List of all OpenHelix tutorials

This is the full list of tutorials offered by OpenHelix, grouped by category. Please note that a tutorial can appear in multiple categories.

Click on the icons to expand/collapse individual categories. Clicking on a tutorial name will display detailed information, together with a list of all available training materials.

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	Name	Description	Resources
Algorithms and Analysis
	BioMart	Management and querying of many types of biological data	BioMart
	BLAST	Basic Local Alignment and Search Tool	NCBI BLAST
	ClustalW2	Performs multiple sequence alignments	Clustal W
	Consensus	A pattern and motif recognition program	Consensus
	DCODE	DCODE.org Comparative Genomics Developments, a collection of powerful comparative genomics tools	Dcode.org anthology of comparative genomic tools
	FASTA	FASTA sequence algorithm	FASTA
	Galaxy	Analysis tools for researchers	Galaxy
	Gene Expression Omnibus (GEO)	A gene expression/molecular abundance repository and a curated, online resource for gene expression data	Gene Expression Omnibus (GEO)
	Gibbs Motif Sampler	A motif finder and analysis tool	Gibbs
	GoMiner	Ascribe biological significance to large lists of genes by annotating them with their corresponding GO categories	GoMiner
	InterPro	A comprehensive protein signature resource	The InterPro Database
	MDscan	Motif Discovery scan for nucleotide and protein motifs	MDscan
	Melina II	A Web-Based Tool for Promoter Analysis	Melina II
	MEME Algorithm	Multiple Expectation Maximum for Motif Elicitation	MEME
	MEME Suite GLAM2 Algorithm	Part of a motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences.	GLAM2
	MEME Suite Overview	Motif-based sequence analysis tools	MEME
	MEME Suite Sequence Annotation Tools	MEME suite motif finding and annotating tools	MEME
	MEME Suite TOMTOM and GOMO algorithms	Motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences that you provide	MEME
	Primer3	Pick primers from a DNA sequence.	Primer3
	UCSC Genome Browser: An Introduction	The UCSC Genome Browser Introduction	UCSC Genome Browser
	UCSC Genome Browser: Custom Tracks and Table Browser	UCSC Genome Browser advanced topics	UCSC Genome Browser
	UCSC Genome Browser: The Additional Tools	Additional tools at the UCSC Genome Browser	UCSC Genome Browser
	UniProt	UniProt, Universal Protein Resource	UniProt
	VBRC	The Viral Bioinformatics Resource Center	VBRC
	VISTA	Tools for Comparative Genomics	VISTA
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
EBI
	Alternative Splicing and Transcript Diversity (ASTD) database	A bioinformatics resource for alternative splice events and transcripts for human, mouse, and rat	ASTD
	ArrayExpress	A public repository for microarray gene expression data at the EBI	ArrayExpress
	BioMart	Management and querying of many types of biological data	BioMart
	ClustalW2	Performs multiple sequence alignments	Clustal W
	Ensembl	Ensembl Genome Browser	Ensembl
	Ensembl Legacy	Older version of Ensembl Genome Browser	Ensembl
	FASTA	FASTA sequence algorithm	FASTA
	IntAct protein interaction database	IntAct is an open source database and analysis resource for protein interaction data	IntAct
	InterPro	A comprehensive protein signature resource	The InterPro Database
Expression
	Allen Mouse Brain Atlas	Mapped gene expression data in mouse brain	Allen Mouse Brain Atlas
	Alternative Splicing and Transcript Diversity (ASTD) database	A bioinformatics resource for alternative splice events and transcripts for human, mouse, and rat	ASTD
	ArrayExpress	A public repository for microarray gene expression data at the EBI	ArrayExpress
	CleanEx	A Database of Heterogeneous Gene Expression Data Based on A Consistent Gene Nomenclature	CleanEx
	DAVID	A tool that analyzes large lists of genes to provide biological meaning	DAVID
	DBTSS	Database of Transcriptional Start Sites	DBTSS
	Functional Glycomics Gateway	The home for Functional Glycomics research	Consortium for Functional Glycomics
