1. Bioinformatics Data and the Grid: The GeneGrid Data Manager
Noel Kelly

2. GeneGrid Architecture
Workflow
Definition
GDM Service
GeneGrid Environment
GeneGrid Portal
GeneGrid
Workflow Status
GeneGrid
Application
Management
Registry
GeneGrid Workflow Manager Service
GeneGrid Data Manager
Registry
GDM Service
GeneGrid Process Manager Service
GeneGrid Input &Results
Parameters
GDM Service
BeSC
GAM Service
GAM Service
GDM Service
iGAP
GAM Service
GDM Service
Blast
EMBL DB
TMHMM
mpiBlast
SwissProt DB
SignalP
EBI
SDSC
SwissProt Database
EMBL
Database

3. GeneGrid Data Manager Objectives
Integrate specialised public biological data into the Grid
Integrate proprietary data into the Grid
Access and Storage of User Input Parameters
Experiment Tracking
Access and Storage of Experiment Results

4. GeneGrid Databases GeneGrid Workflow Definition Database
Xindice 1.0 Collection
GeneGrid Workflow Status Database
GeneGrid Results & Input Parameter Database
File System

5. Biological Databases Structured File EMBL Bank SwissProt TrEMBL
TrEMBL_new
GenBank
DDJB
ENSEMBL
Fusion Proprietary
Amtec Proprietary
Structured File
MySQL
Oracle
T.B.C.

6. Public Biological Data Integration
GeneGrid
Data Manager Service
Using BioPERL modules
JDBC
Driver
PERL
Scripts
SwissProt

7. Public Biological Data Integration
GeneGrid
Data Manager Service
BeSC
Perl Script
Record
SwissProt
EBI

8. Fusion Antibodies Commercial Use Case
Fasta
File
BlastP
MQNSHSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRY…………
Blast Format
Blast Format
SwissProt
Query
Blast
Formatter
Accession Numbers
Multiple Fasta Records
TMHMM
Multiple TMHMM Format
Multiple TMHMM Format
SignalP
Eliminator
Fasta Records
Multiple SignalP Format
Multiple SignalP Format
Bl2Seq
Eliminator
Fasta Records

9. Fusion Use Case – GDM Perspective
BlastP
SwissProt
Query
Blast
Formatter
TMHMM
SignalP
Eliminator
Bl2Seq
Eliminator

10. Multiple Accession Numbers
Querying SwissProt
Accession Numbers
Task
Params
Fasta Record
GeneGrid
Data Manager Service
(for SwissProt)
GeneGrid
Data Manager Service
(for GRIP)
Multiple Accession Numbers
SwissProt
GRIP

11. Fusion Use Case – GeneGrid Perspective
BlastP
SwissProt
Query
Blast
Formatter
TMHMM
SignalP
Eliminator
Bl2Seq
Eliminator

12. Executing Bioinformatics Applications
Result File
Task
Params
GeneGrid
Application Manager Service
(for SignalP)
GeneGrid
Data Manager Service
(for GRIP)
Multiple Fasta Records
GRIP
Input File

13. GeneGrid Landmarks 1 year through a 2 year project
Successfully integrated a number of bioinformatics applications
Successfully integrated a number of bioinformatics data sets
Number of papers accepted at various conferences (Computing & Bioinformatics)
International collaboration with EOL project (SDSC)

14. GeneGrid at All Hands
A practical Workflow Implementation for a Grid Based Virtual Bioinformatics Laboratory
Session 4.4, Thur 2nd Sep, 14:10 -15:50
Bioinformatics Application Integration and Management in GeneGrid: Experiments and Experiences
Session 6.4, Fri 3rd Sep, 11:05 – 13:10

15. GeneGrid Demonstrations
Tuesday, 1st September
18:15 – 20:15
Thursday, 2nd September
10:00 – 11:30
17:30 – 19:30
Friday, 3rd September
13:00 – 14:30