Ken's Biology links

Finally the main links page has got too big so I moved the biology links over here.

Sections

Taxa,   Evolution, Ecology, Genetics,   Taxonomy, Palaeontology, Systematics,   Courses,   Resources,   Bioinformatics,   Modelling,   Projects,   Other stuff.

Other links

Useful stuff,   Christian links,   Science links,   Political links,   Art, literature, sf,   Computers,   Work and university links,   People,   Places,   and Things.

Taxa

God put our ancestors in the Garden of Eden and showed us all the animals to see what we would name them. How many of them will we name before we kill them?

• Prokaryotes & micobiology in general
  • Microbial World at Edinburgh
  • News items about Bacteria at Wisconsin (not to mention football, Orthodoxy, spacefans...) and Timothy Paustian's microbiology textbook (Good for quick reference to pathways & so on)
  • Brock online study-guide by Konopka, Turko & Andrews associated with the text Biology of Microorganisms , eighth edition by Madigan, Martinko, and Parker.
  • Society for General Microbiology (also contains the web pages of what used to be IJSB & a good links page)
  • Society for Applied Microbiology Chattier than the above - and why have one society when you can have two?
  • American Microbiological Society who let you see abstracts but not full text of heaps of journals.
  
  
  
• Plants
  • Multilingual plant name database
  • Autoecological accounts of plants
  • Internet directory for botany: checklists, floras, taxonomic databases, vegetation
  • Global Tree Conservation
  • Growing Common Ferns and links to the American Fern Society.
  • Ferns in Space!
  • Native vascular plants in Britain, by postcode!
  • landplant systematics at Southern Illinois
  • Plantlife look after plants - and fungi:
  • Flora of North America
  • Ozzy New Crops Newsletter with lots of links



• Fungi & assorted other things (some of my best friends are saprophytes)
  • Association of British Fungus Groups> including NI fungi (many links)
  • Mycorrhiza at Tennessee (I think)
  • British Mycological Society - who seem to have a new site
  • Fungal genetics
  • Mycoinfo
  • A project on spores



• Animals
  • Fishbase
  • A key to orders of insects
  • Pictures of crows (from a fantasy role-playing site)
  • Zoological Record Good links site from ZSL, lots about systematics & taxonomy.
  • Spider information and pictures
  • ARACHNOLOGY
  • Spider Eyes
  • Solifugids
  • SIweb American Museum of Natural History Social Insects pages.
  • Entomology Index of Internet Resources
  • Ant links
  • Tardigrades
  • Worms Links to all sorts of things.
  • Cycliophora That is Symbion pandora
  • Xenophyophores
  • Cranes of the World
  • UK Bird Net FAQ
  • Crayfish Huxley's classic - the ref pointed to shows his version of the BSC & also how he distinguished it from a morphological SC.

Evolution, Ecology, Genetics

• Evolutionary Maths at Pandas thumb (with links)
• Evolutionary stuff from NASA
• Some sites dealing with the idea that science and Christianity are naturally opposed, or with so-called creationism.
  • Talk.origins FAQs For years I resisted putting this in my links page on the basis that it is my links page & I can perfectly well remember the URL for talk.origins. But as a Christian who is a scientist as well I think people need to read this stuff. If only to show that I distance myself from the embarrassing so-called creationists.
  • AAAS Dialog Between Science and Religion
  • Science and Christianity
  • Reasons to Believe Is this a Q-site? At first glance yet another semiliterate US creationist website, RTB actually offers serious scientific & historical discussion (& even some dissent!) as well as pointing out that the real problem with the young-earth so-called creationists & genesis-flood weenies is their unorthodox and unchristian attitude to God.
  • Some personal pages, or quotes, apparently from Alan Cresswell, Karl Thornley, Kenneth Miller, Scibel (Michael Roberts & Paul Marston on front page), John Polkinghorne
• Christian Ecology Link
• Michael Stumpf's Introductory Population Genetics at UCL
• Ecological questions & background
  • Alexei Sharov's population ecology class and gypsy moth links
  • Ecological complexity someone's paper, with useful refs
  • Someone's seminar notes on rapid assessment of fungal biodiversity
  • A thesis on indoor fungi (with an overview of methods)
  • A thesis on anti-fungal silage innoculants (with lots of references)
  • A list of links to web pages about extreme environments
  • Research overlapping in all sorts of ways at Cranfield , Wisconsin , somewhere else at Wisconsin , Newcastle
  • Urban Ecology

