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Modeling tools   Scientific computing    Intro kinetics  Intro to Modeling  Glycolysis ref. materials   Professional Development


Modeling tools (in alphabetical order):

Berkeley Madonna: General modeling tool with three interfaces (flow chart, math, chemical) for constructing a model.

CoPasi: This is the latest development effort by Pedro Mendes group. The tool uses a Microsoft Windows like interface and directory structure to develop and simulate numerical models of kinetic reactions.

Computational Neuroscience/Neuroinformatics: A fairly comprehensive list of neuronal simulation tools that can be found at Rolf Kötter's site.

GEPASI: This the precursor to CoPasi. The graphical user interface requires users to enter chemical reactions in biochemical notation.This tool is no longer in development. The site contains software to download, tutorials and FAQ.

Jarnac: This is a programming language for describing cellular systems and has been used to describe metabolic, signal transduction and gene networks.

JDesigner: This application is used to draw biochemical networks and export the drawn network as SBML (Systems Biology Markup Language). It can be used as an interface for developing networks that run on Jarnac.

JigCell: This modeling framework makes uses a spreadsheet interface, solves differential equations, allows users to enter their own rate constants and input conditional statements for the simulation.

MCell: This is a programming language that can be used to describe chemical interactions that are then modeled as Monte Carlo reactions rather than ordinary differential equations (ODE's). Advanced graphic and visualizations tools have been developed to accompany MCell models.

SCAMP: A language for describing metabolic systems. This general simulator is used for metabolic control analysis and simulation.

Stella. This software uses the metaphor of flows and stocks for drafting models of dynamic systems. Model examples and tutorials can be downloaded from the company site.

Virtual Cell: This tool uses ordinary and partial differential equations to model cellular models. Users create models through a graphical user interface or by generating mathematical descriptions using Virtual Cell Math Language.

List of software tools compliant with Systems Biology Markup Language (SBML).

Scientific Computing

Interactive Educational Modules in Computational Science: Based on materials from the text book " Scientific Computing: An introductory survey." by Mike Heath of University of Illinois, Urbana-Champaign. This material provides applets for the user to become familiar with computing principles that form a baseline of knowledge for modeling and computational approaches.

Introductory Materials for Kinetics

Modeling Networks of Signaling Pathways, U.S. Bhalla, Computational Neuroscience 2001 ed. E. De Schutter
This chapter provides easy to understand approaches to developing models of "well, stirred" systems. Rules and hints are provided for describing the kinetics of a few common enzymatic reactions and deciding if it is feasible to develop a complete numerical model for your system.

"THE Medical Biochemistry Page": Online materials for biochemistry including sections on enzyme kinetics. Developed by Dr. Michael W. King, Indiana State University School of Medicine

"An Introduction to Enzyme Kinetics" by Dr. Peter Birch, Department of Biological Sciences, University of Paisley.

Introductory Materials for Modeling

Wofford College: Computational Science Emphasis for Undergraduates
Scinetific Computing, Modeling

Robert Phair's Integrative Bioinformatics:
Practical Kinetic Modeling of Large Scale Biological Systems

Herbert Sauro's Intro to Modeling using JDesigner.

Glycolysis reviews

Online Biology Book: This is an online biology book. It gives a simple overview of Cell Metabolism beginning at glycolysis and then three possible directions for pyruvate at the end of glycolysis (cellular respiration which is our type of aerobic, fermentation to either lactic acid or ethanol whcih is anaerobic) It also gives a good explanation of the path of aerobic metabolism and the 2 additional cycles utilized (Citric Acid Cycle and the Electron Transport System)

Kimball's Biology Pages
Brief overview of the details of glycolysis and subsequent processing of pyruvic acid.


Professional Development

National Computational Science Institute (NCSI) Provides training to undergraduate faculty of all disciplines to learn the basics of modeling and simulation.
BioQuest Curriculum Consortium Provides workshops for biology educators to develop curricular materials taking advantage of modeling and simulation tools.
Advanced Computing in Cell Biology Brings together researchers to advance the use of high performance computing in biological research