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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
Anni text mining literature “Anni” improved to ‘ superanni’ and web enabled, former TextBLAST improved and integrated Martijn Schuemie

and Barend Mons

paper

pubmed:18549479

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

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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 resulting content is managed by the BioExpert Framework. A specific application of BioExpert is the http://www.peroxisomekb.nl/ PeroxisomeKB Andrew Gibson

and Antoine van Kampen

pubmed:18689827

CoPub: a literature based term enrichment tool for microarray data analysis text mining CoPub is a text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. The biomedical concepts included in CoPub are all human, mouse and rat genes, furthermore biological processes, molecular functions and cellular components from Gene Ontology, and also diseases, drugs and pathways. Altogether more than 260,000 search strings are linked with CoPub. Raoul Frijters

and Jacob de Vlieg

pubmed:18442992

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

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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

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
HybQC microarray transcriptomics a pipeline for microarray data quality control Han Rauwerda

and Timo Breit

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

and Jan Bot

download
Phenotype Database framework, database visualization web framework for integration of various types of 'omics data' in the context of a biological study Kees van Bochove

and Phenotype Foundation

paper

pubmed:21052526

Immunophyle phylogenetics Immunophyle is an application that allows for a quick view on evolution of gene families involved in the immune response. Tim Hulsen
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
LocateP genomics LocateP is a computational pipeline combining various tools in order to identify detailed subcellular location of gram-positive bacterial proteins. Miaomiao Zhou

and Roland Siezen

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
MADMAX database (web server) microarray MADMAX is a versatile, platform-independent microarray storage and analysis platform. It is also a potential target for implementation of other tools and data from metabolomics and high-throughput sequencing Anand Gavai

and Jack Leunissen

paper
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
MGV visualisation genomics Visualization for Genomics: The Microbial Genome Viewer Lex Overmars

and Christof Francke

paper

pubmed:14988111

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

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

and Marc van Driel

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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

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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

PhyloDrug phylogenetics Phylodrug allows for a quick view on evolution of gene families for known drug targets Tim Hulsen
Phylopat phylogenetics Phylopat allows for a quick view on gene family evolution in eukaryotes Tim Hulsen
PiCaS framework e-science A Python framework to generate grid output servers Jan Bot download
ProGMap phylogenetics The ProGMap (Protein Group Mappings) is an integrated protein database in which over 14 million proteins and 240,000 group descriptions collected from 9 protein repositories are consistently mapped onto each other, creating a unique network of mappings among these collections. Arnold Kunziar

and Jack Leunissen

paper

pubmed:19494185

ProRepeat sequence analysis ProRepeat collects all perfect and imperfect protein tandem repeats in proteins, plus the corresponding nucleotide sequences Hong Luo

and Jack Leunissen

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
R2: A biologist friendly microarray analysis and visualization platform visualisation; microarray transcriptomics R2: microarray analysis and visualization platform Jan Koster

and Rogier Versteeg

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
Sequence Harmony sequence analysis The Sequence Harmony webserver allows a quick selection of subtype-specific sites from a multiple alignment given a subfamily grouping. This can be useful, e.g., in prioritizing mutation experiments. Application to subtype-specific functional interactions pinpoints major interacting regions and identifies putative associated functions Anton Feenstra

and Jaap Heringa

paper
Sigwin detector microarray transcriptomics SigWin-detector is a grid-enabled workflow application designed to identify significant regions in various kinds of genomic data. A significant region is a part of the input sequence where the median value is higher than expected, if we assume that the ordering of the values in the input sequence does not matter. For example, SigWin-detector enables us to find regions of increased density of gene expression (RIDGES) in transcriptome maps Alves da Inda

and Timo Breit

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

pubmed:19336442

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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
Wikiproteins text mining sub set of for WikiProffesional: Web services for Wiki-annotation (relational) and Knowledge representation and discovery. Barend Mons

