Registration for Workshops is closed. See you Wednesday!
Workshop 1 Workshop 2 Workshop 3 Workshop 4 Workshop 5 Workshop 6 Workshop 7
Workshop 1:
Integrative Cancer Biology Program
Date: Sunday, October 23rd, 2005
Time: 9:00am-5:00pm
Tomas Radivoyevitch
This workshop will provide an introduction to integrative cancer biology (ICB), a field which strives to develop predictive, mechanistic, mathematical models of cancer relevant biological processes. The models couple computational biology, informatics and wet lab experiments to study cancer at the levels of molecules, cells, tissues, organs, individuals and populations. The aims of this workshop are to exchange data and models, to initiate new collaborations, and to discuss and debate various modeling assumptions, inferences and applications. For each session listed below, slides, abstracts, manuscripts, data, models, and R scripts will be provided (where available) 4 weeks prior to the workshop date through a supplementary website http://epbi-radivot.cwru.edu/ICSB2005/ . The R scripts will be described in the final workshop session for those who are interested in implementation details; such attendees should bring their laptops pre-loaded with R, the scripts and the data.
| 9:00 AM | Introduction to NCI's Integrative Cancer Biology Program | Dan Gallahan National Cancer Institute |
| 9:30 AM | Two different ICB approaches to therapeutic gain | Tom Radivoyevitch Case Western Reserve University |
| 10:00 - 10:50 AM | DNA repair and p53/Mdm2/ATM | Herbert Sauro and Vijay Chickarmane Keck Graduate Institute |
| Break | ||
| 11:10 AM - noon | Transcriptional subnetworks from limited expression data | Debopriya Das Lawrence Berkeley National Lab |
| Lunch | ||
| 1:00 PM - 2:00 PM | Tumor growth dynamics | Lynn Hlatky Tufts University |
| 2:00 PM - 3:00 PM | Dynamics of chronic myeloid leukemia | Franziska Michor Harvard University |
| Break | ||
| 3:15 PM - 4:15 PM | Biologically-based risk modeling | Georg Luebeck Fred Hutchinson Cancer Research Center |
| 4:15 PM - 5:15PM | Implementations of analyses in R | Tom Radivoyevitch Case Western Reserve University |
icbp.nci.nih.gov/icbp/edu_outreach/events
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Workshop 2:
Systems Biology Markup Language (SBML)
Date: Sunday, October 23rd and Monday October 24th, 2005
Time: 9:00am-5:00pm
Mike Hucka
Following the tradition of past SBML Forum meetings, this will be a working meeting of the SBML community aimed at enhancing research communication and software interoperability through SBML. Potential attendees are cautioned not to expect any tutorials about SBML itself, and are referred to the documents at sbml.org/documents and the sbml-discuss mailing list for questions of a more basic nature about SBML. All presentations and discussions at this meeting will focus on detailed technical matters concerning SBML, its use, development and evolution, and related software and standards.
For more information and registration:
www.sbml.org/workshops/tenth/
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Workshop 3:
Yeast Systems Biology
Date: Sunday, October 23rd, 2005
Time: 9:00am-5:00pm
Stefan Hohmann
The Yeast Systems Biology Network ( www.ysbn.org) has been started two years ago with the aim to bring experimental and theoretical researchers together. The goal of YSBN is to build the infrastructure and environment to drive systems biology with the crucial model system yeast, S. cerevisiae. The long-term vision is to generate whole-cell computational models of the yeast cell. While this goal is already achievable for low resolution network models, the whole-cell model decribing the dynamics of cell processes is still an ambitous goal. YSBN has just received a 1.3 million Euro grant from the EC to build the infrastructure, i.e. databases, web resources and standards that are need both for data and modelling generation.
For more information and registration:
www.ysbn.org
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Workshop 4:
Systems level studies of model microbial cells: What do we need and how can
we do it?
