Getting help with bioinformatics questions online

There are thousands of bioinformatics databases, servers, algorithms, and apps in the bioinformatics ecosystem. Even though we are immersed in this environment ourselves, it seems that every day there’s something new, and in every workshop we do someone brings us an issue they have which requires some sort of tool that we haven’t explored yet–some species, some data type, or some investigational focus in a field that needs some computational tools.

There are some institutions that have terrific support from a good-sized bioinformatics core group or well-informed science librarians. There are some that have a few go-to folks that can give guidance around their department. But for many people it’s not easy to find what you need locally. In fact, we’ve been stunned sometimes at the lack of support even at some big-name institutions.

Another problem is the way that bioinformatics is growing makes it even more challenging to get appropriate guidance. This is what I mean:

Even when a tool can be identified, documentation and support are frequently missing or obsolete, and often have not anticipated more creative, advanced queries or novel implementations. As an example, the advent of workflow systems like Galaxy and Taverna [1], [2] enables users to weave customized pipelines together that employ multiple and disparate tools and data sources. Because questions and problems relating to workflow systems may cross traditional boundaries and domains of data and software providers, it can be difficult to find guidance from others with relevant experience. Though Taverna’s “MyExperiment” and Galaxy’s “Shared Pages” attempt to address this issue, questions about locating appropriate data, tools, or components beyond the current implementation remain best posed elsewhere. This lack of support can and often does lead to cumbersome bottlenecks during data analysis.

To accomplish some analysis, for example, you might need 5 different databases and tools for mining and running the analysis. But the way that the world is structured you can only get help for one tool at a time at the provider’s site. It’s great to have a tool like Galaxy to access dozens of things you might need. But for each you have to seek out documentation (whose quality may vary) and work it out yourself.

But now there are communities that can offer support across tools and disciplines. One of them in BioStar. We’ve been participating at BioStar for a while now, and each Thursday we highlight a question that might be interesting to our readers.

As BioStar was developing, people were asking how to cite the assistance that they received. And the BioStar participants wanted to also let the wider community know about the site. So an online discussion evolved into a movement to write a paper. A Google doc was provided, and a bunch of us wrote, edited, discussed, generated images, and eventually arrived at a consensus paper. Larry Parnell took the responsibility to work the terrific contributions into a cohesive unit, and voilà!  An article was born. The process was fascinating and fun. Most of us have never met each other, yet we were able to accomplish this in pretty reasonable time.

So have a look at the publication about BioStar to understand how it works and see if it could help you out, or pass it along to students in your classes perhaps. Or if you are a support provider, join us and help us guide others :) .

You might also want to read up on another work that can make your participation in online help communities more effective: Ten Simple Rules for Getting Help from Online Scientific Communities. Some veterans of the forums offer nice advice on how to get the most out of these kinds of interactions.

Visit BioStar:

Parnell, L., Lindenbaum, P., Shameer, K., Dall’Olio, G., Swan, D., Jensen, L., Cockell, S., Pedersen, B., Mangan, M., Miller, C., & Albert, I. (2011). BioStar: An Online Question & Answer Resource for the Bioinformatics Community PLoS Computational Biology, 7 (10) DOI: 10.1371/journal.pcbi.1002216

Dall’Olio, G., Marino, J., Schubert, M., Keys, K., Stefan, M., Gillespie, C., Poulain, P., Shameer, K., Sugar, R., Invergo, B., Jensen, L., Bertranpetit, J., & Laayouni, H. (2011). Ten Simple Rules for Getting Help from Online Scientific Communities PLoS Computational Biology, 7 (9) DOI: 10.1371/journal.pcbi.1002202

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