Search Results for "command line" - Page 4
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Showing 478 open source projects for "command line"
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Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutit
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sgmweka
Weka wrapper for the SGM toolkit for text classification and modeling.
...Has lower time complexity of classification than comparable software due to inference based on sparse model representation and use of an inverted index. The provided .zip file is in the Weka package format, giving access to text classification. Other functions are usable through either Java command-line commands or class inclusion into Java projects. -
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Yali is "Yet Another LCN Interface". "Local Control Network" (LCN) is a building control and automation system, a trademark of Issendorff GmbH. Yali opens the door for MAC and Linux users to control their LCN installation via LAN.
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diasim
Dialogue Similarity
Tools for calculating similarity (including lexical and syntactic) between speakers in dialogue, across standard and randomised corpora. -
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CSV Transformer
transforms xml to csv
The CSV Transformer is a data processing tool which transforms .xml-Files to comma separated values. The CSV Transformer was created in a load and performance testing project, the use case was to be able to transform 2800 configuration files of a big banking application to a single .csv-File. With this single file it was possible to compare the whole configuration between two releases with the already available tool CSV Comparator. This enabled the team to verify if there were any... -
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EV3Utils
LEGO EV3 Utilities and Assembler
EV3Utils are Communication and Assembler utilities written in JAVA for working with the LEGO Mindstorms EV3 from Linux. A command line interface is provided which can be used to up- or download projects as well as assemble new bytecode files. Communication with the brick is currently limited to USB-only, but other transports should be easy to add. The assembler supports all of the functionality of the one provided by LEGO, but uses a slightly different syntax and supports far more error checking. ... -
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jAudio is a project implementing a number of common feature extraction algorithms for analyzing audio in java. Output is either in Weka's ARFF format or the ACE format. Can be used either as a GUI application, command-line application, or embedded. The primary repository is on github (dmcennis) which pushes to this projects github repository.
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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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Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
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CRAFT HPC Floating-point Analysis
CRAFT: Configurable Runtime Analysis for Floating-point Tuning
CRAFT (Configurable Runtime Analysis for Floating-point Tuning) for HPC (High-Performance Computing) uses binary instrumentation to perform runtime analysis of floating-point code, detecting cancellations and making precision level recommendations. NOTE: THIS PROJECT HAS MOVED TO GITHUB!!!! https://github.com/crafthpc/craft -
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came
Identification of chromatin accessibility from NOMe-seq
Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, nucleosome occupancy and methylome sequencing (NOMe-seq) has been developed for simultaneously profiling of chromatin accessibility and DNA methylation on single molecules. However,... -
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FREJ stands for "Fuzzy Regular Expressions for Java" - it is a command-line tool and library which allow you easily compare strings with patterns disregarding nasty typos and considering several variants (like "Barack Obama", "B.H.Obama" etc.) Project sources are moved to github: https://github.com/RodionGork/FREJ
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MARF is a general cross-platform framework with a collection of algorithms for audio (voice, speech, and sound) and natural language text analysis and recognition along with sample applications (identification, NLP, etc.) of its use, implemented in Java.
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Program jobman (Job Manager) glues executables written in different languages according to a given flow. The program can run executables with arguments in parallel (multiprocessed) or in loop or in any combination of them.
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KneeTex is an open–source, stand–alone application for information extraction from narrative reports that describe an MRI scan of the knee. Given an MRI report as input, the system outputs the corresponding clinical findings in the form of JavaScript Object Notation objects. The extracted information is mapped onto TRAK, an ontology that formally models knowledge relevant for the rehabilitation of knee conditions. As a result, formally structured and coded information allows for complex...
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memesa-tools
A collection of tools used in the enumeration of solution spaces
This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function. -
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Toolkit for processing genetic data. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED, PED2RAW conversions; regions of homozygousity and other converters.
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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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Temperature Unit Converter
Temperature Unit Converter
...You can download .apk file from 'Files' section. (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. ... -
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StreamAID
A framework for prototyping and testing P2P live streaming algorithms
StreamAID facilitates fast prototyping of P2P live algorithms that can be built in a modular approach. -
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JMCAD is an program for the modeling and simulation of complex dynamic systems. This includes the ability to construct and simulate block diagrams. The visual block diagram interface offers a simple method for constructing, modifying and maintaining complex system models. The simulation engine provides fast and accurate solutions for linear, nonlinear, continuous time, discrete time, time varying and hybrid system designs. With JMCAD, users can quickly develop software or "virtual"...
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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 proteins' : 1. ... -
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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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An API for manipulating EDIF netlists in Java. We use this API to analyze netlists as a part of our FPGA reliability project. We intend to keep the API as general as possible to support other netlist analysis and manipulation activities. This material is based upon work supported by the National Science Foundation under Grant No. 0801876. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the...
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JGAP is a Genetic Algorithms and Genetic Programming package written in Java. It is designed to require minimum effort to use, but is also designed to be highly modular. JGAP features grid functionality and a lot of examples. Many unit tests included. Legal notice/Impressum: Klaus Meffert An der Struth 25 D-65510 Idstein sourceforge <at> klausmeffert.de
