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