Open Source Java Scientific/Engineering Software - Page 23
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Java Scientific/Engineering Software
View 202 business solutionsBrowse free open source Java Scientific/Engineering Software and projects below. Use the toggles on the left to filter open source Java Scientific/Engineering Software by OS, license, language, programming language, and project status.
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BioPPSy
A biochemical property prediction system
Computationally predicts the pharmacokinetic properties of drug candidates using Quantitative Structure Property Relationships (QSPR) modelling. Assembles a set of tools and databases for predicting the physical properties of small molecules. The program models a given property's dependence on a collection of molecular and structural descriptors using a training set of molecules. Neural networks and support vector regression are available, as well as linear models. The models generated by this analysis can then be used to predict the properties of compounds during the development of new and novel drugs. The program and its databases are all open-source. -
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
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 -
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BitLogic
Simple Java computer algebra calculator
A calculator that solves many types of problems including solving equations computing derivatives and integrals simplifying expressions graphing equations 2d and 3d reverse polish notation, algebraic and word based interpreter infinite writing board for writing out equations requires java 11 or more -
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CalclipseMath
Java math expression parser and script interpreter
CalclipseMath – CalM for short – is a math parser written in Java. With a few lines of code CalM enables your application to evaluate user-supplied mathematical expressions, such as "e^(sin .25pi)" and "(sqrt e)^(sqrt 2)". The standard configuration of the parser has a wide variety of mathematical operations, ranging from basic arithmetic, trigonometry, combinatorics, linear algebra and more. CalM includes a script interpreter which is based on the math parser. The CalM scripting language lets you define your own functions and variables. These may be exported and used in other scripts. The scripting framework supports a component type called MComp (Math Component). MComps are implemented as Java classes and allow further extension to the scripting language. Please visit www.calclipse.com for more information about CalclipseMath and other Calclipse products. -
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Catania Science Gateway Framework
Framework based on standards to build Science Gateways
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IDL specified API for manipulating and processing CellML 1.0 and 1.1. Includes C++ implementation. Accessible from a C++ program, or from any language for which a CORBA language mapping is available Also, a Java wrapper of the API is available.
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Classic Monitor
Android app to monitor a Midnite Solar Classic charge controller
Now available on Google Play at <https://play.google.com/store/apps/details?id=ca.farrelltonsolar.classic> The source code is now maintained on <https://github.com/graham22/Classic> Classic Monitor is a free status monitor for Midnite solar 's, Classic 150, 200, 250 Charge Controller. It is a Read Only Program, it does not write to the Classic. The software is provided "AS IS", WITHOUT WARRANTY OF ANY KIND, express or implied. Classic Monitor is NOT a product of Midnite solar, nor do they support this application! If the app detects a Whizbang Junior current monitor, the State Of Charge will display along with a bi-directional current gauge. Other features include a calendar view of the daily power readings and a chart view of power for the last 24 hours, plus a store and forward feature to upload data to <PVOutput.org>. Basic support for the Tristar MPPT charge controller from Morningstar. Works with Android API level 10 (Gingerbread) and above. -
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This projects intends to develop a complete distributed peer-to-peer environment for running heuristic optimization, modelling, artificial life, etc applications. This involves a network engine, libraries and different user interfaces. All this in java.
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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.
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This project tracks the altitude and position of rockets equipped with an RF signal using the Doppler Effect.
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EDM Calibration Baseline Fitting
EDMFit is an adjustment tool to estimate EDM calibration parameters.
An EDM calibration baseline is used to derive specific instrument errors of the electronic distance measurement (EDM) unit of a total station. EDMFit is a simple adjustment tool to estimate the EDM calibration parameters (addition constant and/or scale parameter). The adjustment process is according to ISO 17123-4. The parameters are checked for significance, to avoid an overestimation. Based on two classical hypothesis testing, EDMFit provides a reliable outlier detection. For uncertainties budgeting, EDMFit makes use of Monte-Carlo simulations and supports different distribution function: - Uniform distribution, - Triangular distribution and - Gaussian (normal) distribution. For refractive index determination, the application supports the following models: - Barrel and Sears (1939), - Edlen (1953, 1966), - Owens (1967), - IAG (1999) and - Ciddor (1996, 2002). The results of the adjustment are reported in a template-based and valid HTML5/CSS3 report. -
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EPICS Version 4
MOVED project - go to: https://epics-controls.org
This project has been merged into EPICS Base. Visit https://epics-controls.org for further information. -
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EXTE recognizes temporal expressions in a text. Temporal expressions are any references to the TIME e.g.: "today", "12th march 2006", "as soon as he woke up". This analyzer will recognize three languages: Spanish, English and French.
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A small Java program for reading, analysing, viewing and animating the data from an EEG machine during a psychology experiment.
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A visualizer for FRAM (Functional Resonance Accident Model), a JCS-model developed by Erik Hollnagel at LiU, Sweden. This tool helps modelling the the FRAM table and visualize it. This project has moved to http://code.google.com/p/framvisualizer/
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Fachwerk calculates strut-and-tie models used by structural engineers for analysing and designing reinforced concrete structures. The program only uses the equilibrium conditions, thus it is not assuming elastic behaviour.
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Fylogenetica
Constructing level-1-networks consistent with a set of quartets
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. -
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G4LTL-ST
Generating PLC programs from formal specifications
G4LTL-ST is a standalone tool and a Java library for automatically generating industrial control software (supporting IEC-61131-3 Structure Text) from LTL or extended logic specifications. See Tutorial.txt inside the package for step-by-step instructions. For technical demails, see CAV'14 paper "G4LTL-ST: Automatic Generation of PLC Programs". The old version (G4LTL; under BSD license) is available under file\arxiv. -
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GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.
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GriF is a new JAVA Collaborative Grid Framework developed by COMPCHEM Virtual Organization operating in the EGI Production Grid environment aimed at running multi-purpose scientific applications empowering Grid massive calculations.
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HermeneutiX
Your graphical tool for Syntactic/Semantic Structure Analysis of texts
HermeneutiX is a tool for diagramming syntactic and semantic structures of complex (not necessarily foreign-language) texts (e.g. bible or other historical excerpts). HermeneutiX is now part of SciToS (the scientific tool set). Starting with version 2.0.0, HermeneutiX can be found on GitHub. Please check out the release summary: https://github.com/scientific-tool-set/scitos/releases For an introduction, check out this video: https://youtu.be/uQjewyG0Ad8 PS: To run a Java application such as HermeneutiX (i.e. SciToS) you need a Java Runtime Environment (JRE). HermeneutiX is currently built to be compatible down to JRE version 6. You may download the current JRE here: http://www.java.com/en/download -
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IAP.G2P
IAP - the Integrated Analysis Pipeline
The Integrated Analysis Platform (IAP) has been designed and developed to support the analysis of large-scale image data sets of different camera systems. It aims in bridging different data domains and in integrating different approaches to data analysis and post-processing. -
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IQM
Scientific Image and Signal Analysis in Java
IQM has moved to GitHub -
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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.
