“…Availability: The CoExpNetViz tool is freely available both as a PHP web server (link: http://bioinformatics.psb.ugent.be/webtools/coexpr/) (implemented in C++) and as a Cytoscape plugin (implemented in Java). Both versions of the CoExpNetViz tool support LINUX and Windows platforms.…”
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“…Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. …”
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“…An analysis of error sources led to the use of a refractory period, more accurate numerical derivatives and a Savitzky-Golay filter to achieve significant improvements in accuracy. Our pure Java implementations of two recently published algorithms reduce computational cost by up to 29% compared to the original implementations. …”
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“…Availability and Implementation: The framework, implemented in Java, is open source and its source code, documentation and tutorial are available at http://www.ibi.vu.nl/programs/BioASF. …”
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“…CONCLUSIONS: This paper proposes a new method to identify key player genes in gene regulatory networks. The Java implementation of the heuristic algorithm explained in this paper is available as a Cytoscape plugin at http://apps.cytoscape.org/apps/mcds. …”
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“…CONCLUSIONS: Je is implemented in JAVA and uses the Picard API. Code, executables and documentation are freely available at http://gbcs.embl.de/Je. …”
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“…The core of MPD is implemented in C for speed and uses a hashed genome to ensure primer uniqueness, avoids placing primers over sites of known variation, and efficiently pools compatible primers. A JavaScript web application (http://multiplexprimer.io) utilizing the MPD Perl package provides a convenient platform for users to make designs. …”
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“…Nonetheless, the use of the SST gradient between the inshore and the oceanic SSTs to characterize upwelling (UI(SST)) was found to be unsuitable because the SST along the ECPM was affected by water advection from the Java Sea and incessant changes in the SST. In order to indicate the major contributor of wind-induced upwelling along the ECPM in terms of the spatiotemporal scale, a comparison between Ekman transport and Ekman pumping was drawn by integrating Ekman pumping with respect to the distance where the positive wind stress curl existed. …”
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“…Halvade-RNA is written in Java and uses the Hadoop MapReduce 2.0 API. It supports a wide range of distributions of Hadoop, including Cloudera and Amazon EMR.…”
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“…OBJECTIVE: To evaluate a home-built Java-based program (GFRcalc) to simplify the calculation of glomerular filtration rate (GFR) after administration of chromium-51 ethylenediaminetetraacetic acid ((51)Cr-EDTA) for routine clinical use. …”
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“…High-resolution BAC maps of the X chromosome on a representative range of cetartiodactyl species from different branches: pig (Suidae), alpaca (Camelidae), gray whale (Cetacea), hippopotamus (Hippopotamidae), Java mouse-deer (Tragulidae), pronghorn (Antilocapridae), Siberian musk deer (Moschidae), and giraffe (Giraffidae) were obtained by fluorescent in situ hybridization. …”
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“…A computational cluster analysis will be conducted using a customized computer program written in JAVA. A Cox proportional hazards analysis will be used to model time-to-event data, while simultaneously adjusting for provider- and patient-level predictors. …”
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“…We found no direct dispersal events between Sumatra and Borneo despite the presence of a terrestrial connection between them during the Pleistocene. Instead, central Java served as an important link allowing termite colonies to be established in Borneo and Sumatra. …”
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“…METHODS: To facilitate NGS data analysis in our clinical molecular diagnostics laboratory, we created a custom bioinformatics tool termed Houston Methodist Variant Viewer (HMVV). HMVV is a Java-based solution that integrates sequencing instrument output, bioinformatics analysis, storage resources and end user interface. …”
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“…The aim of this study was to investigate the reliability for quantitative measurement of glutamate concentration in the nucleus accumbens using a 70-cm wide-bore clinical 3T MRI. (1)H-MRS of the nucleus accumbens was acquired using the Point-Resolved Spectroscopic Sequence (PRESS) with echo time of 40 ms from 10 healthy volunteers (5 female; age range: 18–30 years) on two separate visits (a baseline, and 1-month time point). The Java-based Magnetic Resonance User Interface (jMRUI) software package was used to quantitatively measure the absolute metabolite concentrations. …”
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“…Then, we implemented a tool to enrich the raw relational data and convert it into the openEHR model using the openEHR Java reference model library. The ORBDA dataset is available in composition, versioned composition and EHR openEHR representations in XML and JSON formats. …”
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“…BACKGROUND: This research assesses knowledge amongst drug deliverers about the implementation of mass drug administration (MDA) for lymphatic filariasis (LF) in Agam District (West Sumatera Province), the City of Depok (West Java Province) and the City of Batam (Kepulauan Riau Province), Indonesia. …”
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“…We also developed open-source JavaScript libraries as plug-ins to the web based graph visualization library named Cytsocape.js to implement these methods as complexity management operations. …”
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“…We developed a computer program that automatically generates a PBS draft report based on CBC parameters and age- and sex-matched reference ranges. METHODS: The Java programming language was used to develop a computer program that supports a graphical user interface. …”
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“…On a 16-node multi-core cluster, HSRA is on average 2.3 times faster than previous Hadoop-based tools. Source code in Java as well as a user’s guide are publicly available for download at http://hsra.dec.udc.es.…”
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