A SLiM chance for viruses

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Viruses have evolved a clever way of reproducing. They hijack the signalling pathways used to instruct cells in their host, and fool them into producing copies of the virus. If we could understand these signalling pathways, we could develop treatments for viruses – and for diseases that operate in a similar way. This is a massive task which, in the human body, requires an understanding of the interactions between about 20,000 proteins. Massive problems are well suited to e-Research, so a team of biologists from the University of Southampton have teamed up with OMII-UK and Engage to find a solution.

Richard Edwards, the head of the Bioinformatics and Molecular Evolution group at Southampton, studies how proteins interact. He is specifically interested in short, linear motifs, known as SLiMs. ‘A protein can be thought of as a sequence of amino acids, like beads on a string’ explains Richard ‘[SLiMs] consist of about three-to-five specific amino acids in the protein’. SLiMs control some signalling pathways, because they control the way that some proteins interact. They are potentially useful to viruses, because their small size means that it is relatively easy for the virus to evolve and mimic them. It’s not just viruses, SLiMs could be involved in a variety of diseases, so a clear understanding of them could be vital to the development of new treatments.

Being one of a rare breed of researchers who is adept in his chosen field and in computer science, Richard wrote SLiMFinder: a program to discover SLiMs. The program originally ran on a Unix machine, which limited access to researchers who were happy with the command line. ‘It’s one of those Catch-22 situations’ says Richard ‘the kind of people who are able to download and run [SLiMFinder] are the kind of people who are likely to develop their own software’.

The Engage project is a free service that helps researchers benefit from e-Research techniques. They heard about Richard’s work and realised that it was perfect for e-Research: a massive – yet highly parallelisable – problem, with the need to accesses disparate databases and to include a wide community of researchers. After meeting with Richard, Engage began a collaboration during which OMII-UK experts were commissioned to develop SLiMFinder.

Development focused on the creation of a Taverna workflow for SLiMFinder. This allowed the automation of repetitive tasks, such as data collection from databases. ‘Data management is a non-insignificant part of the work’ explains Richard ‘the time-saving potential is more than it now runs in a day, it also didn’t need someone to spend a day setting everything up’. OMII-UK developers also developed one of SLiMFinder’s sub-programs so that it could execute on a cluster, which significantly reduced execution time.

Taverna will add a user-friendly interface to SLiMFinder, making it easier for researchers to use. It will also be easy to share work through the myExperiment website. Richard believes that this will lead to the real benefit for the new SLiMFinder: any biologists, regardless of computing experience, could use it to study the protein interactions that they know well. The superior ease of use, combined with the faster execution times, has made SLiMFinder into a tool that could be of great interest throughout biological sciences, as Richard explains ‘It’s made the difference between a tool that people would think ‘that’d be interesting, but I’m never going to use it’ and something that people could try out to see if it’s interesting’.

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