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BioJava

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  Analyzed 3 months 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

23 current contributors

3 months since last commit

14 users on Open Hub

Activity Not Available
4.5
   
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Biopython

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  Analyzed 3 months 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]

291K lines of code

62 current contributors

3 months since last commit

13 users on Open Hub

Activity Not Available
4.66667
   
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Bioclipse

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  Analyzed 12 months ago

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from ... [More] Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. [Less]

1.13M lines of code

12 current contributors

almost 6 years since last commit

5 users on Open Hub

Activity Not Available
4.66667
   
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GenoViz

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  Analyzed about 2 months 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

Activity Not Available
5.0
 
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PathVisio

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  Analyzed 3 months ago

Utility for creating / edit biological pathways and and visualizing high-throughput data (e.g. microarray data) in the context of pathways.

168K lines of code

1 current contributors

about 1 year since last commit

4 users on Open Hub

Activity Not Available
0.0
 
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nexml

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  Analyzed 12 months ago

XML-based data exchange standard for phylogenetics. In honor of the commonly-used "nexus" flat file format, the working title for this standard is nexml.

1.11M lines of code

0 current contributors

almost 5 years since last commit

3 users on Open Hub

Activity Not Available
0.0
 
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Icy Imaging

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  Analyzed about 2 months ago

Icy is an open source bio image analysis software.

156K lines of code

5 current contributors

3 months since last commit

3 users on Open Hub

Activity Not Available
4.5
   
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Chaste

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  Analyzed 2 months ago

Chaste - Cancer Heart And Soft Tissue Environment Chaste is a computational biology simulation package. It provides a cardiac simulation package which provides a way to use CellML electrophysiology models in tissue simulations. The cardiac code is suitable for high performance computing on large ... [More] supercomputers. The cell-based side of the code provides a variety of agent-based models (cellular automata, cell-centre-based (on and off mesh), cell vertex, cellular Potts models) for use in biological settings where cells divide and die according to other models. For details please see the recent overview paper in PLoS Computational Biology www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002970 [Less]

1.72M lines of code

15 current contributors

3 months since last commit

3 users on Open Hub

Activity Not Available
5.0
 
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Bio::Phylo

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  Analyzed about 2 months ago

Phylogenetic analysis using perl.

124K lines of code

3 current contributors

5 months since last commit

2 users on Open Hub

Activity Not Available
0.0
 
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Licenses: Artistic-2.0, GPL-2.0+

BioDAS

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  Analyzed 11 months ago

The Distributed Annotation System (DAS) defines a communication protocol used to exchange biological sequence annotations. DAS is a client-server system in which a single client integrates data from multiple servers. Data distribution, performed by DAS servers, is separated from visualization ... [More] , which is done by DAS clients. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community for sharing information about gene and protein sequences as well as protein structures. [Less]

76.5K lines of code

0 current contributors

over 6 years since last commit

2 users on Open Hub

Activity Not Available
0.0
 
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Licenses: No declared licenses