	Gene Expression Omnibus (GEO)	A gene expression/molecular abundance repository and a curated, online resource for gene expression data	Gene Expression Omnibus (GEO)
	GENSAT	Provides an extensive amount of high quality images of gene expression in the central nervous system of the mouse.	GENSAT
	PhenomicDB	Phenotypes database	PhenomicDB
	UCSC Genome Browser: The Additional Tools	Additional tools at the UCSC Genome Browser	UCSC Genome Browser
	VISTA	Tools for Comparative Genomics	VISTA
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
Genome Databases (eu)
	BioMart	Management and querying of many types of biological data	BioMart
	ENCODE	ENCyclopedia of DNA Elements	ENCODE Data Coordination Center
	Ensembl	Ensembl Genome Browser	Ensembl
	Ensembl Legacy	Older version of Ensembl Genome Browser	Ensembl
	FlyBase	A resource for the genes, genome and molecular biology of Drosophila melanogaster and related species.	FlyBase
	GBrowse	GBrowse User Introductory Tutorial	GBrowse
	Gramene	A resource on rice and other grass genomes	Gramene
	Map Viewer	Map Viewer Genome Browser from NCBI	NCBI Map Viewer
	Mouse Genome Informatics (MGI)	The Mouse Genome Informatics resource provides data, tools, and analyses for the mouse model organism.	Mouse Genome Informatics (MGI)
	Overview of Genome Browsers	Various Genome Browsers examined	Ensembl NCBI Map Viewer GBrowse IMG
	PlantGDB	Plant Genome Database	PlantGDB
	Rat Genome Database (RGD)	Rat Genome Database	Rat Genome Database (RGD)
	Saccharomyces Genome Database (SGD)	Saccharomyces Genome Database	SGD
	TAIR	The Arabidopsis Information Resource	The Arabidopsis Information Resource (TAIR)
	UCSC Genome Browser: An Introduction	The UCSC Genome Browser Introduction	UCSC Genome Browser
	UCSC Genome Browser: Custom Tracks and Table Browser	UCSC Genome Browser advanced topics	UCSC Genome Browser
	UCSC Genome Browser: The Additional Tools	Additional tools at the UCSC Genome Browser	UCSC Genome Browser
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
	WormBase	molecular and genetic information on Caenorhabditis elegans and related species	WormBase
	ZFIN	The Zebrafish Information Network	ZFIN
Genome Databases (pro)
	CMR	Comprehensive Microbial Resource	TIGR Comprehensive Microbial Resource
	Complete Microbial Genomes	An extensive collection of data, resources and tools for prokaryotic genomic analysis	Complete Microbial Genomes
	Ensembl Legacy	Older version of Ensembl Genome Browser	Ensembl
	GBrowse	GBrowse User Introductory Tutorial	GBrowse
	Integrated Microbial Genomes (IMG)	IMG is a powerful community resource for the comparative analysis and annotation of microbial genome data.	IMG
	Integrated Microbial Genomes with Microbiome samples (IMG/M)	IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence	IMG/M
	Overview of Genome Browsers	Various Genome Browsers examined	Ensembl NCBI Map Viewer GBrowse IMG
	UCSC Archaeal Genome Browser	Provides 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.	The UCSC Archaeal Genome Browser
	VBRC	The Viral Bioinformatics Resource Center	VBRC
	Viral Genomes at NCBI	Viral genome resources including single-stranded or double-stranded RNA or DNA viruses	NCBI Viral Resources
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
Literature and Text Mining
	Controlled Vocabularies	Standardized term lists that can enhance interactions with biological databases	Controlled Vocabularies (including Open Biomedical Ontologies)
	Gene Ontology	Gene Ontology controlled vocabularies in biology	Gene Ontology (GO)
	iHOP	Information Hyperlinked Over Proteins text mining resource	iHOP
	PubMatrix	PubMatrix, an on-line tool for multiplex literature mining of the PubMed database.	PubMatrix
	PubMed	PubMed access to biomedical research literature	NCBI PubMed
	STRING	known and predicted protein-protein interactions	STRING
	Textpresso	Text-mining the biological literature	Textpresso
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
	XplorMed	eXploring Medline abstracts	XplorMed
