Tag: Escherichia coli

CellAging – Study Segregation and Partitioning in Division in Cell Lineages of Escherichia coli

CellAging

:: DESCRIPTION

CellAging is a tool designed to automatically extract information on the segregation of aggregates to the cell poles and their partitioning in division and on cellular vitality from temporal images of E. coli cells, obtained by parallel brightfield and fluorescence microscopy.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MatLab

:: DOWNLOAD

 CellAging

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1708-9. doi: 10.1093/bioinformatics/btt194. Epub 2013 Apr 23.
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli.
Antti Hakkinen, Muthukrishnan AB, Mora A, Fonseca JM, Ribeiro AS.

Periscope 20150806 – A Predictor for Soluble Protein Expression in the Periplasm of Escherichia coli

Periscope 20150806

:: DESCRIPTION

Constructed based on the rising popularity of periplasmic expression, Periscope is a sequence-based predictor with a two-stage architecture that estimates the expression level and yield of soluble protein in the periplasm of E. coli.

::DEVELOPER

Periscope team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 Periscope

:: MORE INFORMATION

Citation

Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli.
Chang CC, Li C, Webb GI, Tey B, Song J, Ramanan RN.
Sci Rep. 2016 Mar 2;6:21844. doi: 10.1038/srep21844.

iFBA 1.0 – Integrated Flux Balance Analysis Model of Escherichia coli

iFBA 1.0

:: DESCRIPTION

iFBA (Integrated Flux Balance Analysis Model of Escherichia coli) includes several MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches — iFBA, rFBA, and ODE. The project also includes several MATLAB scripts that simulate biochemical networks using 1) integrated flux balance analysis (iFBA) — a combined FBA, boolean regulatory, and ODE approach; 2) regulatory flux balance analysis (rFBA); and 3) ordinary differential equations (ODE). Additionally, the project includes several MATLAB and php scripts for visualizing metabolic simulations.

::DEVELOPER

Covert Systems Biology Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • MATLAB

:: DOWNLOAD

 iFBA

:: MORE INFORMATION

Citation:

Covert, M.W., Xiao, N., Chen, T.J., and Karr, J.R. (2008)
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
Bioinformatics. 24(18): 2044-2050.