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• C-wap
  |{{#vardefine:app|c-wap}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/C-WAP}}
  2 KB (281 words) - 13:16, 15 August 2022
• NetCDF-C
  |{{#vardefine:app|netcdf-c}}
  2 KB (279 words) - 14:53, 3 June 2022
• NCBI C++ Toolkit
  NCBI C++ Toolkit provides free, portable, public domain libraries with no restrict
  3 KB (306 words) - 17:47, 15 August 2022

• File:2012-04-19-Parallel Processing-C Taylor.ppt (1.42 MB) - 16:10, 19 April 2012

Page text matches

• Compilers
  ...n-us/intel-parallel-studio-xe Intel Compiler Suite] provides Fortran and C/C++ compilers and is preferred compiler option on hipergator. The [https://gcc.gnu.org GNU Compiler Suite] provides Fortran and C/C++ compilers.
  1 KB (159 words) - 22:30, 26 July 2021
• Intel MPI
  mpicc ( C source) mpiCC (C++ source)
  3 KB (298 words) - 19:00, 15 August 2022
• SWIG
  ...the 'glue code' required for the above target languages to call into the C/C++ code. SWIG can also export its parse tree in the form of XML and Lisp s-e
  3 KB (414 words) - 17:48, 15 August 2022
• HiC-Pro
  ...ng dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data. ..., Heard E., Barillot E. HiC-Pro: An optimized and flexible pipeline for Hi-C processing. Genome Biology 2015, 16:259 doi:10.1186/s13059-015-0831-x
  3 KB (432 words) - 18:17, 15 August 2022
• Boost
  "Boost provides free peer-reviewed portable C++ source libraries. We emphasize libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and u
  3 KB (350 words) - 13:06, 15 August 2022
• Amber Job Sample Scripts
  sander -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd mpiexec sander.MPI -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd
  1 KB (167 words) - 17:38, 26 June 2017
• Xerces
  |{{#vardefine:url|http://xerces.apache.org/#xerces-c}} ...or parsing, generating, manipulating, and validating XML documents. Xerces-C++ is faithful to the XML 1.0 and 1.1 recommendations and many associated st
  3 KB (306 words) - 21:29, 6 December 2019
• LDhat
  ...n rates from population genetic data. The package is available either as C/C++ source code.
  2 KB (296 words) - 17:09, 10 June 2022
• GCC
  The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc+
  2 KB (251 words) - 16:55, 15 August 2022
• CryptoMiniSat
  ...ython interface provides a high-level yet efficient API to use most of the C++ interface with ease.
  3 KB (325 words) - 14:13, 15 August 2022
• Juicer
  ...stq raw data files and command line tools for feature annotation on the Hi-C maps.
  2 KB (273 words) - 19:12, 15 August 2022
• Freesasa
  FreeSASA is a C library and C++ command line tool for calculating Solvent Accessible Surface Area (SASA) Simon Mitternacht (2016) FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5:1
  2 KB (276 words) - 16:49, 15 August 2022
• Asaq
  ...possible tree topology. To run ASAQ it is necessary to have installed the C++ linear algebra library Armadillo ...//arma.sourceforge.net/armadillo_joss_2016.pdf Armadillo: a template-based C++ library for linear algebra]. Journal of Open Source Software, Vol. 1, pp.