Taxonomy, Palaeontology, & Systematics

Taxonomy, systematics, Life As We Know It, (or used to)

• Palaeontologia Electronica
• Is it stratocladistics or cladostratigraphy ?
• The International Code of Botanical Nomenclature You know it makes sense!
• Tree of Life and Crown Eukaryotes
• U Cal Berkeley Paleontology Museum
• NCBI Taxonomy
• Peter Kuhlman's ideas on large-scale phylogeny (really just notes but lots of references to follow)
• What is a Species and What is Not? Ernst Mayr in 1996. The best of biology. And back up the same tree for the rest of "Dialog Between Science and Religion".
• Species definitions for ethnobotanists

Courses

• Birkbeck Bioinformatics at Crystallography
  • Crystallography
  • Birkbeck library
  • Bioinformatics Modules
  • Genome Analysis
  • Databases


• Links useful for my MSc project at
  • Bioinformatics MSc at Birkbeck Crystallography
  • Clostridium perfringensat TIGR
  • Samuael Karlin and Allan Campbell at Stanford


• Some other online teaching aids
  • Cool Cell Biology Animations from John Kyrk
  • Chemistry of Amino Acids and University of Arizona's Biology Project.


• Links that were useful for the Birkbeck Biology BSc
  • Biology dept at Birkbeck
  • Course Units
  • Birkbeck College Biology Society
  • Biology at Durham
  • Ed Friedlander has notes on hormone-related diseases that could be useful revision for the endo exam.
  • Metabolic pathways also good revision.
  • THCME medical biochemistry page.
  • Millport Marine Biology Station

Resources

Useful Stuff

• NIST chemistry webbook
• A Periodic Table of the Elements at Los Alamos National Laboratory - and another one at Bristol which has more text.
• Metapress online journals
• Biodiversity worldmap
• Communicable Disease weekly report from PHLS
• Morbidity and Mortality weekly report from CDC
• Urban Forestry Bibliography
• Databases at Birkbeck library including pointers to Biosis at edina and ISI at mimas - there are other links to UK academic computing resources above.
• Kew
• Society of Environmental Journalists Tip sheets & the like.
• Care and Feeding of various easy cultures of live organisms, from Flinn (a US supplier).
• US FDA Bad Bug Book
• Natural History Museum Don't forget the Extreme Eukaryotes page.
• NHBS Welcome to BookNet Natural History Book Shop.
• Home page for Cameron Laird Lots of anthropology links here.
• Anthropology Exhibits Kent University social anthropology links.
• American archaeological society
• Society for Economic Botany and also in the UK
• Europes climate history
• NIST chemistry web book, for the Truth about Chemistry :-)
• ACS publications
• CGAP HowTo - lots of ways to find things out
• Remedial maths for real biologists (:-)
  • S.O.S. Mathematics tells you about Matrices
  • Resources for mathematics education for biology students
  • Mathematics at Knoxville
  • The most common errors in undergraduate mathematics
  • Eric Weisstein's mathworld (wonderful, but too concise for most people, including me!)
  • Biographies of mathematicians at St. Andrew's
• And some of the peculiar approaches to statistics and probability the bionformatics MSc took
  • UCLA cognitive systems lab and
  • Judea Pearl with links to loads of their stuff. Straight to the horse's mouth.
  • Brief introduction to and lots of links about graphical representations of probability, Bayes nets, HMM, et.c. No idea of how reliable it is
  • A tutorial on belief nets by Amos Storkey, a bloke of whom I have never heard. But it looks pretty.
  • Lorenz Wernisch here at Birkbeck
  • Radford Neal at Toronto
  • An essay by Dirk Husmeier that overlaps with my revision notes...
  • Computational systems Biology at CMU from which I downloaded papers by Spirtes, Glymour, Scheines & others

Bioinformatics and genomics

• Some well-known sites:
  • NCBI/NIH
  • Sanger
  • EMBL
  • Sanger
  • CGAP
  • chlc
  • tigr
  • "Expert Protein Analysis System" The Swiss. Links to Swissprot & other places.


