Search Results for "system linux"
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Showing 44 open source projects for "system linux"
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Lush is a Lisp dialect with extensions for object-oriented and array-oriented programming. Lush is intended for prototyping numerically intensive applications and is designed for easy integration of existing C/C++/Fortran codes.
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SBW (Systems Biology Workbench)
Framework for Systems Biology
The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as... -
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.
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MOIRAI
Simple Scientific Workflow System for CAGE Analysis
Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data.... -
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SoundRuler is a tool for acoustic analysis, graphing and teaching. It interactively recognizes and measures 35 temporal and spectral properties of each sound in a file. It also features several measurement, graphing and didactic modules.
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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting... -
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ExAM-Exome_Analysis_And_Mining
A whole exome sequencing analysis package and its graphical interface
During the past few years, whole exome sequencing has imposed itself for genetic research, largely due to its use for detection of causative mutations responsible for Mendelian disorders. As a consequence of their power and of the rapidly decreasing cost of these technologies, massive amount of exome sequencing data are generated and becoming available to a broadening community of scientists. However, these data remain difficult to analyze and interpret by the general scientific community,... -
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TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.
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The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.
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XNBC: neurobiology simulation tool
XNBC is a graphic application to simulate biologic neural networks.
XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows. Web site : http://ticemed-sa.upmc.fr/xnbc/ All recent versions are on this site. -
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Gene Ontology Browser
Browser for viewing Gene Ontology (GO) .obo files.
Go Browser allows you to view a gene ontology on your local machine. You can go up and down the hierarchy and inspect the terms. It's a good way of familiarising yourself and orienting yourself in the GO system. It's built using the Baby X toolkit, so has no dependencies other than xlib. Baby X has now also been ported to Windows, so a Windows version is available. -
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GENESIS (GEneral NEural SImulation System) is a software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.
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fqzcomp
A fastq compression program
Fqzcomp is a basic fastq compressor, designed primarily for high performance. Despite that it is comparable to bzip2 for compression levels. -
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A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8
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parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS. A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run. A...
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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection
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Juggernaut is a high throughput out of core sequence assembly algorithm. This program is very useful in assembly projects involving massive number of short reads which originate from high coverage of the genome.
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The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network. Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!
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Stand-alone software tool for the interactive CE analysis of microarray data. The software is a user-friendly and allows on-the-fly study of CE
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The EvoGrid is an effort to develop a distributed simulation system to simulate potential pre-biotic chemical environments.
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Palex is a two-stage biological sequence searching system. Library will contain functions for searching patterns, palindromes and structures in DNA sequence.
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ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.
