Search Results for "gene" - Page 2

GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.

Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R.

The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads.

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

Ontologizer is an Open Source tool with the purpose of identifing enriched Gene Ontology terms in lists of names of genes or gene products.

TOPS provides the benchtop scientist with a free toolset to analyze, filter and visualize data from functional genomic gene-gene and gene-drug interaction screens with a flexible interface to accommodate various different technologies and analysis algorithms in addition to those already provided here.

LocusVu is a novel Java based software tool that accepts a list of genomic loci (positions on the chromosome) as input and automates fetching of related information (cytogenetic band, gene name, OMIM data etc.) from public databases such as the UCSC genome browser database. It then enables multiple workflows on the retrieved results, like comparing multiple datasets (comparative genomics), viewing neighboring genes for a loci from within the tool itself, or graphically representing these results in bar / pie charts. ...

The characterization of genomic sites is a major challenge in the understanding and exploitation of next generation sequencing data. Most genomic sites are represented by short, degenerated motifs with a scattered distribution and sometimes with biological function (ex: regulation of gene expression, splicing patterns or epigenetics signals). These motifs are associated with a huge amount of noise and thus, the development of a computational platform for accurate detection of genomic sites requires the integration of various large-scale biological data in order to filter out false positives. PARSEC represents an intuitive, modular (easily extensible) and all-in-one solution for the efficient integration of lots of diverse genomic information in order to perform nonlinear localization and characterization of biological sites in a user-friendly environment. ...

GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods.

This plugin allow to visualize several e.g. gene expression values simultanously using pie charts. * Please cite http://www.biomedcentral.com/1752-0509/4/164 *

GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.

...The main function of the software at the current development stage is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome although it can be used to optimize genes into other hosts as well. The main tool in CUO, Moptimizer, introduces a semi-automatic way of gene optimization which provides more flexibility and accuracy during the optimization process. The future plan for CUO is to be developed into a multipurpose bioinformatics software where data, findings, planning and learning in biology labs can be created and shared at finger tips.

FastMap is Java based software that performs quantitative trait locus mapping for gene expression data (eQTL Mapping).

Easily find and extract specific chemical reactions from the BioModels database.

A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions

PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.

RssGsc (Rank Sum Statistics for Gene Set Collections) is a bioinformatics tool used to find meaningful gene sets using a ranked list of genes (obtained form an experiment).

HATS (Haplotype Amplification in Tumor Sequences) is a tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. The amplified haplotype may reveal gene variants.

GEAX is a Java application used to visualize and analyze cross-species gene expression microarray data.The program allows comparisons based on fold-change, p-value, quantile matching, or a combination of criteria.

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)

Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies.

SAFEGUI is a graphical interface to the safe R package which performs resampling based categorical significance testing for gene expression data.

GEM is a computational method for identification of transcription factor modulators, using expression datasets. The method tests if the correlation between factor and target gene depends on the expression of the modulator.

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74

Moara is a biological text mining tool and consists of a Java library and some auxiliary MySQL databases for gene/protein training and extraction of mentions and its further normalization and disambiguation.