Patent Publication Number: US-2021180043-A1

Title: Magnet assembly to prevent extraction particle carryover

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of U.S. Provisional Application No. 62/948,003, filed Dec. 13, 2019, which is hereby incorporated by reference in its entirety. 
    
    
     TECHNICAL FIELD 
     The present disclosure generally relates to automated platforms for performing polynucleotide extraction from biological samples and preparing the polynucleotides into a PCR-ready form. More specifically, the present disclosure relates to a fixed magnet assembly usable with such automated platforms in order to provide magnetic energy to a container containing magnetic particles and a reaction mixture of polynucleotides, in order to bring about a separation of the magnetic particles from the reaction mixture. 
     BACKGROUND 
     The medical diagnostics industry is a critical element of today&#39;s healthcare infrastructure. At present, however, diagnostic analyses no matter how routine have become a bottleneck in patient care. There are several reasons for this. First, many diagnostic analyses can only be done with highly specialist equipment that is both expensive and only operable by trained clinicians. Such equipment is found in only a few locations—often just one in any given urban area. This means that most hospitals are required to send out samples for analyses to these locations, thereby incurring shipping costs and transportation delays, and possibly even sample loss or mishandling. Second, the equipment in question is typically not available ‘on-demand’ but instead runs in batches, thereby delaying the processing time for many samples because they must wait for a machine to fill up before they can be run. 
     Understanding that sample flow breaks down into several key steps, it would be desirable to consider ways to automate as many of these as possible. For example, a biological sample, once extracted from a patient, must be put in a form suitable for a processing regime that typically involves using an amplification method, including but not limited to polymerase chain reaction (PCR), TMA, SDA, NASBA, LCR, and Rolling-Cycle Amplification, to amplify a vector of interest. Once amplified, the presence of a nucleotide of interest from the sample needs to be determined unambiguously. Preparing samples for PCR is currently a time-consuming and labor intensive step, though not one requiring specialist skills, and could usefully be automated. By contrast, steps such as PCR and nucleotide detection have customarily only been within the compass of specially trained individuals having access to specialist equipment. 
     Sample preparation is labor intensive in part because most samples must be heated at one or more stages, and in part because target polynucleotides are typically captured by some kind of retention member which must then be effectively isolated from the surrounding milieu. Thus, even where various liquid transfer operations can be optimized, and even automated, there is still a need for controlled application of heat, and efficient capture of extracted polynucleotides in situ. 
     The discussion of the background herein is included to explain the context of the inventions described herein. This is not to be taken as an admission that any of the material referred to was published, known, or part of the common general knowledge as at the priority date of any of the claims. 
     Throughout the description and claims of the specification the word “comprise” and variations thereof, such as “comprising” and “comprises”, is not intended to exclude other additives, components, integers or steps. 
     SUMMARY 
     The systems, methods, and devices described herein each have several aspects, no single one of which is solely responsible for its desirable attributes. Without limiting the scope of this disclosure, several non-limiting features will now be discussed briefly. 
     Disclosed herein are embodiments of a fixed magnet assembly that can be implemented into automated platforms for performing polynucleotide extraction from biological samples and preparing the polynucleotides into a PCR-ready form. The fixed magnet assembly can be used to provide magnetic energy to a container containing magnetic particles and a reaction mixture of polynucleotides, in order to bring about a separation of the magnetic particles from the reaction mixture. This can prevent or reduce magnetic particle carryover in the prepared PCR-ready sample, thereby improving PCR results. 
     In various embodiments, a system for analyzing nucleic acids is contemplated, and the system may include a receiving bay configured to receive a plurality of lysing tubes aligned along a lysing axis and a plurality of mixing tubes aligned along a mixing axis generally parallel to the lysing axis. The receiving bay may include: one or more first magnets aligned along a first magnet axis (which is generally parallel to the lysing and the mixing axes) and one or more second magnets aligned along a second magnet axis (which is generally parallel to the first magnet axis). The one or more first magnets may be configured to move between a position below the plurality of lysing tubes to a position adjacent to the plurality of lysing tubes when the plurality of lysing tubes are received in the receiving bay. The one or more first magnets may be configured to apply a first magnetic force to contents of the plurality of lysing tubes when the plurality of lysing tubes are received in the receiving bay and the one or more first magnets are positioned adjacent to the plurality of lysing tubes. The one or more second magnets may be configured to remain stationary when the plurality of mixing tubes are received in the receiving bay, the one or more second magnets configured to apply a second magnetic force to contents of the plurality of mixing tubes when the plurality of mixing tubes are received in the receiving bay. 
     In some embodiments, the one or more second magnets are included in a fixed magnet assembly, which may include a mounting plate, a support plate having a height relative to the mounting plate, and a first plurality of fasteners mechanically coupling the support plate to the mounting plate. The first plurality of fasteners may enable the height of the support plate relative to the mounting plate to be user-adjustable. In some cases, each of the first plurality of fasteners may include a jack screw. 
     In some embodiments, when the plurality of lysing tubes and the plurality of mixing tubes are received in the receiving bay, the first magnetic force is applied to contents of each of the plurality of lysing tubes along a direction that is generally perpendicular to the lysing axis, and the second magnetic force is applied to contents of each of the plurality of mixing tubes along a direction that is generally parallel to the mixing axis. In some embodiments, when the plurality of lysing tubes and the plurality of mixing tubes are received in the receiving bay, the first magnetic force is applied to contents of each of the plurality of lysing tubes along a direction that is generally perpendicular to the lysing axis, and the second magnetic force is applied to contents of each of the plurality of mixing tubes along a direction that is generally perpendicular to the mixing axis. In some embodiments, the receiving bay is further configured to receive a processing device comprising the plurality of lysing tubes and the plurality of mixing tubes. In some embodiments, the first magnet axis is spatially separate from the second magnet axis a distance such that the one or more first magnets do not exert the first magnetic force on contents of the plurality of mixing tubes when the plurality of mixing tubes are received in the receiving bay, and the one or more second magnets do not exert the second magnetic force on contents of the plurality of lysing tubes when the plurality of lysing tubes are received in the receiving bay. 
     In some embodiments, the system may further include a plurality of second magnets enclosed within a plurality of housings aligned along the second magnet axis, with each housing of the plurality of housings enclosing two of the plurality of second magnets. In some embodiments, when the plurality of mixing tubes are received in the receiving bay, a first of the two magnets in each housing is configured to apply the second magnetic force to contents of a first mixing tube at a first position of the first mixing tube, and wherein a second of the two magnets in each housing is configured to apply the second magnetic force to contents of a second mixing tube that is adjacent to the first mixing tube, the second of the two magnets configured to apply the second magnetic force at a second position of the second mixing tube that is about 180 degrees or less than 180 degrees from a first position of the second mixing tube. In some embodiments, when the plurality of mixing tubes is received in the receiving bay, the ratio of mixing tubes to housings is two-to-one. 
     In some embodiments, the system may further include a plurality of first magnets aligned along the first magnet axis, and when the plurality of lysing tubes is received in the receiving bay, the ratio of lysing tubes to first magnets is one-to-one. In some embodiments, each housing may include two faces that are each angled a different angle relative to the second magnet axis, and each of the two second magnets (enclosed in the housing) is positioned adjacent to an interior wall of one angled face of the housing. 
     In some embodiments, the system may further include a unitary structure that includes the plurality of housings. In some embodiments, the plurality of housings are separated by a plurality of connectors. 
     In some embodiments, the system may include one second magnet formed of a magnetic material, with the second magnet including a plurality of magnet structures aligned along the second magnet axis. Each magnet structure may include two angled magnet faces that are each angled a different angle relative to the second magnet axis. In some embodiments, when the plurality of mixing tubes are received in the receiving bay, a first angled magnet face of each magnet structure is configured to apply the second magnetic force to contents of a first mixing tube at a first position of the first mixing tube, and a second angled magnet face of each magnet structure is configured to apply the second magnetic force to contents of a second mixing tube that is adjacent to the first mixing tube. The second angled magnet face may be configured to apply the second magnetic force at a second position of the second mixing tube that is about 180 degrees or less than 180 degrees from a first position of the second mixing tube. 
     In some embodiments, when the plurality of mixing tubes is received in the receiving bay, the ratio of mixing tubes to magnet structures is two-to-one. In some embodiments, the system may further include a plurality of first magnets aligned along the first magnet axis, and, when the plurality of lysing tubes is received in receiving bay, the ratio of lysing tubes to first magnets is one-to-one. In some embodiments, the receiving bay may further include a support plate positioned between the one or more second magnets and a cover of the receiving bay. In some embodiments, the support plate includes a plurality of recesses each configured to receive a bottom portion of one mixing tube when the plurality of mixing tubes are received in the receiving bay. 
     In some embodiments, the system may further include a plurality of second magnets enclosed within a plurality of housings aligned along the second magnet axis, and the plurality of housings are movable relative to the support plate when the plurality of mixing tubes are not received in the receiving bay. In some embodiments, the system may further include the plurality of lysing tubes and the plurality of mixing tubes received in the receiving bay. 
     In various embodiments, a system for analyzing nucleic acids is contemplated, and the system may include: a receiving bay configured to receive a device having a lysing tube and a mixing tube aligned along each of a plurality of parallel processing axes. The receiving bay may include one or more first magnets aligned along a first magnet axis generally perpendicular to the plurality of processing axes, and may also include one or more second magnets aligned along a second magnet axis generally perpendicular to the first magnet axis. The one or more first magnets may be configured to move between a position below the plurality of lysing tubes to a position adjacent to the plurality of lysing tubes when the device is received in the receiving bay. The one or more first magnets may be configured to apply a first magnetic force to contents of the plurality of lysing tubes when the device is received in the receiving bay and the one or more first magnets are positioned adjacent to the plurality of lysing tubes. The one or more second magnets may be configured to remain stationary when the plurality of mixing tubes are received in the receiving bay. The one or more second magnets may be configured to apply a second magnetic force to contents of the plurality of mixing tubes when the device is received in the receiving bay. 
     In some embodiments, when the device is received in the receiving bay, the first magnetic force is applied along the respective processing axis of each of the plurality of lysing tubes, and the second magnetic force is applied at a point offset from the respective processing axis of each of the plurality of mixing tubes. In some embodiments, when the device is received in the receiving bay, the first magnetic force is applied along the respective processing axis of each of the plurality of lysing tubes, and the second magnetic force is applied along the respective processing axis of each of the plurality of mixing tubes. 
     In some embodiments, the first magnet axis is spatially separate from the second magnet axis a distance such that the one or more first magnets do not exert the first magnetic force on contents of the plurality of mixing tubes when the device is received in the receiving bay, and the one or more second magnets do not exert the second magnetic force on contents of the plurality of lysing tubes when the device is received in the receiving bay. 
     In some embodiments, the system may further include a plurality of second magnets enclosed within a plurality of housings aligned along the second magnet axis, and each housing of the plurality of housings encloses two of the plurality of second magnets. In some embodiments, when the device is received in the receiving bay, a first of two magnets in each housing is configured to apply the second magnetic force to contents of a first mixing tube at a first position of the first mixing tube. A second of the two magnets in each housing may be configured to apply the second magnetic force to contents of a second mixing tube that is adjacent to the first mixing tube, and the second of the two magnets may be also configured to apply the second magnetic force at a second position of the second mixing tube that is about 180 degrees or less than 180 degrees from a first position of the second mixing tube. 
     In some embodiments, when the device is received in the receiving bay, the ratio of mixing tubes to housings is two-to-one. In some embodiments, the system may further include a plurality of first magnets aligned along the first magnet axis, and, when the device is received in the receiving bay, the ratio of lysing tubes to first magnets is one-to-one. In some embodiments, each housing includes two faces that are each angled relative to an adjacent processing axis, and each of the two second magnets is positioned adjacent to an interior wall of one angled face. 
     In some embodiments, the system may further include a unitary structure that includes the plurality of housings. In some embodiments, the receiving bay further includes a support plate positioned between the one or more second magnets and a cover of the receiving bay. In some embodiments, the support plate includes a plurality of recesses each configured to receive a bottom portion of one mixing tube when the device is received in the receiving bay. In some embodiments, the system may further include a plurality of second magnets enclosed within a plurality of housings aligned along the second magnet axis, and wherein the plurality of housings are movable relative to the support plate before the device is received in the receiving bay. In some embodiments, the system may further include the device received in the receiving bay. 
     Additional embodiments of the disclosure are described below in reference to the appended claims, which may serve as an additional summary of the disclosure. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1A  illustrates an image of a device for PCR amplification (e.g., a microfluidics cartridge) that is mechanically clogged by carried over magnetic extraction particles, in accordance with embodiments disclosed herein. 
         FIG. 1B  illustrates a schematic overview of an automated diagnostic or preparatory apparatus for carrying out automated sample preparation on multiple samples in parallel, in accordance with embodiments disclosed herein. 
         FIG. 2A  illustrates an isometric view of an exemplary reagent holder, in accordance with embodiments disclosed herein. 
         FIG. 2B  illustrates a side profile view of an exemplary reagent holder, in accordance with embodiments disclosed herein. 
         FIG. 2C  illustrates a top-down view of an exemplary reagent holder, in accordance with embodiments disclosed herein. 
         FIG. 2D  illustrates a side profile view of an exemplary reagent holder, in accordance with embodiments disclosed herein. 
         FIG. 2E  illustrates a top-down view of an exemplary reagent holder, in accordance with embodiments disclosed herein. 
         FIG. 3A  illustrates an isometric view of an exemplary heater assembly and a magnetic separator, in accordance with embodiments disclosed herein. 
         FIG. 3B  illustrates an isometric and side profile view of an independently-controllable heater unit of a heater assembly, in accordance with embodiments disclosed herein. 
         FIG. 3C  illustrates a side profile view of a magnetic separator and an independently-controllable heater unit of a heater assembly, which shows the interaction between the magnetic separator and the heater unit, in accordance with embodiments disclosed herein. 
         FIG. 4A  illustrates a perspective view of a rack for holding reagent holders, in accordance with embodiments disclosed herein. 
         FIG. 4B  illustrates an isometric view of a rack for holding reagent holders, in accordance with embodiments disclosed herein. 
         FIG. 5A  illustrates an isometric view of an empty loading bay (or receiving bay) of an automated diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 5B  illustrates a front perspective view of an example automated diagnostic apparatus having two loading bays occupied with corresponding sample racks, in accordance with embodiments disclosed herein. 
         FIG. 6A  illustrates a top-down conceptual view of a set of reagent holders in a loading bay or receiving bay of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 6B  illustrates a top-down conceptual view of the positions of certain components of the reagent holders of  FIG. 6A  relative to magnets in a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 6C  illustrates a top-down conceptual view of another set of reagent holders in a loading bay or receiving bay of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 6D  illustrates a top-down conceptual view of the positions of certain components of the reagent holders of  FIG. 6C  relative to magnets in a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 6E  illustrates a side profile conceptual view of the positions of certain components of a reagent holder relative to magnets in a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIGS. 7A-7B  illustrate perspective views of an embodiment of a fixed magnet assembly that can be implemented into an automated diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 7C  illustrates a side profile view of the dimensions of an embodiment of a fixed magnet assembly that is positioned between certain components of a reagent holder, in accordance with embodiments disclosed herein. 
         FIG. 8A  illustrates an isometric view of an embodiment of a fixed magnet assembly that can be implemented into an automated diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 8B  illustrates an isometric view of an embodiment of a fixed magnet assembly affixed to a cover of an automated diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 9  illustrates an isometric view of an embodiment of a fixed magnet assembly that can be implemented into an automated diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 10A  illustrates an isometric view of an embodiment of a fixed magnet assembly that can be implemented into a diagnostic and preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 10B  illustrates a transparent perspective view of a reagent holder interacting with an embodiment of fixed magnet assembly, in accordance with embodiments disclosed herein. 
         FIG. 11  illustrates an isometric view of the internals of some embodiments of an automated diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 12A  illustrates an isometric view of a processing plate used in some embodiments of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 12B  illustrates a top-down view of an arrangement of two processing plates receiving in the receiving bay of some embodiments of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 13A  illustrates an isometric view of the internals of some embodiments of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 13B  illustrates a side profile view of a processing plate and the internals of some embodiments of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 14A  illustrates a top-down conceptual view of a processing plate used in some embodiments of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 14B  illustrates a top-down conceptual view of the positions of certain components of a processing plate relative to magnets in some embodiments of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 14C  illustrates a side profile conceptual view of the positions of certain components of a processing plate relative to magnets in some embodiments of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIGS. 15A-15D  illustrate isometric views of a fixed magnet assembly used in some embodiments of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIGS. 16A-16C  illustrate isometric views of an embodiment of a fixed magnet assembly used with an automated diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIG. 16D  illustrates a perspective view of a fastening mechanism used in an embodiment of a fixed magnet assembly, in accordance with embodiments disclosed herein. 
         FIG. 16E  illustrates a side cutaway view of a fastening mechanism used in an embodiment of a fixed magnet assembly, in accordance with embodiments disclosed herein. 
         FIG. 16F  illustrates an isometric view of an embodiment of a fixed magnet assembly affixed to a cover of an automated diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
         FIGS. 17A-17D  illustrate isometric views of an embodiment of a bridge for installing a fixed magnet assembly within an automated diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
     
    
    
     DETAILED DESCRIPTION 
     Automated platforms (which can be alternatively referred to as an automated diagnostic or preparatory apparatus) exist for processing biological samples for diagnostic or preparatory purposes. For instance, these automated platforms can be used for performing polynucleotide extraction from biological samples and preparing polynucleotides into a PCR-ready form. 
     Some embodiments of these automated platforms perform polynucleotide extraction and preparation by mixing the cells in a biological sample with a lysing reagent in a process tube and heating the process tube, which lyses the cells and releases the polynucleotides contained in the cells. In order to isolate the polynucleotides from the rest of the mixture, magnetic extraction particles (e.g., surface-modified magnetic beads) configured to bind to those polynucleotides can be added to the mixture. Magnetic extraction particles are also referred to herein as magnetic substrates or magnetic binding particles. The magnetic extraction particles can include, for example, beads modified with PAMAM, dendritic polyamines, poly(allylamine) (PAA), polypropylenimine tetramine dendrimer (DABAM), or any other suitable material. Once the polynucleotides bind to the magnetic extraction particles, magnets can be used to apply a magnetic force for holding the magnetic extraction particles in place and separating them from the rest of the mixture. Some embodiments of these automated platforms may have a magnetic separator that can be moved up and down relative to the process tube, in order to raise the magnetic extraction particles out of the rest of the mixture and remove the rest of the mixture. 
     Once the magnetic extraction particles have been isolated in the process tube, chemical eluents can be added to the process tube in order to detach the polynucleotides from the magnetic extraction particles. Some embodiments of the automated platforms may use the magnetic separator again to capture and hold the magnetic extraction particles in place while the polynucleotides are extracted from the process tube and transferred to a separate mixing tube. The polynucleotides can then be added to a mixture of primers and probes used in PCR amplification, which can then be loaded into a device (e.g., a microfluidics cartridge) for PCR amplification. 
     However, there can be some chemical components present, either within a sample&#39;s cellular matrix or other substances present during sample collection, which can prevent sufficient magnetic capture of the magnetic extraction particles to separate them from the rest of the contents in the process tube. Some examples of substances present during sample collection may include medical lubricants, antifungal creams, antibacterial creams, contraceptive gels and foams, vaginal moisturizing creams, and so forth. Any of the chemical components present may interact with the modified surface of the magnetic extraction particles, the cellular matrix, captured polynucleotides, or a combination of any of these, and interrupt magnetic capture of the magnetic extraction particles. As a result, when the polynucleotides are extracted from the process tube and transferred to the mixing tube, there may be magnetic extraction particles that carry over to the mixing tube and, from there, end up in the device used for PCR amplification (e.g., microfluidics cartridge). This magnetic extraction particle “carryover” can cause either mechanical or chemical failures of PCR amplification that trigger assay failures, such as non-reportables (NRs). Mechanically, the carryover particles can clog the loading ports or microfluidics in the PCR amplification device (e.g., the microfluidics cartridge). An example of this is shown in  FIG. 1A , which illustrates an image of a device for PCR amplification (e.g., a microfluidic cartridge) that is mechanically clogged by carried-over magnetic extraction particles. Chemically, the problematic components of the cellular matrix or other interfering substances, which bind to the carried-over magnetic extraction particles, can interfere with or inhibit the PCR reaction and subsequent detection of the amplification products. 
