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OpenHelix

List of all OpenHelix tutorials

This is the full list of tutorials offered by OpenHelix. Clicking on a tutorial name will display detailed information, together with a list of all available training materials. To get a list of all tutorials in a particular category, click on the category name or display all tutorials grouped by category.

NameDescriptionCategoryResources
Subscription requiredAllen Mouse Brain AtlasMapped gene expression data in mouse brainExpressionAllen Mouse Brain Atlas
Subscription requiredAlternative Splicing and Transcript Diversity (ASTD) databaseA bioinformatics resource for alternative splice events and transcripts for human, mouse, and ratExpression, Nucleotides, EBIASTD
Subscription requiredArrayExpressA public repository for microarray gene expression data at the EBIExpression, EBIArrayExpress
Subscription requiredBiologicalNetworksAnalyze and visualize molecular interaction networksYe Olde TutorialsBiologicalNetworks
Subscription requiredBioMartManagement and querying of many types of biological dataGenome Databases (eu), Algorithms and Analysis, EBIBioMart
Subscription requiredBioSystemsDatabase of Biological SystemsPathways, NCBI NCBI BioSystems
Subscription requiredBLASTBasic Local Alignment and Search ToolAlgorithms and Analysis, NCBI NCBI BLAST
Subscription requiredCGAPCharacterize the molecular genetic changes that cause a normal cell to become a cancer cellVariation & MedicalCGAP
Subscription requiredCleanExA Database of Heterogeneous Gene Expression Data Based on A Consistent Gene NomenclatureExpressionCleanEx
Subscription requiredClustalW2Performs multiple sequence alignmentsAlgorithms and Analysis, EBIClustal W
Subscription requiredCMRComprehensive Microbial ResourceGenome Databases (pro), NucleotidesTIGR Comprehensive Microbial Resource
Subscription requiredComplete Microbial GenomesAn extensive collection of data, resources and tools for prokaryotic genomic analysisGenome Databases (pro), NCBI Complete Microbial Genomes
Subscription requiredConsensusA pattern and motif recognition programNucleotides, Proteins, Algorithms and AnalysisConsensus
Subscription requiredControlled VocabulariesStandardized term lists that can enhance interactions with biological databasesLiterature and Text MiningControlled Vocabularies (including Open Biomedical Ontologies)
Subscription requiredCytoscapeAn open-source software platform used for visualization and analysis of molecular interaction and network dataPathwaysCytoscape
Subscription requiredDAVIDA tool that analyzes large lists of genes to provide biological meaningExpression, PathwaysDAVID
Subscription requireddbGaPA database of genotypes and phenotypes with extensive variation data and clinical detailsVariation & Medical, NCBI dbGaP
Subscription requireddbSNPNCBI's SNP databaseVariation & Medical, NCBI NCBI dbSNP
Subscription requiredDBTSSDatabase of Transcriptional Start Sites Expression, NucleotidesDBTSS
Subscription requiredDCODEDCODE.org Comparative Genomics Developments, a collection of powerful comparative genomics toolsAlgorithms and Analysis, NCBI Dcode.org anthology of comparative genomic tools
Subscription requiredDGV: Database of Genomic VariantsDatabase of Genomic Variants, DGV, catalogs and displays structural variation in the human genomeVariation & MedicalDGV: Database of Genomic Variants
Subscription requiredDrugBankA chemoinformatics and bioinformatics resourceGenome Databases (eu)DrugBank
Subscription requiredENCODE Data at UCSCENCODE Data at UCSCGenome Databases (eu)ENCODE Data Coordination Center at UCSC
Subscription requiredENCODE FoundationsENCyclopedia of DNA ElementsGenome Databases (eu)ENCODE Data Coordination Center at UCSC
Subscription requiredEnsemblEnsembl Genome BrowserGenome Databases (eu), EBIEnsembl
Subscription requiredEnsembl LegacyOlder version of Ensembl Genome BrowserGenome Databases (eu), Genome Databases (pro), EBIEnsembl
Subscription requiredEntrez GeneNCBI's Entrez tool for gene-centric informationNucleotides, NCBI NCBI Entrez Gene
Subscription requiredEntrez OverviewOverview of NCBI's Entrez Search ResourceMiscellaneous, NCBI NCBI Entrez
Subscription requiredEntrez ProteinNCBI's Entrez Protein for amino acid-centric informationProteins, NCBI NCBI Protein database
Subscription requiredFASTAFASTA sequence algorithmAlgorithms and Analysis, EBIFASTA
Subscription requiredFlyBaseA resource for the genes, genome and molecular biology of Drosophila melanogaster and related species.Genome Databases (eu)FlyBase
Freely availableFunctional Glycomics GatewayThe home for Functional Glycomics researchExpression, ProteinsConsortium for Functional Glycomics
Subscription requiredGAD: Genetic Association DatabaseAn archived database associating human genes and polymorphisms with diseasesVariation & MedicalGAD: Genetic Association Database