Date: Sunday, October 23rd, 2005
Time: 9:00am-1:00pm
Barry Wanner & Hans Westerhoff
The contrast between our tremendously increased computational and biological powers and technologies on the one hand, and our continuing lack of understanding of any whole cell on the other, has been the major inspiration for the formation of the IECA – the International E. coli Alliance (Holden, 2002. Science 297: 1459-60). The IECA effort is emblematic of systems biology as a whole. The ambitious goal of the IECA is beyond the means of any single investigator or laboratory. It requires an integrative research program and collaborations between scientists with expertise in biology, chemistry, computer sciences, engineering, mathematics and physics. Success will depend crucially on bringing to bear both social and technological tools: namely, consortia that help forge collaborations and common understanding, computational tools that permit analysis of vast and complex data, and agreed-upon standards and tools that enable researchers to communicate, integrate, and use their results in practical and unambiguous ways.
Understanding a living cell will require concerted efforts on many fronts. We need new software tools and modeling that can facilitate interactions and collaboration among diverse groups. We need enabling technology to share these models. We need standardization and ways to carry out standardized experiments in different groups and locations. We need new databases that are readily accessible and interoperable that would not only store massive amounts of data in different formats but would have the capability of interrogating other meaningful databases. We need biological resources, strains of different kinds, measurement technologies, high-throughput detection systems for different biomolecules. We need ways that not only the "big" groups can participate but also smaller groups can contribute as well. The goal of this workshop will be to present examples in these areas and to help formulate a plan for moving forward in model organism systems biology. When appropriate, examples will be taken from studies with different microbial systems, both bacteria and single-cell eukaryotes.
Download agenda here
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Workshop 5:
Systems Biology of Receptor Tyrosine Kinases
Date: Sunday, October 23rd, 2005
Time: 9:00am-2:00pm
Boris Kholodenko, Steven Wiley and Mariko Hatakeyama
Receptor tyrosine kinases (RTKs) are central components of cell signaling networks and play crucial roles in normal physiological processes, such as embryogenesis, cell proliferation and cell death. However, it is difficult to gain in-depth understanding of RTK networks because of their enormous complexity and multiplicity. Systems biology provides novel and promising approaches to improve our understanding of RTK networks.
This workshop is held under the auspices of the International Consortium on Systems Biology of RTK Regulatory Networks (RTK Consortium). The goal of the Consortium is to encourage the application of Systems Biology for quantitative analyses of RTK signaling networks and to develop predictive models, with particular emphasis on interception by pharmacological agents.
| 9:00-9:15 | Introduction Yoshiyuki Sakaki, RIKEN Genomic Sciences Center, Japan. |
| 9:15-9:30 | Intracellular gradients of signaling activities: a distinction between electronic and living circuitry. Boris N. Kholodenko, Thomas Jefferson Univ., USA. |
| 9:30-10:15 | TBA. Joseph Schlessinger, Yale University School of Medicine, USA |
| 10:15-10:30 | Break |
| 10:30-11:00 | The EGFR System Couples Cell Response to Context. Steven Wiley, Pacific North West National Laboratory, USA. |
| 11:00-11:30 | TBA. Walter Kolch, Beatson Institute for Cancer Research, UK. |
| 11:30-11:45 | Temporal encoding of ERK activation. Shinya Kuroda, University of Tokyo, Japan. |
| 11:45-12:00 | Break |
| 12:00-12:15 | Mathematical modeling of the mammalian ErbB signaling network—reduction of combinatorial complexity and analysis of ligand-dependent responses. Marc R Birtwistle, University of Delaware, USA. |
| 12:15-12:30 | A dual role of Gab1 in EGF-induced signaling. Nick Markevich, Thomas Jefferson University, USA. |
| 12:30-12:45 | Structural and modular analysis of RTKs signaling pathways. Julio Saez Rodriguez, Max-Planck-Institute for Dynamics of Complex Technical Systems, Germany. |
| 12:45-13:15 | TBA. Hiroaki Kitano, Sony Computer Science Laboratories, Inc, Japan. |
The organizational meeting of the RTK Consortium was held at RIKEN Genomic Sciences Center in Yokoyama, Japan on January 17-19, 2005. This workshop aims at developing an effective agenda to implement its goals. The meeting will be held from 9:00 to 14:00 and include oral and poster presentations by current Consortium members and other interested investigators, followed by an extended discussion.
