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Companion Website

Sansom & Horton: Internet for Molecular Biologists

Chapter 11

Web resources
BioPerl bio.perl.org A collection of software libraries for developers of Perl-based life-science tools
CPAN www.cpan.org Perl modules, scripts, and documentation
ActiveState www.activestate.com Perl (and other languages) for Windows and Linux
MacPerl www.macperl.com For Macintosh OS 7.0 and later. Note that MacPerl runs as a Classic environment on OS X, and that OS X comes with a native version of Perl that runs from the Unix prompt
2D illustraion of propsed relationship of Prostaglandin H2 synthase to membrane blanco.biomol.uci.edu/MolGraph/1prh.html From the 'Membrane Proteins of Known 3D Structure' collection of the Stephen White Laboratory at the University of California at Irvine
'Average' composition of a protein sequence ca.expasy.org/tools/pscale/A.A.composition.html -
SVG www.adobe.com/svg/viewer/install/main.html This is the download site for the Adobe SVG Viewer, a web browser plugin. It has links to more information
ChemML www.xml-cml.org Follow the "information" link for white papers and other references
MathML www.w3.org/Math Includes links to tools and tutorials
MAGE-ML www.mged.org/Workgroups/MAGE/mage-ml.html A proposed standard data exchange format for microarray expression experiments
XSLT Processors
Saxon
saxon.sourceforge.net A version called 'Instant Saxon' is partcularly convenient to install on Windows machines. It uses the Microsoft Java Virtual Machine (JVM) that came with Internet Explorer, so you do not have to bother with installing and configuring a JVM
Xalan xml.apache.org Cross-platform XSLT processor (written in Java)
NCBI Data in XML ftp://ftp.ncbi.nih.gov/toolbox/xml/ncbixml.txt Comparison of the ASN.1 format used to structure most NCBI data with XML. Describes how one form is transliterated to the other
Creating a Bioinformatics Nation www.nature.com/nature/links/020509/020509-2.html Dr. Lincoln Stein's article prmoting a web services model for bioinformatics resources
Beginning Perl for Bioinformatics, Chapter 10, GenBank http://www.oreilly.com/catalog/begperlbio/chapter/ch10.html Parsing GenBank files
NCBI BLAST Home Page www.ncbi.nlm.nih.gov/BLAST/ See Chapter 2 for more information
XSL www.w3.org/Style/XSL/ Overview and links to the specifications
Free On-Line dictionary of computing wombat.doc.ic.ac.uk/foldoc See entries for 'Perl', 'CGI', 'scripting', etc.