  3 KB (374 words) - 15:10, 1 June 2022
• GNU Compiler Collection
  The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libs
  2 KB (298 words) - 20:44, 15 August 2022
• Doxygen
  annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba and
  3 KB (406 words) - 14:47, 15 August 2022
• Intel Compilers
  Intel® Cluster Studio features the acclaimed Intel Fortran and C++ Compilers. These performance-oriented compilers can deliver a remarkable Intel Compilers support OpenMP. Developers using C or C++ can create and manage portable, shared-memory parallelism in their applic
  3 KB (332 words) - 19:30, 10 June 2022
• Nvhpc
  ...GPU acceleration of HPC modeling and simulation applications with standard C++ and Fortran, OpenACC® directives, and CUDA®. GPU-accelerated math libra
  3 KB (334 words) - 19:06, 6 June 2022
• ProtExcluder
  ...e, G. D., Hunagel, D. E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C. J., Ware, D., Shiu, S-H., Childs, K. L., Sun, Y., Jiang, N, Yandell, M. 20
  3 KB (329 words) - 21:22, 6 December 2019
• Dlib
  ...ing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. See http://dlib.net for the main project do
  2 KB (269 words) - 13:11, 4 May 2020
• SALSA
  A tool to scaffold long read assemblies with Hi-C Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact in
  2 KB (267 words) - 20:06, 10 June 2022
• Armadillo
  Armadillo is a high quality C++ linear algebra library, aiming towards a good balance between speed and e ...://arma.sourceforge.net/armadillo_nicta_2010.pdf Armadillo: An Open Source C++ Linear Algebra Library for Fast Prototyping and Computationally Intensive
  2 KB (269 words) - 14:33, 12 August 2022
• SUNDIALS
  ...marsh, P. N. Brown, K. E. Grant, S. L. Lee, R. Serban, D. E. Shumaker, and C. S. Woodward, "SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equa * R. Serban and A. C. Hindmarsh, "CVODES: the Sensitivity-Enabled ODE Solver in SUNDIALS," Proce
  3 KB (367 words) - 13:45, 13 June 2022
• ImageMagick
  ...re (C), MagickWand (C), ChMagick (Ch), ImageMagickObject (COM+), Magick++ (C++), JMagick (Java), L-Magick (Lisp), Lua, NMagick (Neko/haXe), Magick.NET (
  3 KB (380 words) - 18:46, 15 August 2022
• C-wap
  |{{#vardefine:app|c-wap}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/C-WAP}}
  2 KB (281 words) - 13:16, 15 August 2022
• NetCDF
  ...e that the Fortran module man not have all supporting binaries that netcdf-c module has.
  3 KB (383 words) - 14:53, 3 June 2022
• GRACKLE
  ...ry for astrophysical simulations and models. Grackle has interfaces for C, C++, Fortran, and Python codes and provides:
  2 KB (294 words) - 17:18, 15 August 2022
• BERTopic
  BERTopic is a topic modeling technique that leverages transformers and c-TF-IDF to create dense clusters allowing for easily interpretable topics wh [https://zenodo.org/record/4719700 BERTopic: Leveraging BERT and c-TF-IDF to create easily interpretable topics.]
  2 KB (283 words) - 14:00, 27 May 2022
• Plinkseq
  PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus
  2 KB (296 words) - 20:25, 12 August 2022
• HOOMD
  J. A. Anderson, C. D. Lorenz, and A. Travesset. General purpose molecular dynamics simulation ...D. Nguyen, J. A. Anderson, P. Liu, F. Spiga, J. A. Millan, D. C. Morse, S. C. Glotzer. Strong scaling of general-purpose molecular dynamics simulations
  5 KB (607 words) - 15:40, 6 June 2022
• GSL
  The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General
  2 KB (300 words) - 17:27, 15 August 2022
• OpenCV
  ...des several hundreds of computer vision algorithms. Written in optimized C/C++, the library can take advantage of multi-core processing. Enabled with Op
  2 KB (283 words) - 21:31, 6 December 2019
• Quantisnp
  ...M., Mirza, G., Butler, H., Clouston, P., Basset, A.S., Seller, A., Holmes, C., and Ragoussis, J. QuantiSNP: an Objective Bayes Hidden-Markov Model to de
  2 KB (297 words) - 20:29, 12 August 2022
• GEOS
  ...te (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the ​OpenGIS Simple Features for SQL spatial predica
