Open Source Java Scientific/Engineering Software - Page 27

Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj

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.

CySBGN adds support to Cytoscape to import, export, visualize and analyse System Biology Graphical Notation (SBGN) maps.

This project implements a Cytoscape plugin for viewing and manipulating pathway maps for metabolic models created by the Model SEED (http://www.theseed.org/models). See the "Files" area for README. See Project Homepage for Tutorial.

The Databionics ESOM Tools offer many data mining tasks using Emergent Self-Organizing Maps. Visualization, clustering, and classification of high-dimensional data using databionics principles can be performed interactively or automatically.

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.

New Zealand Distributed Information Systems (NZDIS) Distributed, heterogenous, agent-based framework for intelligent/semantic information and services integration.

This project tracks the altitude and position of rockets equipped with an RF signal using the Doppler Effect.

DotPlot is an Eclipse plug-in to graphically compare word sequences of any type of text. Matches will be plotted as dots on a graph. Similarities in thousands of lines of text or code will result in typical textures and diagonals in the plot.

A small Java program for reading, analysing, viewing and animating the data from an EEG machine during a psychology experiment.

This project is an implementation of an algorithm by J. Keijsper and R. Pendavingh. The goal of the algorithm is to construct a phylogenetic level-1-network that is consistent with a given set of quartets.

GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. Contact: bmhoan@gmail.com or walter.vincent.fr@gmail.com

GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/.

GRAIL Real Time Location Service (RTLS)

GUI Ant-Miner is a tool for extracting classification rules from data. It is an updated version of a data mining algorithm called Ant-Miner (Ant Colony-based Data Miner).

HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2 (http://samtools.github.io/hts-specs/VCFv4.2.pdf). HTDP provides quick filtering functionality and can process data consisting of single or multiple input files. Citation: Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, et al. (2018) High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets. PLoS ONE 13(2): e0192858. https://doi.org/10.1371/journal.pone.0192858

InterPSS is an internet technology based software system for design, analysis, and simulation of power systems. Please visit www.interpss.org and wiki.interpss.org for more information.

JABM is a Java framework for building agent-based simulation models using a discrete-event simulation framework.

JCad is a project to create a fully function 2D CAD program written entirely in Java. It\\\'s Purpose is to create a cross platform smart 2D CAD program with Java2D/Swing.

Create ports : TCP/UDP/Terminal/File/RS232(txrx)/DB/System/Bluetooth/JNA/ETH(jpcap)/Sound. Simply configure with GUI/SFC XML file/CLI. Display, modify, replay, store (tcpdump), decode flow of bytes or objects. Implement : loop/echo/paddings/... and delai/DB2XML/Stacks/Matrix/... management. Stream conversations with a dynamic packet analyse.

In the regulatory assessment of chemicals (e.g. under REACH), Quantitative Structure Activity Models (QSAR) are playing an increasingly important role in predicting properties for hazard and risk assessment. This implies both a need to be able to identify relevant QSARs and to use them to derive estimates and/or have access to their precalculated estimates. To help meet these needs, the JRC QSAR Model Database is established and freely accessible through http://qsardb.jrc.ec.europa.eu/qmrf The QSAR Model Reporting Format (QMRF) is a harmonised template for summarising and reporting key information on QSAR models, including the results of any validation studies. The information is structured according to the OECD validation principles. Download the QMRF Editor in order to describe your models in QMRF format and send the descriptions to JRC-COMPUTOX@ec.europa.eu to have them included in the database. More at http://qmrf.sourceforge.net/

Multipresicion calculator, based on Bigdecimal Java class . It has a library (BigMath) that makes calculations with Bigdecimal. It has also an expression parser to parse the user input. It allows you to store user defined variables and functions . You can operate with them to be used for calculations or for creating new functions with composition. With the new version, you can also calculate the derivative of a function. JDK-17 compatibility You can find more about it at this web site: https://www.frojasg1.com:8443/downloads_web/web/html/calculadora.html?origin=sourceforge

JavaSeis.org: Java based software for processing and storing petroleum industry seismic data.

The new version is available at https://sourceforge.net/projects/ghawwasv4/

LARS (Lightning Assessment of Risk for a Structure). LARS is a simple tool for the lightning assessment of risk for a structure, according to standard IEC 62305-2, second edition.