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ersilia-os / ersilia

The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.
https://ersilia.io
GNU General Public License v3.0
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Outreachy Documentation Project: <Harshita> #144

Closed harshita214 closed 2 years ago

harshita214 commented 2 years ago

Applicant: harshita214

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.

Initial steps:

harshita214 commented 2 years ago

Hello @GemmaTuron

I created a PR https://github.com/ersilia-os/ersilia/pull/178 for the issue

  1. https://github.com/ersilia-os/ersilia/issues/11
  2. https://github.com/ersilia-os/ersilia/issues/49
harshita214 commented 2 years ago

While working on Readme, I saw many readme files and came across the point that a Contributing.md is also required and so I want to modify it as well. This readme file basically contains the following point

@GemmaTuron I am really keen to know your response on this and to know your feedback. If all seems good, I am ready to form a Draft "Contributing.md" with all the points mentioned to get it reviewed

harshita214 commented 2 years ago

In India, there is a proverb " पहला सुख निरोगी काया " which means First happiness is a healthy body. This means whether it be anyone or everyone health and healthcare are a priority for all! So when I came across this project through Outreachy and understood the concept, which became more clear after attending the meet by @GemmaTuron.

One line "Ersilia aims to provide AI models to enable scientists to make drug discovery much quicker" made me realize the impact of Ersilia. This line made me intrigued to know more and more about Ersilia and eventually to be part of Ersilia. The reason behind, I understand the gravity of the situation, I know how important drug discovery is! Especially in India, where infants, children, and most importantly women especially all those who are pregnant or suffer from chronic diseases like cancer, etc. die from illnesses that have few or insufficient drugs.

I am as a part community it's my duty to give back to society ,and Ersilia is doing the same noble cause. I will be glad and honored to be part of community and give my best.

harshita214 commented 2 years ago

Under Graphic material

For third checkpoint, click here

@GemmaTuron kindly provide feedback for the same 😄

harshita214 commented 2 years ago

Twitter Template for The Release of New Models

Did you know our "Model name" is out which can predict in just a single click?! Join the main contributor and another main contributor on (Any date) for a Talk and Q/A session to know more about it 🤩

This is another step of Ersilia in helping researchers and towards our aim 💯

1/3

This model is one of the best releases till now due to many reasons like ... ... Isn't this interesting to know more click here (link) 🔗

Also, don't forget to check out our codebase on GitHub(link) which is absolutely open for enthusiastic contributors like you!

2/3

The main creditors behind this accomplishment are ( Twitter handles of all the persons )

Also checkout our blog and website for more information

GemmaTuron commented 2 years ago

Hi @harshita214

I have merged your readme. You made a lot of work on the installation and instructions, and have a direct way of introducing the project which I think is nice. For a README though, it is a bit too long. I think the information and images from the website do not need to be on the README which should focus on the Hub only. Can you modify it?

GemmaTuron commented 2 years ago

Twitter Template for The Release of New Models

Did you know our "Model name" is out which can predict in just a single click?! Join the main contributor and another main contributor on (Any date) for a Talk and Q/A session to know more about it 🤩

This is another step of Ersilia in helping researchers and towards our aim 💯

1/3

This model is one of the best releases till now due to many reasons like ... ... Isn't this interesting to know more click here (link) 🔗

Also, don't forget to check out our codebase on GitHub(link) which is absolutely open for enthusiastic contributors like you!

2/3

The main creditors behind this accomplishment are ( Twitter handles of all the persons )

Also checkout our blog and website for more information

I like the style, but some re-wording of the first sentence would be good! Did you know our "Model name" is out which can predict in just a single click?! - predict what?

harshita214 commented 2 years ago

Hi @harshita214

I have merged your readme. You made a lot of work on the installation and instructions, and have a direct way of introducing the project which I think is nice. For a README though, it is a bit too long. I think the information and images from the website do not need to be on the README which should focus on the Hub only. Can you modify it?

Sure yes, I am getting your point, I will do the modifications. Thank you so much for your feedback. For the installation part can we make a new readme with pictures since I believe Installations are essential and are actually the first step so it will help contributors a lot. On the website, pictures are not there.

harshita214 commented 2 years ago

Twitter Template for The Release of New Models Did you know our "Model name" is out which can predict in just a single click?! Join the main contributor and another main contributor on (Any date) for a Talk and Q/A session to know more about it 🤩 This is another step of Ersilia in helping researchers and towards our aim 💯 1/3 This model is one of the best releases till now due to many reasons like ... ... Isn't this interesting to know more click here (link) 🔗 Also, don't forget to check out our codebase on GitHub(link) which is absolutely open for enthusiastic contributors like you! 2/3 The main creditors behind this accomplishment are ( Twitter handles of all the persons ) Also check out our blog and website for more information

I like the style, but some re-wording of the first sentence would be good! Did you know our "Model name" is out which can predict in just a single click?! - predict what?