     In order to reduce and prevent this undesired magnetic extraction particle carryover, various embodiments of a fixed magnet assembly are contemplated and disclosed herein that can be implemented with these automated platforms. In some embodiments, the fixed magnet assembly may include a set of angled magnets within a housing positioned in close proximity to the mixing tubes. In some of such embodiments, the individual magnets may be 0.25×0.25×0.0625″ NdFeB, Grade N52 square magnets, that have a pull force of 1.77 lbs and field strength of 3032 Gauss. However, for other embodiments, suitable magnets may include magnets of various different materials, sizes, and/or strengths, as long as the selected magnet configuration combined with the positioning of the magnets by the mixing tubes enable the magnets to capture some or all of the magnetic extraction particles that have been carried over to the mixing tubes. The magnets may be positioned close enough to the mixing tubes to generate a magnetic field of sufficient strength to retain or “trap” carried-over magnetic extraction particles in the mixing tube, and in particular against an interior wall of the mixing tube. Thus, the fixed magnet assembly of the disclosed technology may provide a secondary set of magnets (in addition to the first set of magnets in the magnetic separator), which can be positioned in fixed locations near mixing tubes to provide a secondary magnetic capture for any undesired magnetic extraction particles that are carried over to the mixing tube (e.g., extraction particles not captured during earlier steps in the workflow), in order to prevent those magnetic extraction particles from being carried over into the PCR amplification device. 
     Embodiments of the disclosed technology can be advantageously implemented in any apparatus that receives a holder for processing and manipulating magnet substrates within a container of the holder. Implementations of the fixed magnet assembly according to the disclosed technology can be placed in a very small, predefined volume or envelope that exists between a cover of a receiving bay and a processing device received in the bay. As a result, existing diagnostic or preparatory apparatuses with a particular receiving bay configured to receive a particular processing device can be retrofitted with the fixed magnet assembly without having to re-design the processing device (such as a reagent holder or processing plate) or components that snap-in to the device (such as reagent tubes or containers). Despite being retrofitted into apparatuses that have been implemented across numerous sites and that have some variation in components, magnets of the fixed magnet assembly still effectively and consistently apply a magnetic force to the contents of the processing devices received by these field-deployed systems. Further significant advantages of the disclosed technology is that it can be implemented in field-deployed systems very quickly, with minimal down time to the customer or the laboratory employing the apparatus. 
     Installation of fixed magnet assemblies according to the disclosed technology can be adjusted for site-specific characteristics and constraints. As will be described in detail below, a fixed magnet assembly can be installed with a shim between the assembly and the cover of the receiving bay, where the height of the shim is selected based on site-specific considerations. This can be particularly advantageous when a fixed magnet assembly is retrofitted into existing preparatory and diagnostic apparatuses in the field, in view of very slight differences in the dimensions and tight tolerances associated with receiving bays and processing devices implemented in the apparatuses. 
     As another example of the advantageous adjustability and versatility of the disclosed technology, some embodiments of the fixed magnet assembly include a spring-mounted support plate that is movable in a z-direction relative to a mounting plate that is fixed to the cover of the receiving bay. The mounting plate can be fixed using any suitable mechanism, including but not limited to screws or adhesive tape (including double-sided tape). The support plate can move upward or downward in the z-direction in the receiving bay before and during insertion of a processing device in the receiving bay. This feature may allow for tubes or containers of a processing device to be accurately and consistently positioned relative to magnets in the fixed magnet assembly, without requiring that exact magnet positioning (e.g., via designing, building, and positioning the fixed magnet assembly with very tight tolerances) be accurately and consistently reproduced across each of a plurality of apparatuses in which a fixed magnet assembly is installed. 
     As yet another example of the advantageous adjustability and versatility of the disclosed technology, some embodiments of the fixed magnet assembly include a support plate that is mechanically coupled to a mounting plate using a plurality of adjustable fasteners, which allows the support plate to be movable in the z-direction relative to the mounting plate by adjusting the fasteners. The support plate can be mechanically coupled to the mounting plate using any suitable fastener that can be adjusted to modify the distance between the support plate and the mounting plate. For instance, the support plate can be mechanically coupled to the mounting plate with a plurality of jack screws, which can be threaded clockwise or counter-clockwise in order to increase or decrease the distance between the support plate and the mounting plate (e.g., raise or lower the height of the support plate in the z-direction), respectively. The mounting plate may be fixed to the cover of the receiving bay using any suitable mechanism, including but not limited to screws or adhesive tape (including double-sided tape). This feature may allow for an installer of the fixed magnet assembly (e.g., including but not limited to a user of the system) to manually adjust the height of the support plate based on the particular apparatus the fixed magnet assembly is installed in, such that tubes or containers of a processing device are accurately and consistently positioned relative to magnets in the fixed magnet assembly, without requiring the fixed magnet assembly to be pre-configured with that exact magnet positioning be (e.g., via designing, building, and positioning the fixed magnet assembly with very tight tolerances) and thereby enabling the fixed magnet assembly to be used with various apparatuses that may have inconsistent dimensions. 
     Embodiments of fixed magnet assemblies according to the disclosed technology can include a plurality of magnet housings or structures. As will be described in detail below, the magnet housings and structures can include faces that are advantageously oriented to align very closely with (for example, within 1-2 mm of) a tube or container containing magnetic structures while also avoiding interference with the tube (or features surrounding the tube) when the tube is inserted into the receiving bay. The faces can be angled relative to a processing axis on which the tube lies, while still maintaining very close proximity to the tube. In the case of magnet housings, magnets that are coupled to inner walls of the faces can be advantageously oriented. In the case of magnet structures formed of a magnetic material, angled faces can be advantageously oriented. The shape and dimensions of the magnet housings/structures and the shape and dimensions of connecting structures that connect the magnet housings/structures can be advantageously tailored, such that they do not interfere with a skirt or flange on the underside of a processing device that receives a snap-in reagent tube or container. The magnet housings/structures can thus avoid undesirable physical interference with a tube containing magnetic substrates as well as nearby tubes that do not contain magnetic substrates, while still positioning a magnet in very close physical proximity to the tube containing magnetic substrates. 
     Embodiments of fixed magnet assemblies according to the disclosed technology can include magnet housings/structures that are configured to simultaneously apply a magnetic force to two different tubes or containers that are arranged on parallel processing axes. For example, in the case of a magnet housing enclosing two magnets, one magnet housed in the magnet housing can apply a magnetic force to one side of a first container of a processing device, and another magnet housed in the magnet housing can apply a magnetic force to an opposing side of a second container of the processing device, where the first and second containers are positioned on parallel processing axes. In other words, the magnets in a magnet housing may apply magnetic force to opposite sides of the containers of adjacent processing axes. In a non-limiting example, in which reagents holders are received in a rack that is inserted into a receiving bay, magnets within a single magnet housing can apply magnetic force to opposite sides of snap-in containers of adjacent reagent holders. Although magnetic force is applied to different sides of snap-in containers depending on which magnet is in close proximity to the snap-in containers, the problem of magnetic extraction particle carry-over is effectively and consistently addressed for each of the reagent holders. Advantageously, this implementation can avoid having to place the magnets in a very tight space (e.g., between the snap-in container that includes magnetic particles and another snap-in container aligned along the same processing axis). Instead, the magnets of the disclosed technology can be Advantageously arranged at an oblique angle relative to the processing axis of each reagent holder, rather than being arranged on the processing axis. 
     As described above, the fixed magnet assembly may be designed to be quickly and efficiently implemented, even into existing automated diagnostic or preparatory apparatuses without any hardware modifications to the apparatus. Different embodiments of the fixed magnet assembly of the disclosed technology may be designed, configured, and tailored for use with a specific embodiment of an automated diagnostic or preparatory apparatus. Some specific examples of the various embodiments of the fixed magnet assembly are shown and discussed herein. 
     For instance,  FIGS. 1B, 2A-2E, 3A-3C, 4A-4B, 5A-5B  provide context for a first embodiment of an automated diagnostic or preparatory apparatus.  FIGS. 6A-6C  provide a conceptual overview of how a fixed magnet assembly can be configured, positioned, and implemented with respect to this first embodiment of the automated diagnostic or preparatory apparatus, in order to reduce or prevent magnetic extraction particle carryover.  FIGS. 7A-7B, 8A-8B, 9, 10A-10B, and 16A-16F  illustrate various different embodiments of a fixed magnet assembly that demonstrate additional features and concepts outlined in connection with  FIGS. 6A-6C . The example fixed magnet assemblies described with reference to  FIGS. 6A-6C  can be implemented in the first embodiment of the automated diagnostic or preparatory apparatus in order to prevent magnetic extraction particle carryover. It will be understood that these are non-liming examples and other suitable configurations and implementations are also consistent with the disclosed technology. 
     Additionally,  FIGS. 11, 12A-12B, and 13A-13B  provide context for a second embodiment of an automated diagnostic or preparatory apparatus in which a fixed magnet assembly of the disclosed technology can be implemented.  FIGS. 14A-14C  provide a conceptual overview of how a fixed magnet assembly can be configured, positioned, and implemented with respect to this second embodiment of the automated diagnostic or preparatory apparatus, in order to prevent magnetic extraction particle carryover.  FIGS. 15A-15D  illustrate an embodiment of a fixed magnet assembly that demonstrate additional features and concepts outlined in connection with  FIGS. 14A-14C . The example fixed magnet assemblies described with reference to  FIGS. 15A-15D  can be implemented with the second embodiment of the automated diagnostic or preparatory apparatus in order to prevent magnetic extraction particle carryover. It will be understood that these are non-liming examples and other suitable configurations and implementations are also consistent with the disclosed technology. 
     Example Automated Apparatus, Reagent Holder, and Rack of the Disclosed Technology 
       FIG. 1B  illustrates a schematic overview of an apparatus  181  for carrying out automated sample preparation on multiple samples in parallel, according to steps exemplified elsewhere herein. The geometric arrangement of the components of system  181  is exemplary and not intended to be limiting. The apparatus may additionally include (not shown in  FIG. 1B ) a device, in a receiving bay, and configured to carry out a diagnostic test on the sample, such as by detecting presence of an amplified polynucleotide in the cartridge. The device can include, for example, a microfluidic cartridge, configured to receive polynucleotides that have placed into a PCR-ready form. Such additional features are also described in U.S. patent application Ser. No. 12/173,023, filed on Jul. 14, 2008 (and entitled “Integrated Apparatus for Performing Nucleic Acid Extraction and Diagnostic Testing on Multiple Biological Samples”, in the name of Williams, et al.). Unless specifically made clear to the contrary, where the term PCR is used herein, any variant of PCR including but not limited to real-time and quantitative, and any other form of polynucleotide amplification is intended to be encompassed. 
     A processor  180 , such as a microprocessor, is configured to control functions of various components of the system as shown, and is thereby in communication with each such component requiring control. It is to be understood that many such control functions can optionally be carried out manually, and not under control of the processor. Furthermore, the order in which the various functions are described, in the following, is not limiting upon the order in which the processor executes instructions when the apparatus is operating. Thus, processor  180  can be configured to receive data about a sample to be analyzed, e.g., from a sample reader  190 , which may be a barcode reader, an optical character reader, or an RFID scanner (radio frequency tag reader). 
     Processor  180  can be configured to accept user instructions from an input device  184 , where such instructions may include instructions to start analyzing the sample, and choices of operating conditions. Processor  180  can be also configured to communicate with a display  182 , so that, for example, information about an analysis is transmitted to the display and thereby communicated to a user of the system. Such information includes but is not limited to: the current status of the apparatus; progress of PCR thermocycling; and a warning message in case of malfunction of either system or cartridge. Additionally, processor  180  may transmit one or more questions to be displayed on display  182  that prompt a user to provide input in response thereto. Thus, in certain embodiments, input  184  and display  182  are integrated with one another. Processor  180  can be optionally further configured to transmit results of an analysis to an output device  186  such as a printer, a visual display, a display that utilizes a holographic projection, or a speaker, or a combination thereof. Processor  180  can be still further optionally connected via a communication interface such as a network interface to a computer network  188 . 
     Processor  180  can be further configured to control various aspects of sample preparation and diagnosis, as follows in overview. In  FIG. 1B , the apparatus  181  is configured to operate in conjunction with a complementary rack  170 . Apparatus  181  may be capable of receiving multiple racks, such as 1, 2, 3, 4, or 6 racks. 
     Embodiments of rack  170  are further described in U.S. patent application Ser. No. 12/173,023, filed on Jul. 14, 2008 (entitled “Integrated Apparatus for Performing Nucleic Acid Extraction and Diagnostic Testing on Multiple Biological Samples”, in the name of Williams, et al.), and U.S. patent application Ser. No. 12/178,584, filed on Jul. 23, 2008 (entitled “Rack For Sample Tubes And Reagent Holders”, in the name of Duffy, et al.), both of which are incorporated herein by reference in their entireties. A rack  170  is itself configured to receive a number of biological samples  196  in a form suitable for work-up and diagnostic analysis, and a number of holders  172 —as further described herein, such as in connection with  FIGS. 2A-2C , that are equipped with various reagents, pipette tips and receptacles. The rack is configured so that, during sample work-up, samples are processed in the respective holders, the processing including being subjected, individually, to heating and cooling via heater assembly  177 . 
     The heating functions of the heater assembly  177  can be controlled by the processor  180 . Heater assembly  177  operates in conjunction with a separator  178 , such as a magnetic separator, that also can be controlled by processor  180  to move into and out of close proximity to one or more processing chambers associated with the holders  172 , wherein particles such as magnetic particles are present. Assembly  177  and separator  178  are further described herein. 
     Liquid dispenser  176 , which similarly can be controlled by processor  180 , is configured to carry out various suck and dispense operations on respective sample, fluids and reagents in the holders  172 , to achieve extraction of nucleic acid from the samples. Liquid dispenser  176  can carry out such operations on multiple holders simultaneously. 
     Sample reader  190  is configured to transmit identifying indicia about the sample, and in some instances the holder, to processor  180 . In some embodiments a sample reader is attached to the liquid dispenser and can thereby read indicia about a sample above which the liquid dispenser is situated. In other embodiments the sample reader is not attached to the liquid dispenser and is independently movable, under control of the processor. Liquid dispenser  176  is also configured to take aliquots of fluid containing nucleic acid extracted from one or more samples and direct them to storage area  174 , which may be a cooler. The storage area  174  contains, for example, a PCR tube corresponding to each sample. Additionally, or as an alternative, liquid dispenser  126  can be configured to take aliquots of fluid containing nucleic acid extracted from one or more samples and direct them to a device configured to receive and amplify the nucleic acid. The device can include, for example, a microfluidic cartridge received in a receiving bay of the apparatus  181  (not illustrated). 
     Embodiments of the apparatus shown in outline in  FIG. 1B , as with other exemplary embodiments described herein, are advantageous because they do not require locations within the apparatus suitably configured for storage of reagents. Therefore, the apparatus in  FIG. 1B  is self-contained and operates in conjunction with holders  172 , wherein the holders are pre-packaged with reagents, such as in locations within it dedicated to reagent storage. 
     The apparatus of  FIG. 1B  may be configured to carry out operation in a single location, such as a laboratory setting, or may be portable so that they can accompany, e.g., a physician, or other healthcare professional, who may visit patients at different locations. The apparatus is typically provided with a power-cord so that they can accept AC power from a mains supply or generator. The apparatus may also be configured to operate by using one or more batteries and therefore is also typically equipped with a battery recharging system, and various warning devices that alert a user if battery power is becoming too low to reliably initiate or complete a diagnostic analysis. 
     The apparatus of  FIG. 1B  may further be configured, in other embodiments, for multiplexed sample analysis and/or analysis of multiple batches of samples, where, e.g., a single rack holds a single batch of samples. Each component shown in  FIG. 1B  may therefore be present as many times as there are batches of samples, though the various components may be configured in a common housing. 
     The apparatuses as described herein find application to analyzing any nucleic acid containing sample for any purpose, including but not limited to genetic testing, and clinical testing for various infectious diseases in humans. 
     The apparatus herein can be configured to run on a laboratory benchtop, or similar environment, and can test approximately 45 samples per hour when run continuously throughout a normal working day. Results from individual raw samples are typically available in less than 1 hour. 
       FIG. 2A  shows an isometric view of an exemplary holder (e.g., holder  172  shown in  FIG. 1B ) as described herein. The holders described herein are reagent holders for holding and transporting reagents for various purposes, including but not limited to sample preparation in a clinical context, and configured to be received by a rack as described herein. The reagent holders also typically provide a container in which various reagents can be mixed one with another and/or with a sample. The holders are also configured for use in an automated apparatus that can carry out sample preparation on samples in more than one holder simultaneously. 
     This exemplary holder, as well as others consistent with the written description herein though not shown as specific embodiments, are now described. Further details of reagent holders can be found in U.S. patent application Ser. No. 12/218,416, filed on Jul. 14, 2008 in the name of Wilson, et al., (entitled “Reagent Tube, Reagent Holder, and Kits Containing Same”), which is incorporated herein by reference. 
     The exemplary holder  200  of  FIG. 2A  includes a connecting member  210  having one or more characteristics as follows. Connecting member  210  serves to connect various components of the holder together. Connecting member  210  has an upper side  212  and, opposed to the upper side, an underside (not shown). 
     The reagent holder  200  will now be described in order to illustrate certain features of the disclosed technology, it will be understood that the disclosed technology can be implemented with any suitable holder that receives magnetic substrates, such as magnetic binding particles. The reagent holder  200  of  FIG. 2A  of this particular, non-limiting embodiment includes a process tube  220  having an aperture  222  located in the connecting member; two or more reagent tubes  240  disposed on the underside of the connecting member, each of the reagent tubes having an inlet aperture  242  located in the connecting member; and one or more receptacles  250 , located in the connecting member, wherein the one or more receptacles  250  are each configured to receive a complementary container  254 , such as a reagent tube, inserted from the upper side  212  of the connecting member. In the illustrated embodiment of  FIGS. 2A-2C , the reagent holder  200  includes 4 receptacles  250 , each configured to receive a snap-in container  254 . In another non-limiting embodiment described below with reference to  FIGS. 2D and 2E , the reagent holder includes 3 receptacles  250 , each configured to receive a snap-in container  254 . Implementations of the disclosed technology can be implemented in holders having any suitable number of receptacles, as well as in holders having containers  254  integrally formed with, rather than snapped into, the connecting member. The reagent holder  200  can optionally include at least one socket, located in the connecting member, the socket configured to accept a disposable pipette tip, and at least one pipette sheath. In this non-limiting embodiment, the reagent holder includes 4 sockets and 4 pipette sheaths. The lanes of the rack described herein are designed to have sufficient depth and width to accommodate the various reagent tubes, receptacles, process tube, and pipette sheath of a given reagent holder, and to position the process tube in communication with a heater/separator unit. 
     The containers  254  have been inserted into their corresponding receptacles  250 . The one or more receptacles  250  are configured to accept reagent tubes that contain quantities of one or more reagents for carrying out extraction of nucleic acids from a sample that is associated with the holder. The reagents can be in solid form, such as in lyophilized form. The receptacles can be all of the same size and shape, or may be of different sizes and shapes from one another. Receptacles  250  are shown as having open bottoms, but are not limited to such topologies, and may be closed other than the inlet  252  in the upper side of connecting member  210 . Preferably the receptacles  250  are configured to accept commonly used containers in the field of laboratory analysis, or containers suitably configured for use with the holder herein. For example, the containers  254  may be 0.3 ml tubes. 
     The embodiment of a reagent holder  200  is shown configured with a waste chamber  260 , having an inlet aperture  262  in the upper side of the connecting member  210 . Waste chamber  260  is optional and, in embodiments where it is present, is configured to receive spent liquid reagents. In other embodiments, where it is not present, spent liquid reagents can be transferred to and disposed of at a location outside of the holder, such as, for example, a sample tube that contained the original sample whose contents are being analyzed. 
     Process tube  220  can be configured as a snap-in tube, similar to containers  254 , or it can be integrally formed in the connecting member  210 . Process tube  220  can be used for various mixing and reacting processes that occur during sample preparation. For example, cell lysis can occur in process tube  220 , as can extraction of nucleic acids, such as DNA or RNA of a patient, and DNA or RNA of a pathogen. Process tube  220  can be advantageously positioned in a location that minimizes, overall, pipette head moving operations involved with transferring liquids to process tube  220 . Process tube  220  is also located in the holder in such a position that, when the holder is inserted in a rack as further described herein, the process tube is exposed and accessible to a heater and separator, as further described herein. 
     Some of the reagents contained in the holder are provided as liquids, and others may be provided as solids. In some embodiments, a different type of container or tube is used to store liquids from those that store the solids. 
     Reagent wells  240  are typically configured to hold liquid reagents, one per well. For example, in reagent holder embodiment  200 , three reagent wells are shown, containing respectively wash buffer, release buffer, and neutralization buffer, each of which is used in a sample preparation protocol. Other numbers and configurations of reagent wells can be suitably implemented in embodiments of the disclosed technology. 
