Search Results for "java to c++ converter"
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Showing 65 open source projects for "java to c++ converter"
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Systems Biology Markup Language (SBML)
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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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 SED-ML, SBML and MIRIAM. -
Desktop and Mobile Device Management SoftwareDesktop Central is a unified endpoint management (UEM) solution that helps in managing servers, laptops, desktops, smartphones, and tablets from a central location.
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Quadric
Application for simple base-2 binary to base-4 DNA-code conversion
Quadric is an opensource file converter created by the Jomcraft Network development team. In it's core functionality this small utility can transform base-2 binary files into base-4 DNA-coded human-legible ASCII-files. -
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fcGENE: Genotype format converter
Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)
Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. Similarly all kinds of imputation of outputs are also accepted. Formats which can be generated by... -
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This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are... -
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Projects and applications developed from the lab of Yuval Kluger at the Pathology department at Yale
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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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erne
ERNE - Extended Randomized Numerical alignEr
We present ERNE (Extended Randomized Numerical alignEr), a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners), -
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GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
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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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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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SBSI (Systems Biology Software Infrastructure) is a suite of tools for systems biology, such as parallelized numerical algorithms, and a Java, Eclipse RCP based client for visualizing results, running simulations, and integrating SBML based plugins.
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CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information: [1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU.... -
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scipion-xmipp
Image processing framework to integrate EM software packages.
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. It is integrated... -
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FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
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NIKS
NIKS (Needle in a K-stack) - detection of mutations in NGS data
To get access to the code, please check it out with svn as described in the code section. -
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Genetic data converter
Convert genetic data for hapmixmap software
Genetic data converter, for hapmap.org and hapmixmap data formats. Reads data in tabular format and writes in hapmixmap format. It's possible to add extensions to output different data formats. -
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IDL specified API for manipulating and processing CellML 1.0 and 1.1. Includes C++ implementation. Accessible from a C++ program, or from any language for which a CORBA language mapping is available Also, a Java wrapper of the API is available.
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PARSEC - PAtteRn SEarch / Context
PARSEC - PAtteRn SEarch and Contextualization
The characterization of genomic sites is a major challenge in the understanding and exploitation of next generation sequencing data. Most genomic sites are represented by short, degenerated motifs with a scattered distribution and sometimes with biological function (ex: regulation of gene expression, splicing patterns or epigenetics signals). These motifs are associated with a huge amount of noise and thus, the development of a computational platform for accurate detection of genomic sites... -
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