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Bioinformatics

Unit 1

Unit 4

Index sites

Unit 2

Unit 5

Unit 3

Unit 6
.

 [Last updated: 10/10/01] Under construction- Expect this page to grow.

Background reference support

Use links in this section for review, expanded background, support in other courses, etc.

General

World Lecture Hall: [worldwide course resources literally from A to Z]

http://www.utexas.edu/world/lecture/cs/

For lifelong learning, StudyWeb has something for everybody at a wide range of levels: [There is an extensive list of computer science support & tutorials. Try out other areas as well.]

http://www.studyweb.com/

 

Biology

To use the On-line Biology Book for review and reference go to:

http://gened.emc.maricopa.edu/bio/bio181/BIOBK/bioBookTOC.html

This online dictionary for cell biology was well recommended :

http://www.mblab.gla.ac.uk/~julian/Dict.html

For a rapid ramp-up in molecular genetics, inspired by the Human Genome Project, try:

http://www.bis.med.jhmi.edu/Dan/DOE/intro.html

For some background in ecology and evolution:

http://www.zo.utexas.edu/faculty/sjasper/bio304/syl304.html

http://www.virtual-worlds.net/lifedrop/  [try the applet for an interactive experience]

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Chemistry

Computational chemistry tutorials, a super list of links from basic to advanced, including a dictionary:

http://antas.agraria.uniss.it/tutorials.html

General chemistry resources:

http://www.ch.ic.ac.uk/GIC/ [great site, lots of links]

http://www.chem.vt.edu/chem-ed/vt-chem-ed.html [hypertext & tutorials]

http://antoine.fsu.umd.edu/chem/senese/101/tutorials/index.shtml

Organic chemistry tutorials:

http://www.dcu.ie/~chemist/pratt/cs204/cs204b.htm

http://www.ch.ic.ac.uk/local/organic/tutorial/

Biochemistry tutorials:

http://molvis.sdsc.edu/visres/ [super worldwide index site]

http://www.biology.arizona.edu/biochemistry/tutorials/chemistry/main.html

http://www.umanitoba.ca/faculties/medicine/biochem/coursenotes/blanchaer_tutorials/ [clinical case applications]

http://wbiomed.curtin.edu.au/teach/biochem/ [a well designed site]

http://alpha2.bmc.uu.se/Courses/Bke1/Tutorials/Tutorialindex.html

http://www.massey.ac.nz/~wwbioch/Prot/tutehome/tutepage.htm [proteins]

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Computing

A nice site: Introduction to Computing: [There's more here than you think at first.]

http://www.uen.org/utahlink/train/compintro/frontpage.html

Two general support sites with tutorials:

http://www.geocities.com/donaldpen/tutorials.html

http://www.askkenny.com/

Try also listings at World Lecture Hall and StudyWeb.

Online text & tutorial introducing Web use and search strategies:

http://www.december.com/web/text/

Two good online dictionaries for computing & IT terms:

http://www.tekmom.com/buzzwords/ [a great place to start]

http://www.techweb.com/encyclopedia/ [TechEncyclopedia is comprehensive]

Free Online Dictionary of Computing: [Fully searchable. You can even add a link on your browser tool bar.]

http://foldoc.doc.ic.ac.uk/foldoc/index.html

For a look into the future: a fusion of biology and computer design- DNA based computers: [not required reading, but pretty cool stuff]

http://dna2z.com/dnacpu/dne.html [basic introduction]

http://www.mitre.org/research/nanotech/biocomputers.html [intro & links]

http://www.pcola.gulf.net/~netboy/index2.html [informative links]

http://crypto.stanford.edu/~dabo/biocomp.html [references]

http://www.wired.com/wired/archive/3.08/molecular.html [in the beginning...]

http://www.corninfo.chem.wisc.edu/writings/DNAcomputing.html [the most up-to-date of all]

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Statistics and probability

http://gasbone.herston.uq.edu.au/teach/stats/home.html [good stats intro]

http://www.meandeviation.com/tutorials/stats/ [thumbs up]

http://cgs.edu/wise/index.html [general stats]

http://icp.giss.nasa.gov/education/statistics/ [good reference site]

http://www.gcse.com/Maths/tprob1.htm [intro to probability, & other tutorials also]

http://www.mathsyear2000.org/alevel/pure/purtutpro.htm [probability]

http://www.probability.net/ [a major workout in probability]

http://www.andypryke.com/university/TheDataMine.html [intro to data mining with links]

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Bioinformatics: Background, tutorials, etc.

