Search Results for "java open source" - Page 20
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Showing 2101 open source projects for "java open source"
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Atera all-in-one platform IT management software with AI agentsAtera’s AI agents don’t just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
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BANNER is a named entity recognition system intended primarily for biomedical text. It uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.
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A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/
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TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.
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OpenCryobank is an attempt to develop a simple, free and open database system for frozen samples inventory in biological laboratories. It is mainly aimed at semen and embryo cryobanks, but it can be used for any kind of biological sample. Visit us: http://reprobio.unileon.es/services/analisis-cromatina-espermatica/
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Shoplogix Smart Factory PlatformReal-time Visibility into Your Shop Floor's Performance. The Shoplogix smart factory platform enables manufacturers to increase overall equipment effectiveness, reduce operational costs, sustain growth and improve profitability by allowing them to visualize, integrate and act on production and machine performance in real-time. Manufacturers that trust us to drive efficiency in their factories. Real-time visual data and analytics provide valuable insights to make better informed decisions. Uncover hidden shop floor potential and drive rapid time to value. Develop a continuously improving culture through training, education and data-driven decisions. Compete in the i4.0 world by making the Shoplogix Smart Factory Platform the cornerstone of your digital transformation. Connect to any equipment or device to automate data collection and exchange it with other manufacturing technologies. Automatically monitor, report and analyze machine states to track real-time production.
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rainbow
short reads clustering and local assembly
Efficient tool for clustering and assembling short reads, especially for RAD. -
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LDhat
Estimate Recombination Rates from Population Genetic Data
LDhat is a package written in the C language for the analysis of recombination rates from population genetic data. This package has migrated to github: https://github.com/auton1/LDhat -
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FMFilter
Fast Model Based Variant Filtering Tool
Filtering out the prominent portion through the excessive amount of information produced by next generation techniques is a challenging task. Current tools enable to analyze next generation sequencing data in various methods. However, there is still need for fast, easy to use and efficacious tools. We provide an efficient filtering tool for next generation sequencing data produced by genetic disease studies. FMFilter allows to choose one of the inheritance models (recessive, dominant,... -
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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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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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Predict and Mitigate Operational Risk While Streamlining Regulatory CompliancePredict360 is a risk and compliance intelligence platform developed by 360factors, an enterprise risk and compliance technology and services company. Predict360 is an artificial intelligence (AI)-powered platform that integrates risks and controls, KRIs, regulations and requirements, policies and procedures, audit and examinations, and training in a unified, cloud-based system. Predict360’s SaaS architecture platform and deliver predictive analytics, data insights for predicting risk, and streamlined compliance.
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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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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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ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric analysis and advanced constructions.
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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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starrynite is an image analysis tool for tracking fluorescently-labeled nuclei during C. elegans embryogenesis.
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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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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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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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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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This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...
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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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EVidenceModeler (aka EVM) combines ab initio gene predictions and spliced protein and transcript alignments into weighted consensus gene structure predictions.
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ChemClipse 3rd Party Libraries
ChemClipse Third Party Libraries
The ChemClipse 3rd Party Libraries are plug-ins which encapsulate the functionality of other open-source projects to be usable through Eclipse/OSGi bundles within the ChemClipse Rich Client Platform (RCP). -
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877,...
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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..
