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July 2010

12 participants
12 discussions

Workshop "Modeling Angiogenesis: Joining Cells, Maths and Computers", Lorentz Center, Leiden, Netherlands
by Roeland Merks 07 Jul '10

07 Jul '10

Modeling Angiogenesis: Joining Cells, Maths and Computers Lorentz Center, Leiden, the Netherlands, 4th-8th October Registration at: http://www.lorentzcenter.nl/lc/web/2010/407/info.php3?wsid=407 Scientific organizers: R.M.H. Merks (NISB / CWI, Netherlands) E. Giraudo (IRCC Torino, Italy) P. Koolwijk (VU University Medical Center, Netherlands) B. Ribba (INRIA Grenoble, France) The outgrowth of new blood vessels from pre-existing vessels, called angiogenesis, is a crucial step in myriad physiological and pathological mechanisms. Unfortunately, the complicated causes and effects of angiogenesis make it very difficult to control. Computational models and simulations help unravel both the basic mechanisms of angiogenesis and can help identify the steps in the mechanisms most amenable to intervention. A wide range of mathematical and computational models range from is currently available. Single cell-based models predict how vascular-like patterns follow from the behaviors and interactions of individual endothelial cells. Many discrete models describe the branching conditions of blood vessels, and predict the morphology of vascular trees near tumors. Continuum models often focus at the tissue level, and describe densities of blood vessels rather than individual vascular structures. Despite the biological insights these mathematical models have produced, modeling rarely finds application in experimental angiogenesis research yet. Why is that? One reason is a different focus: experimental and pharmaceutical research necessarily focus on the molecular level, whereas most angiogenesis models take single interacting endothelial cells or vessel branches as the smallest units of their models. Another reason is the lack of predictive, quantitative models and the required quantitative experimental data to feed such models. We will need models that bridge organizational scales, by showing how molecular intervention modifies the behavior of endothelial cells and, consequently, changes the dynamics of angiogenesis. Our workshop will host both experimental researchers and computational models working in vascular biology, endothelial cell biology, angiogenesis, and pharmaceutics. We will a) identify the requirements for computational models to make a true impact in basic angiogenesis research, tissue engineering and drug innovation, b) inventarize pre-existing and missing components of such a model, and c) discuss how we can couple such components. Monday, 4th October, State of the art of angiogenesis research 09.00 – 10:00 Registration and coffee 10:00 – 10:15 Welcome by Lorentz Center and the organizers 10:15 – 11:15 Lecture: Thomas Sato; Discussant: James Glazier 11:15 – 12:15 Discussion: Arjan Griffioen and Roeland Merks Available in vitro and in silico models 12:15 – 13:30 Lunch and informal discussions 13:30 – 14:30 Lecture: Aleksander Popel; ; Discussant: Thomas Sato 14:30 – 15:30 Poster flash presentations 15:30 – 16:00 Coffee break 16:00 – 17:00 Lecture: András Czirók; ; Discussant: Aleksander Popel 17:00 – 19:00 Wine and Cheese party with poster session Tuesday, 5th October, Characterizing and modeling endothelial cell behavior 09:30 – 10:30 Lecture: Andrea Gamba; Discussant: Cynthia Reinhart-King 10:30 – 11:00 Coffee break 11:00 – 12:00 Lecture: Cynthia Reinhart-King; Discussant: Andrea Gamba 12:00 – 13:30 Lunch and informal discussions 13:30 – 16:00 Tutorial: András Czirók Extracting and analyzing quantitative information for time-lapse microscopy, aimed at modelers 16:00 Departure by conference bus to the boat 16:30 – 20:30 Boat trip on Kaag Lakes and Conference Diner Wednesday, 6th October, Integrating cell behavior to explain angiogenesis 09:30 – 10:30 Lecture: James Glazier; Discussant: Peter Friedl 10:30 – 11:00 Coffee Break 11:00 – 12:00 Lecture: Peter Friedl; Discussant: András Czirók 12:00 – 13:30 Lunch and informal discussions 13:30 – 14:30 Lecture: Federico Bussolino; Discussant: Mats Karlsson 14:30 – 16:00 Tutorial: Systems Biology Toolbox 2 / SBPOP by Henning Schmidt, Novartis Pharma, Basel 16:00 – 16:30 Coffee Break 16:30 – 17:30 Keynote lecture: Peter Carmeliet Thursday, 7th October: Applications to drug development 09:30 – 10:30 Lecture: Zvia Agur; Discussant: Pascal Girard 10:30 – 11:00 Coffee Break 11:00 – 12:00 Discussion: Benjamin Ribba, INRIA, France; Discussant: Iñaki Troconiz Preclinical tumor growth models and requirements for angiogenesis models in drug development 12:00 – 13:30 Lunch and informal discussions 13:30 – 16:00 Tutorial: Maciej Swat Cell-based angiogenesis modeling with CompuCell3D, aimed at experimental biologists 16:00 – 16:30 Coffee break 16:30 – 17:30 Lecture: Paolo Magni; Discussant: Enrico Giraudo Friday, 8th October: Applications to tissue engineering 09:30 – 10:30 Lecture: Victor van Hinsbergh; Discussant: Roeland Merks 10:30 – 11:00 Coffee Break 11:00 – 12:00 Lecture: Hans Van Oosterwyck; Discussant: Pieter Koolwijk 12:00 – 13:30 Lunch and informal discussions 13:30 – 14:30 Lecture: Marco Harmsen; ; Discussant: Hans van Oosterwyck 14:30 – 15:00 Coffee break 15:00 – 16:00 Discussion: Hans Van Oosterwyck; ; Discussant: Victor van Hinsbergh Requirements for a computational angiogenesis model in tissue engineering 16:00 – 17:00 Wrap up: Pieter Koolwijk and Roeland Merks, Summary of findings ----- Roeland M. H. Merks Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde & Informatica (CWI) Science Park 123, 1098 XG Amsterdam, The Netherlands Mailing address: P.O. Box 94079, 1090 GB Amsterdam CWI Office Room M246 Roeland.Merks(a)sysbio.nl / Roeland.Merks(a)cwi.nl http://www.cwi.nl/~merks Phone +31 20 592 4117 Fax +31 20 592 4199

