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References
provided during workshop |
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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
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Cell
Cycle Research References |
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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. http://www.jcb.org
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 |
|
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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 |
|
|
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 |
|
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Stella
Demo, Stella Player. Download from ISEE
.
JDesigner.
Downloads with System Biology Workbench. See www.sys-bio.org
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 |
|
BioGenNet,
a software tool for modeling multiple species
http://cellsignaling.lanl.gov/bionetgen/
Protein
family/motif databases
see http://ccb.raquell.us/ccb/ProteinDatabases/
Pfam; Smart; Blocks; Prosite
List
of SBML compatible tools
http://www.sbml.org |
| |
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Getting Started section on biological processes
contains some simple examples for modeling the first
steps of glycolysis.
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JWS
online simulations of glycolysis and other models
http://jjj.biochem.sun.ac.za/database/index.html
The site is useful
for showing the rate equations associated with already
published models and the biochemical reactions diagramed
in the concept map.
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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.
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Metabolic
Pathway Databases
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One of the original pathway databases, an initial
focus was on the implementation of pathways from
a genomic level.
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MetaCyc
http://metacyc.org/
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.
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