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HOWTO-MySQL.html
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HOWTO-MySQL.html
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</head>
<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
<div class=Section1>
<div style='border:none;border-bottom:solid windowtext 1.5pt;padding:0in 0in 1.0pt 0in'>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]> <![endif]><o:p></o:p></p>
</div>
<h3 style='margin-left:0in'>BioTeam.Net HOWTO #1</h3>
<h3 style='margin-left:0in'><![if !supportEmptyParas]> <![endif]><o:p></o:p></h3>
<h3 align=center style='margin-left:0in;text-align:center'>MyGENBANK with
MySQL: </h3>
<h3 align=center style='margin-left:0in;text-align:center'>Rolling your own
relational sequence database</h3>
<p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
color:black'>Additional titles considered:<o:p></o:p></span></b></p>
<p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<ul style='margin-top:0in' type=disc>
<li class=MsoNormal style='color:black;mso-list:l12 level1 lfo6;tab-stops:
list .5in'><span style='font-size:10.0pt;font-family:Arial'>Oracle DBA
not required :)</span><span style='font-family:Arial'><o:p></o:p></span></li>
<li class=MsoNormal style='color:black;mso-list:l12 level1 lfo6;tab-stops:
list .5in'><span style='font-size:10.0pt;font-family:Arial'>Escape from
flatfile hell? </span><span style='font-family:Arial'><o:p></o:p></span></li>
</ul>
<p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal><b><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
font-family:Arial;color:black'>Summary:<o:p></o:p></span></b></p>
<p class=MsoBodyText>A step-by-step diary written by a database novice
describing how to use freely available tools and schemas from the Open
Bioinformatics Foundation to create a MySQL-based relational database
repository for biological sequence and annotation data.</p>
<p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
color:black'>Author:</span></b><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'>Chris
Dagdigian, <a href="mailto:dag@sonsorol.org">dag@sonsorol.org</a> </span><span
style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'><a
href="http://bioteam.net/">http://BioTeam.net</a><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
color:black'>Version:</span></b><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'>1.1
- Last updated May 30, 2002 <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
color:black'>Revision History:<o:p></o:p></span></b></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'>1.0;
Original version May 2002<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'>1.1;
Reader feedback and error corrections; first complete revision May 2002<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
color:black'>Acknowledgements:<o:p></o:p></span></b></p>
<ul style='margin-top:0in' type=disc>
<li class=MsoNormal style='color:black;mso-list:l16 level1 lfo17;tab-stops:
list .5in'><span style='font-size:10.0pt;font-family:Arial'>Open
Bioinformatics Foundation, <a href="http://www.open-bio.org/">http://www.open-bio.org</a><o:p></o:p></span></li>
<li class=MsoNormal style='color:black;mso-list:l16 level1 lfo17;tab-stops:
list .5in'><span style='font-size:10.0pt;font-family:Arial'>Bauer Center
for Genomics Research, Harvard University, <a
href="http://cgr.harvard.edu/">http://cgr.harvard.edu</a><o:p></o:p></span></li>
</ul>
<p class=MsoBodyText style='margin-left:.5in;text-indent:-.25in;mso-list:l16 level1 lfo17;
tab-stops:list .5in'><![if !supportLists]><span style='mso-bidi-font-size:10.0pt;
font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='mso-bidi-font-size:10.0pt'>Keith Allen,
PhD, Paradigm Genetics, USA<o:p></o:p></span></p>
<p class=MsoBodyText style='margin-left:.5in;text-indent:-.25in;mso-list:l16 level1 lfo17;
tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol'>·<span
style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='mso-bidi-font-size:10.0pt'>Mark </span>Lambrecht,
PhD - University of Leuven, Centre of Microbial and Plant Genetics, Belgium</p>
<p class=MsoBodyText style='margin-left:.5in;text-indent:-.25in;mso-list:l16 level1 lfo17;
tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol'>·<span
style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Adam Witney, St. Georges Hospital Medical School,
University of London, UK</p>
<p class=MsoNormal style='margin-left:14.45pt'><span style='mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Additional Resources:<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Open Bio Database Access website, <a
href="http://obda.open-bio.org/">http://obda.open-bio.org</a><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Open-bio-l mailing list, <a
href="http://open-bio.org/mailman/listinfo/open-bio-l">http://open-bio.org/mailman/listinfo/open-bio-l</a><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></b></p>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
color:black'>Contents:</span></b><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-bidi-font-family:Arial;color:black'><span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Background & purpose</span><span style='font-family:Arial;
color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-bidi-font-family:Arial;color:black'><span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Assumptions</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-bidi-font-family:Arial;color:black'><span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>About the OBDA effort</span><span style='font-family:Arial;
color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-bidi-font-family:Arial;color:black'><span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>About BioSQL</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-bidi-font-family:Arial;color:black'><span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>About Bioperl-db</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-bidi-font-family:Arial;color:black'><span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Step-by-step guide</span><span style='font-family:Arial;
color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>1.<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Installing MySQL the lazy way (via RPM) and configuring</span><span
style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>2.<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Installing perl interfaces to MySQL</span><span style='font-family:
Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>3.<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Installing Bundle::BioPerl via CPAN.pm</span><span
style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>4.<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Installing BioPerl via CPAN.pm</span><span style='font-family:
Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>5.<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Downloading & installing bioperl-db directly from the OBF CVS
repository</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>6.<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Downloading biosql-schema directly from the OBF CVS repository</span><span
style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>7.<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Putting it all together: creating a biosql instance within MySQL</span><span
style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>8.<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Loading a test protein dataset: SwissProt release 40</span><span
style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>9.<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Observations</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
color:black'>10.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]><span
style='font-size:10.0pt;font-family:Arial;color:black'><span
style="mso-spacerun: yes"> </span>Next steps
</span><span style='font-family:
Arial;color:black'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:Arial;
color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
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color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:Arial;
color:black'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
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<p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>Background & purpose<o:p></o:p></span></b></p>
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<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'>While working on an
informatics/Bio-IT project at Harvard Universitys new Bauer Center for
Genomics Research (<a href="http://cgr.harvard.edu/">http://cgr.harvard.edu</a>)
I met some people who were interested in storing sequence data into a
relational database so they could avoid having to parse or index big flat text
files.<o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'>Knowing that (a) The Open
Bioinformatics Foundation had started work on solution and (b) I am a complete
and utter moron when it comes to relational databases I thought that it would
be a fun experiment to document my efforts at building such a server starting
with a bare-bones RedHat Linux 7.2 server.<o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'>This document is essentially a
diary of my experiences. It took me roughly a day to get to the point where I
could load Swissprot into a biosql database via Jason Stajichs
load_seqdatabase.pl script.<o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'>Another reason I wrote this is
that as a member of the Open Bioinformatics Foundation board of directors I am
well aware that our website(s) are horrific and that our documentation often
lags behind the functionality of our code base. <o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'>In particular the bioperl website
gives little or no mention to bioperl-db and the related obda.open-bio.org
website is totally devoid of any real information.<o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'>In fact- one practically needs to
be an existing developer on one of our existing projects to even know that this
stuff exists.<o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'>So- besides being a fun way to
spend a day this is also a way for me to get myself more up to speed with the
OBDA website and related work so that I can eventually help contribute to the
website and project documentation efforts.<o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'>Comments/corrections/additions/flames
regarding this document are welcome. Just send them along to me at <a
href="mailto:dag@sonsorol.org">dag@sonsorol.org</a><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
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<p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>Assumptions<o:p></o:p></span></b></p>
<p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></b></p>
<p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
style='font-family:Symbol;mso-bidi-font-family:Arial'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-family:Arial'>This document describes
installing a biosql-compliant database on an x86-based server running RedHat
7.2. <o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
style='font-family:Symbol;mso-bidi-font-family:Arial'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-family:Arial'>Different hardware
architectures or OSs may require different install procedures. Specifically
the server used for this process was a Dell PowerEdge 6450 system with dual
Xeon CPUs, 4GB physical memory and the 2.4.18 linux kernel.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
style='font-family:Symbol;mso-bidi-font-family:Arial'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-family:Arial'>This document assumes
the user has root access to the server system for the purposes of installing
software and perl modules.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
style='font-family:Symbol;mso-bidi-font-family:Arial'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-family:Arial'>This document assumes
at least basic knowledge of RPM packages and how to install them<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
style='font-size:12.0pt;mso-bidi-font-size:10.0pt;font-family:Symbol;
mso-bidi-font-family:Arial;mso-bidi-font-weight:bold'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span style='font-family:Arial'>The process described
here includes downloading code from the internet via anonymous CVS which some
firewalls may not allow. Explaining the use of CVS-over-SSH is not within the
scope of this document.</span><b><span style='font-size:12.0pt;mso-bidi-font-size:
10.0pt;font-family:Arial'> <o:p></o:p></span></b></p>
<p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></b></p>
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<p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>About the Open Bio Database Access (OBDA) effort<o:p></o:p></span></b></p>
<p class=MsoBodyText><![if !supportEmptyParas]> <![endif]><o:p></o:p></p>
<p class=MsoBodyText>OBDA is standard developed by the <a
href="http://www.open-bio.org/">Open Bioinformatics Foundation</a> to
standardize the way all of the OBF-affiliated projects access sequence data
resources. This includes local sequence resources (indexed flatfiles), remote
databases (web accessible sequence resources), CORBA servers (implementing the <a
href="http://www.biocorba.org/">BioCORBA/BSANE</a> specification) and
relational databases using the <a
href="http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/?cvsroot=biosql">BioSQL</a>
schema.</p>