Search Results for "java modelling tools" - Page 9
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Showing 499 open source projects for "java modelling tools"
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SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
SLiMScape adds Short linear motif discovery tools to Cytoscape, transforming it into a SLiM discovery platform. A tutorial is available at the following URL: http://bioware.ucd.ie/slimscape/ -
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ADOPS
Automatic Detection Of Positively Selected Sites
ADOPS is a bioinformatics tool that automatizes the detection of positively selected sites given a set of unaligned nucleotide sequence data. ADOPS implements a complete workflow that integrates three well-known bioinformatic tools: T-Coffee, MrBayes and Codeml (PAML). -
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SMLEditor
Prototype editor for the SDEM Mapping Language
The Gateways Team of the Live-Virtual-Constructive Architecture Roadmap Implementation (LVCAR-I) effort is developing a set of tools that will support the gateway community. One of these tools is the Simulation Data Exchange Model (SDEM) Mapping Language (SML) Editor. The tool provides the ability to import two SDEMs in their native language and subsequently view the entities that need to be mapped between the two SDEMs. The SDEM Editor also allows the user to create these mappings and... -
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ns-2 Trace Toolkit
This toolkit allows you to analyze and validate ns-2 traces
ns-2 Trace Toolkit was developed to help users to manage and debug ns-2 trace files. It is particularly useful for users that generate ns-2 trace files with other tools such as VanetMobiSim or SUMO (Simulation of Urban Mobility). With ns-2 Trace Toolkit, users can debug their trace files by generating histograms for: (1) node speed, (2) node x-position, and (3) node y-position. These histograms can give hits about concentration of nodes. Additionally, the tool allows users to simulate... -
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Security Officers Management and Analysis Project (SOMAP) is all about defining security management work methods and supplying Security Officers with tools to do their job more efficient and following standards easily.
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HLAgile
Tools for distributed simulation
This project is devoted to producing tools to help HLA developers write software that is less tied to vendor specific libraries and/or particular FOMs. -
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openSCADA
openSCADA® is an open source SCADA system written in JAVA
openSCADA is an open source Supervisory Control And Data Acquisition System. It is platform independent and based on a modern system design that provides security and flexibility at the same time. openSCADA is flexible. It is not an out of the box solution, but a set of tools that can be combined in many different ways. It provides development libraries, interface applications, mass configuration tools, front-end and back-end applications. openSCADA is ready to rock. It is used 24/7 in... -
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cnvHiTSeq
cnvHiTSeq is a set of tools for detecting CNVs using sequencing data.
cnvHiTSeq is a set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. cnvHiTSeq uses standard BAM files as input. -
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Java & MPEG-7 based tools for annotation and retrieval of digital photos and images (Caliph & Emir). LIRE has moved to https://github.com/dermotte/lire. Caliph & Emir have moved to https://github.com/dermotte/CaliphEmir.
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TreeGrOSS Forest Growth Simulation
Software for modelling tree growth
Tree Growth Open Source Software is a Java based version of the forest growth simulator for north west Germany BWINPro. -
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The Prajna project is a collection of tools and utility classes combining visualization, geographic displays, data fusion, and semantic reasoning into a cohesive toolkit for enhancing information discovery and reasoning.
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SPiM2Eclipse
Eclipse plugin for Stochastic Pi Machine
Stochastic Pi Machine (SPiM), created by Microsoft, is a programming language for modeling biological processes. Two tools are available from Microsoft for simulation. A web application Visual SPiM, and a destkop application SPiM Player. Both simulation tools require to be run on a Windows platform. Fortunately Microsoft has also released a command line version for Linux and Mac OS based on OCAML however this version will only output a CSV file for the simulation results.... -
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Open Rocket Toolkit
Simulation of historical and contemporary launch vehicles
ORT is a tool for modelling and flying launch vehicles of arbitrary size and complexity. Unlike OpenRocket, it does not focus on amateur rockets but on real-world launch vehicles. The bundle includes a graphical design tool with an integrated simulation engine for rocket launches. Also included in the bundle is a playback application and a headless driver for logging simulations into spreadsheets. ORT integrates JME3 for 3D rendering. -
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GIIAF Microscopy Library
The GIIAF Microscopy Library, that uses customised OMERO software
This project incorporates a suite of tools that aim to allow researchers within Griffith's Imaging and Image Analysis Facility (GIIAF) to efficiently and effectively provide secure, centralised, web-accessible data storage, management and manipulation. The open-source Java-based OMERO software was customised to provide most of the features of this project. -
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ELECANS
Electronic Computational Cancer Systems Biology Simulation Studio
A computational model development and simulation environment for cancer systems biology. ELECANS is the state of the art in the multi agent simulation tools available for computational modeling of tumorigenesis in a variety of tissues. -
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MionChrom
Signal processing for chromatography
MionChrom interprets ASCII data from GC-C-IRMS systems, plots it, identifies peaks and autointegrates the results. The user can manually integrate peaks with different tools. The results is reported in *.XLS, *.TXT and *.PNG. ------------------------------------------------------ MionChrom is soon to be replaced by MionMass which isn't a open sourced project. -
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Ontology Testing
Part of the XD Tools plugin for ontology testing.
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Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files
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Darwin 2: Java Framework for Evolutionary Computation (genetic algorithm, GA). A true framework with out-of-the-box functionality and extensibility of all classes. Interface-based pattern with dependency-injection to configure components.
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Decision Table Preprocessor
Ccide is a Decision Table preprocessor.
Ccide reads a source program, in one of several programming languages, expands all embedded decision tables, and generates the new, expanded source. Ccidew processes C language programs directly. The script, ccide, uses ccidew and m4, to process BASIC, JAVA, CC, C++, BASH, QB, VB, and EX(euphoria), source files containing embedded decision tables. Ccide checks all conditions once and only once, avoiding side effects. Ccide checks tables for conflicts and other... -
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Jnomics
Jnomics is a collection of cloud-scale DNA sequence analysis tools
Jnomics is a collection of cloud-scale DNA sequence analysis tools -
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CUO
Codon Usage Optimizer
CUO is a GUI-based multiplatform software written in Java. It is open source and built with a user/developer-friendly structure. The main function of the software at the current development stage is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome although it can be used to optimize genes into other hosts as well. The main tool in CUO, Moptimizer, introduces a semi-automatic way of gene optimization which provides more flexibility and accuracy during... -
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Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).