Forum:Open Source Bioinformatics projects for beginners

Question

[Eugenia84]

Hello to everyone,

First of all, I would like to apologize in advance if there is already similar posts. I am a molecular biologist with a PhD in immunology and 4 years of postoctoral experience in molecular biology. A little more that one year ago, I started to be interested in bioinformatics and I realized I wanted to persue a career in this field. I had done the Bioinformatics specialization and genomic data science specialization in coursera and learned Python and R. Now, I feel like I need to start to put hands on, in order to really get involved in the subject. I would like to focus on topics applied to biomedical science, as it is my background. Does someone know if there are open source projects or remote internship where I can collaborate or participate and learn from this experience?

Thanks in advance

[GenoMax]

Have you looked locally to see if there are opportunities to participate in bioinformatics projects (there generally are, especially if you are willing to work for free)? If you are just getting started it would be beneficial to have personal interactions with people you are working with (you could do that via Skype etc but it would not be the same thing as being able to drop by/sit/chat in someone's office).

Do you have an independent source of income (while you are doing this)?

[Eugenia84]

Thanks for the answer!! Yes, I have a source of income. I am currently a postdoctoral researcher in biomedical science in Germany. I am originally from Argentina, and I want to make the transition when I go back (in 1 year probably). That is why I am trying to gain experience remotely before I leave.

[Denise CS]

If you have a proposal in mind, you can send it our away. Open Targets is a public-private partnership that uses human genomics data for systematic drug target identification. If you know Python and can code with confidence, you may want to apply for our python software developer post.

[gretchen.m.wright]

Hi Eugenia84, Thanks for posting this. I had a similar question so I am also interested in the answers. I am coming from a background in mathematics and software development and am interested in working on open source projects. I'll be interested to know what you end up deciding on, if you don't mind sharing.

[Saransh]

I also want to join your work

Answer 1

[chen]

Hi Eugenia84, maybe you will be interested in participating the OpenGene projects: https://github.com/OpenGene

Following are some OpenGene projects:

• fastp: A ultra-fast FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...)
• MutScan: Detect and visualize target mutations by scanning FastQ files directly
• GeneFuse: Gene fusion detection and visualization
• ...

[Eugenia84]

Thank you very much for the info! I'll look through the project!

Answer 2

[Zhilong Jia]

A list of Bioinformatics projects for volunteers

[Eugenia84]

Thanks for the info! It's very useful!