Abstract:
The invention is an improved multiplex capillary electrophoresis instrument or module with at least four and preferably six user-accessible vertically stacked drawers. An x-z stage moves samples from the user accessible drawers to the capillary array for analysis. A computer program allows users to add capillary electrophoresis jobs to a queue corresponding to the analysis of rows or plates of samples without stopping or interrupting runs in progress.

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
       [0001]    This application is a continuation in part of commonly owned co-pending earlier filed design case, U.S. Ser. No. ______ filed Mar. 15, 2012, and claims priority of earlier filed provisional application U.S. Ser. No. 61/643,411 filed May 7, 2012, which applications are hereby incorporated by reference in their entirety. 
     
    
     BACKGROUND OF THE INVENTION 
       [0002]    1. Field of the Invention 
         [0003]    This invention relates to a system and software for multi-channel capillary electrophoresis. 
         [0004]    2. Description of Related Art 
         [0005]    The current next-generation sequencing (NGS) platforms use a variety of technologies for sequencing, including pyrosequencing, ion-sequencing, sequencing by synthesis, or sequencing by ligation. Although these technologies have some minor variations, they all have a generally common DNA library preparation procedure, which includes genomic DNA quality &amp; quality assessment, DNA fragmentation and sizing (involving mechanical shearing, sonication, nebulization, or enzyme digestion), DNA repair and end polishing, and a last step of platform-specific adaptor ligation. With a rapidly growing demand for DNA sequence information, there is a critical need to reduce the time required for the preparation of DNA libraries. 
         [0006]    A labor-intensive step in DNA library preparation is the qualification (size determination) and quantification of both un-sheared genomic DNA and downstream fragmented DNA. Existing methods for DNA fragment analysis include agarose gel electrophoresis, capillary electrophoresis, and chip-based electrophoresis. Agarose gel electrophoresis is labor intensive, requiring gel preparation, sample transfer via pipetting, and image analysis. The images obtained by agarose electrophoresis are often distorted, resulting in questionable or unreliable data. It is impossible to use agarose gel electrophoresis for accurate quantification of DNA, which means that a separate, second method (UV or fluorescence spectroscopy) is required for quantification. Finally, agarose gel electrophoresis is difficult to automate. Chip or micro-chip based electrophoresis provides an improvement in data quality over agarose gel electrophoresis but is still labor intensive. For example, chip-based methods require manual steps to load gel, markers and samples. Even though these microchip or chip based electrophoresis units can run a single sample in seconds or minutes, the sample and gel loading are barriers to ease-of-use, especially when running hundreds or thousands of samples. Also, existing chip-based systems are unable to quantify genomic DNA. Capillary electrophoresis (CE) offers advantages over both agarose electrophoresis and microchip electrophoresis in that gel-fill and sample loading is automated. 
         [0007]    Multiplex capillary electrophoresis is known. For example Kennedy and Kurt in U.S. Pat. No. 6,833,062 describe a multiplex absorbance based capillary electrophoresis system and method. Yeung et al. in U.S. Pat. No. 5,324,401 describe a multiplex fluorescent based capillary electrophoresis system. Although these systems offer the advantage of analyzing multiple samples simultaneously, and can run several plates sequentially, they lack the ability to load or change multiple sample plates while the system is running, and they also lack a simple workflow for efficient sample analysis. 
         [0008]    While existing commercial CE systems can be automated with a robotic system, stand-alone systems are not fully automated or lack the sensitivity and data quality required for adequate DNA library analysis. An example of a CE instrument with a robot-capable interface is given by Kurt et al. in U.S. Pat. No. 7,118,659. For the construction of DNA libraries, as well as other applications such as mutation detection, it is often necessary to run thousands of samples per day, but the implementation of a robotic system for sample handling is prohibitively expensive, and many labs lack the expertise necessary for the maintenance and operation of sophisticated robotic systems. Automated forms of micro-slab-gel electrophoresis have been developed, such as those described in United States Patent Application number 20100126857. These allow for automatic analysis of multiple samples, but the techniques either still require significant human intervention, or they do not have the throughput required for high-volume applications. Amirkhanian et al. in U.S. Pat. No. 6,828,567 describe a 12-channel multiplex capillary electrophoresis system capable of measuring up 12 samples at a time using multiplex capillary electrophoresis. However, this system is not capable of measuring multiple 96-well plates, and does not have the workflow that allows the analysis of thousands of samples per day. 
