Template:AllNBICTools

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| 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

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| 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

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

and Barend Mons

| paper

pubmed:18549479

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| 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

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pubmed:20195360

| download

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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

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pubmed:18689827

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| CoPub: a literature based term enrichment tool for microarray data analysis
| text mining 
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| 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

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pubmed:18442992

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| 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

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| 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

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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

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pubmed:21045054

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| 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

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

and Timo Breit

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

and Jan Bot

| 
| download

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| Immunophyle
| phylogenetics 
| 
| Immunophyle is an application that allows for a quick view on evolution of gene families involved in the immune response. 
| Tim Hulsen 
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| 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

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pubmed:17346331

| download

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| 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

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| 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

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| 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
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| 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

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

and Christof Francke

| paper

pubmed:14988111

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

and Dick de Ridder

| 
| download

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| MetID_GC/MS
| metabolomics 
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| 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

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

and Marc van Driel

| 
| download

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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

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pubmed:18817533

| download

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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

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pubmed:18689827

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| PhyloDrug
| phylogenetics 
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| Phylodrug allows for a quick view on evolution of gene families for known drug targets 
| Tim Hulsen 
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| Phylopat
| phylogenetics 
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| Phylopat allows for a quick view on gene family evolution in eukaryotes 
| Tim Hulsen 
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| PiCaS
| framework 
| e-science
| A Python framework to generate grid output servers 
| Jan Bot 
| 
| download

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| 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

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

and Jack Leunissen

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| 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

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

and Rogier Versteeg

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| 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

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| RoVar
| variant detection, ngs 
| genomics
| Robust Variant detection in genome sequences using Next Generation Data from various platforms 
| Victor de Jager 
| 
| download

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| 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

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

pubmed:19336442

| download

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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

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| 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

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| 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

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pubmed:21045054

| download

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| 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

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| Wikiproteins
| text mining 
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| sub set of for WikiProffesional: Web services for Wiki-annotation (relational) and Knowledge representation and discovery. 
| Barend Mons 
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pubmed:18507872

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| 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

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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
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| 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

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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

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| 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

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| 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 
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| 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 
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| 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 
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| De novo assembly software benchmarking
| Framework 
| genomics
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| Jan van Haarst, Leon Mei 
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| Alignment software benchmarking
| Framework 
| genomics
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| Frans Paul Ruzius, Freerk van Dijk, Leon Mei 
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| 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
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| 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 
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