• Some actual data at
  • US National Center for Biotechnology Information (ncbi.nlm.nih) has Locus Link, (to be discontinued 2004) and Mapview, and bacterial genomes, and OMIM "Online Mendelian Inheritance in Man", and Genbank linking to DNA DataBank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL), and most generally: Entrez
  • BLOCKS - match protein sequences against blocks (multiply aligned ungapped segments)
  • BLOSUM and PAM matrices
  • UCSC genome browser (Jim Kent et al)
  • MIT GENSCAN
  • PDB at Rutgers (structures from XRC, NMR & so on since 1972)
  • Mouse Genome Server
  • Ribosomal Database Project
  • Jax for mouse and other stuff.
  • "Expert Protein Analysis System" includes SwissProta curated protein sequence database, and one of the many online copies of the Enzyme Data Bank including IUB enzyme classification (ECN)
  • IBC Washington
  • HapMapHuman genetic variation between populations - Haplotypes, SNPs etc.


• Labs, research teams, & individuals
  • Ronald Breaker at Yale (riboswitches et.c)


• Links to many sites at Cambridge, and MRC , and bacteriamuseum


• Using Perl and so on:
  • Parsing Protein Domains with Perl James Tisdall"s code to read Prosite data, and also part of a book on reading
  • GenBank files.
  • BioPerl , and the BioPerl tutorial
  • AcePerl interface to AceDB and parsing biological data files in Perl (From Lincoln Stein at Cold Spring Harbor).
  
  
  • Assorted tools that have proved useful:
    • ClustalW - global multiple sequence alignment - download by FTP
    • dialign local multiple sequence alignment
    • GENSCAN web server at MIT via HCMP at Hinxton
    • RepeatMasker
    • Kognitor
    • Check chimera
    • treeview?
    • Chromas (can read SCF)
    • BLAST (at NIH)
    • GigAssembler !!!
  
  
  • Jargonification, glossaries, taxonomies, sematic bobbles:
    • Genomic glossaries
    • Sequence formats
    • for EC numbers
    • Genetic codes in different taxa
    • Gene Ontology
    • CATH domains (protein domain classification: (Class, Architecture, Topology, Homologous family)
  
  
  • Bioinfomatics conferences, symposia &c.: 1995 AAAI genetic programming seminar , ISMB01 and Bioinfomatics Open Source at Tivoli Gardens, ISMB02 at Edmonton
  • Expressed sequence tags (ESTs) and sequence tagged sites (STSs) ands so on via Genome Database (GDB), Whitehead/MIT , and the CEPH/Genethon , human-mouse homology map (clickable "b" next to mouse ordered in the order genes come in human chromosome Mouse chromosomes acrocentric with no small arm
  • And on to microRNA! HapMap - their gene browser davidson lab embryonic gene expression sea urchin development genetic network (strongylocentrotus purpuratus)
  • Looking for repeat masker: genome.ucsc.edu and their genome browser - click submit - right at the bottom it shows repeat masker thingy (should be no hits on cdna etc!)
  
  
  • I liked these:
    • - kegg Kyoto Encyclopedia of Genes and Genomes - Japanese enzymes and stuff with neat metabolic pathways.
    • - index to pathways
    • Drospohila protein map!!!!!
    • Biopathways Systems biology links
  
  
  • And Yet More: Core-Promoter Prediction Program put in seq UPSTREAM of gene of interest Transcription Element Search System - ditto (usu < 5kbase uopstream but can be 30 kbase!) Meme & Mast - motif discovery by HMM - look for short highly conserved sequences, islands of similarity, good for things like tfbs jr2, Stanford (for Microarrays etc) - see gene explorer software on breast cancer pictures each row is a gene, each column a tumour sample. Compares samples with a standard red is highly expressed, up-regulated; green is down regulated. CGAP cDNA tissue profiler Try "include brain" both pools. Bulk prep gives lots of libraries Mitelman Database of Chromosome Aberrations in Cancer (hand-crafted!)
  
