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Middleware for In silico Biology

Middleware for In silico Biology. Phillip Lord http://www.mygrid.org.uk. UK e-Science Pilot Project. Oct 2001 – April 2005. £3.4 million. £0.4 million studentships. Newcastle. Sheffield. Manchester. Nottingham. Hinxton. Southampton. Data-intensive bioinformatics.

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Middleware for In silico Biology

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  1. Middleware for In silico Biology Phillip Lord http://www.mygrid.org.uk

  2. UK e-Science Pilot Project. • Oct 2001 – April 2005. • £3.4 million. • £0.4 million studentships. Newcastle Sheffield Manchester Nottingham Hinxton Southampton

  3. Data-intensive bioinformatics ID MURA_BACSU STANDARD; PRT; 429 AA. DE PROBABLE UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE DE (EC 2.5.1.7) (ENOYLPYRUVATE TRANSFERASE) (UDP-N-ACETYLGLUCOSAMINE DE ENOLPYRUVYL TRANSFERASE) (EPT). GN MURA OR MURZ. OS BACILLUS SUBTILIS. OC BACTERIA; FIRMICUTES; BACILLUS/CLOSTRIDIUM GROUP; BACILLACEAE; OC BACILLUS. KW PEPTIDOGLYCAN SYNTHESIS; CELL WALL; TRANSFERASE. FT ACT_SITE 116 116 BINDS PEP (BY SIMILARITY). FT CONFLICT 374 374 S -> A (IN REF. 3). SQ SEQUENCE 429 AA; 46016 MW; 02018C5C CRC32; MEKLNIAGGD SLNGTVHISG AKNSAVALIP ATILANSEVT IEGLPEISDI ETLRDLLKEI GGNVHFENGE MVVDPTSMIS MPLPNGKVKK LRASYYLMGA MLGRFKQAVI GLPGGCHLGP RPIDQHIKGF EALGAEVTNE QGAIYLRAER LRGARIYLDV VSVGATINIM LAAVLAEGKT IIENAAKEPE IIDVATLLTS MGAKIKGAGT NVIRIDGVKE LHGCKHTIIP DRIEAGTFMI

  4. Bioinformaticians Tool Providers Service Providers Service Stack Work bench Taverna Talisman Web Portal Applications Gateway Personalisation Registries Service and Workflow Discovery Provenance Event Notification Ontologies Ontology Mgt Views Metadata Mgt Core services myGrid Information Repository OGSA-DQP Distributed Query Processor FreeFluo Workflow Enactment Engine Web Service (Grid Service) communication fabric External services SoapLab GowLab Native Web Services AMBIT Text Extraction Service Legacy apps Legacy apps

  5. Physical Map CTA-315H11 CTB-51J22 GTF2IRD2P Gap FKBP6T POM121 GTF2IP NOLR1 NCF1P PMS2L STAG3 Block B Block A Block C Williams-Beuren Syndrome Microdeletion A-cen B-cen C-cen C-mid B-mid A-mid B-tel A-tel C-tel WBSCR1/E1f4H WBSCR5/LAB GTF2IRD1 WBSCR21 WBSCR22 WBSCR18 WBSCR14 GTF2IRD2 POM121 NOLR1 BAZ1B BCL7B FKBP6 GTF2I CLDN3 CLDN4 CYLN2 STX1A LIMK1 NCF1 TBL2 RFC2 FZD9 ELN ~1.5 Mb 7q11.23 Patient deletions * * WBS SVAS Chr 7 ~155 Mb

  6. WBS Workflows: Query nucleotide sequence RepeatMasker ncbiBlastWrapper Pink: Outputs/inputs of a service Purple: Taylor-made services Green: Emboss soaplab services Yellow: Manchester soaplab services Grey: Unknowns GenBank Accession No URL inc GB identifier Translation/sequence file. Good for records and publications prettyseq GenBank Entry Amino Acid translation Sort for appropriate Sequences only Identifies PEST seq epestfind 6 ORFs Seqret Identifies FingerPRINTS pscan MW, length, charge, pI, etc Nucleotide seq (Fasta) pepstats sixpack ORFs transeq Predicts Coiled-coil regions RepeatMasker pepcoil tblastn Vs nr, est, est_mouse, est_human databases. Blastp Vs nr Coding sequence GenScan ncbiBlastWrapper Restriction enzyme map restrict SignalP TargetP PSORTII Predicts cellular location CpG Island locations and % cpgreport InterPro PFAM Prosite Smart Identifies functional and structural domains/motifs RepeatMasker Repetative elements Hydrophobic regions Pepwindow? Octanol? Blastn Vs nr, est databases. ncbiBlastWrapper

  7. Semantic discovery • Query-ontology – discovering workflows and services described in the registry by building a query in Taverna. • A common ontology is used to annotate and query. • Look for all workflows that accept an input of semantic type nucleotide sequence. • Aim to have semantic discovery over public view on the Web.