     The reagent holder  200  has a connecting member that is configured so that the at least one socket, the one or more receptacles, and the respective apertures of the process tube, and the two or more reagent tubes, are all arranged linearly with respect to one another (i.e., their midpoints lie on the same axis). As will be described in more detail below with reference to  FIGS. 6A-6B , this axis can be a processing axis along which features of the holder are aligned. It will be understood that, in embodiments of the disclosed technology, features of the holder can be aligned in a substantially linear arrangement, such that the midpoints of the features do not lie precisely on a common processing axis. Further, the holders herein are not limited to particular configurations of receptacles, process tube, sockets, reagent tubes, and waste chamber if present. For example, a holder may be made shorter, if some apertures are staggered with respect to one another and occupy ‘off-axis’ positions. The various receptacles, etc., also do not need to occupy positions with respect to one another that are the same as those shown in  FIG. 2A . 
     It would be understood that alternative configurations of the various parts of the holder  200  give rise only to variations of form and can be accommodated within other variations of the apparatus as described, including but not limited to alternative instruction sets for a liquid dispensing pipette head, heater assembly, and magnetic separator, as further described herein. Each such configuration of the reagent holder can be accommodated by a corresponding variation in form of the rack described herein that receives one or more such holders. 
     In some embodiments, the holder  200  includes a registration member such as a mechanical key. Typically such a key is part of the connecting member  210 . A mechanical key ensures that the holder is accepted by a complementary member in, for example, a supporting rack as described herein (e.g., the rack  170  of  FIG. 1B ) or a receiving bay of an apparatus that controls pipetting operations on reagents in the holder. Thus, embodiment  200  has a mechanical key  292  that includes a pair of rectangular-shaped cut-outs on one end of the connecting member. This feature as shown additionally provides for a tab by which a user may gain a suitable purchase when inserting and removing the holder into a rack or another apparatus. The illustrated embodiment of the holder  200  also has a mechanical key  290  at the other end of connecting member  210 . Key  290  is an angled cutout that eases insertion of the holder into a rack, as well as ensures a good registration therein when abutting a complementary angled cut out in a recessed area configured to receive the holder. 
     A reagent holder for use with a rack as described herein is typically made of a plastic such as polypropylene. The plastic is such that it has some flexibility to facilitate placement into a rack, as further described herein. The plastic is typically sufficiently rigid, however, so that the holder will not significantly sag or flex under its own weight and will not easily deform during routine handling and transport, and thus will not permit reagents to leak out from it. 
     The holder  200  is typically such that the connecting member  210 , process tube  220 , the two or more reagent tubes  240 , and the waste chamber  260  (if present) are made from a single piece, made from a material such as polypropylene. It will be understood that other configurations of holder  200  can be suitable implemented in the disclosed technology. 
     The illustrated embodiment of the reagent holder  200  has four receptacles  250  and corresponding containers  254 .  FIG. 2B  illustrates a side profile view of this embodiment of the reagent holder  200 , and  FIG. 2C  illustrates a top-down view of this embodiment of the reagent holder  200 . It can be seen that the four receptacles  250  (e.g., receptacles  250 - 1 ,  250 - 2 ,  250 - 3 , and  250 - 4 ) are configured to accept corresponding containers  254  (e.g., containers  254 - 1 ,  254 - 2 ,  254 - 3 ,  254 - 4 ). Some of the containers  254  may contain quantities of one or more reagents typically in solid form, such as in lyophilized form, for carrying out extraction of nucleic acids from a sample that is associated with the holder. 
     In other embodiments, such as the embodiment of the holder  202  illustrated in  FIGS. 2D and 2E , there may be a different number of receptacles  250  and containers  254 . For instance,  FIG. 2D  illustrates a side profile view of an embodiment of the holder  202 , with  FIG. 2E  illustrating a corresponding top-down view of the embodiment of the holder  202 . In this embodiment of the reagent holder  202 , there are three receptacles  250  (e.g., receptacles  250 - 1 ,  250 - 2 , and  250 - 3 ) which are configured to accept corresponding containers  254  (e.g., containers  254 - 1 ,  254 - 2 , and  254 - 3 ). Some of the containers  254  may contain quantities of one or more reagents typically in solid form, such as in lyophilized form, for carrying out extraction of nucleic acids from a sample that is associated with the holder. Although example holders  200  and  202  are described as containing reagents for carrying out extraction of nucleic acids from a sample, it will be understood that the disclosed technology is not limited to holders that contain such reagents and can be suitably implemented on any holders in which magnetic substrates, such as magnetic binding particles, in solution are manipulated or processed. 
     Example heater and magnetic separator assemblies that can apply thermal and magnetic energy to the process tube of a plurality of holders will now be described with reference to  FIGS. 3A-3C . It will be understood that embodiments of the disclosed technology can be suitably implemented in other heater and magnetic separator assemblies.  FIG. 3A  illustrates an isometric view of an exemplary heater assembly  300  having independently controllable heater units and a magnetic separator  370 .  FIG. 3B  provides an isometric and side profile view of one of these independently-controllable heater units  301 .  FIG. 3C  provides a side profile view of the interaction of the magnetic separator  370  with the independently-controllable heater units of the heater assembly  300 . 
     More specifically, the heater assembly  300  shown in  FIG. 3A  may include one or more independently-controllable heater units  301 , each of which comprises a heat block  303 . Each of the heat blocks  303  is configured to align with and to deliver heat to a process tube  302 . Each heat block  303  can be optionally secured and connected to the rest of the apparatus using one or more fasteners, such as one or more screws  307  or other adhesive device(s). This securing mechanism is not limited to such a configuration. 
     In certain embodiments there are 2, 3, 4, 5, 6, 8, 10, 12, 16, 20, 24, 25, 30, 32, 36, 40, 48, or 50 heater units in a heater assembly  300 . Still other numbers of heater units, such as any number between 6 and 100 are consistent with the description herein. The one or more heat blocks  303  may be fashioned from a single piece of metal or other material, or may be made separately from one another and mounted independently of one another or connected to one another in some way. Thus, the term heater assembly connotes a collection of heater units but does not require the heater units or their respective heat blocks to be attached directly or indirectly to one another. The heater assembly  300  can be configured so that each heater unit  301  independently heats each of the one or more process tubes  302  (e.g., the process tube of a reagent holder, such as process tube  220  of the holder  200  shown in  FIG. 2A ), for example by permitting each of the one or more heat blocks to be independently controllable, as further described herein. 
     In certain embodiments, there may be a magnetic separator  370 . The magnetic separator  370  may be configured to move one or more magnets  304  relative to the one or more process tubes  302  and separate magnetic particles in the process tubes  302 . In some embodiments, the magnets  304  may be moved into close proximity to the process tubes  302  (e.g., with each magnet  304  having a face less than 2 mm, between 2 mm and 1 mm, or less than 1 mm away from the exterior surface of a corresponding process tube  302  without being in contact with the process tube  302 ). The magnets  304  of the magnetic separator  370  may be aligned on a common axis (e.g., a common axis may pass through the midpoints of each of the magnets  304 ). This common axis may be located behind the process tubes  302  and run parallel to the process tubes  302  (more specifically, run parallel to a common axis passing through all the process tubes  302  when they are disposed in the heat blocks  303 ). In some cases, this common axis passing through the magnets  304  of the magnetic separator  370  may be referred to as a first magnet axis, such as the example of the first magnet axis  380  shown in  FIG. 3B . The magnetic particles may be microparticles, beads, or microspheres capable of binding one or more biomolecules, such as polynucleotides, and commonly available as retention members. Separating the particles, while in solution, typically comprises collecting and concentrating, or gathering, the particles into one location in the inside of the one or more process tubes  302 . 
     Structurally, the magnetic separator  370  may include: one or more magnets  304  affixed to a supporting member; a motorized mechanism configured to move the supporting member in such a manner that the one or more magnets move backwards and forwards along a fixed axis, and during at least a portion of the motion, the one or more magnets maintain close proximity to one or more receptacles which contain the magnetic particles in solution; and control circuitry to control the motorized mechanism. The supporting member and motorized mechanism are not shown in  FIG. 3A , but are described in further detail in connection to  FIG. 3C . 
     The magnetic separator  370  may operate together with the heater assembly  300  to permit successive heating and separation operations to be performed on liquid materials in the one or more process tubes without transporting either the liquid materials or the process tubes to different locations to perform either heating or separation. Such operation is also advantageous because it means that the functions of heating and separation which, although independent of one another, are both utilized in sample preparation, may be performed with a compact and efficient apparatus. 
     In some embodiments, the heater assembly  300  and the magnetic separator  370  can be controlled by electronic circuitry such as on printed circuit board  309 . The electronic circuitry can be configured to cause the heater assembly  300  to apply heat independently to the process tubes  302  to minimize the cost of heating and sensing. It can also be configured to cause the magnetic separator  370  to move repetitively relative to the process tubes  302 . The electronic circuitry can be integrated into a single printed circuit board (PCB). 
     In some cases, the magnetic separator  370  can be integrated with the heater assembly  300 , and they may be collectively referred to as an integrated magnetic separator and heater assembly. Thus, an integrated magnetic separator and heater may include: a heater assembly, wherein the heater assembly includes a plurality of independently-controllable heater units, each of which has a heat block configured to accept and to heat one of a plurality of process tubes; one or more magnets affixed to a supporting member; a motorized mechanism configured to move the supporting member in such a manner that the one or more magnets move backwards and forwards along a fixed axis, and during at least a portion of the motion the one or more magnets maintain close proximity to one or more of the process tubes in the heater assembly, wherein the one or more process tubes contain magnetic particles; and control circuitry to control the motorized mechanism and to control heating of the heater units. 
     Although not shown in  FIG. 3A , an enclosure can cover the magnetic separator  370  and the heater assembly  300  for protection of sub-assemblies below and aesthetics. The enclosure can also be designed to keep the heat blocks  303  spaced apart from one another to ensure efficiency of heating and cooling. The enclosure can be configured to enable sufficient air flow around the process tubes  302  so as not to significantly inhibit rate of cooling. The enclosure can have a gap between it and the heat blocks  303  to facilitate cooling. The magnetic separator  370  and heater assembly  300  can, alternatively, be enclosed by separate enclosures. For instance, the heater assembly  300  can be optionally contained in an enclosure that surrounds the heater units  301  and heat blocks  303 . The one or more enclosures can be made of plastic, but is not so limited. The one or more enclosures may be configured to appear aesthetic to a user. 
     In the specific configuration shown in  FIG. 3A , the heater assembly  300  comprises twelve heat blocks  303  aligned parallel to one another. Each heat block  303  is made from aluminum, and has an L-shaped configuration having a U-shaped inlet for accepting a process tube  302 . The magnetic separator  370  comprises twelve magnets  304  aligned parallel to one another. Each magnet  304  may be a rectangular block of Neodymium (or other permanent rare earth materials with magnetic fields) disposed behind each heat block  304  and mounted on a supporting member. The magnets  304  may be configured to move up and down relative to the process tubes  302  in the heater assembly  300 . This mechanism is described in further detail in connection with  FIG. 3C . 
     Certain embodiments of the automated diagnostic or preparatory apparatus described herein have more than one independently-controlled heater unit  301  in a single heater assembly  300 , as further described herein. For example, a single heater assembly  300  may be configured to independently heat 6 or 12 process tubes, and an apparatus may be configured with two or four such heater assemblies  300 . It will be understood that embodiments of the disclosed technology can be implemented in a heater assembly that does not independently heat each process tube, or that applies heat to a subset of a plurality of process tubes received in the heater assembly. 
     Although a cross-sectional view of one heat block  303  is shown in the right-hand panel of  FIG. 3B , it should be understood that this is consistent with having multiple heat blocks aligned in parallel to one another and such that their geometric midpoints all lie on a single linear axis (e.g., as in  FIG. 3A ), though it is not so limited in configuration. Thus, the one or more heat blocks may be positioned at different heights from one another, in groups or, alternately, individually, or may be staggered with respect to one another from left to right, in groups or alternately, or individually. Additionally, and in other embodiments, the heat blocks are not aligned parallel to one another but are disposed at angles relative to one another, the angles being other than 180°. Furthermore, although the heat block  303  shown in  FIG. 3B  may be one of several that are identical in size, it is consistent with the technology herein that one or more heat blocks may be configured to accept and to heat process tubes of different sizes. 
     The exemplary heat block  303  in  FIG. 3B  (right hand panel) is configured to have an internal cavity that partially surrounds a lower portion of process tube  302 . In the heat block  303 , the internal cavity surrounds the lower portion of process tube  302  on two sides but not the front side (facing away from magnet  304 ) and not the rear side (adjacent to magnet  304 ). In other embodiments, heat block  303  is configured to surround the bottom of process tube  302  on three sides, including the front side. Still other configurations of heat block  303  are possible, consistent with the goals of achieving rapid and uniform heating of the contents of process tube  302 . In certain embodiments, the heat block is shaped to conform closely to the shape of process tube  302  so as to increase the surface area of the heat block that is in contact with the process tube during heating of the process tube. Thus, although exemplary heat block  303  is shown having a conical, curve-bottomed cavity in which a complementary process tube is seated, other embodiments of heat block  303  have, for example, a cylindrical cavity with a flat bottom. Still other embodiments of heat block  303  may have a rectilinear internal cavity such as would accommodate a cuvette. 
     Moreover, although heat block  303  is shown as an L-shape in  FIG. 3B , which aids in the transmittal of heat from heating element  351  and in securing the one or more heat blocks to the rest of the apparatus, it need not be so, as further described herein. For example, in some embodiments heating element  351  may be positioned directly underneath process tube  302 . 
     In one embodiment, the heat block  303  has a mass of {tilde over ( )}10 grams and is configured to heat up liquid samples having volumes between 1.2 ml and 10 μl. Heating from room temperature to 65° C. for a 1 ml biological sample can be achieved in less than 3 minutes, and 10 μl of an aqueous liquid such as a release buffer up to 85° C. (from 50° C.) in less than 2 minutes. The heat block  303  can cool down to 50° C. from 85° C. in less than 3 minutes. The heat block  303  can be configured to have a temperature uniformity of 65±4° C. for heating up 1 ml of sample and 85±3° C. for heating up 10 μl of release buffer. These ranges are exemplary, and the heat block can be suitably scaled to heat other volumes of liquid at rates that are slower and faster than those described. This aspect of the technology is one aspect that contributes to achieving rapid nucleic acid extraction of multiple samples by combination of liquid processing steps, rapid heating for lysis, DNA capture and release and magnetic separation, as further described herein and elsewhere, such as U.S. patent application Ser. Nos. 12/172,208 and 12/172,214, both of which are incorporated herein by reference. 
     As shown in  FIG. 3B , an independently-controller heater unit  301  can also include one or more heating elements (e.g., a power resistor)  351  each of which is configured to thermally interface to a heat block  303  and dissipate heat to it. For example, in one embodiment, a power resistor can dissipate up to 25 Watts of power. Although the heating element  351  is shown placed at the bottom of the heat block  303 , it would be understood that other configurations are consistent with the assembly described herein: for example, the heating element  351  might be placed at the top or side of each heat block  303 , or directly underneath process tube  302 . In other embodiments, the heating element has other shapes and is not rectangular in cross section but may be curved, such as spherical or ellipsoidal. Additionally, the heating element may be molded or shaped so that it conforms closely or approximately to the shape of the bottom of the process tube. 
     In the embodiment shown in  FIG. 3B , the independently-controlled heater unit  301  may further comprise one or more temperature sensors  352 , such as resistive temperature detectors, to sense the respective temperatures of each heat block  303 . Although a temperature sensor  352  is shown placed at the bottom of the heat block  303 , it would be understood that other configurations are consistent with the assembly described herein: for example, the temperature sensor might be placed at the top or side of each heat block  303 , or closer to the bottom of process tube  302  but not so close as to impede uniform heating thereof. 
     Also shown is the printed circuit board (PCB)  309 , which enables the heater assembly  300  to apply heat independently to each process tube  302  upon receipt of appropriate instructions. 
       FIG. 3C  provides a cutaway profile view of an independently-controllable heater unit  301  and a magnet  304  of the magnetic separator  370 , in order to demonstrate the interaction of the magnetic separator  370  with the independently-controllable heater units of the heater assembly  300 . 
     While the magnet  304  shown in  FIG. 3C  is shown as a rectangular block, it is not so limited in shape. Moreover, the configuration of  FIG. 3C  is consistent with either having a single magnet that extends across all the heat blocks  303  in the heater assembly  300 , or having multiple magnets operating in concert and aligned to span a subset of the heat blocks  303 , for example, aligned collinearly on the supporting member. The magnet  304  can be made of neodymium and can have a magnetic strength of 5,000-15,000 Gauss (Brmax). An example magnet is from K &amp; J Magnetics, Inc. Other suitable magnets can be implemented. The poles of the magnets  304  can be arranged such that one pole faces the heat blocks  303  and the other pole faces away from the heat blocks  303 . 
     The magnet  304  is mounted on a supporting member  372  that can be raised up and down along a fixed axis using a motorized shaft  305 . The fixed axis can be vertical. The magnetic separator  370  may have gears  306  that communicate rotational energy from a motor  375  to cause the motorized shaft  304  to raise and lower the magnet  304  relative to the heat block. This geared arrangement may enable the motor  375  to be placed perpendicular to the shaft  305 , thereby saving space in the apparatus in which magnetic separator  370  is situated. In other embodiments, the motor  375  is placed underneath shaft  305 . It would be understood that other configurations are consistent with the movement of the magnet  304  relative to the process tubes  302 , including, but not limited to, moving the magnet  304  from side-to-side, or bringing the magnet  304  down from above. 
     The motor  375  can be computer controlled to run at a particular speed; for example at a rotational speed that leads to vertical motion of the magnet  304  in the range 1-20 mm/s. The magnetic separator  370  can thus be configured to move repetitively, e.g., up and down, from side to side, or backwards and forwards, along the same axis several times. In some embodiments there is more than one shaft  305  that operates under motorized control. The presence of at least a second shaft has the effect of making the motion of the separator  370  more smooth and acting as a guiding member. In some embodiments, the supporting member  372  rides on one more guiding members to ensure that the supporting member  372  does not, for example, tip, twist, or yaw, or undergo other internal motions while moving (other than that of controlled motion along the axis) and thereby reduce efficacy of the separation. 
     The supporting member  372  can also be configured to move the magnets  304  between a first position, situated away from the process tubes  302  (e.g., as in the left-hand side of  FIG. 3C ), and a second position situated in close proximity to the process tubes  302  (e.g., as in the right-hand side of  FIG. 3C ), and is further configured to move at an amplitude about the second position where the amplitude is smaller than a distance between the first position and the second position as measured along the shaft  305 . 
       FIGS. 4A and 4B  illustrate various views of a rack, which can hold multiple reagent holders (e.g., holder  200  shown in  FIG. 2A ) in pre-defined positions to ensure that the process tubes of the reagent holders (e.g., process tube  220  of the holder  200  shown in  FIG. 2A ) are precisely disposed in the heater blocks of the heater assembly (e.g., the heater blocks  303  of the heater assembly  300  shown in  FIG. 3A ) when the rack is loaded into the automated diagnostic or preparatory apparatus described herein. More specifically,  FIG. 4A  illustrates a perspective view of the back of the rack, while  FIG. 4B  illustrates an isometric view of the rack.  FIGS. 4A and 4B  are described together. 
     An embodiment of a rack  400  is shown, which is configured to be insertable into, and removable from, a loading bay (alternatively, a receiving bay) of an automated apparatus, such as an automated diagnostic apparatus or an automated preparatory apparatus as described herein. An example of a loading bay of an automated apparatus is shown in  FIG. 5A . Additional details for such an apparatus are provided in U.S. patent application Ser. No. 12/173,023, filed on Jul. 14, 2008 (entitled “Integrated Apparatus for Performing Nucleic Acid Extraction and Diagnostic Testing on Multiple Biological Samples”, in the name of Williams, et al.), and incorporated by reference herein. The automated apparatus may have multiple loading bays, which allows processing of samples in multiple racks at the same time. 
     Each rack may be configured to receive a plurality of reagent holders. In some examples the rack is also configured to receive a plurality of sample tubes. The apparatus is configured to receive the plurality of reagent holders and the plurality of samples tubes such that the reagent holders are in one-to-one correspondence with the sample tubes, and wherein the reagent holders each contain sufficient reagents to extract polynucleotides from a sample and place the polynucleotides into a PCR-ready form. In implementations in which the rack receives a plurality of sample tubes, the rack may accept any number of sample tubes (e.g., 2, 4, 6, 8, 10, 12, 16, or 20 sample tubes) containing samples and a corresponding number of reagent holders. The rack may be configured to hold the reagent holders in place, either permitting access on a laboratory benchtop to reagents stored in the holders, or situated in a dedicated region of the apparatus permitting the holders to be accessed by one or more other functions of the apparatus, such as automated pipetting, heating of the process tubes, and magnetic separating of affinity beads. The reagent holders may have at least one process tube and one or more containers for reagents. The reagent holders are described in further detail herein (e.g., in connection to  FIGS. 2A-2E ), and additional details for reagent holders are further provided in U.S. patent application Ser. No. 12/218,416, filed on Jul. 14, 2008 (entitled “Reagent Tube, Reagent Holder, and Kits Containing Same”, in the name of Wilson, et al.) and incorporated herein by reference. 
