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BioPerl
Analyzed 4 months 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
Licenses:
Artistic_...
BioJava
Analyzed 4 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
Avogadro
Analyzed 4 months ago
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.
Jmol
J
Analyzed 4 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.
The Chemistry Development Kit
T
Analyzed 4 months 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.
JChemPaint Applet and Swing Application
J
Analyzed 4 months ago
JChemPaint is a program for drawing 2D chemical structures like those found in most chemistry textbooks.
GenoViz
G
Analyzed 4 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
Licenses:
common_pu...
PathVisio
Analyzed 4 months ago
Utility for creating / edit biological pathways and and visualizing high-throughput data (e.g. microarray data) in the context of pathways.
Mostly written in language not available
Licenses:
apache_2
JOELib
J
Analyzed 4 months ago
JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
Generic Model Organism Database Project
G
Analyzed 4 months ago
This project is to develop a set of software modules to be used to develop a generic model organism system database. Such databases contain information about the genomes and biology of laboratory organisms.