FastPros 1.0.0 – Screening of Reaction Knockout Strategies for Metabolic Engineering

FastPros 1.0.0

:: 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

Shimizu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • MatLab

:: DOWNLOAD

 FastPros

:: 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.

Redi 1.0 – REaction-DIffusion simulator

Redi 1.0

:: 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

Redi

:: REQUIREMENTS

  • Windows
  • .Net Framework

:: DOWNLOAD

 Redi

:: 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

MaRIboES 2.1.0 – Metabolite and Reaction Inference based on Enzyme Specificities

MaRIboES 2.1.0

:: 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

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Matlab
  • C++ Compiler

:: DOWNLOAD

  MaRIboES

:: 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.

Pycellerator 1.0 – Biological Simulation using Reaction-Like Arrows

Pycellerator 1.0

:: DESCRIPTION

Pycellerator provices python libraries, a command line interface, and an ipython notebook interface for Cellerator arrow notation.

::DEVELOPER

Pycellerator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • python

:: DOWNLOAD

 Pycellerator

:: MORE INFORMATION

Citation

Pycellerator: an arrow-based reaction-like modelling language for biological simulations.
Shapiro BE, Mjolsness E.
Bioinformatics. 2015 Oct 26. pii: btv596.

HLA Assignment 2 – Determine which HLA Genes are responsible for Patient’s Reaction

HLA Assignment 2

:: 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

Microsoft Biology Initiative

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • .NET

:: DOWNLOAD

 HLA Assignment

:: 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.

PCRsetup – Tool for Planning PCR and qPCR Reactions

PCRsetup

:: 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

PrimerDigital

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PCRsetup

:: 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).

ChemicPen 2.6 – Draw 2D Chemical Formulae & Reactions

ChemicPen 2.6

:: DESCRIPTION

ChemicPen is a software for drawing 2D chemical formulae and reactions. Allows you to print and export formulae in other documents.

::DEVELOPER

Cetramax

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft Office XP or later

:: DOWNLOAD

ChemicPen

:: MORE INFORMATION

Order ChemicPen