EhecRegNet v2 – Database of Pathogenic E. coli Transcriptional Gene Regulatory Networks

EhecRegNet v2

:: DESCRIPTION

EhecRegNet is a database of gene regulations conserved between E. coli K12 and human pathogenic EHEC strains.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Integr Biol (Camb). 2012 Jul;4(7):728-33. doi: 10.1039/c2ib00132b.
On the trail of EHEC/EAEC–unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria.
Pauling J1, Röttger R, Neuner A, Salgado H, Collado-Vides J, Kalaghatgi P, Azevedo V, Tauch A, Pühler A, Baumbach J.

Desharky – Computational Design of Metabolic Pathways in E. coli.

Desharky

:: DESCRIPTION

DESHARKY is a Monte Carlo algorithm that finds a metabolic pathway from a target compound by exploring a database of enzymatic reactions. DESHARKY outputs a biochemical route to the host metabolism together with its impact in the cellular context by using mathematical models of the cell resources and metabolism.

::DEVELOPER

Jaramillo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 DESHARKY

 :: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 1;24(21):2554-6. doi: 10.1093/bioinformatics/btn471. Epub 2008 Sep 5.
DESHARKY: automatic design of metabolic pathways for optimal cell growth.
Rodrigo G1, Carrera J, Prather KJ, Jaramillo A.

CellSegment Tool 1.0 – Image Analysis of E. coli and other Bacteria

CellSegment Tool 1.0

:: DESCRIPTION

MAMLE is a novel segmentation method for detecting cells within dense clusters. MAMLE executes cell segmentation in two main stages. The first relies on state of the art filtering technique, edge detection in multi resolution with morphological operator and threshold decomposition for adaptive thresholding. From this, a correction procedure is applied that exploits maximum likelihood estimate as an objective function. Also, it acquires morphological features from the initial segmentation for constructing the likelihood parameter, after which the final segmentation results are obtained.

::DEVELOPER

Sharif Chowdhury & Andre S. Ribeiro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

 CellSegment Tool

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013;14 Suppl 10:S8. doi: 10.1186/1471-2105-14-S10-S8. Epub 2013 Aug 12.
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE).
Chowdhury S, Kandhavelu M, Yli-Harja O, Ribeiro AS.

FBA 2.0 – Flux Balance Analysis E.coli Model

FBA 2.0

:: DESCRIPTION

FBA (flux-balance analysis) is an software used in the analysis of metabolic behavior. FBA can be used to study metabolic systems.  The fundamental principle of FBA is the conservation of mass.

Another FBA website @ UCSD

::DEVELOPER

Jeremy S. Edwards & Bernhard Palsson

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

FBA

:: MORE INFORMATION

Citation:

Edwards JS, Ibarra RU, Palsson BO. (2001) Nat Biotechnol Feb;19(2):125-30 In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

Edwards JS, Palsson BO (2000) Proc Natl Acad Sci May 9;97(10):5528-33. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.