AfCS > AfCS laboratories > Data Modeling and Network Analysis Laboratory
ALLIANCE FOR CELLULAR SIGNALING
DATA MODELING AND NETWORK ANALYSIS LABORATORY
University of California
Berkeley, CA
Overview
The primary goal of the Alliance for Cellular
Signaling (AfCS) Data Modeling and Network Analysis (DMNA) Laboratory is to
build model-based tools to facilitate extraction and testing of hypotheses about
how signals propagate in the large-scale signaling networks of interest to the
AfCS. There are two main subtasks of the laboratory:
- 1. the data modeling effort is designed to
extract key features of the data that should be predicted from network models
and to infer new interactions among network components from the data; and
- 2. the network analysis effort is designed to deeply curate legacy
information about the signal transduction pathways into computable models of
network dynamics that can be directly compared to the AfCS data.
The laboratory will provide innovative methods for
quantifying the consistency of the experimental observations with the network
model and for ranking models of alternative hypotheses. The results of these
analyses will be to enumerate the parts of the model that are either
unconstrained by the data (meaning there is not enough data to know if the model
is correct in that area) or are inconsistent with the data. The laboratory will
develop formal and informal methods for optimal experimental design to
discriminate between alternative network hypotheses and to clear up
inconsistencies or critical under-constraint in the model. In collaboration with
other AfCS laboratories, these suggestions will then be used to direct new
experiments.
This effort is critical to understanding signal
flows in these networks. The number of network constituents and their
interactions and the complexity of the data being collected is such that
reasoning about these networks without model-based computational tools will be
difficult at best. Models and data analyzed by the DMNA Laboratory will be
summarized on the AfCS Web site.
Staff
Alliance for Cellular Signaling
Data Modeling and Network Analysis Laboratory
University California
1 Cyclotron Road, MS3-144
Berkeley, California 94720
Phone: 510-495-2116
Fax: 510-486-6059
| Director | Adam Arkin, Ph.D. |
| Lead Programmer | Alex Gilman, Ph.D. |
| Graduate Student | Keith Erickson |
| Graduate Student | Patrick Flaherty |
| Graduate Student | Matthew Onsum |
| Data Manager | Janet Jacobsen |
| Lab Administrator | Gwyneth Terry |
| Consultant | Michael Frenklach |
| Consultant | Andrew Packard |
| Consultant | John Doyle |
Slide Presentations from May 23-26, 2004, AfCS Annual Meeting
Goals for Year 5 (9/04-8/05)
- Extension of the Pathway Builder pathway knowledge representation and
modeling tool for more efficient representation of AfCS pathways.
- Connection of Pathway Builder to the bioinformatics core's molecule page
database.
- Completion of C5a, UDP/UTP, and FcGamma receptor models and the macrophage
calcium dynamics model.
- Comparison of model to ligand screen, dose-response, and siRNA data
currently available in the laboratory.
- Begin development of models of the other receptors and more of the PIP3
module.
- Continue development of parameter estimation, model sensitivity, and model
invalidation tools.
- Communication of results to the wider AfCS and scientific
communities.
