[Internship Project]: Hellen Namulinda

[GemmaTuron]

Summary

Hello,

This is a public issue for a virtual daily stand-up. We will use this to briefly share the tasks of the day and the challenges and advances made, so that we can ensure smooth support from the Ersilia mentors and alignment between daily tasks and overall internship goals.

Scope

Initiative 🐋

Objective(s)

Internship goals:

• Learn how to work in an Open Source Community
• Improve the infrastructure of the Ersilia Model Hub
• Improve the usability and platform compatibility of Ersilia Models, mainly via Docker Images
• Learn about AI/ML models for drug discovery
• Identify new relevant AI/ML models and datasets and add them to this discussion
• Incorporate new AI/ML models in the Hub
• Improve the documentation of the Ersilia Model Hub for users
• Improve the documentation of the Ersilia Model Hub for developers

Team

Role & Responsibility	Username(s)
Intern	@HellenNamulinda
Mentor	@GemmaTuron
Coordinator	@GemmaTuron

Timeline

Before starting your work, line up a few tasks and short description. This should not take long. For example, it could be something like: Wednesday 21st June

• [ ] Create Intern daily task tracker
• [ ] Update the Ersilia GitHub Project
• [ ] Make sure Git Actions start upon success of the other workflows
• [ ] Work on the documentation for model testing
• [ ] Attend the Drug Discovery intro by WCAIR

Documentation

No response

[HellenNamulinda]

Hello @GemmaTuron, I'm going to work on these. Model eos96ia is one of the molgrad models and therefore will have the same docker file as eos43at. I'm testing this locally and will have a proper discussion for these molgrad models with Riley(eos96ia), Febie(eos1af5) and Zakia(eos6ao8).

Thank you!

[HellenNamulinda]

Thursday 10th August: Tasks

• [x] Test/Debug model eos96ia: https://github.com/ersilia-os/eos96ia/issues/3#issuecomment-1672098391
• [x] Refactor and debug model eos935d: https://github.com/ersilia-os/eos935d/issues/6#issuecomment-1673228127, made a PR; https://github.com/ersilia-os/eos935d/pull/9
• [x] Re-test Model eos6fza: https://github.com/ersilia-os/eos6fza/issues/5
• [x] Present progress at the Weekly Lab meeting

[HellenNamulinda]

Friday 11th August: Tasks

• [x] Testing the Ersilia test module: This was done on two models; eos43at(eos43at_test.txt) , and eos6f7za(eos6fza_test.txt)
• [x] ChEMBL data cleaning. Previously, I had generated summary files for all the assays(pathogens of interest). For each pathogen assays, the summary file shows the different standard types, the total of molecules for each type, a list of standard units for each type, and the number of molecules for each unit. I started with cleaning the Enterococcus faecium assays, merging some standard types into one, and converting all units to one standard unit. For example, EC50: Merging EC50 with ED50 and converting the different units to one, IC50: Merging IC50 with IC80, and MBC: Merging MBC, MBEC, MBC90, MBC99.9, MBIC & MBIC90

[GemmaTuron]

perfect @HellenNamulinda

Let's try to meet on Monday to discuss the ChEMBL data!

[HellenNamulinda]

Monday 14th & Tuesday 15th, August: Tasks

• [x] Meeting with my mentor, Gemma, to discuss the next steps for the ChEMBL data.
• [ ] Prepare ML datasets from the ChEMBL data using the example automated pipeline, antimicrobial-ml-tasks
• [x] Attend weekly team meeting

[HellenNamulinda]

Wednesday 16th, August: Tasks

• [x] Re-test Model eos6fza: https://github.com/ersilia-os/eos6fza/issues/5#issuecomment-1679650479
• [ ] Compare ChEMBL datasets generated using the automated pipeline with the data prepared manually.

[HellenNamulinda]

Thursday 17th August: Tasks

• [x] Test Model eos5qfo: https://github.com/ersilia-os/eos5qfo/issues/3#issuecomment-1681848301
• [x] Final team Internship meeting

[GemmaTuron]

Hi @HellenNamulinda !

It was great to work with you, thanks so much for your contributions to Ersilia, we hoped you learnt and enjoyed as much as we did! Please, remain engaged with the community and feel free to open any issues or contribute to open ones :) I'll now close this issue as completed !