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

210/16/2009SP Intervets BioInformatics Portal

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


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


Default Pipeline Pilot Webport

• Standard customization options available– Not enough, do not meet our requirements


BioInformatics Portal

Re-designed webport(header & navigation)

New starting window

All protocols can be accessed dependingon the user dataset (nucleotide, protein)


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


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)


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


Example Workflow (BLASTn) – Results II

Detail View



Detail View

Formatted Alignment

External Links



Detail View

Formatted Alignment

External Links

BioInfPortal_SystemDatabases.xls


Example Workflow (BLASTn) – Results III

Result Refinement

Postfilter Tool



Result Refinement

Postfilter Tool


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");


Database Connectivity


Upload of User Datasets


Automatic Database Update

Scheduled download of FASTA databases from NCBI (Genbank), Expasy (Uniprot), and RCSB

(PDB) via FTP

Processing and indexing


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


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


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





Schistosomamansoni

Caenorhabditiselegans

Drosophilamelanogaster





Schistosomamansoni

Caenorhabditiselegans

Drosophilamelanogaster

Potential Target associated to

severe Phenotype





Isentris Integration• Database Synchronization• Structure Registration• Property Calculations


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


Acknowledgement

Andreas RohwerRichard J. MarhöferHon TranAndreas KraskyPaul M. Selzer

Pedro Gomez FabreScott MarkelAccelrys Support Team

sp intervets bioinformatics portal - a customized global pipeline pilot webportal

Health & Medicine

user requirements user

user contextvar url

user expectations similar

user dataset nucleotide

gb ram

job context

database accesspresentation

pp solution application