iGEM 2017 — Team BostonU_HW

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# Team:BostonU HW/Notebook

BostonU\_HW

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[![MARS Logo](https://static.igem.org/mediawiki/2017/3/32/MARSNAV.png "MARS was developed and designed by the 2017 BU iGEM HW Team")](https://2017.igem.org/Team%3ABostonU_HW)

* Team
  + [Meet The Team](https://2017.igem.org/Team%3ABostonU_HW/Team)
  + [Attributions](https://2017.igem.org/Team%3ABostonU_HW/Attributions)
  + [Contribution](https://2017.igem.org/Team%3ABostonU_HW/Contribution)
  * Project
    + [Project Description](https://2017.igem.org/Team%3ABostonU_HW/Description)
    + [Microfluidics 101](https://2017.igem.org/Team%3ABostonU_HW/IntrouF)
    + [MARS Repository](https://2017.igem.org/Team%3ABostonU_HW/Demonstrate)
    + [Fluid Functionality](https://2017.igem.org/Team%3ABostonU_HW/Model)
    + [iGEM Collaborations](https://2017.igem.org/Team%3ABostonU_HW/Collaborations)
  * Notebook
    + [Timeline](https://2017.igem.org/Team%3ABostonU_HW/Notebook)
    + [Improve](https://2017.igem.org/Team%3ABostonU_HW/Improve)
  * Human Practices
    + [Silver](https://2017.igem.org/Team%3ABostonU_HW/HP/Silver)
    + [Gold](https://2017.igem.org/Team%3ABostonU_HW/HP/Gold_Integrated)
  * Medal Criteria
    + [Bronze](https://2017.igem.org/Team%3ABostonU_HW/Bronze)
    + [Silver](https://2017.igem.org/Team%3ABostonU_HW/Silver)
    + [Gold](https://2017.igem.org/Team%3ABostonU_HW/Gold)

Attributions

![](https://static.igem.org/mediawiki/2017/9/94/LARGE_background_MARS.png)

![](https://static.igem.org/mediawiki/2017/2/22/MARSLogo2.png)

Notebook

# May

* The BostonU Wetlab and Hardware iGEM teams participated in joint Wetlab safety and protocol training
* The team performed an initial literature review in order to learn more about the types of microfluidic devices being design
* The team was given a software overview/explanation of the three CIDAR lab microfluidic design tools: 3Duf, Fluigi, and Neptune
* The team was given an overview/explanation of the CIDAR lab microfluidic design manufacturing process: Makerfluidics

# June

* From the literature review, each member chose one chip of interest to replicate and test

1. LAMP Chip[1]
   + 3 iterations designed in Fluigi
   + 5 iterations designed in 3Duf and tested
2. Multiplex Drug Testing Chip[2]

+ 2 iterations designed in 3Duf and tested
+ 1 iteration designed in Fluigi

3. Magnetic Mixer Chip[3]

+ 5 Iterations milled and tested
+ Magnetic particles introduced into chip
+ Experimented with different protocols

* BostonU Wetlab iGEM Team Collaboration began

+ At the initial meeting BostonU Wetlab provided BostonU Hardware with a protocol they thought could be performed in a microfluidic device
+ 6 potential chips designed for Wetlab collaboration

* Submitted Microfluidics iGEM Poll to the iGEM collaborations page
* Volume Dispensing Chips
  + 3 iterations designed in 3Duf and tested
* Alternative Tree Primitive Designs
  + Given repeat difficulties faced while using trees in designs, alternative designs were tested to determine if there was a better design
  + 3 iterations designed in 3Duf and tested
* Transformation Chip
  + 6 Iterations designed in Fluigi
  + 2 Iterations designed in 3Duf and tested
* Cell Sorting
  + 1 iteration milled and tested
  + Magnetic particles run through chip
* Attended Northeastern iGEM practice conference (NEGEM) at BU
  + Received feedback on iGEM narrative
  + Developed project ideas based off of feedback
* MARS Repository begins to form after talking with researchers from CILSE’s Biological Design Center

