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The Stanford Microarray Database

G. Sherlock
2001 Nucleic Acids Research  
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data.  ...  The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published,  ...  SMD will be supported as long as the microarray community at Stanford University supports and uses it.  ... 
doi:10.1093/nar/29.1.152 pmid:11125075 pmcid:PMC29818 fatcat:clcw423uevehjhaqqu4o5uetey

The Stanford Tissue Microarray Database

R. J. Marinelli, K. Montgomery, C. L. Liu, N. H. Shah, W. Prapong, M. Nitzberg, Z. K. Zachariah, G. J. Sherlock, Y. Natkunam, R. B. West, M. van de Rijn, P. O. Brown (+1 others)
2007 Nucleic Acids Research  
The Stanford Tissue Microarray Database (TMAD; is a public resource for disseminating annotated tissue images and associated expression data.  ...  The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license.  ...  Funding to pay the Open Access publication charges for this article was provided by HHMI. P.O.B. is an investigator of the Howard Hughes Medical Institute.  ... 
doi:10.1093/nar/gkm861 pmid:17989087 pmcid:PMC2238948 fatcat:pplfutifkjcjlojknn3oipkwom

Implementation of GenePattern within the Stanford Microarray Database

J. Hubble, J. Demeter, H. Jin, M. Mao, M. Nitzberg, T. B. K. Reddy, F. Wymore, Z. K. Zachariah, G. Sherlock, C. A. Ball
2009 Nucleic Acids Research  
Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd. to store, annotate, view, analyze and share microarray data.  ...  In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base.  ...  the GenePattern instance within SMD.  ... 
doi:10.1093/nar/gkn786 pmid:18953035 pmcid:PMC2686537 fatcat:wefawczrgfgyziketziwreshyy

The Stanford Microarray Database accommodates additional microarray platforms and data formats

C. A. Ball
2004 Nucleic Acids Research  
The Stanford Microarray Database (SMD) (http:// is a research tool for hundreds of Stanford researchers and their collaborators.  ...  In addition to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the ability to store, retrieve, display and analyze the complete raw data produced  ...  ACKNOWLEDGEMENTS This work was supported by grants from the US National Institutes of Health to P.O.B. (5R01 CA77097) and to G.S. (1R01 HG002732).  ... 
doi:10.1093/nar/gki006 pmid:15608265 pmcid:PMC539960 fatcat:sqekj2ckarhjhkjogcikdzita4

The Stanford Microarray Database: data access and quality assessment tools

J. Gollub
2003 Nucleic Acids Research  
The Stanford Microarray Database (SMD; http:// serves as a microarray research database for Stanford investigators and their collaborators.  ...  In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code and providing full public access to data published by SMD users, along with  ...  The Stanford Microarray Database (SMD;, a research database for Stanford-affiliated and other registered users, makes freely available the data for over 3500  ... 
doi:10.1093/nar/gkg078 pmid:12519956 pmcid:PMC165525 fatcat:pa4emp44ebag5foguix6r74lzi

The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

Patrick J Killion, Gavin Sherlock, Vishwanath R Iyer
2003 BMC Bioinformatics  
It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases.  ...  The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux.  ...  One of the most successful, proven, and heavily utilized microarray databases is the Stanford Microarray Database (SMD - [5] .  ... 
doi:10.1186/1471-2105-4-32 pmid:12930545 pmcid:PMC194174 fatcat:gijrnimgw5dwrlrejrnzg6jxtm

The Stanford Microarray Database: implementation of new analysis tools and open source release of software

J. Demeter, C. Beauheim, J. Gollub, T. Hernandez-Boussard, H. Jin, D. Maier, J. C. Matese, M. Nitzberg, F. Wymore, Z. K. Zachariah, P. O. Brown, G. Sherlock (+1 others)
2007 Nucleic Acids Research  
The Stanford Microarray Database (SMD; http://smd. is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray  ...  The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis  ...  ACKNOWLEDGEMENTS We thank the users of SMD for their constant feedback that helps us to improve SMD, and to the remote installers of SMD for detailed reports as to the ease of installing SMD that have  ... 
doi:10.1093/nar/gkl1019 pmid:17182626 pmcid:PMC1781111 fatcat:3q2yf3tf25hydkgfrgblk3nzqa

