neurodudes

Cognitive Atlas, a machine-readable ontology and semantic database of assertions about cognitive studies, with bibliographic links and brain area localization.

Quartzy is a webapp for collaborative reagent inventory and lab protocol management.

Two neat tools concerned with the “connectome” (i.e. the pattern of connections in the nervous system):

Semantic wiki:
http://www.connectome.ch/wiki/Main_Page

Desktop viewer:
http://connectomeviewer.org/viewer “Multi-Modal Multi-Level Network and Neuroimaging Visualization and Analysis” (screencasts)

Expression data is now available for over 60K gene probes over the entire human brain. Click here to access this monster data set!

More info after the jump.

(more…)

Want to run your research computations on Amazon’s cloud computing service?

http://aws.amazon.com/education/

No word as to when the next grant applicatiion deadline is, but it looks like an ongoing program.

Thanks to Brad Aimone, who got about $3000 worth of compute time for his research project, for alerting us to this.

http://mloss.org/software/

In addition to an index of over 200 open source machine learning software projects, the “about” section notes that there is an open source tools track of the journal JMLR, and that there are MLOSS workshops sometimes at NIPS and ICML.

You can help with protein folding research!

http://fold.it/

According to the website, currently they are collecting data from the game to see if humans can actually contribute anything beyond what the computers can already do.

Neurodudes reader (and optogeneticist) Feng Zhang has designed some vector manipulation tools that are freely available online. He writes

My colleague Robert Wang and I created an online collaborative DNA Vector analysis program called everyVECTOR. We were initially motivated because all of the existing commercial software are really expensive and the free ones are not as nicely designed/intuitive to use. Also, I was always frustrated with collaborators sending me text files of DNA sequences that weren’t annotated and confusing to read.

[...] You can also the public interface (without registration) by visiting here.

We released everyVECTOR last week and so far we have received good responses from people. We have around 200 users now from the past week, mostly from the Stanford and bay area universities.

I hope all of you molecular biologists can give everyVECTOR a try and give Feng some feedback. It certainly seems much more affordable (ie. free) than its well-known competitors. I’m a big fan of web-based tools myself and find them invaluable in doing simple sequence calculations for my own projects (one of my favs is the Sequence Manipulation Suite).

Also, apologies for the decreased posting frequency… I’m trying to graduate these days and there just doesn’t seem to be enough hours for everything. I hope to return to full force soon.