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Comp Biol Postdoc , Amsterdam, The Netherlands
by Lodewyk Wessels 04 Jul '10

04 Jul '10

POSTDOCTORAL COMPUTATIONAL BIOLOGIST (NKI-AVL and the VU University, Amsterdam, The Netherlands) COMPUTATIONAL MODELING OF SIGNALING AND REGULATORY PATHWAYS IN Th17 DIFFERENTIATION Lymphocytes are central in the regulation of immune response. T-lymphocytes differentiate into functionally distinct subsets. Proper regulation of the balance between various subsets is crucial for an optimal immune system and for host defense against pathogens and cancer. Recently, a new T-cell subset, Th17, which plays a central role in host defense, was discovered. In this project, our aim is to identify the underlying regulatory mechanisms and molecular networks that govern the formation of Th17 cells. We will achieve this by generating comprehensive datasets and performing state-of-the art computational modeling based on these data. The data sets will include time series RNA and miRNA expression data, siRNA perturbation experiments based on kinome and phosphatome libraries, (phospho)protein expression and Chip-Seq data. To construct the computational models, we will build both data-driven machine learning models and knowledge-driven (logical and Petri-net) models of the regulatory networks. Our aim is to fuse the results of these two approaches to obtain a single, hybrid model. Computational predictions of key control mechanisms will be tested experimentally and the resulting data will be employed to refine the models. The successful candidate will be primarily responsible for constructing models of the regulatory Th17 developmental networks, developing new computational methodologies where required and liaising with the computational and biological partners in this project. EMPLOYER INFORMATION The Netherlands Cancer Institute is a dedicated cancer center conducting research in all major areas of cancer, with a strong emphasis on translational research. The Bioinformatics and Statistics group provides leadership on the collection and analysis of data for the research programs of the institute, by developing novel compuational approaches and performing state of the art analyses of a wide array of data types, including laboratory and animal experiments, clinical trials, and epidemiologic studies. The Centre for Integrative Bioinformatics (IBIVU) is a broad-based research centre at the VU University that is carried by the Faculty of Sciences (FEW) and the Faculty of Earth and Life Sciences (FALW) with strong endorsement from the University Board. Its main missions are carrying out a strong and internationally competitive research program in Integrative Bioinformatics with an additional focus on Systems Biology, and providing an excellent educational program at bachelor and master level; the latter including two-year international master's programmes in Bioinformatics and in Systems Biology. REQUIREMENTS The vacancy is a research position within the field of bioinformatics/computational biology and the research will be carried out in close collaboration with the involved partners. The ideal candidate has a background in bioinformatics, computer science, statistics, physics, or biology, strong algorithmic and/or machine learning skills, and experience with the analysis of high-throughput data. EMPLOYMENT CONDITIONS The temporary employment will be for a period of three years. The gross monthly salary for a Postdoc will range from ? 3140,- to ? 3.495,- and depends on previous experience. We can help you find housing. The NKI-AVL has been listed in the top 25 of 'Best Employers' in 2009 offering a specialized cancer research institute and hospital with good working conditions and an excellent atmosphere. INTERESTED? To apply, and for further information please contact Lodewyk Wessels, tel.: +31-20-5127987, e-mail: l.wessels(a)nki.nl or Jaap Heringa, tel.: heringa(a)few.vu.nl +31 20 59 87649 (direct) or +31 20 59 87483 (secr.) CLOSING DATE 1 July 2010 L.F.A.Wessels, Ph.D Bioinformatics and Statistics The Netherlands Cancer Institute Plesmanlaan 121, 1066 CX Amsterdam The Netherlands Tel: +31 (0)20 5127987 Fax: +31 (0)20 6691383 Mobile: +31 (0)634485714 http://bioinformatics.nki.nl/

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