Thanks for the compliment 😄 Okay I will make the changes and modify it

harshita214 commented 2 years ago

Under 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
  • [ ] Incorporate feedback from the mentor

For third checkpoint, click here

https://bitmesra-my.sharepoint.com/:p:/g/personal/btech25053_20_bitmesra_ac_in/EVGAfhC6ElBJga-59f_KIoIB-If6bTfCIF5c-kP8Y4G8ng?e=XbF3MO

@GemmaTuron kindly provide feedback for the same 😄

harshita214 commented 2 years ago

image

Made this while thinking about Ersilia. All types of feedback are appreciated :)

Ps: It's not any task-related, I can delete it as well if it's violating any rule.

harshita214 commented 2 years ago

For Newsletter, Kindly view this doc file @GemmaTuron

https://docs.google.com/document/d/1PP-qEORGE4PVUoNxgc4P4wFxYK9KMVv00DqBezvwShg/edit?usp=sharing

harshita214 commented 2 years ago

Strategic plan 2021-2023 blogpost link

https://docs.google.com/document/d/1SJE5IWMzxyu2hDj7jwj2Uq0h-KY5PEaEcWxtmvoN9e4/edit?usp=sharing

@GemmaTuron Kindly review it :)

GemmaTuron commented 2 years ago

Hi @harshita214

You have done a lot of work, thank you for your efforts!

If you are working in any other tasks add them here in the comments, otherwise check my feedback and start preparing your final application!

harshita214 commented 2 years ago

Hi @harshita214

You have done a lot of work, thank you for your efforts!

  • I have left some comments in the Newsletter, but good template
  • Strategic goals: thanks for the infographic!
  • Mission and Vision: I like how you emphasize that healthcare researchers may not have the tech skills to use AI/ML, not everyone is aware of it. I would avoid generalistic comments such as "Our goal is to work for people"

If you are working in any other tasks add them here in the comments, otherwise, check my feedback and start preparing your final application!

@GemmaTuron Thanks for the feedback I am happy to contribute :), Yes, I will make all the changes by tomorrow and will revert to you.

For the newsletter, I will make the appropriate changes Yes I will keep in mind to avoid generalistic comments

Currently, I am working on the Scientific Content task of writing a Technical card. Apart from it, I am also working on issue #198

harshita214 commented 2 years ago

Twitter Template for The Release of New Models

Holla people!

Ersilia is excited to share that we have released our new model which predicts the detection of cancer cells in just one click! Isn't this intriguing?! Sure it is so join us on 18th April at 17:00 GMT to interact with the main contributor and another main contributor for a Talk and Q/A session to know more about it 🤩

This is another step of Ersilia in helping researchers and toward our aim 💯

1/3

This model is one of the best releases till now due to many reasons like ... ... Isn't this interesting to know more click here (link) 🔗

Also, don't forget to check out our codebase on GitHub(link) which is absolutely open for enthusiastic contributors like you! We are also open to new ideas, funders and researchers 😄

2/3

The main creditors behind this accomplishment are ( Twitter handles of all the persons )

Also, check out our blog and website for more information

@GemmaTuron Modified the template as suggested

harshita214 commented 2 years ago

Modified the following @GemmaTuron

harshita214 commented 2 years ago

@GemmaTuron I didn't find any comments on Strategic post Is there any modification which is needed there also?

harshita214 commented 2 years ago

Technical Card

Model ID: eos65rt

Model: LogP calculation based on fluorescent data

Description:

LogP calculation is used for fluorescent data for membrane permeability Small-molecule fluorescent probes are becoming powerful biomedical reagents to advance cell biology and drug discovery research, as well as cancer diagnostics. For Ersilia it's a really important model and for the medic world also. Especially since this model is used for cancer diagnostics. When it comes to cell permeability the LogP descriptor is the most significant descriptor 8–11. It has been shown that drugs with good cell permeability exhibit moderate LogP values 12,13. The Lipinski rule of five that is used to evaluate the drug-likeness of compounds indicates a moderate LogP range (− 0.5 < LogP < 5) for sub- stances with good cell permeability 14. Various LogP descriptors have already been developed that can be used to build models for cell permeability. Another class of algorithms, e.g. MLogP19, calculate LogP by using molecular properties such as 3-D structures or topological indices. The consensus LogP (cLogP) descriptor calculates the average LogP from multiple LogP models with improved accuracy 20.

Hyperparameter tuning in neural network-based models is essential for accurate predictions.

Algorithm: fingerprint algorithm, deep neural network (DNN)

Input : Compounds

Output: Permeability, Physicochemical property

Github Repository: here

Publication: here

harshita214 commented 2 years ago

Created a PR @GemmaTuron

Issue the PR is solving

wintermornings00 commented 2 years ago

Great work! @harshita214

harshita214 commented 2 years ago

Thank you @wintermornings00 :)

GemmaTuron commented 2 years ago

Hi @harshita214

Thanks, I have merged all your PR!

sophiee-blip commented 2 years ago

Nice job!

harshita214 commented 2 years ago

Submitted my final application ✨ Closing this Issue

Thank you @GemmaTuron and @miquelduranfrigola for the guidance ❤️