Tag Archives: genmapp

Wanna code? Student opportunities

From the Cytoscape mailing list this evening:

We are looking for students to help build Cytoscape, GenMAPP
and WikiPathways through the Google Summer of Code 2009
program. If you are a student and are interested in open
source and biology, then you should apply!

There are more details at the link. I love the part where they give you a major HINT on how to strengthen your application….

More on Summer of Code and the different projects involved: http://socrates2.cgl.ucsf.edu/GenMAPP/wiki/Google_Summer_of_Code_2009

If you aren’t familiar with the tools the links to those sites are:

GenMAPP: http://genmapp.org/

Cytoscape: http://cytoscape.org/

WikiPathways: http://www.wikipathways.org/index.php/WikiPathways

PathVisio: http://www.pathvisio.org/

Open source molecular modeling–finally?

My Bio SmartBrief newsletter today had a reference to a paper in a rather…um…obscure journal. Maybe it is just something I have missed over the years, but the Journal of the Royal Society Interface has really just never come across my desk before. Nevertheless, Wired seems to think this software is finally meeting our needs in biological modeling. Finally?

The open-source software movement has finally met the world of biological modeling.

Both a language and a program, “little b” gives systems biologists an infrastructure for building and sharing models of cellular activity.

Ok–this may be fabulous software. I’ll have a look. But to say that this is the one we have been holding our breath for is rather presumptuous. I’m not paying $49 for the paper, so I can’t assess it from the text. I will go and evaluate it at the developer’s site. For software evaluation I do read the papers (unless they cost $49), but I don’t believe anything until I kick the tires quite a bit anyway.

But from the breathless Wired article I can’t see why this is the solution rather than GenMapp, or BiologicalNetworks, or Cytoscape, or NAViGaTOR, or VisANT or….the half a dozen other that we are looking at for tutorial development. Or the ones I intend to learn about at the ISSB meeting in Sweden next month. The choice of tutorials there had me stumped on which ones I could fit into my schedule.

This Wired line about the image they show cracked me up:

Image: Detail from a gene regulation network, courtesy of PNAS. Wouldn’t it be great not to have to duplicate this in every new model?

Um….I can reproduce most of that now with about 10 different tools. If I wanted to do it quickly with stored information I could go to MINT and check out the curated interaction data and their very cool MINT Viewer (you can watch me do that in a movie here). Well, except it doesn’t show a picture of the Golgi in the background. Is that what’s new–despite that being from some unreferenced PNAS paper that may have nothing to do with this software? I would bet if I asked most of these teams would let me load up a cell graphic in the background, or I could create a network and layer it in with my image editing software. But I don’t think that’s it.

I hope little b is great. But like most software in this field there are other options–and some tools are right for some tasks, others are right for other tasks, even when they are in the same space. As we say in the blogosphere, YMMV {your mileage may vary}.

Another Wiki, WikiPathways

ResearchBlogging.orgPLoS Biology reports today on WikiPathway. The paper entitled “WikiPathways: Pathway editing for the people,” announces a new wiki for the ‘public curation’ of pathway data. The authors argue that

 The exponential growth of diverse types of biological data presents the research community with an unprecedented challenge to keep the flood of biological data as accessible, up-to-date, and integrated as possible.

I agree with this. We’ve seen it here and mentioned it many times, the growth of data is exponential and difficult to keep track of. The proposed solution for pathway data, as there has been for other data types and curation that I’ve written about lately, is a wiki: WikiPathways to be exact. The authors have high hopes for this wiki, as they state:

WikiPathways will be a powerful resource for the research community and a vital forum for pathway curation, And we are hopeful that it will serve as an example for how the continuing flood of biological data can be managed and utilized by the community to irrigate future hypotheses and discoveries

I’ve already made known my “skeptical optimism” for wikis for biological data known in a previous post, reading this later paper, that would still apply here. But right now I’m not going to write beyond that, I’m just going to point you to this paper and wiki. Later (this week, next at the latest) I’ll be critiquing this paper more fully and more generally look at this trend currently to use wikis for community curation and documentation of biological data and databases.

Pico, A.R., Kelder, T., van Iersel, M.P., Hanspers, K., Conklin, B.R., Evelo, C. (2008). WikiPathways: Pathway Editing for the People. PLoS Biology, 6(7), e184. DOI: 10.1371/journal.pbio.0060184