Search Results for "gnu linux" - Page 33

""" E-Cell's source code repository has moved to GitHub! https://github.com/ecell The development of E-Cell now continues on GitHub. The Subversion repository was abandoned. """ E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components driven by multiple algorithms with different timescales to coexist in a model.

A population-based method for DNA copy number analysis: recurrent copy number aberration indentification in multiple samples (with no need of single-sample calling). Developed for a quick analysis of high resolution and large population data.

The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.

Skittle is a 2D visualization of genome sequence files. The program assigns four colors to the four nucleotides and text wraps the sequence to create a 2D picture based on the DNA sequence. Great for researching tandem repeats and chromosome structure. Compiled downloads available at http://dnaskittle.com/ Source maintained at https://github.com/josiahseaman/skittle

Foad is an open source software which receive an EKG Signal from scanner, WFDB database or heart sensors. Finding patient disease started by taking Fourier transform (FFT) from input signal and extract a single cycle. Based on some heuristic algorithm the most important feature like P , Q , R , S , T captured and feed to trained neural network. and so the final decision made by CNN library. As mentioned before this software also capable do some image processing on scanned paper to lower...

JHeatChart is a simple Java library for generating heat map charts.

The GPDE is a biological protein database based on the PRIDE xml format. It combines proteomics experiments based on the investigated cell type and creates a biological meta-analysis. Try it out at http://www.meduniwien.ac.at/proteomics/database.

Perl code scafflod for the automatic execution of main Next Generation Sequencing data processing and analysis.

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

Cloe (Closure Editor) is a graphical, Java based tool used for editing contigs, resolving contig features, and closing both sequencing and physical gaps.

Open Source project for visualizing protein structure. Written in C++ with Qt and OpenGL the software is designed to be multi-platform (Linux, FreeBSD and Windows). On web: www.msprot.com Copyright 2008 Federal University of Sao Paulo - UNIFESP

SARSE is a scientific data editor that uses the extendable column format, allows interactive overview, tracks editing history, and has a user extendable tool box.

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.

FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra

An R package implementation of a consensus clustering methodology. This package allows users to perform re-sampling statistics based clustering using multiple clustering algorithms to assess the robustness of both clusters and members of clusters.

This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. "Novel computational methods for increasing PCR primer design effectiveness in directed sequencing". BMC Bioinformatics 2008, 9:191.

A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.

DuffyRNAseq is an R package that implements an analysis pipeline for processing RNA-seq data from Illumina NextGen sequencers, to measure gene transcription and differential expression.

Protein Data Bank transformed into an SQL database with a very powerful search engine and a rich web interface. The engine combines chemical, sequence and 3D structure searches. The interface provides statistics, sequence and 3D structure alignments.

Fast search using a standard SQL on Oracle or PostgreSQL database. The package includes the database creator, loader and web application. It supports SMILES and SMARTS substructure searches, similarity search, stereochemistry.

Suite of software tools for transcription factor binding site search, gene annotation, and orthology filtering. Some tools in the CisOrtho package are required along with MAQ for use in MAQGene.

MTMP is a multi-threaded multiple pattern matching algorithm based on the Wu-Manber algorithm.

A C++ Library for modelling and analyzing biochemical networks

Graphical editor using HTML5 canvas for input of chemical structures, molecule interactions, as well as protein sequence and 3D structural motifs. Facilitates searches in chemo-informatics, bioinformatics and structural biology .

Algorithm Based Automatic Contiguation of Assembled sequences (ABACAS) is an integrated platform for quickly contiguating reference based assemblies.