Open Source Project For Beginner

Question

[Phil]

Possible Duplicate: How To Get Started In Bioinformatics?

Hi,

I'm a software engineer interested in bioinformatics. To make the transition, I'd like to get involved in an open source project.

What bioinformatics open source project could welcome beginners in the field (I have nothing more than high school level in chemistry and biology but, being interested in these subjects, I'm willing to learn more).

Thanks in advance for your suggestions.

[Pierre Lindenbaum]

What is your specialty as a software engineer ?

Answer 1

[Martijn Van Iersel]

There are so many. It depends on the type of bioinformatics you're interested in (protein structure, sequence analysis, data mining, ...) and it depends on the programming language that you're familiar with. The best project to work on is one that you actually use yourself, because that way you know what the most useful improvements are.

In my experience, bioinformatics software projects are often more lacking in software engineering expertise than in bioinformatics expertise, so you'll be most welcome.

Please forgive me for plugging my own projects here, but to give two examples:

• Cytoscape is an open source network analysis tool written in Java. It has a plug-in interface, so an easy way to start is by creating a plug-in.

• PathVisio is another open source tool written in Java. PathVisio focusses on visualization and analysis of pathway knowledge. It also has a plug-in interface, so that's another good place to start. There is a guide for plug-in developers, and there is a list of "low hanging fruit" bugs that's good for newcomers.

After you choose your project (and by all means, don't restrict yourself to the above two options), here are some tips to hit the ground running:

• Start by checking out the source and setting it up in your IDE. For any reasonable sized project, this is already challenging, and it's a good way to familiarize yourself with the code.
• Find the mailing list of the project and introduce yourself. Not every project is equally welcoming to newcomers, but on the mailinglist you''ll find out quickly
• Find the bug tracker. Look for a bug that you can reproduce, and then try to solve it. This has two advantages: fixing bugs is a really good way to get to know the internals of a project, and it's also a good way to prove your worth to the other developers.

Another good place to start is the annual Google Summer of Code, because Google only selects projects that welcome newcomers, and the project will assign a mentor to you. Unfortunately GSOC 2011 has just finished. Look around for the next one around spring 2012. You'll increase your chances to get in if you already set up contacts with the developers on beforehand.

There are over 175 open source projects participating in GSOC, not all of them are related to bioinformatics, but at least these are:

• Genome Informatics (Umbrella for wormbase, reactome and GMOD)
• Orange
• National resource for network biology (Umbrella for WikiPathways, GenMAPP and Cytoscape)
• TBP@HU
• NESCent

[Graslevy]

Great answer Martijn, hope to read more from you...

[Phil]

Hi Martijn! Thanks for your complete answer. I guess I can start preparing myself for next year...:) Cytoscape and NESCent projects look very interesting. I'm going to check-out the documentation on Cytoscape and see how to get started with plug-ins. Thanks

Answer 2

[brentp]

Find practical problems. You could post an answer to this question.

Once you are familiar with some formats or problems, you'll find projects that are interesting. Submit a patch and get started.

[Phil]

Thank you for your answer. I'll have a look there.