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Advanced SQL Querying of Bioinformatics Databases
  Did you miss the recent class entitled Advanced SQL Querying of Bioinformatics Databases? If so, you can catch up by watching the videorecording and get the slides and examples.
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  •   
    - Database (organized collection of data)
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    - Tool (used to performs analyses)
  • - Resource requires a login
  • - Tutorial available
  • - Licensed for Stanford community
  • - Produced by Stanford researchers
 
—Databases  
 
—Tools
Genomes 
More info about CMR CMR: Comprehensive Microbial Repository database        
More info about Ensembl Ensembl genome databases        
GO ontologies     Video tutorials
Go to BioFAQ on MGD MGD: Mouse Genome Informatics database        
Go to BioFAQ on Ensembl NCBI Genome databases        
UCSC Genome Browser UCSC Genome Browser       Video tutorials
WormBase        
Genes, proteins & sequence analysis 
Go to BioFAQ on BKL BIOBASE Knowledge Library: curated protein data (formerly PROTEOME) Stanford only Resource requires a login for SOME FUNCTIONS - click here to get one   Video tutorials
Go to BioFAQ on Biology Workbench Biology Workbench: web-based molbio tools   Resource requires a login - click here to get one    
Go to BioFAQ on ExPASy ExPASy: proteomics databases and tools        
Go to BioFAQ on GeneCards GeneCards: gene summaries        
Go to BioFAQ on iHOP iHOP: gene-function mappings from literature        
Go to BioFAQ on LOCATE LOCATE: predicted protein localization & structure        
Go to BioFAQ on Bioinformatik Harvester Bioinformatik Harvester: gene properties new class        
Go to BioFAQ on NCBI Gene NCBI Gene        
Go to BioFAQ on Oligo Oligo Stanford only Resource requires a login - click here to get one    
Go to BioFAQ on Sequencher Sequencher Stanford only Resource requires a login - click here to get one    
Go to BioFAQ on Vector NTI Vector NTI: molbio tools        
Go to BioFAQ on UniProt UniProt: principal repository of protein sequences & function data       Video tutorials
Genetics & phenotypes 
Go to BioFAQ on PharmGKB PharmGKB     Video tutorials
Go to BioFAQ on dbSNP dbSNP        
Pathways & enzymes 
Go to BioFAQ on BioCyc BioCyc: pathway/genome databases       Video tutorials
Go to BioFAQ on BRENDA BRENDA: enzyme database        
Go to BioFAQ on IPA Ingenuity Pathways Analysis Stanford only Resource requires a login - click here to get one   Video tutorials
Go to BioFAQ on KEGG KEGG: pathways, protein and cellular functions        
Expression & function 
Go to BioFAQ on SMD SMD: Stanford University Microarray Database     Video tutorials
search engine specialized in finding and characterizing biological information, especially microarray data NextBio search engine [Enterprise-level trial access]        
Go to BioFAQ on GeneSpring GeneSpring microarray data analysis Stanford only Resource requires a login - click here to get one   Video tutorials
Go to BioFAQ on IPA Ingenuity Pathways Analysis Stanford only Resource requires a login - click here to get one   Video tutorials
Go to BioFAQ on BodyMap BodyMap: gene expression        
Info on GEO GEO: Gene Expression Omnibus       Video tutorials
Go to BioFAQ on MeV MeV: Microarray multiexperiment viewer        
Go to BioFAQ on NCBI Probe NCBI Probe       Video tutorials
Go to BioFAQ on SAM SAM: Significance Analysis of Microarrays   Resource requires a login - click here to get one  
Go to BioFAQ on SymAtlas SymAtlas: gene expression        
Drugs & chemistry 
Go to BioFAQ on DiscoveryGate DiscoveryGate: MDL chemistry & pharmacology search engine Stanford only This resource is restricted to holders of a SUNet ID; click here to see how to get one   Video tutorials
Go to BioFAQ on SciFinder web SciFinder web Stanford only Resource requires a login - click here to get one   Video tutorials
Go to BioFAQ on CAS CAS Online: chemical Abstracts databases Stanford only This resource is restricted to holders of a SUNet ID; click here to see how to get one    
Go to BioFAQ on DrugBank DrugBank: comprehensive drug and drug target data        
Structures 
Go to BioFAQ on CATH CATH: protein family classifications        
Go to BioFAQ on Cn3D Cn3D NCBI molecular viewer       Video tutorials
Go to BioFAQ on DS Visualizer Accelrys DiscoveryViewer        
Go to BioFAQ on FistGlance FistGlance viewer        
Go to BioFAQ on MMDB NCBI MMDB: structure database        
Go to BioFAQ on PDB PDB: Biomolecular structures of all types       Video tutorials
Go to BioFAQ on SCOP SCOP: structural classification of proteins        
Literature & patents 
search engine specialized in finding and characterizing biological information, especially microarray data NextBio search engine  [click for Enterprise-level trial access]        
search engine that offers powerful filtering features for PubMed records novoseek search engine         
search engine that presents PubMed search records according to GO ontology GoPubMed search engine         
Go to BioFAQ on SCI SCI: Science Citation Index database Stanford only This resource is restricted to holders of a SUNet ID; click here to see how to get one    
Go to BioFAQ on Derwent Innovations Index Derwent Innovations Index (patents) Stanford only This resource is restricted to holders of a SUNet ID; click here to see how to get one   Video tutorials
Go to BioFAQ on SciFinder web SciFinder web Stanford only Resource requires a login - click here to get one   Video tutorials
Google Patents        
Go to BioFAQ on Google Scholar Google Scholar        
Data mining 
Go to BioFAQ on GraphPad Prism GraphPad Prism       Video tutorials
search engine specialized in finding and characterizing biological information, especially microarray data NextBio search engine  [click for Enterprise-level trial access]        
Go to BioFAQ on MS Excel statistics MS Excel statistics        

