Thursday, July 23, 2009

Quick poll for next STITCH version concerning chemical names

I'm conducting a small poll over at FriendFeed about abbreviations of chemical names. If you have a opinion about which abbreviation is better in the following cases, please leave your feedback (either on FriendFeed or in the comments here):

  • 10-formyltetrahydrofolate: "10-formyltetra." or "10-formyl-THF"?
  • acetyl-L-carnitine: "acetyl-L-carni." or "ALCAR"?
  • dihydrotestosterone: "androstanolone" or "dihydrotestost."?

Tuesday, July 21, 2009

STRING Cytoscape plugin

Users of Cytoscape can now natively retrieve interaction networks from STRING !

During a recent workshop at the EBI, a common web service API to query interaction databases (called PSICQUIC) was finalized. Once all interaction databases have implemented this interface, it will be possible to use a single client (a Cytoscape plugin for example) to interact with all of them. We are committed to this initiative, and look forward to the implementations.

In the interim, we have decided to also release a small, custom-made plugin for Cytoscape called StringWSClient, which interacts only with the STRING database.

This allows us to offer users the full range of features that the STRING API allows (e.g. to show all available species, or to resolve ambiguous inputs). Version 1.0 (1.1) supports only the import of interaction networks; upcoming versions will be able to extend existing networks, filter them using STRING specific criteria, etc. The 1.0 version works only with Cytoscape 2.6.1, and 1.1 was released to support the whole 2.6.x branch.

To install it, fire up Cytoscape, open Plugins/Manage Plugins dialog and pick StringWSClient v1.0 from "Network and Attribute I/O" section. You may have to restart Cytoscape to load the plugin. See Cytoscape documentation for details.

Once you have the plugin installed, open File/Import/Network from web services... dialog and
pick the String plugin.

The plugin resembles STRING's web user interface: a field to type queries and the organisms selector. In the background, the query is sent to the STRING database and the resulting interaction network is fetched and displayed.

We're looking forward to your feedback !
Milan Simonovic and the STRING team.

Wednesday, July 1, 2009

100 API accesses per minute: not a good idea

STRING was unreachable for some time this morning while it was busy processing ~10,000 API requests in about 1.5 hours. 100 API accesses per minute is not a good idea, as this overloads our server, making STRING (and STITCH) unavailable for everyone. Don't run scripts that access the API in parallel.

If you want to do large-scale analysis on STRING data, you can make your and our life much easier by signing an academic license agreement and downloading the full dataset.