         [0009]    As can be seen, there a need for an automated capillary electrophoresis system that a) eliminates the complexity, cost, and required expertise of a robotic system b) enables users to run from one to several thousand samples per day and c) allows users to conveniently load several plates or samples onto a capillary electrophoresis system while the system is running other samples and d) has the small size and footprint of a stand-alone capillary electrophoresis unit. 
         [0010]    This invention has as a primary objective the fulfillment of the above described needs. 
       BRIEF SUMMARY OF THE INVENTION 
       [0011]    The present invention is a multiplex capillary electrophoresis system and console with an improved sample handling and control method for the analysis of samples. One embodiment of the invention is a console with a series of at least four and preferably at least six vertically stacked user-accessible drawers that can each hold a plate containing from 1 to 384 sample wells. Preferably, each user accessible drawer holds a sample plate containing 96 sample wells. The system is configured so that sample plates can be loaded onto the system at any time, including during the electrophoresis or analysis of samples. User “A” can walk up to the machine, load a row of 12 samples, enter loading and analysis instructions onto the computer and walk away. While user “A” samples are running, user “B” can walk up to the machine, load a tray of 96 samples, enter loading and analysis instructions and walk away. User “C” can walk up to the machine, load 12 samples, while either user “A” or user “B” samples are running, enter loading and analysis instructions, and walk away. Two of the preferred six user-accessible drawers are used to hold an electrophoresis run buffer and a waste tray. 
         [0012]    Another embodiment of the invention is a mechanical stage that transports sample trays and/or buffer or waste trays from any one of the vertically stacked user-accessible drawers to the injection electrodes and capillary tips of the multiplex capillary array of the capillary electrophoresis subsystem. 
         [0013]    Another embodiment of the invention is uses a computer program that enables a user to create a queue of jobs, with each job representing an analysis of a new set of samples. This computer system enables users to enter job data even when the system is running samples. For example, user “A” loads “sample plate 1” into the system into Drawer 3 and uses a computer program to add a job to a queue, the job representing the injection and capillary electrophoresis of samples in “sample plate 1” in Drawer 3. While the system is running user A′s samples, user B loads plate 2 into Drawer 4 and uses the same computer program to add a job to a queue, the job representing the injection and capillary electrophoresis of samples in “sample plate 2” in Drawer 4. User C loads “sample plate 3” into Drawer 5 and uses the same computer program to add a job to the queue, the job representing the injection and capillary electrophoresis of samples in “sample plate 3” in Drawer 5. 
         [0014]    A preferred embodiment of this invention is a system capable of allowing the user to enter 24 or more individual jobs to a queue, with each job representing an injection and analysis of a plurality of samples. 
         [0015]    An even more preferred embodiment is a system capable of allowing the user to enter 48 or more individual jobs to a queue, with each job representing an injection and analysis of a plurality of samples. 
         [0016]    Another embodiment is a system capable of allowing the user to enter 100 or more individual jobs to a queue, with each job representing an injection and analysis of a plurality of samples. 
     
    
     
       BRIEF SUMMARY OF THE DRAWINGS 
         [0017]      FIG. 1  shows a left-front-view of the instrument, with 6 drawers for holding sample and buffer plates. 
           [0018]      FIG. 2  shows a right-front view of the instrument with one drawer pulled out for placement of a buffer plate and the top and side door compartments open. 
           [0019]      FIG. 3  shows the x-z stage assembly. 
           [0020]      FIG. 4  shows a drawer, stage assembly, tray holder, and sample plate. 
           [0021]      FIG. 5  shows the bottom of a tray holder. 
           [0022]      FIG. 6  shows a right-side view of the instrument without the cover. 
           [0023]      FIG. 7  shows the left-side view of the instrument without the cover. 
           [0024]      FIG. 8  shows a capillary array cartridge 
           [0025]      FIG. 9  shows the flow-chart for the software control program for creating a queue of jobs. 
