Tuesday, March 16, 2010

Combining scores the right way

With STRING version 8, we began to add prior correction to the scores. That means that we consider how close scores are to the background rate of about 6% for protein–protein interactions, and we remove the random expectation from the scores before we combine them.  (At the end, we put the random contribution back in to make it consistent with the case that only a single evidence channel contributes to the score.)

For some applications, you might want to remove certain evidence types from the STRING download files. To compute a new combined score, you can now use the same prior correction we've been using internally. We have started a new BitBucket repository, and added a script to discard channels from the full STRING download files. 

Monday, November 9, 2009

STRING 8.2 and STITCH 2.0 released

We have released new versions of STRING and STITCH!

Here are some of the changes:

  • protein-protein actions like binding or post-translational modifications are now included
  • most download files are now under Creative Commons licenses, so academics usually don't need to fill license agreements anymore
  • bugfix: version 8.1 had accidentally omitted homology transfer in the textmining channel, this is now fixed.
  • the Flash interactive network viewer has further matured; a simple, lean version is now enabled by default. The full-featured version can be activated by clicking on the "advanced" button below the network
  • STITCH 2 uses the protein universe of STRING 8
  • the number of interactions has further increased

Tuesday, September 1, 2009

API for STRING 8.0 still accessible

After the release of STRING 8.1, the previous version, 8.0, can still be accessed: http://string80.embl.de. Under this URL, the API continues to work, e.g.:


This pattern will continue for upcoming releases (you could also use "string81" as host name now to stay on this version even if we update to a new version).

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.

Wednesday, June 24, 2009

New Release of STRING: Version 8.1

We are happy to announce that STRING 8.1 has just been released. We have updated the interaction data, fixed a number of bugs and greatly improved the web interface. As always, we keep older versions around to guarantee reproducibility of earlier work (see here).

The interactive network viewer has been re-implemented (it's now based on Adobe Flash version 10), and it gives users the new opportunity to "play around" with the network while keeping the same look and feel as previously.

The proteins in the network can now also be clustered, 'live', via two different methods: k-means and markov chain clustering. The topology can be relaxed after clustering, or in real time by turning on "relaxation" and "cooling". The graph layouting is done by force-directed placement (see here), and the cooling is done by gradually lowering the relaxation variable hat determines the strength of node movements, to zero. Of course, this is merely a first version of the interactive viewer and future versions may well have additional features (in particular in case our users have specific requests).

We have also extended the protein structure previews. These are now not only based on PDB, but we also incorporate homology models from the SWISS-MODEL Repository. And, structure previews are finally shown in the proper context of the protein's domain architecture.

Lastly, we fixed several 'known issues' (i.e., bugs) - such as missing minor chromosomes for some species, and viewer problems with the textmining predictions.

To start playing with the new release, visit STRING 8.1 - and p
lease don't hesitate to send us any feedback, criticism or suggestions...

Have Fun !

The STRING team