Comments on: Thoughts from BOSC 2009; Python in bioinformatics

By: Daiwa Rods

Daiwa Rods — Sun, 01 May 2011 23:47:53 +0000

Hey Brad,
It seems like most things that communication between groups sharing information and working together usually gets the best results, good luck with that!

By: Venus Hair

Venus Hair — Thu, 28 Apr 2011 13:07:20 +0000

I also think that there must be wrong if SciPy’s bio community is that far removed from Biopython’s user base. Is for technical issue, where Pythonistas are repelled by Biopython’s API.

By: Brad Chapman

Brad Chapman — Sun, 26 Jul 2009 21:10:22 +0000

Eric;
That’s an interesting link. Looking at the history it appears as if the last update was 2007, so hopefully this does not reflect current thinking about what is needed. My guess is that the proposal is due to a lack of familiarity with Biopython, rather than an intense dislike of the API.

For the larger question, my take on the right answer is that the various projects need to be proactive in learning the other code bases. In the short term, this can be documentation and cross-project contributions. Medium term, it would be great to meet and discuss common problems and solutions to flesh out more cross-project links.

Longer term, a meta-project as you are proposing may evolve from this communication. My sense is to let these evolve organically as trying to create something new will stretch the limited resources of Python bioinformatics programmers even more.

Nice discussion,
Brad

By: Eric Talevich

Eric Talevich — Sat, 25 Jul 2009 13:23:48 +0000

Should there be a Turbogears of bioinformatics packages for Python?

Looking at SciPy’s “most wanted” page, it seems like none of these distinct bio-oriented packages are getting enough mindshare to keep Python programmers from duplicating the same basic functions:

http://bio.scipy.org/wiki/index.php/Most_wanted

The requested cookbook items are all core features of Biopython and PyCogent — I think something must be wrong if SciPy’s bio community is that far removed from Biopython’s user base. Is it a technical issue, where Pythonistas are repelled by Biopython’s API, or find the features inadequate? Or is it just a matter of evangelism? Neither seems insurmountable.

By: Brad Chapman

Brad Chapman — Mon, 20 Jul 2009 22:44:10 +0000

James;
I have only played with the workflows a bit and am at the point of being happy they are thinking about the problem. From this naive viewpoint, I’d like to see integration with something like myExperiment (http://www.myexperiment.org/). Workflows are a hard problem and working towards a single solution makes a lot of sense.

Responsiveness is a key component of Galaxy being a successful platform. This is the only way to engage the wider community by encouraging outside programmers to contribute. I know the difficulties of keeping up coming from Biopython, but it’s essential to doing it right. You can fork the code and provide patches as new issues on the bitbucket site (http://bitbucket.org/galaxy/galaxy-central/), which is a good start. But ultimately you need someone from the project to integrate, or at least recognize and discuss your ideas, in a timely fashion. I submitted a patch there for something I needed with the secondary goal of finding out how it would be addressed.

Thanks for the thoughts; these are really interesting discussion points.

By: James Casbon

James Casbon — Mon, 20 Jul 2009 11:08:50 +0000

Galaxy needs two things to be really compelling:
* the ability to run workflows from the command line
* the ability to compose workflows from other workflows

It also needs a lot of work in making workflows really usable such as named outputs, parameters, etc. Of course, you could say that I should contribute these myself, only the core team aren’t that responsive in dealing with simple patches (YMMV).