Search Results for "c code compiler"
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Showing 41 open source projects for "c code compiler"
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Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc
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GenForm
Generation of molecular formulas by high-resolution MS and MS/MS data
This is an open source implementation of molecular formula calculation by high resolution MS and MS/MS data as described in M. Meringer, S. Reinker, J. Zhang, A. Muller: MS/MS Data Improves Automated Determination of Molecular Formulas by Mass Spectrometry. MATCH Commun. Math. Comput. Chem. 65, 259-290, 2011. The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can... -
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are... -
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dualword-chem
chemical viewer
chemical viewer written in C++ (Qt, RDKit) Source code: http://github.com/dualword/dualword-chem -
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Fast and efficient 3D pharmacophore search developed by the Camacho Lab (http://smoothdock.ccbb.pitt.edu) at the University of Pittsburgh. Source code is available through the svn repository.
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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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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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Patlac--Xml2cpp is a totally customizable code generator that generates classes (c++ for now) automatically from a xsd schema. Classes are described in google-ctemplate files and a xml options file allow precise definition of projects.
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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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Stop vibe-debugging.AppSignal's MCP server hands Claude, Cursor, or Zed your real errors, traces, and the deploy that shipped them. AI writes the fix; you review the diff.
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GenCodeGenerator
C++ class to generate biologically plausible genetic codes
The "GeneticCode" C++ class is designed to generate versions of the genetic code subject to the requirements of the three major models of the genetic code origin and evolution (about these models see, e.g., Koonin & Novozhilov, 2009, IUBMB Life). This class was written specifically to perform statistical test for the paper Makukov & shCherbak (2017), but it might be used for a wider class of studies related to the genetic code. -
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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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...Source Code for Biology and Medicine, 2014 9:30] HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. HeatmapGenerator is released under the GNU GPL.
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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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Moose
Multiscale Neuroscience and Systems Biology Simulator
Moose is the core of a modern 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. We have moved Github.com. This should be your source for the latest version of the code. -
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Madeline 2.0 Pedigree Drawing Engine
Madeline 2.0 Pedigree Drawing Engine (PDE)
The Madeline 2.0 Pedigree Drawing Engine is a pedigree drawing program designed to handle large and complex pedigrees with an emphasis on readability and aesthetics. PLEASE NOTE THAT as of 2015.09.30, the most current Madeline source code tree is now maintained on GITHUB at https://github.com/piratical/Madeline_2.0_PDE . -
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parSRA
Portable Framework for the Parallel Execution of Short Read Aligners
...It uses the following techniques in order to improve scalability: 1) a fast splitting of the input reads using the FUSE kernel module available in most of current Linux distributions; 2) a balanced on-demand distribution of the reads based on the shared locks of UPC++, an extension of C++ for parallel computing that follows the Partitioned Global Address Space (PGAS) paradigm. parSRA is portable as its configuration file allows the users to parallelize the execution of existing SRA tools without the need to modify the source code of parSRA or the aligner. -
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Virus QSP Modeling
C++ and Python code for simulating RNA virus replication
Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files. -
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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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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
From Amat et al., Nature Methods, 2014*: "The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types of... -
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SOAP3-DP
Fast, Accurate and Sensitive GPU-based Short Read Aligner
...SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. Citation: Luo R, Wong T, Zhu J, Liu C-M, Zhu X, et al. (2013) SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE 8(5): e65632. doi:10.1371/journal.pone.0065632 -
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MICA-aligner
Next-generation sequencing short reads aligner based on Intel® MIC
Latest Code in GitHub: https://github.com/aquaskyline/MICA-aligner To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core. Experiments on aligning 150bp paired-end reads show that MICA using one MIC board is ~4.85 times faster than the CPU-(multi-core)-based BWA-MEM and about the same speed as the GPU-based SOAP3-dp. Furthermore, MICA’s... -
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MSL
http://dx.doi.org/10.1002/jcc.22968
MSL is a C++ library that enables the computational study of macromolecules. The MSL library is not a program (although some applications are distributed) but a tool for scientist to code their own molecular modeling methods. Philosophy The main goal is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications (protein modeling or design). ... -
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A Scalable Multicore Code for RNA Secondary Structure Prediction
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Percolator, binary downloads
Binary download site for percolator the proteomics post processor
Binary download site for the proteomics data post processor percolator. The source code is hosted on git hub, https://github.com/percolator/percolator