# July

* Alternative Tree Primitive Designs
  + 1 iteration designed in 3Duf and tested
  + 1This design was markedly better at dispensing liquid equally, therefore it was used in later designs
* Cell Lysis Chip
  + 3 iterations designed in 3Duf and tested
  + Changes made to fix issues with fluid input and mixing
  + Initial draft of protocol written
* Wetlab Collaboration Chip
  + 4 iterations milled
  + Sealing issues improved upon
  + Testing done with shared liquid input
* DNA Digestion Chip
  + 4 iterations milled
  + Iterations made to better replicate protocol on a chip
  + Pipetting chamber designed and optimized for chip
* BostonU Hardware visits BosLab during monthly showcase
  + Provided insight into what small scale biohacker space is like, and what synthetic biology community is looking for in microfluidics
* Fluid Functionality begins to be developed
  + Idea of primitive level analysis developed along with some qualitative failures
* Worked with Neptune (2016 BostonU Hardware Team) automated syringe pumps tried to increase accuracy and improve function
* MARS Repository chips began to be placed in subsections of isolation, modification, and quantification
* Transformation Chip
  + 2 iterations designed in Fluigi
  + 8 iterations designed in 3Duf and tested
  + Changes made to overall design as well as valve sizes
* Summer Pathways
  + Participated in Summer Pathways alongside the BostonU Wetlab Team
  + Created an interactive microfluidics design activity for the attending high school students
  + Engaged with students to design microfluidic devices based on synbio protocols
* Harvard iGEM Team Collaboration
  + Initial meetings to discuss plans
* WPI iGEM Team Collaboration
  + During the initial Skype call we discussed the nature of their lead assay and how it might be moved onto a microfluidic
  + Their team visited our lab and performed verified their assay’s functionality on the BU spectrometer
* Tutorial Videos
  + PDMS video filmed
* Peristaltic Pump Chip[4]
  + Design inspired by another paper with different geometries
  + 4 iterations designed in 3Duf and tested
* Metering Primitive
  + In order to allow for accurate volume dispensing on a microfluidic device, a metering primitive inspired by the peristaltic pump was designed
  + 2 iterations designed in 3Duf and tested

# August

* Transformation Chip
  + 13 iterations designed in 3Duf and tested
  + Different valve dimensions tested
* Ligation Chip
  + 2 iterations designed in 3Duf
* Tutorial Videos
  + PDMS Video finalized
  + Milling Video recording and scripting completed
* DNA Digestion
  + 2 iterations milled and tested
* Wetlab Collaboration Chip
  + 1 iteration milled and tested
* Cell Lysis Chip
  + Design finalized
  + Testing with magnetic particles in chamber
* Cell Culturing[6]
  + Initial CAD model designed and tested
  + Spin coated PDMS
  + Second and final CAD model designed and tested
* Wiki
  + Initial pages started to be constructed
  + Wiki architecture organized
* Fluid Functionality
  + Quantitative tests begin to be developed

# September

* Transformation Chip
  + 1 iteration designed in 3Duf and tested
  + Different valve dimension tested
* Tutorial Videos
  + Milling video finalized
  + Assembly video filmed and scripted
  + Cleaning video filmed and audio recorded
* Fluid Functionality
  + Channels quantitative tests finalized
* Antibiotic Resistance[5]
  + Initial design developed
* Wetlab Collaboration Chip
  + 2 Iterations milled and tested
  + Protocol and design finalized
  + Chip tested by Wetlab

# October

* Transformation Chip
  + 4 iterations designed in 3Duf and tested
  + Different metering scales tested
* PCR Chip
  + 4 iterations designed in 3Duf and tested
* Cell Sorting
  + 2 iterations milled and tested
  + Protocol finalized and documented
* Ligation Chip
  + 1 iteration designed in 3Duf
* Video tutorials
  + Assembly video finalized
  + Cleaning video finalized
* WPI iGEM Team Collaboration chip design documented finalized
* Attended Northeastern iGEM practice conference #2 (NEGEM) at MIT
  + Received feedback on iGEM presentation
  + Incorporated feedback for final presentation
* Fluid Functionality
  + Valve quantitative test finalized
  + Mixer quantitative test finalized
* Antibiotic Resistance
  + Design finalized using 3Duf
  + Milled and documented
* Harvard iGEM Collaboration
  + Validated Harvard optical density sensor