For more information and registration:
www.rtkconsort.org/
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Workshop 6:
Gene network models and their applications: From gene function to drug discovery
Date: Sunday, October 23rd, 2005
Time: 10:00am-5:00pm
Diego di Bernardo
One of the grand challenges in the future of genomics research has been recently described by Collins and colleagues: the need to develop "computational and experimental methods to detect gene-gene and gene-environment interactions" for identifying the genetic contributions to disease and drug response. Scientists have been successful in cataloguing genes through genome sequencing projects, and we can now generate vast quantities of gene expression data using microarrays. However, the scientific community has had far less success in understanding how genes and proteins are connected and operate within networks. When a cell is perturbed (whether by a drug or in a disease state), it is important to understand how it will respond in terms of gene expression and protein interactions.
Preliminary Agenda:
D. di Bernardo, TIGEM, Naples, Italy
Prof. G. Church, Harvard University, Boston, USA
T.S. Garder, Boston University, Boston, USA
A. Califano, Columbia University, New York, USA
E.P. Van Someren, TU Delft, Netherlands
1:30 Lunch break
A. Hartemink, Duke University, USA (to be confirmed)
T. Ideker, University of California - San Diego, USA
4:10 Coffee break
C Maranas, Penn State Univeristy, USA
P. Lio, Cambridge University (to be confirmed)
For more information:
genet2005.tigem.it
Registration is closed.
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Workshop 7:
Vertically Integrated System Modeling
Date: Sunday, October 23rd, 2005
Time: 9:00am-12:00pm
Sylvia Nagl and Manish Patel
One of the central questions of systems biology is how integrated genome-wide networks produce robust whole cell behaviour. Biomolecular networks are located midway between the genome and the phenome, and can be conceptualised as an 'extended genotype' or 'elementary phenotype'. Thus, networks provide a steppingstone to the integrative study of gene function in complex living systems. To study the function of genes, it is necessary (i) to interpret their expression dynamics (at the level of the transcriptome and the proteome) within the context of gene regulatory and protein interaction networks, and (ii) to go beyond network topology and address the global dynamics of networks that will reveal the collective behaviour of the interacting gene products. These aims require advanced statistical analysis and mining of the large amounts of data on genome activation obtained through -omic technologies to be integrated with mathematical modeling of metabolic and signaling network dynamics.
The SCIpath project - A particular challenge is posed by the need for software tools that can effectively visualize, analyze and model both the functional and dynamic relationships between genome structure, expression and dynamic cell processes. Integrative in silico environments are needed that can jointly deploy data mining tools and mathematical modeling of pathway and cell dynamics. This vision lies at the heart of the Systems Complexity Interface for pathways (SCIpath) project which delivers an object-oriented framework acting as an integrative hub together with new data mining, modeling and visualization tools and SBML-enabled software connectivity. SCIpath can be thought of as a toolkit of many different visualization and analytical Java programs and a medium through which these programs can communicate, share information and visualizations. SCIpath is specifically designed to facilitate exploitation of vertically integrated (multi-scale) datasets generated by systems biology which may include karyotypic, transcriptomic, proteomic and quantitative cell physiology data. SCIpath links to Systems Biology Workbench-powered simulator modules (e.g., Virtual Cell, E-Cell, Gepasi) for dynamic network modeling.
For more information, please go to www.scipath.org.uk
Preliminary agenda:
-
1. Introduction (Powerpoint presentation): Vertically integrated systems modelling – the scientific
promise and the informatics challenge (20 min)
- a. Software demonstration 30 min
- b. Guidelines for programmers 20 min
- a. Case study: Systems biology at the frontline - treatment resistance in cancer
- a. Networking and collaboration
- b. Method and tool development
- c. Collaborative generation of multi-scale datasets, frequently sampled over appropriate timeframes - potential focus: DNA damage response in cancer
- d. Standardization of experimental protocols, data quality, standards and exchange formats for multi-scale data
- e. A summary of the discussion will be made available on the web
2. Software demonstration: The SCIpath project (50 min)
4. Vertically integrated systems modelling and the future of drug discovery (30 min)
6. Discussion: How can we take vertically integrated modelling forward as a community? (50 min)
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