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BioPerl

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  Analyzed 9 days ago

Bioperl is a large, object-oriented toolkit of interacting perl modules useful for building bioinformatics solutions in Perl. The collection of modules in the bioperl-live repository contains the core functionality. Additional packages for creating graphical interfaces (bioperl-gui), setting up ... [More] persistent ORM storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (bioperl-run), and software to automate bioinformatic analyses (bioperl-pipeline) are all available from our Subversion repository. [Less]

384K lines of code

11 current contributors

3 months since last commit

22 users on Open Hub

Moderate Activity
4.22222
   
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BioJava

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  Analyzed 10 days 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

26 days since last commit

14 users on Open Hub

Moderate Activity
4.5
   
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Jmol

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  Analyzed 7 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

2 current contributors

about 1 year since last commit

12 users on Open Hub

Activity Not Available
4.0
   
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SeqAn

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  Analyzed 9 days ago

Seqan is a C++ template library of efficient data structures and algorithms for sequence analysis.

509K lines of code

16 current contributors

13 days since last commit

12 users on Open Hub

Moderate Activity
5.0
 
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SHOGUN

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  Analyzed 9 days 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]

277K lines of code

32 current contributors

9 days since last commit

11 users on Open Hub

High Activity
5.0
 
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Biopython

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  Analyzed 10 days ago

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source ... [More] code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. We work along with the Open Bioinformatics Foundation, who generously host our website, bug tracker, and mailing lists. [Less]

293K lines of code

82 current contributors

14 days since last commit

11 users on Open Hub

High Activity
4.66667
   
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Galaxy Bioinformatics Platform

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  Analyzed 8 days 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]

852K lines of code

158 current contributors

8 days since last commit

8 users on Open Hub

Very High Activity
5.0
 
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XNAT

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  Analyzed 9 days ago

XNAT is an open-source imaging informatics software platform dedicated to helping you perform imaging-based research. XNAT’s core functions manage importing, archiving, processing and securely distributing imaging and related study data. But its extended uses continue to evolve.

1.43M lines of code

21 current contributors

25 days since last commit

6 users on Open Hub

Very High Activity
5.0
 
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mdanalysis

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  Analyzed 22 days ago

MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, NAMD, LAMMPS, or Gromacs. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively fast ... [More] framework for complex analysis tasks. In addition, CHARMM-style atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out. Some time-critical routines are written in C or Cython and require a working C compiler. MDAnalysis comes with an expanding library of analysis functions such as RMSD-fitting or analysis of lipid membrane bilayers. [Less]

55.1K lines of code

29 current contributors

25 days since last commit

6 users on Open Hub

High Activity
5.0
 
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Cytoscape

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  Analyzed over 1 year ago

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

8.98M lines of code

25 current contributors

over 1 year since last commit

6 users on Open Hub

Activity Not Available
5.0
 
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