Search Results for "c programming framework"
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32 projects for "c programming framework" with 2 filters applied:
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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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PhysiCell
physics-based multicellular simulator
PhysiCell is a cross-platform C++ framework for large, physics-based multicellular simulations. -
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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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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. -
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bioweb
polyglot language framework to analyze genetic data
polyglot framework using Python/C++/JavaScript to fast develop applications to analyze biological sequences -
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An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
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Phaistos is a framework for all-atom Monte Carlo simulations of proteins. It incorporates several advanced probabilistic models of protein structure for conformational sampling, efficient move-algorithms and the OPLS and PROFASI forcefields.
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LightPCC
Parallel pairwise correlation computation on Intel Xeon Phi clusters
The first parallel and distributed library for pairwise correlation/dependence computation on Intel Xeon Phi clusters. This library is written in C++ template classes and achieves high speed by exploring the SIMD-instruction-level and thread-level parallelism within Xeon Phis as well as accelerator-level parallelism among multiple Xeon Phis. To facilitate balanced workload distribution, we have proposed a general framework for symmetric all-pairs computation by building provable bijective functions between job identifier and coordinate space for the first time. -
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bio-cargo
CARGO - Compressed ARchival for GenOmics
CARGO is a high-level framework that can semi-automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of CARGO methods to compress FASTQ and SAM format archives require only a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors, and scale well to multi-TB datasets. -
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openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.
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SPA
SPA: a short peptide assembler for metagenomic data
The metagenomic paradigm offers the opportunity to study protein families, and therefore the metabolic and functional potential, of the constituent microbes in a community. A nucleotide assembly-based strategy does not fare much better since metagenomic assemblies are typically very fragmented and also leave a large fraction of reads unassembled. We present a method for reconstructing complete protein sequences directly from NGS metagenomic data. Our framework is based on a novel Short... -
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SOAPdenovo-Trans
A de novo transcriptome assembler.
Latest Codes on GitHub: https://github.com/aquaskyline/SOAPdenovo-Trans SOAPdenovo-Trans is a de novo transcriptome assembler inherited from the SOAPdenovo2 framework, designed for assembling transcriptome with alternative splicing and different expression level. The assembler provides a more comprehensive way to construct the full-length transcript sets compare to SOAPdenovo2. -
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smalt
A mapper for DNA sequencing reads
SMALT aligns DNA sequencing reads with genomic reference sequences. It employs hashing combined with dynamic programming. -
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hrefinder
Detection of homologous recombination events from SNP data
This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of... -
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DeltaQt
Parser for DELTA files (Qt, C++)
DeltaQt is part of the FreeDelta project and aims to implement a parser for DELTA (DEscription Language for TAxonomy) files using the Qt core framework. DeltaQt is a library intended to be incorporated into other applications that require the ability to parse DELTA files. -
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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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A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
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AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general. AnnaF was build upon the pipeline framework Anna.
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4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
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Structlab is a machine learning C++ framework for structured domains, which provides a toolbox of learning methods and tools for preprocessing and visualization. It also provides a GUI to setup elaborate experiments in a visual and intuitive way.
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The JefNET (Java Evolutionary Framework Network) Proj. consists of three subprojects: JEF, Dna, JXTAJef. Our intent is to provide a distributed genetic programming framework for the Java language, and a network in which classes can spontaneously evolve.
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Sehr Gut Libs (sglibs) is a set of utility libraries for general and scientific programming. It includes stack and string manipulation, CGI I/O, config file parsing, and sequence-processing for molecular biology.
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Genetic programming environment to inference context free grammars base on positive and negative examples of language.
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OpenEMS™ is the multi platform Grid framework to seamlessly aggregate all your multi platform resources into a virtual super computer.
