Background

Building a functional simulation of tissue, organ or even an entire organism requires an unprecedented effort to fuse techniques derived from biology, chemistry, physics, computer science and information science. Developing models that can be explored using a range of different simulation techniques requires a common language capable of describing heterogeneous features and behaviors at various scales ranging from molecule to organism.

While languages exist for some necessary subareas (e.g. cell physiology and molecular dynamics), many researchers still use ad-hoc formats and vocabulary to describe cell-based multi-cell models (e.g. Cellular Potts Models, Center Models, FEM). What these models do have in common is that they all describe cellular behaviors and how those behaviors give rise to emergent phenomena (e.g. tumor growth or choroidal neovascularization).

In order to standardize the way multi-cell models are described we have to first be able to unambiguously describe cellular behaviors (e.g. mitosis, taxis) and cellular properties (e.g. size, concentration of adhesion molecules) in a way that is implementation independent. This task is greatly facilitated by Cell Behavior Ontology (http://cbo.biocomplexity.indiana.edu).

Secondly, in order a for multi-cell model description standard to be successful there has to be community buy-in. It is often implicitly assumed that once a standard is in place everybody will adapt his multi-cell modeling software to it, in practice this is rarely the case. It is therefore essential to consult with the broad community to develop an optimal strategy for the development and deployment of the CBMSL.

Motivation & Objectives

The workshop will focus on defining standards for multi-cell model descriptions. In contrast to subcellular models where SBML and CellML greatly facilitated model sharing, validation and reuse, multi-cell modeling community lacks a useable model definition language. Existing multi-cellular models are usually hard coded and therefore very difficult to share or reuse.

The workshop will be 5th in a series of workshop focusing on multi-cell model description language (aka Cell Behavior Model Specification Language - CBMSL). Previous workshops in Bloomington (USA), Edinburgh and Nottingham (UK) demonstrated significant interest of multi-cell modeling community in standardizing multi-cell model description and enabling sharing of models (and data) between various cell-based modeling platforms regardless of their specific mathematical and computational implementations.

Linking CBMSL with existing standards for model description at the molecular level (SBML, CellML) will create an integrated suite of standards capable of describing a much broader range of biological systems than is currently possible. Successful linking of the aforementioned standards will allow us to describe, in a unified fashion, models in which cell behaviors are parameterized based on the state of the internal metabolic network thus creating truly multi-scale models.

Further information on current progress on model description language can be found at
http://cbo.biocomplexity.indiana.edu/wiki/Workshops/CBO4.