:: DESCRIPTION
Pycellerator provices python libraries, a command line interface, and an ipython notebook interface for Cellerator arrow notation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pycellerator: an arrow-based reaction-like modelling language for biological simulations.
Shapiro BE, Mjolsness E.
Bioinformatics. 2015 Oct 26. pii: btv596.
:: DESCRIPTION
FastPros (Fast algorithm of knockout screening for target Production based on shadow price analysis), a new iterative screening algorithm, which uses biomass production maximization to identify sets of metabolic reactions whose simultaneous knockouts result in the production of a target metabolite
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Apr 1;30(7):981-7. doi: 10.1093/bioinformatics/btt672. Epub 2013 Nov 19.
FastPros: screening of reaction knockout strategies for metabolic engineering.
Ohno S1, Shimizu H, Furusawa C.
:: DESCRIPTION
Redi simulates biochemical systems at the mesoscopic scale of interaction
::DEVELOPER
The Microsoft Research – University of Trento Centre for Computational and Systems Biology
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
P. Lecca, A. Ihekwaba, L. Dematte’, C.
Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient.
In Journal of Integrative Bioinformatics, 7, 2010
:: DESCRIPTION
MaRIboES is an algorithm for metabolite and reaction inference based on enzyme specificities. MaRIboES ,has many applications, for example to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. MaRIboES employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Nov 15;25(22):2975-82. Epub 2009 Aug 20.
Metabolite and reaction inference based on enzyme specificities.
de Groot MJ, van Berlo RJ, van Winden WA, Verheijen PJ, Reinders MJ, de Ridder D.
:: DESCRIPTION
HLA Assignment takes lab data from a series of patients and determines probabilistically which HLA genes are responsible for a patient’s reaction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J. Listgarten,N. Frahm, C. Kadie, C. Brander, D. Heckerman.
A statistical framework for modeling HLA-dependent T cell response data,
PLoS Computational Biology, 3(10): e188, October 2007.
:: DESCRIPTION
PCRsetup is a tool for planning PCR and qPCR reactions, mixing solutions. The higher quality of primers is help to save PCR efficiency at changing PCR conditions. PCR reaction can set up in room temperature and performed without hot-start enzymes.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kalendar R, Lee D, Schulman AH 2011.
Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis.
Genomics, 97(7).
:: DESCRIPTION
ChemicPen is a software for drawing 2D chemical formulae and reactions. Allows you to print and export formulae in other documents.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
