Search Results for "web file manager java"

Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. ...

The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.

Our source code is now on GitHub: https://github.com/hci-gnomex/gnomex. Please refer to GitHub for the latest code. GNomEx is Genomic LIMS and Data Repository. It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. Experiment platforms supported include Illumina HiSeq, MiSeq, iScan, ABI Sanger sequencing,...

The Investigation/Study/Assay (ISA) Infrastructure is the first pilot-stage freely available software suite that 1. assists in the reporting and local management of experimental metadata and facilitates submission to international public repositories.

The q utility is a platform for creating and managing data analysis pipelines. 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...

Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.

3D viewer which arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Feedback appreciated. NOTE: requires Java3d installation. Superceded by Cylindrical Alignment App

Index biological data (genbank sheets, Uniprot...) in a Solr indexer, with index shard support and provides a query interface. Project goal is to create a virtual image with indexer and web interface to query and visualize biological data.

A new open-source tool that integrates pipeline automated identification and phylogenetic studies of microbial communities using genes sequences

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

TaxonFinder is an application that annotates taxon found in literature. The application harnesses a hybrid algorithm that is necessarily a combination of morphological analysis, dictionary lookup and Levenstein Distance algorithm.

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

Large set of functions for biological records (ECG, EEG, phono), datastore, datamining and analysis (HRV, QT, RR, ST). The application is written in Java, so that it is assumed to work on all devices. It runs as a desktop or client-server application. It

BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.

A dialect of XUL implementing most of Mozilla XUL's Fourth Draft. XML User Interface Language (XUL) is a method for easily creating GUI applications. Lux XUL supports Python scripting via Jython 2.1.

This project provides software resources for creating solid models of proteins that can be printed on color 3D printers. The main focus is a java program that reads in a PDB file and produces a PLY format stick representation of the protein.

Shred is a fast and scalable faceted data browser. The application allows users to navigate the data in an intuitive way and by any path they wish to take. Immediate intuitive information regarding the data is apparent.