     For instance, in the embodiment shown in  FIGS. 4A and 4B , the rack  400  is configured to accept  12  sample tubes  416  and  12  corresponding reagent holders  404 , in  12  lanes  402 . A lane  402 , as used herein in the context of the rack  400 , is a dedicated region of the rack  400  designed to receive a sample tube and corresponding reagent holder  404 . In some cases, the reagent holders  404  may be the reagent holders  200  shown in  FIG. 2A , which have a process tube  220  at one end. The lanes  402  of the rack  400  may be configured to receive the reagent holders  404  in a certain orientation. For instance, in order to slide each reagent holder  404  into a lane  402 , the end of the reagent holder  404  with the process tube may have to be directed towards the lane  402 . 
     For example, in the embodiments shown here, at least the first lane and the second lane are parallel to one another, a configuration that increases pipetting efficiency. Typically, when parallel to one another, pairs of adjacent sample lanes  402  are separated by 24 mm at their respective midpoints. Other distances are possible, such as 18 mm apart, or 27 mm apart. The distance between the midpoints in dependent on the pitch of the nozzles in the liquid dispensing head, as further described herein. Keeping the spacing in multiples of 9 mm enables easy loading from the rack into a 96 well plate (where typically wells are spaced apart by 9 mm). Typically, also, the rack is such that the plurality of reagent holders in the plurality of lanes are maintained at the same height relative to one another. 
     A lane  402  of the rack  400  may be configured to accept a given reagent holder  404  in such a way that the reagent holder  404  snaps or locks reversibly into place, and thereby remains steady while reagents are accessed in it, and while the rack  400  is being carried from one place to another or is being inserted into, or removed from, a diagnostic or preparatory apparatus. The lanes  402  of the rack  400  can be configured so that the reagent holders  404 , when positioned in the rack  400 , are aligned for proper pipette tip pick-up using a liquid dispenser as further described herein. Furthermore, in examples where the reagent holder houses one or more pipette tips, the second location of each lane can be deep enough to accommodate one or more pipette tips, such as contained in a pipette tip sheath. 
     The rack  400  may include a sample tube holder  410  configured to accept a number of sample tubes  416 , one for each lane  402 . Thus, in the embodiment shown in  FIGS. 4A and 4B , the sample tube holder  410  may be configured to accept up to  12  sample tubes  416 . For each sample tube  416  that the sample tube holder  410  is configured to hold, the sample tube holder  410  may have a first slot  412  and a second slot  414  that the sample tube  416  is inserted through. Each first slot  412  may have a corresponding second slot  414 , and each first slot  412  and its corresponding second slot  414  may be positioned to receive and hold a sample tube  416  at a location adjacent to one of the lanes  402  (e.g., in the same axis as the lane  402 , such that the holder  404  inserted in that lane  402  is aligned with the sample tube  416 ). It will be understood that implementations of the disclosed technology are not limited to racks that include sample tube holders  410  as illustrated in  FIGS. 4A-4B , and that implementations of the disclosed technology can be suitably implemented with racks that do not include a sample tube holder  410  and that do not receive sample tubes  416 . 
       FIG. 5A  illustrates an isometric view of an empty loading bay  500  (or receiving bay) of an automated diagnostic or preparatory apparatus. 
     The loading bay  500  may be a recessed area of the apparatus, which is configured to accept a rack such as the exemplary rack  400  of  FIGS. 4A and 4B . The apparatus may have any number of loading bays  500  for receiving the corresponding number of racks  400 . For instance,  FIG. 5A  illustrates an embodiment of an apparatus that has two loading bays  500  that are located side-by-side, which allows two separate racks  400  to be simultaneously loaded. Also illustrated in  FIG. 5A  is a first magnet axis  580 , which may be a common axis on which the magnets of the magnetic separator are aligned (e.g., the common axis that passes through the magnets of the magnetic separator). This first magnet axis  580  (similar to the first magnet axis  380  shown in  FIG. 3B ) may be located behind the process tubes of the reagent holders in the rack  400  when the rack  400  is inserted into the loading bay  500  and run parallel to those process tubes (more specifically, run parallel to a common axis passing through the process tubes). 
       FIG. 5B  illustrates a front perspective view of an example automated diagnostic apparatus having two loading bays  500  occupied with corresponding sample racks  400 . These loading bays  500  are shown in relation to two microfluidic cartridges  510 , which can be configured to carry out an amplification on a suitably prepared sample, as further described in U.S. patent application Ser. No. 12/173,023, filed on Jul. 14, 2008 (entitled “Integrated Apparatus for Performing Nucleic Acid Extraction and Diagnostic Testing on Multiple Biological Samples”, in the name of Williams, et al.). Other suitably configured recessed areas for receiving other racks differing in shape, appearance, and form, rather than function, are consistent with the description herein. 
     Also shown is a liquid dispensing head  520 , which may be an automated pipette head used to perform liquid processing operations. An exemplary automated pipette head is described in U.S. patent application Ser. No. 12/173,023, filed Jul. 14, 2008 (entitled “Integrated Apparatus for Performing Nucleic Acid Extraction and Diagnostic Testing on Multiple Biological Samples”, in the name of Williams, et al.). 
     The liquid dispensing head  520  can pick up pipette tips (for example, from the one or more sockets in a reagent holder, such as one of the reagent holders  404  in the racks  400 ) and return pipette tips (for example, to such sockets in a reagent holder after use); strip and discard a pipette tip from a pipette head after use or upon encountering an error; and move a pipette tip with precision from one location of a given holder to another so that, for example, liquid reagents can be located and added to solid reagents to make up solutions, and various liquid reagents can be mixed with one another during a sample preparation protocol. Furthermore, it is desirable that such a liquid dispensing head  520  can operate on several holders (e.g., 2, 3, 4, or 6) in a rack  400  simultaneously, and thereby perform certain operations in parallel. The liquid dispensing head  520  can move in three degrees of freedom. 
     Example Fixed Magnet Assemblies According to the Disclosed Technology 
       FIGS. 6A-6E  illustrate various conceptual views associated with implementing a fixed magnet assembly for preventing extraction particle carryover in accordance with the disclosed technology. These conceptual views provide contextual details helpful for understanding how the addition of a fixed magnet assembly prevents extraction particle carryover in implementations of the disclosed technology. 
       FIG. 6A  is a top-down conceptual view of a set of 3 reagent holders  602  in a loading bay or receiving bay  600  of a diagnostic or preparatory apparatus.  FIG. 6A  illustrates how the reagent holders  602  are arranged relative to a first magnet axis  612  (e.g., off a magnetic separator) and a second magnet axis  614  (of a fixed magnet assembly according to the disclosed technology). As will be described below, one or a plurality of magnets of a magnetic separator described above with reference to  FIGS. 3A-3C  can be aligned along the first magnet axis  612 . A set of 3 sample tubes  604  in associated with the reagent holders  602  are also shown adjacent to the reagent holders  602 . In practice, there could be more than 3 reagent holders  602  (and more than 3 corresponding sample tubes  604 ) in the receiving bay  600 , such as the 12 reagent holders held in the rack  400 . For each reagent holder  602 , some of its associated components are shown, including a process tube  606  (e.g., the process tube  220  shown in  FIG. 2A ) and a set of containers  608  (e.g., containers  254  shown in  FIG. 2A ). Each reagent holder  602  and its corresponding sample tube  604  may be aligned along a processing axis  610 , with the diagnostic or preparatory apparatus configured to perform processing and operations (e.g., the transfer of liquids) along each processing axis  610 . Accordingly, a total of n processing axes  610  may be conceptualized—one for each reagent holder  602  and its corresponding sample tube  604 . 
     It will be understood that in some embodiments, the processing axes  610  does not include a sample tube  604  (for example if the sample tube  604  is received in a different part of the apparatus that is not in association with a reagent holder  602 ). In such an example, the processing axis  610  may be defined by the location of the process tube  606  and a location of a container that receives magnetic energy from magnets aligned along the second magnet axis  614  (in the illustrated embodiment, container  608 - 3 ). 
     In some embodiments, each of the reagent holders  602  may be similar to the reagent holder  200  shown in  FIGS. 2A-2C . In other words, the reagent holders  602  may be an embodiment with four snap-in containers  608  (e.g., containers  254  in  FIG. 2A ), which include container  608 - 1 ,  608 - 2 ,  608 - 3 , and  608 - 4  (numbered in order from nearest to furthest away from the process tube  606 ). In such cases, the process tube  606  may be alternatively referred to as either a reaction tube or a lysis tube, container  608 - 1  may be alternatively referred to as an extraction tube, and container  608 - 3  may be alternatively referred to as a mixing tube. It will be understood that alternative reagent holders  602  can be implemented in embodiments of the disclosed technology. For example, a plurality of reagent holders  602  may be joined or formed as a single, monolithic processing device that is configured to be received in the receiving bay. For another example, a unitary device including a plurality of the reagent holders  602  may be received in the receiving bay. 
     A first magnet axis  612  may run horizontally behind the process tubes  606  of the reagent holders  602 . The first magnet axis  612  may be an axis on which the magnets of a magnetic separator (e.g., the magnets  304  of the magnetic separator  370  shown in  FIGS. 3A and 3C ) reside. The first magnet axis  612  may be positioned, such that, when the magnetic separator is raised, the magnets of the magnetic separator come into close proximity with the process tubes  606  (e.g., within 2 mm of the process tubes  606 ). 
     In accordance with embodiments of the fixed magnet assembly of the disclosed technology, a second magnet axis  614  may run horizontally through the containers  608 - 3  of the reagent holders  602 . Alternatively, the second magnet axis  614  can run behind or in front of the containers  608 - 3 , in either case in close enough proximity to impart a magnetic force on the contents of the container  608 - 3 . The second magnet axis  614  may be an axis on which the magnets of a fixed magnet assembly reside. The second magnet axis  614  may be positioned, such that the magnets of the fixed magnet assembly are in sufficiently close proximity with the containers  608 - 3  (e.g., the mixing tubes) of the reagent holders  602 , so as to impart a magnetic force on the contents of the containers  608 - 3 . The magnetic force can be of a sufficient strength to hold magnetic binding particles in solution in the container  608 - 3  against an interior wall of the container  608 - 3 , for example while the solution is being transferred out of the container  608 - 3  during a pipetting operating. Additionally, the second magnet axis  614  may be spaced far enough apart from the first magnet axis  612  such that the magnets of the fixed magnet assembly do not interfere with the magnet of the magnetic separator. For example, the first magnet axis  612  can be spatially separated from the second magnet axis  614  a distance “D” such that the one or more magnets aligned along the first magnet axis  612  do not exert a magnetic force on contents of the containers  608 - 3 , and one or more magnets aligned along the second magnet axis  614  do not exert a magnetic force on contents of the process tubes  606 . 
     The first magnet axis  612  and the second magnet axis  614  are further shown in  FIG. 6B , which is a top-down conceptual view of the positioning of certain components of the reagent holders  602  relative to magnets on the first magnet axis  612  and magnets on the second magnet axis  614 . 
     More specifically,  FIG. 6B  shows for 4 reagent holders, including the positions of the process tube  606 , the snap-in container  608 - 3 , and the processing axis  610  associated with each reagent holder. It can be seen that the magnetic separator  620  includes multiple magnets  622  that are aligned on the first magnet axis  612 , and each magnet  622  is positioned adjacent to the process tube  606  of a reagent holder. In this example implementation, the magnets  622  are in one-to-one correspondence with the process tubes  606 . In practice, when the magnetic separator  620  is raised to bring the magnets  622  into close proximity to the process tubes  606 , the magnets  622  exert a magnetic force (shown as vertical vectors in  FIG. 6B ) on the contents of the process tubes  606 . 
     Also shown in  FIG. 6B  are the magnets  632  of a fixed magnet assembly according to the disclosed technology. In this example implementation, a single magnet  632  exerts a magnetic force on two containers  608 - 3 , such that the magnets  632  are not in one-to-one correspondence with the containers  608 - 3 . In some embodiments, the magnets  632  of the fixed magnet assembly can be arranged in pairs. Each pair of magnets  632  can be located within a housing or structure  630 . A fixed magnet assembly may include multiple housings  630 . In one non-limiting embodiment, a plurality of housings  630  are formed in a unitary structure and each housing is configured to house or enclose two magnets  632 . In another non-limiting embodiment, the fixed magnet assembly includes a unitary structure formed of a magnetic material, the unitary structure including a plurality of magnet structures  630  configured to exert a magnetic force on containers  608 - 3 . The pairs of magnets  632  can be positioned within the diagnostic or preparatory apparatus, such that each pair of magnets  632  is located between the containers  608 - 3  of two adjacent reagent holders (in the manner shown in the figure) when the reagent holders are in the receiving bay of the diagnostic or preparatory apparatus. There may be a magnet  632  for each reagent holder and when the reagent holders are in the receiving bay of the diagnostic or preparatory apparatus, each magnet  632  may be in close proximity with the container  608 - 3  of a reagent holder. All of the magnets  632  of the fixed magnet assembly may be aligned on (or substantially aligned on) the second magnet axis  612 . Each of the magnets  632  may exert a magnetic force (shown as horizontal vectors in  FIG. 6B ) on the contents of adjacent containers  608 - 3 . 
     Implementations of fixed magnet assemblies according to the disclosed technology can include any suitably configured magnet. In one non-limiting example, the individual magnets  632  are 0.25×0.25×0.0625″ NdFeB, Grade N52 square magnets, that have a pull force of 1.77 lbs and field strength of 3032 Gauss. It will be understood that the material, dimensions, and pull force is not limited to this particular example of the disclosed technology. Suitable magnets may include magnets of various different materials, sizes, and/or strengths, as long as the selected magnet configuration combined with the positioning of the magnets by the mixing tubes enable the magnets to sufficiently capture the magnetic extraction particles in the mixing tubes. 
       FIG. 6C  is similar to  FIG. 6A , in that  FIG. 6C  illustrates a top-down conceptual view of a set of 3 reagent holders  602  in a loading bay or receiving bay  600  of a diagnostic or preparatory apparatus is shown. However, in the embodiment illustrated in  FIG. 6C , the second magnet axis  614  does not run through the midpoints of the containers  608 - 3  of each of the reagent holders  602 . Instead, the second magnet axis  614  lies on an off-center chord of each the containers  608 - 3 . This may correspond, for instance, with the embodiment that is shown in  FIG. 6D . 
       FIG. 6D  is similar to  FIG. 6B , in that  FIG. 6D  illustrates a top-down conceptual view of the positions of certain components of the reagent holders  602  relative to magnets on the first magnet axis  612  and magnets on the second magnet axis  614 . However, in the embodiment illustrated in  FIG. 6D , the second magnet axis  614  does not run through the midpoints of the containers  608 - 3  of each of the reagent holders  602 . This second magnet axis  614  is distinct from a mixing axis  616 , which passes through the midpoints of the containers  608 - 3  of each of the reagent holders  602 . The magnets  632  are aligned along the second magnet axis  614  that is generally parallel to the first magnet axis  612  and also generally parallel to the mixing axis  616  (but does not coincide with the mixing axis  616 ). However, the second magnet axis  614  may be close enough to the mixing axis  616 , such that the magnets  632  (residing on the second magnet axis  614 ) may be considered as applying a magnetic force to the contents of each of the containers  608 - 3  along a direction that is generally parallel to the mixing axis  616 .The functions of the magnets  622  of the magnetic separator  620  and the magnets  632  of the fixed magnet assembly may be better understood with additional context provided by  FIG. 6E , which is a side profile conceptual view illustrating the positions of a reagent holder  602  and corresponding sample tube  604  in relation to a first magnet  622  (e.g., from the magnetic separator) and a second magnet  632  (e.g., from the fixed magnet assembly) when the reagent holder  602  and corresponding sample tube  604  are in the receiving bay of the diagnostic or preparatory apparatus. 
     More specifically,  FIG. 6E  shows a reagent holder  602  having a process tube  606 , a set of 4 snap-in containers  608  (e.g., containers  608 - 1 ,  608 - 2 ,  608 - 3 , and  608 - 4 ), a set of reagent tubes (e.g., reagent tubes  640 ,  642 , and  644 ), a waste chamber  646 , and a set of pipette tips disposed within pipette sheaths (e.g., pipette tips  648 ,  650 ,  652 , and  654 ). Although the illustrated embodiment of the reagent holder  602  has 4 snap-in containers  608 , it should be noted that embodiments of the disclosed technology can be suitable implemented with the reagent holders with 3 snap-in containers  608  described with reference to  FIGS. 2D-2E  (e.g., without the container  608 - 4 ). 
     Process tube  606  (similar to process tube  220  shown in  FIG. 2A ) may typically be used during sample preparation for cell lysis and extraction of nucleic acids, such as DNA or RNA of a patient, and DNA or RNA of a pathogen. The process tube  606  may be positioned at the distal end of the reagent holder  602  in a location that minimizes, overall, pipette head moving operations involved with transferring liquids to the process tube  606  when the reagent holder  602  is in the receiving bay of the diagnostic or preparatory apparatus. The process tube  606  is also positioned in a location such that the process tube  606  is disposed within a heater block  660  of a heater assembly (e.g., as shown in  FIGS. 3A and 3B ) when the reagent holder  602  is in the receiving bay of the diagnostic or preparatory apparatus. The first magnet  622  of the magnetic separator may be raised to be in close proximity to the process tube  606  in order to exert a magnetic force on the contents of the process tube  606 . 
     Some of the containers  608  may contain lyophilized reagents (e.g., dried reagents) to which fluid may be added. In some embodiments, container  608 - 1  may be alternatively referred to as an extraction tube. In some embodiments, container  608 - 3  may be alternatively referred to as a mixing tube. In some embodiments, containers  608 - 2  and  608 - 4  may be alternatively referred to as master mix tubes. The reagent tubes  640 ,  642 , and  644  may contain liquid reagents, one per tube. In some embodiments, the reagent tube  640  may contain a wash buffer. In some embodiments, the reagent tube  642  may contain an elution buffer. In some embodiments, the reagent tube  644  may contain a neutralization buffer. The wash buffer, release buffer, and neutralization buffer may each be used in a sample preparation protocol. Spent liquid reagents can be transferred to the waste chamber  646 , where they can be later disposed of. 
     The set of 4 pipette tips (e.g., pipette tips  648 ,  650 ,  652 , and  654 ) may be disposed within pipette sheaths. The pipette tips may be used by the diagnostic or preparatory apparatus (e.g., via the liquid dispensing head  520 ) to perform processing and operations (e.g., the transfer of liquids). The pipette sheaths may serve to catch drips from used pipette tips, and thereby prevent cross-sample contamination, from use of one holder to another in a similar location, and/or to any supporting rack in which the holder is situated. The pipette sheaths may be permanently or removably affixed to the reagent holder  602 , or may be formed, e.g., molded, as a part of a single piece assembly for the holder  602 . 
     Preparation of a sample with the additional fixed magnet assembly may proceed as follows. It should be noted that the following description of an example workflow is provided to provide context for understanding the role of the fixed magnet assembly and the steps are not applicable to all assays, which may use other workflows that have different process steps or order of operations. In some embodiments, the liquid dispensing head of the diagnostic or preparatory apparatus may first pick up the first pipette tip  648  and use it to pierce (e.g., obtain access) to various components of the reagent holder  602 , including the container  608 - 1 , the waste chamber  646 , and the reagent tubes  640 ,  642 , and  644  (containing the wash buffer, release buffer, and neutralization buffer, respectively). 
     The liquid dispensing head of the diagnostic or preparatory apparatus may use the first pipette tip  648  to transfer some raw sample from the sample tube  604  and add it to the process tube  606 . The amount of raw sample transferred may depend on the type of assay or procedure. Some of the sample (e.g., the remainder of the sample not transferred into the process tube  606 ) may be added to the container  608 - 1  (e.g., the extraction tube), which may contain magnetic particles (e.g., beads), a lyophilized extraction reagent (e.g., dried lysis reagent), and internal controls. The magnetic particles may be configured to bind to specific molecules (e.g., DNA/RNA) in the sample. The contents of the container  608 - 1  are rehydrated using the added sample and given time to dissolve into solution. The liquid dispensing head may then use the first pipette tip  648  to transfer the contents of the container  608 - 1  into the process tube  606  (which contains the rest of the transferred sample from the sample tube  604 ) and mix the contents of the process tube  606 . Afterwards, the liquid dispensing head may return the first pipette tip  648  to its pipette sheath. 
