Search Results for "open source project" - Page 19

LaJolla can perform 3D alignments of RNA and protein structures. It is fast, simple to use and well tested. LaJolla is successfully published in a peer reviewed journal. !!!!!! PROJECT MOVED TO GITHUB !!!!!! Please check out http://raphaelbauer.github.io/lajolla/

ZAE is a Zoomable multiple sequence Alignment Editor

JAMBLAST: Java Application Manager for the ncbi BLAST results. It is a graphic application that allow the user to display, filter, sort, import/export, store/manage BLAST results produced with the NOBLAST (https://sourceforge.net/projects/noblast).

Quantitative Evalution of Blush: a program to assess myocardial reperfusion on coronary angiograms. This program calculates a value that can be used for risk classification of STEMI patients or as a surrogate endpoint in clinical trials.

This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.

A sorting tool for Bioinformatics, Biochemistry and/or Molecular biology. This sorts nucleotide sequences aligned using "ClustalW". There may be a way to do this w/ original app, but someone I know couldn't figure out how - thus this project was born

Multimedia, Medicine Computing and BioInformatics --- This Project is a collection of several subprojects for Solutions in Multimedia, Medicine Computing and BioInformatics focus on video-,EEG- & Multichanels-signals developped in Web 20, J2EE.

This project contains a set of files (Perl, Java, and an R package) used to perform analysis of oligonucleotide signatures in metagenomes and genomes.

The MML Framework is a temporal-spatial biological model representation language. The MML Project provides the application tool set which facilitates the goals of representing biological models using the MML specifications.

JRasterCreator allows you to easily & visually build a raster file for the mass spectrometry instrument Bruker Daltonics MS ultraflex II by clicking on various spots/locations.

J2dPathway project are composed of several packages: J2dPathway(biological pathway viewer), Pyrus Pathway Editor (biological CAD), and DNASequenceViewer (platform-independent sequence viewer).

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.

A small java API library for running the MM3 molecular mechanics package from within a java environment. It does not include MM3, nor implement MM3. The MM3 binaries have to be available on the user system.

CILib is a framework for developing Computational Intelligence software in swarm intelligence, evolutionary computing, neural networks, artificial immune systems, fuzzy logic and robotics.

Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!! It has a built-in database and contains information about all the physical properties and lets you to search them

ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the automatic annotation of genome-wide tiling-array data in Arabidopsis. ARTADE is a program originally written by Dr. Tetsuro Toyoda, RIKEN, Japan.

Testing tools source code of the Integrating the Healthcare Enterprise (IHE) Cross-Enterprise Document Sharing for Images (XDS-I) Integration Profile

RepeatMap is a collection of time/memory efficient algorithms and data structures to enable rapid counting & querying of kmers (sequences of length k) counts in large sequences. E.g. a query could be "how many times is 'ACGTCATGGTAC' found in a genome."

Decima is a database that was designed to support time-series data mining. It consists of PostgreSQL custom type definition, implementation of GiST index for that type and snowflake database schema.

jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.

Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.

E-BioFlow enables the scientists to design workflow using three different perspectives: control flow, data flow and resource perspective. The workflow tool is based on the Yawl engine and has support for BioMOBY and WSDL services and Perl and R scripts.

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions of TraceTuner, which support mixed base calling, have been used by the research community, the private biotech sector, and the U.S. government as components of different variant detection, genotyping and forensic software applications (e.g. ...