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

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.

2 thoughts on “Software bonanza…

  1. Chris Edwards

    Hiroaki Kitano talked about Payao at the G2S conference in Manchester earlier this year and I think it first got an outing at the conference in Tokyo before that. His idea is of a “Google Maps” for biological diagrams that would be built around not so much CellDesigner as SBGN. He is very keen on having one unified graphical language, although some people I have spoken to find SBGN too rich for their tastes, preferring annotations to its pretty large symbol set.

    Initially, the idea was that people would annotate the online SBGN diagrams with relevant papers in a form of crowdsourcing. This is something else that has made some biologists nervous but, on the flipside, it looks to be a powerful way of bringing a lot of literature together into one easy interface. To populate the site initially, Manchester Uni is working on text mining software to try to link relevant papers to things like reaction pathways. I think Nf-KB is the first to get the treatment, although there are some significant issues, such as resolving ambiguous names and working out what to do with proteins and other things that turn up in multiple places and what happens if the pathway changes depending on context.

    BTW, Kitano is talking Wednesday and is scheduled to be at the speakers’ corner tomorrow (Tuesday). I was planning to ask how progress is going.

    A Payao is a raft used to help catch fish: palm fronds draped from the raft attract small fish thinking there will be food there.

  2. Mary

    Well, one of my concerns about community annotations is that there are not “carrots” there–maybe the little palm fronds will work ;) Thanks for that description–I was really curious!

    I’m hoping to hear more about it Wednesday. The thing that is most interesting to me is having a web interface. We prefer to provide training using web services because they are easier to access than software downloads and have fewer platform-specific wrinkles.

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