Computational Biology Links

G4120: Introduction to Computational Biology
Columbia University
Department of Microbiology
Fall 2007

Instructor:

Description: This is a collection of links referred to during the course, arranged in the order they were presented.

Columbia University Medical Center Internet Access
http://www.cubhis.org/
http://www.cubhis.org/getting_help/resnet.html
http://www.columbia.edu/acis/software/applemail/config.html
http://www.columbia.edu/acis/software/fugu/
http://fetchsoftworks.com/Licensing/edustore.application.html

Dashboard Widgets
http://www.apple.com/downloads/dashboard/
http://www.dashboardwidgets.com/

Bioinformatics Reference Sites
http://www.iscb.org
http://www.google.com
http://www.sanger.ac.uk
http://www.ncbi.nlm.nih.gov

NCBI Blast
http://www.ncbi.nlm.nih.gov/BLAST/
http://www.ncbi.nlm.nih.gov/blast/blast_FAQs.shtml
http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html
http://www.ncbi.nlm.nih.gov/Education/blasttutorial.html
http://www.geospiza.com/outreach/BLAST/index.html
http://www.geospiza.com/outreach/organelles/index.html
http://www.geospiza.com/outreach/snp_hunting/index.html

Macintosh OS X Troubleshooting and Help Sites
http://www.info.apple.com
http://developer.apple.com/technotes/tn/tn1061.html
http://docs.info.apple.com/article.html?artnum=106482
http://docs.info.apple.com/article.html?artnum=106805
http://discussions.info.apple.com
http://www.macosxhints.com
http://www.bombich.com/mactips/openfirmware.html
http://www.macfixit.com
http://fixa.troubledmac.com

Macintosh OS X Software and Hardware Sites
http://www.versiontracker.com
http://www.dealmac.com

Macintosh OS X News Sites
http://www.macslash.com
http://www.slashdot.com
http://www.macintouch.com

PubMed
http://ncbi.nlm.nih.gov/pubmed
http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/

BLAT
http://hgwdev.cse.ucsc.edu/cgi-bin/hgBlat?command=start
http://www.kentinformatics.com
http://genome.ucsc.edu/goldenPath/help/blatSpec.html/

MFold
http://frontend.bioinfo.rpi.edu/applications/mfold/cgi-bin/rna-form1.cgi
http://www.bioinfo.rpi.edu/applications/mfold/rna/form1.cgi

GRAIL
http://compbio.ornl.gov/grailexp/
http://compbio.ornl.gov/generation/

GeneMark and GeneMark.hmm
http://opal.biology.gatech.edu/GeneMark/

Glimmer and GlimmerHMM
http://cbcb.umd.edu/software/glimmer/
http://cbcb.umd.edu/software/glimmerhmm/

GenScan
http://genes.mit.edu/GENSCAN.html

PROSITE
http://us.expasy.org/prosite/

SMART
http://smart.embl-heidelberg.de/

HMMER
http://hmmer.janelia.org/

Center for Biological Sequence Analysis
http://www.cbs.dtu.dk/services/

Amos Bairoch's List of Protein Resources
http://us.expasy.org/links.html

Protein Prediction
http://bmerc-www.bu.edu/psa/
http://www.predictprotein.org/
http://www.predictprotein.org/meta.php
http://salilab.org/modeller/modeller.html
http://www.expasy.org/swissmod/
http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
http://robetta.bakerlab.org/

CDD
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

MMDB
http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

VAST
http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html

CDART
http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps

Cn3D
ftp://ftp.ncbi.nih.gov/cn3d/Cn3D-4.1.OSX.sit
http://www.geospiza.com/outreach/structure/

Bioinformatics Resources
http://www.ncbi.nlm.nih.gov/
http://www.ensembl.org/
http://www.sanger.ac.uk
http://www.ebi.ac.uk
http://genome.ucsc.edu/
http://us.expasy.org/
http://www.bioinfo.rpi.edu
http://www.rcsb.org/pdb/

Macintosh OS X Bioinformatics Software
http://iubio.bio.indiana.edu/
ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/
http://www.apple.com/science/software/lifescience.html
http://emboss.sourceforge.net/
http://sourceforge.net/
http://www.finkproject.org/
http://pdb.finkproject.org/pdb/browse.php?section=sci
http://www.macports.org
http://www.versiontracker.com

Open Source Bioinformatics Software
http://www.opensource.org/
http://bioinformatics.org
http://open-bio.org
http://cbcb.umd.edu/software/
http://www.tigr.org/software/

Porting Software to Macintosh OS X
http://developer.apple.com/documentation/Porting/Porting.html
http://developer.apple.com/documentation/Porting/index.html
http://www.finkproject.org/doc/porting/index.php

Phylogenetic Software Packages
http://evolution.genetics.washington.edu/phylip.html
http://iubio.bio.indiana.edu/treeapp/treeprint-form.html
http://bips.u-strasbg-fr.fr/Documentation/ClustalX/
http://paup.csit.fsu.edu
http://www.macclade.org/

PEDANT
http://pedant.gsf.de

Kyoto Encyclopedia of Genes and Genomes (KEGG)
http://www.genome.jp/kegg/

NCBI Clusters of Orthologous Groups (COG)
http://www.ncbi.nlm.nih.gov/COG/new

Microbial Genome Database for Comparative Analysis (MBGD)
http://mbgd.genome.ad.jp/

A Quick Guide to Sequenced Microbial Genomes
http://www.genomenewsnetwork.org/resources/sequenced_genomes/ genome_guide_p1.shtml

NCBI Entrez Genomes and Genomic Biology Resources
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome
http://www.ncbi.nlm.nih.gov/Genomes/

The Institute for Genomic Research (TIGR)
http://www.tigr.org
http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi
http://www.tigr.org/software/

Genome Databases
http://www.cbs.dtu.dk/databases/DOGS/index.php

Automation Utilities
http://www.blacktree.com/
http://www.typeit4me.com/
http://www.power4mac.com/renamer/
http://www.skytag.com/
http://archive.macosxlabs.org/rsyncx/rsyncx.html
http://www.barebones.com
http://www.versiontracker.com

AppleScript for Absolute Starters
http://files.macscripter.net/sourcebook/AS4ASb2.pdf

Bash Guide for Beginners
http://www.tldp.org/LDP/Bash-Beginners-Guide/Bash-Beginners-Guide.pdf

Programming Resources
http://applescriptsourcebook.com/
http://www.perl.org/
http://www.php.net/
http://www.lysator.liu.se/c/
http://www.python.org/
http://www.ruby-lang.org/
http://java.sun.com/

Perl Programming Resources
http://www.perl.org/
http://learn.perl.org/
http://learn.perl.org/library/beginning_perl/
http://www.cpan.org/
http://www.bioperl.org/