Bioinformatics Services

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Contents

Main projects

Almost all of these projects are collaborative projects with other research groups, see the individual project pages for details.

  • ArrayAnalysis.org - Quality Control, pre-processing, normalization and statistics of Affymetrix microarrays
  • BridgeDB.org - Software framework for identifier mapping.
  • dbNP.org - Development site for Systems Biology infrastructure.
  • PathVisio.org - Pathway editor and pathway analysis tool.
  • Wikipathways.org - Pathways for the people.

Computing facilities

  • NuGO Blackbox NBX5 (NBX development)
  • NuGO Blackbox NBX7 (Production machine)
  • NuGO Blackbox NBX8 (Production machine)
  • NuGO Blackbox NBX31(Production machine)
  • Blackbox NBX33 (BiGCaT Calculation server)
  • ArrayAnalysis server
  • NTC-R server (NTC calculation server)
  • NTC Data server
  • NTC-ArrayTrack server
  • NTC-Docushare App server
  • NTC-Docushare DB server
  • Wikipathways server
  • BiGCaT FTP server
  • We soon expect to host a LifeScience GRID cluster.

Software

Incomplete list, contact us for anything you might need not on the list
Since the NBX project is based on BioLinux all the NBXs contain the full set of BioLinux software, only some of that is mentioned below.
  • Affymetrix MAS5 and GCOS
  • Agilent Feature Extraction software
  • ArrayTrack [used by NTC]
  • Base2 (as NutriBase): access on NBX7, NBX8, no longer supported
  • Bioconductor/R (statistics)
  • Bioinformatics desktop offering some of the tools mentioned here on your local machine
  • Bowtie (Short read alignment tool)
  • Consed/Phred (sequence data base calling and contig assembly)
  • Cytoscape (network analysis)
  • EMBOSS: European Molecular Biology Open Software Suite access from NBX7, NBX8
  • Eu.gene (pathway statistics)
  • GenePattern (webaccess to tools and workflows): access on NBX7, NBX8
  • GenMAPP: (pathway analysis) visit GenMAPP.org for local install, consider using PathVisio instead
  • Genomatix Bibliosphere and Chipinspector (transcription factor involvement in transcriptomics)
  • GO_Elite (Gene Ontology analysis)
  • Incyte Gemtools (Incyte specific toolbox), no longer actively supported, needs to be booted on old offline server if needed
  • Metacore from GeneGo (pathway and network analysis)
  • PathVisio visit pathvisio.org for local use
  • Primer3 Plus (primer design) from our colleagues at WUR
  • Rosetta Resolver (database and analysis environment)
  • Refiner Genome (Process, visualize and analyze HTS data)
  • SAS JMP (statistics)
  • Spotfire Decisionsite (mainly visual analysis)
  • Taverna (workflows)
  • Wikipathways (pathway editing)
Software usage policies depend on licenses and computing facilities needed, please contact us if there anything you need to use

Website services

Workflows and toolkits

Contact us for collaborations
  • Clustering and PCA (often as a part of QC or a prelude to pathway analysis)
  • Datawarehousing
  • Experiment description (Mage-ML, Tabe2Mage)
  • Experiment publication in Arrayexpress or GEO
  • Gene Ontology (GO) analysis
  • Prediction of protein translation using miRNA data
  • Pathway creation and editing
  • Pathway analysis toolbox
  • Pathway statistics approaches
  • Profile definition for gene expression classes
  • Quality control, normalisation and analysis for two colour microarrays
  • Quality control, GCRMA normalisation and analysis for Affymetrix microarrays
  • Quality control and analysis for methylation arrays (MeDIP)
  • Quality control and analysis for ChiP-on-chip
  • Quality control and analysis for miRNA microarrays
  • Sequence analysis for functional SNPs
  • Sequence and thermodynamic analysis to find miRNA binding sites
  • SNP toolbox
  • Text mining toolbox (most often applied to pathway extensions)
  • Transcription factor binding site analysis (from synteny, expression and databases)
  • Number crunching and scripting in Perl, Java and C++.