           [0026]      FIG. 10  shows a computer screen image of the computer software. 
           [0027]      FIG. 11  shows the positioning of a sample plate under the array by the stage. 
           [0028]      FIG. 12A  shows a view of the capillary electrophoresis reservoir system. 
           [0029]      FIG. 12B  shows a view of the capillary electrophoresis reservoir system. 
           [0030]      FIG. 13A  shows a view of the x-z stage relative to the drawers. 
           [0031]      FIG. 13B  shows a view of the x-z stage with a sample tray lifted. 
       
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
       [0032]    The invention is a multiplexed capillary electrophoresis system with enhanced workflow. The capillary electrophoresis system and apparatus of the present invention includes an absorbance or fluorescence-based capillary electrophoresis sub-system with a light source, a method for carrying light from the light source to the sample windows of a multiplex capillary array containing at least 12 capillaries (preferably 96 capillaries), and a method for detecting light emitted (fluorescence) or absorbed (absorbance) from the sample windows of a multiplex array. The sub-system also includes a method for pumping buffers and gels through the capillaries, as well as a method for application of an electric field for electrophoretic separation. The optics of the fluorescent-based sub system of the present invention are described by Pang in United States Patent Applications 20070131870 and 20100140505, herein incorporated by reference in their entirety. The optics of an applicable absorbance-based system, as well as the fluid handling, reservoir venting, application of electric field, and selection of fluids via a syringe pump and a 6-way distribution valve are discussed by Kennedy et al. in U.S. Pat. Nos. 7,534,335 and 6,833,062, herein incorporated by reference their entirety. 
         [0033]    Referring to  FIG. 1  the multiplex capillary system and/or console  16 , with enhanced workflow has a door  10  for easy access to the loading of gels, two drawers  11  for the easy loading of a buffer tray and a waste tray. Drawers  12  can be opened for easy loading of 96-well PCR plates, tube strips, vials, or other sample containers. A top door  13  can be opened to access a replaceable capillary array, array window, and reservoir. An indicator light  14  is used to for notifying users of the active application of a high-voltage for electrophoresis. A removable back-panel  15  allows access to electronics such as a high-voltage power supply, electrical communication panels, a pump board, pressure transducer board, and stage driver electronics. The back panel  15  also allows maintenance access to the x-z stage, which is used to move sample trays from the drawers  11  and  12  to a capillary array. 
         [0034]      FIG. 2  shows the multiplex capillary system used with the enhanced workflow console  16  with the top and side doors open. A replaceable capillary array  17  holds either 12 or 96 capillaries for multiplex capillary electrophoresis. An LED light guide  67  guides light from a LED engine located in the back compartment to the array window block  22  which is inserted between the array window holder  19  and LED light guide and window holder  18 . In this view, array window block  22  is attached to the capillary array  17  for display. When the capillary array is removed, from the system, the array window block  22  can be attached to the capillary array  17  (as shown). When the capillary array is fully installed, the array window block  22  is not visible because it is sandwiched between the array window holder  19  and LED light guide and window holder  18 . A vent valve  21  is connected to the top of a capillary reservoir  20 . A syringe pump  23  coupled with a 6-way distribution valve  29  delivers fluids and electrophoresis gels from fluid containers  24  and  25  into the capillary reservoir  20 , waste container  26 , or capillaries in the capillary array  17 . A fan  27  is used for forcing cool air from the back compartment through the capillary array  17 , past the outside of the reservoir  20 , down past the fluid containers  24 ,  25  and finally out the bottom of the instrument. LED indicator lights  120  are used to indicate the presence or absence of trays in the drawers. A buffer tray  28  is shown in a drawer ( 11 ,  FIG. 1 ). The capillary array reservoir tip  91  is shown inserted into the reservoir  20 . 
         [0035]    The concepts and practical implementation of motion control systems are known. For example, Sabonovic and Ohnishi; “Motion Control” John Wiley and Sons, 2011, herein incorporated by reference in its entirety, discusses practical methods for the design and implementation of motion control. It does not, however, show an enhanced CE workflow console  16  as depicted here. 
