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Latest revision as of 03:20, 20 October 2016
MEDAL CRITERIA: BRONZE
Bronze Medal Requirements
Register for iGEM, have a great summer, and attend the Giant Jamboree
We're very excited to be part of the Jamboree, to see all the other amazing projects, to show everyone what we've accomplished through our hard work this summer. And we're excited to see you there too :)
Meet all deliverables on the Requirements page (section 3), except those that specifically mention parts
- Team Wiki: You're looking at her.
- Poster: Come by our table and take a look.
- Presentation: You'll love what you see.
- Project Attributions: Please see out attributions page.
- Registry Part Pages: Hardware track.
- Safety Forms: Complete.
- Judging Forms: Complete.
Meet all deliverables on the Requirements page (section 3), except those that specifically mention parts
Neptune is a design tool that implements the research done by many mentors and graduate student. Before us, other students developed single, abstract software tools toward microfluidic design. These tools saw limited to no use because they failed to integrate into a bigger system. We created the software for the Neptune user interface that wraps these different projects, and we created the hardware control infrastructure for the microfluidics that are generated from this workflow. We have also contributed to the algorithmic libraries of Neptune by developing a tool called Mushroom Mapper, which allows for a higher level of abstraction when specifying microfluidic chip designs. Here we attribute the different components behind Neptune, the ones created by other students and mentors.
3DuF:
3DuF is a user friendly, open source application for creating microfluidic designs and design components that can then be fabricated with CAD tools. This application is embedded in Neptune as a visualization tool for the microfluidic chip design. This tool is currently in development by our mentor Josh Lippai.
MakerFluidics:
MakerFluidics is a microfluidic fabrication protocol that leverages open, low cost, and easily accessible tools to fabricate microfluidics. In this toolchain, microfluidics are created using a CNC mill to create channels in a thermoplastic, biocompatible stock. MakerFluidics uses open source software, including 3DuF, and now Neptune. Neptune is developed to be compatible with MakerFluidics; in Neptune SVG design schematics are generated, ready to fabricate with a CNC mill. This protocol was developed by our mentor Ryan Silva.
Fluigi Core:
Fluigi Core is a place and route tool that takes MINT files that the user inputs into Neptune, and it performs an optimization placing of channels, valves, and other components onto the microfluidic chip. In essence, Fluigi Core generates design schematics from the MINT standard microfluidic specification format you provide it. Neptune wraps Fluigi Core, it is the algorithmic library to our software. This program is currently in development by our mentor Radhakrishna Sanka.
NetSynth:
NetSynth is a logic minimization library for Verilog. The original purpose of NetSynth was to take a Verilog description of a circuit, and convert this into a netlist of wires and gates that realize the design description. Our iGEM team has joined the prior work of Prashant Vaidyanathan to refactor NetSynth into a tool that can also perform logic minimization on microfluidic designs. Prashant is responsible for originally repurposing NetSynth for microfluidic design, and our team has further contributed to this by integrating NetSynth outputs with the Mushroom Mapper tool we created.
3DuF:
3DuF is a user friendly, open source application for creating microfluidic designs and design components that can then be fabricated with CAD tools. This application is embedded in Neptune as a visualization tool for the microfluidic chip design. This tool is currently in development by our mentor Josh Lippai.
MakerFluidics:
MakerFluidics is a microfluidic fabrication protocol that leverages open, low cost, and easily accessible tools to fabricate microfluidics. In this toolchain, microfluidics are created using a CNC mill to create channels in a thermoplastic, biocompatible stock. MakerFluidics uses open source software, including 3DuF, and now Neptune. Neptune is developed to be compatible with MakerFluidics; in Neptune SVG design schematics are generated, ready to fabricate with a CNC mill. This protocol was developed by our mentor Ryan Silva.
Fluigi Core:
Fluigi Core is a place and route tool that takes MINT files that the user inputs into Neptune, and it performs an optimization placing of channels, valves, and other components onto the microfluidic chip. In essence, Fluigi Core generates design schematics from the MINT standard microfluidic specification format you provide it. Neptune wraps Fluigi Core, it is the algorithmic library to our software. This program is currently in development by our mentor Radhakrishna Sanka.
NetSynth:
NetSynth is a logic minimization library for Verilog. The original purpose of NetSynth was to take a Verilog description of a circuit, and convert this into a netlist of wires and gates that realize the design description. Our iGEM team has joined the prior work of Prashant Vaidyanathan to refactor NetSynth into a tool that can also perform logic minimization on microfluidic designs. Prashant is responsible for originally repurposing NetSynth for microfluidic design, and our team has further contributed to this by integrating NetSynth outputs with the Mushroom Mapper tool we created.
Document at least one new substantial contribution to the iGEM community that showcases a project made with BioBricks. This contribution should be equivalent in difficulty to making and submitting a BioBrick part
Our contribution to the iGEM community is not a single hardware device, nor a one-off software tool. Our contribution to the iGEM community, and the synthetic biology community as a whole, is much greater than that. This summer we built a completely integrated, seamless, end-to-end microfluidic design, fabrication, and control workflow. This workflow enables the rapid, modular, and parametric design of microfluidic chips, and our workflow integrates with low cost, open fabrication methods. This is something that has never been possible in microfluidics before.
Physically, our contribution to the community is twofold:
This summer we created Neptune, an integrated microfluidic design suite. This is a single software tool that spans the entire microfluidic design process. In Neptune, users can create microfluidic chips design schematics with the aid of algorithms that optimize the design. Neptune allows microfluidics to be designed through LFR, a specification we worked to create. With LFR, designs are parametric and the design process is simple. Neptune also allows researchers to run experiments directly through the interface by providing a control page. Users can upload a chip design to Neptune, and then use Neptune to manipulate valve states and actuate pumps to generate fluid flows in the chip.
We did not stop there. This summer we also created a full hardware control infrastructure for microfluidic chips. We developed original designs for controlling valve actuation and fluid dispension using low cost servo motors and 3D printed components. These designs are both parametric, and the they have high precision in their fluid dispension. Further, we designed 3D print schematics for a pump array to control a microfluidic chip; these 3D print schematics are all served through Neptune.
Thus, we have developed everything a researcher would need to design, fabricate, and run experiments on their microfluidic device. Accessibility, though, has always been our biggest goal. We developed this entire workflow with the synthetic biology community in mind. Microfluidics have always been very difficult to fabricate, and costly, with tools for fabrication and design costing nearly $100,000. Further, control infrastructure is also costly, and most software tools to control microfluidics are specialized to single hardware pieces. We developed our workflow to interface with and use only open source, low cost tools. We designed 3D printed hardware for the purpose of providing a more accessible alternative, and we use the MakerFluidics fabrication protocol to keep fabrication costs as low as possible.
Please, follow this link to see the documentation for Neptune, and our hardware pieces.
