Online Research tools and Databases under We The Microbiologist

Openwares is the platform where you will get the links of softwares freely available to download without any trial notice. But as you input the usage of these softwares in your research we would recommend you to cite these softwares in your research papers.

 

S. No.

Name

Details

For citation

1

PyMol

PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!

Visit

2

Cell Designer 4.4

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi.

By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface. CellDesigner is free to use.

DOI:10.1016/S1478-5382(03)02370-9

3

Open Meta Analyst

Completely open-source, cross-platform software for advanced meta-analysis

To cite please contact at open_meta_analyst [at] googlegroups.com

4

FlinchTV

Geospiza’s FinchTV is the popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multi-pane view. And it leads the way with raw data views, BLAST searching and the ability to reverse complement sequences and traces.

Citation not required

5

Allele ID

It is a comprehensive desktop tool to address the challenges in bacterial identification, pathogen detection and species identification. AlleleID® can be used to design species identification/cross species probes for microarrays or real time PCR including SYBR® Green, TaqMan® MGB, TaqMan® probes, Molecular Beacons and real time PCR primers. AlleleID® also offers support for designing microarray experiments for detecting alternative splicing events.

Citation not required