Dr Vincent Robert - EU BOLD Mirror & Fungal Barcoding
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  • 1. EU BOLD Systsem & BioloMICS SoftwareEU BOLD SYSTEM & BIOLOMICSSOFTWAREVincent Robert, v.robert@cbs.knaw.nl CBS-KNAW 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 analyzes BioloMICS 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 centre BioAware 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. Szoke B. Jabas E. Blom Utrecht, The Netherlands Hannut, Belgium S. Ben Daoud A. Ben Hadj Amor O. Chouchen M. Jaidane A. Dridi N. van de Wiele Sousse, Tunisia Sydney, Australia CBS-KNAW fungal biodiversity centre BioAware 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 centre BioAware 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 BIOLOMICS SOFTWARE EXAMPLE STRUCTURE OF A GIVEN COLLECTION DATABASE (COMPLETELY FLEXIBLE AND MODIFIABLE) Bibliography Taxon Files tables table names table … Strains table containing a number of fieldsDatabase of a collection DNA Sequence s table Stock Propertie Host managemen s table table t table CBS-KNAW fungal biodiversity centre BioAware 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 table Taxon names table … Strains table containing a number of fields Database of a collection DNA Sequences table P r o H p o e s rt t i Stock management table t e a s b t l a e b l e CBS-KNAW fungal biodiversity centre BioAware 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 application Connections between (n) collections(usually MS-Windows based) specific databasesTo manage and analyze data B i b l i o T a x o n(for curators and local researchers) g n Ot r a her a m tab p e les h s … y t t a a b b l l e e Strains table containing a number of fields D Database of a collection N A S e q u e n S c t e o s c P k r t o a m p H b a e o l n r s e a t t g i e e t m s a e b n t l t a e b t l a e b l e T Bi a bl x io o gr n Other a n table p a s h m … y e ta s bl ta e bl e Strains table containing a number of fields D N Database of a collection A S e q u e n c e St P s o r c o t k p H a m e o b a r s l n t t e a i g e t e s a m b e t l nt a e ta b bl l e e T Bi a bl x io o gr n Other a n table p a s h m … y e ta s bl ta e bl e Strains table containing a number of fields D N Database of a collection A S e q u e n c e St P s o r c o t k p H a m e o b a r s l n t t e a i g e t e s a m b e t l nt a e ta b bl l e e CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c
  • 16. Internet publication, availability and analyzes of data via specific websitesCollection specific website Collection specific database Other tables Bibliography table Taxon names table … Strains table containing a number of fields Database of a collection DNA Sequences table P r o H p o e s rt t i Stock management table t e a s b t l a e b l e CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c
  • 17. 4. DATABASE MANAGEMENT AND ANALYZES BIOLOMICS SOFTWARE Direct update and availability of data via both desktop application and Internet based application (website)Desktop application Connections 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 collection u 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 collection u 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 collection u 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 group Scientific return on investment and/or collaborations Short & Long termLarge investments Financial 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 (several remote sequence databases; from www.q- bank.eu)• Fungal Barcoding (future EU BOLD mirror; from www.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, infor mation systems and their applications , CBS, The Netherlands, robert@cb s.knaw.nl 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 (several remote sequence databases; from www.q- bank.eu)• Fungal Barcoding (future EU BOLD mirror; from www.fungalbarcoding.org)• Polyphasic Identification (from www.q-bank.eu) CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c
  • 38. THERMOREGULATIONEXAMPLE 1 0.9 0.8 0.7 Total number of strains 0.6 0.5 0.4 0.3 0.2 0.1 0 1 3 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 centre BioAware 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 NetherlandsUniversität für Bodenkultur, Vienna, Austria… CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c
  • 40. 3 SOLUTIONS• Deposit data on default database (free display and upload to BOLD)• User defined structure (Submitted to curators for approaval) and data submitted to curator via website, no access to BioloMICS plateform (free display and upload to BOLD)• User defined structure, access via BioloMICS plateform using Citrix XenApp (not free) CBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c
  • 41. CONTACT Vincent Robert Head of Bioinformatics group Centraalbureau voor Schimmelcultures CBS-KNAW Fungal Biodiversity Center Address: 8 Uppsalalaan, 3584CT Utrecht, The Netherlands Tel: +32(0)478 28 57 64 E-mail: v.robert@cbs.knaw.nl Web: www.cbs.knaw.nlCBS-KNAW fungal biodiversity centre BioAware Company, www.bio-aware.c