Search Results for "java" - Page 17
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Showing 804 open source projects for "java"
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The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.
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FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.
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JHeatChart is a simple Java library for generating heat map charts.
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HeliconiusDB is a project to develop a database schema and web-based software tools for the study of Heliconius butterflies (and other organisms) in evolutionary biology.
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Cloe (Closure Editor) is a graphical, Java based tool used for editing contigs, resolving contig features, and closing both sequencing and physical gaps.
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SAFEGUI is a graphical interface to the safe R package which performs resampling based categorical significance testing for gene expression data.
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SARSE is a scientific data editor that uses the extendable column format, allows interactive overview, tracks editing history, and has a user extendable tool box.
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Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies.
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IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.
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PocketDepth helps determine binding grooves for protein molecules. Applicable in Bioinformatics and Drug discovery. Literature - http://www.ncbi.nlm.nih.gov/pubmed/17949996 Author's thesis - http://openwetware.org/wiki/Kalidas_Y
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JFlux is a java library and graphical user interface to work with flow cytometry data. In particular, it is adapted to the COPAS biosorter and can analyze expression profiles.
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It's a project to predict peptide fragmentation of mass spectrometry. Check the detail at Anal Chem. 2011 Feb 1;83(3):790-6. On the accuracy and limits of peptide fragmentation spectrum prediction. Li S, Arnold RJ, Tang H, Radivoja
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A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.
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A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.
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Protein Data Bank transformed into an SQL database with a very powerful search engine and a rich web interface. The engine combines chemical, sequence and 3D structure searches. The interface provides statistics, sequence and 3D structure alignments.
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Graphical editor using HTML5 canvas for input of chemical structures, molecule interactions, as well as protein sequence and 3D structural motifs. Facilitates searches in chemo-informatics, bioinformatics and structural biology .
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Algorithms that optimally & efficiently map atomic reactions. See 1) Atomic Reaction Mapping {Crabtree: amazon, b&n} 2) J. of Exp. Algorithmics, Vol 13 {Crabtree, Mehta} 3) J. Chem. Inf. Model., 2010, 50 (9), pp 1751–1756 {Crabtree, Mehta, Kouri}.
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Basic Electronical Medical Management (BEMM) is an application to control medical data of a set of patients. It is built on top of open source technologies, to provide an integration skeleton of mvn, Datanucleus, Spring, Vaadin, Acceleo technologies.
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Small set of utilities used by the 2010 iGEM Mexico-UNAM-CINVESTAV Team to automate biobricks from files
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DIVAT (Diagnostic Immunohistochemistry Visualization and Analysis Tool) is designed to graphically analyse comprehensive data sets of immunohistochemical results as those used in clinical diagnostic pathology.
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CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
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ChiBE
Chisio BioPAX Editor
ChiBE (Chisio BioPAX Editor) is an open source pathway editor for biological pathways in BioPAX format. ChiBE converts BioPAX graphs into process diagrams where complexes and compartments are represented with compound nodes. !!! For latest version, please see !!! http://code.google.com/p/chibe -
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Visualize chromatographic properties for peptides from replicate, multi-site HPLC-MRM Mass Spectrometry experiments. RT Viewer was developed to easily visualize and troubleshoot chromatographic properties of a study across multiple laboratories.
