Abstract
BackgroundWe observe two trends in bioinformatics: (i) analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii) multiple CPU clusters and Grids are available to more scientists. The traditional solution to the problem of running workflows across multiple CPUs required programming, often in a scripting language such as perl. Programming places such solutions beyond the reach of many bioinformatics consumers.ResultsWe present Wildfire, a graphical user interface for constructing and running workflows. Wildfire borrows user interface features from Jemboss and adds a drag-and-drop interface allowing the user to compose EMBOSS (and other) programs into workflows. For execution, Wildfire uses GEL, the underlying workflow execution engine, which can exploit available parallelism on multiple CPU machines including Beowulf-class clusters and Grids.ConclusionWildfire simplifies the tasks of constructing and executing bioinformatics workflows.
Highlights
We observe two trends in bioinformatics: (i) analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii) multiple CPU clusters and Grids are available to more scientists
The usability gap in bioinformatics has moved from individual applications to both construction and execution of workflows
We construct a workflow for analysis of human tissue-specific transcripts by comparing them against the known exons
Summary
We construct a workflow for analysis of human tissue-specific transcripts by comparing them against the known exons. This example shows how Wildfire can make use of the parallel capabilities of supercomputers. Component rscript uses the R-project to cluster the amino acid sequences from a database of known allergens. The resulting motifs are used to construct HMM profiles using hmmbuild We use these profiles with hmmpfam to predict allergenic sequences.
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