wholecellsimdb.org
WholeCellSimDBDatabase of whole-cell model predictions.
http://www.wholecellsimdb.org/
Database of whole-cell model predictions.
http://www.wholecellsimdb.org/
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WholeCellSimDB | wholecellsimdb.org Reviews
https://wholecellsimdb.org
Database of whole-cell model predictions.
wholecellsimdb.org
WholeCellSimDB › Simulation › – –
http://www.wholecellsimdb.org/download
IFBA simulation GLC/G6P diaxuic growth. IFBA simulation GLC/LCTS diaxuic growth. ODE simulation GLC/G6P diaxuic growth. ODE simulation GLC/LCTS diaxuic growth. RFBA simulation GLC/G6P diaxuic growth. RFBA simulation GLC/LCTS diaxuic growth. Single gene disruption-MG 0001. Single gene disruption-MG 0002. Single gene disruption-MG 0003. Single gene disruption-MG 0004. Single gene disruption-MG 001. Single gene disruption-MG 002. Single gene disruption-MG 003. Single gene disruption-MG 004. Single gene disr...
WholeCellSimDB › Organisms
http://www.wholecellsimdb.org/list/organism
Last updated March 24, 2014, 3:16 pm. Contact wholecell@lists.stanford.edu.
WholeCellSimDB › Investigators
http://www.wholecellsimdb.org/list/investigator
Last updated March 24, 2014, 3:09 pm. Contact wholecell@lists.stanford.edu.
WholeCellSimDB › Parameters
http://www.wholecellsimdb.org/list/parameter
FBA to ODE est init biomass ratio. 357, 1.07, 0.56]. 428, 1.1, -7.4]. 086, 0.01, 0.12, 0.01]. Last updated March 22, 2014, 7:32 pm. Contact wholecell@lists.stanford.edu.
WholeCellSimDB › Tutorial
http://www.wholecellsimdb.org/tutorial
Use the "Browse" menu at the top-left to explore WholeCellSimDB including the available in silico organisms and simulation batches. Use the "Browse" menu at the top-left to explore WholeCellSimDB including the available in silico organisms and simulation batches. Use the basic plotting tool. To preview simulations. Use the Python API to construct more advanced visualizations (see examples. Storing simulations in WholeCellSimDB. See the developer instructions. See the developer instructions.
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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.
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...
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
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...
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
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 | 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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