Tag Archives: biostar

What’s the answer? (how to stay current)

This week is a bit different than the usual “What’s the Answer?” post where we highlight a question from a forum that our readers might be interested in. However–in this post, one of the answers includes BioStar–so it sort of comes back around!

Stephen Turner (aka @genetics_blog) wrote up a blog post recently in response to people asking him how he stays current in bioinformatics/genomics. I know a lot of people retweeted that post at the time, and his very kind inclusion of OpenHelix led to some good traffic to this blog and new twitter followers. And just last night I saw this as well, confirming my impression of this post:

There are blogs, forums, automated searches, Twitter, and literature–of course. A lot of people might know about some of these, but it’s nice to see someone assemble a collection. It is also interesting to see how similar it is to my strategy.

So it seemed like this might be a fun item to highlight as a good source of answers on a number of things, and a good way to find useful sites and folks to be aware of in this field. Check it out.

How to Stay Current in Bioinformatics/Genomics

So much data and information. You gotta have some strategies. And you have to have more than the literature.

What’s the Answer? (Online mouse resources)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Need online resources for mouse research? Andrew Su at Biostar asked for a list of such resources and started it with a couple dozen:

I’d like to create a collection of the most useful online resources for mouse researchers. Here’s my list so far…

A comment thread continues with some great addition including many from Mary such as the Mouse resource browser: http://bioit.fleming.gr/mrb/, Jax: http://informatics.jax.org/and others which Andrew added to the list.

What’s the Answer? (Bioinformatics Tools on Biostar)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Just about a month ago, BioStar added a tool section as a place to announce and update new and old bioinformatics tools. So, in a sense, today’s post is are answers in search of your questions :):

We just added a new section to the site called **Tools** We designate this section to announcements regarding bioinformatics software tools, both new and old.

There are about 10 tools listed currently for various areas of analysis. This dovetails nicely with a the “obituary” section Mary created at Biostar for no longer supported tools and databases she discussed earlier this week. Circle of life and all that :).

What’s the Answer? (Next-Generation Sequencing -NGS- courses)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This question was created 18 months ago, but new slides and comments have been added and is still an excellent resource for a course on NGS:

Question: I am preparing a course on NGS: any suggestion ?

The first answer (with 22 up votes!) is a treasure trove of material, along with some excellent resources from other answers. Want to learn more about analysis of NGS data?… here you go.

What’s the Answer? (Gene ID conversion)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question:

What is a good “gene ID conversion tool

This is an older question, from 2 years ago, but still relevant and the answers still quite helpful and full of resources such as DAVID, BioDBnet, BioMart and others.

Check it out. Also, might want to check out the third exercise of our UCSC Advanced Tutorial .  The exercise:

“From a list of UCSC genes, add gene symbols and GO IDs for additional information about the gene set. Bonus step: add GO terms.”

Walks through how you might be able to do this with the UCSC Table Browser with some simple modifications.

BioStar, moved

We here at OpenHelix love BioStar. If you haven’t noticed, we highlight an answer from Biostar every Thursday in our “What’s the Answer” thread. For those new to Biostar, a quick intro: Biostar is a Q&A site for bioinformatics and genomics or, as it describes on the about page:

This site’s focus is bioinformaticscomputational genomics and biological data analysis.

Well, that’s not particularly descriptive, but read on and you’ll find that BioStar is an excellent question and answer site. The questions and answers can be quite detailed and complex, or as they say on the about page, “No question is too trivial or too “newbie”.  We’ve found a lot of use and a lot of good answers (and questions). Mary and I are both there (Mary is a moderator) and every week we search the site for questions and answers that are particularly useful for our readers.

But that’s describing BioStar wasn’t the title of this post (and we’ve done that before :), but to remind folks that BioStar has moved to it’s own home. It used to be housed at StackExchange, but for various reasons (discussion history if you want to plunge) the decision was made to migrate BioStar to a new site. That migration took place last weekend, to http://www.biostars.org. It’s a nice new site with all the functions and features you remember, a few changed things (reputation is calculated differently). A smooth and happy move. Your old URL should redirect to the new one, but if it doesn’t, you have it here. Congratulations to the community at Biostars to a new site and start.

 

What’s the Answer? Lipid-binding protein database or tool?

 

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question:

How to identify the lipid binding region (amino acid residues) in the protein? Any specialized online/commercial tools is there.

The first answer starts off:

You can try CGDB - a database of membrane protein/lipid interactions. You can also try the predictive algorithm for lipid-binding sites using three-dimensional structural data, described by Scott, et al.

And then continues with more to read and some description. There is (at this time) another answer using PFAM.

What’s the Answer? databases of disease SNPs

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s question is searching for databases of SNPS ‘causal’ for diseases. As the answers point out, the word ‘causal’ should be used with hesitation when talking about SNPs. That said, the answers gave some good suggestions to this perennially asked question, here’s the first one (others are as useful, so check them out):

Human Gene Mutation Database

http://www.hgmd.cf.ac.uk/ac/index.php

Paid subscription for up-to-date information. Otherwise less up-to-date public version of the database is freely available only to registered users from academic institutions/non-profit organisations.

What’s the Answer? Alternatives to Galaxy

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is

What are the “alternatives to Galaxy for wrapping a command line tool in GUI?

Or in other words, what workflow systems are out there in addition to Galaxy (a great tool, but sometimes people need something different :).  The answers to this question will help both bioinformaticists who create tools and biologists who use them, giving the former alternatives for doing this if need be and the latter other workflow systems to try out.

Several were highlighted including TavernaYabi and Knime and a list was provided from wikipedia. Check out the answers for more examples.

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: http://biostar.stackexchange.com/

References:
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