Computational Biology Links

G4120: Introduction to Computational Biology
Columbia University
Department of Microbiology
Fall 2005

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/IC/support_center/resnet.html
webcal://microbiology.columbia.edu/Calendar/micro.ics

Bioinformatics Reference Sites
http://bio.oreilly.com
http://www.iscb.org
http://www.ncbi.nlm.nih.gov
http://www.google.com

NCBI Blast
http://www.ncbi.nlm.nih.gov/BLAST/
http://www.geospiza.com/outreach/BLAST/index.html

Macintosh OS X Troubleshooting and Help Sites
http://www.info.apple.com
http://discussions.info.apple.com
http://www.macosxhints.com
http://www.macfixit.com
http://www.macosxfaq.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
http://www.macminute.com

PubMed
http://ncbi.nlm.nih.gov/pubmed

BLAT
http://www.genomeblat.com/genomeblat/
http://www.soe.ucsc.edu/~kent/exe/osX/
http://genome.ucsc.edu/goldenPath/help/blatSpec.html/

MFold
http://www.bioinfo.rpi.edu/applications/mfold/old/rna/

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

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.wustl.edu/

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://salilab.org/modeller/modeller.html
http://www.expasy.org/swissmod/
http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
http://robetta.bakerlab.org/

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

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

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

Bioinformatics Resoource
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.rcsb.org/pdb/

Macintosh OS X Bioinformatics Software Resources
http://iubio.bio.indiana.edu/
ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/
http://corba.ebi.ac.uk/biocatalog/
http://www.apple.com/science/software/lifescience.html
http://www.emboss.org/
http://bioteam.net/MacOSX/biotools-1/
http://www.tigr.org/software/
http://sourceforge.net/
http://fink.sourceforge.net/
http://pdb.finkproject.org/pdb/section.php/sci
http://darwinports.opendarwin.org/ports/
http://www.versiontracker.com

Open Source Software
http://www.opensource.org/
http://bioinformatics.org
http://open-bio.org

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.sinauer.com/

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://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl
http://www.tigr.org/software/

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

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

AppleScript for Absolute Starters
http://www.applescriptsourcebook.com/tips/AS4AS.html

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

Programming Resources
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://www.cpan.org/
http://www.bioperl.org/