Outreachy Code Project: Name: Anamika Yadav about ersilia HOT 19 CLOSED

@anamika-yadav99 Is this the format that issue is meant to have going forward?

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Hi @anamika-yadav99
You have done some good work on the CLI! Can you link the relevant issues / PR's that you have contributed to? This way we can better follow your work!
Thanks

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@GemmaTuron I have completed most of these tasks. Can I do it after a couple of days? I have my exams going on currently.

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I have fetched and run chemprop-antibiotic model

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Fetched 3 models

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Select one issue related to improving the CLI and request to be assigned to it.

I was assigned issue #13
to add model search functionality in CLI : $ersilia catalog --text "chemprop-antibiotic" and $ersilia catalog --mode 'pretrained' to cli.

I have completed the task and the issue was closed.
Pull Request successfully merged : #41

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Suggest at least one missing feature in the CLI

1. Discussion on issue #60 . I had suggested to add tag word to the model card which could be used to search for model related to they tag keywords. Later these keywords could also be added to $ersilia --help.
   #60 (comment) by @miquelduranfrigola approving the idea.
2. Improve Model search functionality to display the closely related model in case of typo or wrong spelling in Model catalog table search. #241

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

1. issue #9
   Added conda recipe which is used to build conda package . Then uploaded my built package to anaconda to test the
   package.

• To build conda recipe for Ersilia I used the recipe used by Tensorflow a few years ago. The recipe downloads the .whl file of Ersilia and then builds it in conda using conda build command.

Raised PR for the same.
PR #89 successfully merged
2. Better model catalog display #12

• I improved the model display according to discussion in comment #12 (comment)

• I added a class to slice the catalog table into table of 15.

• I also added ersilia catalog --next and ersilia catalog --previous in cli which displays the next and previous table
  consequently.

• I have done so by storing a counter in an auxillary file. Every time the command ersilia catalog is called the counter is set to 1 and table 0 is displayed. Counter variable is used as index for next table. ersilia catalog --next displays the next table and increases the counter by 1. In case, the user enters command even after the table is finished the counter is frozen to index of last table and table and the user is prompted to return back. Vise versa in ersilia catalog --previous.
  Raised a pr.
  PR #238

3. Improved ModelSearcher functionality as discussed in issue #241

• I have added 2 methods to ModelSearcher Class to search using --text and --mode . To search using --text search_text method is added which also performs fuzzy match on the input to the data in catalog table. Fuzzy match is performed on model_id, description and slug.

Raised a PR #262

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Hi @anamika-yadav99 thanks for documenting all of this so nicely

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Add a screenshot showing that you are able to run predictions using ersilia as a Python library (find more information here). Ideally, use a Jupyter notebook.

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

1. issue Make ersilia conda-installable #9
   Added conda recipe which is used to build conda package . Then uploaded a package from my end to test the package.
   Raised PR for the same.
   PR added conda recipe  #89 successfully merged.
2. Currently working on Better model catalog display #12 Implementing the suggestions mentioned in the comment
   Better model catalog display #12 (comment)

Hi @anamika-yadav99 , you have done a great job over all. I really like your approach in solving issue #13 add model search functionality in CLI . Well done!

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

1. issue Make ersilia conda-installable #9
   Added conda recipe which is used to build conda package . Then uploaded a package from my end to test the package.
   Raised PR for the same.
   PR added conda recipe  #89 successfully merged.
2. Currently working on Better model catalog display #12 Implementing the suggestions mentioned in the comment
   Better model catalog display #12 (comment)

Hi @anamika-yadav99 , you have done a great job over all. I really like your approach in solving issue #13 add model search functionality in CLI . Well done!

Thanks @Amna-28 . You did an amazing job with the streamlit app yourself. The app looks great!

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

DeepDTA: deep drug–target binding affinity prediction:
https://academic.oup.com/bioinformatics/article/34/17/i821/5093245.

AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery:
https://arxiv.org/abs/1510.02855

ChemBO: Bayesian Optimization of Small Organic Molecules with Synthesizable Recommendations:
https://arxiv.org/abs/1908.01425

DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations
https://pubs.rsc.org/en/content/articlelanding/2020/sc/c9sc03414e

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Write a docstring for the ErsiliaModel class. Use the Google Python Style guide.

@GemmaTuron Will this be all or should I also write for the methods in ErsiliaModel Class?

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Hi @anamika-yadav99, I think that your CLI feature suggestion is a really nice idea

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

1. issue Make ersilia conda-installable #9
   Added conda recipe which is used to build conda package . Then uploaded a package from my end to test the package.
   Raised PR for the same.
   PR added conda recipe  #89 successfully merged.
2. Currently working on Better model catalog display #12 Implementing the suggestions mentioned in the comment
   Better model catalog display #12 (comment)

Hi @anamika-yadav99 , you have done a great job over all. I really like your approach in solving issue #13 add model search functionality in CLI . Well done!

Thanks @Amna-28 . You did an amazing job with the streamlit app yourself. The app looks great!

Thank you so much @anamika-yadav99

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Create a simple Streamlit app using the ersilia Python library. The app can have an input and an output box, and perhaps a few models to select. Add a screenshot of the app as seen in your browser.

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Add your card as a comment to this issue

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Comment under this issue explaining why you are interested in this project.

I’m a 3rd year undergraduate student from New Delhi, India. I’m currently pursuing engineering from GGS Indraprastha University, New Delhi. I’m a big supporter of open science and open source. I’m intrigued by the support and opportunities open source could provide to the scientific community and people. I have always wanted to work on projects which build tools for the scientific research community. It’s one of the driving forces to pursue this project. None the less, this project is aimed for developing country.
I'm passionate about the application of ML in healthcare, drug discovery, genetic engineering etc . I wish to further pursue post grad in one of the fields like computational biology, biotechnology, AI+health(not sure, still exploring) but somewhere along the lines. This project gives me an opportunity to work closely with the ML papers in drug discovery.
I'm fluent in python and very well familiar with implementing ML papers, ML Toolboxes. This project is apt for my skillset and interest.

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