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J2dPathway project are composed of several packages: J2dPathway(biological pathway viewer), Pyrus Pathway Editor (biological CAD), and DNASequenceViewer (platform-independent sequence viewer).
The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.
A project to help students calculate symbolic derivatives and integrals. Plus, a Java expression tree library for developers who may need to do such things in their programs.
The project has moved to github: https://github.com/generalpenguin89/calchelper
iGOR: interactive graphical ogr reprojector. iGOR is a windows graphical user interface for the GDAL ogr2ogr {http://www.gdal.org/ogr2ogr.html} developed in Java.
The project is targeted at building a framework for
describing businesses with natural language or structured natural
language. Starting from these definitions different components for
automated code and workflow generation will be integrated
Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!!
It has a built-in database and contains information about all the physical properties and lets you to search them
This project is an easy to use Java application framework, providing enough functionalities to be fully usable. It has been developed for a scientific articles library software, but I hope it's sufficiently generic to be usable on different contexts.
A program for organizing and commenting textual citations from texts (books, articles or other published works) for use in producing scientific or academic publications. Works together with EndNote, RefWorks and BibTeX. Exports to PDF and Word (RTF).
G.A.V. (Graph Algorithm Visualizer) is a tool that visualizes algorithms from graph theory. A step-by-step visualization from each different algorithm allows the user to understand the particular algorithm very easily.
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ElectroMimic is an electronic circuit simulator in Java™. The simulator is focused on the piecewise-linear models normally used by undergraduate students, but can also be linked with external simulation software for more realistic results.
This research project seeks to use compiler techniques to perform an attribute-based data-flow analysis on (MOF/UML)models allowing for a syntax-driven validation of a model's static semantics as well as an abstract interpretation of i dynamic behavior.
propose a support for defining mappings between elements in generic models and elements in the designer’s models,help to create consistent and relevant models integrating the generic and specific ones and taking into account the mappings between them
The PlanetLab Visualizer is intended to help users to run their experiments on PlanetLab hosts. The main advantages are the ease of use and the support for Linux and Windows OSes.
This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
A small java API library for running the MM3 molecular mechanics package from within a java environment. It does not include MM3, nor implement MM3. The MM3 binaries have to be available on the user system.
Extensible framework that enables productive design, analysis, and execution of arbitrary-sized neural-networks or system on a distributed, scalable, high-throughput runtime platform. Enables synapse-oriented-programming.
Convert a "line string" from a .kml file to a "route" in another .kml file. I started this project to use google maps for routing at home and a very simple GPS-device for following the route while on the road.
JIPL (Java Image Processing Library) is an attempt to provide an efficient way to load, filter, manipulate, and save images. The goal is to provide an intuitive and extensible library.
A Controlled Language Programming (CLP) compiler, runtime engine, and development IDE for writing software in a natural (but somewhat restricted) language that clearly represents the real world concerns and maps to a 3GL (Java/Groovy) for execution.
BioWebAuth (Biometrics for Web Authentication) is an open source Java framework intended to provide single sign-on web authentication based on BioAPI-compliant biometric software or devices. It uses the JA-SIG Central Authentication Service architecture.
The Vyper Dynamic Server framework is a pure-javalibrary for use in the creation of backend / server platforms. VDS is specifically tailored for financial applications, and suited for many high-throughput, asynchronous and distributed environments.