dialing the ibivu vrije universiteit amsterdam jaap heringa centre for integrative bioinformatics vu...
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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 [email protected]; http://ibivu.cs.vu.nl
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The Centre for Integrative Bioinformatics VU (IBIVU)
Vrije Universiteit Amsterdam
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Bioinformatics at the VUCore Bioinformatics Section andIntegrative 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
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The IBIVU
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The IBIVU
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The IBIVU
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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
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IBIVU organisation
ThematicExecutive Committees
Governing Boarddean FALW | dean FEW
VU-Board (CvB)Vrije Universiteit
DirectorateDirector | co-director
Executive committeeThematic Committee chair persons
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IBIVU advisory structure
ManagementAdvisory Committee
Governing Boarddean 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
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Direction
Theme
Ecogenomics
Centre
Centre for Medical Systems Biology
Central FEW/
FALW
VUMC
Microarray facilities*
VUMC Brain Imaging Centre*
Systems Biology*
1. Sequence-Structure-Function relationships
X X X X X
2. Computation & tool creation X X X X X X3. Data/method/model integration X X X X X X4. Comparative genomics / gene prediction
X X X X X
5. Network modeling X X X X X6. Vertical (integrative) genomics X X X X X7. Integrative visualisation X X X X X X8. Gene expression (microarray) analysis
X X X X X
9. Biostatistics X X X X X10. Biomolecular informatics (meso scale)
X X X
11. Silicon cell (E-cell) X X X12. Bacterial informatics X X X13. Tumor informatics X X X X
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Current core bioinformatics group @ Informatics Dept.
• Victor Simossis (PhD)• Radek Szklarczyk (PhD)• Mischa Sammeth (temp.)(PhD)
• John Romein (Postdoc)
• Jens Kleinjung (UD)
• Jaap Heringa
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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
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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
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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)
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Theme Integrative Visualisation
Porting and developing SaraGene The CAVE @ SARA The ICwall @ VU
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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.
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Data Integration, Analysis and Logistics (DIAL) @ IBIVU
• Biostatistics– Plans completed (Aad van der Vaart)– Postdoc
• Systems Biology-directed integrative bioinformatics– Postdoc