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BioPerl

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  Analyzed 27 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]

296K lines of code

9 current contributors

11 months since last commit

22 users on Open Hub

Very Low Activity
4.22222
   
1 Review
I Use This
Mostly written in Perl
Licenses: artistic
Tags bio-informatics bioinformatics cross-platform open_bioinformatics_foundation perl toolkit

BioJava

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  Analyzed 26 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

13 current contributors

3 months since last commit

14 users on Open Hub

Moderate Activity
4.5
   
0 Reviews
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Mostly written in Java
Licenses: lgpl
Tags bio-informatics bioinformatics biology cross-platform development java research science toolkit

Biopython

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  Analyzed 27 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]

1.39M lines of code

56 current contributors

2 months since last commit

13 users on Open Hub

Moderate Activity
4.66667
   
0 Reviews
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Mostly written in Python
Licenses: Biopython...
Tags bio_informatics bioinformatics biology biopython cross_platform python science toolkit

Jmol

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  Analyzed 26 days 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.

629K lines of code

0 current contributors

over 1 year since last commit

12 users on Open Hub

Very Low Activity
4.0
   
0 Reviews
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Mostly written in Java
Licenses: lgpl
Tags bio-informatics bioinformatics cheminformatics chemistry computer_aided_instruction java molecular_science research visualization

Galaxy Bioinformatics Platform

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  Analyzed 26 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 https://usegalaxy.org where you ... [More] can do all this with nothing more than a web browser. [Less]

1.86M lines of code

164 current contributors

2 months since last commit

12 users on Open Hub

Very High Activity
5.0
 
0 Reviews
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Mostly written in Python
Licenses: AFL1-1
Tags bioinformatics ngs planemo research science toolshed usegalaxy workflow

SeqAn

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  Analyzed 27 days ago

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

460K lines of code

9 current contributors

3 months since last commit

12 users on Open Hub

Low Activity
5.0
 
0 Reviews
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Mostly written in C++
Licenses: BSD-3-Clause
Tags bioinformatics c++ sequenceanalysis templatelibrary

SHOGUN

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  Analyzed 26 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]

271K lines of code

24 current contributors

over 1 year since last commit

11 users on Open Hub

Very Low Activity
5.0
 
0 Reviews
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Mostly written in C++
Licenses: gpl3_or_l...
Tags bioinformatics kernels kmeans large-scale learning machinelearning matlab matplotlib optimization python research standalone 4 more...

mdanalysis

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  Analyzed 27 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]

92.6K lines of code

37 current contributors

2 months since last commit

6 users on Open Hub

Moderate Activity
5.0
 
0 Reviews
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Mostly written in Python
Licenses: gpl
Tags analysis bioinformatics charmm dcd gromacs lammps moleculardynamics namd python science simulations timeseries 1 more...

XNAT

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  Analyzed 26 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.

1.64M lines of code

14 current contributors

4 months since last commit

6 users on Open Hub

Moderate Activity
5.0
 
0 Reviews
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Mostly written in JavaScript
Licenses: bsd_2clau...
Tags bioinformatics dicom imaging medical neuroimaging neuroinformatics research xnat

The Chemistry Development Kit

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  Analyzed 26 days ago

The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.

602K lines of code

10 current contributors

2 months since last commit

6 users on Open Hub

Moderate Activity
4.33333
   
0 Reviews
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Mostly written in Java
Licenses: lgpl
Tags 3d_rendering bio-informatics bioinformatics cheminformatics chemistry chemoinformatics development java medical_science