Educational and Modeling

This page contains links to books, projects and exercises used in undergraduate and graduate courses to teach quantitative cell biology. Quantitative cell biology is defined here as the research field that measures biological properties and uses those measurements to posit the behavior of the biological system. Quantitative Cell Biology makes use of computer modeling to test the hypothesis generated from experimental measurements.

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Educational Resources

Curricular Materials for Modeling Biology - The CompCellBio web site contains materials for teaching computational modeling of cell biology to biology students in undergraduate and graduate courses. These materials are organized in teaching modules and courses.

Virtual Cell Curricular Exercises - Compilation of materials that use the Virtual Cell to teach biological concepts or aspects of modeling.

Modeling Resources

Binding and Kinetics for Molecular Biologists - James A. Goodrich, Jennifer F. Kugel, Cold Spring Harbor Laboratory Press, Cold Spring Harbor NY, 2007.

A Cell Biologist's Guide to Modeling and Bioinformatics - Raquell Holmes. This book contains a chapter with step by step discussion on creating a spatial calcium model originally published by Fink et. al., 2000.

Computational Cell Biology - Christopher P. Fall, Eric S. Marland, John M. Wagner, John J. Tyson, Springer, 2004. This textbook provides an introduction to dynamic modeling in cell biology. Access the VCell Models for Computational Cell Biology, under the 2002 tab.

The Geometry of Biological Time - Art Winfree, Springer, 2001. Written for advanced undergraduates, graduate students and researchers, this book presents a mathematical description of periodic processes in biological systems and their non-living analogues.

Modeling Links

BioNetGen - A web-based tool for automatically generating a biochemical reaction networks from user-specified rules for biomolecular interactions.

B10NUMB3R5 - (BIONUMBERS) A database of useful biological numbers.

cellmigrationgateway - modeling software

CellML- The CellML language is an open standard based on the XML markup language at the University of Auckland and affiliated research groups.

CompCell Bio Web - Development site for teaching modules on quantitative cell biology.

DOQCS - Quantitative Cellular Signaling (DOQCS) is a repository of models of signaling pathways.

E-Cell - A Multi-Algorithm, Multi-Timescale Simulation Software Environment.

Kitware - Professional Visualization Solutions, Tools and Support.

MCell - General Monte Carlo Simulator of Cellular Microphysiology.

Minimotif Miner - Application to search for short sequence motifs in Proteins.

SBML - The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks.

sys-bio.org - Systems Biology Workbench, an open source framework connecting heterogenous software applications.

QuB - Kinetic Analysis made Easy. Programs for analyzing single-molecule kinetics, in particular single ion channels.

Cell Databases

Cell Centered Database -  Cell Centered Database (CCD) from the National Center for Microscopy and Imaging Research

Cell Image Library - The Cell an Image Library from the American Society for Cell Biology

Cell Organizer - From the Center for Bioimage Infromatics

SLIF - Subcellular Location Image Finder  - Finds fluorescent images in on-line journal articles and indexes them based on cell line, labeled proteins and resolution.