Search Results for "informatics" - Page 3
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Showing 163 open source projects for "informatics"
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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.
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eHealth Charter
GUI for the coocking hacks eHealth
GUI for the cooking hacks eHealth Biomedic Sensor Platform. It reads the data through the USB. -
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AJT is a set of utility classes for Java for handling some bioinformatics data, graphics file export, GUI widgets, and classes that should long have been added to the official Java API.
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WM Hyperintensities Segmentation Toolbox
Open Source White Matter Hyperintensities Segmentation Toolbox
Wisconsin White Matter Hyperintensity Segmentation [W2MHS] and Quantification Toolbox is an open source MatLab toolbox designed for detecting and quantifying White Matter Hyperintensities (WMH) in Alzheimer’s and aging related neurological disorders. WMHs arise as bright regions on T2- weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer’s disease (AD) with regard to its prognosis. Our toolbox... -
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PPSeq: Parallel NGS Analysis
Parallel Processing for Next-Generation Sequencing (NGS) Analysis
High-throughput next generation sequencing (NGS) technology has quickly emerged as a powerful tool in many aspects of biomedical research. However, along with its rapid development, the data magnitude and analysis complexity for NGS far exceed the capacity and capability of traditional small-scale computing facilities, such as multithreading algorithms on standalone workstations. To address this issue, here we present a solution using the ever-increasing supply of processing power by massive... -
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Critterding
Evolving Artificial Life
Critterding is a "Petri dish" universe in 3D that demonstrates evolving artificial life. Critters start out with completely random brains and bodies, but will automatically start evolving into something with much better survival skills. -
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The Boolean Network Toolkit is an efficient and easy-to-use object-oriented C++ library which enables researchers to simulate ad carry out experiments (like attractor sampling and Derrida plot computation) on large boolean networks.
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The Systems Biology Ontology project (SBO) goal is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. !!!! Important Announcement !!!! We have moved the curation and development of Systems Biology Ontology (SBO) to a git-hub repository https://github.com/EBI-BioModels/SBO. Hence, this SourceForge SBO project has also been retired. Please use the Git-Hub...
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El proyecto central es la conformación de un Sistema de Información Hospitalaria, se pretende ir por subproyectos los cuales formaran las piezas fundamentales que se integraran mediante perfiles IHE que vayan estableciéndose para la norma HL7v3
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein... -
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parFE is fully-parallel high-performance finite element code targeted to the modeling of trabecular bones in humans. It employs scalable multigrid solvers for efficient solutions on massively parallel computers.
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ISAD
Individual Synaptic Activity Detection (ISAD)
ISAD is a peak detection software that detects individual (pre-)synaptic activity in microscopy images from neuronal cultures transfected with pHluorin. It computes synaptic signals from automatically segmented regions of interest and detects peaks that represent vesicle fusion events, thus, pre-synaptic activity. ISAD is based on MWA, which is a continuous wavelet transform based algorithm that employs multiple wavelets and is published as: Sokoll, S., Tönnies, K., and Heine, M. Detection... -
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The goal of this project is a collection of free educational textbooks, articles, lectures and any other kind of textmaterials for the students of the informatic department of Eötvös Loránd Tudományegyetem university in Budapest shipped with GFDL license.
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TRMSim-WSN (Trust and Reputation Models Simulator for Wireless Sensor Networks) is a Java-based simulator aimed to test Trust and Reputation models for WSNs. It provides several Trust and Reputation models and new ones can be easily added.
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If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).