Difference between revisions of "NBIC Tools"

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| structomics
 
| structomics
 
| The GPCR-specific PDF reader allows you to enrich your scientific literature with information and knowledge from the GPCRDB. Relevant information for genes, proteins, residues and mutations is automatically retrieved from the GPCRDB and made available to you. This information is integrated with the article in a non-obtrusive way; it is only there where and when you want it. This software helps you put your literature in the context of the total body of knowledge related to GPCRs, providing you with instant access to current, integrated, validated, internally consistent data and information.  
 
| The GPCR-specific PDF reader allows you to enrich your scientific literature with information and knowledge from the GPCRDB. Relevant information for genes, proteins, residues and mutations is automatically retrieved from the GPCRDB and made available to you. This information is integrated with the article in a non-obtrusive way; it is only there where and when you want it. This software helps you put your literature in the context of the total body of knowledge related to GPCRs, providing you with instant access to current, integrated, validated, internally consistent data and information.  
| [http://www.nbic.nl/about-nbic/who-is-who/details/prof-dr-gert-vriend/ Gert Vriend]
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| Bas Vroling and [http://www.nbic.nl/about-nbic/who-is-who/details/prof-dr-gert-vriend/ Gert Vriend]
 
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| [http://www.gpcr.org/7tm/?wicket:bookmarkablePage=:nl.ru.cmbi.mcsis.web.pages.info.UtopiaDocumentGPCRDBPage download]
 
| [http://www.gpcr.org/7tm/?wicket:bookmarkablePage=:nl.ru.cmbi.mcsis.web.pages.info.UtopiaDocumentGPCRDBPage download]
 
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Revision as of 15:09, 5 August 2011

Package Category Domain Description Author/contact Publication Software
Genevis visualisation transcriptomics GENeVis is an application for integrated visualization of genome expression and network dynamics in both regulatory networks and metabolic pathways. Michel A. Westenberg paper download
BMRF protein function, prediction proteomics BMRF is an easy to use R program for protein function prediction using Markov Random Field analysis. Inferences are made by Markov Chain Monte Carlo. Besides function prediction this method estimates accurately the network parameters. Yiannis Kourmpetis and Cajo ter Braak pubmed:20195360 download
PeroxisomeKB database integrative The peroxisomal knowledge base focuses on peroxisomal pathways and several related genetic disorders. The knowledgebase is based on a new framework to construct knowledge bases with concept maps for presentation of information and the web ontology language OWL for the representation of information [BioExpert]. Marcel Willemsen and Antoine van Kampen pubmed:18689827
BioExpert framework, database integrative The BioExpert project is working towards an environment that allows the creation of high-qualilty knowledge bases (KB) about specific demains of biology. The aim is to engage experts in rich, free-form semantic content creation through the development of concept maps. The resultaing content is managed by the BioExpert Framework. A specific application of BioExpert is the PeroxisomeKB Andrew Gibson and Antoine van Kampen pubmed:18689827
WikiPathways pathway, visualisation integrative WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Thomas Kelder and Alex Pico doi:10.1371/journal.pbio.0060184 development site
PathVisio pathway visualisation integrative PathVisio is a tool for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as you would in any drawing program, like PowerPoint or Photoshop. But the difference is that PathVisio can understand the biological context of a pathway, because you can link biological entities (genes or proteins) in your pathways to biological data using database identifiers. This will let you map experimental data (e.g. microarray data) and visualize it on top of the pathway drawing. Martijn van Iersel and Chris Evelo pubmed:18817533 download
LOFT Orthology, gene function, prediction, phylogeny genomics LOFT(levels of orthology) can be used to describe the multi-level nature of gene relations. This is implemented in a program LOFT that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large) trees. René van der Heijden and Martijn Huynen pubmed:17346331 download
Topos framework, distributed computing escience The Token Pool Server (ToPoS) is a ReST webservice that supports distribution of large computational tasks on distributed systems, such as clusters, compute clouds, the Grid or processes on a super computer. Pieter van Beek download
CytoscapeRPC communication integrative CytoscapeRPC is a plugin for Cytoscape which allows users to create, query and modify Cytoscape networks from any programming language which supports XML-RPC. This enables them to access Cytoscape functionality and visualize their data interactively without leaving the programming environment with which they are familiar Jan Bot pubmed:21712249 download
RoVar variant detection, ngs genomics Robust Variant detection in genome sequences using Next Generation Data from various platforms Victor de Jager download
StatQuant toolbox proteomics A post quantification analysis toolbox for improving quantitative mass spectrometry Bas van Breukelen pubmed:19336442 download
LysNDeNovo peptide identication proteomics LysNDeNovo analyses ETD spectra which utilizes the presence of a single fragment ion series to assign the peptide sequence. Our de novo sequencing approach results in a significant higher number of peptides identified than searching a dataset with other methods. Moreover, the de novo results allow the determination of point mutations as well as conserved regions between proteins of different species. Bas van Breukelen pubmed:20077410 download
GPCRDB database structomics The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models. Bas Vroling and Gert Vriend pubmed:21045054
Utopia/GPCRDB-PDF-Reader database, visualisation structomics The GPCR-specific PDF reader allows you to enrich your scientific literature with information and knowledge from the GPCRDB. Relevant information for genes, proteins, residues and mutations is automatically retrieved from the GPCRDB and made available to you. This information is integrated with the article in a non-obtrusive way; it is only there where and when you want it. This software helps you put your literature in the context of the total body of knowledge related to GPCRs, providing you with instant access to current, integrated, validated, internally consistent data and information. Bas Vroling and Gert Vriend download