openTECR: an open database for Thermodynamics of Enzyme-catalyzed Reactions

[rgiessmann]

Project Lead: @rgiessmann, @teddygroves

Mentor: @NPalopoli

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Week 1: Meet your mentor!

• Meet mentor for 30 minutes
• Create an account on GitHub
• Check if you have access to the HackMD notes set up for your meetings with your mentor
• Prepare to meet your mentor(s) by completing a short homework provided in your shared notes
• 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.
• Make sure you know when and how you'll be meeting with your mentor.

Before Week 2: Cohort Call (Welcome to Open Life Science!)

• Attend call or catch up via YouTube
• Create an issue on the OLS-8 GitHub repository for your OLS work and share the link to your mentor.
• Draft a brief vision statement using your goals
• Leave a comment on this issue with your draft vision statement & be ready to share this on the call
• Check the Syllabus for notes and connection info for all the cohort calls.

Before Week 3: Meet your mentor!

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

Before Week 4: Cohort Call (Tooling and roadmapping for Open projects)

• Attend call or catch up via YouTube
• Look up two other projects and comment on their issues with feedback on their open canvas.

Week 5 and later

• Meet mentor
• Create a GitHub repository for your project
• Add the link to your repository in your issue
• Use your canvas to start writing a README.md file, or landing page, for your project
• Link to your README in a comment on this issue
• Add an open license to your repository as a file called LICENSE.md
• Add a Code of Conduct to your repository as a file called CODE_OF_CONDUCT.md
• Invite new contributors to into your work!

This issue is here to help you keep track of work as you start Open Life Science program. Please refer to the OLS-4 Syllabus for more detailed weekly notes and assignments past week 4.

Week 6

• Attend call or catch up via YouTube

Week 7

• Meet mentor

Week 8

• Attend call or catch up via YouTube

Week 9

• Meet mentor

Week 10

• Attend call or catch up via YouTube

Week 11

• Meet mentor

Week 12

• Attend call or catch up via YouTube

Week 13

• Meet mentor

Week 14

• Attend call or catch up via YouTube

Week 15

• Meet mentor

[rgiessmann]

https://docs.google.com/document/d/1dv7FHCRR6SGs9EKu39MBUZIxndygexdo/edit#heading=h.ppvvf2q72wj6

One-sentence Vision Statement:

We're creating an open database that simplifies access to and sharing of energy data for biochemical reactions in living organisms, built by and for modellers and experimentalists alike.

The long version:

We are making a free, open, FAIR, online database containing important information about the energies of chemical reactions in living organisms.

Our project will facilitate quantitative biological modelling by providing easy access to data as well as a place to share the results of new measurements with the scientific community.

Our users are people who want data about biochemical reaction energies and people who have measured these energies experimentally and want to share their results. These people are also our intended contributors

[virginiagarciaalonso]

Hi @rgiessmann and @teddygroves!

Nice project you have going on. I was wondering, are you going to focus on specific living organisms and/or biochemical reactions at the beginning?

[rgiessmann]

Hi @virginiagarciaalonso , no, the equilibrium constants are independent of the specific organism (this sentence contains a slight simplification; let me know if you need more info).

We are aiming to collect as many biochemical reactions as possible. There is a lot already available (~500 reactions), and filling the gaps experimentally would require some funding and lab space. Let me know if you would like to learn more and/or want to collaborate on anything in this space. :)

[rgiessmann]

Reading recommendations we received so far:

Ten quick tips for biocuration

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Bad Identifiers are the Potholes of the Information Superhighway: Take-Home Lessons for Researchers

what motivates people to use&contribute to PomBase: https://pubmed.ncbi.nlm.nih.gov/32353878/

Based on the survey results it seems that most people did not contribute because no one had asked them: https://pubmed.ncbi.nlm.nih.gov/20167071/

https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies/

[ykho001]

Hi @rgiessmann and @teddygroves,
You have a really interesting project here, and I like how you laid out your vision statement (short, long, and full form) so that we can learn about your project easily. (We may have to emulate your model here for when we develop our vision statement!)
I'd be interested to see how you create your open database, and how you make it interactive and accessible to the community. Looking forward to seeing the development of your project, and hearing the feedback from your user and contributor base! :)

[rgiessmann]

Our open canvas is at: https://docs.google.com/presentation/d/13l2gEKGwpgQdXzgPfpBXw1ju-r4SMFFNkUGsxEm-hIE/edit#slide=id.p6

[rgiessmann]

Our github repo is here: https://github.com/opentecr/opentecr

[rgiessmann]

Our README draft is here: https://docs.google.com/document/d/1bmV44za0rPykaQ0ykv80JhR2Ax6Ja9Slb4-mRRsbsKw/edit

[rgiessmann]

a collection of tasks, hopefully leading to a Roadmap: https://docs.google.com/document/d/1UFTLCb9QeDxPBj_j29_Tx1d-om2dKlVdqkhcGboit8I/edit