# Citations

1. Tourlousse, D. M., Ahmad, F., Stedtfeld, R. D., Seyrig, G., Tiedje, J. M., & Hashsham, S. A. (2012). A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomedical Microdevices, 14(4), 769–778. <https://doi.org/10.1007/s10544-012-9658-3>
2. Mohan, R., Mukherjee, A., Sevgen, S. E., Sanpitakseree, C., Lee, J., Schroeder, C. M., & Kenis, P. J. A. (2013). A multiplexed microfluidic platform for rapid antibiotic susceptibility testing. Biosensors and Bioelectronics, 49, 118–125. <https://doi.org/10.1016/j.bios.2013.04.046>
3. Liang-Hsuan Lu, Kee Suk Ryu, & Chang Liu. (2002). A magnetic microstirrer and array for microfluidic mixing. Journal of Microelectromechanical Systems, 11(5), 462–469. <https://doi.org/10.1109/jmems.2002.802899>
4. Nguyen, T. V., Duncan, P. N., Ahrar, S., & Hui, E. E. (2012). Semi-autonomous liquid handling via on-chip pneumatic digital logic. Lab on a Chip, 12(20), 3991. <https://doi.org/10.1039/c2lc40466d>
5. Hou, H. W., Bhagat, A. A. S., Lin Chong, A. G., Mao, P., Wei Tan, K. S., Han, J., & Lim, C. T. (2010). Deformability based cell margination—A simple microfluidic design for malaria-infected erythrocyte separation. Lab on a Chip, 10(19), 2605. <https://doi.org/10.1039/c003873c>
6. Lee KS, Boccazzi P, Sinskey AJ, Ram RJ. Microfluidic chemostat and turbidostat with flow rate, oxygen, and temperature control for dynamic continuous culture. Lab Chip. 2011;11(10):1730-9.<https://doi.org/10.1039/c1lc20019d>

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# Team:BostonU HW/Experiments

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MENU

[HOME](https://2017.igem.org/Team%3ABostonU_HW)

TEAM

[Team](https://2017.igem.org/Team%3ABostonU_HW/Team)
[Collaborations](https://2017.igem.org/Team%3ABostonU_HW/Collaborations)

PROJECT

[Description](https://2017.igem.org/Team%3ABostonU_HW/Description)
[Design](https://2017.igem.org/Team%3ABostonU_HW/Design)
[Experiments](https://2017.igem.org/Team%3ABostonU_HW/Experiments)
[Notebook](https://2017.igem.org/Team%3ABostonU_HW/Notebook)
[InterLab](https://2017.igem.org/Team%3ABostonU_HW/InterLab)
[Contribution](https://2017.igem.org/Team%3ABostonU_HW/Contribution)
[Model](https://2017.igem.org/Team%3ABostonU_HW/Model)
[Results](https://2017.igem.org/Team%3ABostonU_HW/Results)
[Demonstrate](https://2017.igem.org/Team%3ABostonU_HW/Demonstrate)
[Improve](https://2017.igem.org/Team%3ABostonU_HW/Improve)
[Attributions](https://2017.igem.org/Team%3ABostonU_HW/Attributions)

PARTS

[Parts](https://2017.igem.org/Team%3ABostonU_HW/Parts)
[Basic Parts](https://2017.igem.org/Team%3ABostonU_HW/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3ABostonU_HW/Composite_Part)
[Part Collection](https://2017.igem.org/Team%3ABostonU_HW/Part_Collection)

[SAFETY](https://2017.igem.org/Team%3ABostonU_HW/Safety)

HUMAN PRACTICES

[Silver HP](https://2017.igem.org/Team%3ABostonU_HW/HP/Silver)
[Integrated and Gold](https://2017.igem.org/Team%3ABostonU_HW/HP/Gold_Integrated)
[Public Engagement](https://2017.igem.org/Team%3ABostonU_HW/Engagement)

AWARDS

[Applied Design](https://2017.igem.org/Team%3ABostonU_HW/Applied_Design)
[Entrepreneurship](https://2017.igem.org/Team%3ABostonU_HW/Entrepreneurship)
[Hardware](https://2017.igem.org/Team%3ABostonU_HW/Hardware)
[Measurement](https://2017.igem.org/Team%3ABostonU_HW/Measurement)
[Model](https://2017.igem.org/Team%3ABostonU_HW/Model)
[Plant](https://2017.igem.org/Team%3ABostonU_HW/Plant)
[Software](https://2017.igem.org/Team%3ABostonU_HW/Software)

[JUDGING FORM](https://igem.org/2017_Judging_Form?team=BostonU_HW)

# BostonU\_HW

# Experiments

Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.

