Conflux Protocols: Reproducible Opensource Biological Automation Protocols

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Project Lead:

• W.R. Jackson

Mentor:

• Yo Yehudi
• Malvika Sharan

Welcome to OLS-3! This issue will be used to track your project and progress during the program. Please use this checklist over the next few weeks as you start Open Life Science program :tada:.

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Week 1 (week starting 8 February 2021): Meet your mentor!

• [x] Create an account on GitHub
• [x] Check if you have access to the HackMD notes set up for your meetings with your mentor
• [x] Prepare to meet your mentor(s) by completing a short homework provided in the HackMD notes
• [x] Complete your own copy of the open leadership self-assessment and share it to your mentor If you're a group, each teammate should complete this assessment individually. This is here to help you set your own personal goals during the program. No need to share your results, but be ready to share your thoughts with your mentor.
• [x] Make sure you know when and how you'll be meeting with your mentor.

Before Week 2 (week starting 15 February 2021): Cohort Call (Welcome to Open Life Science!)

• [x] Create an issue on the OLS-3 GitHub repository for your OLS work and share the link to your mentor.

• [x] Draft a brief vision statement using your goals

  This lesson from the Open Leadership Training Series (OLTS) might be helpful

• [x] Leave a comment on this issue with your draft vision statement & be ready to share this on the call

• [x] Check the Syllabus for notes and connection info for all the cohort calls.

Before Week 3 (week starting 22 February 2021): Meet your mentor!

• [ ] Look up two other projects and comment on their issues with feedback on their vision statement
• [x] Complete this compare and contrast assignment about current and desired community interactions and value exchanges
• [x] Complete your Open Canvas (instructions, canvas)
• [x] Share a link to your Open Canvas in your GitHub issue
• [x] Start your Roadmap
• [x] Comment on your issue with your draft Roadmap
• [x] Suggest a cohort name at the bottom of the shared notes and vote on your favorite with a +1

Before Week 4 (week starting 1 March 2021): Cohort Call (Tooling and roadmapping for Open projects)

• [ ] Look up two other projects and comment on their issues with feedback on their open canvas.

Week 5 and later

• [x] Create a GitHub repository for your project
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This issue is here to help you keep track of work as you start Open Life Science program. Please refer to the OLS-3 Syllabus for more detailed weekly notes and assignments past week 4.

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Vision Statement

Biological automation has the potential to increase the speed at which discovery in the life science space happens and allows for consistent reproducible results across institutions and laboratories. These aid in interoperability between research projects and minimize the rework required to get biological protocols operational.

However, this information is not freely disseminated or available due to a number of factors:

• Hardware Fragmentation across commercially available liquid handlers and robotics.
• An impetus to keep protocols in house, either to avoid getting 'scooped' in a research context or act as a competitive advantage against other researchers.
• A disconnect between the needs of biologists and robotic implementation.

Conflux seeks to fix these issues by acting as an open-source repository for automation protocols and a linuga franca by acting as a translator for different automation platforms.

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Link to Open Canvas

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Link to Github Projects

[sjb287]

I really like your idea, this is such an important issue to solve! A couple of questions: How exactly are the protocols to be stored (raw files or more like something along the lines of protocols.io?) How will Conflux act as a translator between different automation platforms? will you use something like Antha? https://www.synthace.com/antha/ and https://github.com/antha-lang

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Thanks! I really appreciate the positive feedback. I had heard mention of Synthace and Antha previously but never had actually read the repository, so I appreciate the link!

To answer the questions:

1. Something more along the lines of Protocols.io. My current implementation is very heavily inspired by the Github UI/UX workflow, so each protocol currently lives in something that looks like a repository and has a number of visuals that correspond to a network graph representation of the protocol as well as a 'Recipe' view of the protocol that I think is more parseable by folks coming at this from the wet lab side of things.

2. Most of the Protocols I've written for Conflux so far are actually graphs where the nodes represent bioautomation primitives (Pipette this much liquid to this well, heat location to N degrees, etc.). I have something akin to a simplistic compiler that maps those primitives to the various APIs or Languages for each of the targets. To be fair, it's more than a little janky at the moment. The upshot of this is that each graph can flow into each other, so I can arbitrarily combine and create macros out of complex systems.