     The contents of process tube  606 , which is disposed in the heater block  660  (e.g., the process tube  606  is received within the heater block  660 ) of a heater unit of a heater assembly of the diagnostic or preparatory apparatus, are heated by the heater block  660 . The temperature and duration of the heating is determined by the type of assay or procedure. The heating and lysis reagent causes the cells from the sample to break open, and some of the target nucleic acid (for example, DNA or RNA) contained in the cells and the internal controls may attach or bind to the magnetic particles (e.g., magnetic binding particles or beads). 
     The first magnet  622  of the magnetic separator may be raised until it is in close proximity to the process tube  606 . The magnet  622  may exert a magnetic force on the magnetic particles in the process tube  606 , drawing the magnetic particles and the attached nucleic acid to the side of the process tube  606 . The liquid dispensing head may use the first pipette tip  648  to extract the liquid from the process tube  606  while the magnet  622  is still drawing the magnetic particles and attached nucleic acid to the side of the process tube  606 . Ideally under normal operating, this liquid should not contain the magnetic particles and attached nucleic acid, which are held against the inner side wall of the process tube  606  as the liquid is extracted. The liquid dispensing head may dispense the extracted liquid to the waste chamber  646  and return the first pipette tip  648  to its pipette sheath. 
     The first magnet  622  of the magnetic separator may be lowered, thereby removing the magnetic force holding the magnetic particles and the attached nucleic acid to the side of the process tube  606 . The liquid dispensing head may use the second pipette tip  648  to transfer wash buffer from the reagent tube  640  to the process tube  606 . The second pipette tip  650  can also be used to mix the added wash buffer with the magnetic particles bound to nucleic acid in the process tube  606 . Afterwards, the first magnet  622  of the magnetic separator may be raised against until it is in close proximity to the process tube  606 . The magnet  622  may exert a magnetic force on the magnetic particles in the process tube  606 , again drawing the magnetic particles and the attached nucleic acid to the side of the process tube  606 . 
     With the magnetic particles moved to the side of the process tube  606 , the liquid dispensing head may use the second pipette tip  650  to extract the liquid contents (e.g. primarily the added wash buffer) of the process tube  606  and transfer the liquid to the waste chamber  646 . Ideally under normal operating conditions, this liquid should not contain the magnetic particles and attached nucleic acid, which are held against the inner side wall of the process tube  606  as the liquid is extracted. Afterwards, the liquid dispensing head may return the second pipette tip  650  back to its pipette sheath and the first magnet  622  of the magnetic separator may be lowered, thereby removing the magnetic force holding the magnetic particles and the attached nucleic acid to the side of the process tube  606 . 
     The liquid dispensing head may then use the third pipette tip  652  to transfer release buffer from the reagent tube  642  to the process tube  606  containing the magnetic particles and attached nucleic acid. The release buffer may cause the magnetic particles to separate from the nucleic acid and internal controls. The liquid dispensing head may then use the third pipette tip  652  to transfer neutralizing buffer from the reagent tube  644  to the snap-in container  608 - 3  (e.g., mixing tube), which is empty at this point. Afterwards, the liquid dispensing head may return the third pipette tip  652  back to its pipette sheath. At this point, the process tube  606  will contain the magnetic particles, the extracted nucleic acid (e.g., DNA/RNA extracted from the cells and attached to the magnetic particles), and internal controls. The snap-in container  608 - 3  (e.g., mixing tube) contains neutralizing buffer. 
     The heater block  660  is activated a second time to heat the contents of the process tube  606 . The temperature and duration of the heating will be dependent on the assay or procedure performed. The first magnet  622  of the magnetic separator may be raised yet again, until it is in close proximity to the process tube  606 . The magnet  622  may exert a magnetic force on the magnetic particles in the process tube  606 , drawing the magnetic particles to the inner side wall of the process tube  606  (but not the nucleic acid, e.g., DNA/RNA molecules, which are no longer attached to the magnetic particles). While the magnetic particles are drawn to and held against the inner side wall of the process tube  606  by the magnet  622 , the liquid dispensing head may use the third pipette tip  652  to extract the liquid contents (e.g. the nucleic acid mixture) from the process tube  606  without extracting the magnetic particles. The nucleic acid mixture can be transferred to container  608 - 3  (e.g., the mixing tube) now containing the neutralizing buffer. The neutralizing buffer is configured to lower the pH of the nucleic acid mixture to a neutral pH. The third pipette tip  652  may be returned to its pipette sheath and the first magnet  622  of the magnetic separator may be lowered. 
     At this point, for the embodiment of the reagent holder  602  with 4 snap-in containers  608 , the liquid dispensing head may use the fourth pipette tip  654  to puncture (e.g., gain access) container  608 - 2  and/or container  608 - 4 . The containers  608 - 2  and  608 - 4  may be alternatively referred to as master mix tubes, and which of these containers are used may depend on the assay or procedure performed. The first master mix tube (e.g., container  608 - 2 ) may contain primers and probes to test for a first analyte of interest, and the second master mix tube (e.g., container  608 - 4 ) may contain primers and probes to test for a second analyte of interest. 
     As a very specific example, in some embodiments, the reagent holder  602  may be used to perform an assay of enteric bacteria, and both container  608 - 2  and container  608 - 4  may be used. In such cases, the container  608 - 2  may be referred to as an enteric bacterial panel master mix tube containing enteric bacterial panel master mix for identifying one set or panel of enteric bacteria, and the container  608 - 4  may be referred to as an extended bacterial panel master mix tube containing extended bacterial panel master mix for identifying a second set or panel of enteric bacteria. Thus, some of the neutralized DNA/RNA mixture from container  608 - 3  could be transferred to both master mix tubes. 
     In some embodiments, the reagent holder  602  may be used to extract polynucleotides (e.g., DNA or RNA) from a sample and place the polynucleotides into a PCR-ready form. In such cases, either the snap-in container  608 - 4  or the snap-in container  608 - 2  may serve as a PCR master mix tube, which contains PCR master mix (e.g., primers, probes, and other PCR reagents for the PCR reaction). For example, if the snap-in container  608 - 2  is the PCR master mix tube containing PCR master mix, the liquid dispensing head may first use the fourth pipette tip  654  to puncture (e.g., obtain access to) container  608 - 2 . The liquid dispensing head can then extract the neutralized nucleic mixture in container  608 - 3  (e.g., the mixing tube) and transfer it to container  608 - 2 . This container  608 - 3  may be in close proximity with the second magnet  632  (e.g., of a fixed magnet assembly) when the reagent holder  602  is inserted for processing by the diagnostic or preparatory apparatus. Additional context for the possible positions and orientations of the second magnet  632  is provided in  FIG. 6B . The second magnet  632  may exert a magnetic force on the contents of the container  608 - 3  as the liquid dispensing head extracts the neutralized nucleic acid mixture from the container  608 - 3 . In particular, there may be some magnetic particles (e.g., beads) that were transferred into the container  608 - 3  from the process tube  606  despite efforts to prevent this from occurring (e.g., using the first magnet  622  to keep the magnetic particles in the process tube  606 ). The second magnet  632  may be used as part of an additional filtering step to remove any leftover magnetic particles carried over from the process tube  606  (e.g., “carryover” magnetic particles) from the neutralized nucleic mixture as it is extracted from container  608 - 3 . 
     The extracted neutralized nucleic mixture is then transferred to the container  608 - 2  (e.g., PCR master mix tube). In some embodiments, the PCR master mix in the container  608 - 2  may be in the form of a lyophilized pellet. Adding the neutralized RNA/DNA mixture may dissolve the PCR master mix pellet. The PCR master mix pellet may be allowed to dissolve, and the liquid dispensing head may use the fourth pipette tip  654  to mix together the contents of the container  608 - 2 . The liquid dispensing head may then use the fourth pipette tip  654  to withdraw the mixed solution (now an amplification-ready sample) from the container  608 - 2  and transfer it to a device, including a storage device where the sample is stored or a microfluidic cartridge where it is amplified (e.g., the microfluidic cartridges  510  shown in  FIG. 5B ). 
     It should be noted that this sample preparation process for extracting and preparing polynucleotides into PCR-ready form can be used with other embodiments of the reagent holder, such as reagent holders with only 3 snap-in containers (e.g., similar to the reagent holder  202  shown in  FIGS. 2D and 2E ). Without the fourth snap-in container available (e.g., container  608 - 4 ), the second snap-in container (e.g., container  608 - 2 ) is used as the master mix tube, which will hold the prepared PCR-ready solution that will be transferred to the storage device or the microfluidic cartridge. 
       FIGS. 7A and 7B  illustrate two perspective views of an embodiment of a fixed magnet assembly according to the disclosed technology that can be implemented into an automated diagnostic or preparatory apparatus.  FIG. 7C  illustrates a side profile view of the dimensions of the fixed magnet assembly  700  in  FIGS. 7A-7B  relative to the dimensions of the snap-in containers of reagent holders received in a diagnostic or preparatory apparatus. 
     In particular, the magnets  732  of a fixed magnet assembly  700  are shown to be positioned in close proximity with the third snap-in containers  708 - 3  (e.g., third snap-in container, such as container  608 - 3  in  FIGS. 6A-6E ) of reagent holders received in a diagnostic or preparatory apparatus. In this non-limiting example, for each reagent holder, a magnet  732  is positioned behind the third snap-in container  708 - 3  (e.g., between the third snap-in container  708 - 3  and where the second snap-in container would reside, if shown). Furthermore, in this embodiment of the fixed magnet assembly  700 , the magnets  732  are oriented at an angle that makes them parallel to the sloped wall of the snap-in containers  708 - 3  (e.g., resulting in magnetic forces that are normal to the sloped wall). 
     As shown in  FIG. 7A , the fixed magnet assembly  700  (and its magnets  732 ) may be configured to fit in between the second snap-in container (not shown) and the third snap-in container (e.g., between containers  608 - 3  and  608 - 2  in  FIG. 6E ) once the fixed magnet assembly  700  is installed and a rack with loaded reagent holders is received in the receiving bay of the diagnostic or preparatory apparatus. The fixed magnet assembly  700  may be configured to fit in the very small volume between the snap-in containers, despite variations in dimensions across diagnostic or preparatory apparatus and the differences in the exact placement of each fixed magnet assembly  700  within the receiving bays of diagnostic or preparatory apparatuses. In one non-limiting example, the fixed magnet assembly  700  can be positioned so that the magnets are as little as 0.01 inches distance away from the sloped wall of the containers, and the fixed magnet assembly  700  may have dimensions that enable it to be positioned in the space between containers. For instance, the fixed magnet assembly  700  may have a width that ranges from between 0.15-0.3 inches and a height below 0.4 inches. The ability to fit the fixed magnet assembly  700  into such a small volume may advantageously allow for existing diagnostic or preparatory apparatuses to be retrofitted with the fixed magnet assembly  700  without having to re-design reagent holders or the snap-in containers, while also enabling the magnets  732  of the fixed magnet assembly  700  to effectively and consistently apply a magnetic force to the snap-in containers  708 - 3 . 
     This advantageous aspect of the fixed magnet assembly  700  is better visualized in  FIG. 7C , which shows a side profile of the fixed magnet assembly  700  positioned between the third snap-in container  708 - 3  and second snap container  708 - 2 . In some embodiments, the distance  750  between the sloped wall of the third snap-in container  708 - 3  and a magnet  732  of the fixed magnet assembly  700  may be 0.011 inches or less, the horizontal distance  752  between the walls of the third snap-in container  708 - 3  and the second snap-in container  708 - 2  of a reagent strip may be 0.152 inches or less, and the length  754  of the sloped wall of one of the snap-in containers may be approximately 0.407 inches. The fixed magnet assembly  700  may be sized and shaped to fit within this space between the third snap-in container  708 - 3  and second snap-in container  708 - 2  of a reagent strip when the reagent strip is loaded into a rack received in the receiving bay of the diagnostic or preparatory apparatus. 
     Although the example fixed magnet assemblies  700  in  FIGS. 7A and 7B  are shown to be configured to exert a magnetic force on the third snap-in container, it will be understood that they can be suitably positioned to exert a magnetic force on any other snap-in container, depending on the particular assay or process that is implemented and which container is likely to include carryover particles. 
     It should be noted that the magnets  732  of the embodiment of the fixed magnet assembly  700  shown in  FIGS. 7A and 7B  can be thought of as arranged along a single linear axis (e.g., an axis that is perpendicular to the longitudinal axis of the reagent holders, as well as perpendicular to a processing axis of the reagent holders). Thus, despite the magnets  732  of the fixed magnet assembly  700  being arranged in a different manner than the magnets  632  shown in  FIG. 6B , the second magnet axis  614  shown in  FIGS. 6A and 6B  would still be applicable if adjusted to run between the second and third snap-in containers (the magnets  732  would reside on that axis, similarly to the magnets  622  on the first magnet axis  612 , and exert a magnetic force on the third snap-in containers that would be best represented as a vertical vector in  FIG. 6B ). 
       FIG. 8A  illustrates an isometric view of an embodiment of a fixed magnet assembly that can be implemented according to the disclosed technology into an automated diagnostic or preparatory apparatus. More specifically,  FIG. 8A  shows an embodiment of a fixed magnet assembly  800  having fixed height when implemented into the diagnostic or preparatory apparatus.  FIG. 8B  illustrates the fixed magnet assembly of  FIG. 8A  implemented in a receiving bay of a diagnostic or preparatory apparatus, such as within the receiving bay  500  described with reference to  FIGS. 5A-5B . 
     The fixed magnet assembly  800  may include a support plate  802 , which may have dimensions suited to the particular diagnostic or preparatory apparatus in which the fixed magnet assembly  800  is implemented. In some embodiments, the support plate  802  may be a machined aluminum plate. The support plate  802  may include a set of recesses or holes  806 , each of which is configured to receive the bottom end of a container (e.g., mixing tube), such as container  708 - 3  shown in  FIGS. 7A-7B  or container  608 - 3  shown in  FIGS. 6A-6E . For instance, the indicated positions of the containers  608 - 3  shown in the conceptual view of  FIG. 6B  may coincide with the positions of the holes  806  on the support plate  802 . 
     The fixed magnet assembly  800  may also include a magnet holder  804 , which may similarly have dimensions suited to the particular diagnostic or preparatory apparatus in which the fixed magnet assembly  800  is implemented. In some embodiments, the magnet holder  804  may be made of a material that is chemically resistant to cleaning agents. The magnet holder  804  may include a set of magnet housings  812  and connectors  814 . The magnet housings  812  and the connectors  814  can be integrally formed as a single, monolithic piece. In another example, the magnet housings  812  and the connectors  814  are coupled to form the magnet holder  804 . Other configurations can be suitably implemented. In some embodiments, each magnet housing  812  may have a trapezoidal shape when viewed from top-down. In this example, each magnet housing  812  houses two magnets (not shown) that are located adjacent to a first face  820  and a second face  822  of the magnet housing  812 , respectively. This arrangement may be similar to how  FIG. 6B  shows the pair of magnets  632  are arranged within the housing  630 . 
     In one non-limiting example, the fixed magnet assembly  800  is a single, monolithic piece that includes a plurality of magnet housings  812  separated by connectors  814 . In some cases, the fixed magnetic assembly is a unitary structure that includes a plurality of magnet housings  812 . A unitary fixed magnet assembly  800  can be formed, for example, of a magnetic material. In another non-limiting example, a unitary fixed magnet assembly  800  is formed of one or more non-magnetic materials, and a magnetic material is coupled to interior walls of the housing adjacent to the first face  820  and the second face  822  of each magnet housing  812 . Other configurations are possible. 
     The magnet holder  804  may have mounting holes  816  (e.g., in the connectors  814 ) for attaching the magnet holder  804  to the support plate  802 . For instance, fasteners (e.g., screws) can be inserted into the mounting holes  816  to affix the magnet holder  804  to the support plate  802  and form the fixed magnet assembly  800 . The support plate  802  of the fixed magnet assembly  800  can then be installed in (for example, affixed to) the diagnostic or preparatory apparatus using any suitable mechanism. In some embodiments, the fixed height (e.g., the up/down position) of the magnet holder  804  relative to the support plate  802  and the rest of the diagnostic or preparatory apparatus may be adjusted by adding a shim of a desired height measured in the z-direction between the magnet holder  804  and the supporting plate  802 . Installation of the fixed magnet assembly  800  can include selecting one of a plurality of shims of different heights from an installation kit, installing the selected shim in a receiving bay, and installing the fixed magnet assembly  800  over the shim in the z-direction. This can be particularly advantageous when a fixed magnet assembly is retrofitted into existing preparatory and diagnostic apparatuses in the field, in view of very slight differences in the dimensions and tight tolerances associated with receiving bays and racks implemented in the apparatuses. 
     Thus, the mixing tubes (e.g., container  608 - 3  or container  708 - 3 ) of the reagent holders may be received in the holes  806  of the support plate  802 , resulting in each mixing tube being in close proximity with a magnet in an adjacent magnet housing  812  (e.g., a magnet located behind either a first face  820  or second face  822  of the adjacent magnet housing  812 ). In some embodiments, the first face  820  and the second face  822  of each magnet housing  812  may be oriented at an angle that makes them parallel to the sloped wall of the mixing tubes (e.g., container  608 - 3  or container  708 - 3 ) when the mixing tubes are disposed in the holes  806 . Thus, the magnet located behind each first face  820  or second face  822  of the magnet housings  812  may also be oriented so as to be parallel to the sloped wall of the adjacent mixing tube, resulting in magnetic forces that are normal to the sloped wall of the mixing tube. 
     The shape and dimensions of the magnet housings  812  and the shape and dimensions of the connectors  814  that connect the magnet housings  812  can be advantageously tailored, such that they do not interfere with a skirt or flange of the receptacles of the reagent holder (e.g., receptacles  250 ) that receive the second snap-in container or the third snap-in container (e.g., containers  608 - 2  and  608 - 3 , respectively), when the fixed magnet assembly  800  is installed in the diagnostic or preparatory apparatus and a rack containing the reagent holder is loaded into a receiving bay of the diagnostic or preparatory apparatus. For example, the connectors  814  may have a selected depth (measured in the y-direction) and height (measured in the z-direction) in the portions near the holes  806 , such that the connectors  814  fit between the very small space between the second snap-in container and the third snap-in container of a reagent holder housed in a rack inserted into the receiving bay. This allows a magnetic force to be applied by the magnet housings  812  to the third snap-in container without physically interfering with the second snap-in container, which would otherwise be pushed through its receptacle and out the top of the reagent holder when the rack housing the reagent holder is inserted in the receiving bay if the dimensions of the magnet housings  812  and connectors  814  were not configured properly. 
     As in the illustrated embodiment, the fixed magnet assembly  800  can advantageously include magnet housings  812  that are configured to apply a magnetic force to the snap-in containers of two different reagent holders simultaneously (e.g., as with the magnet housing  630  in  FIG. 6B ). More specifically, a magnet housing  812  of the fixed magnet assembly  800  may include two magnets (not shown), one of which may apply a magnetic force to one side of a snap-in container of a reagent holder, and the other of which may apply a magnetic force to an opposing side of another snap-in container of a different reagent holder. In other words, the magnets in a magnet housing  812  may apply magnetic force to opposite sides of the snap-in tubes of adjacent reagent holders; adjacent magnets in the fixed magnet assembly  800  apply magnetic force to opposite sides of snap-in tubes of adjacent reagent holders. Although magnetic force is applied to different sides of snap-in containers depending on which magnet is in close proximity to the snap-in containers (as shown in  FIG. 6B ), the problem of magnetic extraction particle carry-over is effectively and consistently addressed for each of the reagent holders. This implementation may avoid having to place the magnets in a very tight space (e.g., between the third snap-in container and the second snap-in container of a reagent holder, as in the example of  FIGS. 7A-7B ). Instead, the magnets can be arranged at an oblique angle relative to the processing axis of each reagent holder, rather than being arranged on the processing axis. An example of this is shown by the arrangement of each pair of magnets  632  in the magnet housings  630  shown in  FIG. 6B . 
     In some embodiments, the fixed magnet assembly  800  may be implemented in a particular diagnostic or preparatory apparatus by affixing the support plate  802  to a cover  850  of the apparatus using a fastener, such as using very high bond tape. This approach may allow the fixed magnet assembly  800  to be inexpensively and quickly implemented into a particular apparatus on-site (e.g., at the location of the diagnostic or preparatory apparatus), but there may be unknown component variation among different apparatuses and also variation among all the potential personnel installing the fixed magnet assembly  800  into different apparatuses.  FIG. 8B  illustrates the same fixed magnet assembly  800  shown in  FIG. 8A  (including the support plate  802  and the magnet holder  804 ) affixed to the cover  850  of a diagnostic or preparatory apparatus. 