  3 KB (307 words) - 17:05, 15 August 2022
• DCMTK
  ...orage and worklist servers. DCMTK is is written in a mixture of ANSI C and C++. It comes in complete source code and is made available as "open source"
  3 KB (304 words) - 20:31, 10 June 2022
• Pbmm2
  pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets o
  3 KB (303 words) - 20:08, 31 May 2022
• Tuning Analysis Utilities
  ...olkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python. ...methods, basic blocks, and statements as well as event-based sampling. All C++ language features are supported including templates and namespaces. The A
  3 KB (443 words) - 17:37, 6 June 2022
• Segemehl
  Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "F Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, H
  3 KB (404 words) - 20:38, 12 August 2022
• GDSL
  ...ary fully written from scratch in pure ANSI C. It is designed to offer for C programmers common data structures with powerful algorithms, and hidden imp
  3 KB (305 words) - 15:37, 6 June 2022
• TAU
  ...olkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. ...h instrumentation of functions, methods, basic blocks, and statements. All C++ language features are supported including templates and namespaces. The A
  4 KB (575 words) - 21:31, 6 December 2019
• LAMMPS
  ...liquid, solid, or gaseous state. It is a open source software, written in C++ and developed at Sandia laboratory. It can be used to model atomic, polym ...CMAKE_INSTALL_PREFIX=<target_lammps_dir> -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake ../cmake
  3 KB (467 words) - 23:34, 20 August 2021
• Allhic
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data ...embly of allele-aware, chromosomal scale autopolyploid genomes based on Hi-C data. Nature Plants, doi:10.1038/s41477-019-0487-8 (2019).
  3 KB (299 words) - 12:35, 12 August 2022
• KIM
  * C * C++
  3 KB (322 words) - 19:19, 15 August 2022
• 3d-dna
  ...n: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. ...A.P., et al. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science eaal3327. Published online ahea
  3 KB (328 words) - 17:51, 10 June 2022
• SHARCGS
  Dohm JC, Lottaz C, Borodina T, Himmelbauer H SHARCGS, a fast and highly accurate short-read a Dohm JC, Lottaz C, Borodina T, Himmelbauer H Substantial biases in ultra-short read data sets
  3 KB (310 words) - 14:30, 3 June 2022
• OpenCL
  ...evelopers can launch compute kernels written using a limited subset of the C programming language on a GPU. ...wget -q https://raw.github.com/smistad/OpenCL-Getting-Started/master/main.c
  3 KB (363 words) - 20:47, 10 June 2022
• Minimac
  ...rnals.org/content/early/2014/10/22/bioinformatics.btu704.short Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatic Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR. Fast and accurate genotype imputa
  3 KB (332 words) - 18:31, 10 June 2022
• PICRUSt
  ...le, D. E.; Vega Thurber, R. L.; Knight, R.; Beiko, R. G.; and Huttenhower, C. Nature Biotechnology, 1-10. 8 2013.]
  3 KB (344 words) - 18:28, 10 June 2022
• HOMER
  ...many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.
  3 KB (330 words) - 18:19, 15 August 2022
• Phenix
  .... Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).
  3 KB (322 words) - 13:32, 13 June 2022
• Maq
  maqindex -i -c consensus.cns all.map; maqview -c consensus.cns all.map
  3 KB (377 words) - 19:47, 12 August 2022
• Biolite
  BioLite is a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks proven * A C++ library 'seqio' for efficient I/O of large NGS data files
  3 KB (362 words) - 12:54, 15 August 2022
• BUCKy
  [http://mbe.oxfordjournals.org/content/24/2/412.abstract?etoc C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas (2007). Bayesian estimati ...l.pdf?ijkey=BIwQBlPEqeEiojQ&keytype=ref B. Larget, S.K. Kotha, C.N. Dewey, C. Ané (2010). BUCKy: Gene tree / species tree reconciliation with the Bayes
  3 KB (386 words) - 13:15, 15 August 2022
• Elastix
  ...Elastix, making it available in languages like C++, Python, Java, R, Ruby, C# and Lua.
