<TITLE>University of Minnesota Medical School</TITLE>
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<H1>Computational Biology Centers</H1>
<H1>Medical School</H1>
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<p>
<h4>Copyright  1994, 1995 The Regents of the University of Minnesota</h4>
This server is under virtually continuous development, and has not yet
formally been made public.  There is nothing in here that we presently
consider finished, and several of the sections are very much in the 
"proof of concept" stage.  All textual, image and software material associated
with this server which is original to this site is to be considered 
copyrighted, at least by the Regents of the University of Minnesota, and, 
in some cases, by other entities.
<P>
<ADDRESS>Ernie Retzel</ADDRESS>
<ADDRESS>ernest@lenti.med.umn.edu</ADDRESS>
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<H1>Research Projects</H1>
<img src ="red.line.gif"><p>

<p>
<dd>
<a href="MSU.arab/arab_top_page.html">
<IMG align=top SRC="cs-907.small.gif">
</a>

<DL> 
<dt><h2> <a href="MSU.arab/arab_top_page.html">Arabidopsis 
cDNA Sequence Analysis Project</A>
</h2>

<dd>The <i>Arabidopsis</i> cDNA Sequence Analysis Project is a joint effort
between the University of Minnesota's Plant Molecular Informatics Center
(PMIC) and Michigan State University, and it is
funded by the National Science Foundation, under grants
BIR 940-2380 and BIR 931-3751.
This project combines both software and database development, seeking to
provide alternative views into analyzed data.
<HR>

<dt><h2> Additional cDNA Sequence Analysis
Projects at the Plant Molecular Informatics Center:</h2
>
<h3> Rice, Corn, Pine and Others</h3>

<P>
In addition to the work with <i>Arapidopsis</i>, other cDNA analysis projects have been undertaken by PMIC to transfer
<a href="general_cdna/general_top.html">sequence analysis tools</a> developed
for
<i>Arabidopsis</i> to other plants:

<P>
<UL>
<LI>The <a href="Rice/top.html"> Rice cDNA Project
</a>
at the Rice Genome Research Program at STAFF Institute in Tsukuba, Japan;

<LI>The <a href="AZ.corn/top.html"> Corn cDNA Project
</a>
at the University of Arizona;

<LI>The <a href="Loblolly/top.html"> Loblolly Pine cDNA Project
</a>
at the Institute of Forest Genetics, USDA Pacific Southwest Research
Station of the Forest Service; and

<LI>A sequencing project for an anonymous client.

</UL>

<P>
We are grateful for the cooperation of
Carolyn Tolstoshev and Mark Boguski of NCBI's dbEST; their assistance and
encouragement in this work has been invaluable and appreciated.

<P>
You may be interested in finding out about having PMIC process your sequences.
(UNDER CONSTRUCTION. A link will be put in shortly.)
<P>
Note:  We have also applied these tools to other organisms, as seen in the
<a href="zebrafish/zfish_top_page.html">
Zebrafish Project.
</a>
<HR>

<a href="http://alces.med.umn.edu/start.html">
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</a>

<dt><h2><a href="http://alces.med.umn.edu/start.html">Alces Server</A></h2>

<dd>Home of the <a href="http://alces.med.umn.edu/VGC.html">
Virtual Genome Center </a> with
   information about <a href="http://alces.med.umn.edu/Candida.html"><i>Candida albicans</i> molecular biology</a>.
<HR>

<dt><a href="http://www.cs.umn.edu/neural/index.html">
<IMG align=top SRC="NEURON_BRAIN/zBRAIN3.gif">

<dt><h2><a href="http://www.cs.umn.edu/neural/index.html">Neuroscience 
Database Program</A></h2>

<dd>The main goal of this research is to provide an
interdisciplinary environment that facilitates development of a
zoomable database of brain structure and function.

</dl>
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<img src ="red.line.gif"></a><p>
<H1>Virtual Library </H1>
<img src ="red.line.gif"></a><p>

<dl>
<dt><h2>The PCR <I>In Situ</I></h2>
<dd>
While the polymerase chain reaction provides an extremely powerful tool
for the analysis of populations of cells, the PCR <I>In Situ</I> extends this 
technology to the single cell level.  In part due to the newness of the
technique, and in part to respond to demand for detailed information, 
pre-prints of articles and in-press book chapters, as well as a cookbook of protocols,
have been made <a href="insitu_pcr/top_page.html">available</a>.

