# Bringing data science and AI/ML tools to infectious disease research

Welcome to the hands-on workshop on Artificial Intelligence methods for Drug Discovery!

## Introduction

This GitBook contains all the necessary information to follow the course, as well as links to the relevant materials.

Each day is organised in four main activities:

* Keynote Lecture: a presentation by H3D and Ersilia staff introducing key concepts that we will put into practice during the day. It will include a 15 min Q/A section
* Skills Workshop: a hands-on training where the course facilitators will walk the participants through a specific ML exercise
* Breakout: participants will be divided in small groups to complete an exercise related to the skills workshop
* Group Discussion: each group will give a short (10 min) presentation on their breakout activity.

### Schedule

<figure><img src="https://4053923198-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fiegy9L2sZKTXtwOkGHUO%2Fuploads%2FsRo5e579TirPCbDQ9lzl%2FEvent%20Brainstorm.jpg?alt=media&#x26;token=aa254a5f-433f-4131-bcdd-06d55c0337c3" alt=""><figcaption><p>Course schedule overview</p></figcaption></figure>

## Course Contents

| Activity           | Session 1                                                                                                                                                                                                                                                                                                                                    | Session 2                                                                                                                                                                                                                                                                                                                                                            | Session 3                                                                                                                                                                                                                                                                                                                            | Session 4                                                                                                                                                                                                                                                                                |
| ------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Keynote            | [Slides](https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/presentations/session1_keynote.pptx)                                                                                                                                                                                                                           | <p><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/presentations/220928_session2_keynote.pdf">Slides</a><br><a href="https://www.youtube.com/watch?v=7iJ5TmJa0Xc">Video</a></p>                                                                                                                                                        | <p><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/presentations/session3_keynote.pdf">Slides</a><br><a href="https://www.youtube.com/watch?v=Xj6QScBeiOI">Video</a></p>                                                                                                                               | <p><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/presentations/session4_keynote.pdf">Slides</a><br><a href="https://www.youtube.com/watch?v=uVijDg8me7Q">Video</a></p>                                                                                   |
| Skills development | <p><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/presentations/session1_skills.pptx">Slides</a><br><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/notebooks/session1_skills.ipynb">Notebook</a><br><a href="session-1/skills-open-chemistry-datasets">Guide</a></p>           | <p><a href="https://ersilia.slides.com/gturon/eventfund_session2_skills">Slides</a><br><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/notebooks/session2_skills.ipynb">Notebook</a><br><a href="session-2/skills-building-an-ml-model-for-chemistry">Guide</a><br><a href="https://www.youtube.com/watch?v=zfHxRE_vyIw">Video</a></p> | <p><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/presentations/session3_skills.pdf">Slides</a><br><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/notebooks/session3_skills.ipynb">Notebook</a><br><a href="https://www.youtube.com/watch?v=Xj6QScBeiOI">Video</a></p> | <p><a href="https://ersilia.slides.com/gturon/eventfund_session4_skills-3bba3f">Slides</a></p><p><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/notebooks/session4_skills.ipynb">Notebook</a><br><a href="session-4/skills-using-os-models">Guide</a></p> |
| Breakout           | <p><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/presentations/session1_breakout.pptx">Slides</a><br><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/notebooks/session1_breakout.ipynb">Notebook</a><br><a href="session-1/breakout-working-with-chemistry-data">Guide</a></p> | <p><a href="https://ersilia.slides.com/gturon/eventfund_session2_breakout">Slides</a><br><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/notebooks/session2_breakout.ipynb">Notebook</a><br><a href="session-2/breakout-the-ersilia-model-hub">Guide</a></p>                                                                           | [Slides](https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/presentations/session3_breakout.pdf)                                                                                                                                                                                                                   | <p><a href="https://ersilia.slides.com/gturon/eventfund_session4_breakout">Slides</a><br><a href="https://github.com/ersilia-os/event-fund-ai-drug-discovery/blob/main/notebooks/session4_breakout.ipynb">Notebook</a><br><a href="session-4/breakout-generative-models">Guide</a></p>   |

### Extra Content

Contains content we have not covered during the course but can help to those participants that are looking for further information.

### Tools

A short description of the different tools and Python packages we will use during the workshop is available in the [Documents](https://ersilia.gitbook.io/event-fund/documents/tools) section.

### Glossary

During the course, facilitators will collect the terminology specific of the field and add it to the [Glossary](https://ersilia.gitbook.io/event-fund/documents/glossary) in the Document section of this GitBook, with the goal to facilitate understanding and create a lasting resource for the participants.

## Requirements

To attend the course, participants will need:

* Their own laptop
* Access to Internet
* A Google account to access Drive and Colab

## Code of Conduct

Participants are required to abide by the [code of conduct](https://ersilia.gitbook.io/event-fund/documents/code-of-conduct) for the duration of the event, both during the workshop and in social activities before, during or after the event. Breaches of the Code of conduct will be taken seriously.

### Image and media

Images, photos and/or videos will be taken during the event. Please review our [media policy](https://ersilia.gitbook.io/event-fund/documents/image-and-media-policy).

## Funding

This workshop has been possible thanks to the sponsorship of Wellcome Trust through the Event Fund series organised by Code by Science and Society.