Background and on-line instruction using Darwin 2000:

http://www.rickhershberger.com/darwin2000/

Other on-line instruction and support:

A basic general introduction:

http://biotech.icmb.utexas.edu/pages/bioinfo.html

A detailed, highly linked site: [Note: Some applications have restricted access, but there is still a significant amount of useful information.]

http://www-biology.ucsd.edu/others/dsmith/workshop.html

Nick Ewing's Bioinformatics course resources, including perl script tutorial:

http://gaia.ecs.csus.edu/~mei/biox01/syllabus/bio296c.html
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Multi-linked index sites of interest

[Come back to these frequently and explore. Make note of and share the destinations you like by posting them on the bulletin. I'll post links on updated versions of this page.]

http://mcb.harvard.edu/BioLinks.html 

http://biotech.icmb.utexas.edu/

 

Unit 1: Databases & Queries

Living Textbook: [a look at a possible future]

http://kaluza.physik.uni-konstanz.de/LT/Welcome.html

Citation of online resources:

http://www.tekmom.com/cite/index.html

http://www.lib.duke.edu/libguide/citing.htm

Avoid plagiarism:

http://www.indiana.edu/~wts/wts/plagiarism.html

Introduction to databases & WWW: [a comprehensive tutorial]

http://cdr.cs.uiuc.edu/pubs/de97tutorial/index.htm
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Journal databases and text access sites

Schultz Center

Journals: http://libweb.sonoma.edu/collections/journals.html
[Here you can access Elsevier's Science Direct via the Database list, use the journal locator, and connect to New Jour- a full text resource. Also, periodically check Trial databases for new things. Although your PIN will allow access to most databases, you'll have to get the password from the reference desk to use Biosis.]

Cell Molecular Guide: http://libweb.sonoma.edu/research/subject/cellmol.html

Interscience: [with full text journal articles available]

http://www3.interscience.wiley.com/cgi-bin/simplesearch

Highwire Press: a huge source for free full text literature

http://www.highwire.org/

PubMed: [with full text journal articles available]

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

BioMedNet: [with full text journal articles available] & home of the free e-journal H.M.S. Beagle [worth having for fun and info]

http://www.bmn.com/

MedBioWorld: broad range search site for journals & more

http://www.sciencekomm.at/
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Bioinformatics databases & interfaces

National Center of Biotechnology Information [NCBI] homepage:

http://www.ncbi.nlm.nih.gov/

For site map to ease navigation: [You can click on the boxes and see how they are linked.]

http://www.ncbi.nlm.nih.gov/Sitemap/index.html

Pittsburgh Supercomputing Center's A Tutorial on Searching Sequence Databases and Sequence Scoring Methods

http://www.psc.edu/biomed/training/tutorials/sequence/db/index.html

National Biotechnology Information Facility- 1000's of link resources, including the game Origin: Unknown, which provides a fun way to learn bioinformatics:

http://www.nbif.org/

San Diego Supercomputing Center has lots of useful links and resources:

http://restools.sdsc.edu/

For a more general look at what all else they have try: http://www.sdsc.edu/

European Bioinformatics Institute:

http://www.ebi.ac.uk

ExPASy [Expert Protein Analysis System] is dedicated to proteomics:

http://www.expasy.ch/

TIGR [The Institute for Genomic Research] is of use for genomics:

http://www.tigr.org/

Resource list at NOAA is nicely organized:

http://www.nwfsc.noaa.gov/bioinformatics.html

 

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Biology Workbench:

A powerful integrated tool, allowing you to search multiple databases simultaneously and to use a very wide variety of tools to examine proteins, nucleotide sequences, alignments, and structures:

http://workbench.sdsc.edu

[All you need to do the first time is to choose a user name & password. The cool thing is that it can save your work sessions, so you can come back to them, even months later. You can upload and download from it as well, so you can easily transfer material to a log, and to a report. The downside to using Biology Workbench is that it takes a little practice to navigate following a simple rule of not using the "back" button, because it can cause problems.]