<HR>
<dt><h2>Research Papers</h2>
<dd>
The Computational Biology Centers has converted several of its
<a href="research_papers.html">research papers</a> into a format for WWW
browsing.
<p>
<HR>

<dd>
<a href="recombinant_dna/recombinant_flowchart.html">
<IMG align=top SRC="book2.gif">
</a>

<dt><h2>The Hidden Layers: A Fluid Molecular Biology Didactic Platform</h2>
<dd>
Teaching a course on state of the art molecular biology is challenging
as the underlying technologies advance faster than print support media can
accomodate.  In addition, the essential computational tools are generally
ignored as the difficulty of supporting multiple platforms and capacities
are virtually insurmountable.  This project 
<a href="recombinant_dna/recombinant_flowchart.html">(A Recombinant DNA 
Technology Course)</A> seeks to remove the barriers
by using net-based resources [Mosaic], desktop publishing technologies,
client-server computing, device-independent graphics and imaging and
an array of computational tools operating on remote servers.
<HR>

<dt><H2>Web page creation</H2>
<dd>
A set of pages containing <A Href = "/~hansen/www.class.html">
information</A> and tips, such as design
considerations, for new web authors.
Originally written for the Bio-Medical Library's Beginning WWW class.
<HR>

<dt><h2>On-line Software Documentation</h2>
Software documentation for several molecular biology programs and
packages have been put on-line: 

<ul>
<li>The <a href="doc/staden/staden-94.2.html">Staden Software Suite Manual</a>, for sequence analysis and
manipulation.
<li>An unofficial <a href="MolBio_man/MolBio_man.html">GCG Software Guide</a>.
<li><a href="zuker/mfold.html">Zuker's Mfold Manual</a>, for prediction of RNA Secondary Structure.
<li>The <a href="doc/osp/intr2.html">Oligo Selection Program</a>, an aid in selecting oligonucleotide primers
for DNA sequencing an PCR.
<li><a href="http://xplor.csb.yale.edu">X-PLOR</a>, used to determine molecular structure by X-ray
crystallography and solution nuclear magnetic resonance spectroscopy.
<li><a href="/software/server_software.html>Other documentation</a>, useful for
making Web server pages.
</ul>

<HR>

<dt><h2>Additional Medical School Resources</h2>
<dd>
<a href="gopher://lenti.med.umn.edu/11/biomed"><IMG align=top SRC="xgopher.gif">
The Bio-Medical Library Gopher Information System
</a>
</dl>
<P>

<dt>
<dd>
<a href="http://lenti.med.umn.edu/~ihg/index.html"><IMG align=top SRC="http://lenti.med.umn.edu/~ihg/Images/chem.model.GIF">
The Institute of Human Genetics</a>, Medical School
</dl>
<dd>

<dt>
<dd>
<a href="~valeriya/top.html"><IMG align=top SRC="bipl.gif">The Biomedical 
Imaging and Processing Lab</a>
</dl>

<dt><ul>
<li>
Home of the <a href="linkage/linkage.html"> Genetic Linkage
Analysis</a> Information Guide.  This locally created summary points to frequently asked
questions (FAQs) and information sources, such as databases, software
and newsletters, pertaining to linkage analysis.
</ul></li>

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<img src ="red.line.gif"></a><p>
<H1>Other Interesting Points </H1>
<img src ="red.line.gif"></a><p>

<p>
<dl>
<li><a href="other_sites.html">Useful sites</a> on the WWW, 
including internet information and navigation, bio-resource and bio-research 
servers, and high performance computer servers.
<li>The <a href =
"http://lenti.med.umn.edu/usage/list.html">usage statistics</a>
for this server.
</dl>

<HR>
This server is brought to you by <A NAME=10
HREF="personnel/uofm_personnel.html">the members</A> of the
University of Minnesota Medical School Computational Biology Centers.

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