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DIALing the IBIVU

Vrije Universiteit Amsterdam. DIALing the IBIVU. Jaap Heringa Centre for Integrative Bioinformatics VU (IBIVU) Faculty of Sciences / Faculty of Earth and Life Sciences Free University, Amsterdam, The Netherlands heringa@cs.vu.nl; http://ibivu.cs.vu.nl.

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DIALing the IBIVU

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  1. Vrije Universiteit Amsterdam DIALing the IBIVU Jaap Heringa Centre for Integrative Bioinformatics VU (IBIVU) Faculty of Sciences / Faculty of Earth and Life Sciences Free University, Amsterdam, The Netherlands heringa@cs.vu.nl; http://ibivu.cs.vu.nl

  2. The Centre for Integrative Bioinformatics VU (IBIVU) Vrije Universiteit Amsterdam

  3. Bioinformatics at the VU Core Bioinformatics Section and Integrative Bioinformatics Institute VU (IBIVU) • Two founding faculties (FEW, FALW) • Towards including three faculties (FEW, FALW, FPP) and VUMC • Expertise covering Mathematics (statistics /stochastics), AI (machine learning), (Theoretical) Biology, Molecular Biology/Medicine and Bioinformatics • Embeds a number of national and international initiatives

  4. The IBIVU

  5. The IBIVU

  6. The IBIVU

  7. What kind of bioinformatics research at the IBIVU • Integrative bioinformatics • Integrate expertise: Mathematics (statistics), HTP computing, AI, Machine learning, (Molecular) biology, Genomics, Clinical medicine, etc. • Integrate data (e.g. vertical genomics), models and methods • Integrate tool creation and experimental validation • Tools directed bioinformatics • strong embedding in computer science (FEW Computer Science Department) Both components give the IBIVU a competitive edge

  8. IBIVU organisation VU-Board (CvB) Vrije Universiteit Governing Board dean FALW | dean FEW Directorate Director | co-director Executive committee Thematic Committee chair persons ThematicExecutive Committees

  9. IBIVU advisory structure Industrial Platform IBIVU Assembly Management Advisory Committee Board (CvB) Vrije Universiteit Bsik Ecogenomics Scientific Advisory Committee Governing Board dean FEW/FALW CMSB Scientific Director | co-director Executive committee IOP-Genomics NWO, STW, EU Thematic Committees

  10. Current core bioinformatics group @ Informatics Dept. • Victor Simossis (PhD) • Radek Szklarczyk (PhD) • Mischa Sammeth (temp.)(PhD) • John Romein (Postdoc) • Jens Kleinjung (UD) • Jaap Heringa

  11. Tools-directed research in the IBIVU core Bioinformatics Section • Integrating external information (e.g. predicted secondary structure) and Multiple Sequence Alignment • Genomic and protein internal repeats detection • Repeats-filtered multiple sequence alignment • Energy-based protein fold recognition (threading) • Integrative homology searching (function-biased and knowledge biased searching) • Structure-based alignment and alignment verification

  12. Centre for Integrative Bioinformatics@ Faculty of Sciences + Faculty of Earth and Life Sciences • Includes: • 2 professors • 3 group leaders • 2.4 assistant professors • 2.5 postdocs • 1 PhD student

  13. Wider Centre for Integrative Bioinformatics • Will include more than 16 research groups supporting: • Research directions (e.g. CMSB, Ecogenomics (inter)national initiatives) • Contributed projects (at VU faculty level) • Small external projects (partially embedded within IBIVU)

  14. Theme Integrative Visualisation Porting and developingSaraGene The CAVE @ SARA The ICwall @ VU

  15. SaraGene • 3D visualisation important for large genomic data sets: • Clustering and mapping genes onto location, expressome, metabolome, etc. • Many data objects (labels): need 3D to place objects and high resolution to read labels • CAVE has good 3D but low resolution (e.g. labels not easily readable) • ICwall has bit less 3D capability but much higher resolution.

  16. Data Integration, Analysis and Logistics(DIAL) @ IBIVU • Biostatistics • Plans completed (Aad van der Vaart) • Postdoc • Systems Biology-directed integrative bioinformatics • Postdoc

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