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<h3 style='margin-left:0in'>BioTeam.Net HOWTO #1</h3>
<h3 style='margin-left:0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></h3>
<h3 align=center style='margin-left:0in;text-align:center'>“BioSQL with
MySQL: </h3>
<h3 align=center style='margin-left:0in;text-align:center'>Rolling your own
relational sequence database”</h3>
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<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]>&nbsp;<![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]>&nbsp;<![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]>&nbsp;<![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]>&nbsp;<![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]>&nbsp;<![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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]>Adam Witney, St. George’s 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]>&nbsp;<![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]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Background &amp; 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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
color:black'>Downloading &amp; 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"'>&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;
</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"'>&nbsp;&nbsp;&nbsp;&nbsp;
</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]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:Arial;
color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in'><span style='font-family:Arial;
color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<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]>&nbsp;<![endif]><o:p></o:p></p>
</div>
<p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>Background &amp; purpose<o:p></o:p></span></b></p>
<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'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![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 University’s 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]>&nbsp;<![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]>&nbsp;<![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 Stajich’s
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]>&nbsp;<![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]>&nbsp;<![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]>&nbsp;<![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]>&nbsp;<![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]>&nbsp;<![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]>&nbsp;<![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'><![if !supportEmptyParas]>&nbsp;<![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'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
</div>
<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]>&nbsp;<![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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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]>&nbsp;<![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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style='font-family:Arial'>Different hardware
architectures or OS’s 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]>&nbsp;<![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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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]>&nbsp;<![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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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]>&nbsp;<![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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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]>&nbsp;<![endif]><o:p></o:p></span></b></p>
<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]>&nbsp;<![endif]><o:p></o:p></p>
</div>
<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]>&nbsp;<![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>
<p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
<p class=MsoBodyText>The website for the OBDA effort will eventually be <a
href="http://obda.open-bio.org/">http://obda.open-bio.org/</a> . At this time
though the site is only online in template form. The OBF is actively soliciting
people to take over the website and OBDA documentation efforts. </p>
<p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
<p class=MsoBodyText>The primary discussion forum for the OBDA effort is the
“open-bio-l” mailing list. The list signup page is located at: <a
href="http://open-bio.org/mailman/listinfo/open-bio-l">http://open-bio.org/mailman/listinfo/open-bio-l</a>
. The list archives are online at <a
href="http://open-bio.org/pipermail/open-bio-l/">http://open-bio.org/pipermail/open-bio-l/</a>.
</p>
<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'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![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'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></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'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
</div>
<p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>About BioSQL<o:p></o:p></span></b></p>
<p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
<p class=MsoBodyText>The website and primary email discussion list for all
things BioSQL related will be the ones listed above in the OBDA section.</p>
<p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
<p class=MsoBodyText>A BioSQL ER diagram in PDF form can be <a
href="http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/biosql-schema/doc/biosql-ERD.pdf?rev=HEAD&amp;cvsroot=biosql">downloaded
directly</a> (PDF) from the OBF anonymous CVS server. A formatted listing of
the tables described in the schema can be <a
href="http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/biosql-schema/doc/biosql.html?rev=HEAD&amp;cvsroot=biosql&amp;content-type=text/html">viewed
online directly</a> (HTML) from the same server.</p>
<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]>&nbsp;<![endif]><o:p></o:p></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'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
</div>
<p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>About BioPerl-db<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]>&nbsp;<![endif]><o:p></o:p></span></b></p>
<p class=MsoBodyText>The bioperl-db project was started by Ewan Birney with
major work contributed by Elia Stupka and continued support coming from the
bioperl community.<span style="mso-spacerun: yes">  </span>Its purpose is a
standalone sequence database with little external dependencies and tight
integration with the bioperl distribution.<span style="mso-spacerun: yes"
</span>Support for more databases and bindings in java and python by Biojava
and Biopython projects are welcomed and encouraged.<span style="mso-spacerun:
yes">  </span>All questions and comments should be directed to the bioperl list
&lt;<a href="mailto:bioperl-l@bioperl.org">bioperl-l@bioperl.org</a>&gt; and
more information can be found about the related projects at <a
href="http://bio.perl.org">http://bio.perl.org</a> and <a
href="http://www.open-bio.org.">http://www.open-bio.org.</a></p>
<p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
<p class=MsoBodyText>Bioperl-db is a standalone module located within the CVS
code repository operated by the BioPerl Project. Anonymous CVS access and
tarball downloads are available at <a href="http://cvs.bioperl.org/">http://cvs.bioperl.org</a>.