         [0036]      FIG. 3  shows the x-z stage assembly  48 , which is used to transport sample trays ( 50 ,  FIG. 4 ) and associated tray holders ( 51 ,  FIG. 4 ) from the drawers ( 12   FIG. 1 ) to the injection capillaries ( 72 ,  FIG. 8 ) and injection electrodes ( 71 ,  FIG. 8 ) of the capillary array ( 17 ,  FIG. 8 ). The x-z stage assembly  48  is also used to position a buffer tray or waste tray ( 28 ,  FIG. 2 ) from the drawers ( 11 ,  FIG. 1 ) to the injection capillaries and electrodes of the capillary array ( 72 ,  FIG. 8 ). The x-z stage assembly has a tray carrier  31  with alignment pins  32 , which align with holes ( 57 ,  FIG. 5 ) on the bottom of the tray holder ( 51 ,  FIG. 4 ) to prevent subsequent sliding or movement of the tray holders during transport. A protective cover  34 , made of metal or plastic, is used to prevent gels or other liquids from spilling onto the x-direction guide rails  38  and x-direction drive belt  37  of the stage assembly. An x-drive stepper motor  35  is used as the electro-mechanical driver for motion in the x-direction. A drive pulley  36  is attached to the stepper motor  35  and x-direction drive belt  37  which drives the stage carrier  39  back-and forth along the guide-bars  38 . A second drive pulley (not shown) is used on belt  37  towards the back-end of the stage, which allows the belt to make a full loop when affixed to stage carrier  39 . Any motor-induced movement of the belt induces a x-direction movement of the stage carrier  39  on the guide rails  38 . A stepper-motor for the z-position is located at  41 , which is attached to a drive pulley/belt configuration similar to that shown in the x-direction. The x-direction drive belt is shown as  43 . The z-position motor/pulley/belt is used to move the tray carrier  31  up and down the guide bars  40 . Top plate  33  serves as a structural support for the guide bars  40 . An electrical communication strip  44  is used to communicate between an electrical motor control board  46  and the stepper motors  41  and  35 . An x-direction membrane potentiometer strip  49 , along with appropriate control electronics, is used to determine and control the absolute position of the stage carrier  39  in the x-direction. A z-direction membrane potentiometer strip  42 , along with appropriate control electronics, is used to determine the absolute position of the tray carrier  31  in the z-direction. Linear encoders or rotational encoders (on the stepper motor) are alternative forms of positional measurement and control. Bearings  45  are located on each guide bar  40  and guide rail  38  to enable friction-free movement of both the tray carrier  31  and the stage carrier  39 . Note that there are two guide bars or guide rails per axis. Electrical cord guide straps  47  are attached to a back support, which also holds the electrical control board  46  for the x-z stage assembly. 
         [0037]      FIG. 4  shows a drawer  12 , superimposed on an image of the stage assembly  48 , tray holder  51 , and 96-well sample tray  50 . The tray holder  51  is molded to specifically hold a 96-well plate, shown here as  50 . Alternative moldings of the tray holder allow for different sample plates. Holes ( 57 ,  FIG. 5 ) on the bottom of the tray holder  51  align with the alignment pins  32  of the tray carrier ( 31   FIG. 4 ). Notches  53  in the tray holder  51  align with alignment pins  52  on the drawer  12  to enable the tray holder to fit in a tight, reproducible way within the sample drawer. 
         [0038]      FIG. 6  Shows a right side view of the electrophoresis system, with a chassis  66 , pump motor and control system  61 , pump control board  62 , LED light engine  69 , LED light line  67 , high voltage power supply board  65 , capable of applying 0.0 kV to 15 kV across the electrodes of the array, a CCD camera  64 , capillary array cartridge  17 , array window holder  19 , reservoir  20 , drawers  11 , drawers  12 , fluid lines  68 , waste container  26 , gel containers  25  and syringe  23 . A USB electronic distribution bard is shown as  63 . 
