Forum:How can I contribute to the Bioinformatics community as a Software Engineer

Question

[Chen Sun]

I got my Ph.D. in Computer Science with research directions of bioinformatics and computational biology. I published several first-author papers in journal Bioinformatics and conferences like RECOMB. I also have a Master degree in Genomics.

Now I am a full-time Software Engineer in Silicon Valley, but I still want to contribute to the bioinformatics community with my expertise, after work and during the weekend. I consider myself very good at software development and algorithm design.

Can anyone give me some practical suggestions on how I can continue to contribute? By contributing, I mean writing software or applications.

Thanks in advance

[Kevin Blighe]

Just start contributing. Just answer questions that you feel you can answer. Your number of publications, your qualifications, and where you have worked are not important to an online support community. How you help users is important.

[Chen Sun]

By contributing, I mean writing software or applications

[Kevin Blighe]

I see. There is actually a big need for that in bioinformatics. I find that some bioinformaticians are already more aligned toward software engineering than they are toward, say, statistics. I did undergrad in Computer Science (Dublin, Ireland) and then undergrad in Industrial Biology, before a PhD in a wet-lab / bioinformatics area.

In Silicon Valley, whilst there is no shortage of employment in bioinformatics, I think that most are looking for full-time workers in this area. You don't imply that you are willing to give up your current full-time job in software engineering, for which I imagine you have a higher salary than most bioinformaticians ever will.

You can always advertise your skills on job boards for freelance work.

[S]

Hi Chen,

You could contact PIs in different biology research areas that are into developing tools to address biological questions. Even though most of them would require some kind of "commitment" with the tool development time frame but I am pretty sure majority will appreciate your contribution. Evaluate your expertise and interests as far as what tools you are thinking of developing and make contacts.

All the best!

[Ahill]

You could reach out to an open source bioinformatics project that could use experienced developer help. This earlier post had listed a few examples Open Source projects to contribute to but I'm sure others can offer many more ideas.

[zx8754]

We can start with GitHub advanced search

Answer 1

[Joe]

I will play Devils Advocate and say that it will be difficult if you aren’t actively researching in an area of your own.

Many tools are written because that person happens to bump up against a challenge that hasn’t been satisfactorily solved, in the pursuit of some greater project/task.

The key, therefore, is going to be finding problems that people need solving, and that won’t be so easy from the outside looking in.

2 options I can see however might be:

• Work your way around github and the like, and apply some ‘proper’ software engineering to existing tools. There are plenty of tools written by people like me (biologist turned programmer, amateur bioinformatician etc). The tools might be perfectly functional, but could maybe benefit from someone with a taught understanding of algorithms, data structures, dev best practices etc. Might be as simple helping set up continuous integration, building tests and making the software more robust etc (Lord knows most bioinformatics tools need that).

• The same thing that others suggested: get in touch with PIs and research groups that you have an interest in and become something of a ‘gun for hire’ (though whether your time will be paid for is another matter entirely). I say this because most universities are very averse to the freelancer model. If you simple want to keep tow in the bioinformatics waters for your own satisfaction and not for monetary gain, this shouldn’t be an issue, as PIs are unlikely to ever shy away from free expert advice in an area like this.

Answer 2

[Charles Yin]

If you have time, you may consider to do independent research in bioinformatics and computational biology, research results can be published as papers, ePrints, and patents.

[ATpoint]

By contributing, I mean writing software or applications