Search Results for "apache"
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Showing 28 open source projects for "apache"
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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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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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ProteoWizard development moved to GitHub in 2018. The ProteoWizard Library is a set of software libraries and tools for rapid development of proteomics data analysis software. The libraries are cross-platform and built from the ground up using modern C++ techniques.
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libSBOL provides the core C/C++ interfaces and their implementation for the Synthetic Biology Open Language (SBOL). Version 2.1.1 of libSBOL provides an API to construct SBOL 2.1.0 designs and to read and write SBOL version 2.1.0 XML/RDF files.
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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... -
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Crux-Toolkit
Software toolkit for tandem mass spectrometry analysis
Crux is a software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. If you use Crux in your research, please cite Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and William Stafford Noble. "Rapid and accurate peptide identification from tandem mass spectra." Journal of Proteome Research. 7(7):3022--3027, 2008. -
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MSAProbs: Multiple Sequence Alignment
One of the most accurate multiple protein sequence aligners
MSAProbs is an open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. -
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LightSpMV
lightweight GPU-based sparse matrix-vector multiplication (SpMV)
LightSpMV is a novel CUDA-compatible sparse matrix-vector multiplication (SpMv) algorithm using the standard compressed sparse row (CSR) storage format. We have evaluated LightSpMV using various sparse matrices and further compared it to the CSR-based SpMV subprograms in the state-of-the-art CUSP and cuSPARSE. Performance evaluation reveals that on a single Tesla K40c GPU, LightSpMV is superior to both CUSP and cuSPARSE, with a speedup of up to 2.60 and 2.63 over CUSP, and up to 1.93 and... -
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CUSHAW3 is an open-source parallelized, sensitive and accurate short-read aligner. This aligner proposes a general approach to properly aligning both easy and hard reads to large genomes such as the human genome. Perform evaluation on alignment quality reals that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novalign3 for short-reads...
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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SWAPHI: Smith-Waterman on Intel Xeon Phi
The first protein sequence database search on shared-host Xeon Phis
The first parallel algorithm to accelerate the Smith-Waterman protein database search on shared-host multiple Intel Xeon Phi coprocessors. By searching against the UniProtKB/TrEMBL database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on a single Xeon Phi and up to 228.4 GCUPS on four Xeon Phis. -
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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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SplitMEM
Graphical pan-genome analysis with suffix skips
With the rise of improved sequencing technologies, genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach with multiple individuals represented and analyzed together. Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. To achieve this time complexity, we augment the suffix tree with suffix skips, a new construct that... -
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CUSHAW2: Parallel Gapped Read Alignment
One of the leading short-/long-read aligner to large genomes
CUSHAW2 is a fast and parallel gapped read alignment to large genomes, such as the human genome. The performance evaluation, by aligning simulated and real datasets to the human genome, shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads. -
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ParaBWT - parallel BWT construction
a parallel and space-efficient Burrows-Wheeler transfrom constructor
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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 -
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MSA-CUDA: multiple sequence aligner
multiple sequence alignment on CUDA-enabled GPUs.
This project is not active any more since we failed to get the permit from the Clustal team to distribute our software. You can refer to the paper "Yongchao Liu, Bertil Schmidt, Douglas L Maskell:MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA. ASAP 2009" for more details. -
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Musket - short read error corrector
a parallel short-read error corrector for Illumina sequencing
Musket is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing substitution-error-based correctors. In addition, Musket is multi-threaded using a master-slave model and demonstrates... -
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PASHA: Parallelized Short Read Assembly
One of the fastest parallel short read assemblers for large genomes.
PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates... -
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DecGPU: CUDA-based Error Correction
The first distributed and parallel short-read error corrector on GPUs
DecGPU (Distributed Error correction on GPUs) is a parallel and distributed error correction algorithm for large-scale short read assembly. It is implemented using CUDA C++ and MPI, running on a GPU cluster. -
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CUSHAW: CUDA-based Short Read Alignment
the first aligner introducing a complete paired-end alignment on GPUs
CUSHAW is a CUDA compatible short read aligner to large genomes, such as the human genome, based on the Burrows Wheeler transform. -
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NHP-IMS
Non-Human Primate Information Management System
This project will enable a research lab using Non-Human Primates to control and track the Non-Human primates and the experiments associated with each. -
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Corra [BMC Bioinformatics 2008] is a computational framework & tools for discovery proteomics using label free LC-MS and ATAQS [BMC Bioinformatics 2011] is a computational framework & tools for validation proteomics using SRM LC-MS method.
