Workflows & Grid services

Alf has an informative post over at Hublog about bioinformatics workflows, which is an interesting area (you could also check out Fabrice's post on this subject at Propeller Twist). I had a look at Taverna a wee while ago when I wrote this faintly ranty post about the Grid, but only really sat down with it properly last week.

I thought it was promising (there's a "but" coming up in the next paragraph, but my take home message is that it's pretty nice). You select pipeline components from a big list of web services - which you can add to, obviously - and pipe input from one to the other, then the final output goes to a component which draws a graph, or outputs some text, or whatever. I'm not sure who these workflows are aimed at, though - people who do a lot of work with the same components all of the time?

The thing that stops me from using it regularly... well, the main thing is that I don't think it would save me any time or effort, so the cost / benefit of leaving behind my comfortable IDE just doesn't work out. That might change in the future, but anyway - there's also the fact that while 50% of the components I use during bioinformatics work might be stable objects that I need regularly - to fetch sequences, convert from GFF to FASTA, get some GO terms, etc. - the remaining 50% change frequently, and there's often some non-pluggable piece of software involved. To be able to add it to my workflow I need to wrap it somehow (so it can be used as a component) and have some sort of code glue to convert inputs and outputs into recognizable formats. I've not delved into the Taverna docs deeply enough to know for sure that there's not an easy way to do this, but I suspect Beanshell has to be involved as glue. That's a lot of coding in different languages when I can make both SOAP and system calls in a three line Perl script. The increase in complexity just doesn't translate into added productivity, yet.