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BioJava

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  Analyzed 1 day 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

6 months since last commit

14 users on Open Hub

Low 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 about 3 hours 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]

1.44M lines of code

56 current contributors

7 days 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

Bioclipse

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  Analyzed over 1 year 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]

537K lines of code

0 current contributors

over 4 years since last commit

5 users on Open Hub

Activity Not Available
4.66667
   
0 Reviews
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Mostly written in Java
Licenses: eclipse
Tags bioinformatics biology cheminformatics chemistry chemoinformatics eclipse framework java molecular visualization

PathVisio

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  No analysis available

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

0 lines of code

0 current contributors

0 since last commit

4 users on Open Hub

Activity Not Available
0.0
 
0 Reviews
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Mostly written in language not available
Licenses: apache_2
Tags bio-informatics bioinformatics biology genes genomics java metabolomics pathway-tools proteomics scientific

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]

187K lines of code

35 current contributors

about 2 years since last commit

4 users on Open Hub

Inactive
5.0
 
1 Review
I Use This
Mostly written in Java
Licenses: common_pu...
Tags bio-informatics bioinformatics biology cross-platform genetics java research science scientific visualisation visualization

Chaste

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  Analyzed about 18 hours 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]

459K lines of code

9 current contributors

2 months since last commit

3 users on Open Hub

Moderate Activity
5.0
 
0 Reviews
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Mostly written in C++
Licenses: BSD-3-Clause
Tags biology cancer cardiac electrophysiology mathematical_model simulation soft-tissue vertex

COPASI

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  Analyzed about 14 hours ago

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

2.91M lines of code

0 current contributors

4 months since last commit

3 users on Open Hub

Low Activity
0.0
 
0 Reviews
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Mostly written in C++
Licenses: Artistic_...
Tags biology chemistry computationalbiology differential_equations dynamics numericalmodeling optimization parameterestimation sbml sensitivity_analysis simulation stochastic

Debian Science

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Claimed by Debian No analysis available

The main goal of the Debian Science project is to provide a system with all the most important free scientific software in each scientific field.

0 lines of code

0 current contributors

0 since last commit

3 users on Open Hub

Activity Not Available
4.0
   
0 Reviews
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Mostly written in language not available
Licenses: CoreSystemIV, Multiple_...
Tags astronomy biology chemistry computeralgebrasystem dataacquisition debian engineering geography gridcomputing logic mathematics maths 6 more...

Icy Imaging

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  Analyzed about 23 hours ago

Icy is an open source bio image analysis software.

167K lines of code

3 current contributors

over 5 years since last commit

3 users on Open Hub

Inactive
3.5
   
0 Reviews
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Mostly written in Java
Licenses: gpl3
Tags biology icy image image_analysis imageanalysis imagej image_processing imageprocessing visualization

BioDAS

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  No analysis available

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]

0 lines of code

0 current contributors

0 since last commit

2 users on Open Hub

Activity Not Available
0.0
 
0 Reviews
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Mostly written in language not available
Licenses: No declared licenses
Tags annotation bio-informatics bioinformatics biology client cross-platform data_formats data_integration distributed genomics science scientific 2 more...