  
  
  
  
   

  Modelling in ecology & evolution

  • Modelling in ecology.
    • Individual-based modelling in ecology
      • Jan Kreft does IbMs of bacteria
      • Fish simulations at Humboldt State
      • Highly relevant lists of links from Craig Reynolds (so many there isn't much point it adding more here!)
      • Some publication references for Donald DeAngelis
      • NIgel Franks does ants at Bath
    • Other kinds of modelling in ecology
      • Ecobas Register of Ecological Models
      • Ecomachines & spatial modelling from the Primordial Soup Kitchen
      • tiem (Gross & others)
      • Canadian Environmental Modelling Centre model index
      • Ecosystem Dynamics at Canberra
      • Ecological Dynamics at Strathclyde
  • Other resources for modelling.
    • population genetic simulations
    • CAS, Alife, games, non-ecological applications, Psanta-feud's corner, whatever
      • Complex at UCL
      • Swarm
      • Primordial Soup Kitchen - looks good but S L O O O W, too much Java!
      • Agent-based modelling in Economics
      • Look for links from: UTK Mathematical Life Sciences Archives at UTK with their alife software links page
      • Steve Harper .
      • Paul Fishwick has stuff anbout visualisations & models in the polystyrene sense
      • Santa Fe Institute
      • Uri Alon lab at Weizmann, NB network motifs
      • Stuff about redundancy & "immune systems" in computer networks partly here for the link to citeseer.
    • More general ideas on computing and models
      • Petri Nets World
      • Introduction to Monte-Carlo methods
      • A dissertation on state events in continuous modelling
      • Systems simulation , Hossein Arsham
      • A survey of web-based simulations
  
  
  
   

  Links were relevant to other projects

  • Extraction of DNA from environmental samples
    • Promega/Wizard
    • Field preservation in CTAB
    • Tennessee
    • Stewart & Via (1993)
    • Eric Boehm
    • Vaillancourt maxiprep
    • Vaillancourt miniprep
    • Algal stuff from a list
    • A selection of DNA methods
    • WIT Evgeny Selkov & others at Argonne try to find our what is in there from gene sequences.
  • Genetics, DNA manipulation and Stuff Like That
    • database of genome sizes just a sideshow of their Really Useful (though maybe a little OOD) bioinformatics pages
    • Glossary at Johns Hopkins.
    • PCR, gels, & other techniques
      • Karen Hughes links to various techniques for fungi.
      • John Mundy's big list of plant protocols
      • Old teliospores
      • a little tutorial on SDS gels
      • Highveld has an online library of otechniques and protocols
    • From a forensic point of view:
      • Conference papers FS labs.
      • New Approaches to DNA Fingerprint Analysis (a bit commercial)
      • STR links including Validating STR
  • Proprietary techniques, suppliers, chemicals used, material safety data sheets: Primus PCR kit (MWG) Wizard DNA purification kit (Promega) Acrylamide (Bio-rad) Nucleospin manual (Clontech's version of the whole thing)
  
  
  
   

  Other things

  • Bill Hamilton tribute site
  • The Natural Pharmacist refers to serious studies, unlike most health-fetish sites
  • A website about Alfred Russel Wallace
  • Marsbugs
  • Steve Hoffman's photosSome nice pictures of garden creatures, amongst other stuff.
  • The Net Vet Hundreds and hundreds of links about animals - things like Caring for Pets with Cancer and The Llama Web and Penises of the Animal Kingdom the Pig Disease Information centre and the Interactive Frog Dissection Tutorial Updated weekly for over 2 years, it is all here...
  • Genesis of Eden Chris King's biodiversity pages in NZ. The guy is a bit of a gnostic but we let him off because of all the good articles assembled here.
  • Curiosities of Biological Nomenclature (Mark Isaak) and Curious Scientific Names (This is also Doug Yanega's links page & a good one it is too. About 50% overlap with this one so it must be...). Doris the Sea-Slug has many relatives. Like Lo the rabbitfish, Scabies the clam, Sirius the snail, Iyaiyai the fly (apparently it works better if you're Dutch) Zappa the goby, Abra cadabra the ant (or was it a bivalve?) and of course Clitoria the pea (and that's due to Linnaeus!). And there is a special dispensation allowing us to continue to use Megalosaurus instead of Scrotum which has priority.
  • headlice.org A strange site. Not so much about lice as about public health as a means of social control for fun & profit. It's what happens when a community abandons its common responsibility for health to commercial interests. Thank God for the NHS.
   

  Last update: 8th April 2005, some stats 18th November 2004, stuff on amino acids, 16th January 2004, copied from main links page 15th May 2004