Open Source Java Scientific/Engineering Software - Page 52

AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general. AnnaF was build upon the pipeline framework Anna.

Set of Ant filters that can be used to gather statistics from files or resources. It is mainly used for log files analysis. It allows to: - count inputs - count occurrences of each input - calculate average, max and min values of floats in input

Apolda is a plugin for the Gate framework (see http://sourceforge.net/projects/gate/) that annotates texts with labels of concepts from an arbitrary OWL-ontology.

The goal of this project is to develop a flexible and easy to use dive logbook for Palm OS based PDA. The advantages of the old paper logbook should be combined with the power of a computer.

An ontology based portable question-answering system which takes queries expressed in natural language and an ontology as input and returns answers drawn from one or more knowledge bases (KBs)

A Java argumentation tool kit. Calculate the Dung acceptability of an argument given a source of conflicting arguments, with this library.

Aricom is a file compressor. It is based on arithmetic coding compression. Just a proof of concept of the implementation of a statistical compressor. Aimple Java GUI interface provided. Best efficiency than huffman compressor. Entropy and information

Ariel is an implementation of the quadratic sieve in Java. Ariel is simple to use and requires minimal knowledge of the sieve's mechanisms for factorizations.

This project contain application to extract images from arch.H format used by Asteroid Data Hunter, and also compiled releases of updated versions of Asteroid Data Hunter itself.

Astro Info is a multi-lingual astronomical ephemeris for the PalmOS that provides data for our solar system and other objects. If you wish to get involved, please download a copy of the source code from CVS.

Astrosoft is a free indian astrology software program for astrologers and astrological students. Its a Java Swing based GUI Application. It provides Birth chart of individual with details of Lagna, Rasi, Nakshata, Thithi, Paksha and many more features.

This project assists you in performing population genetic analyses by taking over the ugly, boring and error-prone data manipulation steps. Starting from well specified input formats VCF, BED and FASTA and a unique configuration file describing data (f.e. from SNP-arrays or sequencing) as well as filtering one can create standard POPGEN formats like Eigenstrat, PEDMAP (PLINK), Treemix ... In addition there are several utilities for * generating VCF from SNPArray data (NCBI - GEO, Illumina call files) * work with genetic maps ...

Modified version of AutoGrow, autogrow.ucsd.edu/ , with a mutation script added in the class files, and a global change of the defined mutation point from Hydrogen atoms to Calphas, to allow placement of Amino Acids. Deposited are 3 versions, used for my PhD Thesis. These allow for mutation of short 2-15 amino acid peptides, and associated screening of these using AutoDock or AutoDock Vina, allowing for 8 CPU systems to screen 10K peptides a day or 1-2K with flexible residues added in. A detailed method for determining the peptide ligand for any sequenced and modeled T cell receptor will be published and link added at some point. These scripts are written quickly in a couple weeks to meet a task and could be re-written more eloquently. I may or may not work on this project again, the goal would be to introduce amino acids into any protein in openCL to allow automated design on GPU's.Limits-The standard PDB codes used slightly modified, proline not at angles, peptide shld be linear,

Control-Center for Automation. Control your PLC's and I/O's through a Database or Web-Interface DEPRECATED, NEW LOCATION: https://github.com/rudin-io/s7connector

Web service providing access to the Autshumato Machine Translation (MT) and other Moses Statistical MT systems. Functionality includes: - Automatic sentence, document, web page translation. - Improvements for translations. - Reviewer requests and interface to review improvements - Connection to the latest version of the Autshumato ITE, Post Edits done on inserted automatic translations are automatically submitted to the MTWS. - Administration interface to add users, reviewers and MT systems. - Exposed API for all of the services. - Ability to log into the system using your Google or Facebook ID. - All requests are logged by IP. Licensed under the GNU GPL v3 (or later): http://www.gnu.org/licenses/gpl-3.0.txt

AvroraZ is the branch of Avrora from the Cork Institute of Technology, Cork, Ireland aimed at improving MicaZ support thus enabling IEEE 802.15.4 compliant emulations

Aware.MPS is a maintenance productivity suite designed to measure productivity, set productivity goals, and track progress toward those goals. It is best combined with a CMMS system to monitor productivity and suggest areas for productivity improvement.

BANNER is a named entity recognition system intended primarily for biomedical text. It uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.

The BEAM project has moved away from SourceForge.net to a dedicated web site at http://envisat.esa.int/beam

The BioEnergy Allocation and Simulation Tool (BEAST) is a tool dedicated to assess political goals of woody bioenergy production in the context of available biomass potentials and corresponding economic and ecological criteria on a regional level. It is a useful tool in participative decision making processes by iterative simulation and visualization of complex issues. BEAST is a data- and model-driven Decision Support System (DSS) evaluating woody biomass potentials from forests, hedges and trees outside forests as well as short rotation coppice (SRC). The latter one is modelled spatially explicit. This opens the possibility to identify prefered areas for SRC production under different restrictions and goals. Forest wood and wood from outside forests are treated only aggregated.

An API for manipulating EDIF netlists in Java. We use this API to analyze netlists as a part of our FPGA reliability project. We intend to keep the API as general as possible to support other netlist analysis and manipulation activities. This material is based upon work supported by the National Science Foundation under Grant No. 0801876. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Baldr, aka Balder, is a plagiarism prevention software. Inspired by late researches in computer sciences, it’s able to compare documents using only properties linked to data compression.

The Bamformatics project aims to provide a coherent and consistent approach to analysis of high-throughput sequencing data. Its toolkit includes, among others, programs to identify variants and to compute various types genomic tracks. It also provides a graphical user interface to facilitate general bioinformatic workflows. The project wiki contains further details.

Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).

BeastCalc is portable, cross-platform graphing calculator utility written in Java.