     More specifically,  FIG. 8B  shows how the fixed magnet assembly  800  can be implemented within a receiving bay of a diagnostic or preparatory apparatus, such as the receiving bay  500  of the diagnostic or preparatory apparatus shown in  FIGS. 5A-5B , so that when the receiving bay receives a rack with reagent holders inserted into the rack, the process tubes of those reagent holders are received in the holes  806  of the support plate  802  of the fixed magnet assembly  800 . Furthermore, the one or more movable magnets of a magnetic separator (not shown in this figure, but described above with reference to  FIGS. 3A-3C ) can apply a magnetic force to each process tube of the reagent holders in the rack. In addition, with the fixed magnet assembly  800  installed in this position, a constant, consistent magnetic force from the magnets of the fixed magnet assembly  800  (e.g., the magnets in the magnet housings  812 ) is also applied to each third snap-in container of the reagent holders in the rack. 
       FIG. 9  illustrates an isometric view of an embodiment of a fixed magnet assembly according to the disclosed technology that can be implemented into an automated diagnostic or preparatory apparatus. More specifically,  FIG. 9  shows an embodiment of a fixed magnet assembly  900  that is compliant in the z-direction (e.g., can move upward or downward in the z-direction when implemented in in the receiving bay of the diagnostic or preparatory apparatus). 
     The fixed magnet assembly  900  may include a support plate  902 , which may have dimensions suited to the particular diagnostic or preparatory apparatus in which the fixed magnet assembly  900  is implemented. In some embodiments, the support plate  902  may be a machined aluminum plate. The support plate  902  may include a set of recesses or holes  908 , each of which is configured to receive the bottom end of a container (e.g., mixing tube), such as container  708 - 3  shown in  FIGS. 7A-7B  or container  608 - 3  shown in  FIGS. 6A-6E . For instance, the indicated positions of the containers  608 - 3  shown in the conceptual view of  FIG. 6B  may coincide with the positions of holes  908  on the support plate  902 . 
     The fixed magnet assembly  900  may also include a magnet holder  904 , which may similarly have dimensions suited to the particular diagnostic or preparatory apparatus in which the fixed magnet assembly  900  is implemented. In some embodiments, the magnet holder  904  may be made of a material that is chemically resistant to cleaning agents. The magnet holder  904  may include a set of magnet housings  912  and connectors  914 . In some embodiments, each magnet housing  912  may have a trapezoidal shape when viewed from top-down. In this example, each magnet housing  912  houses two magnets (not shown) that are located adjacent to a first face  920  and a second face  922  of the magnet housing  912 , respectively. This arrangement may be similar to how  FIG. 6B  shows the pair of magnets  632  are arranged within the housing  630 . 
     The fixed magnet assembly  900  includes a mounting plate  906  positioned below the support plate  902 . The fixed magnet assembly includes a set of springs  924  (not visible in this view), with one end of each spring attached to the mounting plate  906  and an opposite end of each spring attached to the magnet holder  904  and/or the support plate  902 . Other biasing mechanisms, in addition to or as an alternative to springs  924 , can be suitable implemented. The springs  924  exert a biasing force against the support plate  902  in order to create a desired spacing between the mounting plate  906  and the support plate  902  when the springs are in an uncompressed state. To assemble the fixed magnet assembly  900  of this non-limiting embodiment, the magnet holder  904  is affixed to the support plate  902 . In some embodiments, the magnet holder  904  can be mechanically coupled to the support plate  902  using fasteners  919 , which may be received in mounting holes  918  of the magnet holder  904  and corresponding mounting holes of the support plate  902  (not shown). Next, the support plate  902  is affixed to the mounting plate  906 . The support plate  902  can be affixed using springs  924  that are coupled to the support plate  902  and the mounting plate  906 , which allow the support plate  902  to move up and down in the z-axis (e.g. by compressing or uncompressing the springs  924 ) relative to the mounting plate  906 . In some embodiments, the support plate  902  may additionally be mechanically coupled to the mounting plate  906  via fasteners  919 . The fasteners  919  may be inserted through mounting holes in the magnet holder  904  (e.g., mounting holes  918 ) and corresponding mounting holes of the support plate  902  (not shown) to affix the support plate  902  to the mounting plate  906 . In some embodiments, the fasteners  919  may be screws or shoulder bolts, and they may limit the maximum spacing between the mounting plate  906  and the support plate  902 . The fasteners  919  may place an upward limit to the upward movement of the support plate  902  in the z-direction away from the mounting plate  906 , but do not limit downward movement of the support plate  902  in the z-direction toward the mounting plate  906 . In some embodiments, the fasteners  919  may additionally restrict the movement of the support plate  902  in the x-axis and y-axis. The fixed magnet assembly  900  can then be affixed to the receiving bay of a diagnostic or preparatory apparatus, such as by affixing the mounting plate  906  to the cover of the diagnostic and preparatory apparatus using a fastener, such as a very high bond tape or fasteners received in the mounting plate  906 . Other fasteners can be suitably implemented in accordance with the disclosed technology. 
     Advantageously, the support plate  902  of the installed fixed magnet assembly  900  can move upward or downward in the z-direction in the receiving bay before and during insertion of a rack in the receiving bay, because the springs  924  allow movement of the support plate  902  in the z-direction relative to the mounting plate  906  fixed to the cover. This feature may allow for the mixing tubes (e.g., container  608 - 3  or container  708 - 3 ) of the reagent holders to be properly positioned relative to the magnets in the magnet holder  904  without requiring that exact magnet positioning (e.g., via designing, building, and positioning the fixed magnet assembly with very tight tolerances) be accurately and consistently reproduced across each of a plurality of apparatuses in which a fixed magnet assembly is installed. For example, as a rack is inserted into the receiving bay, a bottom surface of the rack can contact a top surface of the magnet holder  904 . In one non-limiting example, this contact takes place between a bottom surface of the rack and a top surface of one or more magnet housings  912 . This contact can cause the magnet holder  904  and the support plate  902  to lower in the z-direction, thereby compressing the springs  924  located between the support plate  902  and the mounting plate  906 . As the rack continues to be inserted into the receiving bay, the magnet holder  904  and the support plate  902  continue to lower in the z-direction until they reach a position that precisely positions the magnet housings  912  relative to the mixing tubes of the reagent holders, as well as precisely positions the mixing tubes of the reagent holders in the holes  908  of the support plate  902 . In one non-limiting embodiment, as the springs  924  are compressed, the support plate  902  lowers relative to the mounting plate  906  until it reaches a point where the rack has reached its lowermost position within the receiving bay, at which point the bottom portions of the mixing tubes of the reagent holders will be reliably and accurately disposed in the holes  908  of the support plate  902 . This arrangement results in each mixing tube being in close proximity with a magnet in an adjacent magnet housing  912  (e.g., behind either a first face  920  or second face  922  of the adjacent magnet housing  912 ), independent of specific dimensional variations in the rack that is used to insert the holders into the receiving bay and independent of specific dimensional variations in the receiving bay that receives the holders. Accordingly, this arrangement for providing magnetic energy to the mixing tube of a plurality of holders using a support plate  902  that is adjustable in the z-direction can be reliably and accurately reproduced across many different apparatuses, independent of variations in the dimensions and tolerances between the receiving bay and the rack of the apparatus. 
     In some embodiments, the first face  920  and the second face  922  of each magnet housing  912  may be oriented at an angle that makes them parallel to the sloped wall of the mixing tubes (e.g., container  608 - 3  or container  708 - 3 ) when the mixing tubes are disposed in the holes  908 . Thus, the magnet located adjacent to each first face  920  or second face  922  inside the magnet housings  812  may also be oriented so as to be parallel to the sloped wall of the adjacent mixing tube, resulting in magnetic forces that are normal to the sloped wall of the mixing tube. 
     Advantageously, embodiments of the fixed magnet assembly  900  according to the disclosed technology can allow the fixed magnet assembly  900  to be implemented into a particular diagnostic and preparatory apparatus on-site (e.g., at the location of the diagnostic and preparatory apparatus) using nominal magnet positioning. 
       FIG. 10A  illustrates an isometric view of an embodiment of a fixed magnet assembly that can be implemented accordingly to the disclosed technology into an automated diagnostic or preparatory apparatus. More specifically,  FIG. 10A  shows an embodiment of a fixed magnet assembly  1000  that is compliant in the z-direction (e.g., can move upward or downward in the z-direction when implemented in the receiving bay of the diagnostic or preparatory apparatus).  FIG. 10B  illustrates a transparent perspective view of a reagent holder interacting with the fixed magnet assembly  1000  of  FIG. 10A , in order to demonstrate how a third snap-in container  1030  of the reagent holder may be seated in a hole  1008  of the support plate  1002  of the fixed magnet assembly  1000 , once the fixed magnet assembly  1000  is installed and a rack containing the reagent holder is loaded into the receiving bay of the diagnostic or preparatory apparatus. 
     The fixed magnet assembly  1000  may include a support plate  1002 , which may have dimensions suited to the particular diagnostic or preparatory apparatus in which the fixed magnet assembly  1000  is implemented. In some embodiments, the support plate  1002  may be a machined aluminum plate. The support plate  1002  may include a set of recesses or holes  1008 , each of which is configured to receive the bottom end of a container (e.g., mixing tube), such as container  708 - 3  shown in  FIGS. 7A-7B  or container  608 - 3  shown in  FIGS. 6A-6E . For instance, the indicated positions of the containers  608 - 3  shown in the conceptual view of  FIG. 6B  may coincide with the position of holes  1008  on the support plate  1002 . 
     The fixed magnet assembly  1000  may also include a set of magnet housings  1012 . In some embodiments, the magnet housings  1012  may be made of a material that is chemically resistant to cleaning agents. The magnet housings  1012  may have a trapezoidal shape when viewed from top-down. In this example, each magnet housing  1012  houses two magnets (not shown in  FIG. 10A  but visible in  FIG. 10B ) that are located adjacent to a first face  1020  and a second face  1022  of the magnet housing  1012 , respectively. This arrangement may be similar to how  FIG. 6B  shows the pair of magnets  632  are arranged within the housing  630 . 
     The fixed magnet assembly  1000  includes a mounting plate  1006  positioned below the support plate  1002 . The fixed magnet assembly  1000  includes a set of springs  1024  with one end of each spring attached to the mounting plate  1006  and an opposite end of each spring attached to the magnet housings  1012  and/or the support plate  1002 . Other biasing mechanisms, in addition to or as an alternative to springs  1024 , can be suitably implemented. There may be spacing between the support plate  1002  and the mounting plate  1006  when the springs  1024  are in an uncompressed state. 
     The springs  1024  exert a biasing force against the support plate  1002  in order to create a desired spacing between the mounting plate  1006  and the support plate  1002  when the springs are in an uncompressed state. In some embodiments, the support plate  1002  may additionally be mechanically coupled to the mounting plate  1006  via fasteners  1019 . The maximum spacing between the mounting plate  1006  and the support plate  1002  may be limited by fasteners  1019  (e.g., screws or shoulder bolts) inserted through mounting holes  1018  in the support plate  1002 . These fasteners  1019  are inserted into the mounting holes  1018  to affix the support plate  1002  to the mounting plate  1006  to form the fixed magnet assembly  1000 . In this example, the heads of the fasteners  1019  inserted in the mounting holes  1018  place an upward limit to the upward movement of the support plate  1002  in the z-direction away from the mounting plate  1006 , but do not limit downward movement of the support plate  1002  in the z-direction toward the mounting plate  1006 . In some embodiments, the fasteners  1019  may additionally restrict the movement of the support plate  1002  in the x-axis and y-axis. The fixed magnet assembly  1000  can then be affixed to the diagnostic or preparatory apparatus, such as by affixing the mounting plate  1006  to the cover of the diagnostic and preparatory apparatus using a fastener, such as a very high bond tape or other suitable fastener. 
     Advantageously, the spring-mounted support plate  1002  of the installed fixed magnet assembly  1000  can move upward or downward in the z-direction in the receiving bay before and during insertion of a rack in the receiving bay, because the springs  1024  allow movement of the support plate  1002  in the z-direction relative to the mounting plate  1006  fixed to the cover. This feature may allow for the mixing tubes (e.g., container  608 - 3  or container  708 - 3 ) of the reagent holders to be accurately and consistently positioned relative to the magnets in the magnet housings  1012  without requiring that exact magnet positioning be accurately and consistently reproduced across each of a plurality of apparatuses in which a fixed magnet assembly is installed. For example, the mixing tubes of the reagent holders may be received in the holes  1008  of the support plate  1002 , and the mixing tubes (or another portion of the rack in contact with the complaint support plate  1002 ) may press down in the z-direction on the support plate  1002 , compressing the springs  1024  located between the support plate  1002  and the mounting plate  1006 . As the springs  1024  are compressed, the support plate  1002  lowers relative to the mounting plate  1006  until it reaches a point where the rack has reached its lowermost position within the receiving bay, at which point the bottom portions of the mixing tubes of the reagent holders will be reliably and accurately disposed in the holes  1008  of the support plate  1002 . This arrangement results in each mixing tube being in close proximity with a magnet in an adjacent magnet housing  1012  (e.g., behind either a first face  1020  or second face  1022  of the adjacent magnet housing  1012 ), independent of specific dimensional variations in the rack that is used to insert the holders into the receiving bay and independent of specific dimensional variations in the receiving bay that receives the holders. Accordingly, this arrangement for providing magnetic energy to the mixing tube of a plurality of holders using a support plate  1002  that is adjustable in the z-direction can be reliably and accurately reproduced across many different apparatuses, independent of variations in the dimensions and tolerances between the receiving bay and the rack of the apparatus. 
     In some embodiments, the first face  1020  and the second face  1022  of each magnet housing  1012  may be oriented at an angle that makes them parallel to the sloped wall of the mixing tubes (e.g., container  608 - 3  or container  708 - 3 ) when the mixing tubes are disposed in the holes  1008 . Thus, the magnet located adjacent to each first face  1020  or second face  1022  inside the magnet housings  1012  may also be oriented so as to be parallel to the sloped wall of the adjacent mixing tube, resulting in magnetic forces that are normal to the sloped wall of the mixing tube. 
     This can be more easily understood from  FIG. 10B , which illustrates a transparent view of the fixed magnet assembly  1000  to more easily demonstrate features of the disclosed technology. Embodiments of the fixed magnet assembly, the mixing tube, and the holder need not be transparent. A mixing tube  1030  of a holder (e.g., a container in the third position from the process tube at the distal end of the holder) is shown seated in a hole  1008  of the fixed magnet assembly  1000 . In this position, the mixing tube  1030  is positioned in close proximity to a magnet housing  1012  having a first face  1020  and a second face  1022 . It can be seen from  FIG. 10B  that a magnet  1040  is positioned behind the first face  1020  and a magnet  1042  is positioned behind the second face  1022 . The magnet  1042  is in close proximity to (within about 2 mm of) the mixing tube  1030  when the mixing tube  1030  is seated in the hole  1008  of the fixed magnet assembly  1000 , and it can be seen that the magnet  1042  has a sloped orientation at an angle that matches the sloped wall of the mixing tube  1030 . 
     Advantageously, the magnet housing  1012  is dimensioned such that it does not interfere with the second snap-in container (not shown, but analogous to container  608 - 2  shown in  FIG. 6E ) of the reagent holder. Furthermore, the magnet housing  1012  may also be advantageously dimensioned to not interfere with the skirt or flange of either the second or third receptacle that receives the second snap-in container or third snap-in container  1030 , respectively. 
     It will be understood that embodiments of the disclosed technology are not limited to applying a fixed magnetic force to a holder as described above with reference to  FIGS. 2A-10B . Similarly, it will be understood that embodiments of the disclosed technology are not limited to applying a fixed magnetic force to a holder in an automated diagnostic or preparatory apparatus discussed above with reference to  FIG. 1B . The disclosed technology can be advantageously implemented in any apparatus that receives a holder for processing and manipulating magnet substrates within a container of the holder. A non-limiting example automated apparatus configured to apply a fixed magnetic force to a non-limiting example holder in accordance with the disclosed technology will now be described with reference to  FIGS. 11-15D  to further illustrate certain advantageous features of the disclosed technology.  FIG. 11  is an isometric view of the internals  1100  of some embodiments of a diagnostic or preparatory apparatus. 
     This illustrated embodiment of a diagnostic or preparatory apparatus may be similarly used to extract polynucleotides from samples and prepare them in PCR-ready form. This diagnostic or preparatory apparatus may be similar to the one disclosed in PCT Application No. WO2017/184244, filed on Feb. 17, 2017 (entitled “Automated Diagnostic Analyzer and Method for its Operation”), the disclosure of which is hereby incorporated here by reference in its entirety. 
     Notably, this embodiment of the diagnostic or preparatory apparatus may not use reagent holders containing pre-packaged reagents used in sample preparation, such as reagent holders in the form shown in  FIGS. 2A-2C  that are loaded into racks to be received by the diagnostic or preparatory apparatus. Instead, this diagnostic or preparatory apparatus may receive processing plates  1140  that do not include pre-packaged reagents, and the reagents for sample preparation may be stored separately at a different location on a processing deck  1116 . The processing plates  1140  are described in more detail in connection to  FIGS. 12A-12B . 
     For instance, there may be a dry reagent plate  1150  that includes a plurality of dry reagent compartments that are sealed by a penetrable membrane placed over each of the dry reagent compartments. In some embodiments, there may be  96  total dry reagent compartments in the dry reagent plate  1150 , and each reagent compartment within the same plate  1150  is loaded with the same reagent so that the reagent plate is assay specific. However, multiple dry reagent plates  1150  can be used, depending on the assay or procedure, and separate reagent plates each with reagents specific to that assay can be utilized. For instance, to prepare a sample into PCR-ready form, there may be a first dry reagent plate (e.g., an extraction reagent plate) containing lysis buffer and magnetic particles (e.g., extraction beads) and a second dry reagent plate (e.g., an amplification reagent plate) containing master mix reagent. In other embodiments, different reagents can be combined on a single dry reagent plate  1150  (e.g., the extraction reagent plate and amplification reagent plate can be combined). 
     The apparatus may also include a liquid reagent plate  1160 . The liquid reagent plate  1160  may include a plurality of reagent compartments organized in four processing rows, and each processing row may include four compartments where each compartment holds a reagent for a sample processing step. For example, each processing row may include a first compartment for a reconstitution buffer, a second compartment for a wash buffer, a third compartment for an elution buffer, and a fourth compartment for a neutralization buffer. These compartments can be arranged in the order in which they are used. However, they could be in other arrangements. In addition, each compartment holds enough reagent to process a full batch of samples, for example a batch of 24 total samples. A penetrable membrane (not shown) is placed over each of these compartments and is sealed to the liquid reagent plate  1160  so that if the membrane is penetrated to obtain access to one compartment, the remaining compartments remain sealed. This allows liquid reagent plate  1160  to be stored until needed for another batch of samples. 
     In some embodiments, the processing plates  1140  may have holes in which pipette tips may be parked, and there may be elongate openings  1117  on the processing deck  1116  that allows the reusable pipette tips parked in the processing plates  2040  to extend therethrough. In some embodiments, the processing deck  1116  may include a pipette tip chute  1135 , in which used pipette tips may be disposed. In some embodiments, the internals  1100  of the diagnostic or preparatory apparatus may include a bay configured to receive an amplification cartridge  1170  that includes microfluidic channels and amplification chambers for performing amplification of a processed sample. 
       FIG. 12A  is an isometric view of an example processing plate  1240  used in some embodiments of a diagnostic or preparatory apparatus describe with reference to  FIG. 11 .  FIG. 12B  is a top-down view of an arrangement of two processing plates  1240  when inserted for use into a receiving bay of some embodiments of the diagnostic or preparatory apparatus. This arrangement of the two processing plates  1240  may allow for 24 samples to be processes (12 from each processing plate  1240 ).  FIGS. 12A and 12B  are described together. The processing plate  1240  may the same or substantially similar to the processing plate  1140  described above with reference to  FIG. 11 . It will be understood that the disclosed technology is not limited to the specific features of the example processing plate  1240  and other suitably-configured processing plates can be implemented in the disclosed technology. 
     The processing plate  1240  may include a plate body  1241 , which may partially define a plurality of process tubes  1244 , mixing tubes  1246 , and pipette tip holding stations  1247 . The plate body  1241  may have a circular opening for each of the process tubes  1244 , mixing tubes  1246 , and pipette tip holding stations  1247 . The process tubes  1244  may have a tube body  1245  that extends from the bottom of the plate body  1241 , and the tube body  1245  may have a conical surface of revolution. The mixing tubes  1246  may also have a tube body (not shown, but visible in  FIG. 13B ) that extends from the bottom of the plate body  1241 , which may also have a conical surface of revolution. The pipette tip holding stations  1247  may have a sleeve (not shown, but visible in  FIG. 13B ) that extends from the bottom of the plate body  1241 . The sleeve may keep a pipette tip parked in the pipette tip holding station  1247  stable when disposed therein, even if the processing plate  1240  is moved. 
