Gaggle

I hadn't heard of Gaggle before but both Deepak and Sutee Dee (who needs a homepage.. ;)) from the ISB mentioned it last week so I figured it was worth a look. It's a system built by Paul Shannon at the ISB in Seattle to share data between different bioinformatics applications on the fly. It has been around for a while, I think - there was a BMC Bioinformatics paper describing the system in March 2006.

A small server program (the ´Gaggle Boss´) provides communication among analysis and display programs (the ´geese´) which are modest and minimal adaptations of existing (or novel) bioinformatics and computational biology programs, and web resources. The Boss and the geese all run as separate programs on the user´s desktop computer, communicating with each other, at the user´s behest, by passing simple messages.

(from the ISB's 'about Gaggle' page)

I ran through a tutorial showing data sharing between (modified versions of) Cytoscape (also developed by ISB), R and a data matrix viewer no problem. Quite cool.

You can't share data from an arbitrary application (I don't think?), they need to be modified to send messages to the Boss goose. Having said that there's a Firefox extension called Firegoose which lets you pass messages to and from web apps, Entrez etc. I couldn't get it working properly but suspect that's something to do with my install rather than the extension itself.

Anyway, it's good to see stuff like this. Truth be told it's not the slickest thing ever, but it's still pretty cool - and it works. I wonder if you could turn it into a simple lab notebook - could you write a brief description of what you're going to try and do for the Boss app every time you send data to another app or something?