Outreachy Documentation Project: Anita Igbine

[AIgbine]

Applicant: @AIgbine

Welcome to the Ersilia Open Source Initiative. This issue will serve to track all your contributions for the project “Improve the documentation and outreach material of the Ersilia Model Hub”.

Please tick the tasks as you complete them. To make a final application it is not required to have completed all tasks. Only the Initial Steps and Community sections are REQUIRED. The tasks are not ordered from more to less important, they are simply related to different skills. Start where you feel most comfortable. This project can be adapted to the applicants interests, please focus on the type of tasks that you prefer / have better skills / would like to work on as an intern.

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Initial steps:

• [x] Record your application for the project in the outreachy website referencing this issue. Please make sure to select the right project on the website.
• [x] Join the Slack channel to follow public communications

• [x] Comment under this issue explaining why are you interested in this project

  GitHub documentation:

• [ ] Create a README file with the name under the /documentation folder
• [ ] Link the #PR in a comment under this issue

• [ ] Incorporate feedback from the mentor

  Writing dissemination material

• [x] Read the Strategic plan 2021-2023 for Ersilia and create a 1-page blogpost with the main points
• [x] Comment under this issue with a link to the blogpost (a google docs for example)
• [x] Incorporate feedback from the mentor
• [x] Choose your own topic related to Ersilia (AI/ML for biomedical research, neglected diseases, drug discovery…) and write a 1-page blogpost to communicate to a non-expert audience
• [x] Comment under this issue with a link to the blogpost (a google docs for example)
• [x] Incorporate feedback from the mentor
• [x] Create a template for a twitter post to release every time a new model is incorporated in the Hub (twitter: 280 characters, you can suggest a main post + thread with extra information) and add it as a comment under this issue

• [x] Create a template short Newsletter (1 paragraph) to send every month to our community (funders, users, contributors). It should mention metrics (models in the hub, number of users, funding…), thank you etc

  Technical skills (required for the tutorial only)

• [x] Install the Ersilia Model Hub
• [ ] Test one model
• [ ] Add a screenshot under this issue showing the model running in your computer

• [ ] Write a docstring for the ErsiliaModel class. Use the Google Python Style guide. Paste the docstring as a comment below (do not use a PR).

  Graphic material

• [x] Read the Ersilia Brand Guidelines
• [x] Read “Why Ersilia?”
• [x] Create one image / slide to explain Ersilia’s mission and vision
• [x] Link to the image/slide as a comment under this issue
• [x] Incorporate feedback from the mentor
• [ ] Create two slides / short video showing how to use the Ersilia Model Hub and add them under the /tutorial folder
• [ ] Link the #PR in this issue

• [ ] Incorporate feedback from the mentor

  Scientific content

• [x] Check the models available in the Hub
• [x] Select one model from the list and write a technical card (what is the model for, what input, which data was used to create it, what kind of ML algorithm uses…) for it
• [x] Add your card as a comment to this issue

• [ ] Search the scientific literature and suggest 3 new models (comment in this issue) that would be relevant to incorporate in the Hub.

  Community

• [ ] Look up two other projects and comment on their issues with feedback on one of their tasks

• [x] If you have feedback from your peers, answer it in this issue.

  Other

  If you have interest in working on related topics, or have new suggestions, please do the following

• [ ] Add a comment in this issue with your new idea, tagging the mentor
• [ ] Get feedback from the mentor and act accordingly

• [ ] Link in the comments any other PR you have contributed to.

  Final application

• [x] I have answered all comments from mentors and contributors
• [x] All PR or issues assigned to me are complete
• [x] I have submitted my final application to the project

[AIgbine]

Hi, I'm Anita Igbine. A data analyst and technical writer. I am contributing to this documentation for the following reasons:

1. I started out learning python on my own and documentation, how-to tutorials were my go-to whenever I got stuck
2. I enjoy contributing to learning resources and have done so for a year now
3. For my final year project at school (class of 2020) I build a machine learning model. It gave me an opportunity to learn the basics of building a model and intend to use this knowledge to contribute to this project.
4. I would love to contribute to Open Source. It's something that scares and excites me.

[GemmaTuron]

Hi @AIgbine !

Thanks for your interest! Given your background and description, perhaps your skills are better suited to the coding project? If you have python knowledge and are interested in the computational aspects of our work check the second open project!

[AIgbine]

Hi @GemmaTuron

I will definitely be contributing to the coding project. On the outreachy website I noticed that you only need one intern so I plan to contribute to both the documentation and the coding projects.

I'll jump on the second project right away!

[AIgbine]

Hi @GemmaTuron

Here is my link for a one-page blog on the Strategic Plan 2021 - 2023

https://docs.google.com/document/d/1lM3w3Ojdmj3edkneJi4XjjPzfNrk9pjJtNl1aUndC20/edit

[victorabba]

Hi @AIgbine. Your Blogpost is superb, but you need to add a title to the blog.

[AIgbine]

Hey @victorabba,

I put the title as the document name initially but I have now put it at the top of the post Thank you for taking time out to read it!

[GemmaTuron]

Hi @Algbine!

Good job on this post! I left some comments for your consideration, check them before going onto other tasks but continue this good work, thanks!

