ShareYourCloning: a web application to generate molecular cloning strategies in json format, and share them with others

[manulera]

Project Lead: @manulera

Mentor: @DimmestP

Welcome to OLS-4! 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 🎉.

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Week 1 (week starting 13 September 2021): 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 (week starting 20 September 2021): Cohort Call (Welcome to Open Life Science!)

• Attend call or catch up via YouTube

• Create an issue on the OLS-4 GitHub repository for your OLS work and share the link to your mentor.

• Draft a brief vision statement using your goals

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

• 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 (week starting 27 September 2021): 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

[manulera]

Week 1 and 2 assignments

Self-assesment notes (click to expand)

Taking the self-assesment survey felt a bit unrealistic. I have barely participated as a contributor to OS projects, much less as a leader. I tried to answer following what I think I would do as a project leader. I think the main areas of learning for me would be how to engage people to contribute, and how to share the governance / development decissions of a project with the community

Vision statement notes (click to expand)

The problem to solve

ShareYourCloning is the first step towards the development of a bigger web application called Genestorian. Genestorian will be an Open Source web application for experimental researchers to keep an audit trail of the sequences of recombinant DNA and model organism strains in a laboratory collection. The application will track all genetic engineering operations performed on strains and recombinant DNA up to the entry point of sequences into the collection (e.g. when a strain or plasmid is requested from another laboratory or repository). ShareYourCloning is the first step towards this goal, and is concerned with the documentation of molecular cloning.

How openness and open leadership will help solve it

Genestorian tries to address a fundamental challenge that remains unaddressed in genetics: How to document the lineages of recombinant DNA molecules and model organism strains. This is an Open Science matter as it concerns the documentation and reproducibility of research.

A project like this will require a combination of software development skills and understanding of a broad range of experimental use-cases that will be best addressed as a community of developers/ users.

How meeting your personal goals will help you and help solve the problem

My personal open science goals:

• Learn how to make the project community inclusive and accessible for new contributors
• Learn how to share/open the governance of a project that initially started as a personal project

I think OLS-4 can help train me in best practices to grow an inclusive and accessible community around the project, which will help it grow and serve the various use cases. I expect this to be particularly challenging for a project with this characteristics, where most often there will be a distinction between users and developers.

I think open managing of a project's governance is one of the key challenges that I hope to learn to address. Beyond transparency on reporting why some decisions are taken, I believe having a participative decision process will greatly benefit the project.

Short vision statement

I’m working with biologists interesting in coding and developers interested in biology to build ShareYourCloning, a web application so that researchers working with recombinant DNA can document molecular cloning.

[manulera]

Open Canvas

This is an Open Canvas for Genestorian, of which ShareYourCloning would be the first component.

[acocac]

Hi @manulera, nice project. I've found very interesting the project repo and README. The short vision statement is also great, however, it's worth mentioning the platform will evolve to a big web application, Genestorian. Also, is the platform only focused on biologists with programming skills? I note you have a well-established front- and back-end so it might be also good to leave open contributions from the computer science community or developers interested in molecular cloning and/or DNA data applications.

[manulera]

Project README file

Link

[manulera]

Project roadmap

Link

[manulera]

Hi @manulera, nice project. I've found very interesting the project repo and README. The short vision statement is also great, however, it's worth mentioning the platform will evolve to a big web application, Genestorian. Also, is the platform only focused on biologists with programming skills? I note you have a well-established front- and back-end so it might be also good to leave open contributions from the computer science community or developers interested in molecular cloning and/or DNA data applications.

Hi @acocac, thanks for having a look! I bounce back between mentioning Genestorian or not, as this project will be a standalone tool, but also a first brick for Genestorian. I will include it in the mission statement.

Ideally the project will be used by biologists with or without programming skills, and as you said the goal is that developers that are not biologists can make contributions as well. This is in the contributing file but maybe a link to it on the readme will help. Thanks for having a look!

• Adding contributing personas to the readme and link to the contributing.md
• Adding Genestorian to vision statement

[Elisa-on-GitHub]

Hi @manulera, I really enjoyed going through your README file. Although I don't know much about the field, it was clear how I should get started and it was good that you provided samples of code. I also read your contributor guidelines and code of conduct, and I just wanted to compliment you: it all looks complete and very clear!