     In some embodiments, the process tubes  1244  may be alternatively referred to as extraction tubes or lysis tubes. In some embodiments, the mixing tubes  1246  may be alternatively referred to as mixing wells. The process tubes  1244  may be located closer to the middle of the plate body  1241  than the mixing tubes  1246 , and the mixing tubes  1246  may be located closer to the middle of the plate body  1241  than the pipette tip holding stations  1247 . Other configurations can be suitably implemented in the disclosed technology. 
     In some embodiments, the processing plate  1240  may include two rows of process tubes  1244 , mixing tubes  1246 , and pipette tip holders  1247  that are arranged parallel to each other. In the illustrated embodiment, the processing plate  1240  includes two rows of 6 process tubes  1244 , two rows of 6 mixing tubes  1246 , and two rows of 6 pipette tip holding stations  1247 . However, more or less is contemplated (e.g., the processing plate  1240  can include two rows of 12 process tubes  1244 , mixing tubes  1246  and pipette tip holding stations  1247  or even a single row of such). The processing of a single sample may involve one of the process tubes  1244  and its corresponding mixing tube  1246  and pipette tip holding station  1247  that are aligned with it in the same column. Thus, a single processing plate  1240  may allow 12 samples to be processed therein. 
     In some embodiments, the processing plate  1240  may include engagement members  1249  on the top surface of the processing plate  1240 . The engagement members  1249  may include engagement notches  1242 . The engagement members  1249  and the engagement notches  1242  may allow the processing plate  1240  to be grasped and moved by features (e.g., a robotic arm) of the diagnostic or preparatory apparatus for sample processing. 
       FIG. 13A  is an isometric view of the internals of some embodiments of a diagnostic or preparatory apparatus.  FIG. 13B  is a side profile view of the internals of some embodiments of a diagnostic or preparatory apparatus, with a processing plate in position for sample processing.  FIGS. 13A and 13B  are described together. 
     As can be seen in  FIG. 13A , a first extractor  1340  and a second extractor  1350  are visible as part of a single assembly, which may include, among other things, a housing  1342 , printed circuit boards  1347  (“PCB”), a motor  1344 , a number of heater assemblies  1348 , and a number of magnetic separators  1341 . There may be any number of heating assemblies  1348  and magnetic separators  1341 . In some embodiments, the heater assemblies  1348  and the magnetic separators  1341  can be controlled by electronic circuitry such as on the PCBs  1347  (e.g., to cause the heater assemblies  1348  to apply heat independently to the process tubes of the processing plate(s)). It can also be configured to cause the magnetic separators  1341  to move up and down relative to the process tubes of the processing plate(s). 
     Similarly to the heater assembly  300  shown in  FIGS. 3A-3C , a heater assembly  1348  may comprise one or more independently-controllable heater units, each of which comprises a heat block  1349 . The heat blocks  1349  may be fashioned from a single piece of metal or other material, or may be made separately from one another and mounted independently of one another or connected to one another in some way. Thus, a heater assembly  1348  may include a collection of heater units but does not require the heater units or their respective heat blocks  1349  to be attached directly or indirectly to one another. Each of the heat blocks  1349  may be configured to align with and to deliver heat to a process tube  1314  of a processing plate  1310  (similar to a process tube  1244  of the processing plate  1240  shown in  FIG. 12A ), and the heater assembly  1348  can be configured so that each heater unit independently heats each of the one or more process tubes  1314  of the processing plate  1310 , for example by permitting each of the one or more heat blocks  1349  to be independently controllable, as further described herein. There may be any number of independently-controllable heater units in one of the heater assemblies  1348 . In various embodiments, there may be 2, 3, 4, 5, 6, 8, 10, 12, 16, 20, 24, 25, 30, 32, 36, 40, 48, or 50 independently-controllable heater units in a heater assembly  1348 . There may be any number of heating assemblies  1348  used in the diagnostic or preparatory apparatus. 
     Similarly to the magnetic separator  370  shown in  FIGS. 3A-3C , a magnetic separator  1341  may be configured to move one or more magnets  1354  relative to the one or more process tubes  1314  of processing plate  1310  (similar to process tubes  1244  of the processing plate  1240 ). The magnetic separator  1341  may move magnets  13541350  into close proximity to the process tubes  1314  (e.g., with each magnet  1354  of the magnetic separator  1341  having a face less than 2 mm, between 2 mm and 1 mm, or less than 1 mm away from the exterior surface of an adjacent process tube without being in contact with the process tube) in order to separate magnetic particles in the process tubes. 
     Structurally, a magnetic separator  1341  may include: one or more magnets  1354  affixed to a supporting member  1352 ; a motorized mechanism configured to move the supporting member  1352  in such a manner that the one or more magnets  1354  move backwards and forwards along a fixed axis (e.g., see motor  1344 ), and during at least a portion of the motion, the one or more magnets  1354  maintain close proximity to one or more process tubes  1314  which contain the magnetic particles in solution; and control circuitry to control the motorized mechanism (e.g., PCB  1347 ). The magnetic separators  1341  may operate together with the heater assemblies  1348  to permit successive heating and separation operations to be performed on liquid materials in the one or more process tubes  1314  without transporting either the liquid materials or the process tubes to different locations to perform either heating or separation. Such operation is also advantageous because it means that the functions of heating and separation which, although independent of one another, are both utilized in sample preparation, may be performed with a compact and efficient apparatus. 
     In the illustrated embodiment, there are four heating assemblies  1348 , with each heating assembly  1348  having 6 independently-controllable heater units each comprising a heater block  1349 . Up to two processing plates  1310  can be used at a time, and each processing plate  1310  involves the use of two heating assemblies  1348  with a magnetic separator  1341  between those two heating assemblies  1348 . The magnetic separator  1341  may have two rows of 6 magnets (e.g., a row of 6 magnets on each side of the magnetic separator  1341 ), so as to form six pairs of adjacent magnets which face the two heating assemblies  1348  straddling the magnetic separator  1341 . This side-by-side pairing of magnets may enhance the magnetic attraction of magnetic extraction particles within a process tube  1314  of a processing plate  1310  over that of a single magnet. Each magnet in the magnetic separator  1341  may be positioned to be adjacent to a heat block  1349  of one of the two heating assemblies  1348  when the magnetic separator  1341  is in a raised position. Each of the 12 heat blocks  1349  among those two heating assemblies  1348  may be specifically positioned to receive one of the 12 process tubes  1314  of the processing plate  1310  (e.g., the two rows of 6 process tubes  1244  shown in  FIG. 12A ). When motor  1344  is operated, the rows of magnets in the magnetic separator  1341  may be moved up into a space between the two rows of heat blocks  1349  to be in close proximity to the process tubes  1314  disposed therein. 
     As described earlier, in some cases, the magnetic separators  1341  can be integrated with the heater assemblies  1348  (e.g., one of the magnetic separators  1341  and the two heating assemblies  1348  straddling it), and they may be collectively referred to as an integrated magnetic separator and heater assembly. Additionally, although not shown in  FIGS. 13A and 13B , an enclosure can cover the internals of the diagnostic or preparatory apparatus (including the magnetic separators  1341  and heater assemblies  1348 ) for protection of sub-assemblies and aesthetics. 
       FIG. 14A  illustrates a top-down conceptual view of a processing plate used in some embodiments of a diagnostic or preparatory apparatus. More specifically,  FIG. 14A  shows an example processing plate  1400  (similar to the processing plate  1240  shown in  FIGS. 12A and 12B ) that can be used with some embodiments of an automated diagnostic or preparatory apparatus (e.g., the ones described in  FIGS. 11, 13A, and 13B ). The processing plate  1400  may have two rows of process tubes  1442 , two rows of mixing tubes  1444 , and two rows of pipette tip holding stations  1446 . 
     Each process tube  1442  may be associated with a mixing tube  1444  and a pipette tip holding station  1446 , and they may be aligned along a processing axis  1410 , with the diagnostic or preparatory apparatus configured to perform processing and operations (e.g., the transfer of liquids) along each processing axis  1410 . Accordingly, a total of n processing axes  1410  may be conceptualized—one for each process tube  1442  in the processing plate  1400 . 
     When the processing plate  1400  is in use by the automated diagnostic or preparatory apparatus, a magnetic separator (e.g., magnetic separator  1341 ) having two rows of magnets may be positioned between the two rows of process tubes  1442 . This can be seen in  FIG. 13B . Each row of magnets of the magnetic separator may be aligned on a common axis (e.g., the common axis that passes through the midpoint of the magnets in that row), which may be referred to as a first magnet axis. Thus, a magnetic separator having two rows of magnets may have a first magnet axis for each of the two rows, which are represented by the first magnet axes  1412  in  FIG. 14A . Each first magnet axis  1412  may run horizontally, parallel to the adjacent row of process tubes  1442 . Each first magnet axis  1412  may be positioned, such that, when the magnetic separator is raised, the magnets of the magnetic separator that are aligned on that first magnet axis  1412  come into close proximity with the process tubes  1442  in the adjacent row of process tubes  1442  (e.g., within 2 mm of each process tube  1442  in the row). 
     In some embodiments, two separate fixed magnet assemblies may be implemented into the automated diagnostic or preparatory apparatus. Each fixed magnet assembly may include a set of magnets in a row, which may be aligned on a common axis (e.g., the common axis that passes through the midpoint of all the magnets). This common axis associated with a fixed magnet assembly may be referred to as a second magnet axis. The second magnet axes for both fixed magnet assemblies are represented by the second magnet axes  1414  in  FIG. 14A . The two fixed magnet assemblies can be positioned so that each of the second magnet axes  1414  is close to one of the two rows of mixing tubes  1444 , such that the magnets of a fixed magnet assembly are in close enough proximity to the adjacent row of mixing tubes  1444  to exert a magnetic force on any magnetic extraction particles contained in those mixing tubes  1444 . The magnetic force can be of a sufficient strength to hold magnetic extraction particles in solution in the mixing tubes  1444  against an interior wall of the mixing tubes  1444 , for example while the solution is being transferred out of the mixing tubes  1444  during a pipetting operation. With two separate fixed magnet assemblies, each second magnet axis  1414  may run horizontally through one of the two rows of mixing tubes  1444 . Alternatively, a second magnet axis  1414  can run behind or in front of a row of mixing tubes  1444 , in either case in close enough proximity to impart a magnetic force on the contents of the mixing tubes  1444  and capture any magnetic extraction particles contained therein. Additionally, each second magnet axis  1414  may be spaced far enough apart from the closest first magnet axis  1414  such that the magnets of the fixed magnet assembly do not interfere with the magnets of the magnetic separator. For example, each first magnet axis  1412  can be spatially separated from a corresponding second magnet axis  1414  a distance “D” such that the one or more magnets aligned along the first magnet axis  1412  do not exert a magnetic force on contents of the mixing tubes  1444 , and one or more magnets aligned along the second magnet axis  1414  do not exert a magnetic force on contents of the process tubes  1442 . 
     The first magnet axes  1412  and the second magnet axes  1414  are further shown in  FIG. 14B , which may provide additional context for understanding the first magnet axes  1412  and the second magnet axes  1414 .  FIG. 14B  illustrates a top-down conceptual view of the positions of certain components of a processing plate relative to magnets in some embodiments of a diagnostic or preparatory apparatus, in accordance with one configuration of a fixed magnet assembly. 
     More specifically,  FIG. 14B  shows the positions of two rows of process tubes  1442  and mixing tubes  1444  of a processing plate, along with the processing axis  1410  associated with each of the process tubes  1442 . A magnetic separator  1420  having two rows of magnets  1422  is located between the two rows of process tubes  1442 . It can be seen that there are two different first magnet axes  1412 , which correspond to each of the two rows of magnets  1422  of the magnetic separator  1420 . In this example implementation, the magnets  1422  are in one-to-one correspondence with the process tubes  1442 . In practice, when the magnetic separator  1420  is raised to bring the magnets  1422  into close proximity to the process tubes  1422 , the magnets  1422  exert a magnetic force (shown as vertical vectors in  FIG. 14B ) on the contents of the process tubes  1442 . 
     Also shown in  FIG. 14B  are the magnets  1432  of two separate fixed magnet assemblies according to the disclosed technology. In some embodiments, the magnets  1432  of a fixed magnet assembly can be arranged in pairs. Each pair of magnets  1432  can be located within a housing  1430 . A fixed magnet assembly may include multiple housings  1430 . The pairs of magnets  1432  can be positioned within the diagnostic or preparatory apparatus, such that each pair of magnets  1432  is located between two adjacent mixing tubes  1444  of a processing plate (in the manner shown in the figure) when the processing plate is in the receiving bay of the diagnostic or preparatory apparatus. There may be a magnet  1432  for each mixing tube  1444  in the processing plate, and when the processing plate is in the receiving bay of the diagnostic or preparatory apparatus, each magnet  1432  may be in close proximity with an adjacent mixing tube  1444 . All of the magnets  1432  of a fixed magnet assembly may be aligned on (or substantially aligned on) a second magnet axis  1414 . With two separate fixed magnet assemblies, there are two separate second magnet axes  1414 , each of which corresponds to the row of magnets  1432  in one of the two fixed magnet assemblies. In this example implementation, the magnets  1432  are in one-to-one correspondence with the mixing tubes  1444 , and each of the magnets  1432  may exert a magnetic force (shown as horizontal vectors in  FIG. 14B ) on the contents of an adjacent mixing tube  1444 . 
       FIG. 14C  illustrates a side profile conceptual view of the positions of certain components of a processing plate relative to magnets in some embodiments of a diagnostic or preparatory apparatus, in accordance with embodiments disclosed herein. 
     More specifically,  FIG. 14C  shows a process tube  1442 , a mixing tube  1444 , and a pipette tip holding station  1446  associated with one processing axis  1410  of a processing plate  1400 . The process tube  1442  may be used during sample preparation for cell lysis and extraction of nucleic acids, such as DNA or RNA of a patient, and DNA or RNA of a pathogen. The process tube  1442  may be positioned in a location such that the process tube  1442  disposed within a heater block  1460  of a heater assembly (e.g., heater assembly  1348  shown in  FIG. 13A ) when the processing plate  1400  is in the receiving bay of the diagnostic or preparatory apparatus. A first magnet  1422  of the magnetic separator may be raised to be in close proximity to the process tube  1442  in order to exert a magnetic force on the contents of the process tube  14442 . The mixing tube  1444  may be positioned in a location that is in close proximity to a second magnet  1432  of a fixed magnet assembly, such that the second magnet  1432  exerts a magnetic force on the contents of the mixing tube  1444 . 
     Preparation of a sample with this added fixed magnet assembly may proceed as follows. In some embodiments, the diagnostic or preparatory apparatus may pierce the extraction tube of an extraction plate (e.g., sealed dry reagent compartments of a dry reagent plate  1150 ) containing extraction reagent, which can include magnetic extraction particles, a lyophilized extraction reagent (e.g., dried lysis reagent), and internal controls. The magnetic particles may be configured to bind to specific molecules (e.g., DNA/RNA) in the sample. The diagnostic or preparatory apparatus may also pierce the relevant reagent compartments of a liquid reagent plate  1160 . The diagnostic or preparatory apparatus may then transfer some raw sample into the process tube  1442 . The amount of raw sample transferred may depend on the type of assay or procedure. The diagnostic or preparatory apparatus may move some of the extraction reagent (e.g., an extraction buffer) from the extraction tube of the extraction plate into the process tube  1442 . 
     The contents of process tube  1442 , which is disposed in the heater block  1460  of a heater unit, are then heated by the heater block  1460 . The temperature and duration of the heating is determined by the type of assay or procedure. The heating and lysis reagent causes the cells from the sample to break open, and some of the target nucleic acid (for example, DNA or RNA) contained in the cells and the internal controls may attach or bind to the magnetic particles (e.g., magnetic binding particles or beads). 
     The first magnet  1422  of the magnetic separator may be raised until it is in close proximity to the process tube  1442 . The magnet  1422  may exert a magnetic force on the magnetic particles in the process tube  1442 , drawing the magnetic particles and the attached nucleic acid to the side of the process tube  1442 . The diagnostic or preparatory apparatus may extract the liquid from the process tube  1442  while the magnet  1422  is still drawing the magnetic particles and attached nucleic acid to the side of the process tube  1442 . Ideally under normal operating, this liquid should not contain the magnetic particles and attached nucleic acid, which are held against the inner side wall of the process tube  1442  as the liquid is extracted. The diagnostic or preparatory apparatus may dispense of the extracted liquid. 
     The first magnet  1422  of the magnetic separator may be lowered, thereby removing the magnetic force holding the magnetic particles and the attached nucleic acid to the side of the process tube  1442 . The diagnostic or preparatory apparatus can transfer wash buffer into the process tube  1442  (e.g., from a reagent compartment of a liquid reagent plate  1160 ) to be mixed in with the magnetic particles bound to nucleic acid in the process tube  1442 . Afterwards, the first magnet  1422  of the magnetic separator may be raised again until it is in close proximity to the process tube  1442 . The magnet  1422  may exert a magnetic force on the magnetic particles in the process tube  1442 , again drawing the magnetic particles and the attached nucleic acid to the side of the process tube  1442 . 
     With the magnetic particles moved to the side of the process tube  1442 , the liquid contents (e.g. primarily the added wash buffer) can be extracted from the process tube  1442  and disposed of. Ideally under normal operating conditions, this extracted liquid should not contain the magnetic particles and attached nucleic acids, which are held against the inner side wall of the process tube  1442  as the liquid is extracted. Afterwards, the first magnet  1422  of the magnetic separator may be lowered, thereby removing the magnetic force holding the magnetic particles and the attached nucleic acid to the side of the process tube  1442 . 
     An elution or release buffer (e.g., from a reagent compartment of a liquid reagent plate  1160 ) can be added to the process tube  1442 , which contains the magnetic particles and attached nucleic acid. The release buffer may cause the magnetic particles to separate from the nucleic acid and internal controls. The diagnostic or preparatory apparatus can transfer neutralizing buffer (e.g., from a reagent compartment of a liquid reagent plate  1160 ) to the mixing tube  1444 , which is empty up to this point. At this point, the process tube  1442  will contain the magnetic particles, the separated nucleic acid (e.g., DNA/RNA), and internal controls. The mixing tube  1444  contains neutralizing buffer. 
     The heater block  1460  is activated a second time to heat the contents of the process tube  1442 . The temperature and duration of the heating will be dependent on the assay or procedure performed. The first magnet  1422  of the magnetic separator may be raised yet again, until it is in close proximity to the process tube  1442 . The first magnet  1422  may exert a magnetic force on the magnetic particles in the process tube  1442 , drawing the magnetic particles to the inner side wall of the process tube  1442  (but not the nucleic acid, e.g., DNA/RNA molecules, which are no longer attached to the magnetic particles). While the magnetic particles are drawn to and held against the inner side wall of the process tube  1442  by the first magnet  1422 , the liquid contents (e.g. the nucleic acid mixture with the added release buffer) are extracted from the process tube  1442  without extracting the magnetic particles. The nucleic acid mixture can be transferred to the mixing tube  1444  that contains the neutralizing buffer. The neutralizing buffer is configured to lower the pH of the nucleic acid mixture to a neutral pH. The first magnet  1422  of the magnetic separator may be lowered. 
     In some embodiments, a dry reagent compartment of an amplification reagent plate, which contains PCR master mix reagent containing probes and primers used in PCR amplification, may be accessed. The PCR master mix reagent may be in the form of a lyophilized bead. The diagnostic or preparatory apparatus may transfer the contents of the mixing tube  1444  into the compartment of the amplification reagent plate containing the PCR master mix reagent, and the neutralized nucleic acid mixture from the mixing tube  1444  may dissolve the PCR master mix pellet. However, as the contents are extracted from the mixing tube  1444 , the second magnet  1432  of the fixed magnet assembly may exert a magnetic force on the contents of the mixing tube  1444 . In particular, there may be some magnetic particles (e.g., beads) that were transferred into the mixing tube  1444  from the process tube  1442  despite efforts to prevent this from occurring (e.g., using the first magnet  1422  to keep the magnetic particles in the process tube  1422 ). The second magnet  1432  may be used as part of an additional filtering step to remove any leftover magnetic particles, carried over from the process tube  1422  (e.g., “carryover” magnetic particles), from the neutralized nucleic acid mixture as it is extracted from mixing tube  1444 . 
     The resulting mixed solution in the dry reagent compartment of the amplification reagent plate, which contains rehydrated PCR master mix reagent and the neutralized nucleic acid mixture, can be transferred to a device, including a storage device where the sample is stored or a microfluidic cartridge where it is amplified (e.g., the microfluidic cartridge  1170  shown in  FIG. 11 ). 
       FIGS. 15A-15D  illustrate isometric views of a fixed magnet assembly according to the disclosed technology used in some embodiments of a diagnostic or preparatory apparatus. 