[AIgbine]

Hey @GemmaTuron

I've implemented the corrections. Thank you for taking time to read through the document https://docs.google.com/document/d/1lM3w3Ojdmj3edkneJi4XjjPzfNrk9pjJtNl1aUndC20/edit

[AIgbine]

Hi @GemmaTuron

Here is my submission for the Ersilia newsletter template: https://docs.google.com/document/d/1V27kRIyaNNsRuW4N3hBVX3ttctjvZKxFuSuw7bTyyyY/edit?usp=sharing

I have also written a one-page blog post on Drug Discovery here: https://docs.google.com/document/d/11Pig-9SFFV5LZQeTJsHhsZ2X7EEuGfPyMPx5KeDR4cA/edit?usp=sharing

Please find the link to an image of Ersilia's Mission and Vision here: https://www.canva.com/design/DAE9nrBdWV8/9_B0sT9lx18i9UnYCObtoA/edit?utm_content=DAE9nrBdWV8&utm_campaign=designshare&utm_medium=link2&utm_source=sharebutton

[AIgbine]

@GemmaTuron, had to put this in a separate comment

Here is a template for announcing new models on Twitter:

New at Ersilia!

We’re happy to introduce the drug-discovery-ai model. Credit to @[account name/just name] and her team for working hard on this model. The drug-discovery-ai model improves drug discovery with an accuracy of more than 98%. Head over to the Ersilia Model Hub to use this model! [Link] (1/2)

Not sure where to start? The model documentation will help you get your model running in no time! Read the model documentation here or watch this video on Youtube to get started. [Link to resources] (2/2)

[I introduced the model in a catchy way while briefly stating its benefits and lastly, providing a link to the model. Further information can be given in subsequent threads or a simple link to the documentation and other resource materials as I have done here]

[Dedme]

@AIgbine, thanks for the Tag (Xxis - old account), but I is not Her. and would be a shame for them to miss out on the praise tag!

[AIgbine]

@AIgbine, thanks for the Tag (Xxis - old account), but I is not Her. and would be a shame for them to miss out on the praise tag!

Oh my. I actually just came up with it as a place holder. Never thought it would belong to anyone 😅

[GemmaTuron]

Hi @AIgbine

Thanks for the effort in the project! Well done in the blogpost, and I like that you introduce new funders and donors for the newsletter. Can I ask you to add here the Mission and Vision template as a .png or .jpg file for easy download? You have done a lot of work. To complete your application, I would suggest to focus in one of the tasks of the Scientific content, and you will be ready for making the final application on the website. Thanks for the effort

[AIgbine]

Thanks for going through my work @GemmaTuron!

Here is the .png file of the Mission and Vision

[AIgbine]

@GemmaTuron here is my submission for model technical card

Model Summary Name: chemprop-antibiotic Code: e0s4e40 Input: A compound Output: Antibiotic activity of the compound Function: The model predicts the antibiotic activity of molecules that are structurally different from known antibiotics.

Data and Algorithm Training Data: The model training data consists of data available from US Food and Drug Administration (FDA) data and natural products isolated from plants, animals, and microbial sources. A total of 2335 unique compounds. Algorithm: Deep neural network model

Resources Publication: https://pubmed.ncbi.nlm.nih.gov/32084340/ GitHub: https://github.com/ersilia-os/eos4e40 Source: http://chemprop.csail.mit.edu/checkpoints

License MIT

[paulinebanye]

@GemmaTuron, had to put this in a separate comment

Here is a template for announcing new models on Twitter:

New at Ersilia!

We’re happy to introduce the drug-discovery-ai model. Credit to @[account name/just name] and her team for working hard on this model. The drug-discovery-ai model improves drug discovery with an accuracy of more than 98%. Head over to the Ersilia Model Hub to use this model! [Link] (1/2)

Not sure where to start? The model documentation will help you get your model running in no time! Read the model documentation here or watch this video on Youtube to get started. [Link to resources] (2/2)

[I introduced the model in a catchy way while briefly stating its benefits and lastly, providing a link to the model. Further information can be given in subsequent threads or a simple link to the documentation and other resource materials as I have done here]

Well done @AIgbine with the twitter template. I loved that you gave credit where due. I did feel that a link to a YouTube video would be perfect here.

[AIgbine]

@GemmaTuron, had to put this in a separate comment Here is a template for announcing new models on Twitter: New at Ersilia! We’re happy to introduce the drug-discovery-ai model. Credit to @[account name/just name] and her team for working hard on this model. The drug-discovery-ai model improves drug discovery with an accuracy of more than 98%. Head over to the Ersilia Model Hub to use this model! [Link] (1/2) Not sure where to start? The model documentation will help you get your model running in no time! Read the model documentation here or watch this video on Youtube to get started. [Link to resources] (2/2) [I introduced the model in a catchy way while briefly stating its benefits and lastly, providing a link to the model. Further information can be given in subsequent threads or a simple link to the documentation and other resource materials as I have done here]

Well done @AIgbine with the twitter template. I loved that you gave credit where due. I did feel that a link to a YouTube video would be perfect here.

Thanks for the review @pauline-banye. Yes, that's a good idea. YouTube videos and other resources can be linked to the second tweet.

[GemmaTuron]

Hi @AIgbine

Thanks for the technical card, really well-thought! Now focus on creating a good final application in the Outreachy website please!