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Companion Website

Sansom & Horton: Internet for Molecular Biologists

Chapter 06

Web Resources for cell and developmental biology
Carnegie Stages of embryo development http://embryo.soad.umich.edu/carnStages/carnStages.HTML Illustration of developmental stages, with links to resources about each stage
Flybase http://flybase.bio.indiana.edu The Drosophila central web site. Everything you want to know about flies.
Gene Ontology Consortium http://www.geneontology.org Controlled vocabulary of gene and protein roles
Mouse 3D altas http://genex.hgu.mrc.ac.uk/ 3D volumetric pixel models of mouse embryos that can display tissue or gene expression domains
STKE http://stke.sciencemag.org/ A growing site that aims to link all transduction pathways
Society for Developmental Biology (SDB) http://sdb.bio.purdue.edu/dbcinema/ Various movies and animations, fly morphegenesis, calcium waves, filopodial dynamics, and more.
Multidimensional human embryo (SDB) http://embryo.soad.umich.edu/ A collection of magnetic resonance microscopy images plus optical photographs
Rotating animation of stage 16 embryo http://embryo.soad.umich.edu/carnStages/stage16/stage16.mov QuickTime movie
Morph of human development http://embryo.soad.umich.edu/resources/morph.mov QuickTime movie
WWW Virtual Library--Cell Biology http://www.biochemweb.org/ Designed for scientists, students and educators
Virtual Library--Developmental Biology http://sdb.bio.purdue.edu/Other/VL_DB.HTML Maintained by the SDB
Wormbase http://wormbase.org The C. elegans community site
Xenbase http://xenbase.org Community site for Xenopus research
Xenopus Molecular Marker Resource http://www.xenbase.org/xmmr/Welcome.HTML A Xenopus site that includes morphs and movies


Web Searching
Search engines

Altavista
www.altavista.com Advanced search lets you construct Boolean queries, sort results by various criteria, etc.
Google www.google.com Results are ranked by the number of other sites that link to that page, a surprisingly effective method of focusing on the more useful sites.
Yahoo www.yahoo.com _
Metasearch

Sherlock
http://www.apple.com/macosx/jaguar/sherlock.HTML Included in Mac OS X
OmniWeb browser http://www.omnigroup.com/applications/omniweb/ A commercially available web browser for Mac OS X
Datamonster www.datamonster.com Web-based meta-search engine that compiles results from various search sites
Dogpile www.dogpile.com Another web-based metasearch engine
Create bookmarkable search URLs

AutoPOST
http://www.io.com/~jsm/autopost/ Attempts to add a GET-method query string to a search form URL (see Protocol 1)
frmget bookmarklet http://www.squarefree.com/bookmarklets/forms.html A javascript snippet that changes PSOT forms to GET (See Protocol 1)
Add searching to your site

ht://Dig
http://www.htdig.org/ WWW indexing and searching system for a domain or intranet


Smart links in PubMed
Search for papers on Xenopus in the last 7 days
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd= search&term=Xenopus&db=PubMed&orig_db=PubMed&filters=on&pmfilter_EDatLimit=7+Days"
Search for papers by J.D.Watson
http: //www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=PubMed&term=watson+jd"
Search for papers on the Xenopus heart that appeared in the last 120 days
http://www.ncbi.nlm.nih.gov/entrez/query.f cgi?cmd=search&term=Xenopus+heart&db=PubMed&orig_db=PubMed&filters=on&pmfilter_EDatLimit =120+Days"
Search for papers on microtubule dynamics that appeared in the last 120 days
http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?cmd=search&term=microtubule+dynamics&db=PubMed&orig_db=PubMed&filters=on&pmfilt er_EDatLimit=120+Days"


Molecular biology and genomics resources
ArrayViewer http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/images.HTML A Java Applet for analysing array data
Blast http://www.ncbi.nlm.nih.gov/blast/indelx.HTML Compares sequences
eMotif motif.stanford.edu/emotif Protein sequence motifs
ESTs http://www.ncbi.nlm.nih/gov/dbEST/ Expressed sequence tags database at the NCBI
Expression profiler http://ep.ebi.ac.uk:80/ A clustering program for array analysis
Homologene http://www.ncbi.nlm.nih.gov/HomoloGene/stats.HTML Finds the closest related gene in other species
SMD http://genome-www4.stanford.edu/MicroArray/SMD/ The Stanford microarray database. Stores raw and normalized array data
Unigene http://www.ncbi.nlm.nih.gov/UniGene/index.HTML Compilation of sequnce data into individual contigs
Gene expression sites
Mouse Genome Informatics
http://www.informatics.jax.org/ Genetic, genomic, and biological data on laboratory mice
The Edinburgh Mouse Atlas Project http://genex.hgu.mrc.ac.uk 3D atlas showing gene expression in mouse embryo
ZFIN: the Zebrafish Information Network http://www.zfin.org Zebrafish model organism database
Xenbase: a Xenopus web resource http://xenbase.org Cell and developmental biology of the frog, Xenopus
Axeldb http://www.dkfz-heidelberg.de/abt0135/axeldb.htm A database focusing on gene expression data gathered by large-scale in situ hybridization screening in Xenopus laevis embryos
Microarrays
Micro Array Gene Expression Markup Language (MAGE-ML)
http://genomebiology.com/2002/3/9/research/0046 XML-based data format to facilitate the exchange of microarray data.
SMD Microarray Links: Software & Tools http://genome-www5.stanford.edu/MicroArray/SMD/restech.HTML Links to sources of various microarray analysis tools.
ScanAlyze http://rana.lbl.gov/EisenSoftware.htm Microarray image analysis program.
Cluster and TreeView http://rana.lbl.gov/EisenSoftware.htm Cluster analysis and visualization
XCluster http://genome-www.stanford.edu/~sherlock/cluster.HTML Cluster analysis on UNIX
ExpressionProfiler http://www.ebi.ac.uk/microarray/ExpressionProfiler/ep.HTML A set of tools for analysing and clustering gene expression and sequence data