ExonScan 1.0 – Simulating the RNA Splicing Pattern of a Primary Transcript Sequence

ExonScan 1.0

:: DESCRIPTION

ExonScan expects a primary transcript sequence, preferably excluding the first and last exon. It also currently needs at least about 20 bases upstream of the first exon it can locate, and at least about 60 bases downstream of the last. Numbers in the sequence are discarded, so you can cut and paste from, e.g., a GenBank file.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Cell. 2004 Dec 17;119(6):831-45.
Systematic identification and analysis of exonic splicing silencers.
Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB.

SPiM 0.05 / SPiM Player 1.13 – Programming Language for Designing and Simulating Computer Models of Biological Processes

SPiM 0.05 / SPiM Player 1.13

:: DESCRIPTION

The SPiM (Stochastic Pi Machine) is a programming language for designing and simulating computer models of biological processes. The language is based on a mathematical formalism known as the pi-calculus, and the simulation algorithm is based on standard kinetic theory of physical chemistry. The language features a simple graphical notation for modelling a range of biological systems, and can be used to model large systems incrementally, by directly composing simpler models of subsystems.

The SPiM Player is a graphical interface to SPiM

::DEVELOPER

Andrew Phillips, Luca Cardelli, Matthew Lakin, Filippo Polo, Microsoft Research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
.NET
Silverlight

:: DOWNLOAD

SPiM / SPiM Player

:: MORE INFORMATION

paper-ng-sam – Pipeline for simulating NG-SAM experiments

paper-ng-sam

:: DESCRIPTION

paper-ng-sam is a pipeline for simulating NG-SAM experiments

::DEVELOPER

Botond Sipos

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
r package
biopython

:: DOWNLOAD

paper-ng-sam

:: MORE INFORMATION

Citation:

Botond Sipos, Tim Massingham, Adrian M. Stütz, Nick Goldman (2012)
An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and Next Generation Sequencing.
PLoS ONE 7(8):e43359 doi:10.1371/journal.pone.0043359.

PEDAGOG 1.23 – Simulating Eco-evolutionary Population Dynamics

PEDAGOG 1.23

:: DESCRIPTION

PEDAGOG is a Windows program that simulates population dynamics at the individual level, allows for heritability and selection of traits, records individual genotype and pedigree information, and allows for several types of errors to manifest in the output which can be formatted for 57 existing software programs.

::DEVELOPER

Jason Coombs ,jcoombs@cns.umass.edu ,Ben Letcher, and Keith Nislow

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

PEDAGOG

:: MORE INFORMATION

Citation

Coombs, J. A., B. H. Letcher and K.H. Nislow. 2010.
PEDAGOG: Software for simulating eco-evolutionary population dynamics,
Molecular Ecology Resources, 10: 558-563.

NetBuilder 0.94 – Graphical Tool for Representing and Simulating Genetic Regulatory Networks

NetBuilder 0.94

:: DESCRIPTION

NetBuilder is an interactive graphical tool for representing and simulating genetic regulatory networks in multicellular organisms. Although the diagrams created in NetBuilder represent biological processes, the underlying concepts have their roots in electronic engineering.

::DEVELOPER

NetBuilder Development team

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

NetBuilder

:: MORE INFORMATION