Search Results for "mchange-commons-java" - Page 37
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Showing 4563 open source projects for "mchange-commons-java"
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Virmid
Virtual Microdissection for SNP calling
...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). ... -
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OpenTRV
Open-Source Thermostatic Radiator Valve
Retrofit completely-open reference mechanical/hardware/software design for zoned heating control not relying critically on any proprietary/hacked components. The aim is to include at least one complete mechanical and software design for a replacement TRV head that can be retrofitted without any plumbing plus at least one simple boiler control to allow end-to-end open soft heating zoning, with the ability to connect to home automation system or the Net if required. -
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merlin is an user-friendly Java application that performs the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs several steps of the reconstruction process, including the functional genomic annotations of the whole genome. Moreover, merlin includes tools for the identification and annotation of transport proteins encoding genes, as well as the generation of transport reactions for such carriers.
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eyeCure
eyeCure helps you cure your ill eyes, tired or intermittent exotropia.
eyeCure helps you cure your tired eyes or intermittent exotropia (exodeviation) by forcing you take rest regularly, if you don't feel good in eyes, or even have headache for too much computer usage. eyeCure did help me feel much better. Hope it helps you too. -
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Temperature Unit Converter
Temperature Unit Converter
...(Or by visiting this page from your Android device) ---------------------------- A simple and useful GUI(Linux only) and command line program that lets you convert widely used temperature units to each other: Fahrenheit, Celsius and Kelvin. ------------------------------- Written by İ. Yuşa Çetin Using Python and gtk for GUI, C for algorithms and command line usage, Java for the Android version. ------------------------------------- This is still a Beta, so no one in the universe is responsible for anything happens :) I have it on my own computer and it's working properly. If you find any bugs feel free to tell me : yusha493@gmail.com --------------- If you are interested in translating the Android app to another language,current languages: *English *Turkish -Both by me :) ,please contact me: yusha493@gmail.com -
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available... -
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MOEA Framework
A Free and Open Source Java Framework for Multiobjective Optimization
The MOEA Framework is a free and open source Java library for developing and experimenting with multiobjective evolutionary algorithms (MOEAs) and other general-purpose multiobjective optimization algorithms. The MOEA Framework supports genetic algorithms, differential evolution, particle swarm optimization, genetic programming, grammatical evolution, and more. A number of algorithms are provided out-of-the-box, including NSGA-II, NSGA-III, ε-MOEA, GDE3 and MOEA/D. -
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Ichnaea
Performance Timing Tools
Ichnaea is a set of tools that aid in collecting and tracking parameters and timings for parallel applications. The Performance Modelling Timing Module, PMTM, is a library that wraps system timing calls to abstract these from code developers and aid portability. It also has functionality to store parameters and print those, along with the timing information to a comma separated variable file. The Performance Modelling Analysis Tool, PMAT, is coming soon. This is able to read in and... -
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Krowface (Krowdix 3.0) is a simulation and implementation tool of social networks. To visualize and analyze the evolution of different social networks in real time. And the creation of a social network, configuring the parameters that define it. All this through a simple web interface and user friendly.
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Lompad
Metatagging Editor for Learning Object Metadata (IEEE's LOM)
Lompad is a metatagging tool for learning object. It supports the IEEE-lom spec and SCORM, CANCORE and Normetic profiles. The interface is available in French, English and Spanish Consult the project's Web Site for more information. -
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Transcriptome assembly ORA
Reference-based transcriptome reconstruction software
Sofware for reference-based transcriptome reconstruction. It performs reconstruction starting from short reads obtained from RNA-seq. It is best suited to manage the transcriptomes of lower eukaryotes with a low number of introns per gene and it can be used also for procariotes. It needs a SAM file with the reads aligned on the reference genome and (optional) a gff file with the position of genes on the reference genome. It provides in output the positions of the transcripts identified,... -
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Tellervo
Dendrochronological sample measurement, curation and analysis program
Tellervo enables users to measure, curate and analyse dendrochronological samples. It has a server/client architecture enabling users to collaborate within and between laboratories. -
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xorlisp
Bit level lambda continuations and nothing else - Queue automata
Not working yet. To deal with the Halting Problem, computing and data are navigated using debugger ops: linearForward and treeForward, which navigate an astronomically large bit string where 1 is ( and 0 is ). All pairs are derived from (). For example, true is represented as ((()())()), and false is (()(()())). It appears related to the church encoding of lambda where T chooses first parameter and F chooses second, of a pair. Continuations are nearly finished code and are represented as a... -
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MD PnP | OpenICE
Open Source Integrated Clinical Environment
As of 2015-06-23, this project may now be found at http://www.github.com/mdpnp/mdpnp. A prototype reference implementation of the standard for the Integrated Clinical Environment (ASTM F2761-2009) -
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SEWOL: Security-oriented Workflow Lib
Java Library for workflow handling
SEWOL provides support for the handling of workflow traces. It allows to specify the shape and content of process traces in terms of entries representing the execution of a specific workflow activity. Currently it supports plain text, Petrify, MXML and XES log file types. In order to specify security-related context information, SEWOL provides access control models such as access control lists (ACL) and role-based access control models (RBAC). SEWOL uses and encloses the following... -
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SEPIA: Security-oriented PN Framework
Petri net framework for security related modeling and reasoning.
SEPIA provides implementations for various types of Petri nets. Along Place/Transition-nets, it supports Petri nets with distinguishable token colors and defines coloured workflow nets, where coloured tokens are interpreted as data elements used during process execution. To support information flow analysis of processes, SEPIA defines so-called IF-Nets, tailored for security-oriented workflow modeling which enable users to assign security-levels (HIGH, LOW) to transitions, data elements and... -
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XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
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DbOutputter4RS
Plugin for Repast Simphony that supports storage of results in a DB
Insalling the plugin it is possible to direct data collected by data gatherers into a MySQL database. The database connection is configured via a wizzard. The whole process is similar to putting data to a file. -
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Interactive Web Physics is a Java, Web-based animation and problem designer tool. Anyone can quickly design mathematics or physics animations and simulations that run in a web browser. Unlike other solutions, no knowledge of programming is required.
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Protein Contact Matrix Generator
Command line application to generate contact matrix from proteins (3D)
A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). Contact Maps can be used to understand... -
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Usul
Foundation bolt load for Pressure Vessel
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Moved to GitHub. This is the old, unmaintained source code. https://github.com/zet-evacuation A tool to model and simulate evacuation situations in buildings using flows on graphs and cellular automatons. It allows visualization of both models in OpenGL.
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XMLPipeDB is a suite of tools for building relational databases from XML sources with minimal manual processing of the data. While the applicability is general, our motivation was to facilitate the management of biological data from different sources.
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