1. Martin John Bishop UK HGMP Resource Centre Hinxton Cambridge CB10 1 SB

2. Bioinformatics scope Genome sequences - DNA Transcripts - RNA Proteins
Protein interactions
Macromolecular assemblies
Development and cellular function
Genetic linkage analysis

3. Molecular biology needs bioinformatics
Biological data - molecules
Sequences
Structures
Gene expression
Proteomes
Pathways
Evolution
Computer analysis – methods
Comparison
Modelling
Co-regulation
Mass spectrometry
Knowledge bases
Phylogenetics

4. Molecular biology is about information
Central dogma
DNA
<-> RNA
-> protein
-> phenotype
<- DNA
Molecules
Processes
Central paradigm
Genome repository
<-> RNA world
-> Protein sequence
-> Protein structure
-> Protein function
-> Phenotype
<- Fed back to genome
Information processing

5. The activities of HGMP-RC

6. On-line service

7. HGMP-RC SERVICE Web menu Telnet menu / Unix login X (or VNC) Java

8. GENOME WEB Up to date Relevant Fully searchable Fully verified
Extensive

9. INTEGRATED ANALYSIS
BLAST
NIX
PIX
GLUE
PIE
MAGI
PINT

10. COMMON OPTIONS
EMBOSS
GCG
PINE
CLUSTAL
STADEN
PASSWORD

11. GENOMICS APPLICATIONS
Linkage Analysis
Radiation Hybrid Mapping
Sequence Ready Clone Maps
Genome Databases
Polymorphisms
Sequence Analysis
Gene Prediction
Expression Profiling
Phylogenetic Analysis
Integrated Tools - GLUE, RHYME, NIX, PIE

12. PROTEOMICS APPLICATIONS
Protein Sequence Analysis
Protein Structure Analysis
Protein Structural Modelling
Proteome Databases
Tools for Peptide Sequence Determination
Protein Cellular Localisation
Protein Functional Studies
Pathways and Protein Interactions
Integrated tools and databases - PIX

13. NETWORK / JANET SERVICE
LONDON
Currently 34 Mbps main link
Future keep 34 Mbps link for backup
CAMBRIDGE
Currently 8 Mbps redundant link
Future Gigabit Ethernet

14. SERVERS More than 80 servers 1, 4 and 8 cpu SMP Sparc and Intel
Solaris and Linux
Databases doubling every 14 months

15. LOADS Load is the percentage of processes trying to run
Interactive load 50%
Job queues load 100%
Jobs waiting can be 6-10 times the work being processed

16. PROCESSES AND QUEUES Menu service (hot swop)
General analysis (overloaded)
Sun BLAST and NIX queue
Dell BLAST queue
BLAST data file server
Interactive Linkage queue
Heavy Linkage queue

17. USERS’ REAL WORLD PROBLEMS
Comparative method
Extrapolate from known to similar
Hints to reduce the amount of experimental work that needs to be done

18. SOFTWARE SYSTEMS A variety of technical solutions are used BLAST
NCBI Entrez
SRS
GeneCards
NIX
ENSEMBL

19. HELPING THE USER Information discovery – completeness
Communication – multiple sites
Ontology – uniformity?
Software integration – ease of use
Reasoning about results
Monitoring – repeat queries

20. MAJOR CHALLENGES
User interface
Back end processing
Cost recovery

21. NEW TECHNOLOGIES? Web services GRID (EMBnet)
Object-orientated computing
Multi-agent systems

22. TREASURE Web service with top level container Customise for the user
User selects a service and opens it as an application
An alternative view can be built around user data as the fundamental objects

23. IMPLEMENTATION
EMBREO library written in Java handles web service layer (also CORBA, XML-RPC, JDBC and other connectivity)
Also handles file access and transfer and display of results (including use of VNC)
Simple Object Access Protocol (SOAP)
Browser channel uses XML format

24. USER ACCOUNTING AND CUSTOMIZATION
Currently very complex
HED
NIS+
Filesystem configuration files
Future a single database
Lightweight Directory Access Protocol (LDAP)

25. CREDITS Gary Williams Geoff Gibbs Peter Tribble
Menu systems and Genome Web
Geoff Gibbs
Network and systems
Peter Tribble
Web servers, Queues, Treasure