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.
The Java Penrose Empires Package allows you to compute the empires (forced tiles) for an arbitrary initial patch of tiles. Tilings may be saved for later, and may be exported to PDF, EPS, or PNG. This software represents a new method of computing forced tiles. Rather than using a "growth" approach (where some tiles are randomly forced), this system only shows the forced tiles in the system, leaving all unforced areas blank.
The Atropos (formerly AVNMP) Toolkit allows experimentation with predictive capability inside a network while the network is operating: this might be best described as 'in vitro' prediction experimentation. Its purpose is to facilitate experimentation towards addressing a severe limitation in state-of-the-art network management: current management techniques are reactive. The toolkit is an active application that executes in real time within a network that has an overlay active network. Active networking provides a framework in which executable code within data packets executes upon intermediate network nodes. The Atropos Toolkit provides the infrastructure to develop and inject numerous, small, interacting network component models in support of network prediction. Research results in Complexity Theory using Atropos can be found in the DARPA-funded GE Fault Tolerant Networking Project.
XiStrat (aka 'Extended Strategy') is in particular about turn-based, networked multiplayer, non-cooperative, zero-sum, abstract strategy board games (e.g., Chess, Go, Reversi variants, etc.) on 3D-visualized polyhedra and contains a server, client GUI, autoplayer engine, utilities, and documentation. Related recreational modern mathematics (single agent, cellular automata, graph/group/complexity/knot theory, discrete geometry, algebra, combinatorics, and mathematical physics) is also dealt with.
DigitizeIt digitizes scanned graphs and charts. Graphs can be loaded in nearly all common image formats (including gif, tiff, jpeg, bmp, png, psd, pcx, xbm, xpm, tga, pct), pasted from the clipboard, or imported via a screenshot. Digitizing of line and scatter plots occurs automatically, and manual digitizing via mouse clicks is also possible. Data values are transformed to a specified axes system and can be saved in ASCII format, ready to use in many other applications such as Microcal Origin or Excel. Axes can be linear, logarithmic, or reciprocal scale. Multiple data sets can be defined and edited. Tilted and distorted graphs can be handled. Comprehensive online help is included. Java 1.4 is required.
The NumericalChameleon converts numbers with a precision of up to 1000 significant figures. It supports more than 3200 units in 82 categories, including lengths, areas, volumes, durations, bits & bytes, angles, temperatures, exchange rates, Roman numerals, spoken numbers, all 35 radixes, unicode, colorcode, int. dial codes, timezones, date calculations and more. You have unlimited access for adding, modifying, and deleting categories, units, and icons. Update exchange rates with the GUI or at the command line. All configuration data are stored in flat files.
MST is a very simple Java application for calculating a minimum spanning tree from a weighted, undirected graph. The graph is read from a standard ASCII text file. One of the possible minimum spanning trees for the graph is then printed to the screen, along with the total weight of the tree.