Search Results for "informatics" - Page 3
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Showing 196 open source projects for "informatics"
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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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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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vrecko
virtual environment framework
Vrecko is a component-based system capable of management and display of virtual worlds using various input and output devices. It is in development by HCI (Human-Computer Interaction) laboratory at Faculty of Informatics, Masaryk University, Czech Republic. -
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW....
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math lib for .NET. n-dim arrays, complex numbers, linear algebra, FFT, sorting, cells- and logical arrays as well as 3D plotting classes help developing algorithms on every platform supporting .NET. Sources from SVN, binaries: http://ilnumerics.net
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The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.
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jMDFLib
This is a small Java library which reads MDF Files up to Version 3.00
This Library for Java shall enable developers to use (at first read, maybe later writer) MDF Files, as described by the Format Specification MDF Format by Vector Informatics. The MDF file format is widely used in automotive engineering and other fields for the recording of measurement data. This Java library parses MDF files and enables different kind of read access. If this library is not helpful for a particular purpose it can at least be used to see how the parsing (and therefore how the file format itself) works. -
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Pipeline Builder for NGS tools
Scripting tool for automatize and managing complex NGS analysis
Handling with NGS tool configuration files is a real challenge for modern biologists and biotechnologist. To increase productivity, specificity and enhance the data processing, this tool provides a collection of commands already structured, leading the user in building the correct pipeline for the data he has to analyse. Pipeline Builder is a scripting tool for managing complex NGS analysis pipelines. It helps the user in composing NGS tool commands and composing his own analysis... -
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CQRlib is an ANSI C implementation of a utility library for quaternion arithmetic and quaternion rotation math.
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DVN
An extended Subversion client enabling versioning of database schemas
...Emphasis is put on the client to be extensible, though, so it is possible to implement a connector for another database system. This project is supported by the Faculty of Informatics, Masaryk University, Brno, Czech Republic, as a research project MUNI33/112013, http://www.muni.cz/research/projects/23565 -
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BMF
Bio Medical Framework (BMF)
The BMF is a Software Framework developed in Java language for the creation of web applications on the server platform also Open source, in clinical, administrative and management for a healthcare company. -
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HRDAG
Framework for Hierarchical Graph Decomposition
This is a framework used to decompose hierarchical graphs, i.e.,graphs which were created from or contain a hierarchy of modules. Each module is reused several times in the hierarchy. This may be useful to reverse-engineer human constructs like electronic equipment, manufactured machines, or bureaucratic hierarchies; but also to decompose natural constructs like gene-relation or protein-relation nets. -
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Online Signature Verification
Real time signature verification using MATLAB and C#
Online Signature Verification technology requires primarily a digitizing tablet and a special pen connected to the USB port of a computer. An individual can sign on the digitizing tablet using the special pen regardless of his signature size and position. The signature is characterized as pen-strokes consisting x-y coordinates and pressure with the data being stored in a signature database. Dynamic time warping (DTW) and quadratic discriminant analysis (QDA) is used to get results where the... -
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RSSA
Rejection-based stochastic simulation algorithm (RSSA)
Rejection-based stochastic simulation algorithm (RSSA) is an efficient exact algorithm for doing stochastic simulation of biochemical reaction systems. RSSA improves over state of the art of stochastic simulations by avoiding and collapsing as much the number of propensity updates. -
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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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...However, there are few tools available to the integration of these tools, which would be suitable for the application of SBST (Search Based Software Testing). Furthermore, such tools require an advanced knowledge of software testing techniques and optimization techniques. Thinking about it, the SBST Group from Informatics Institute at Universidade Federal de Goiás, are developing the SBSTFrame focuses in the integration of these two types of tools to facilitate the application of search techniques in problems of Software Testing area. The SBSTFrame plays the role of a top layer compared with software testing tools and frameworks of search techniques layer, to the communication between them could be done transparently to the user.
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Java Machine Learning Library is a library of machine learning algorithms and related datasets. Machine learning techniques include: clustering, classification, feature selection, regression, data pre-processing, ensemble learning, voting, ...
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This is a project for Andre to share CellML related tools he works on that other people might find useful.
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The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.
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ParaBWT - parallel BWT construction
a parallel and space-efficient Burrows-Wheeler transfrom constructor
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.
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q pipeline manager
q: integrated platform for pipeline configuration and management
...It expands the value of your existing job scheduler - either Grid Engine or TORQUE PBS - through numerous functions that help you organize, submit, monitor, manage and share your informatics work. Data processing pipelines require high-level organization and parallelization of work to optimize resource utilization and decrease the time to results. q (from queue) allows complex job sequences to be efficiently assembled and managed, including dependency tracking, parallelization, and pipeline-level monitoring, error recovery, and data protection. ... -
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K-Surfer
A KNIME extension for the management and analysis of FreeSurfer Data
...References: Sarica Alessia, Giuseppe Di Fatta, and Mario Cannataro. "K-Surfer: A KNIME Extension for the Management and Analysis of Human Brain MRI FreeSurfer/FSL Data." Brain Informatics and Health. Springer International Publishing, 2014. 481-492. Sarica A, Di Fatta G and Cannataro M (2014). K-Surfer: A KNIME-based tool for the management and analysis of human brain MRI FreeSurfer/FSL Data. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014. doi: 10.3389/conf.fninf.2014.18.00003 -
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TopiaryExplorer has moved to GitHub. Find the new project info page here: https://github.com/qiime/Topiary-Explorer. If you need help or would like to add a bug/feature request, please do so there.
