Posts Tagged ‘announcement’

First release of LibSBGN

Thursday, February 10th, 2011

After months of work, last week we finally released the first version of LibSBGN.

LibSBGN logo

So what is LibSBGN? The Systems Biology Graphical Notation (SBGN), is a standard for drawing pathways. It prescribes exactly how to draw a biochemical reaction, how one can display the effect of heat on protein degradation, or how you should present the formation of a protein complex. It’s unambiguous: no matter how complex the drawing gets, it can be interpreted in only one way. SBGN is the result of many discussions, arguments and debates, over the course of several years and it’s therefore really well thought out.

Good software support is essential to make SBGN succeed as a standard. LibSBGN was created in an attempt to encourage uptake. As the name implies, LibSBGN is a software library that should make it easy to incorporate SBGN in pathway tools.

LibSBGN is only a software component, it’s not a ready to use end-product by itself. So this announcement is probably only interesting to bioinformatics developers. Nevertheless, I hope that it will soon lead to an increased uptake of SBGN in pathway tools, which should benefit end-users of those tools as well.

LibSBGN is already supported by a few applications, including of course PathVisio. To make sure that it works exactly the same in each tool, we’ve created a comparison gallery, containing several test-cases rendered by each tool. All the diagrams should look exactly the same for each tool. This comparison page has proven tremendously useful to check for bugs and misunderstandings.

This is only the first release, there is still a lot to do. This first release only supports a part of SBGN called process description (PD). The coming months will see lots of work on the remaining parts of SBGN, entity relationships (ER), and activity flow (AF). And after that we’ve planned more features, such as validation rules and file format conversion.

This is the first tangible result from something that was set in motion at a meeting in Wittenberg. LibSBGN community: thanks for your hard work and congratulations on this first milestone.

PathVisio 2 released

Sunday, October 18th, 2009

This week we released version 2.0 of PathVisio. There has been over a year of active development since the last major release, and a ton of new features.

What is PathVisio? PathVisio is a tool for biological pathways. Stay organized! Use PathVisio as a simple notebook to collect all the various bits of information related to a biological research subject. Create images suitable for presentation or publication. Draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl or Entrez gene, and add comments and literature references from pubmed.

With PathVisio you draw pathways just like you would in powerpoint:

What is new? New in PathVisio 2.0 is the ability to import experimental datasets and visualize them on top of pathways. Explore large datasets in a way that is more interesting and understandable than just a huge spreadsheet. Import microarray, proteomics or metabolomics data. Microarray reporters will be automatically linked to genes and protein identifiers in pathways. You can customize the visualization, using gradients, boolean color rules, or colored icons.

Here is an example of visualized microarray data:

Perform over-representation analysis to find the pathway that was most affected by experimental conditions. This is great for hypothesis-generating experiment types, where you really don’t know anything in advance about your experiment.

Download pathway sets or share pathways on WikiPathways, a wiki where any researchers can contribute pathway knowledge. PathVisio is fully compatible.

Check our visual tour if you want to know more. Click here to Download PathVisio

For Developers: PathVisio has a plugin interface that lets users customize it to new analysis types, new visualization methods and new pathway formats. PathVisio is fully open source, and we’re always looking for Java developers who are interested in contributing, either to new plugins or to the core of the program. Contact us on our mailinglist.