Cell modeling and simulation:

National Resource for Cell Analysis and Modeling
University of Connecticut - “Virtual Cell Project”

 “NRCAM provides advanced research tools for the study of cell physiology. The primary technology development project is the Virtual Cell, a general computational framework for modeling cell biological processes. Specifically, computational cell biology is coupled with high resolution light microscopy to facilitate the interplay between experimental manipulation and computational simulation of cellular events. This new technology associates biochemical and electrophysiological data describing individual reactions with experimental microscopic image data describing their subcellular locations. Cell physiological events can then be simulated within the empirically derived geometries, thus facilitating the direct comparison of model predictions with experiment. Access to the Virtual Cell modeling software is available via the internet using a Java based interface. Distinct biological and mathematical frameworks are encompassed within a single graphical interface”.

University of California, Berkeley

Bio/Spice is a biological data analysis and modeling workspace and database based loosely on SPICE tools used by Electrical Engineers for the design and analysis of their circuitry… The computational aspects of the laboratory are dedicated to creating methods for the numerical analysis of biological systems. The efforts cover roughly four areas: 1) Databasing, 2) Data mining/analysis, 3) Model building, 4) Numerical simulation and analysis. Database efforts entail the creation of complex biological databases containing more that just sequence and molecular structure information, but also containing information on developmental, signal transduction and metabolic pathways, models and parameters for various cellular processes, primary molecular profiling and image data. The datamining and analysis efforts involve developing informative relationships among the different datatypes to identify biological components and subsystems responsible for experimental observations. Model building tools are central to aiding in the rapid evaluation of theories of biochemical reaction network functioning and in explaining complex experimental data such a gene microarrays. Numerical simulation and analysis tools allow models, at various levels of abstraction and different types (stochastic or deterministic, differential or algebraic), to be evaluated for their dynamical behavior and the dependency of behavior on parameters and model structure.


“E-CELL Simulation Environment (E-CELL SE) is a software package for cellular and biochemical modeling and simulation. E-CELL attempts to provide a framework not only for analyzing metabolism, but also for higher-order cellular phenomena such as gene regulation networks, DNA replication, and other occurrences in the cell cycle… Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behaviour of living cells. Previous work in biochemical and genetic simulation have isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico.”

Cell Markup Language (CellML)
 “The CellMLTM language is an XML-based markup language being developed by Physiome Sciences Inc. in Princeton, New Jersey, in conjunction with the Bioengineering Research Group at the University of Auckland's Department of Engineering Science and affiliated research groups. The purpose of CellML is to store and exchange computer-based biological models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying biological processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). CellML includes mathematics and metadata by leveraging existing languages, including MathML and RDF. In the future, CellML may also use other existing languages to specify data and define simulation and rendering information”.

Systems Biology Workbench Development Group
“Our Mission is to develop an integrated, easy-to-use environment, the workbench, which will enable biologists to create, manipulate, display and analyze biological models at molecular, cellular and multicellular levels.  We are focusing on biochemical networks including mass action kinetics, metabolic pathways, stochastic simulation, gene expression and regulation… One of the key aspects of out project is to facilitate collaboration among existing developers and users of system biology software. We aim to do this by providing an open-source software infrastructure which will enable collaborators to freely use and share each other's computational resources."