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

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Presentation on theme: "Martin John Bishop UK HGMP Resource Centre Hinxton Cambridge CB10 1 SB"— Presentation transcript:

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

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

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

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

5 The activities of HGMP-RC

6 On-line service

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

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



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

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

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

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

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

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

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

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

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

20 MAJOR CHALLENGES u User interface u Back end processing u Cost recovery

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

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

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

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

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

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