Post on 13-Jan-2016
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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 Netherlandsheringa@cs.vu.nl; http://ibivu.cs.vu.nl
The Centre for Integrative Bioinformatics VU (IBIVU)
Vrije Universiteit Amsterdam
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
The IBIVU
The IBIVU
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 Boarddean FALW | dean FEW
VU-Board (CvB)Vrije Universiteit
DirectorateDirector | co-director
Executive committeeThematic Committee chair persons
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
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
Current core bioinformatics group @ 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 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
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 CAVE @ SARA The ICwall @ 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 (DIAL) @ IBIVU
• Biostatistics– Plans completed (Aad van der Vaart)– Postdoc
• Systems Biology-directed integrative bioinformatics– Postdoc