The Galaxy Experience.
I am an Outreachy applicant and we had 3weeks to contribute to any of the listed open source projects to be eligible for the internship. I remember scrolling through the lists and being indecisive, I finally settled on 2 projects; Galaxy community and Zulip. I tried both projects and on the third day, I decided to go for the Galaxy projects because their documentation and specifics were clear.
When I first joined the Galaxy community, I was excited to learn about stars, astronomy, galaxies, planetary bodies but I was wrong, actually, the Galaxy
“is an open, web-based platform for accessible, reproducible, and transparent computational research.”
what this means is that it’s an open-source web-based platform for research and data-intensive analysis on any subject. The Galaxy graphical interface is equipped with tools to run complex computational analyses and visualize results in different forms. It is a great application for scientists, biologists, ecologists including those with limited or no programming knowledge. In the Galaxy GUI, a user can upload or get data from data centers, the Galaxy tools are used to run analysis on the data and the analysis can be published, shared, and reproduce on any of the Galaxy servers.
The Galaxy community is a unique community with wonderful people from across the world, working together to ensure that the platform is effective and the resources are available for newcomers.
The experience so far:
I contributed to the “ Galaxy Community Mentor Network” project. The goal of the project is to “establish a Galaxy Mentor Network that connects newcomers with experienced community members to help prevent newcomers from getting lost”. As an Outreachy intern, I followed the stated specifics to contribute to the project.
I started with the introductory resources( Introduction to Galaxy Analyses) and I went on to sign-up on the Galaxy Europe server(usegalaxy.eu) to practice. On the Galaxy, I learned the “From Peak To Gene” tutorial. I had challenges understanding the data names, Galaxy tools, and switching histories, but after my second attempt, I fully understood how to navigate the Galaxy interface and tools. I finished off publishing my histories.
I also went through the “Introduction to Genomics and Galaxy” tutorial and published it successfully.
I contributed to raising issues on GitHub for challenges and suggestions on how to improve the Galaxy training resources. Some of the issues I observed while using the resources include wrong use of images, wrong content syntax.
I encountered an error in the “NGS data logistics” tutorial and I raised an issue too
The contribution guide was so helpful and clear and I was able to access the project and make the necessary changes. I joined the October Papercuts CoFest session which was great too, it offered the opportunity to talk about the internship and other issues, etc.
- Challenges Faced
Being my first time working on a data analysis platform, some of the data and concepts were alien to me. Some hands-on were not detailed. Finding the right Galaxy tools was a challenge not until the mentor directed me to the Galaxy training material on the Galaxy server(Hat ) where tools are easily accessible. I could not debug the errors I got during practice because the source of the error was unknown.
- Experience gained
I am happy to contribute to the Galaxy Community. I learned how to use the Galaxy interface and tools to analyze data on various subjects. I learned about the Zenodo database center. I learned about Gitpod(i knew GitHub and GitHub CLI only.) I enjoyed the experience of collaborating with the mentors and colleagues to clear blockers, the mentors were available and helpful, they gave timely responses and direction in resolving issues.
- Improvement /Suggestions
From my experience, I would say the Galaxy community is doing a great job improving the training materials. The effort in this direction is great and should continue.
Pending issues should be reviewed to reduce the backlog.
More scientific background information should be added to tutorials.
More details in the Hands-on tutorial.
All in all... it‘s been a wonderful experience🥰 and I look forward to contributing to building the Galaxy Community Mentor Network.