Team:BostonU HW/Attributions
ATTRIBUTIONS
The NEPTUNE Flow
Neptune abstracts a very intricate workflow to provide an intuitive experience for its user. Below is a detailed depiction of all of the components that are under Neptune's hood.
Each of BostonU Hardware Team's members played an integral part in the success of Neptune's development.
Liquid Flow Relations & User Constraints File | Shane McCormack
In order to increase accessibility of our tool (and microfluidics in general), a method for describing microfluidics in a few simple lines was formed! This standard consists of Liquid Flow Relations (or LFR), and the User Constraints File (or UCF). The LFR file is where the user describes the inputs, outputs, and tells of any operations which occur on those inputs and outputs. These operations are described as symbols on the LFR, but are informed by the UCF. The few lines of LFR are the only things needed to run a chip through Neptune; a sample UCF is provided with Neptune that can be fine-tuned, but will not need to be written in its entirety.
The UCF can be thought of as a library of microfluidic components where, once a component is defined, it will never have to be written again! In more detail, once a component is defined inside the UCF, all subsequent LFR files can utilize the symbol the component is linked to without redefining the details of the component. The UCF leverages the MINT standard of describing parametric microfluidics. This parametrization unlocks great potential in the rapid prototyping of designs, where one number can be changed in the UCF, and all subsequent designs will have the updated component! For example, if our fictional synthetic biologist Dr. Ali found that his mixer's bends were too short in length, with one number edit in the UCF he could fix every bend of every mixer in all of his designs thereafter! This is far more accessible than redrawing every bend by hand on AutoCAD.
The UCF can be thought of as a library of microfluidic components where, once a component is defined, it will never have to be written again! In more detail, once a component is defined inside the UCF, all subsequent LFR files can utilize the symbol the component is linked to without redefining the details of the component. The UCF leverages the MINT standard of describing parametric microfluidics. This parametrization unlocks great potential in the rapid prototyping of designs, where one number can be changed in the UCF, and all subsequent designs will have the updated component! For example, if our fictional synthetic biologist Dr. Ali found that his mixer's bends were too short in length, with one number edit in the UCF he could fix every bend of every mixer in all of his designs thereafter! This is far more accessible than redrawing every bend by hand on AutoCAD.
MμShroom Mapper | Shane McCormack
With the new facilitated design method of Liquid Flow Relations, a behind-the-scenes software tool was needed to interpret and translate the LFR and UCF into a functional MINT file. This task is fulfilled with muShroomMapper; muShroomMapper takes LFR and UCF as inputs, maps the LFR into a graph with the support of NetSynth, then informs that graph with the UCF. The informed graph is then translated into a MINT file, to be placed and routed to a blueprint for fabrication.
MμShroom Mapper-Neptune Integration | Kestas Subacius & Shane McCormack
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Fluigi-Neptune Integration | Kestas Subacius & Shane McCormack
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Control Infrastructure Prototyping | Zach Lasiuk & Priya Kapadia
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Parametric Control Infrastructure | Zach Lasiuk
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Neptune's Specify & Design Pages | Kestas Subacius
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Neptune's Build & Assembly Pages | Priya Kapadia
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Neptune's Control Page | Becca Wolf
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3DuF Integration | Becca Wolf
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Neptune-Arduino Integration | Johan Ospina & Becca Wolf
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Arduino Firmware | Zach Lasiuk
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Firmware-Neptune Integration | Zach Lasiuk & Becca Wolf
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Even Fluid Dispension | Zach Lasiuk
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Even Fluid Dispension-Neptune Integration | Zach Lasiuk, Becca Wolf, & Priya Kapadia
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Microfluidic Chip Prototyping | Shane McCormack
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We stand on the shoulders of giants.
Our work would not have been possible without the foundations laid by our mentors. Neptune’s microfluidic design and fabrication tool leverages projects such as Fluigi Place and Route, Mint description language, MakerFluidics, and 3DuF in order to provide the most intuitive and cohesive experience for users. These projects have been built and expanded on by our graduate student mentors. We would like to thank our mentors for all of the work they have done to allow us to bring Neptune to life.
Fluigi | Radhakrishna Sanka
A place and route tool for microfluidic devices. Fluigi takes a MINT file as input and strategically routes the features specified in the MINT into an optimized microfluidic design. Fluigi outputs the design in a series of visual formats: SVG files (which can be used to mill out the different layers of the microfluidic chip using a CNC mill), a JSON file (which can be used to visualize the microfluidic design with 3DuF), and EPS files (which can be used to build the chip using photolithography if the user so chooses).
MINT | Radhakrishna Sanka
A microfluidic description language generated as an output of MuShroom mapper and used as an input to Fluigi. This language is used to describe the features of the specified microfluidic device in great detail including specification of feature shape, size and spacing.
Netsynth | Prashant Vaidyanathan
Netsynth is a software tool that was originally built by Prashant Vaidyanathan to translate Verilog logic descriptions into wire and gate lists. Netsynth has been modified for use in Neptune through a collaboration between Shane McCormack (BostonU_HW Team member) and Vaidyanathan to produce output formatted for interpretation in the context of microfluidic design. MuShroom mapper (a tool build by McCormack) uses this output alongside a variety of other inputs to produce a MINT file output in the Specify stage of Neptune.
3DuF | Joshua Lippai
A CAD-like drawing web application. 3DuF can be used to manually draw a microfluidic design if the user wishes to bypass high-level specifications. 3DuF will then output SVG files (for CNC milling layers of the microfluidic chip) and a JSON file for later visualization and editing purposes. When used in the context of Neptune, 3DuF is leveraged to visualize the JSON output of Fluigi so that the user may control his or her microfluidic device intuitively through the Neptune interface.
MakerFluidics | Ryan Silva
MakerFluidics is an accessible, inexpensive microfluidic fabrication technique used to manufacture microfluidic chips. A user will use an SVG file to mill out both the control and flow layers of a microfluidic chip. Then he or she will use these 2 layers to sandwich a piece of PDMS and vacuum the chip to create a seal. Through Neptune, the user is encouraged to use this fabrication infrastructure to make their chip so that they may rapidly prototype many chips inexpensively for any iterations of their experiment and easily control their microfluidic system through the Neptune interface.
Microfluidic Application | Ali Lashkaripour
Explorations into the biological applications for Neptune’s workflow are spearheaded by Ali Lashkaripour. He designs and tests features to be added to our UCF repo as relevant primitives to chip designs for synthetic biological application. Design constraints of microfluidic design through Neptune’s toolchain are also investigated by Lashkaripour.
Thank you to our sponsors for their support
