Distributed computing
I've been looking into distributed services in bioinformatics (sub required) again recently. A lot of research in this area seems to be Grid related.
Like most things in computer science the Grid is an old idea dressed up in spangly pants. It's not rocket science to have a client ask a server to do some computation and then return the result. You wouldn't know it to look at the descriptions of most Grid related projects, though - there's so much guff surrounding the central idea. Here in the UK, at least, there's a great deal of money available for Grid projects, so perhaps people feel that they need to justify their grants by inventing new acronyms and giving older technologies new, swisher names.
(I'm not saying that I think the Grid is a bad idea, because it's definitely not. It's just that it's sometimes being wrapped in needless complexity and presented as some sort of magical panacea for all our computational problems.)
Anyway, you can already do various NCBI searches with REST (i.e. sending variables on the URL line). The SOAP::Lite Perl library lets you access bioinformatics web services quickly and easily - not that there are all that many out there, but hey - all of which is Grid-lite, I guess.
Projects like BioMOBY take things one step further, introducing centralized lists of services, formally defining inputs and outputs and so on. I don't know if anybody reading this uses it frequently, or knows of any projects where it's been used successfully; as impressed as I am with the work that has gone into it BioMOBY never grabbed me simply because it took as long to sort out all of the kinks and overhead involved as it did to obtain, parse and analyse the data I wanted to look at in the old fashioned BioPerl way. Maybe that'll change in the future, as APIs get slimmed down, network negotiations get faster and more services become available.
In any case, I'm still unsure of why the Grid is a hot topic. For large scale projects and pipelines, sure, the Grid could come in useful (check out SETI@Home or that United Devices protein folding app) but are the changes it might make to the majority of bioinformatics work really all that revolutionary? If not, why all the funding?
Like most things in computer science the Grid is an old idea dressed up in spangly pants. It's not rocket science to have a client ask a server to do some computation and then return the result. You wouldn't know it to look at the descriptions of most Grid related projects, though - there's so much guff surrounding the central idea. Here in the UK, at least, there's a great deal of money available for Grid projects, so perhaps people feel that they need to justify their grants by inventing new acronyms and giving older technologies new, swisher names.
(I'm not saying that I think the Grid is a bad idea, because it's definitely not. It's just that it's sometimes being wrapped in needless complexity and presented as some sort of magical panacea for all our computational problems.)
Anyway, you can already do various NCBI searches with REST (i.e. sending variables on the URL line). The SOAP::Lite Perl library lets you access bioinformatics web services quickly and easily - not that there are all that many out there, but hey - all of which is Grid-lite, I guess.
Projects like BioMOBY take things one step further, introducing centralized lists of services, formally defining inputs and outputs and so on. I don't know if anybody reading this uses it frequently, or knows of any projects where it's been used successfully; as impressed as I am with the work that has gone into it BioMOBY never grabbed me simply because it took as long to sort out all of the kinks and overhead involved as it did to obtain, parse and analyse the data I wanted to look at in the old fashioned BioPerl way. Maybe that'll change in the future, as APIs get slimmed down, network negotiations get faster and more services become available.
In any case, I'm still unsure of why the Grid is a hot topic. For large scale projects and pipelines, sure, the Grid could come in useful (check out SETI@Home or that United Devices protein folding app) but are the changes it might make to the majority of bioinformatics work really all that revolutionary? If not, why all the funding?
posted by Stew @ 10:37 AM
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