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SP Intervets BioInformatics Portal - A customized global Pipeline Pilot Webportal

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Accelrys European User Group Meeting, Barcelona, Spain, October 16, 2009

Accelrys European User Group Meeting, Barcelona, Spain, October 16, 2009

Published in: Health & Medicine, Technology
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  • 1. SP Intervets BioInformatics Portal A customized global Pipeline Pilot Webportal 10/16/2009 Accelrys European User Group Meeting, Barcelona
  • 2. Background / Motivation Former Bioinformatics Software • Metalife BioInformatics Suite • Client-Server application • Tools for expert users & non-specialists • Highly customized (developed with Intervet) • Large, complex Microsoft SQL Server backend (specific stores) • Globally used in SP animal health by expert users and lab scientists Reasons for Change • SP / OBS Merger: Software Consolidation • Limitations in Metalife – Database Updates (time-consuming, complex) – Enhancements (too few, takes too long) • Pipeline Pilot was already used in our group since one year SP Intervets BioInformatics Portal 10/16/2009 2
  • 3. Requirements for PP Solution • Application-like instead of Web-Service like • Meet user expectations / similar to former solution – Usability – Functionality • • • • • Easy to use for non-specialist lab scientists Sufficient capabilities for expert users Flexible (allow fast response on changed user requirements) User context instead of job context Allow combination with other software packages and databases SP Intervets BioInformatics Portal 10/16/2009 3
  • 4. Default Pipeline Pilot Webport • Standard customization options available – Not enough, do not meet our requirements SP Intervets BioInformatics Portal 10/16/2009 4
  • 5. BioInformatics Portal Re-designed webport (header & navigation) New starting window All protocols can be accessed depending on the user dataset (nucleotide, protein) SP Intervets BioInformatics Portal 10/16/2009 5
  • 6. Job Context versus User Context New User folder window • Windows Explorer-like • based on PP file chooser framework All protocols write PDF reports that are stored in the corresponding subfolders SP Intervets BioInformatics Portal 10/16/2009 6
  • 7. Example Workflow (BLASTn) - Input Presentation according Schering-Ploughs corporate identity → using HTML attribute of reporting components and standard includes but also limitations! Not static! Information will be retrieved during protocol execution (e.g. database access) Presentation follows the representation and functionality of the NCBI Web-services → critical !!! SP Intervets BioInformatics Portal 10/16/2009 7
  • 8. Example Workflow (BLASTn) – Results I Summary View Several Limitations: 1. Custom CSS styles can not be defined to influence the table design 2. The Link-Webport Issue SP Intervets BioInformatics Portal 10/16/2009 8
  • 9. Example Workflow (BLASTn) – Results II Detail View SP Intervets BioInformatics Portal 10/16/2009 9
  • 10. Example Workflow (BLASTn) – Results II Detail View External Links Formatted Alignment SP Intervets BioInformatics Portal 10/16/2009 10
  • 11. Example Workflow (BLASTn) – Results II Detail View External Links Formatted Alignment SP Intervets BioInformatics Portal 10/16/2009 11
  • 12. Example Workflow (BLASTn) – Results II Detail View External Links Formatted BioInfPortal_SystemDatabases.xls Alignment SP Intervets BioInformatics Portal 10/16/2009 12
  • 13. Example Workflow (BLASTn) – Results III Result Refinement Postfilter Tool SP Intervets BioInformatics Portal 10/16/2009 13
  • 14. Example Workflow (BLASTn) – Results III Result Refinement Postfilter Tool SP Intervets BioInformatics Portal 10/16/2009 14
  • 15. Example Workflow (BLASTn) – Results III Result Refinement Postfilter Tool SP Intervets BioInformatics Portal 10/16/2009 15