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More databases- many types with different kinds of use

Human genome database:

http://gdbwww.gdb.org/ or go to:

http://www.ncbi.nlm.nih.gov/Entrez/ and click on "Genome"

Select bacterial genomes:

http://genolist.pasteur.fr/

Genomes on-line:

http://wit.integratedgenomics.com/GOLD/

http://www.tigr.org/tdb/

Kabat Database of proteins of immunological interest:

http://immuno.bme.nwu.edu/

Environmental & Biodiversity interface:

http://biodi.sdsc.edu/

Ecology database resources:

http://www.brc.ac.uk/

Metabolic pathways:

KEGG: KEGG's search and computation tools
http://www.genome.ad.jp/kegg/kegg3.html
Paper introducing KEGG:
http://igs-server.cnrs-mrs.fr/~ogata/Paper/ogata98BioSys.html

Pathway database of inherited metabolic diseases: http://oxmedinfo.jr2.ox.ac.uk/Pathway/Miscell/welcome.htm

WIT database:
http://wit.mcs.anl.gov/WIT2/

ERGO database:
http://wit.integratedgenomics.com/IGwit/

Metabolic part of SoyBase: part of USDA's Plant Genome Project
http://cgsc.biology.yale.edu/metab.html

 

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Unit 2: Genomics

Introduction to Human Genome Computing via the World Wide Web by Lincoln Stein

http://formaggio.cshl.org/talks/BioWWW/chapter/

Project preparation:

http://www.pnas.org/cgi/content/full/95/5/1971

Maize DB:

http://nucleus.agron.missouri.edu/

Comparative mapping:

http://nucleus.agron.missouri.edu/cMap/cMap.html

 

Unit 3: Molecular Genetics

A great resource site for all sorts of things molecular: DNA Information Corner

http://www.dur.ac.uk/~dbl0www/Bioinformatics/DNA_corner.htm

Plasmid information:

Selection of plasmids: See under "Vectors" at DNA Information Corner above.

Tutorial exercises in plasmid mapping: Get a partner to do some of these- it's more fun that way.

http://www.carolina.com/biotech/plasmid_problems/plasmid_guide.asp

 

Background, resources and tools for restriction enzymes:

http://www.accessexcellence.org/AE/AEC/CC/restriction.html

http://www.ultranet.com/~jkimball/BiologyPages/R/RestrictionEnzymes.html [This site also gives links to information on DNA sequencing and recombinant DNA.]

Resource list of restriction enzymes by type & commercial availability: [Also, a very fitting cartoon]

http://internalmed.wustl.edu/divisions/enzymes/INDEX.HTM

 

Background & tools for primer design:

http://www.chemie.uni-marburg.de/~becker/

http://www.hgmp.mrc.ac.uk/GenomeWeb/nuc-primer.html

 

Introduction to microarrays:

http://www.bio.davidson.edu/courses/genomics/chip/chip.html

http://www.bio.davidson.edu/courses/genomics/chip/chipreal.html

http://www.bsi.vt.edu/ralscher/gridit/intro_ma.htm

Resource list for microarrays:

http://www.deathstarinc.com/science/biology/chips.html

 

HLA and tissue typing:

An excellent tutorial on HLA and tissue typing, with information on the different screening methods:

http://www.umds.ac.uk/tissue/what1.html

LiPA HLA assay system, with some background on HLA:

http://www.innogenetics.com/Website/Website.nsf/7df3b6bb9c0862e8c12567380052687f/69a6ff86644d314ac12569a700578cec?OpenDocument

Anthony Nolan Bone Marrow Trust, another good resource:

http://www.anthonynolan.org.uk/HIG

 

Ethics: Some selected papers & resources

Several relevant papers may be accessed through Stanford's Biochemistry 118: Genomics, Bioinformatics & Medicine [Scroll down to papers on ethical issues.] http://cmgm.stanford.edu/biochem118/

Resource site on biotechnology, bioinformatics, and ethics:

http://www.denniskennedy.com/bioinformaticslaw.htm

 

 

 

Unit 4: Phylogenetics

ClustalW, tree-building & other tools

 

Unit 5: Protein Structure Prediction

3D viewers & modeling tools

PDBsum:

http://www.biochem.ucl.ac.uk/bsm/pdbsum

Protein Explorer:

http://molvis.sdsc.edu/protexpl/

 

Unit 6: Metabolism & Networks

KEGG & WIT & more tools 
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Updated 8/26/01 by thatcher@sonoma.edu