BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
Weka is a collection of machine learning algorithms for solving real-world data mining problems. It is written in Java and runs on almost any platform. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka is also well-suited for developing new machine learning schemes. The development version contains a GUI with visualization tools and direct database access.
Artemis is a DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. It can read and write complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK, or GFF format.
JMV (The Java Molecular Viewer) is a molecule viewer program/component written in Java and Java3D. It is designed to be an easy-to-use, platform neutral molecular visualization tool which can be used standalone or integrated into a larger program. It provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities. It loads PDB files over the web, from the RCSB protein databank, from BioCoRE filesystems, and from local filesystems. The interface can be customized by users, and can be disabled for web-based presentations of molecules to save browser space.
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.
JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, and conversion of different chemical file formats. It is written in 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
BioCoRE is a collaborative work environment for biomedical research, research management, and training. It features easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and other practical features.