Bioresearch Notifications

Solution biotool: Ingenuity Pathways Analysis

Need to analyze microarray or proteomics data? If so, have look at the Ingenuity Pathways Analysis (IPA), a highly curated database + analytical functions for understanding how proteins work together to effect cellular changes. More
Already an IPA user? Then join the online Stanford IPA user group and share in your colleagues' expertise.

So What? Success Tip #12

So What? Tip If you're a Mac user, you should consider installing MS Windows (XP or Vista). Why? Both operating systems can be run on a single machine can enable you to use valuable Windows-only, such as Stanford's free Electronic Laboratory Notebook. Also, MS Office programs on Windows are susbtantially better and are more reliable than their Mac-version.

Find Biotools

Search BioWareDB BiowareDB is a search engine for biosoftware and databases

  Browse Biodatabases:
  NAR database survey NAR provides a yearly listing of molecular biology databases, organized by subject area   Browse Bio web services:
  NAR web services survey NAR provides a yearly listing of molecular biology web services, organized by subject area

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portal mission

PharmGKB is a major repository of pharmacogenomic data for Homo sapiens. Its principal investigator is Stanford Professor of Bioengineering Russ B. Altman. The GO Ontologies are the principal ontologies describing the properties of genes and proteins of many organisms. One of its architects is Stanford Genetics Professor J. Michael Cherry. SMD is a major repository of microarray gene expression. The database is a joint project in the Departments of Biochemistry and Genetics at the School of Medicine, Stanford University. SOURCE is a data retrieval tool provided by the Department of Genetics at the School of Medicine, Stanford University.
[more] SGD is the main repository of genome data from Saccharomyces cerevisiae. Its principal investigator is Stanford Genetics Professor J. Michael Cherry.
[more] TGD is the main repository of genome data from Tetrahymena thermophila. Its principal investigator is Stanford Genetics Professor J. Michael Cherry. TGD is the main repository of genome data from Candida albicans. Its principal investigator is Stanford Genetics Assistant Professor Gavin Sherlock. SAM is a powerful tool for evaluating the statistical significance microarray gene expression data. The tool is provided by Stanford Professor of Statistics Robert Tibshirani. TGD is the main repository of genome data from Tetrahymena thermophila. Its principal investigator is Stanford Genetics Professor J. Michael Cherry. TAIR is the main repository of genome data from Arabidopsis thaliana. It is curated by personnel form Stanford's Department of Plant Biology. Using microarray data, BioProspector examines the upstream region of genes in the same gene expression pattern group, looking for regulatory sequence motifs. It was developed by Stanford Biochemistry Professor Douglas L. Brutlag. A powerful tool for microarray and genome data analysis, BioProspector examines the upstream region of genes in the same gene expression pattern group, looking for regulatory sequence motifs. It was developed by a team that includes a number of Stanford researchers. Using combined tiling array and comparative genomics data, CisGenome was developed by a team that includes Stanford Professor of Statistics Wing Wong. This resource is restriced to holders of a SUNet ID. StepMiner was developed by a team that includes Stanford Professor of Statistics Robert Tibshirani, Stanford Associate Professor of Radiology Sylvia K. Plevritis, and Stanford Professor of Computer Science David L. Dill.
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