Search Results for "gnu linux" - Page 14
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Showing 1553 open source projects for "gnu linux"
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Library of various Java Swing user interface components, with emphasis on views and editors for complex data structures, like collections, sets, lists, maps, graphs, and matrices.
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starrynite is an image analysis tool for tracking fluorescently-labeled nuclei during C. elegans embryogenesis.
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parSRA
Portable Framework for the Parallel Execution of Short Read Aligners
parSRA is a framework to execute short read aligners on compute clusters. 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... -
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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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JGAP is a Genetic Algorithms and Genetic Programming package written in Java. It is designed to require minimum effort to use, but is also designed to be highly modular. JGAP features grid functionality and a lot of examples. Many unit tests included. Legal notice/Impressum: Klaus Meffert An der Struth 25 D-65510 Idstein sourceforge <at> klausmeffert.de
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merlin is an user-friendly Java application that performs the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs several steps of the reconstruction process, including the functional genomic annotations of the whole genome. Moreover, merlin includes tools for the identification and annotation of transport proteins encoding genes, as well as the generation of transport reactions for such carriers. Also, merlin includes tools for the...
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NetView P
Population Genomics Network Analysis Pipeline
NetView P has been re-structured as a package for R and moved to GitHub: https://github.com/esteinig/netview -
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available... -
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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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HTQC
Quality control and filtration for illumina sequencing data
A toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. -
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The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparision, exchange and verification.
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Protein Contact Matrix Generator
Command line application to generate contact matrix from proteins (3D)
A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). Contact Maps can be used to understand... -
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BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
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XMLPipeDB is a suite of tools for building relational databases from XML sources with minimal manual processing of the data. While the applicability is general, our motivation was to facilitate the management of biological data from different sources.
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BLESS: NGS Error Correction Tool
Bloom-filter-based Error Correction Tool for NGS reads
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Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.
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TRiDaS is a universal data exchange standard for the dendrochronology community. This project contains the data standard itself as well as libraries and tools useful for reading, writing and converting dendro data files.
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Muninn
A software package for estimating generalized ensemble weights in Mark
We have moved to GitHub: https://github.com/muninnorg/muninn As of July 2015 we have moved to GitHub. The SourceForge page will preserved, with the old releases. Muninn is a software package for estimating generalized ensemble weights in Markov chain Monte Carlo (MCMC) simulations. The method is full automated and makes use of the generalized multihistogram (GMH) equations for estimation the density of states [1]. The package is implemented in C++ and has a convenient interface. -
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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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RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.
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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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Taxy is a tool for browsing and quering data organized as a taxonomy. Through the use of plugins it allows to connect to different data sources, such as the NCBI species taxonomy or the catalogue of biomedical services of the EU project ACGT.
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DEAPathways
Differential Expression Analysis for Pathways
This project contains the source code associated with the PLoS Computational Biology publication: "Differential Expression Analysis for Pathways". The paper text can be found here: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002967 -
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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees.