Miscellaneous
	Entrez Overview	Overview of NCBI's Entrez Search Resource	NCBI Entrez
	NCBI Overview	Home to many commonly used publicly available databases and tools in molecular biology.	Database resources of the National Center for Biotechnology Information
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
NCBI
	BioSystems	Database of Biological Systems	NCBI BioSystems
	BLAST	Basic Local Alignment and Search Tool	NCBI BLAST
	Complete Microbial Genomes	An extensive collection of data, resources and tools for prokaryotic genomic analysis	Complete Microbial Genomes
	dbGaP	A database of genotypes and phenotypes with extensive variation data and clinical details	dbGaP
	dbSNP	NCBI's SNP database	NCBI dbSNP
	DCODE	DCODE.org Comparative Genomics Developments, a collection of powerful comparative genomics tools	Dcode.org anthology of comparative genomic tools
	Entrez Gene	NCBI's Entrez tool for gene-centric information	NCBI Entrez Gene
	Entrez Overview	Overview of NCBI's Entrez Search Resource	NCBI Entrez
	Entrez Protein	NCBI's Entrez Protein for amino acid-centric information	NCBI Protein database
	Gene Expression Omnibus (GEO)	A gene expression/molecular abundance repository and a curated, online resource for gene expression data	Gene Expression Omnibus (GEO)
	GeneTests	GeneTests, a current, comprehensive genetic testing resource	GeneTests
	GENSAT	Provides an extensive amount of high quality images of gene expression in the central nervous system of the mouse.	GENSAT
	Map Viewer	Map Viewer Genome Browser from NCBI	NCBI Map Viewer
	MMDB	Molecular Modeling Database at NCBI	MMDB
	NCBI Overview	Home to many commonly used publicly available databases and tools in molecular biology.	Database resources of the National Center for Biotechnology Information
	PubMed	PubMed access to biomedical research literature	NCBI PubMed
	RefSeq	Provides molecular sequence records to help locate gene and protein data.	RefSeq
	Viral Genomes at NCBI	Viral genome resources including single-stranded or double-stranded RNA or DNA viruses	NCBI Viral Resources
Nucleotides
	Alternative Splicing and Transcript Diversity (ASTD) database	A bioinformatics resource for alternative splice events and transcripts for human, mouse, and rat	ASTD
	CMR	Comprehensive Microbial Resource	TIGR Comprehensive Microbial Resource
	Consensus	A pattern and motif recognition program	Consensus
	DBTSS	Database of Transcriptional Start Sites	DBTSS
	Entrez Gene	NCBI's Entrez tool for gene-centric information	NCBI Entrez Gene
	Gibbs Motif Sampler	A motif finder and analysis tool	Gibbs
	MDscan	Motif Discovery scan for nucleotide and protein motifs	MDscan
	Melina II	A Web-Based Tool for Promoter Analysis	Melina II
	MEME Algorithm	Multiple Expectation Maximum for Motif Elicitation	MEME
	miRBase	microRNA sequences, targets and gene nomenclature	miRBase
	Primer3	Pick primers from a DNA sequence.	Primer3
	RefSeq	Provides molecular sequence records to help locate gene and protein data.	RefSeq
	UCSC Genome Browser: The Additional Tools	Additional tools at the UCSC Genome Browser	UCSC Genome Browser
	VISTA	Tools for Comparative Genomics	VISTA
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
Pathways
	BioSystems	Database of Biological Systems	NCBI BioSystems
	Cytoscape	An open-source software platform used for visualization and analysis of molecular interaction and network data	Cytoscape
	DAVID	A tool that analyzes large lists of genes to provide biological meaning	DAVID
	GeneMANIA	GeneMANIA: Fast Gene Function Predictions	GeneMANIA
	GenMAPP	A freely available open source software application for visualizing microarray data in the context of biological pathways.	GenMAPP--Gene Microarray Pathway Profiler
	IntAct protein interaction database	IntAct is an open source database and analysis resource for protein interaction data	IntAct
	KEGG	KEGG, The Kyoto Encyclopedia of Genes and Genomes	KEGG
	MINT	Molecular Interaction Database	MINT