Free access costs money

Peg Brickley
2003 Genome Biology  
But the Stanford microarray database serves 85 laboratories on campus, and 400 scientists.  ...  Twice, the National Institutes of Health (NIH) has refused to fund the Stanford Microarray Database, a homegrown effort that may be the largest free and open collection of microarray research data in the  ... 
doi:10.1186/gb-spotlight-20030225-01 fatcat:yaa7al4i7nh7pm5ddkornrlwiy

ARROGANT: an application to manipulate large gene collections

A. V. Kulkarni, N. S. Williams, Y. Lian, J. D. Wren, D. Mittelman, A. Pertsemlidis, H. R. Garner
2002 Bioinformatics  
ARROGANT can relate different sequence identifiers to their common reference sequence using the UniGene database, allowing for the comparison of data from two different microarray experiments.  ...  The objective is to enable users to compile gene/clone collections from different databases, allowing them to design experiments and analyze the collections as well as associated experimental data efficiently  ...  We would like to thank Affymetrix, Inc for providing accession numbers for the sequences on their microarrays.  ... 
doi:10.1093/bioinformatics/18.11.1410 pmid:12424110 fatcat:akg7auncifbf5exs2yl3yofdha

The Second International Meeting on Microarray Data Standards, Annotations, Ontologies and Databases

Andy Hayes
2000 Yeast  
In the Stanford database alone, Mike Cherry (SGR, Stanford) anticipated a billion rows of data and 0.75 terabytes of images per year by the end of 2000.  ...  YAMAD (yet another microarray database) The next session of talks was introduced by Terry Gaasterland (Rockefeller University) as a`marathon of databases'. A marathon it was too!  ... 
doi:10.1002/1097-0061(20000930)17:3<238::aid-yea35>;2-x pmid:11025536 pmcid:PMC2448378 fatcat:odatk5hoevdizjnn2u3oqwifeu

Submission of Microarray Data to Public Repositories

Catherine A Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C Matese, Helen Parkinson, John Quackenbush, Martin Ringwald, Susanna-Assunta Sansone, Gavin Sherlock (+6 others)
2004 PLoS Biology  
While NCBI and the EBI had developed nascent microarray data repositories, and work was underway to create a similar database at the DDBJ, submitting data to these databases was a considerable burden for  ...  Ball is in the Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America; Alvis Brazma is at the European Bioinformatics Institute, European Molecular  ... 
doi:10.1371/journal.pbio.0020317 pmid:15340489 pmcid:PMC514887 fatcat:oj7qvl34vbc2bbopak5tsyflk4

Navigating Public Microarray Databases

Christopher J. Penkett, Jürg Bähler
2004 Comparative and Functional Genomics  
Here we provide a guide to the use of these public microarray resources.  ...  With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this  ...  Acknowledgements The authors wish to thank Alvis Brazma for valuable additions to the paper.  ... 
doi:10.1002/cfg.427 pmid:18629145 pmcid:PMC2447434 fatcat:d7gmuubz45fqlaqs3jaukkdaj4

The bioinformatics resource for oral pathogens

T. Chen, K. Abbey, W.-j. Deng, M.-c. Cheng
2005 Nucleic Acids Research  
Microarray Database.  ...  Different gene identification schemes and functional annotation methods used in these databases present a challenge for cross-referencing and the efficient use of the data.  ...  Hanson of the Office of Computing and Network Technology at The Forsyth Institute for their assistance. This work was supported by the NIDCR grant K22 DE14742.  ... 
doi:10.1093/nar/gki361 pmid:15980574 pmcid:PMC1160122 fatcat:g2dun5esb5czxox3xk4e6sq2mu

Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification

P. M. Haverty
2004 Nucleic Acids Research  
Biology (Stanford University) Computational Molecular Biology (Stanford University) Protein Architecture, Dynamics, and Structure Prediction (Stanford University) Research Highlights: Introduction to  ...  Lectured and gave personal instruction in the use of the PERL programming language and the UNIX operating system for bioinformatics research.  ... 
doi:10.1093/nar/gkh183 pmid:14704355 pmcid:PMC373293 fatcat:ahgztmavgjditp6ty464t3gsxa

Arabidopsis Microarray Service Facilities

Ellen Wisman, John Ohlrogge
2000 Plant Physiology  
In this regard, all experimental data generated by AFGC are deposited in the Stanford Microarray Database (SMD; http://genome www4.  ...  STANFORD MICROARRAY DATABASE Microarrays can, in one experiment, provide information on expression patterns for thousands of genes and this information often can supply new insights about already described  ... 
doi:10.1104/pp.124.4.1468 pmid:11115861 fatcat:ouyqwzxagrgvxhb6u55ziujjue
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