Tag Archives: CellDesigner

Software bonanza…

Still enjoying the ICSB meeting, and it is a gorgeous fallish morning in Göteborg. What a great city and terrific people here. Not entirely sure I want to come home….

My brain is approaching “full” already, and there are still several days to go. I’ll have a lot of tools to talk about in the coming weeks as I check more of them out. But I wanted to talk about a couple of neat tools that I have heard about so far. First–CellDesigner 4.0, that I mentioned the other day, was a good choice of tutorials to attend for sure. You can access their tutorial material here. Turns out they are also about to release a web-based version of this that will be a collaborative community editing tool for networks and pathways. It is called Payao–which I’m told means a type of “fish-aggregating device” according to their poster. I was unable to catch the poster authors so far to discuss it further, but it looked like a neat tool. I can’t find a release on the web yet and there was no URL on the poster. I’ll try to track them down again today.

Update: Found it here http://celldesigner.org/payao/payaopreview.html

Another fun tool (which I haven’t had a chance to use much yet) is BioMyn. The idea behind BioMyn is that it is something like a Google search for systems biology and other relevant biological data types. It aggregates a lot tools into a single search, here’s a partial list: ensembl, MINT, GAD, HPRD, Corum, InterPro, PDB, OMIM, GO, Reactome, KEGG, UniProt, HiMap, IntAct, GNF, and DIP. I spoke to Fidel Ramirez, the creator, about this tool and he was very eager to have users and feedback on this new beta phase. He was saying that people have suggested the results link should be re-organized a bit. If you do a search you get a list of results and some context. The link at the top goes to your “best” resource hit–leaving BioMyn. But if you click the link at the bottom of the result ( View all annotations for ) you go to the aggregated results in BioMyn. Organized into a collection of data in tabs, you can find a wealth of information on this gene. You can find gene links, of course, but also diseases, pathways, interactions, GO terms, and on and on. Anyway–check it out. And keep in mind it is beta. Feel free to offer feedback here and I will pass it along to the developers–they don’t have a feedback link on the site yet. But they do have a blog, I suppose you could put comments over there. In fact, I’ll suggest that to the team today if I see them.

Systems biology software day for me

I’m in Göteborg today, at the ICSB International Conference on Systems Biology. I’m taking a couple of the tutorials today. My first one is on the Edinburgh Pathway Editor or EPE (description of this can be found in this PDF of the session). They have made available a 2.0 version for the attendees here. I’m eager to learn more about this.

The next session I signed up for is CellDesigner 4.0. You can learn more about it from the session PDF here.

Both of these tools require downloading and installation. We usually focus more on web-based software, but these systems biology tools often require you to install and run it locally. You can get the software directly from these sites:

Edinburgh Pathway Editor: http://www.bioinformatics.ed.ac.uk/epe/index.shtml

CellDesigner: http://celldesigner.org/

Have fun! I expect I’ll post more thoughts on them after I have had a chance to dive in and swim around some.