  3 KB (365 words) - 15:30, 3 June 2022
• Intel Compilers and Libraries
  | C || icc || ''icc compiler_options example.c'' | C++ || icpc || ''icpc compiler_options -o example.exe example.cxx''
  5 KB (662 words) - 18:58, 15 August 2022
• CUDA Examples
  ===cuda_bm.c=== {{#fileAnchor: cuda_bm.c}}
  11 KB (1,462 words) - 20:33, 21 June 2017
• Mamba
  Mamba is a reimplementation of the conda package manager in C++. core parts of mamba are implemented in C++ for maximum efficiency
  3 KB (429 words) - 20:16, 3 June 2022
• Tensorboard
  ...orBoard 2.4.0 at '''<nowiki>http://localhost:6006/</nowiki>''' (Press CTRL-C to quit)
  1 KB (184 words) - 18:18, 20 January 2022
• ChartDirector
  VBScript, VBA, JavaScript, .NET (C#/VB), Java, JSP, C++, PHP, Perl, Python,
  3 KB (397 words) - 13:26, 15 August 2022
• USEARCH
  Edgar, Robert C. - Search and clustering orders of magnitude faster than BLAST Author : Edgar, Robert C.
  4 KB (557 words) - 20:53, 12 August 2022
• PICSL
  [1] H. Wang, J. W. Suh, S. Das, J. Pluta, C. Craige, P. Yushkevich, "Multi-atlas segmentation [2] H. Wang, S. R. Das, J. W. Suh, M. Altinay, J. Pluta, C. Craige, B. B. Avants, and P. A. Yushkevich,
  3 KB (390 words) - 20:22, 3 June 2022
• Xpra Windows Installation
  "/drives/c/Program Files/Xpra/Xpra" "$@"
  2 KB (300 words) - 17:27, 30 July 2019
• CASM
  [ref2] J. C. Thomas, A. Van der Ven, Finite-temperature properties of strongly anharmon [ref4] A. Van der Ven, J. C. Thomas, Q. Xu, J. Bhattacharya “Linking the electronic structure of soli
  4 KB (453 words) - 13:20, 15 August 2022
• EDTA
  ...J., Lugo C. S. B., Elliott T. A., Ware D., Peterson T., Jiang N.✉, Hirsch C. N.✉ and Hufford M. B.✉ (2019). Benchmarking Transposable Element Annot
  4 KB (479 words) - 16:31, 27 May 2022
• MetaBCC LR Job Scripts
  -c 25000 \
  1 KB (194 words) - 13:23, 6 June 2022
• Using SSH Keys To Access HPG
  ssh-keygen -o -a 100 -t ed25519 -f ~/.ssh/id_ed25519 -C "Comment to make the key recognizable among many" ssh-keygen -o -a 100 -t ed25519 -f ~/.ssh/id_ed25519 -C "Comment to make the key recognizable among many"
  3 KB (590 words) - 16:53, 18 May 2022
• AMBER
  ...Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation progra ...-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (20
  5 KB (763 words) - 12:39, 12 August 2022
• NAMD
  James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Eliza
  2 KB (249 words) - 17:04, 6 September 2017
• Persistent Terminal Sessions
  ...eate as many terminal windows in the screen session as needed with 'Ctrl+a c' key combination. See [[Screen]] documentation. Ctrl+a c
  4 KB (701 words) - 15:51, 9 July 2020
• FFTW
  Fastest Fourier Transform in the West, is a C library for computing the Discrete Fourier Transform (DFT) in one or more d
  2 KB (223 words) - 16:41, 15 August 2022
• Mach2VCF
  Mach2VCF is a C++ tool to convert MaCH files to VCF files.
  2 KB (242 words) - 14:49, 10 June 2022
• Vcf-validator
  Validation suite for Variant Call Format (VCF) files, implemented using C++11
  2 KB (247 words) - 21:29, 6 December 2019
• AI Help
  ...loped by Facebook AI Research Lab and has interfaces for Python, Java, and C++, but is most commonly used with Python. It supports training on both GPU ...-GPU and distributed training. APIs are available for Python, Java, Go and C++. See our [[TensorFlow|TensorFlow quickstart page]] for help getting start
  4 KB (584 words) - 18:44, 16 August 2022
• DosageConvertor
  DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther format
  2 KB (252 words) - 15:04, 10 June 2022
• OpenSim
  SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
  2 KB (247 words) - 17:47, 22 September 2021
• OpenSlide
  OpenSlide is a C library that provides a simple interface to read whole-slide images
  2 KB (248 words) - 21:22, 6 December 2019
• CellProfiler
  ...arch Computing. To run CellProfiler in batch mode, you should include the -c or --run-headless option. Also, you want to use CELLPROFILER_USE_XVFB="1" -c, --run-headless Run headless (without the GUI)
  8 KB (889 words) - 13:24, 15 August 2022
• Aster
  ...family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL).