  8. Semantic Discovery Pedro data capture tool View annotations on workflow Drag a workflow entry into the explorer pane and the workflow loads. Drag a service/ workflow to the scavenger window for inclusion into the workflow

  9. ..masked_sequence_of .. nucleotide_sequence project ..part_of organisation >gi|19747251|gb|AC005089.3| Homo sapiens BAC clone CTA-315H11 from 7, complete sequence AAGCTTTTCTGGCACTGTTTCCTTCTTCCTGATAACCAGAGAAGGAAAAGATCTCCATTTTACAGATGAG GAAACAGGCTCAGAGAGGTCAAGGCTCTGGCTCAAGGTCACACAGCCTGGGAACGGCAAAGCTGATATTC AAACCCAAGCATCTTGGCTCCAAAGCCCTGGTTTCTGTTCCCACTACTGTCAGTGACCTTGGCAAGCCCT GTCCTCCTCCGGGCTTCACTCTGCACACCTGTAACCTGGGGTTAAATGGGCTCACCTGGACTGTTGAGCG experiment definition rdf:type ..part_of group urn:lsid:taverna:datathing:13 ..part_of ..author workflow definition ..works_for ..invocation_of ..author person ..BLAST_Report workflow invocation ..similar_sequences_to ..run_for ..run_during service description rdf:type 19747251 AC005089.3 831 Homo sapiens BAC clone CTA-315H11 from 7, complete sequence 15145617 AC073846.6 815 Homo sapiens BAC clone RP11-622P13 from 7, complete sequence 15384807 AL365366.20 46.1 Human DNA sequence from clone RP11-553N16 on chromosome 1, complete sequence 7717376 AL163282.2 44.1 Homo sapiens chromosome 21 segment HS21C082 16304790 AL133523.5 44.1 Human chromosome 14 DNA sequence BAC R-775G15 of library RPCI-11 from chromosome 14 of Homo sapiens (Human), complete sequence 34367431 BX648272.1 44.1 Homo sapiens mRNA; cDNA DKFZp686G08119 (from clone DKFZp686G08119) 5629923 AC007298.17 44.1 Homo sapiens 12q22 BAC RPCI11-256L6 (Roswell Park Cancer Institute Human BAC Library) complete sequence 34533695 AK126986.1 44.1 Homo sapiens cDNA FLJ45040 fis, clone BRAWH3020486 20377057 AC069363.10 44.1 Homo sapiens chromosome 17, clone RP11-104J23, complete sequence 4191263 AL031674.1 44.1 Human DNA sequence from clone RP4-715N11 on chromosome 20q13.1-13.2 Contains two putative novel genes, ESTs, STSs and GSSs, complete sequence 17977487 AC093690.5 44.1 Homo sapiens BAC clone RP11-731I19 from 2, complete sequence 17048246 AC012568.7 44.1 Homo sapiens chromosome 15, clone RP11-342M21, complete sequence 14485328 AL355339.7 44.1 Human DNA sequence from clone RP11-461K13 on chromosome 10, complete sequence 5757554 AC007074.2 44.1 Homo sapiens PAC clone RP3-368G6 from X, complete sequence 4176355 AC005509.1 44.1 Homo sapiens chromosome 4 clone B200N5 map 4q25, complete sequence 2829108 AF042090.1 44.1 Homo sapiens chromosome 21q22.3 PAC 171F15, complete sequence urn:lsid:taverna:datathing:15 service invocation ..described_by ..created_by ..filtered_version_of A B Provenance tracking Relationship BLAST report has with other items in the repository Other classes of information related to BLAST report

  10. Using IBM’s Haystack GenBank record Portion of the Web of provenance Managing collection of sequences for review

  11. Acknowledgements myGrid is an EPSRC funded UK eScience Program Pilot Project Particular thanks to the other members of the Taverna project, http://taverna.sf.net

  12. myGrid People Core • Matthew Addis, Nedim Alpdemir, Tim Carver, Rich Cawley, Neil Davis, Alvaro Fernandes, Justin Ferris, Robert Gaizaukaus, Kevin Glover, Carole Goble, Chris Greenhalgh, Mark Greenwood, Yikun Guo, Ananth Krishna, Peter Li, Phillip Lord, Darren Marvin, Simon Miles, Luc Moreau, Arijit Mukherjee, Tom Oinn, Juri Papay, Savas Parastatidis, Norman Paton, Terry Payne, Matthew Pockock Milena Radenkovic, Stefan Rennick-Egglestone, Peter Rice, Martin Senger, Nick Sharman, Robert Stevens, Victor Tan, Anil Wipat, Paul Watson and Chris Wroe. Users • Simon Pearce and Claire Jennings, Institute of Human Genetics School of Clinical Medical Sciences, University of Newcastle, UK • Hannah Tipney, May Tassabehji, Andy Brass, St Mary’s Hospital, Manchester, UK Postgraduates • Martin Szomszor, Duncan Hull, Jun Zhao, Pinar Alper, John Dickman, Keith Flanagan, Antoon Goderis, Tracy Craddock, Alastair Hampshire Industrial • Dennis Quan, Sean Martin, Michael Niemi, Syd Chapman (IBM) • Robin McEntire (GSK) Collaborators • Keith Decker

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