InforBIO 5.28 – E-Workbench for Databasing, Classification & Identification of Microbes

InforBIO 5.28

:: DESCRIPTION

InforBIO is an e-Workbench for databasing, classification and identification of microbes. InforBIO can identify the phenotypic characteristics that discriminate and are associated with the clusters of a phylogenetic tree.

::DEVELOPER

WFCC-MIRCEN World Data Centre for Microorganisms

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

InforBIO

:: MORE INFORMATION

Citation

Hideaki Sugawara, Naoto Tanaka, and Satoru Miyazaki (2003)
An e-Workbench for the study of microbial diversity,
The system design and basic functions. Microbial. Cult. Coll., 19, 59-67 (InforBIO.pdf)

BacSim – Simulator of Bacterial Growth

BacSim

:: DESCRIPTION

BacSim is a simulator for individual-based modelling of bacterial colony growth. The potential of this approach is in relating the properties of microscopic entities – cells – to the properties of macroscopic, complex systems such as biofilms. Here, the growth of a single Escherichia coli cell into a colony was studied.

::DEVELOPER

the Kreft Group at the University of Birmingham

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

BacSim the colony model and the biofilm/EPS models ; Java Source Code

:: MORE INFORMATION

Citation:

Jan-Ulrich Kreft, Ginger Booth, and Julian W. T. Wimpenny (1998)
BacSim, a simulator for individual-based modelling of bacterial colony growth.
Microbiology 144:3275-3287.

COP 0.3 – Competition Plotter

COP 0.3

:: DESCRIPTION

One of the measures of virulence of different strains of an organism is the competitive index. In this model, a mixed infection is performed in a single host with the assumption that the more fit strain will outperform the other. The current standard is to report competitive index (CI), the ratio of recovered colony forming units of one strain to the other. While this information is informative, it discards overall organ-load information due to the one-dimensional nature of the CI.

COP is for generation of plots which preserve this information. Paired t-test statisitcs are calculated.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac Os / Linux
Perl
TK

:: DOWNLOAD

COP for Win ; Source Code ; Sample data file

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.