         [0039]      FIG. 7  shows a left side-view of the electrophoresis unit showing the x-z stage assembly  48 , which moves tray holders  51  and sample trays  50  from a drawer  12  or  11  to the bottom of array  17 . The stage unit  48  can move the sample tray holder  51  and sample tray  50  up in the z-direction to lift the tray holder/sample tray off of the drawer, move back in the x-direction away from the sample drawers, and then move the sample plate up in the z-direction to the bottom of the capillary array  17 . After electrokinetic or hydrodynamic injection, the stage unit  48  can move the sample tray holder/sample tray back down to the target drawer position (down in the z-direction), move forward in the x-direction just above the sample plate, and then drop down in the z-direction to set the sample tray holder/sample tray onto the drawer. When the sample tray holder  51  is resting in a drawer, the back edge of the sample tray holder  51  and sample tray  50  are aligned so that they do not lie directly underneath the array  17 . This allows the sample stage tray carrier ( 31 ,  FIG. 3 ) to move up and down along the entire z-axis with a tray holder/sample tray without colliding into other tray holders/sample trays in the drawers. The alignment pins ( 70 ,  FIG. 8 ) on the bottom of array  17  are used to align the tray holder with a tray so that the capillary and electrode tips dip into each sample well of the sample plate and do not collide with other areas of the sample plate. This is shown in more detail in  FIG. 11 , which shows a sample tray holder  51  with a sample tray  50  aligned underneath a capillary array. Alignment holes  56  on the tray holder  51  force the alignment of the tray holder with the capillary array alignment pins  70 . 
         [0040]      FIG. 7  also shows high voltage power supply board  65  and high voltage power supply cable (to the array)  75 . 
         [0041]      FIG. 8  shows an array cartridge  17 , with rigid plastic support structure  77 , window storage and transport screw  80 , capillary support cards  76 , high voltage power supply cable  75 , and insulating support structure  73  onto which the electric circuit board  74  is placed. Electrodes,  71  protrude through the electric circuit board  74 , through the insulating support structure  73 , and protrude through the bottom of the array. The electrode material is stainless steel or tungsten. The electrode dimension, which is not a critical aspect of the invention, is 50 mm diameter×29 mm length. The protrusion from the bottom of the cartridge base is 20.0 mm. The electrodes are soldered onto the circuit board  74 . The high voltage power supply cable  75  is also soldered to the same circuit of the electrical circuit board, which enables contact of the electrodes  71  with the high voltage power supply ( 65 ,  FIG. 6 ). Capillary tips  72  are threaded through the electric circuit board  74  and insulated support structure  73  and are aligned immediately adjacent and parallel to the electrode tips. 
         [0042]    The distance between the capillary tips and electrodes are from 0.1 mm to 4 mm. The ends of the capillaries and the ends of the electrode lie in a single plane (i.e. the capillary tips and electrode tips are the substantially the same length, with length variation of no more than about +/−1 mm. Preferably, the length variation of capillary tips and electrode tips is less than 0.5 mm. The capillaries thread through the bottom of the capillary array, through the insulating support structure  73 , through the electric circuit board  74 , through the capillary support cards  76  (which are supported by the rigid plastic support structure  77 ) through the capillary window holder  70  with capillary windows  79  centered in the opening of the window holder, and then finally through the capillary reservoir tip  91 , in which all capillaries (in this case  12 ) are threaded through a single hole. For  96  capillary arrays, capillaries are threaded in groups of  12  in the capillary reservoir tip  79 . The capillaries are held in place in the reservoir tip  91  with an adhesive, such as a thermally or uv-curable epoxy. 
         [0043]      FIG. 12A  shows the reservoir, with reservoir body  20 , capillary reservoir tip  91 , slider bar  130  (for locking capillary reservoir tip into the reservoir, through alignment of a notch on the capillary reservoir tip  91  and the slider bar  130 ), vent block valve  21 , waste tube out  138 , waste block valve  132 , and pressure transducer cavity  133 . 
         [0044]      FIG. 12B  shows an alternate cut-out view of the reservoir, with reservoir body  20 , capillary reservoir tip  91 , slider bar  130 , vent block valve  21 , waste tube out  138 , waste block valve  132 , electrode for attachment to ground  135 , pressure transducer cavity  133 , pressure transducer  136 , pressure transducer cable for attachment to analog/digital board  137 , and fluid tube input  134  (from syringe pump  23   FIG. 2 ). 