     An embodiment of a fixed magnet assembly  1500  is shown that can be implemented for the embodiments of the diagnostic or preparatory apparatus shown and described in  FIGS. 11, 13-13B, and 14A-14C . Four separate fixed magnet assemblies  1500  can be installed as shown, each of which may include a support plate  1502 , which may have dimensions suited to the particular diagnostic or preparatory apparatus in which the fixed magnet assembly  1500  is implemented. In some embodiments, the support plate  1502  may be a machined aluminum plate. The support plate  1502  may include a set of recesses or holes  1508 , each of which is configured to receive the bottom end of a mixing tube  1546  (similar to the mixing tube  1316  shown in  FIG. 13B  or the mixing tube  1444  shown in  FIG. 14A-14C ) of a processing plate  1540 . 
     The fixed magnet assembly  1500  may also include a set of magnet housings  1512 . The magnet housings  1512  can be integrally formed as a single, monolithic piece. The magnet holder  1500  may include a set of magnet housings  1512  and connectors  1514 . The magnet housings  1512  and the connectors  1514  can be integrally formed as a single, monolithic piece. In another example, the magnet housings  1512  and the connectors  1514  are coupled to form the magnet holder  1500 . Other configurations can be suitably implemented. In some embodiments, each magnet housing  1512  may have a trapezoidal shape when viewed from top-down. In this example, each magnet housing  1512  houses two magnets (not shown) that are located adjacent to a first face  1520  and a second face  1522  of the magnet housing  1512 , respectively. This arrangement may be similar to how  FIG. 14B  shows the pair of magnets  1432  are arranged within the housing  1430 . The fixed magnet assembly  1500  may include mounting holes  1518  for attaching the magnet housings  1512  to the support plate  1502 . For instance, fasteners (e.g., screws) can be inserted into the mounting holes  1518  to affix the magnet housings  1512  to the support plate  1502  and form the fixed magnet assembly  1500 . The support plate  1502  of the fixed magnet assembly  1500  can then be installed in (for example, affixed to) the diagnostic or preparatory apparatus using any suitable mechanism. 
     In one non-limiting example, the fixed magnet assembly  1500  is a single, monolithic piece that includes a plurality of magnet housings  1512  separated by connectors  1514 . In some cases, the fixed magnetic assembly is a unitary structure that includes a plurality of magnet housings  1512 . A unitary fixed magnet assembly  1500  can be formed, for example, of a magnetic material. In another non-limiting example, a unitary fixed magnet assembly  1500  is formed of one or more non-magnetic materials, and a magnetic material is coupled to interior walls of the housing adjacent to the first face  1520  and the second face  1522  of each magnet housing  1512 . Other configurations are possible. 
     In some embodiments, the magnet housings  1512  of each fixed magnet assembly  1500  may have a fixed height (e.g., up/down position) relative to the support plate  1502  and the rest of the diagnostic or preparatory apparatus. This fixed height may be adjusted by adding a shim of a desired height measured in the z-direction between the magnet housings  1512  and the supporting plate  1502 . Installation of the fixed magnet assembly  1500  can include selecting one of a plurality of shims of different heights from an installation kit, installing the selected shim in a receiving bay, and installing the fixed magnet assembly  1500  over the shim in the z-direction. This can be particularly advantageous when a fixed magnet assembly is retrofitted into existing preparatory and diagnostic apparatuses in the field, in view of very slight differences in the dimensions and tight tolerances associated with receiving bays and racks implemented in the apparatuses. In some other embodiments, the spring-based mechanism shown in  FIGS. 9 and 10A-10B  can be used for the fixed magnet assembly  1500  to allow for the support plate  1502  of the installed fixed magnet assembly  1500  to move upward or downward in the z-direction. 
     Thus, the mixing tubes  1546  of the processing plate  1540  may be received in the holes  1508  of the support plate  1502 , resulting in each mixing tube  1546  being in close proximity with a magnet in an adjacent magnet housing  1512  (e.g., a magnet located behind either a first face  1520  or second face  1522  of the adjacent magnet housing  1512 ). In some embodiments, the first face  1520  and the second face  1522  of each magnet housing  1512  may be oriented at an angle that makes them parallel to the sloped wall of the mixing tubes  1546  when the mixing tubes are disposed in the holes  1508 . 
       FIGS. 16A-16B  illustrate isometric views of an embodiment of another fixed magnet assembly that can be implemented according to the disclosed technology into an automated diagnostic or preparatory apparatus. More specifically,  FIGS. 16A-16B  show an embodiment of a fixed magnet assembly  1600  with user-adjustable height.  FIG. 16C  illustrates the fixed magnet assembly of  FIGS. 16A-16B  with the magnet housings  1612  and connectors  1614  omitted for illustrative purposes only.  FIG. 16D  illustrates a perspective view of the fastening mechanism implemented by the fixed magnet assembly of  FIGS. 16A-16C , while  FIG. 16E  illustrates a side cutaway view of that fastening mechanism.  FIG. 16F  illustrates an isometric view of the fixed magnet assembly of  FIGS. 16A-16C  implemented in a receiving bay of a diagnostic or preparatory apparatus, such as within the receiving bay  500  described with reference to  FIGS. 5A-5B . 
     The fixed magnet assembly  1600  may include a mounting plate  1602 , a support plate  1606 , and a magnet holder  1604 . The mounting plate  1602  may have dimensions suited to the particular diagnostic or preparatory apparatus in which the fixed magnet assembly  1600  is implemented. In some embodiments, the mounting plate  1602  may be a machined aluminum plate. In some embodiments, the mounting plate  1602  may include a plurality of mounting brackets  1640  on one side. For instance, in the embodiment illustrated in the figures, there are two mounting brackets  1640  disposed on a front side of the mounting plate  1602 , which extend upwards from the mounting plate  1602  (e.g., in the z-axis). Each mounting bracket  1640  may have a vertical slot  1644 , through which a fastener  1642  can be disposed. The fastener  1642  may be disposed through the vertical slot  1644  and into a corresponding recess (not shown) in the support plate  1606 , which is configured to receive the fastener  1642 . In some cases, the fasteners  1642  may be screws and tightening the fasteners  1642  may sandwich the mounting brackets  1640  between the fasteners  1642  and the support plate  1606 , thereby mounting the support plate  1606  to the mounting brackets  1640  in order to resist re-positioning of the support plate  1606 . In some embodiments, the mounting plate  1602  may also include fastener housings  1630 , and a fastener  1632  may be disposed in each fastener housing  1630 . In the embodiment illustrated in the figures, there are three fastener housings  1630  spaced along the length of the mounting plate  1602 , with two of the fastener housings  1630  at each longitudinal end of the mounting plate  1602 . It will be understood that other numbers, spacings, and configurations of the fastener housings  1630  are possible. Each fastener  1632  may be disposed through a recess in a fastener housing  1630  and also disposed through a corresponding recess in the support plate  1606  (as shown in  FIG. 16E ). In some cases, the fasteners  1632  may be screws and tightening the fasteners  1632  may thread them deeper through those recesses of the support plate  1606  to raise the support plate  1606  relative to the mounting plate  1602 . 
     As will be described in further detail herein, the mounting brackets  1640  (and their vertical slots  1644 ), fasteners  1642 , fastener housings  1630 , and the fasteners  1632  may be some of the components that are configured to work together to enable the user to adjust the height of the support plate  1606  and/or the magnet holder  1604  of the fixed magnet assembly  1600  (relative to the mounting plate  1602 ). Once the mounting plate  1602  is fixed in place, the support plate  1606  and/or the magnet holder  1604  may be able to move up and down (e.g., along the z-axis) within a limited range, relative to the stationary mounting plate  1602 , through the user-adjustable height feature. In some embodiments, the support plate  1606  may be the component that moves up and down (e.g., along the z-axis) relative to the mounting plate  1602  when using the user-adjustable height feature, such as when the fasteners  1632  (disposed in the fastener housings  1630 ) are turned clockwise and/or counter-clockwise. 
     The support plate  1606  may sit on top of the mounting plate  1602 , sandwiched between the mounting plate  1602  and the magnet holder  1604 . The magnet holder  1604  may include a set of magnet housings  1612  and connectors  1614 . The magnet housings  1612  and the connectors  1614  can be integrally formed as a single, monolithic piece, or the magnet housings  1612  and the connectors  1614  may be coupled to form the magnet holder  1604 . Other configurations can be suitably implemented. The dimensions of the support plate  1606  and the magnet holder  1604  may be suited to the particular diagnostic or preparatory apparatus in which the fixed magnet assembly  1600  is implemented. In some embodiments, the magnet holder  1604  may be made of a material that is chemically resistant to cleaning agents. In some embodiments, each magnet housing  1612  may have a trapezoidal shape when viewed from top-down. In this example, each magnet housing  1612  may house two magnets (not shown) that are located adjacent to a first face  1620  and a second face  1622  of the magnet housing  1612 , respectively. This arrangement may be similar to how  FIG. 6B  shows the pair of magnets  632  are arranged within the housing  630 . 
     In one non-limiting example, the fixed magnet assembly  1600  is a single, monolithic piece that includes a plurality of magnet housings  1612  separated by connectors  1614 . In some cases, the fixed magnetic assembly is a unitary structure that includes a plurality of magnet housings  1612 . A unitary fixed magnet assembly  1600  can be formed, for example, of a magnetic material. In another non-limiting example, a unitary fixed magnet assembly  1600  is formed of one or more non-magnetic materials, and a magnetic material is coupled to interior walls of the magnet housings  1612 , adjacent to the first face  1620  and the second face  1622  of each magnet housing  1612 . Other configurations are possible. 
     The magnet holder  1604  may have mounting holes  1616  (e.g., in the connectors  1614 ) for mechanically coupling the magnet holder  1604  to the mounting plate  1602 . For instance, in some embodiments, fasteners  1617  (e.g., screws or shoulder bolts) can be inserted into the mounting holes  1616  (and also inserted through corresponding mounting holes in the support plate  1606 , which are not shown) to mechanically couple the magnet holder  1604  to the support plate  1606  and/or the mounting plate  1602 . In some embodiments, the fasteners  1617  may limit the maximum spacing between the support plate  1606  and the mounting plate  1602 . The fasteners  1617  may place an upward limit to the upward movement of the support plate  1606  in the z-direction away from the mounting plate  1602 , but do not limit downward movement of the support plate  1606  in the z-direction toward the mounting plate  1602 . In some embodiments, the fasteners  1617  may additionally restrict the movement of the support plate  1606  in the x-axis and y-axis. With these fasteners  1617  in place, the magnet holder  1604  may be affixed to the support plate  1606 , such that the two may move together as a single unit. These fasteners  1617  inserted through the mounting holes  1616  should not be mistaken for the fasteners  1632  disposed in the fastener housings  1630 , which may serve a different purpose (e.g., enabling a user to adjust the height of the fixed magnet assembly  1600 , such as the position of the magnet holder  1604  and support plate  1606  relative to the mounting plate  1602  on the z-axis). With the magnet holder  1604 , support plate  1606 , and the mounting plate  1602  mechanically coupled together, the mounting plate  1602  of the fixed magnet assembly  1600  can then be installed in (for example, affixed to) the diagnostic or preparatory apparatus using any suitable mechanism. In some embodiments, the fixed magnet assembly  1600  may be implemented in a particular diagnostic or preparatory apparatus by affixing the mounting plate  1602  to a cover  1650  of the apparatus using a fastener, such as using very high bond tape. 
     In some embodiments, the fixed height (e.g., the up/down position) of the magnet holder  1604  and/or the support plate  1606 , relative to the mounting plate  1602  and the rest of the diagnostic or preparatory apparatus, may be adjusted by a user, such as by using the following technique or procedure. First, the fasteners  1642  in the mounting brackets  1640  can be loosened (e.g., by turning the fasteners  1642  counter-clockwise). The fasteners  1642  may serve to lock-in the height once the correct height is determined (e.g., by tightly fastening the magnet holder  1604  to the mounting brackets  1640 ); loosening the fasteners  1642  allows the height to be adjusted. The fasteners  1642  can remain loose during height adjustment, after which they can be tightened to ensure that the support plate  1606  remains at the correct position. 
     After loosening the fasteners  1642 , the fasteners  1632  in the fastener housings  130  can be individually adjusted or adjusted in-sync, in order to adjust the height of the support plate  1606 . For instance, in some cases, each of the fasteners  1632  may be a jack screw which is disposed through a recess of a fastener housing  1630  and threaded through a recess of the support plate  1606 . Thus, the support plate  1606  may move up and down, accordingly, as the jack screw is threaded further into, or out of, the support plate  1606 . For instance, turning the jack screw in a clockwise direction may thread the jack screw further into the support plate  1606  and bring that portion of the support plate  1606  towards the fastener housing  130 , thereby raising that portion of the support plate  1606 . Turning the jack screw in a counter-clockwise direction may thread the jack screw out of the support plate  1606  and distance that portion of the support plate  1606  away from the fastener housing  130 , thereby lowering that portion of the support plate  1606 . 
     In some embodiments, when installing the fixed magnet assembly  1600  into a particular diagnostics or preparatory apparatus and performing the height adjustment, there may be an alignment fixture (e.g., a separate device not shown in the figures) that can be loaded into the same holes that containers of a rack would occupy when the rack is placed in a receiving bay of the apparatus. The alignment fixture can be used as a guide during the height adjustment in order to determine when the support plate  1606  and/or the magnet holder  1604  are at the correct height for that particular diagnostics or preparatory apparatus. Advantageously, the above-described height adjustment can be a one-time height adjustment that is performed once and it is not repeated once the system is placed back into operational use. 
     Once the support plate  1606  and/or the magnet holder  1604  are adjusted to be at the desired heights, the fasteners  1642  can be tightened in order to maintain those heights. In some embodiments, there may be an additional fixture (e.g., another separate device not shown in the figures) that enables the adjusted height of the support plate  1606  and/or the magnet holder  1604  to be checked in order to confirm they are within +/−1 mm of the nominal position expected, which can inform if the heights need to be re-adjusted during this installation procedure. This particular configuration of the fixed magnet assembly  1600  may allow the fixed magnet assembly  1600  to be inexpensively and quickly implemented into a particular apparatus on-site (e.g., at the location of the diagnostic or preparatory apparatus), despite any unknown component variation that may exist among different apparatuses.  FIG. 16F  illustrates the same fixed magnet assembly  1600  shown in  FIGS. 16A-16C  (including the mounting plate  1602  and the magnet holder  1604 ) affixed to the cover  1650  of a diagnostic or preparatory apparatus. 
     More specifically,  FIG. 16F  shows how the fixed magnet assembly  1600  can be implemented within a receiving bay of a diagnostic or preparatory apparatus, such as the receiving bay  500  of the diagnostic or preparatory apparatus shown in  FIGS. 5A-5B , so that when the receiving bay receives a rack with reagent holders inserted into the rack, the process tubes of those reagent holders rest on the mounting plate  1602  of the fixed magnet assembly  1600  next to the magnets in the magnet holder  1604 . Furthermore, the one or more movable magnets of a magnetic separator (not shown in this figure, but described above with reference to  FIGS. 3A-3C ) can apply a magnetic force to each process tube of the reagent holders in the rack. In addition, with the fixed magnet assembly  1600  installed in this position, a constant, consistent magnetic force from the magnets of the fixed magnet assembly  1600  (e.g., the magnets in the magnet holder  1604 ) is also applied to each third snap-in container of the reagent holders in the rack. 
       FIGS. 17A-17D  illustrate isometric views of an example structure for installing and implementing a fixed magnet assembly  1710  into an automated diagnostic or preparatory apparatus. More specifically,  FIG. 17A  shows an embodiment of a bridge  1700  used to support the fixed magnet assembly  1710 .  FIGS. 17B-17D  illustrate how the bridge  1700  and fixed magnet assembly  1710  of  FIG. 17A  can be installed and implemented within the receiving bay of an automated diagnostic or preparatory apparatus, according to this non-limiting embodiment. It will be understood that the present disclosure is not limited to installing a fixed magnet assembly in accordance with this embodiment, and other structures can be suitably implemented. 
     In one non-limiting example, the bridge  1700  may include multiple portions, such as a first bridge portion  1702  and a second bridge portion  1706 , which can be used to support the fixed magnet assembly  1710 . For instance, the first bridge portion  1702  may be configured to support a first end of the fixed magnet assembly  1710  and the second bridge portion  1706  may be configured to support an opposing second end of the fixed magnet assembly  1710 , thereby forming a bridge. 
     In some embodiments, the bridge  1700  may have a first bridge portion  1702  and a second bridge portion  1706  that are mirror symmetrical. The first bridge portion  1702  and the second bridge portion  1706  may be configured to engage with slots on the opposing sides of a cover  1720  in the receiving bay of an automated diagnostic or preparatory apparatus, resulting in the bridge  1700  straddling the cover  1720  as shown in  FIG. 17B . 
     This can be better seen in  FIGS. 17C and 17D , which show the first bridge portion  1702  installed on one end of the cover  1720 . The second bridge portion  1706  is not shown, but it would be on the opposing end of the cover  1720 . The opposing ends of the fixed magnet assembly  1710  can be seated respectively on the first bridge portion  1702  and the second bridge portion  1706 , which hold the fixed magnet assembly  1710  above the cover  1720  and position the fixed magnet assembly  1710  in the proper place to precisely exert magnetic force on the magnetic particles residing within the corresponding tubes of a rack that has been placed in the receiving bay. 
     In some embodiments, the first bridge portion  1702  and the second bridge portion  1706  may have recesses that allow the first bridge portion  1702  and the second bridge portion  1706  to fit cleanly on the ends of the cover  1720  without disturbing any components of the diagnostic or preparatory apparatus that may reside under the cover  1720 . For example,  FIGS. 17C and 17D  show the first bridge portion  1702  having a recess  1704  shaped and sized to receive components (e.g., printed circuit boards) of the diagnostic or preparatory apparatus. 
     Many variations and modifications may be made to the above-described embodiments, the elements of which are to be understood as being among other acceptable examples. All such modifications and variations are intended to be included herein within the scope of this disclosure. The foregoing description details certain embodiments. It will be appreciated, however, that no matter how detailed the foregoing appears in text, the systems and methods can be practiced in many ways. As is also stated above, it should be noted that the use of particular terminology when describing certain features or aspects of the systems and methods should not be taken to imply that the terminology is being re-defined herein to be restricted to including any specific characteristics of the features or aspects of the systems and methods with which that terminology is associated. 
     Conditional language, such as, among others, “can,” “could,” “might,” or “may,” unless specifically stated otherwise, or otherwise understood within the context as used, is generally intended to convey that certain embodiments include, while other embodiments do not include, certain features, elements, and/or steps. Thus, such conditional language is not generally intended to imply that features, elements and/or steps are in any way required for one or more embodiments or that one or more embodiments necessarily include logic for deciding, with or without user input or prompting, whether these features, elements and/or steps are included or are to be performed in any particular embodiment. 
     The term “substantially” when used in conjunction with the term “real-time” forms a phrase that will be readily understood by a person of ordinary skill in the art. For example, it is readily understood that such language will include speeds in which no or little delay or waiting is discernible, or where such delay is sufficiently short so as not to be disruptive, irritating, or otherwise vexing to a user. 
     Conjunctive language such as the phrase “at least one of X, Y, and Z,” or “at least one of X, Y, or Z,” unless specifically stated otherwise, is to be understood with the context as used in general to convey that an item, term, etc. may be either X, Y, or Z, or a combination thereof. For example, the term “or” is used in its inclusive sense (and not in its exclusive sense) so that when used, for example, to connect a list of elements, the term “or” means one, some, or all of the elements in the list. Thus, such conjunctive language is not generally intended to imply that certain embodiments require at least one of X, at least one of Y, and at least one of Z to each be present. 
     The term “a” as used herein should be given an inclusive rather than exclusive interpretation. For example, unless specifically noted, the term “a” should not be understood to mean “exactly one” or “one and only one”; instead, the term “a” means “one or more” or “at least one,” whether used in the claims or elsewhere in the specification and regardless of uses of quantifiers such as “at least one,” “one or more,” or “a plurality” elsewhere in the claims or specification. 
     The term “comprising” as used herein should be given an inclusive rather than exclusive interpretation. For example, a general purpose computer comprising one or more processors should not be interpreted as excluding other computer components, and may possibly include such components as memory, input/output devices, and/or network interfaces, among others. 
     While the above detailed description has shown, described, and pointed out novel features as applied to various embodiments, it may be understood that various omissions, substitutions, and changes in the form and details of the devices or processes illustrated may be made without departing from the spirit of the disclosure. As may be recognized, certain embodiments of the inventions described herein may be embodied within a form that does not provide all of the features and benefits set forth herein, as some features may be used or practiced separately from others. The scope of certain inventions disclosed herein is indicated by the appended claims rather than by the foregoing description. All changes which come within the meaning and range of equivalency of the claims are to be embraced within their scope.