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BioJava

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  Analyzed about 12 hours ago

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and ... [More] powerful analysis and statistical routines including a dynamic programming toolkit. BioJava is used in several real-world bioinformatics applications and has been used for bioinformatics analysis in a number of published studies. [Less]

1.07M lines of code

22 current contributors

3 months since last commit

14 users on Open Hub

Moderate Activity
4.5
   
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Jmol

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  Analyzed about 2 months ago

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs.

516K lines of code

3 current contributors

7 months since last commit

12 users on Open Hub

Activity Not Available
4.0
   
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SHOGUN

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  Analyzed about 1 month ago

The SHOGUN machine learning toolbox's focus is on large scale kernel methods and especially on Support Vector Machines (SVM). It comes with a generic interface for SVMs, features several SVM and kernel implementations, includes LinAdd optimizations and also Multiple Kernel Learning algorithms. ... [More] SHOGUN also implements a number of linear methods. It allows the input feature-objects to be dense, sparse or strings and of type int/short/double/char. It provides efficient implementations several kernels but also linear methods, hidden markov models etc. and interfaces to matlab,octave,python,R and has a cmdline interface and allows C++ extensions via a library. [Less]

295K lines of code

34 current contributors

about 1 month since last commit

11 users on Open Hub

Activity Not Available
5.0
 
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Galaxy Bioinformatics Platform

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  Analyzed 7 months ago

Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more... We provide a public Galaxy instance at http://usegalaxy.org where you can ... [More] do all this with nothing more than a web browser. [Less]

686K lines of code

123 current contributors

7 months since last commit

8 users on Open Hub

Activity Not Available
5.0
 
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Apache Taverna

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Claimed by Apache Software Foundation Analyzed 12 months ago

The Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community.

640K lines of code

15 current contributors

over 2 years since last commit

4 users on Open Hub

Activity Not Available
4.6
   
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GenoViz

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  Analyzed 1 day ago

The GenoViz project provides tools for genomics data visualization. It consists of the following: 1) the GenoViz SDK, a library of re-usable components, 2) the Genometry data model to represent relationships between biological sequences, and 3) the Integrated Genome Browser (IGB, "igbee"), an ... [More] application built upon the GenoViz SDK and Genometry for visualization and exploration of genomes and corresponding annotations from multiple data sources. IGB supports the Distributed Annotation System (DAS) protocol, version 1 and 2, as well as other optimized binary data formats that are designed for efficient exploration of large, whole genome data sets. [Less]

202K lines of code

3 current contributors

12 months since last commit

4 users on Open Hub

Very Low Activity
5.0
 
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tranSMART

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  Analyzed about 2 months ago

tranSMART is an OSS for translational research. The tranSMART Foundation (www.transmartfoundation.org) coordinates the community that is developing around the tranSMART platform.

1.54M lines of code

22 current contributors

3 months since last commit

2 users on Open Hub

Activity Not Available
5.0
 
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QuteMol

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  Analyzed about 2 months ago

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilities through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding ... [More] of the 3D shape and structure of large molecules or complex proteins. * Real Time Ambient Occlusion * Depth Aware Silhouette Enhancement * Ball and Sticks, Space-Fill and Liquorice visualization modes * High resolution antialiased snapshots for creating publication quality renderings * Automatic generation of animated gifs of rotating molecules for web pages animations * Interactive rendering of large molecules and protein (>100k atoms) * Standard PDB input [Less]

11.1K lines of code

0 current contributors

almost 10 years since last commit

2 users on Open Hub

Activity Not Available
0.0
 
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bio-charm

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  Analyzed 7 months ago

CHarm provides codon harmonization for heterologous expression systems.

552 lines of code

0 current contributors

about 3 years since last commit

1 users on Open Hub

Activity Not Available
0.0
 
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R'MES

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  Analyzed 10 months ago

R'MES is a set of command-line tools to assess the exceptionality of words or families of words in biological sequences. Using different mathematical models it gives a statistical measure of how much occurrences of words in sequences deviate from their expected values, an can thus single out words ... [More] having a potential biological interest. It has already been used to prove on a statistical basis that a specific motif (called CHI) is over-represented in certain kind of bacteria. R'MES is an initiative of the Applied Mathematics and Computing division of the french Agronomical Research Institute (INRA). [Less]

31.7K lines of code

0 current contributors

almost 7 years since last commit

1 users on Open Hub

Activity Not Available
0.0
 
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