         [0045]    The reservoir body can be made of any solid material such as acrylic, Teflon, PETE, aluminum, polyethylene, ABS, or other common metals or plastics. The key criterion is that the material is durable and chemically resistant to the materials used. A preferred material is acrylic or Teflon. 
         [0046]      FIG. 13A  shows the x-z stage unit  48  in relation to the drawers  11  and  12 . The x-z stage is located directly behind the drawers, and can move the stage carrier ( 39 ,  FIG. 13B ) back-and forth in the x-direction using the stepper-motor for the z-position  41 . A sample tray is removed from a drawer by first moving the stage forward, towards the drawers, in the x-direction. The tray carrier ( 31 ,  FIG. 3 ) lifts a tray holder up and off a drawer in the z-direction using the z-direction stepper motor ( 41 ,  FIG. 3 ). The stage carrier is then moved back in the x-direction, away from the drawers, as shown in  FIG. 13B . The stage carrier  39  is then moved up in the z-direction to move the tray holder  51  and sample tray  50  to the injection position of the capillary array ( FIG. 11 ). 
         [0047]    A typical strategy for pumping fluids for capillary electrophoresis is as follows. Consider the following 6 positions of the six-way distribution valve ( 29 ,  FIG. 2 ) on the syringe. Position 1 is connected to the bottom of the reservoir ( 134 ,  FIG. 12B ); position 2 is connected through a tube to a bottle of conditioning fluid (a fluid for conditioning the walls of the capillaries); position 3 is connected to a “Gel 1” which is used for the analysis of genomic DNA, position 4 is connected to a “Gel 2” which is used for the analysis of fragmented DNA, position 5 is unused, and position 6 is connected to the waste bottle. 
         [0048]    Step A: The reservoir is first emptied by opening position 1 (reservoir), filling the syringe with fluid that is in the reservoir, closing position 1, opening position 6, and empting fluid to the waste. This is repeated until the reservoir is empty. Block valves  21  and  132  are kept open during this process to enable efficient draining of the reservoir. Step B: The reservoir is then filled with conditioning solution by opening position 2, filling the syringe with conditioning solution, closing position 2, opening position 1, and filling the reservoir with conditioning solution. Block valve  21  is closed, but block valve  132  to waste is open, enabling the over-filling of the reservoir with conditioning solution. 
         [0049]    Step C: The capillaries are filled by closing both vent block valve  21  and waste vent valve  132 . The syringe is filled with capillary conditioning solution. Position 1 is opened, and fluid is pressure filled through the capillaries at a minimum of 100 psi for a pre-determined time, which may range from 1 minute to 20 minutes. 
         [0050]    Step D: The reservoir is emptied by step A, and then re-filled with gel using the same process as in Step B, except that position 3 for the gel is used on the 6-way distribution valve. 
         [0051]    Step E: The capillaries are filled with gel using a process analogous to Step C. After steps A-E, the capillaries are ready for electrophoresis. 
         [0052]    A general strategy and process for analyzing samples using electrophoresis is as follows. 
         [0053]    Samples are placed into a 96-well plate for analysis. The user places the sample plate into a sample drawer ( 12 ,  FIG. 1 ), and then adds jobs to a computer-based queue, corresponding to the analysis of a specific row or the entire sample plate in the drawer. 
         [0054]    The computer, which is the control system of the instrument, executes the analysis of the row or entire tray of interest. 
         [0055]    A key embodiment of the invention is the workflow of the capillary electrophoresis system. Drawers ( 11 ,  FIG. 1 ) allow easy placement of buffer and waste trays into the system. Drawers ( 12 ,  FIG. 1 ) allow easy placement of sample trays into the system. Of particular importance is the ability to place or remove sample trays from drawers ( 12 ,  FIG. 1 ) while the system is performing capillary electrophoresis. Indicator lights ( 120 ,  FIG. 1 ) show if a tray is present or absent in a drawer, which let users know if a drawer is in place. A typical workflow for a 12-capillary multiplex system is as follows: User A walks up to the machine with sample tray 1, and places it into the third drawer from the top (one of drawers  11 ,  FIG. 1 ). User “A” then fills a queue with three jobs, which correspond to performing capillary electrophoresis on the three rows of samples: sample tray 1 row A, sample tray 1 row B, and sample tray 1 row C. User “A” then instructs the computer to execute the queue, and as a result, the system begins capillary electrophoresis of sample tray 1, row A, and will continue executing jobs in the queue until there are no more jobs. 
