“…Availability: All data and a JAVA applet to check SBML-models is available from http://www.minet.uni-jena.de/csb/prj/ot/tools Contact: dittrich@minet.uni-jena.de Supplementary information: Supplementary data are available at Bioinformatics online.…”
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“…BACKGROUND: The largest living lizard species, Varanus komodoensis Ouwens 1912, is vulnerable to extinction, being restricted to a few isolated islands in eastern Indonesia, between Java and Australia, where it is the dominant terrestrial carnivore. …”
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“…SLIMS was developed using Java 1.6.0, JSPs, Hibernate 3.3.1.GA, DB2 and mySQL, Apache Tomcat 6.0.18, NetBeans IDE 6.5, Jasper Reports 3.5.1 and JasperSoft's iReport 3.5.1. …”
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“…The software is independent of the operating system, due to the fact that the Rich Client Platform is written in Java. OpenChrom is released under the Eclipse Public License 1.0 (EPL). …”
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“…RESULTS: We developed a Java-based framework to integrate existing tools and methods for ncRNA detection. …”
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“…CONCLUSIONS: BMGE is able to perform biologically relevant trimming on a multiple alignment of DNA, codon or amino acid sequences. Java source code and executable are freely available at ftp://ftp.pasteur.fr/pub/GenSoft/projects/BMGE/.…”
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“…RESULTS: We have developed PathMAPA, a web-based application written in Java that can be easily accessed over the Internet. …”
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“…A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.…”
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“…We use our model to estimate the duration of post-cytokinetic attachment between a S.cerevisiae mother and daughter cell. The Java implementation is fast and extensible, and includes a graphical user interface. …”
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“…BACKGROUND: RNAexinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes. …”
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“…METHODS: Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. …”
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“…The algorithm was implemented in Java, supports any ontology in OBO format, and is available for non-commercial and academic usage under: https://compbio.charite.de/svn/hpo/trunk/src/tools/significance/…”
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“…We therefore conducted a field survey in 19 locations on Sumatra, Java and the Mentawai islands to record male loud-calls of wild surilis (Presbytis), a genus of Asian leaf monkeys (Colobinae) with disputed taxanomy, and compared the structure of their loud-calls with a molecular genetic analysis. …”
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“…Over the last decade systems specific for the automatic quantification of RIF have been developed for this purpose, however to ask more mechanistic questions on the spatio-temporal aspects of RIF, an automated RIF analysis platform that also quantifies RIF size/volume and relative three-dimensional (3D) distribution of RIF within individual nuclei, is required. RESULTS: A java-based image analysis system has been developed (AutoRIF) that quantifies the number, size/volume and relative nuclear locations of RIF within 3D nuclear volumes. …”
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“…Chemical operations are carried out by calling Java code modules which use the CDK, JChemPaint and OPSIN libraries to provide cheminformatics functionality. …”
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“…The layout algorithm is available as open source Java code. CONCLUSIONS: Visualization of large molecular data sets using the Molecule Cloud approach allows scientists to get information about the composition of molecular databases and their most frequent structural features easily. …”
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“…High performance of CytoKavosh is achieved by dynamically linking highly optimized functions of Kavosh's C++ to the Cytoscape Java program, which makes this plug-in suitable for analyzing large biological networks. …”
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“…The content of ontologies is mapped to a graph of connected objects which is compatible to the object-oriented programming style in Java. Semantic functions implement knowledge about the complex semantics of an ontology beyond the class hierarchy and “partOf” relations. …”
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“…An implementation of the method in Java for the generation of wavelet-based surrogates is available online as supporting material.…”
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“…METHODS: PWID were recruited by respondent-driven sampling in an urban setting in Java, Indonesia and interviewed with the Addiction Severity Index (ASI), Blood-Borne Virus Transmission Risk Assessment Questionnaires, and Knowledge Questionnaire on HIV/AIDS. …”
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