✍️ Contribution period: Aml

Aml-Hassan-Abd-El-hamid commented 1 year ago

Week 1 - Get to know the community

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

Week 2 - Install and run an ML model

[x] Select a model from the suggested list
[x] Install the model in your system
[ ] Run predictions for the EML
[ ] Compare results with the Ersilia Model Hub implementation!
[ ] Install and run Docker!

Week 3 - Propose new models

[ ] Suggest a new model and document it (1)
[ ] Suggest a new model and document it (2)
[ ] Suggest a new model and document it (3)

Week 4 - Prepare your final application

[ ] Submit the final application in the Outreachy website

Aml-Hassan-Abd-El-hamid commented 1 year ago

Hi Guys! if you wonder how I took the decision to join your project so fast! It's because I was contributing to Ersilia's last outreachy contribution period. I didn't get accepted last time so I set my mind to re-apply again in the winter! maybe this time I can get :) Here's a link to my issue: https://github.com/ersilia-os/ersilia/issues/621

DhanshreeA commented 1 year ago

Hi @Aml-Hassan-Abd-El-hamid welcome back! Please go ahead and tick off the tasks completed from week 1, and proceed with the remaining tasks, like installing ersilia and testing out the simplest model. Thanks.

Aml-Hassan-Abd-El-hamid commented 1 year ago

Thank you very much @DhanshreeA

DhanshreeA commented 1 year ago

Hi @Aml-Hassan-Abd-El-hamid I see that you have ticked off ersilia installation and motivation letter from week 1 tasks. Can you confirm if you have a working installation of ersilia on your system? In addition, could you please add a motivation letter here.

Aml-Hassan-Abd-El-hamid commented 1 year ago

Hi @DhanshreeA Sorry for not updating that earlier. Here's a screenshot from my terminal after fetching, serving and running the eos3b5e model :

Screenshot from 2023-10-05 04-17-13

Aml-Hassan-Abd-El-hamid commented 1 year ago

My motivation statement to work at Ersilia

A little brief on my background:
I'm a fresh computer engineering graduate, I'm an open-source enthusiast with some experience in contributing to different open-source projects and packages -mostly related to ML and research-, My skill set includes Python -including ML libraries such as PyTorch, and SkLearn,....-, C/C++, Git, Conda, Docker, Ubuntu, Technical writing.

When I came across the Ersilia project this March, I was fascinated -and I'm still :) - by how much value such a project can give to the world. For me having a sensible value associated with my work is the greatest goal of my life, and working on such a project can help me achieve that goal, Knowing that I can work on a project that helps to enhance the quality of medical research in Low-Middle Income Countries -I was born into one and I was a student in a governmental university and I'm aware of how little the resources that are available for scientific research- is my greatest motivation.

Not only that but also the fact that Ersilia has a very helpful and responsive team that I can learn from to sharpen my technical and communication skills, I know that from my last experience with Ersilia during the last contribution period, I was new to a lot of tools such as Conda and Docker and I learned a lot about them during that period, also learned how to communicate better and how to report an issue professionally.

My plan during this internship is to learn from Ersilia as much as I can, do my best to contribute as much as I can to Ersilia and leave a good mark on this project, sharpen my communication skills and strengthen my network.

After the internship, I plan to use the outreach reword to continue my learning journey and fund my master's degree, and also continue to be in touch with my peers and mentors from the internship period, asking for their advice regarding my professional and research life, and helping them as much as I can.

Aml-Hassan-Abd-El-hamid commented 1 year ago

I chose to work with STOUT, I installed the model following the instructions from its readme,

I ran into 2 errors while trying to install that model,

1- during the installation, while I was using conda install -c decimer stout-pypi, I ran into the same issue last continuation period and I knew that the solution was to run pip install STOUT-pypi

2- While trying to import translate_forward, translate_reverse, I ran into jvm dll not found: define/path/or/set/java_home/variable/properly, I know that @ZakiaYahya -thanks :) - ran into the same error last contribution period and she solved it by by installing OpenJDK manually using "sudo apt install default-jre" command, so I followed the same procedure and fixed the issue.

DhanshreeA commented 1 year ago

Hi @Aml-Hassan-Abd-El-hamid thanks for the updates. I would also recommend that you create a contribution on the Outreachy website.

HellenNamulinda commented 1 year ago

Hello @Aml-Hassan-Abd-El-hamid, You are yet to complete week 2 tasks. Were you able to make predictions using the STOUT model? Is there any assistance we can offer to support you?

Aml-Hassan-Abd-El-hamid commented 1 year ago

I'm sorry to say that but due to personal reasons I wasn't able to continue the contribution period work, I'll close this issue.

ersilia-os / ersilia