Search Results for "knowledge"

...In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.

FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc. - to be as automatic as possible (i.e. the FusionCatcher will choose automatically the best parameters in order to find candidate fusion genes, e.g. finding automatically the adapters, building the exon-exon junctions automatically based on the length of the input reads, etc.) while providing the best possible detection rate for finding fusion genes.

The Collaborative Computational Project for NMR (CCPN) provides tools and knowledge to maximise the impact of the biological NMR studies. The CCPN software facilitates data analysis and software integration. The project actively promotes the exchange of knowledge and provides training and best practices for the NMR community. CCPN also has a leading role in the development of a NMR data-sharing standard and coordination of NMR instrumentation proposals for RCUK and BIS. ...

MoSGrid focuses on the configuration and provision of Grid services for molecular simulations and annotation of the results with metadata and their provision for data mining and knowledge generation. It is based on Liferay technology togethe with gUSE.

An interactive data entry, querying, and editing system based on a generic conceptual schema for taxonomic databases. It combines the automated use of scientific names and synonyms in a species checklist with online access to geographical data and common knowledge data (morphological descriptors, genomics, ecology, vernacular names, economic uses, structured notes and conservation status) about the species. All these data can be cross-indexed to a citation list. The design and standard permits rapid customization to suit any taxonomic group.

This advanced machine learning algorithm is a Michigan-style learning classifier system (LCS) developed to specialize in classification, prediction, data mining, and knowledge discovery tasks. Michigan-style LCS algorithms constitute a unique class of algorithms that distribute learned patterns over a collaborative population of of individually interpretable IF:THEN rules, allowing them to flexibly and effectively describe complex and diverse problem spaces. ExSTraCS was primarily developed to address problems in epidemiological data mining to identify complex patterns relating predictive attributes in noisy datasets to disease phenotypes of interest. ...

Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).

Ontologies, which are made up by standardized and defined controlled vocabulary terms and their inter-relationships, are comprehensive and readily searchable repositories for knowledge in a given domain

Web application to make user-friendly requests on large XML database. Tools to XML-ize large bodies of semi-formal texts (like floras). Computer-assisted specimen identification. Uses natural language processing, 2D/3D images analysis and generation.

ProteinShop is an interactive protein manipulation tool. Users apply their knowledge and intuition to quickly create a set of protein configurations that can be subjected to local or global optimization. More information at http://proteinshop.org

FunctSNP is an R interface to an SQL database for linking single nucleotide polymorphisms (SNPs) to functional knowledge. FunctSNP should work on any OS on which R runs.

OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.

Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.

The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects in OBO, OWL, and other commonly used ontology representation

Extraction of binding sites of ligands and search for unknown binding sites on apoproteins. Some call it docking. Some call it binding site detections. Some call it knowledge based.

ASKGene (Automated Sequence Knowledge GENErator) - a customizeable integration platform for sequence-processing bioinformatics tools.

GSCope3 performs microarray data analysis to find correlations between BLSOM clusters and any form of omic knowledge expressed in OSML. Includes example metabolic pathway, gene ontology, genome position, transcription and PPI knowledge in OSML format.

A neuroscientific knowledge management system for the published literature

SENTENSA Knowledge Miner is a platform independent tool for searching any text. SENTENSA uses robust methods of indexing and searching text, leveraging on experience from more than 20 years of information retrieval.

Our goal is to create an open source framework and toolset for modeling dynamic cellular network functions, and to develop a user community committed to using, extending and exploiting these tools to further our knowledge of biologic processes.

Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.

BioNote is a knowledge base that combines unstructured wiki technology with structured annotation to form a collaborative environment. BioNote adds the concepts of page types and semi-structured annotation to extend the unstructured nature of wiki pages

HC is a C++ library for assisting the development of knowledge discovery systems and experiments.

BIRBU (BIological Relationship BUilder) is a Java tool for microarray gene expression data analysis. BIRBU identifies biologically significant relationship between genes using microarray data and prior knowledge on relationships between genes.

The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.