pubmed:18507872

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

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multi-RELIEF sequence analysis The multi-RELIEF webserver allows a quick selection of subtype-specific sites from a multiple alignment given a subfamily grouping. This can be useful, e.g., in prioritizing mutation experiments. Application to subtype-specific functional interactions pinpoints major interacting regions and identifies putative associated functions. Anton Feenstra

and Jaap Heringa

paper
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

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‘Watskeburt?’ text mining genomics Heuristic support for hypothesis construction from literature. See AIDA toolkit Marco Roos

and Pieter W Adriaans

paper

pubmed:19796406

BioVenn visualisation generic A web application for the comparison and visualization of biological lists using area-proportional Venn diagrams Wynand Alkema

and Tim Hulsen

paper

pubmed:18925949

Diagnostic Variant Database Database genomics Diagnostic Variant Database (DVD) is to share all genetic variants detected in the course of next-generation sequencing (NGS) application next-generation sequencing (NGS) applications between collaborators. This will help medical researchers to distinguish between functionally relevant and benign genetic variants. Therefore, researchers or clinicians can quickly narrow down to those variants that are the potential genetic cause of a particular disease. Jeroen Laros
CLI-mate Framework generic In the agile development environment of bioinformatics, many command line tools are created quickly to fill in gaps between complex information processes. A command line interface (CLI) is sometimes sufficient for the task, but it limits adoption by a broader audience. As such, it's often necessary for the developer to create a CLI wrapper that provides a more user friendly interface. CLI-mate was developed to systematize and expedite this very time consuming process. Zuotian Tatum, Jeroen Laros
Mutalyzer Framework genomics Mutalyzer is a tool primarily designed to check descriptions of sequence variants according to the standard human sequence variant nomenclature of the Human Genome Sequence Variation Society (HGVS) (For an overview, visit http://www.hgvs.org/mutnomen/). Mutalyzer aims to encourage the proper use of nomenclature in publications and reduce redundancy in sequence variation databases. In principle, Mutalyzer can check descriptions of sequence variants detected in other organisms, provided that the standard HGVS nomenclature is applied. Jeroen Laros, Martijn Vermaat paper
De novo assembly software benchmarking Framework genomics A Galaxy module that wraps existing de novo assembly program and reports the assembly program's quality (e.g. max contig, N50, etc) and performance (CPU time, memory use, etc). Jan van Haarst, Leon Mei
Alignment software benchmarking Framework genomics A Galaxy module that wraps existing mapping alignment program and reports the alignment program's quality (e.g. nr of mapped reads, accuracy, etc) and performance (CPU time, memory use, etc). Frans Paul Ruzius, Freerk van Dijk, Leon Mei
Narwhal Framework, pipeline genomics the NARWHAL software pipeline has been developed to automate the primary analysis of massive parallel sequencing data. NARWHAL has been specifically developed to deal with large num-bers of samples and diverse sequencing applications. NARWHAL performs de-multiplexing, alignment and quality control with a minimum of hands-on time. Rutger Brouwer paper
GAPSS Framework, pipeline genomics SNP calling, CAGE/SAGE analysis pipeline. Also available at NBIC Galaxy. Matthew S. Hestand, Jeroen Laros
Rite Framework, distributed computing escience Rite provides a client and server programs to aid the distributed execution of programs. Using a pilot job infrastructure rite provides a java framework for specifying jobs in addition to a text based (JSON) representation for these jobs and sequences of jobs (recipes or workflows). Mathijs Kattenberg
FGWeb Framework, pipeline escience FGWeb is a web-interface that allows to integrate functional genomics data and bioinformatic tool flows with a minimum of time investment in robust web-based software. David van Enckevort, Sacha van Hijum
FAME Environment systems biology FAME, the Flux Analysis and Modeling Environment. FAME is your one stop shop for stoichiometric modeling, featuring model construction, model execution, results visualization, and friendly elephants. Joost Boele

and Bas Teusink

paper

pubmed:22289213

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