NBIC Tools With Download Link

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Package Category Domain Description Author/contact Publication Software
2Dwarp mass spectrometry proteomics A Two-Dimensional Method for Time Aligning Liquid Chromatography Mass Spectrometry Data. The algorithm called 2Dwarp correct the time shift occurring in LC-MS chromatograms. Modifications in the COW algorithm have been made using overlapping peak area of 3 dimensional Gaussian which size were obtained from extracted peaks of the reference and sample chromatogram. The software is to be used by data analysts working on LC-MS data. Frank Suits

and Peter Horatovitch

paper

pubmed:21349866

download
2Dwarp - Taverna Workflow mass spectrometry proteomics A Two-Dimensional Method for Time Aligning Liquid Chromatography Mass Spectrometry Data. The algorithm called 2Dwarp correct the time shift occurring in LC-MS chromatograms. Modifications in the COW algorithm have been made using overlapping peak area of 3 dimensional Gaussian which size were obtained from extracted peaks of the reference and sample chromatogram. The software is to be used by data analysts working on LC-MS data. Frank Suits

and Peter Horatovitch

paper

pubmed:21349866

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


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

and Marcel Reinders

pubmed:21712249

download
FluxES metabolomics metabolomics FluxEs is a program for metabolic flux analysis using NMR spectra of tracer experiments. FluxEs 1.0 is freely available via a web interface. FluxEs 2.0 is a development version and is available upon request. Thomas Binsl

and Hans van Beek

paper

pubmed:20097912

download
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
Ibidas framework, database an integration platform for various sorts of biological data. Mark Hulsman

and Jan Bot

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
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
MASDA mass spectrometry proteomics R-package for Mass Spectrometry Data Analysis, The package includes routines for loading mass spectrometry data from CSV files, doing baseline correction and normalization, peak detection and filtering, peak clustering across spectra, peak filtering and some visualization of results Wouter Meuleman

and Lodewyk Wessels

paper

pubmed:18257918

download
MaRIboES metabolomics an algorithm for metabolite and reaction inference based on enzyme specificities (Matlab, C++) Marco de Groot

and Dick de Ridder

download
MetID_GC/MS metabolomics Quantitative structure – retention index prediction using multiple linear regression and genetic algorithms for descriptor selection. Retention index – time conversion and filtering of the hit lists obtained from experiments analyzed with AMDIS Velitchka Mihaleva

and Roeland van Ham

paper

pubmed:19176550

download
MetiDB database metabolomics {{{description}}} Velitchka Mihaleva

and Marc van Driel

download
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


PiCaS framework e-science A Python framework to generate grid output servers Jan Bot download


R package “penalized” statistics statistics L1 (lasso) and L2 (ridge) regression for generalized linear models and the Cox proportional hazards model, with cross-validation. Jelle Goeman download
ReConn visualisation metabolomics, network A Java plug-in for Cytoscape that connects the visualization program Cytoscape with the database Reactome. Pathways from Reactome are retrieved and visualized with Cytoscape and data (e.g. gene expression) is mapped on the pathways. ReConn has different features, like calculating routes between reactions, partial simulation of knock-out experiments, “growing” reaction pathways starting with a given metabolite, etc. Wim Ligtenberg

and Peter Hilbers

download
RoVar variant detection, ngs genomics Robust Variant detection in genome sequences using Next Generation Data from various platforms Victor de Jager download
SIM statistics statistics R package for the to analyse simultaneously copy number and gene expression microarray data, to identify candidate genes involved in tumorigenesis Renee de Menezes

and Judith Boer

paper

pubmed:19563656

download


StatQuant toolbox proteomics A post quantification analysis toolbox for improving quantitative mass spectrometry Bas van Breukelen

pubmed:19336442

download
The AIDA toolbox text mining The AIDA toolbox is a suite of web services for ontology-supported information extraction on the Grid. AIDA has routines for ontology alignment, ontology supported query construction, named entity recognition and concept learning. It is a modular platform for dynamic adaptive information extraction in an e-Science environment. Scott Marshall

and Marco Roos

paper 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
Utopia/GPCRDB-PDF-Reader database 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. Bas Vroling

and Gert Vriend

pubmed:21045054

download
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 paper download
globaltest statistics omics Testing groups of covariates/features for association with a response variable, with applications to gene set testing Jelle Goeman paper

pubmed:14693814

download
mzMatch framework, pipeline metabolomics mzMatch is a modular, open source and platform independent data processing pipeline for metabolomics LC/MS data written in the Java language Richard Scheltema

and Rainer Breitling

paper

pubmed:21401061

download







GRASS ngs genomics GRASS,a generic algorithm for scaffolding next-generation sequencing assemblies. Alexey A. Gritsenko

and Dick de Ridder

paper download
GO-Elite pathway omics GO-Elite is designed to identify a minimal non-redundant set of biological Ontology terms or pathways to describe a particular set of genes or metabolites. Default resources include multiple ontologies (Gene, Disease, Phenotype), pathways (WikiPathways, KEGG, Pathway Commons), putative regulatory targets (transcription, microRNA, domains) and cellular biomarkers. Multiple options for pathway visualization are also available. This software can be run using an intuitive graphical user interface, through command-line arguments, using a web interface and through the program GenMAPP-CS Chris Evelo paper download