Subscription requiredGalaxyAnalysis tools for researchersAlgorithms and AnalysisGalaxy
Subscription requiredGBrowseGBrowse User Introductory TutorialGenome Databases (eu), Genome Databases (pro)GBrowse
Subscription requiredGene Expression Omnibus (GEO)A gene expression/molecular abundance repository and a curated, online resource for gene expression dataExpression, Algorithms and Analysis, NCBI Gene Expression Omnibus (GEO)
Subscription requiredGeneMANIAGeneMANIA: Fast Gene Function PredictionsProteins, PathwaysGeneMANIA
Subscription requiredGene OntologyGene Ontology controlled vocabularies in biologyLiterature and Text MiningGene Ontology (GO)
Subscription requiredGeneSNPsAn integrated view of gene structure and SNP variationsYe Olde TutorialsGeneSNPs
Subscription requiredGeneTestsGeneTests, a current, comprehensive genetic testing resourceYe Olde TutorialsGeneTests
Subscription requiredGenetics Home ReferenceA collection of data describing the effects of genetic variability on human health and diseaseVariation & MedicalGenetics Home Reference
Subscription requiredGenMAPPA freely available open source software application for visualizing microarray data in the context of biological pathways. PathwaysGenMAPP--Gene Microarray Pathway Profiler
Freely availableGenoCADComputer-Assisted Design software for synthetic biologyNucleotidesGenoCAD
Freely availableGenoCAD Advanced TopicsComputer-Assisted Design software for synthetic biologyNucleotidesGenoCAD
Subscription requiredGenome Variation Server (GVS)A database providing rapid access to human genotype data and analysis tools.Variation & MedicalGVS
Subscription requiredGENSATProvides an extensive amount of high quality images of gene expression in the central nervous system of the mouse.
Expression, NCBI GENSAT
Subscription requiredGibbs Motif SamplerA motif finder and analysis toolNucleotides, Proteins, Algorithms and AnalysisGibbs
Subscription requiredGoMiner Ascribe biological significance to large lists of genes by annotating them with their corresponding GO categoriesAlgorithms and AnalysisGoMiner
Subscription requiredGrameneA resource on rice and other grass genomesGenome Databases (eu)Gramene
Subscription requiredHapMapHapMap, a database and analysis resource of human variationVariation & MedicalHapMap
Subscription requirediHOPInformation Hyperlinked Over Proteins text mining resourceLiterature and Text MiningiHOP
Subscription requiredIntAct protein interaction databaseIntAct is an open source database and analysis resource for protein interaction dataProteins, Pathways, EBIIntAct
Subscription requiredIntegrated Microbial Genomes (IMG)IMG is a powerful community resource for the comparative analysis and annotation of microbial genome data.Genome Databases (pro)IMG
Subscription requiredIntegrated Microbial Genomes with Microbiome samples (IMG/M)IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome sequenceGenome Databases (pro)IMG/M
Subscription requiredInterProA comprehensive protein signature resourceProteins, Algorithms and Analysis, EBIThe InterPro Database
Subscription requiredKEGGKEGG, The Kyoto Encyclopedia of Genes and GenomesPathwaysKEGG
Subscription requiredMadeline 2.0Human pedigree diagram toolsVariation & MedicalMadeline 2.0
Subscription requiredMap ViewerMap Viewer Genome Browser from NCBIGenome Databases (eu), NCBI NCBI Map Viewer
Subscription requiredMDscanMotif Discovery scan for nucleotide and protein motifsNucleotides, Proteins, Algorithms and AnalysisMDscan
Subscription requiredMelina IIA Web-Based Tool for Promoter AnalysisNucleotides, Algorithms and AnalysisMelina II
Subscription requiredMEME AlgorithmMultiple Expectation Maximum for Motif ElicitationNucleotides, Proteins, Algorithms and AnalysisMEME
Subscription requiredMEME Suite GLAM2 AlgorithmPart of a motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences.Algorithms and AnalysisGLAM2
Subscription requiredMEME Suite OverviewMotif-based sequence analysis toolsAlgorithms and AnalysisMEME
Subscription requiredMEME Suite Sequence Annotation ToolsMEME suite motif finding and annotating toolsAlgorithms and AnalysisMEME
Subscription requiredMEME Suite TOMTOM and GOMO algorithmsMotif discovery tool that can detect conserved motifs in a set of DNA or protein sequences that you provideAlgorithms and AnalysisMEME
Subscription requiredMINTMolecular Interaction DatabaseProteins, PathwaysMINT
Subscription requiredmiRBasemicroRNA sequences, targets and gene nomenclatureNucleotidesmiRBase
Subscription requiredMMDBMolecular Modeling Database at NCBIProteins, NCBI MMDB
Subscription requiredMouse Genome Informatics (MGI)The Mouse Genome Informatics resource provides data, tools, and analyses for the mouse model organism. Genome Databases (eu)Mouse Genome Informatics (MGI)
Subscription requiredNCBI OverviewHome to many commonly used publicly available databases and tools in molecular biology.Miscellaneous, NCBI Database resources of the National Center for Biotechnology Information
