Open Source Java Scientific/Engineering Software - Page 19

This program is a simulator for managing arrival and departure for different train traffic for different station , here the player acts just like a station master . Trains are created at different intervals of time with some metadata , the player is supposed to modify the signals and the switches to stop trains at the station or let them pass without any interruption. The goal will be to prevent delays , achieve maximum throughput and most importantly not cause collisions .

Triple-A (Automatic Analysis with Automata) is a full-featured library for (finite) automata written in Java with two powerful analysis tools (dealing with LTL model checking and Presburger arithmetics) and a graphical user interface built around it.

This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.

NEWS: 11-07-2013 A new version Virmid 1.1.0 has been uploaded. 08-29-2013 Virmid paper is now published in Genome Biology. Kim S et al, "Virmid: accurate detection of somatic mutations with sample impurity inference", Genome Biology 2013, 14:R90 http://genomebiology.com/2013/14/8/R90/abstract Virmid (Virtual Microdissection for SNP calling) is a Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha). The important features of Virmid are: •Estimation of accurate proporation of control sample in a (mixed) disease sample •Improved SNP and somatic mutation calling with regard to the estimated proportion

jCAE is a JAVA based environment for CAE applications. It provides meshing and visualization capabilities. It is targetted to run on a maximal number of platform.

Netsim is a mobile ad hoc network simulator targeted at large heterogeneous node configurations. It is written in Java and is easily extensible through its modular concept.

PileWorks provides the organizational structure for coordinating several different projects which approach some aspect of Pile Technology. PileWorks defines a set of interfaces and implements some basic infrastructure for Pile engines and agents.

TreeSoft is a collection of softwares that build or manipulate phylogenetic trees.

Cuttlefish aims to be a highly extensible visualization and analysis platform for all kinds of network data. IMPORTANT: The Cuttlefish project has been migrated to github: https://github.com/dev-cuttlefish/cuttlefish

This project is dedicated to open source data quality and data preparation solutions. Data Quality includes profiling, filtering, governance, similarity check, data enrichment alteration, real time alerting, basket analysis, bubble chart Warehouse validation, single customer view etc. defined by Strategy. This tool is developing high performance integrated data management platform which will seamlessly do Data Integration, Data Profiling, Data Quality, Data Preparation, Dummy Data Creation, Meta Data Discovery, Anomaly Discovery, Data Cleansing, Reporting and Analytic. It also had Hadoop ( Big data ) support to move files to/from Hadoop Grid, Create, Load and Profile Hive Tables. This project is also known as "Aggregate Profiler" Resful API for this project is getting built as (Beta Version) https://sourceforge.net/projects/restful-api-for-osdq/ apache spark based data quality is getting built at https://sourceforge.net/projects/apache-spark-osdq/

RAPSim (Renewable Alternative Powersystems Simulation) is a free and open source micro-grid simulation framework for better understanding of power flowing behavior in smart microgrids with renewable sources. It is able to simulate grid-connected or standalone microgrids with solar, wind or other renewable energy sources. The proposed software calculates the power generated by each source in the microgrid and then it conducts a power flow analysis. This software is helpful for optimal placement of distributed generation units in a micro grid. RAPSim is designed for use in science and classroom with a simple to use graphical interface. It is an easily extendable framework that supports users in implementation of their own models, for grid objects, and algorithms for grid control.

JGP is a GUI for gnuplot (http://www.gnuplot.info/). It is made for all those who just love gnuplot but who found that organizing a large number of datasets and plots from the command line is inconvenient. JGP uses gnuplot as plotting engine.

Jafama (Java Fast Math) consists of fast - but not sloppy - counterparts of java.lang.Math treatments, plus additional ones. They are usually about 2-4 (up to 15) times faster, with about 1e-15 accuracy, and handle special cases (NaN, etc.). Since version 2.1, a StrictFastMath class is also provided. It is a strictfp version of FastMath (and not a fast version of StrictMath): for a same version of this library, its methods always return a same result for same arguments, which might not be the case for FastMath depending on JIT or other JVM optimizations. Requires Java 5 or later. Available on Central since 2015/06/05. Also available on github since 2015/12/13: https://github.com/jeffhain/jafama

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).

A text editor for maths. Simple algebra should be faster and more intuitive to perform on a computer than on paper and should look like maths. Write small fragments in plain text; perform simple click-and-drag algebra with the mouse; and explore more involved algebra through keyboard shortcuts. When done, save as plain text files or export to LaTeX and HTML.

Driver support for 3D Controller Hardware. We hope to support SDL Input, DirectInput, and other major controller API's including game consoles and embedded systems.

The goal of project is delivering useful and simple tools to creating charts. Functionality is provided by modules/plugins (OSGi technology). It allows you to create your plugins or customize Analysis application (by changing installed plugins in application). The Application, thanks to JAVA technology, is portable on the most operating system. In Files page you can find the application and also patches to its.

AGTK is a suite of software components for building tools for annotating linguistic signals, time-series data which documents any kind of linguistic behavior (e.g. audio, video). The internal data structures are based on annotation graphs.

Java/XML toolkit for research using Bayesian networks and other graphical models of probability (exact and approximate inference, structure learning, etc.)

A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining.

CNC code generator is a software to generate CNC codes (G & M codes) for maching operations like milling, drilling. At present CNC code generator is limited for end milling. we working on other machining operations like turning, drilling etc.

This application is intended to help students with the basics of chemistry. It can solve basic gas laws equations, and find the molar mass of a compound or element. These tasks allow students to cut the repetition out of basic chemistry.

Crystalsim is a simple freeware program with a neat graphical user interface for X-ray diffraction (XRD) data analysis . It can simulates all possible {hkl} planes data for the selected crystal. Crystallographic Information File (.cif) can also be used. Analyze both powder diffraction and single crystal data . Indexed at International Union of Crystallography (IUCR). Crystalline lattice parameters such as ‘a’, ‘b’, ‘c’ as well as interfacial angles such as alpha, beta, gamma can also be entered manually. Processed data can be saved as .csv file format. Designed by M Kanagasabapathy, Associate Professor, Department of Chemistry, Rajus' College, Affiliated to Madurai Kamaraj University Rajapalayam (TN) India email: rrcmks(at)gmail.com

DLESE (Digital Library for Earth System Education) is a community-supported digital library dedicated to the collection, enhancement, and distribution of materials that facilitate learning about the Earth. Sponsored by the US National Science Foundation.

DicomReader is a simple Java Dicom files decipher. It handles headers and images within as well; data (headers and pixel-value images) will be saved into ascii clear text files. A pgm version of the image files is also provided.