Matthias Lange. gatersleben.de Bioinformatics Progress Seminar, May 08, BI Progress 05/07/2008 M. Lange: Data IPK

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1 Matthias Lange gatersleben.de Bioinformatics Progress Seminar, May 08, 2008 slide #2

2 slide #3 protocols in lab books sample preparation plant treatment technical parameter for devices taxonomy plant tissue materials and methods section in publication electronical meta data storage text file names controlled vocabular slide #4

3 slide #5 MacroArrays 454 Sequencing ABI Sequencing Lemnatek Phenotyping 2 D gel electrophoresis MALDI TOF MS Microscopy Balance slide #6

4 image processing quantification (e.g. spot intensities) data extraction (e.g. base calling) data format converting slide #7 file system gatersleben desktop (e.g. array vision computer in PGRC) CD/DVD several group internal NAS storages (e.g. TerraStations) software embeded databases / project Databases, e.g.: Lemnatek software: plant images in embedded ORACLE Pyro Sequencing software: embedded ORACLE microscope Ag SZB: images MS Access MALDI TOFT software: Mass spec data IPK ORACLE Barley Core Collection: POSTGRES & FOXPRO GBIS, BIC GH, PGRC projects: IPK ORACLE hierarchical storage management combination of disk and tape storage (SamFS) Metatdata managed in ORACLE slide #8

5 1. data analysis 2. analysis result storage a) like raw data storage b) information systems (APEX, JAVA client, Java Server Pages, PHP) slide #9 programming by design generate code for non business logic software components (GUI, reports, formulars, visualization) data model: relational view: WebFrontend control/logic: JAVA stored procedures, PL/SQL, Web Services How to use: pgrc 35.ipk gatersleben.de/pls/htmldb_pgrc slide #10

6 central managed DBMS 2x2GHz Itanium CPUs, 16GByte RAM 1TByte SCSI RAID backend for non raw data 6 TBytetapestorage(HSM) backend for raw data high available (standby environment) build in: data mining, text mining, blast, row level data security, central user management, auditing, historic data versions, Test it: sqlplus gatersleben.de:1521:genophen how to use: gatersleben.de slide #11 Facts heterogeneous system environment almost locked in lab infrastructure with no or poor interfaces no or minimal interaction within single or group of instruments/applications data: huge volumes, often unstructured, inherently distributed, usually file based or isolated databases processes: scripts, command line tools Typical researchers point of view publish a research paper don t care data storage data processing data management data sharing data reproducibility scalability data lies around no reusability of research results no reproducibility of research no semantic search no cross field searches no data quality assurance Required: Data management and integration framework capture and link all relevant data automate/support scientific workflows slide #12

7 Online: API (e.g. SOAP Web WebService in FLAREX, VANTED) Online: SQL access (e.g. MomaVis) Offline: Standard XML (SBML, MAGE ML) #!perl -w use SOAP::Lite; $soap_response = SOAP::Lite -> uri('http://service.crest.agbi.ipk.de') -> proxy('http://pgrc-35.ipkgatersleben.de:7900/crest/crest'); my $var = SOAP::Data -> type('string') -> name ('ListOfLibIDs') -> value('hy'); $soap_response->proxy->timeout(3600); my $result = $soap_response -> getestfastabylibstring($var); unless ($result->fault) { open(filehandle,">estlibhy.fasta"); print FileHandle $result->result(); close(filehandle); } else { print join ', \n',$result->faultcode,$result->faultstring; } slide #13 controlled management of raw data use of central IPK storage warrant 10 years, maintained online access controlled management of meta data link raw data to its meta data relational modeling/decomposition (entities and attributes) use of controlled vocabularies (taxonomy, tissue, traits, units) use the IPK ORACLE database slide #14

8 slide #15 slide #16

9 [Wikipedia]: A Laboratory Information Management System (LIMS) is computer software that is used in the laboratory for the management of samples, laboratory users, instruments, standards and other laboratory functions such as work flow automation. Case study: Open Source System B Fabric (FGC Zürich) (infos: suppl. seminar web page) slide #17 slide #18

10 slide #19 slide #20

11 1. homogenization of IPK data management 2. use of IPK wide Labor Information Mangement System (LIMS) commercial, e.g. Nautilus von Thermo Labs (used in MPI Golm, SunGene, Bayer CS) open source, e.g. B Fabric (FGCZ Zürich) 3. integrative IPK slide #21

Management von Forschungsprimärdaten und DOI Registrierung. Dr. Matthias Lange (Bioinformatics & Information Technology) June 19 th, 2013

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