  • 16. Example Workflow (BLASTn) – Results III Result Refinement Postfilter Tool SP Intervets BioInformatics Portal 10/16/2009 16
  • 17. Example Workflow (BLASTn) – Results IV PDF Reports Remember the User Context var url = "/scitegic-bin/DownloadFile?SID=" + sessionid + "&filename=" + uripath; var w = window.open(url, "_blank", "status=yes,rezizable=yes,location=no"); SP Intervets BioInformatics Portal 10/16/2009 17
  • 18. Database Connectivity SP Intervets BioInformatics Portal 10/16/2009 18
  • 19. Upload of User Datasets SP Intervets BioInformatics Portal 10/16/2009 19
  • 20. Automatic Database Update Processing and indexing Scheduled download of FASTA databases from NCBI (Genbank), Expasy (Uniprot), and RCSB (PDB) via FTP SP Intervets BioInformatics Portal 10/16/2009 20
  • 21. Technical Details Productive System • Dell Power Edge 2950 Server • 8 Intel Xeon X5355 CPUs, 2.66 GHz • 32 GB RAM • 100 GB Swap Space • Storage: – – – – Dell EMC CX700 (Clarion) SAN 3,6 TB 2 redundant controller 8-way FC connection • RedHat Enterprise Linux 5.3 Development System • Dell Precision T5400 Desktop • 8 Intel Xeon E5405 CPUs, 2.00 GHz • 16 GB RAM • 20 GB Swap Space • Storage: – SGI TPS9300 Raid System (our common working raid, NFS) – 3,4 TB • RedHat Enterprise Linux 5.4 • Also used for all other PP runs SP Intervets BioInformatics Portal 10/16/2009 21
  • 22. Outlook: BioInformatics Portal 2.0 • Implementation of additional bioinformatics algorithms – EMBOSS – Blast2sequences • Protein Annotation Workflow • Enhanced Explorer Functionality – Drag & Drop – Copy, Move, Rename, Delete of folders and files – Context Menu (right mouse button) • Enhanced Database functionality – Import of genomes – Advanced search functionalities SP Intervets BioInformatics Portal 10/16/2009 22
  • 23. Other Current Developments Porting our Genlight software to PP • Tool for genome comparison • Developed by Intervet and university of Bielefeld • recently used to identify new drug targets for Schistosomasis Journal of Integrative Bioinformatics Yearbook 2004, ISBN 3-88579-127-7, 2004, 79-94 SP Intervets BioInformatics Portal 10/16/2009 23
  • 24. Other Current Developments Porting our Genlight software to PP • Tool for genome comparison • Developed by Intervet and university of Bielefeld • recently used to identify new drug targets for Schistosomasis Schistosoma mansoni Drosophila Caenorhabditis melanogaster elegans SP Intervets BioInformatics Portal 10/16/2009 24
  • 25. Other Current Developments Porting our Genlight software to PP • Tool for genome comparison • Developed by Intervet and university of Bielefeld • recently used to identify new drug targets for Schistosomasis Potential Target Schistosoma associated to severe Phenotype mansoni Drosophila Caenorhabditis melanogaster elegans SP Intervets BioInformatics Portal 10/16/2009 25
  • 26. Other Current Developments Porting our Genlight software to PP • Tool for genome comparison • Developed by Intervet and university of Bielefeld • recently used to identify new drug targets for Schistosomasis Isentris Integration • Database Synchronization • Structure Registration • Property Calculations SP Intervets BioInformatics Portal 10/16/2009 26
  • 27. Summary  Integrated bioinformatics suite based on Pipeline Pilot webport • Usage of build-in functionalities (CSS) • Self-developed enhancements (html and webport Javascript framework) • Additional functionalities by using ‘hidden’ PP functionalities  Full replacement of former application framework • Easy to use for lab scientists • Powerful enough for expert users  Very flexible and extendable  Further applications will be ported to PP-based solutions SP Intervets BioInformatics Portal 10/16/2009 27
  • 28. Acknowledgement Pedro Gomez Fabre Scott Markel Accelrys Support Team Andreas Rohwer Richard J. Marhöfer Hon Tran Andreas Krasky Paul M. Selzer SP Intervets BioInformatics Portal 10/16/2009 28

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