a free genome 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
Cell Electrophysiology Simulation Environment
Cell Electrophysiology Simulation Environment (CESE) is a comprehensive framework specifically designed to perform computational electrophysiological simulations, for example, simulations of cardiac myocyte electrical activity. CESE is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
FORESTER is being developed as a framework for (automated) sequence function prediction based on phylogenic information - phylogenomics. Currently, it is composed of Java classes representing basic data structures, algorithms and tools to operate on phylogenetic trees.
a cross-platform framework for using Genetic Algorithms for solutions. Written in Java and uses convinient plug-in features for every phase in the genetic development, while maintaining an easy-to-use API for easy integration into applications
GenPlay is a multi-purpose genome analyzer and browser. It is a fast, easy to use and stable tool for rapid analysis and data processing.
iLAP (Laboratory data management, Analysis, and Protocol development) is a workflow-driven information management system specifically designed to create and manage experimental protocols and to analyze and share laboratory data.
a molecular viewer written in Java and Java3D. JMV is designed to be an easy-to-use, platform neutral, molecular visualization tool, which can be used standalone or integrated into a larger program
Java Structure Viewer
Mirth is a cross-platform HL7 interface engine that enables bi-directional sending of HL7 messages between systems and applications over multiple transports.
a graphical tool that links a 2D projection of a protein-protein interface to a 3D view of the protein structures. This Java-based software uses the representation of are projected onto the interface. The second window, WebMol, displays 3D representations of the molecules. The two windows are linked in such a way that mouse manipulations on the 2D-map window change the map and the 3D view
Pfaat is a Java-based protein sequence alignment application designed to facilitate the analysis, curation, and annotation of large protein sequence families. Key features of Pfaat include the ability to align collections of sequences, cluster and/or group sequences into subfamilies, analyze sequences based on a number of similarity criteria, visualize protein structure, and annotate sequences and specific residue positions with text descriptions.
Simbrain is a neural network which emphasizes ease of use, environmental interaction (most networks are abstracted from environments), creative design, and sophisticated gauging.
Spatiotemporal Epidemiological Modeler
The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases. These models could aid in understanding, and potentially preventing, the spread such diseases.
Watchmaker is an extensible, high-performance, multi-threaded, object-oriented framework for implementing platform-independent evolutionary computation (genetic algorithms, etc.) in Java.
Wildlife Stock Monitor
(commercial) Wildlife Stock Monitor is a grid-based GIS system for inventorying biotopes.
a cross-platform artificial life/cellular automaton simulator game written in Java. It is inspired by several principles and ideas used in the well-known a-life programs Tierra and Avida