1 / 11

Bioinformatics Workflows

Bioinformatics Workflows. Chris Wroe (based on material from the myGrid team & May Tassabehji / Hannah Tipney Medical Genetics, St Marys). Bioinformatics pipelines on the web. Copying and pasting from one web based application to annotation by hand

oriole
Download Presentation

Bioinformatics Workflows

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Bioinformatics Workflows Chris Wroe (based on material from the myGrid team & May Tassabehji / Hannah Tipney Medical Genetics, St Marys)

  2. Bioinformatics pipelines on the web • Copying and pasting from one web based application to annotation by hand • Advantages : quick, easy access to distributed resources • Disadvantages: time consuming, error prone, tacit procedure so difficult to share both protocol and results RepeatMasker BLASTn Twinscan

  3. Automating pipelines • Using Perl/ Matlab scripts to implement a pipeline • Advantages : automation, quick to write, significant community resources (e.g. BioPerl) • Disadvantages: hard to explain, hard to relocate, hard to tinker with.

  4. Workflows Predicted genes out Sequence in RepeatMasker Web service BLASTn Web Service TwinscanWeb Service • Simple scripting language aims to specify how steps of a pipeline link together • High level picture of the pipeline separated from any low level fiddling • Application logic and low level fiddling encapsulated in remote web services • Advantages : automation, quick to write, easier to explain, share, relocate, and record provenance of results in a standard way

  5. Workflow components in myGrid • Scufl – Simple Conceptual Unified Flow Language • Developed by myGrid members at EBI. • Designed to be as simple as possible, just enough features to support bioinformatics workflows • Taverna – a tool for writing, running workflows and examining results. (http://taverna.sourceforge.net) • FreeFluo – workflow engine to run workflows (http://freefluo.sourceforge.net)

  6. Workflow use • Newcastle University (Anil Wipat, Peter Li) • Affymetrix Microarray Analysis Workflow • Gene annotation workflow • Manchester University May Tassabehji, PhD student Hannah Tipney, Medical Gentics, St Marys (Wellcome Trust Funded) • Gene alerting service workflow (GAS) • Gene and protein annotation workflow • And others

  7. Workflow experience + • Easy to get started with Taverna (1-2 hours tutorial) • Sharing does happen • Cuts down the time taken to perform one pipeline from 2wks to 2 hours

  8. Workflow experience: outstanding issues • Early days: web services rare; significant time take to wrap applications as web services (licensing, installation, maintenance) • Soaplab and Gowlab try to help (http://industry.ebi.ac.uk/soaplab) • Fiddly bits don’t go away: Many ‘shim’ services needed to ensure the output of one step fits the expected input of another • Automation produces many results in a short amount of time. Issues of result management and display

  9. Other workflow systems • Commercial bioinformatics – drug discovery • Incogen VIBE • TurboWorx Pipeline Pilot • eScience • DiscoveryNet (bioinformatics – proprietary) • Keppler ( US ecology) • Triana (UK Physics astronomy, signal processing)

  10. Workflow standards • Can’t have enough of them! All currently come from e-Business rather than science community • BPEL – Business Process Execution Language • WS – Orchestration • XML Process Definition Language (XPDL) • Business Process Markup Language (BPML)

More Related