Modeling - Collaboration and Release Policy
The Consortium's computational modeling activities comprise a wide spectrum of quantitative approaches that include correlative, systems and physical-chemical models. The centerpiece is an intimate connection between the modeling and the experimental data. For this reason, most of the models are being developed in collaboration with other laboratories, many of which reside outside the Consortium. At this time, the choice of phenomena to model lies with the individuals in the initiative. However, their choice of activity often is limited by the availability of quantitative data describing a phenomenon. Please feel free to contact us if you are generating quantitative, migration related data, the understanding of which could require computer modeling. The data might be useful for activities either planned or in progress, or alternatively, they could result in collaboration for the development of a new model. If you have developed a new model and wish us to assist in publicizing it, we will list your model on our web site. If you are developing a model similar to any of those on our list, please contact us (see below) so that we can coordinate to avoid overlap or duplication of effort.
The Consortium will make the details of the models, .e.g. algorithms or code, available on this web site. The Consortium will also make available key modeling data, when the model is published. Otherwise we can provide a link to the laboratory that generated the data. The Virtual Cell (www.nrcam.uchc.edu) is one of our main modeling venues. It is a web-based application that includes a centrally stored database of models and model components, permitting users to share models and make them publicly accessible. It is designed to allow biologists with little training in physics and mathematics to engage in computational cell biology and construct complex spatial models of biological processes.
- Doug Lauffenburger - [a] bioinformatics-based models relating cell phenotypic behavioral responses to intracellular signals generated by extracellular ligand cues; [b] biophysics-based models for trajectories of cells migrating through three-dimensional matrices, generating predictions of speed and direction movement properties.
- Les Loew - differential equation models of adhesion and cell signaling with emphasis on developing a user-friendly software.
- Alex Mogilner - biophysical modeling of protrusion, contraction and adhesion of cytoskeletal gels and computational integrative models of mechanochemistry of simple shaped cells.