Please remember to put all characterization and measurement data for your parts on the corresponding Registry part pages.

##### What should this page contain?

* Protocols
* Experiments
* Documentation of the development of your project

##### Inspiration

* [2014 Colombia](https://2014.igem.org/Team%3AColombia/Protocols)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Protocols)
* [2014 Caltech](https://2014.igem.org/Team%3ACaltech/Project/Experiments)

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# Team:BostonU HW/Results

[![](http://placehold.it/350x150)](https://2017.igem.org/Team%3ABostonU_HW)

MENU

[HOME](https://2017.igem.org/Team%3ABostonU_HW)

TEAM

[Team](https://2017.igem.org/Team%3ABostonU_HW/Team)
[Collaborations](https://2017.igem.org/Team%3ABostonU_HW/Collaborations)

PROJECT

[Description](https://2017.igem.org/Team%3ABostonU_HW/Description)
[Design](https://2017.igem.org/Team%3ABostonU_HW/Design)
[Experiments](https://2017.igem.org/Team%3ABostonU_HW/Experiments)
[Notebook](https://2017.igem.org/Team%3ABostonU_HW/Notebook)
[InterLab](https://2017.igem.org/Team%3ABostonU_HW/InterLab)
[Contribution](https://2017.igem.org/Team%3ABostonU_HW/Contribution)
[Model](https://2017.igem.org/Team%3ABostonU_HW/Model)
[Results](https://2017.igem.org/Team%3ABostonU_HW/Results)
[Demonstrate](https://2017.igem.org/Team%3ABostonU_HW/Demonstrate)
[Improve](https://2017.igem.org/Team%3ABostonU_HW/Improve)
[Attributions](https://2017.igem.org/Team%3ABostonU_HW/Attributions)

PARTS

[Parts](https://2017.igem.org/Team%3ABostonU_HW/Parts)
[Basic Parts](https://2017.igem.org/Team%3ABostonU_HW/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3ABostonU_HW/Composite_Part)
[Part Collection](https://2017.igem.org/Team%3ABostonU_HW/Part_Collection)

[SAFETY](https://2017.igem.org/Team%3ABostonU_HW/Safety)

HUMAN PRACTICES

[Silver HP](https://2017.igem.org/Team%3ABostonU_HW/HP/Silver)
[Integrated and Gold](https://2017.igem.org/Team%3ABostonU_HW/HP/Gold_Integrated)
[Public Engagement](https://2017.igem.org/Team%3ABostonU_HW/Engagement)

AWARDS

[Applied Design](https://2017.igem.org/Team%3ABostonU_HW/Applied_Design)
[Entrepreneurship](https://2017.igem.org/Team%3ABostonU_HW/Entrepreneurship)
[Hardware](https://2017.igem.org/Team%3ABostonU_HW/Hardware)
[Measurement](https://2017.igem.org/Team%3ABostonU_HW/Measurement)
[Model](https://2017.igem.org/Team%3ABostonU_HW/Model)
[Plant](https://2017.igem.org/Team%3ABostonU_HW/Plant)
[Software](https://2017.igem.org/Team%3ABostonU_HW/Software)

[JUDGING FORM](https://igem.org/2017_Judging_Form?team=BostonU_HW)

# BostonU\_HW

# Results

Here you can describe the results of your project and your future plans.

##### What should this page contain?

* Clearly and objectively describe the results of your work.
* Future plans for the project.
* Considerations for replicating the experiments.

##### You should also describe what your results mean:

* Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for.
* Show data, but remember all measurement and characterization data must be on part pages in the Registry.
* Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project.

##### Project Achievements

You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.

* A list of linked bullet points of the successful results during your project
* A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.

##### Inspiration

See how other teams presented their results.

* [2014 TU Darmstadt](https://2014.igem.org/Team%3ATU_Darmstadt/Results/Pathway)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Results)
* [2014 Paris Bettencourt](https://2014.igem.org/Team%3AParis_Bettencourt/Results)

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