Advanced Computing in Cell Biology:

Workshop in Computational Biology

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References provided during workshop
Botstein, David (Conversation); Learning the Language of Systems Biology

Crampin E.J. et al.; Computational physiology and the physiome project

Henry, C M.; Systems Biology, C&EN Cover Story

Mellman, and Misteli; Computational cell biology – JCB May12, 2003

Schacherer, Frank G.D.; A review of biological network visualization

Cell Cycle Research References
Sha, et al. Hysteresis Drives Cell-Cycle Transitions in Xenopus Leavis Egg Extracts

Tyson, John; Modeling the Cell Division Cycle

Goldbeter, Albert; A Minimal Cascade Model for the Mitotic Oscillator

JCB vol 161, May issues. These issues of the Journal of Cell Biology contain reviews and articles on computational cell biology.

Mueller, P.R., et al. Myt1: A Membrane-Associated inhibitory kinase that phosphorylates Cdc2 on both threonine-14 and Tyrosine-15. Science 1995 270(5233):86-90. (PubMed)

Lee, H. Kumagai, A. and Dunphy, W.G. Positive Regulation of Wee1 by Chk1 and 14-3-3 Proteins. Molecular Biology of the Cell 2001 12: 551-563. (PubMed)
Signal Transduction and JDesigner
Aguda, and Sauro; Computer Simulation of MARK Signal Transduction

Sauro, Herbert; An Introduction to Biochemical Modeling Using JDesigner

Microscopy and modeling
Fink, Charles C. et al.; An Image-Based Model of Calcium Waves in Differentiated Neuroblastoma Cells – Biophysical Journal, V.79, July 2000.

Lippincott-Schwartz, Jennifer, et al.; Studying Protein Dynamics in Living Cells

Book Resources
Voit, E. Computational analysis of biochemical systems

Bower and Bolouri, Computational modeling of genetic and biochemical networks

De Schutter, Computational Neuroscience

Hunt and Murray, Cell Cycle

Sheen, Math and Bio 2010

Software Used 
Stella Demo, Stella Player. Download from ISEE .

JDesigner. Downloads with System Biology Workbench. See
Runs on Windows or Unix.

Virtual Cell. Create account and log in at Virtual Cell homepage
Requires Java runtime on Mac and Windows.

Microsoft Excel 2003. Component of Microsoft office.

Links of Interest to Participants
List of books on dynamics and epidemiology

BioGenNet, a software tool for modeling multiple species

Protein family/motif databases
see Pfam; Smart; Blocks; Prosite

List of SBML compatible tools

Metabolic Models
Integrating computational biology in undergraduate education: Glycolysis

Getting Started section on biological processes contains some simple examples for modeling the first steps of glycolysis.

JWS online simulations of glycolysis and other models

The site is useful for showing the rate equations associated with already published models and the biochemical reactions diagramed in the concept map.
Olivier, B.G and Snoep, J.L, (2004) Web-based kinetic modelling using JWS Online, Bioinformatics, (20), 2143 – 2144. Brief write up of the above website. Provided.

Systems Biology Markup Language http://SBML.Org

This site contains a model repository. The models are common oscillation models and a few metabolic models. Detailed descriptions of the differential equations, rate equations and parameters are provided. As well, an SBML downloadable file is provided. JDesigner, Gepasi, Mathematica.
Metabolic Pathway Databases

One of the original pathway databases, an initial focus was on the implementation of pathways from a genomic level.


MetaCyc is the most recent child from the original EcoCyc pathway database. EcoCyc focused on modeling Ecoli pathways. The next version was BioCyc which was created to allow comparisons of pathways.
Krieger, CJ, et al. MetaCyc: A Multiorganism Database of Metabolic Pathways and Enzymes Nucleic Acids Research, 2004 32(1):D438-42. Provided.
Karp, P.D. and Riley,M. EcoCyc: The Resource and the Lessons Learned, in Bioinformatics Databases and Systems, S. Letovsky, ed., Kluwer Academic Publishers, pp47-62, 1999. Provided.


This material is based upon work supported by the National Science Foundation under Grant No. 0439204. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. If you have a question about materials on these pages please send us an email.