         [0056]    User “B” then comes up and places sample tray 2 into the fourth drawer from the top (one of drawers  11 ,  FIG. 1 ). User “B” then adds 8 jobs to the queue corresponding the performing of capillary electrophoresis on 8 rows of samples: sample tray 2, rows A-H. The computer will continue analyzing user “A” samples until they are finished, and then continue on with the analysis of user “B” samples. In the meantime, user “C” walks up and loads sample tray 3 into the fifth drawer from the top (one of drawers  11 ,  FIG. 1 ). User “C” then adds 1 job to the queue corresponding to the analysis of 1 row of samples: sample tray 3, row A. This process can continue indefinitely, as long as there is sufficient gel in gel containers ( 25  in  FIG. 2 ), or if there is sufficient run buffer in the buffer tray ( 28 ,  FIG. 2 ) located in top drawer  11 ,  FIG. 1 . It is, among other things, the enabling of this workflow, via the drawers sample stage, and computer program with a queue for loading jobs that differentiates the present invention from the prior art systems for CE workflow. 
         [0057]    An important embodiment of the present invention is a computer program that enables users to load a sample plate into the desired vertical drawer ( 12 ,  FIG. 1 ), and instruct the system to run the desired rows or entire sample plate, while the system is running other samples. This allows multiple users to load samples and/or sample plates, or a single user to load multiple samples and/or sample plates without first having to wait for the electrophoresis of other samples to be complete. 
         [0058]      FIG. 9  shows the general flow diagram of the work process and computer program. A user loads a sample tray into a drawer ( 12 ,  FIG. 1 ) of the system. On the computer, user then selects the tray, edits sample names and/or tray name. User further selects or defines a method (time of separation, electric field used for separation, gel selection, etc.). This selected tray, along with an associated method is defined as a “job”, which is then placed into a queue. The computer as an instrument control device, fetches jobs from the queue, and controls the instrument for every task, including operation of the syringe pump, operation of the high voltage power supply, and the motion control stage ( 48 ,  FIG. 3 ). For each run (or job), there may be a variety of tasks, with each task requiring direct command and control of subunits of the system. Tasks associated with control of the syringe pump include emptying/filling the reservoir with conditioning fluid, forcing conditioning fluid through the capillaries, emptying/filling the reservoir with gel, forcing gel through the capillaries. Tasks associated with control of the x-z stage may include moving or removing a waste tray to/from the inlet capillaries and electrodes of the capillary array, moving or removing a buffer tray to/from the inlet capillaries and electrodes of the capillary array, or moving/removing a sample tray to/from the inlet capillaries and electrodes of the capillary array. Tasks associated with control of the high voltage power supply include turning off/on a high voltage for capillary electrophoresis separation. Other tasks are associated with the camera (acquisition of data), and block valves. For each set of samples, the program will complete all tasks required to obtain a set of electropherograms. Once these tasks are complete, the program fetches another job from the queue. If the queue is empty, all sample runs are complete (until the user initiates another queue). 
         [0059]    The graphical result of this computer program is shown in  FIG. 10 , which shows a list of samples to be analyzed in queue  101 , an option to add rows or trays to the queue  102 , and an option to select the tray number for analysis  103 . It is these three aspects that are critical to software portion of the invention: a) Selection of tray  103  (corresponding to a drawer  11   FIG. 1 ) b) Adding the sample set to a queue ( 102 ,  FIG. 10 ) and c) A queue of active samples for analysis ( 101 ,  FIG. 10 ), which are executed in sequence until all jobs are complete. Another critical aspect is the ability to add samples to instrument drawers ( 11 ,  FIG. 1 ) and queue ( 101 ,  FIG. 10 ) while the instrument is running other samples. 
         [0060]    As can be seen from the above description, the system eliminates the need for expensive robots, enables the user to run many samples per day, allows loading of new samples while running others, and yet has a small size footprint.