✍️ Contribution period: Arineitwe Fred

arinetf3321 commented 4 months ago

Week 1 - Get to know the community

[ ] Join the communication channels
[ ] Open a GitHub issue (this one!)
[ ] Install the Ersilia Model Hub and test the simplest model
[ ] Install Docker if needed, and test another model
[ ] Write a motivation statement to work at Ersilia
[ ] Submit your first contribution to the Outreachy site

Week 2 - Get Familiar with Machine Learning for Chemistry

[ ] Select a model from the list suggested in GitBook
[ ] Download and serve the model via the Ersilia Model Hub to ensure it works
[ ] Open a repository on your GitHub user with all the necessary files
[ ] Select and clean a dataset of 1000 molecules (example notebook 1)
[ ] Run predictions for the molecules on the selected model and evaluate the results

Week 3 - Validate a Model in the Wild

[ ] Find a suitable dataset with sufficient experimental results
[ ] Clean and standardize the dataset
[ ] Run predictions and calculate metrics.

Week 4 - Prepare your final application

[ ] Submit the final application in the Outreachy website

arinetf3321 commented 4 months ago

The guiding document https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/installation require additional ordering for the new contributor to avoid package failure during installation. Like Pre-requisite 5: The Isaura data lake. After installation of the Insura data lake and activation, it directs to activate ersilia using the command (conda activate ersilia) without stating the installation command as (conda create -n ersilia python=3.7). Though it references the command, the point of reference is not indicated for a new contributor to clearly install the packages.

arinetf3321 commented 4 months ago

Week 1 tasks

Installation of ubuntu 23.04.
Installation of conda
Instalation of isaura
Installation of ersilia

Bellow steps were followed: Setting up Platform to run Ersilia Model Hub: Installing ubuntu 22.0 on my computer.

Installing gcc compiler using sudo apt install build-essential. Installing Python and Conda using the sequence of steps. installation of anaconda Installing Git and GitHub CLI using conda install gh -c conda-forge. Authenticating installed system with github using gh auth login. Installing Git Large File Storage(LFS) using conda install git-lfs -c conda-forge. Activation of of LFS using git-lfs install. Installation of Isaura data lake using: conda activate ersilia python -m pip install isaura==0.1

Installation of the Docker

Installation of the Ersilia using: conda create -n ersilia python=3.7 conda activate ersilia

Installation of python package using: git clone https://github.com/ersilia-os/ersilia.git cd ersilia pip install -e .

arinetf3321 commented 4 months ago

Motivation Statement Dear Outreachy, I am writing to express my deep-seated passion and unwavering commitment to contribute my skills and expertise to the Ersilia Model Hub Project titled Improvement of the Ersilia Model Hub, a FOSS platform of AI/ML models for biomedical research. Furthermore, I have great desire to learn from the mentioned project so that I can enhance skills and expertise. My skills and expertise are in python programming, AI/ML development and integration, Java programming, node.js, JavaScript, typescript, react, android programming tailored by contribution to open source communities and high level of advanced research. My aim is to make significant contribution to projects that are advanced and require high level skills of which Ersilia Model Hub is the project of the kind. Based on my kills and aim, Ersilia Model Hub Project, like any ambitious project, offers an opportunity to explore, create, and bring new ideas to life. I firmly believe that it is in these endeavors that I find the true essence of human potential. My motivation for working on Ersilia Model Hub Project is rooted in the principles like, Enhancing connections just as the threads of Ersilia Model Hub are woven together to create a complex and vibrant system, I am eager to collaborate with a diverse team of individuals, each bringing their unique talents to build a harmonious AI system. Enriching Innovation where Ersilia Model Hub encourages innovation, and I see it as a canvas for fresh ideas, where I can contribute my knowledge and creativity to make this project an exemplar of Artificial Intelligence / Machine Learning (AI/ML) model in our ever-evolving world of infectious and neglected diseases. Advancing Endurance much like the intricate web of threads that compose Ersilia Model Hub, I am committed to persevering through challenges and setbacks. I see each obstacle as an opportunity to learn and grow, ultimately leading to a more refined and resilient project. Maximizing Inspiration just as I aspire to inspire not only myself but also others by my unwavering dedication to Ersilia Model Hub. I believe that by setting an example of commitment and determination, I can encourage others to embark on similar journeys of exploration and creation. I am excited by the vision of Ersilia Model Hub, and I am ready to invest my time, energy, and expertise to help bring this project to fruition. The prospect of contributing to a project that embodies the beauty of infectious and neglected diseases is not only motivating but also a source of great personal fulfillment. Thank you for considering my motivation statement to work on Ersilia Model Hub Project entitled Improvement of the Ersilia Model Hub, a FOSS platform of AI/ML models for biomedical research. I am eager to be a part of the team that will make this vision a reality and look forward to discussing how I can contribute further.

Sincerely, Arineitwe Fred.

arinetf3321 commented 3 months ago

Security challenges that were limiting traffic flow in and out from jupyter notebook server into the docker container. This was when integrating jupyter notebook server with docker container. This was resolved by revising docker network configuration and enabled traffic flow all through from jupyter notebook server.

ersilia-os / ersilia