Bioinformatics, Translational Bioinformatics, Personalized Medicine
SP Intervets BioInformatics Portal - A customized global Pipeline Pilot Webportal
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Transcript of SP Intervets BioInformatics Portal - A customized global Pipeline Pilot Webportal
Accelrys European User Group Meeting, Barcelona10/16/2009
SP Intervets BioInformatics Portal
A customized global Pipeline Pilot Webportal
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Background / MotivationFormer 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
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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
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Default Pipeline Pilot Webport
• Standard customization options available– Not enough, do not meet our requirements
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BioInformatics Portal
Re-designed webport(header & navigation)
New starting window
All protocols can be accessed dependingon the user dataset (nucleotide, protein)
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Job Context versus User Context
New User folder window• Windows Explorer-like• based on PP file chooser framework
All protocols write PDF reports that arestored in the correspondingsubfolders
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Example Workflow (BLASTn) - Input
Presentation according Schering-Ploughs corporateidentity→ using HTML attribute of reporting components andstandard includesbut also limitations!
Presentation follows the representation and functionality of the NCBIWeb-services→ critical !!!
Not static!Information will be retrievedduring protocol execution(e.g. database access)
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Example Workflow (BLASTn) – Results I
Summary View
Several Limitations:
1. Custom CSS styles can notbe defined to influencethe table design
2. The Link-Webport Issue
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Example Workflow (BLASTn) – Results II
Detail View
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Example Workflow (BLASTn) – Results II
Detail View
Formatted Alignment
External Links
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Example Workflow (BLASTn) – Results II
Detail View
Formatted Alignment
External Links
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Example Workflow (BLASTn) – Results II
Detail View
Formatted Alignment
External Links
BioInfPortal_SystemDatabases.xls
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Example Workflow (BLASTn) – Results III
Result Refinement
Postfilter Tool
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Example Workflow (BLASTn) – Results III
Result Refinement
Postfilter Tool
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Example Workflow (BLASTn) – Results III
Result Refinement
Postfilter Tool
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Example Workflow (BLASTn) – Results III
Result Refinement
Postfilter Tool
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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");
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Database Connectivity
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Upload of User Datasets
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Automatic Database Update
Scheduled download of FASTA databases from NCBI (Genbank), Expasy (Uniprot), and RCSB
(PDB) via FTP
Processing and indexing
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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
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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
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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
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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
Schistosomamansoni
Caenorhabditiselegans
Drosophilamelanogaster
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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
Schistosomamansoni
Caenorhabditiselegans
Drosophilamelanogaster
Potential Target associated to
severe Phenotype
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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
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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
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Acknowledgement
Andreas RohwerRichard J. MarhöferHon TranAndreas KraskyPaul M. Selzer
Pedro Gomez FabreScott MarkelAccelrys Support Team