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FishLAB is an easy-to-use program for tracking aquarium water chemistry. With FishLab you can monitor pH, hardness, NH4, NO2, NO3, Fe, CO2 (the software converts units where needed). The graph function warns you of bad trends in water quality.
Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.
jdwglib is a Javalibrary for accesing DWG files. It is essentially a port from the Pythoncad DWG reading classes by Art Haas. jdwglib manages complex DWG objects allowing users to employ these objects directly in their applications.
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Framework for storing and editing Forestry-related XML data, with a specialised graphical interface for each object type. Plug-in API for adding functionality. Coded in Java, uses WebStart for distribution, swing GUI, ~100k lines of code.
MBAS -- Macro-Biological Analysis System -- provides a set of interoperable tools for aid in the analysis of biological data. The backing database is currently PostgreSQL and the primary language is C, though some data entry tools are written in Java.
jCase is a simulation toolkit for the evaluation of combinatorial auctions. Such auctions are used to allocate resources that are complementarities or substitutes.