Amigo Gene Ontology

Gene Inspector is a unique combination of a versatile electronic laboratory research notebook and a comprehensive sequence analysis product. Using GI, the user has the ability to define an entire 'suite of analyses' that can be performed each time they (or anyone in the lab) has a new sequence,...

The Gene Construction Kit allows graphic manipulation of DNA sequences and sophisticated plasmid drawing options. It has an award winning interface design that allows graphic manipulation of DNA sequences in addition to providing sophisticated drawing capabilities. GCK was named the "Best Plasmid...

Lives discretely in your menu bar, giving you quick and easy access to all your friends on Facebook. Once installed on your computer, Amigo will also notify you when you have new messages or notifications. Get your friend status updates, pokes, messages, wall-posts, group and event invites...


Platforms: Mac

Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.


Platforms: Windows, Mac, Linux

Disease Gene Profiler (DGP) comprises of a set of (bioinformatics) tools that can be used to identify the genes underlying susceptibility to common multifactorial diseases (such as diabetes, asthma and cancer) using freely available datasources.


Platforms: Windows, Mac, Linux

Perl Entrez Gene Parser project provides Perl parsers for NCBI's Entrez Gene based on regular expression, Parse::RecDescent, Parse::Yapp and Perl-byacc. Some can parse human genome annotations in minutes. Documentation and user guides are provided.


Platforms: Windows, Mac, Linux

Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of...


Platforms: Windows, Mac, Linux

GRaPe - a platform-independent software tool for building integrative gene-reaction-protein (GRP) networks. It generates the kinetic equations for each reaction and outputs a SBML document. It also implements two methods for parameter estimation.


Platforms: Windows, Mac, Linux

LiveGMS is a PHP/MySQL driven gene editor for the game Creatures 3 / Docking Station. It provides a platform independent online editor with most features other binary genetics editors have.


Platforms: Windows, Mac, Linux

ONTODerm is a specialty specific ontology for dermatology to integrate dermatology with medical software systems.


Platforms: Windows, Mac, Linux

An open source common API tasks to query existing ontology resources in local files (OWL and OBO) as well as public repositories (Bioportal, OLS) using a standardised, uniform interface.


Platforms: Windows, Mac, Linux

ROO is an (OWL) ontology construction tool based on Protégé 4. ROO makes the ontology building process easier as it provides guidance about the steps involved and it allows to enter knowledge using an easy to learn controlled natural language.


Platforms: Windows, Mac, Linux

a simple function that returns a colormap, C, for visualizing gene expression. C is just a N x 3 matrix [R G B] describing the range of color values.example usage: C = exp_colormap('blue-yellow',64); colormap(C);called without any arguments, it returns a [3 x 64] green-red colormap.options for...


Platforms: Matlab

A research fellow at Harvard asked me to write a program to search for gene sequence, such as d-de?TCCd-deOao, and record the next 4 codes. The data file was 14Gb. He tried some matlab codes, and the system froze, or kept running and never stopped.I first tested using a loop method (V1.0). It...


Platforms: Matlab

The script is a Matlab implementation of reference gene selection reported inJo Vandesompele et al, "Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes", Genome Biology 2002, 3 (7).


Platforms: Matlab

This application is an interactive simulation of gene expression that allows the user to: Explore a sample gene: Explore the correspondence between DNA, pre-mRNA, mature mRNA, and protein Map the functional elements of a gene. Create mutations in a gene and explore their effects. Design...


Platforms: Mac

This is Gene Simmons Adiumy with his kiss custome and his signature Axe Bass, showing his tongue.


Platforms: Mac

This script uses the gene name field(s) in a table downloaded from the UCSC Genome Browser to add gene names to an existing SVS marker map saved in the DSM file format. Note: Though the following instructions specify downloading a table containing genes based on the Mar. 2006 (NCBI36/hg18) Human...


Platforms: Mac

Build a gene network! The lac operon is a set of genes which are responsible for the metabolism of lactose in some bacterial cells. Explore the effects of mutations within the lac operon by adding or removing genes from the DNA. Sample Learning Goals: * Predict the effects on lactose...


Platforms: Mac

Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries. SYNOPSIS use Bio::SAGE::Comparison; $sage = Bio::SAGE::Comparison->new(); This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE)...


Platforms: *nix