Difference between revisions of "Team:BostonU HW/Attributions"

In order to effectively use the MARS system, users need to have a fundamental understanding of microfluidics. With this in mind, we created an introduction to microfluidics that teaches users the basics of microfluidics. This educational component of project MARS consists of an introduction to microfluidic chips as well as a guide to the various primitives used in our microfluidic designs.

In order to make the microfluidic chips we designed accessible to synthetic biologists we developed four fully-narrated tutorial videos. These videos go step by step through the process of manufacturing, assembling, and testing a microfluidic device. The four videos created teach uses how to mill a microfluidic chip, how to make PDMS, how to assemble a microfluidic chip, and how to clean a microfluidic chip. Each of these videos is accompanied by a detailed written protocol as well.

In order to make microfluidics a practical field for synthetic biologists, we created the MARS microfluidic chip repository. This repository hosts nine microfluidic chips that each perform a fundamental synthetic biological protocol. These nine protocols were determined after reaching out to synthetic biologists in the Boston University and iGEM communities. Each chip comes with all the required design files and documentation so that a synthetic biologist could download, manufacture, and test any chip in the repository. The nine chips in the MARS repository are as follows:

For more information regarding each chip, please see our MARS Repository page.

In order to verify whether or not a microfluidic device is functional, a grading system was developed: the Fluid Functionality Checklist. This fluid functionality system was broken up into two portions: a qualitative checklist and a quantitative analysis.

The qualitative portion of the fluid functionality checklist consists of various failure modes. These are visual cues that something has gone wrong while running a chip, such as liquid leaking out of a channel or primitive. If a chip passes each of these qualitative checks, it is deemed “fluid functional.” If a chip does not pass each of these qualitative checks, the user moves to the quantitative analysis to determine why the chip failed.

The quantitative portion of the fluid functionality checklist consists of various quantitative analyses. Two forms of analysis are included in this portion of our evaluation system: physics-based primitive analysis and image processing-based analysis. Physics based analysis helps to determine if a qualitative failure occurred because the incorrect primitive dimensions and/or flow rate were used. Image processing analysis is used to evaluate the functionality of primitives such as mixers. Using these analyses, a user can both determine why their chip failed and evaluate the functionality of key primitives.

3DuF is a microfluidic design software that allows users to draw designs manually similarly to a CAD tool. 3Duf then provides users with CNC millable SVG files, and JSON files which can be used to edit the design in 3DuF later on. 3DuF has been the primary software tool used throughout the project for device design and iteration.

MINT is a detailed microfluidics description language which is taken as an input by Fluigi, a place and route tool for microfluidics, and converted into optimized device designs. These designs are provided to users as CNC millable SVG files, and JSON files compatible with 3DuF.

Throughout the microfluidic design and iteration process Ali provided advice from the perspective of a microfluidic device expert. He also gave input on effective troubleshooting of fabrication, prototyping and testing issues experienced by the team members.

MakerFluidics is a low-cost, rapid microfluidic fabrication workflow. Users mill out the SVG files provided by Fluigi or 3Duf using a CNC to fabricate the flow and control layers of their device. A flexible PDMS layer is then placed between them and vacuum sealed using a desiccator. These chips can then be tested using colored dye and oil.

Over the summer Shane advised the team on utilizing the existing software flow (Neptune, 3Duf, Fluigi) and the basics of fabricating using MakerFluidics. He was also present as a team advisor and liaison during the iGEM season providing support and advice.