Search Results for "java open source" - Page 42

Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.

Web application to make user-friendly requests on large XML database. Tools to XML-ize large bodies of semi-formal texts (like floras). Computer-assisted specimen identification. Uses natural language processing, 2D/3D images analysis and generation.

SeqAnt is an open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform.

Databases to aid Metabolomics projects providing storage functionality for raw and preprocessed data, and integration with existing data analysis environments.

As an NIAID Bioinformatics Resource Center (BRC) Pathema contains in depth curatorial analysis of six target organisms from the list of NIAID category A-C pathogens. Pathema also offers single-genome and comparative multi-genome analyses as well as displ

VELMA stands for Visualization & Exploration of Large Multiple sequence Alignments. VELMA is a Java tool for visualizing alignments of large numbers of biological sequences that exceed the capabilities of existing software.

ODD is a tool for optimal domain decomposition of atomic structure guided by the given molecular dynamics data.

3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.

SyMBA is a Data Archive and Integrator that is based on the Functional Genomics Object Model (http://fuge.sf.net) and which archives, stores, and retrieves raw high-throughput data. See http://symba.sf.net and http://www.cisban.ac.uk

The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types.

Soaplab is a generator of Web Services providing a programmatic access to command-line (and other) applications on remote computers (an example of its usage is available at http://www.ebi.ac.uk/soaplab/)

MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.

A computational tool to discover location of promoter consensus sequences in bacterial genomes.

birgHPC is a Linux Live CD distribution based on PelicanHPC and Debian Live. birgHPC features automated cluster configuration on PCs in the same network specifically for bioinformatics and molecular dynamics. If you are looking for CUDA support, try birgHPCC (https://sourceforge.net/projects/birghpcc/) If you use birgHPC in your work, please cite us: Teong Han Chew, Kwee Hong Joyce-Tan, Farizuwana Akma and Mohd Shahir Shamsir. birgHPC: creating instant computing clusters for...

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

A set of command-line utilities for annotating and manipulating DNA sequences in FASTA format. Generate restriction fragments, ORF's, translations, reverse complement, etc. . - and tie it all together with Unix pipes for complete virtual cloning.

miRDeep-P,miRDP for short, is a computational tool for analyzing the microRNA (miRNA) transcriptome in plants.

OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation

Metaboflux is a generic approach for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments, to increase the biological relevance of the model.

CellNet3D is an application for visualising chemical formula in 3D on Linux platform through PDBlib and X11.

A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.

TaxPub is an extension of the NLM/NCBI Journal Archiving DTD for markup of taxonomic treatments. Maintenance of TaxPub has moved to: https://github.com/plazi/TaxPub

Biologic Institute's Stylus simulation software suite. (See the SVN repository for source code.)

CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

Tangerine is a protein sequence alignment tool based on cross-correlation. Its aim is to provide maximum sensitivity while being computationally efficient.