Dr Vincent Robert - EU BOLD Mirror & Fungal Barcoding

• 1. EU BOLD Systsem & BioloMICSSoftwareEU BOLD SYSTEM & BIOLOMICSSOFTWAREVincent Robert, [email protected] fungal biodiversity centre BioAware Company, www.bio-aware.c

2. OUTLINE 1.History of BioloMICS 2.The team 3.The infrastructure 4.Database management and analyzesBioloMICS software 5.Examples of use 1.QBOL projects 2.Thermoregulation exampleCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 3. HISTORY OF BIOLOMICSCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 4. 1. HISTORY OF BIOLOMICSCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 5. 1. HISTORY OF BIOLOMICS Strain #1234 Species name, J. Smith, Soil, 1 972, UKCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 6. 1. HISTORY OF BIOLOMICSBioAware is created in 2000 as a Spin-off of Centraalbureau voor SchimmelcultureCBS-KNAW (Utrecht, The Netherlands) an Institute of the Dutch Academy of Arts CBS-KNAW fungal biodiversity centreBioAware Company, www.bio-aware.c 7. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 8. 2.THE TEAMV. Robert D. Vu (G. Stegehuis) S. SzokeB. JabasE. BlomUtrecht, The Netherlands Hannut, Belgium S. Ben Daoud A. Ben Hadj Amor O. ChouchenM. Jaidane A. DridiN. van de Wiele Sousse, Tunisia Sydney, AustraliaCBS-KNAW fungal biodiversity centreBioAware Company, www.bio-aware.c 9. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 10. 3. THE INFRASTRUCTUREHousing of the infrastructure in secure datacenter1. Connectivity2. Security3. Triple electrical supply4. Temperature control5. Fire protection6. Direct access to CLOUD computing facility7. Support CBS-KNAW fungal biodiversity centreBioAware Company, www.bio-aware.c 11. 3. THE INFRASTRUCTURE -VIRTUALIZATION VIA CITRIX XENAPP CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 12. 4. DATABASE MANAGEMENT AND ANALYZES BIOLOMICSSOFTWAREEXAMPLE STRUCTURE OF A GIVEN COLLECTION DATABASE(COMPLETELY FLEXIBLE AND MODIFIABLE) Bibliography Taxon Files tables tablenames tableStrains table containing a number of fieldsDatabase of a collectionDNASequence s tableStockPropertie Hostmanagemens tabletablet tableCBS-KNAW fungal biodiversity centreBioAware Company, www.bio-aware.c 13. Simple structure: single database containing a number of interconnected tablesDesktop application Collection specific database(usually MS-Windows based)To manage and analyze data(for curators and local researchers) Other tables Bibliography tableTaxon names table Strains table containing a number of fields Database of a collectionDNASequencestable P r o H p o e s rt t iStock management table t e a s b t l a e b l e CBS-KNAW fungal biodiversity centreBioAware Company, www.bio-aware.c 14. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 15. Simple structure: several databases (from one or several collections) containing a number of interconnected tablesDesktop applicationConnections between (n) collections(usually MS-Windows based) specific databasesTo manage and analyze data B i b l i oTaxon(for curators and local researchers) gn Ot raher amtab peles hs yt ta ab bl le e Strains table containing anumber of fields DDatabase of a collection N A S e q u e n S c t e o s cP kr to a mp H b ae o l nr s e at t gi ee t ms a eb nt l ta eb tl ae b l eTBi abl xio ogr n Other a n table p a s hm y eta sblta ebl eStrains tablecontaining a number of fields D N Database of a collectionA S e q u e n c eStPs or cot kpH am eo b ars l ntt e aig et esamb etlntaetabbll eeTBi abl xio ogr n Other a n table p a s hm y eta sblta ebl e Strains table containing a number of fields D NDatabase of a collection A S e q u e n c eStPs or cot kpH am eo b ars l ntt e aig et esamb etlntaetabbll ee CBS-KNAW fungal biodiversity centreBioAware Company, www.bio-aware.c 16. Internet publication, availability and analyzes of data via specific websitesCollection specific website Collection specific databaseOther tablesBibliography tableTaxon names tableStrains table containing a number of fieldsDatabase of a collection DNA Sequences tableProHpoesrtti Stock management table teasbtlaebleCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 17. 