TidyScreen: a platform to design, execute and document virtual drug screening campaigns

[alfredoq]

Project Lead: Alfredo Quevedo - @alfredoq

Mentor: Gemma Turon - @gemmaturon

Welcome to OLS-9! 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: Meet your mentor!

• [x] Meet mentor for 30 minutes
• [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 your shared 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: Cohort Call (Welcome to Open Life Science!)

• [x] Attend call or catch up via YouTube

• [x] Create an issue on the OLS-9 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: Meet your mentor!

• [x] Meet mentor
• [x] 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
• [ ] Comment on your issue with your draft Roadmap
• [ ] Suggest a cohort name at the bottom of the shared notes and vote on your favourite with a +1

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

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

Week 5 and later

• [x] Meet mentor
• [x] Create a GitHub repository for your project
• [x] Add the link to your repository in your issue
• [x] Use your canvas to start writing a README.md file, or landing page, for your project
• [x] Link to your README in a comment on this issue
• [x] 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
• [x] Invite new contributors to 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-9 Syllabus for more detailed weekly notes and assignments past week 4.

Week 6

• [x] Attend call or catch up via YouTube
• Comment below to share your progress and link to resources for review with your peers and mentors below

Week 7

• [ ] Meet mentor
• Comment below to share your progress and link to resources for review with your peers and mentors below

Week 8

• [ ] Attend call or catch up via YouTube
• Comment below to share your progress and link to resources for review with your peers and mentors below

Week 9

• [ ] Meet mentor
• Comment below to share your progress and link to resources for review with your peers and mentors below

Week 10

• [ ] Attend call or catch up via YouTube
• Comment below to share your progress and link to resources for review with your peers and mentors below

Week 11

• [ ] Meet mentor
• Comment below to share your progress and link to resources for review with your peers and mentors below

Week 12

• [ ] Attend call or catch up via YouTube
• Comment below to share your progress and link to resources for review with your peers and mentors below

Week 13

• [ ] Meet mentor
• Comment below to share your progress and link to resources for review with your peers and mentors below

Week 14

• [ ] Attend call or catch up via YouTube
• Comment below to share your progress and link to resources for review with your peers and mentors below

Week 15

• [ ] Meet mentor

• [ ] Celebrate your participation!

• [ ] Share your presentation on Zenodo and share the link in the comment!

• [ ] Graduate! 🎓

[alfredoq]

TidyScreen is under active development in order to improve its quality as an open source package available to the community.

Following my learning process during the OLS-9-Catalyst cohort the repository is being enhanced:

Please find the first TidyScreen repo here;

The revised repo under development can be found here

Original README.md: here Revised README.md: here

[alfredoq]

[alfredoq]

Our vision of statement:

We have been working in the field of computational chemistry in the Academic environment for several years, with particular focus towards computer-aided drug design. In this way, we have gained experience in the design and execution of bioactive compounds screening using a variaety of publicly available toolkits to aid this kind of studies.

In this context we have identified diverse difficulties associated to the field, not only to newcomers to the area, but also affecting expert users. The main issue detected is the heterogeneity of execution designs and information storage protocols, which hampers the simplicity to advance the project, with an increasing complexity as size and amount of information grows. Also, this heterogeneity complicates a straightforward collaboration since the methodology behind the obtaining results is usually not evident or feasible to be reproduced.

To contribute with a solution in this scenario, we have designed TidyScreen, a Python package implementing most of the common actions executed within a virtual drug screening campaign (i.e. chemical space generation and exploration, molecular docking studies, molecular dynamics simulations and hit prioritization analyses). All the information associated to the screening campaign is stored and organized within a structured-query database.

We aim to provide a platform to help new and expert users a straightforward way to execute screening campaigns, while also making collaboration and discussion of results more easy.