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Companion Website
Sansom & Horton: Internet for Molecular Biologists
Chapter 06
| 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 |
| Search engines Altavista |
www.altavista.com | Advanced search lets you construct Boolean queries, sort results by various criteria, etc. |
| 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 |
| 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" |
| 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 |