4. DATABASE MANAGEMENT AND ANALYZES BIOLOMICS SOFTWAREDirect update and availability of data via both desktop application andInternet based application (website)Desktop applicationConnections between (n) collections Collection specific website(usually MS-Windows based) specific databasesTo manage and analyze data(for curators and local researchers) B T i a b x O l o t i n h o e g n r r S a a t m t p r e a h a s b y i l n t e t s a s a b b t l l a e e b l e c o n t a i n i n g a D N Database of a n A collectionu m S b e e q r u S e o n t f o c c P e f s k r i o e t m p H l a e o a d n r s b s l a t t g i e e e t m s a e b n t l t a e b t l a e b l e B T i a b x O l o t i n h o e g S n r r t a a r m t p a e a h i s b y n l s t e t a s a t b b a l l b e e l e c o n t a i n i n g D a N Database of a A n collectionu S m e b q e u S r e t n o o c c f P e k r s f o m i p H t a e e o a n l r s b a d t t l g s i e e e t m s a e b n t l t a e b t l a e b l e B T i a b x O l o t i n h o e g S n r r t a a r m t p a e a h i s b y n l s t e t a s a t b b a l l b e e l e c o n t a i n i n g D a N Database of a A n collectionu S m e b q e u S r e t n o o c c f P e k r s f o m i p H t a e e o a n l r s b a d t t l g s i e e e t m s a e b n t l t a e b t l a e b l e CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 18. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 19. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 20. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 21. 4. DATABASE MANAGEMENT AND ANALYZESBIOLOMICS SOFTWARESPECIFIC MANAGEMENT OF SEQUENCES RELATEDDATA (LIMS) CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 22. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 23. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 24. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 25. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 26. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 27. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 28. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 29. Growth of data & complexityCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 30. Growth of data & complexityCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 31. CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 32. Bioinformatician IT & Software developers sCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 33. Large investments Bioinformatics groupScientific return on investmentand/or collaborations Short & Long termLarge investmentsFinancial return on investment Sales & collaboration & projects CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 34. 5. EXAMPLES - FES AND QBOLPROJECTS EXAMPLES CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 35. A FEW MOVIES BioloMICS main version (www.bio-aware.com) Qbank Pairwise Sequence Alignments (severalremote sequence databases; from www.q-bank.eu) Fungal Barcoding (future EU BOLD mirror; fromwww.fungalbarcoding.org) CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 36. IT THE PROBLEM ?WHY IS IT SO IMPORTANT TO IDENTIFY PROPERLY ? JUST A MEDICALEXAMPLE Vincent Robert, Collections, information systems and their applications, CBS, The Netherlands, [email protected] CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 37. A FEW MOVIES BioloMICS main version (www.bio-aware.com) Qbank Pairwise Sequence Alignments (severalremote sequence databases; from www.q-bank.eu) Fungal Barcoding (future EU BOLD mirror; fromwww.fungalbarcoding.org) Polyphasic Identification (from www.q-bank.eu) CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 38. THERMOREGULATIONEXAMPLE1 0.9 0.8 0.7 Total number of strains 0.6 0.5 0.4 0.3 0.2 0.10 13 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 Based on 4802 strains of yeasts, belonging to 144 generaCBS-KNAW fungal biodiversity centreBioAware Company, www.bio-aware.c 39. SOME USERSInstitut Pasteur, Paris, FranceCenters for Disease Control and Prevention, Atlanta, Georgia, USAUK Health Protection Agency, Colindale, UKUniversity of California, Davis, California, USAINRA, Montpelier, FranceAtlas of Living Australia and most Australian microbial collectionsWestmead Hospital and University of Sydney, Sydney, AustraliaAnheuser-Busch InBev (the largest brewer in theworld), Leuven, BelgiumMiller Brewing Company, Milwaukee, Wisconsin, USAFrieslandcampina, Lelystad, The NetherlandsUniversitt fr Bodenkultur, Vienna, AustriaCBS-KNAW fungal biodiversity centreBioAware Company, www.bio-aware.c 40. 3 SOLUTIONS Deposit data on default database (free displayand upload to BOLD) User defined structure (Submitted to curatorsfor approaval) and data submitted to curatorvia website, no access to BioloMICS plateform(free display and upload to BOLD) User defined structure, access via BioloMICSplateform using Citrix XenApp (not free) CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c 41. CONTACTVincent RobertHead of Bioinformatics groupCentraalbureau voor SchimmelculturesCBS-KNAW Fungal Biodiversity CenterAddress: 8 Uppsalalaan, 3584CT Utrecht, TheNetherlandsTel: +32(0)478 28 57 64E-mail: [email protected]: www.cbs.knaw.nlCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c