  2 KB (251 words) - 14:57, 12 August 2022
• Tbb
  Widely used C++ template library for task parallelism.
  2 KB (259 words) - 21:29, 6 December 2019
• Talesf
  TALESF is a C library for identifying potential binding sites for transcription activator
  2 KB (256 words) - 21:29, 6 December 2019
• Fastp
  ...e fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
  2 KB (256 words) - 15:23, 15 August 2022
• Glog
  C++ implementation of the Google logging module
  2 KB (269 words) - 17:10, 15 August 2022
• Unanimity
  C++ library and its applications to generate and process accurate consensus s
  2 KB (268 words) - 17:48, 15 August 2022
• GenomeTools
  ...nome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
  2 KB (266 words) - 18:58, 12 August 2022
• LEMON
  Networks. It is a C++ template library providing efficient implementations
  2 KB (268 words) - 15:41, 6 June 2022
• Libunistring
  ...t provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
  2 KB (269 words) - 15:49, 10 June 2022
• IGoR
  IGoR is a C++ software designed to infer V(D)J recombination related processes from seq
  2 KB (271 words) - 13:52, 14 May 2020
• Eagle-rc
  ...s.biomedcentral.com/articles/10.1186/s12920-018-0342-1 Tony Kuo and Martin C Frith and Jun Sese and Paul Horton. EAGLE: Explicit Alternative Genome Like
  2 KB (270 words) - 22:30, 26 August 2020
• MetaSV
  ...oup.com/bioinformatics/article/31/16/2741/321286 Marghoob Mohiyuddin, John C. Mu, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. W
  2 KB (277 words) - 21:21, 6 December 2019
• IMa2p
  IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under
  2 KB (277 words) - 21:21, 6 December 2019
• Phylonet
  C. Than, D. Ruths, L. Nakhleh (2008) PhyloNet: A software package for analyzi
  2 KB (263 words) - 21:23, 6 December 2019
• GLPK
  ...(MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
  2 KB (272 words) - 17:11, 15 August 2022
• QD
  ...ead-safe, but, unlike MPFUN2020, is available with both a Fortran-90 and a C++ high-level interface.
  2 KB (271 words) - 17:47, 15 August 2022
• QT
  QT is a cross-platform application and UI framework for developers using C++ or QML, a CSS & JavaScript like language.
  2 KB (259 words) - 14:09, 13 June 2022
• MiRanda
  ...finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was develo
  2 KB (278 words) - 21:21, 6 December 2019
• NetCDF-C
  |{{#vardefine:app|netcdf-c}}
  2 KB (279 words) - 14:53, 3 June 2022
• Rust
  ...both functional and imperative paradigms. Rust is syntactically similar to C++, but its designers intend it to provide better memory safety while still
  2 KB (285 words) - 21:24, 6 December 2019
• UDUNITS
  1) a C library for units of physical quantities.
  2 KB (276 words) - 20:13, 10 June 2022
• Grib api
  The ECMWF GRIB API is an application program interface accessible from C,
  2 KB (278 words) - 17:22, 15 August 2022
• Gaussian
  gui start -e gv -c 1 -m 8 -t 4 ...aramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G.
  7 KB (1,030 words) - 16:54, 15 August 2022
• FastSpar
  FastSpar is a c++ implementation of the SparCC algorithm published here: Friedman, J. & Alm
  2 KB (283 words) - 15:26, 15 August 2022

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