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.

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