Search Results for "data science" - Page 8

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.

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.

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.

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.

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

Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.

A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.

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.

OpenClinica is a web-based electronic data capture platform for clinical research. See http://www.OpenClinica.org/ for downloads, documentation, and mailing lists.

CEGA is a highly extendable layout plugin for Cytoscape based on an Evolutionary Algorithm. In contrast to other layout algorithms, CEGA lets users decide which features are important for the visualization of their graphs.

The Molwind project aims at developing Open Source software to visualize relationships among molecular entities such as chemical structures on the basis of NASA WorldWind. Different levels of complexity get visible by zooming in areas of interest.

ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.

CyReposition is an open source Cytoscape Plugin for the reuse of existing Cytoscape network layouts in new Cytoscape projects. This project migrated to github https://github.com/matthiaskoenig/cy2reposition

SnoopCGH is a java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.

Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases. See http://bit.ly/bfirSh and http://bit.ly/bwpnSY for latest developments.

SLEDRIDE: Simplified Learning about Expression Data Running in a Desktop Environment. To provide a general workbench for pipe-lining microarray gene expression data from supervised learning results into unsupervised learning methods.

Chipster is a biologist-friendly analysis software for high-throughput data. It contains over 200 analysis tools for next generation sequencing (NGS), microarray and proteomics data. Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates...

Annotare is a tool for annotating Microarray and Gene Expression data. It will help a bench biologist construct a MIAME-compliant MAGE-TAB file.

ZAE is a Zoomable multiple sequence Alignment Editor

This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.

ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the automatic annotation of genome-wide tiling-array data in Arabidopsis. ARTADE is a program originally written by Dr. Tetsuro Toyoda, RIKEN, Japan.

RepeatMap is a collection of time/memory efficient algorithms and data structures to enable rapid counting & querying of kmers (sequences of length k) counts in large sequences. E.g. a query could be "how many times is 'ACGTCATGGTAC' found in a genome."

Decima is a database that was designed to support time-series data mining. It consists of PostgreSQL custom type definition, implementation of GiST index for that type and snowflake database schema.

E-BioFlow enables the scientists to design workflow using three different perspectives: control flow, data flow and resource perspective. The workflow tool is based on the Yawl engine and has support for BioMOBY and WSDL services and Perl and R scripts.

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.