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Biology Workbench
http://workbench.sdsc.edu
The Biology WorkBench is a web-based resource for analyzing and visualizing
molecular data developed at NCSA (the National Center for Supercomputing
Applications). Undergoing continued development at the San Diego Supercomputer
Center, the innovative Biology WorkBench integrates access to many tools
within a simple graphical user interfacse.Database searching is integrated
with access to a wide variety of analysis and modeling tools, all within
a point and click interface that eliminates file format compatibility
problems.
Biology Student Workbench
http://peptide.ncsa.uiuc.edu/
The Biology Student Workbench consists of curricular
materials centered around molecular biological investigations, links
to educational, scientific, computational, and informational resources,
and communication tools to bind together a contributing community of
educators. It is designed to give a transparent introduction to the use
of the Biology Workbench for learning and teaching biology at all levels.
SIB Homepage (Student Interface to the Biology
Workbench) and other Bioinformatics information
http://deltas.animal.uiuc.edu/sibdoc/index.html
Bioinformatics Education section of
the Open Directory project.
http://dmoz.org/Science/Biology/Bioinformatics/Education/
The Open Directory Project is the largest, most comprehensive human-edited
directory of the Web. It is constructed and maintained by a vast, global
community of volunteer editors. Instead of fighting the explosive growth
of the Internet, the Open Directory provides the means for the Internet
to organize itself. As the Internet
grows, so do the number of net-citizens. These citizens can each organize
a small portion of the web and present it back to the rest of the population,
culling out the bad and useless and keeping only the best content.
GeneDoc
http://www.psc.edu/biomed/genedoc
GeneDoc is a full featured multimple sequence alignment editor and shading
utility.
The Inquiry Page
http://inquiry.uiuc.edu/
This is a dynamic virtual community where inquiry-based education can
be discussed, resources and experiences shared, and innovative approaches
explored in a collaborative environment. You can search a growing database
of inquiry units, and you can also build your own inquiry units. You
can see pictures of inquiry-based activities and learn more about some
of our partners who use inquiry methods. Learn how to assess and evaluate
inquiry-based education or look for more inquiry resources to support
what you're doing.
National Center for Biotechnology Information
(NCBI)
http://www.ncbi.nlm.nih.gov
Established in 1988 as a national resource for molecular biology information,
NCBI creates public databases, conducts research in computational biology,
develops software tools for analyzing genome data, and disseminates biomedical
information - all for the better understanding of molecular processes
affecting human health and disease.
NCBI Education
http://www.ncbi.nlm.nih.gov/Education/
OMIM™ Online Mendelian Inheritance
in Man
http://www.ncbi.nlm.nih.gov/omim/
This database is a catalog of human genes and genetic disorders authored
and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins
and elsewhere, and developed for the World Wide Web by NCBI, the National
Center for Biotechnology Information. The database contains textual information,
pictures, and reference information. It also contains copious links to
NCBI's Entrez database of MEDLINE articles and sequence information.
The OMIM Morbid Map, a catalog of genetic diseases and their cytogenetic
map locations arranged alphabetically by disease, is now available.
Protein Explorer
http://molvis.sdsc.edu/protexpl/frntdoor.htm
(PE) version 2.0 enables visualization of macromolecular 3D structure
with exceptional ease of use. Visual analysis of proteins, nucleic acids,
and ligand interactions can be done largely from menus, buttons, and
forms, with context-sensitive help and color keys displayed automatically.
PE employs the Chime plugin that is derived from RasMol, and PE understands
all RasMol commands. However, PE enables visual analysis to considerable
depth without learning a single RasMol-style command, and it is much
more powerful than RasMol. PE enables easy selection of portions of a
molecule, to apply different rendering or coloring schemes, and to hide
selected moieties. In addition it has one-click routines to map sequence
to structure, show contact surfaces (overview of noncovalent bonds to
any moiety), solvent-accessible surfaces, cation-pi interactions, and
salt bridges. Advanced routines simplify finding noncovalent bonds, and
coloring a protein by conservation/mutation from a multiple protein sequence
alignment. Websites can include hyperlinks to Protein Explorer that prespecify
molecule(s). Adopted by the Protein Data Bank as a 3D structure viewer.
Authored by Eric Martz, using MDL Information Systems' Chemscape Chime
freeware. PE is freeware for Windows or Macintosh.
SeqPup
http://iubio.bio.indiana.edu/soft/molbio/seqpup/About-seqpup.text
SeqPup is a biological sequence editor and analysis program. It includes
links to network services and external analysis programs. It is usable
on common computer systems, including Macintosh, MS-Windows and X-Windows.
SWISS-PROT
http://www.expasy.ch/sprot/
SWISS-PROT is a curated protein sequence database which strives to provide
a high level of annotations (such as the description of the function
of a protein, its domains structure, post-translational modifications,
variants, etc.), a minimal level of redundancy and high level of integration
with other databases
Tree Finder
http://www.treefinder.de/
TREEFINDER computes phylogenetic trees from nucleotide sequences. Using
the widely accepted Maximum Likelihood method, it supports six popular
models of sequence evolution up to the general time reversible model
with Gamma distributed rates among sites. All model parameters including
the rate heterogeneity can be estimated from the data. A genetic tree
search algorithm explores tree space for the likeliest trees, having
a good chance to not being trapped in local optima of the likelihood
surface. Its exhaustiveness is accomodable to the users patience.
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