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WholeCellViz :: Mycoplasma genitalium

WholeCellViz is a web-based software program for visually analyzing whole-cell simulations. WholeCellViz enables users to interactively analyze many aspects of cell physiology including:. Cell mass, volume, and shape,. Metabolite, RNA, and protein copy numbers,. Metabolic reaction fluxes,. Molecular machine statuses – DNA polymerase, RNA polymerase, ribosome, FtsZ ring, and the. Chromosome copy number, superhelicity, integrity, and DNA binding status. See the Advanced usage. A single animation timeline.

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WholeCellViz :: Mycoplasma genitalium | wholecellviz.org Reviews
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WholeCellViz is a web-based software program for visually analyzing whole-cell simulations. WholeCellViz enables users to interactively analyze many aspects of cell physiology including:. Cell mass, volume, and shape,. Metabolite, RNA, and protein copy numbers,. Metabolic reaction fluxes,. Molecular machine statuses – DNA polymerase, RNA polymerase, ribosome, FtsZ ring, and the. Chromosome copy number, superhelicity, integrity, and DNA binding status. See the Advanced usage. A single animation timeline.
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1 mycoplasma genitalium
2 start
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5 whole cell model
6 covert lab
7 example views
8 welcome to wholecellviz
9 features
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WholeCellViz :: Mycoplasma genitalium | wholecellviz.org Reviews

https://wholecellviz.org

WholeCellViz is a web-based software program for visually analyzing whole-cell simulations. WholeCellViz enables users to interactively analyze many aspects of cell physiology including:. Cell mass, volume, and shape,. Metabolite, RNA, and protein copy numbers,. Metabolic reaction fluxes,. Molecular machine statuses – DNA polymerase, RNA polymerase, ribosome, FtsZ ring, and the. Chromosome copy number, superhelicity, integrity, and DNA binding status. See the Advanced usage. A single animation timeline.

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WholeCellViz :: Mycoplasma genitalium

http://www.wholecellviz.org/viz.php

WholeCellViz is a web-based software program for visually analyzing whole-cell simulations of the Gram-positive bacterium Mycoplasma genitalium. WholeCellViz enables users to analyze several aspects of cell physiology including. The cell mass, volume, and shape,. The copy number of every metabolite, RNA, and protein,. The flux of every metabolic reaction,. The status of every molecular machine – DNA polymerase, RNA polymerase, ribosome, FtsZ ring, and. 389-401 (2012). Cell. Graduate Student in Biophysics.

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WholeCell.org | About

http://www.wholecell.org/about.html

Covert Lab, Stanford. Karr Lab, Mt Sinai. Covert Lab, Stanford. Karr Lab, Mt Sinai. WholeCell.org is maintained by Jonathan Karr. Derek Macklin, and Markus Covert. Last updated Mar 9, 2015. Contact wholecell@lists.stanford.edu.

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Karr Lab :: Publications

http://www.karrlab.org/publications

Karr Systems Biology Lab. Karr Systems Biology Lab. Cokelaer T, Bansal M, Bare C, Bila E, Bot BM, Neto EC, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR. Küffner R, Menden MP, Meyer P, Nore R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G and Saez-Rodriguez J. DREAMTools: a Python package for scoring collaborative challenges. F1000Res. 4, 1030 (2015). Langner KM and Plewczynski D. Combined systems and structural modeling repositions antibiotics for Mycoplasma genitalium. Sanghvi JC, Macklin D...

karrlab.org karrlab.org

Karr Lab :: Resources

http://www.karrlab.org/resources

Karr Systems Biology Lab. Karr Systems Biology Lab. Please use the links below to use the free, hosted versions of our software and download source code. In addition to the software packages listed here, we have also developed several utility libraries. These can be obtained from our MATLABCentral page. The first "whole-cell" model of the bacterium M. genitalium. Web-based software for creating model organism databases for whole-cell models. Implemented in Python using the Django framework. Graphical use...

wholecell.org wholecell.org

WholeCell.org

http://www.wholecell.org/index.php?title=Frequently_asked_questions

Covert Lab, Stanford. Karr Lab, Mt Sinai. Covert Lab, Stanford. Karr Lab, Mt Sinai. Welcome to WholeCell.org! What is whole-cell modeling? The goal of whole-cell modeling is predict how genotype determines phenotype. Whole-cell models account for the specific function of every gene product and predict the dynamics of every molecule over the entire life cycle. Whole-cell models have the potential to enable engineers to rationally design cells to perform useful functions such as synthesizing drugs,...Sangh...

wholecell.org wholecell.org

Whole-cell Wiki

http://www.wholecell.org/wiki

Welcome to the whole-cell wiki. This is a community resource for whole-cell modeling. Please register. To contribute to the wiki. What is whole-cell modeling? Getting started with whole-cell modeling. What is whole-cell modeling? The goal of whole-cell modeling is predict how genotype determines phenotype. Whole-cell models account for the specific function of every gene product and predict the dynamics of every molecule over the entire life cycle. Whole-cell models have the potential to enable e...30, 8...

wholecell.org wholecell.org

WholeCell.org

http://www.wholecell.org/index.html

Covert Lab, Stanford. Karr Lab, Mt Sinai. Covert Lab, Stanford. Karr Lab, Mt Sinai. Welcome to WholeCell.org! What is whole-cell modeling? The goal of whole-cell modeling is predict how genotype determines phenotype. Whole-cell models account for the specific function of every gene product and predict the dynamics of every molecule over the entire life cycle. Whole-cell models have the potential to enable engineers to rationally design cells to perform useful functions such as synthesizing drugs,...Sangh...

wholecell.org wholecell.org

WholeCell.org | Summer School, April 3-8 2016, Barcelona Spain

http://www.wholecell.org/school-2016.html

Covert Lab, Stanford. Karr Lab, Mt Sinai. Covert Lab, Stanford. Karr Lab, Mt Sinai. Who is the course for? The course is designed for PhD students and postdoctoral scholars who wish to gain training in large-scale dynamical modeling. See the pre-requesites section below for more information. The summer school will be held April 3-8, 2016 at the Center for Regulatory Genomics. In Barcelona, Spain. Associate Professor, University of Pittsburgh. Signaling, rule-based modeling. Group Leader, EMBL Heidelberg.

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WholeCellSimDB

WholeCellSimDB is a database of whole-cell model simulations designed to make it easy for researchers to explore and analyze whole-cell model predictions including predicted:. DNA, RNA and protein expression,. DNA-bound protein positions,. DNA modification positions, and. Reseachers can download entire simulations and groups of simulations from WholeCellKB in HDF5. Format. In addition, researchers can obtain the simulation metadata needed to reproduce simulations in SED-ML. Please view the tutorial.

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WholeCellViz :: Mycoplasma genitalium

WholeCellViz is a web-based software program for visually analyzing whole-cell simulations. WholeCellViz enables users to interactively analyze many aspects of cell physiology including:. Cell mass, volume, and shape,. Metabolite, RNA, and protein copy numbers,. Metabolic reaction fluxes,. Molecular machine statuses – DNA polymerase, RNA polymerase, ribosome, FtsZ ring, and the. Chromosome copy number, superhelicity, integrity, and DNA binding status. See the Advanced usage. A single animation timeline.

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