	Pathway Interaction Database	A resource of pathway and network data and displays	NCI / Nature Pathway Interaction Database
	Reactome	Knowledgebase of biological processes	Reactome
	Reactome Legacy	Older version of the current Reactome knowledgebase of biological processes.	Reactome
	STRING	known and predicted protein-protein interactions	STRING
	VisANT	A web-based or downloadable software platform used for visualization and analysis of networks and interaction pathways	VisANT
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
Proteins
	Consensus	A pattern and motif recognition program	Consensus
	Entrez Protein	NCBI's Entrez Protein for amino acid-centric information	NCBI Protein database
	Functional Glycomics Gateway	The home for Functional Glycomics research	Consortium for Functional Glycomics
	GeneMANIA	GeneMANIA: Fast Gene Function Predictions	GeneMANIA
	Gibbs Motif Sampler	A motif finder and analysis tool	Gibbs
	IntAct protein interaction database	IntAct is an open source database and analysis resource for protein interaction data	IntAct
	InterPro	A comprehensive protein signature resource	The InterPro Database
	MDscan	Motif Discovery scan for nucleotide and protein motifs	MDscan
	MEME Algorithm	Multiple Expectation Maximum for Motif Elicitation	MEME
	MINT	Molecular Interaction Database	MINT
	MMDB	Molecular Modeling Database at NCBI	MMDB
	Pathway Interaction Database	A resource of pathway and network data and displays	NCI / Nature Pathway Interaction Database
	Pfam	Protein Domain families	Pfam
	PROSITE	Database of protein domains, families and functional sites	PROSITE
	RCSB PDB	RCSB Protein Data Bank	RCSB PDB
	SMART	Protein domain annotation and analysis of domain architectures	SMART
	STRING	known and predicted protein-protein interactions	STRING
	Structural Biology Knowledgebase	The Protein Structure Initiative Structural Biology Knowledgebase	The Protein Structure Initiative Structural Biology Knowledgebase
	UCSC Genome Browser: The Additional Tools	Additional tools at the UCSC Genome Browser	UCSC Genome Browser
	UniProt	UniProt, Universal Protein Resource	UniProt
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
Variation & Medical
	CGAP	Characterize the molecular genetic changes that cause a normal cell to become a cancer cell	CGAP
	dbGaP	A database of genotypes and phenotypes with extensive variation data and clinical details	dbGaP
	dbSNP	NCBI's SNP database	NCBI dbSNP
	DGV: Database of Genomic Variants	Database of Genomic Variants, DGV, catalogs and displays structural variation in the human genome	DGV: Database of Genomic Variants
	DrugBank	A chemoinformatics and bioinformatics resource	DrugBank
	GAD: Genetic Association Database	An archived database associating human genes and polymorphisms with diseases	GAD: Genetic Association Database
	GeneTests	GeneTests, a current, comprehensive genetic testing resource	GeneTests
	Genetics Home Reference	A collection of data describing the effects of genetic variability on human health and disease	Genetics Home Reference
	Genome Variation Server (GVS)	A database providing rapid access to human genotype data and analysis tools.	GVS
	HapMap	HapMap, a database and analysis resource of human variation	HapMap
	Madeline 2.0	Human pedigree diagram tools	Madeline 2.0
	NIEHS SNPs	National Institute for Environmental Health Sciences Environmental Genome Project (EGP) SNPs	NIEHS SNPs Program
	OMIM	Online Mendelian Inheritance in Man	Online Mendelian Inheritance in Man (OMIM)
	PhenomicDB	Phenotypes database	PhenomicDB
	PubMed	PubMed access to biomedical research literature	NCBI PubMed
	SeattleSNPs	Human SNPs in genes	SeattleSNPs
	VISTA	Tools for Comparative Genomics	VISTA
	World Tour of Genomics Resources	A World Tour of Genome Resources for finding and learning the right resource for your needs.	UCSC Genome Browser RCSB PDB
Ye Olde Tutorials
	BiologicalNetworks	Analyze and visualize molecular interaction networks	BiologicalNetworks
	GeneSNPs	An integrated view of gene structure and SNP variations	GeneSNPs