Freely availableNIEHS SNPsNational Institute for Environmental Health Sciences Environmental Genome Project (EGP) SNPsVariation & MedicalNIEHS SNPs Program
Freely availableOMIMOnline Mendelian Inheritance in Man (OMIM): A database of human genes, genetic diseases and disordersVariation & MedicalOMIM
Subscription requiredOverview of Genome BrowsersVarious Genome Browsers examinedGenome Databases (eu), Genome Databases (pro)GBrowse
IMG
Ensembl
NCBI Map Viewer
Subscription requiredPathway Interaction DatabaseA resource of pathway and network data and displaysProteins, PathwaysNCI / Nature Pathway Interaction Database
Subscription requiredPfamProtein Domain familiesProteinsPfam
Subscription requiredPhenomicDBPhenotypes databaseExpression, Variation & MedicalPhenomicDB
Subscription requiredPlantGDBPlant Genome DatabaseGenome Databases (eu)PlantGDB
Subscription requiredPrimer3Pick primers from a DNA sequence. Nucleotides, Algorithms and AnalysisPrimer3
Subscription requiredPROSITEDatabase of protein domains, families and functional sitesProteinsPROSITE
Subscription requiredPubMatrixPubMatrix, an on-line tool for multiplex literature mining of the PubMed database. Literature and Text MiningPubMatrix
Subscription requiredPubMedPubMed access to biomedical research literatureLiterature and Text Mining, Variation & Medical, NCBI NCBI PubMed
Subscription requiredRat Genome Database (RGD)Rat Genome DatabaseGenome Databases (eu)Rat Genome Database (RGD)
Subscription requiredRCSB PDBRCSB Protein Data BankProteinsRCSB PDB
Subscription requiredReactomeKnowledgebase of biological processesPathwaysReactome
Subscription requiredReactome LegacyOlder version of the current Reactome knowledgebase of biological processes.PathwaysReactome
Subscription requiredRefSeqProvides molecular sequence records to help locate gene and protein data.Nucleotides, NCBI RefSeq
Subscription requiredSaccharomyces Genome Database (SGD)Saccharomyces Genome DatabaseGenome Databases (eu)SGD
Subscription requiredSeattleSNPsHuman SNPs in genesVariation & MedicalSeattleSNPs
Subscription requiredSMARTProtein domain annotation and analysis of domain architecturesProteinsSMART
Subscription requiredSTRINGknown and predicted protein-protein interactionsLiterature and Text Mining, Proteins, PathwaysSTRING
Subscription requiredStructural Biology KnowledgebaseThe Protein Structure Initiative Structural Biology KnowledgebaseProteinsThe Protein Structure Initiative Structural Biology Knowledgebase
Subscription requiredTAIRThe Arabidopsis Information ResourceGenome Databases (eu)The Arabidopsis Information Resource (TAIR)
Subscription requiredTextpressoText-mining the biological literatureLiterature and Text MiningTextpresso
Subscription requiredUCSC Archaeal Genome BrowserProvides you with many research and analysis tools that can be used to examine the genomes of more than 50 microbial species from the domain archaea.Genome Databases (pro)The UCSC Archaeal Genome Browser
Freely availableUCSC Genome Browser: An IntroductionThe UCSC Genome Browser IntroductionGenome Databases (eu), Algorithms and AnalysisUCSC Genome Browser
Freely availableUCSC Genome Browser: Custom Tracks and Table BrowserUCSC Genome Browser advanced topicsGenome Databases (eu), Algorithms and AnalysisUCSC Genome Browser
Freely availableUCSC Genome Browser: The Additional ToolsAdditional tools at the UCSC Genome BrowserAlgorithms and Analysis, Expression, Genome Databases (eu), Nucleotides, ProteinsUCSC Genome Browser
Subscription requiredUniProtUniProt, Universal Protein ResourceProteins, Algorithms and AnalysisUniProt
Subscription requiredVBRCThe Viral Bioinformatics Resource CenterGenome Databases (pro), Algorithms and AnalysisVBRC
Subscription requiredViral Genomes at NCBIViral genome resources including single-stranded or double-stranded RNA or DNA virusesGenome Databases (pro), NCBI NCBI Viral Resources
Subscription requiredVisANTA web-based or downloadable software platform used for visualization and analysis of networks and interaction pathwaysPathwaysVisANT
Subscription requiredVISTATools for Comparative GenomicsAlgorithms and Analysis, Expression, Nucleotides, Variation & MedicalVISTA
Freely availableWorld Tour of Genomics ResourcesA World Tour of Genome Resources for finding and learning the right resource for your needs.Algorithms and Analysis, Expression, Genome Databases (eu), Genome Databases (pro), Literature and Text Mining, Miscellaneous, Nucleotides, Pathways, Proteins, Variation & MedicalUCSC Genome Browser
Subscription requiredWormBasemolecular and genetic information on Caenorhabditis elegans and related speciesGenome Databases (eu)WormBase
Subscription requiredXplorMedeXploring Medline abstractsLiterature and Text MiningXplorMed
Subscription requiredZFINThe Zebrafish Information NetworkGenome Databases (eu)ZFIN
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