DIALing the IBIVU Vrije Universiteit Amsterdam Jaap Heringa Centre for Integrative Bioinformatics VU (IBIVU) Faculty of Sciences / Faculty of Earth and Life Sciences Free University, Amsterdam, The Netherlands

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

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

The IBIVU

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

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

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

Direction Theme Ecogeno mics Centre Centre for Medical Systems Biology Central FEW/ FALW VUMC Microarray facilities* VUMC Brain Imaging Centre* Systems Biology* 1. Sequence-Structure-Function relationships XXXXX 2. Computation & tool creation XXXXXX 3. Data/method/model integration XXXXXX 4. Comparative genomics / gene prediction XXXXX 5. Network modeling XXXXX 6. Vertical (integrative) genomics XXXXX 7. Integrative visualisation XXXXXX 8. Gene expression (microarray) analysis XXXXX 9. Biostatistics XXXXX 10. Biomolecular informatics (meso scale) XXX 11. Silicon cell (E-cell) XXX 12. Bacterial informatics XXX 13. Tumor informatics XXXX

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

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

Centre for Integrative 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

Wider Centre for Integrative Bioinformatics Will include more than 16 research groups supporting: 1.Research directions (e.g. CMSB, Ecogenomics (inter)national initiatives) 2.Contributed projects (at VU faculty level) 3.Small external projects (partially embedded within IBIVU)

Theme Integrative Visualisation Porting and developing SaraGene The SARAThe VU

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.

Data Integration, Analysis and Logistics IBIVU Biostatistics –Plans completed (Aad van der Vaart) –Postdoc Systems Biology-directed integrative bioinformatics –Postdoc