The document describes a customized Pipeline Pilot web portal developed for SP Intervets to replace their former bioinformatics software. The portal was designed to meet requirements for usability for non-specialists and functionality for experts. It integrates bioinformatics protocols and tools into a user-friendly interface that stores results in a user context rather than job context. Examples demonstrate running BLAST searches, viewing and refining results, and generating PDF reports. The portal provides flexible access to databases and allows updating and extending functionality. It has successfully replaced the former application framework.

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
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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
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4. Default Pipeline Pilot Webport
• Standard customization options available
– Not enough, do not meet our requirements
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5. BioInformatics Portal
Re-designed webport
(header & navigation)
New starting window
All protocols can be
accessed depending
on the user dataset
(nucleotide, protein)
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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
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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 !!!
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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
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9. Example Workflow (BLASTn) – Results II
Detail View
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10. Example Workflow (BLASTn) – Results II
Detail View
External Links
Formatted Alignment
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11. Example Workflow (BLASTn) – Results II
Detail View
External Links
Formatted Alignment
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12. Example Workflow (BLASTn) – Results II
Detail View
External Links
Formatted BioInfPortal_SystemDatabases.xls
Alignment
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13. Example Workflow (BLASTn) – Results III
Result Refinement
Postfilter Tool
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14. Example Workflow (BLASTn) – Results III
Result Refinement
Postfilter Tool
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15. Example Workflow (BLASTn) – Results III
Result Refinement
Postfilter Tool
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16. Example Workflow (BLASTn) – Results III
Result Refinement
Postfilter Tool
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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");
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18. Database Connectivity
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19. Upload of User Datasets
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20. Automatic Database Update
Processing and indexing
Scheduled download of FASTA databases from
NCBI (Genbank), Expasy (Uniprot), and RCSB
(PDB) via FTP
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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
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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
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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
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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
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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
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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
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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
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28. Acknowledgement
Pedro Gomez Fabre
Scott Markel
Accelrys Support Team
Andreas Rohwer
Richard J. Marhöfer
Hon Tran
Andreas Krasky
Paul M. Selzer
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