Look in the bioperl repository for the “bioperl-db” module.</p>
<span style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-ansi-language:EN-US;mso-fareast-language:EN-US;
mso-bidi-language:AR-SA'><br clear=all style='mso-special-character:line-break;
page-break-before:always'>
</span>
<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]>&nbsp;<![endif]><o:p></o:p></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'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
</div>
<p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial'>Step by step guide</span></b><b><span style='font-size:12.0pt;
mso-bidi-font-size:10.0pt;font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='mso-fareast-font-family:"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='mso-fareast-font-family:"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-size:11.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial;mso-fareast-font-family:"MS Mincho"'>Step 1 Install MySQL the
lazy way (via RPM) and configure<o:p></o:p></span></b></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>While logged in as root I installed the following RedHat RPMS:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysqlclient9-3.23.22-6<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-3.23.41-1<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-server-3.23.41-1<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-devel-3.23.41-1<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Arial;
mso-fareast-font-family:"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The install was verified by issuing the following command:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><span style='mso-tab-count:1'>            </span># rpm –qa | grep
mysql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysqlclient9-3.23.22-6<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-3.23.41-1<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-server-3.23.41-1<o:p></o:p></span></p>
<p class=MsoPlainText style='text-indent:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-devel-3.23.41-1</span><span
style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoBodyText><b><span style='mso-fareast-font-family:"MS Mincho"'>MySQL
version warning:</span></b><span style='mso-fareast-font-family:"MS Mincho"'>
Mark Lambrecht recommends the use of MySQL version 3.23 or later. When trying
to install version 3.22 on an Alpha-based system he received errors relating to
the creation of the “</span><span style='font-family:"Courier New"'>fattribute_to_feature</span
table. <span style='mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>By default the RPM MySQL install puts sample configuration files
into /usr/share/mysql/<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The base directory that the RPM MySQL install uses is
/var/lib/mysql<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The global configuration file is kept at /etc/my.cnf<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>It is important to edit the configuration file at /etc/my.conf <b>BEFORE</b>
starting the database for the first time particularly if you want (like me) to
have the MySQL data files live somewhere other than /var/lib/mysql.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>In my case I wanted to do two main things to the global config
file, (a) change the default location to the much larger /usr/local/ partition
and (b) incorporate some of the config suggestions found in /usr/share/mysql/
specific to large dedicated database servers. <o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>WARNING</span></b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>; BioSQL databases can be very large. It may be wise to double
check the size of your /var partition before continuing on with a totally
default RPM-based install. The 1GB /var partition present on the Dell 6450
server is far too small. As an example:<span style="mso-spacerun: yes"
</span>The swissprot40 database is 307MB in size. When this dataset was loaded
into MySQL the resulting database files and indices consumed roughly 399MB of
disk space. <o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoBodyText><b><span style='mso-fareast-font-family:"MS Mincho"'>NOTE</span></b><span
style='mso-fareast-font-family:"MS Mincho"'>: Several BioSQL users have found
that very large sequence records will greatly exceed some of the default
settings that MySQL uses. In particular one may need to set the configuration
value “</span><span style='font-family:"Courier New";mso-fareast-font-family:
"MS Mincho"'>max_allowed_packet</span><span style='mso-fareast-font-family:
"MS Mincho"'>” to a fairly high value (several megabytes at least). If you
encounter any error messages that are similar to: “</span><span
style='font-family:"Courier New"'>DBD::mysql::st execute failed: MySQL server
has gone away…</span>” than it is likely that <span style='font-family:"Courier New"'>max_allowed_packet</span>
needs to be set to a larger value. In an email post to the bioperl-l (<a
href="http://bioperl.org/mailman/listinfo/bioperl-l">http://bioperl.org/mailman/listinfo/bioperl-l</a>)
mailing list Keith Allen covers his experience with this problem in excellent
detail. The full email message can be read at the following URL: <a
href="http://bioperl.org/pipermail/bioperl-l/2002-May/007987.html">http://bioperl.org/pipermail/bioperl-l/2002-May/007987.html</a>
</p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>After revising the value of max_allowed_packet to ‘3M’ due to
feedback from Keith Allen (see above Note) the global configuration file
/etc/my.conf now looks like this:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysqld]<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>port=3306<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>datadir=/usr/local/mysql-database<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>socket=/usr/local/mysql-database/mysql.sock<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>skip-locking<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable= key_buffer=256M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
max_allowed_packet=3M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
table_cache=256<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
sort_buffer=1M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
record_buffer=1M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
myisam_sort_buffer_size=64M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
thread_cache=8<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
thread_concurrency=4<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>server-id= 1<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>tmpdir= /tmp/<span
style='mso-tab-count:1'> </span><span style='mso-tab-count:1'>      </span><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><span
style="mso-spacerun: yes">     </span><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysql.server]<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>user=mysql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>basedir=/usr/lib<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[safe_mysqld]<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>err-log=/var/log/mysqld.log<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>pid-file=/var/run/mysqld/mysqld.pid<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysqldump]<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>quick<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
max_allowed_packet=16M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysql]<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>no-auto-rehash<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>safe-updates<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[isamchk]<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
style='mso-tab-count:1'>      </span>= key_buffer=128M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
style='mso-tab-count:1'>      </span>= sort_buffer=128M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
style='mso-tab-count:1'>      </span>= read_buffer=2M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
style='mso-tab-count:1'>      </span>= write_buffer=2M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[myisamchk]<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
style='mso-tab-count:1'>      </span>= key_buffer=128M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
style='mso-tab-count:1'>      </span>= sort_buffer=128M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
style='mso-tab-count:1'>      </span>= read_buffer=2M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
style='mso-tab-count:1'>      </span>= write_buffer=2M<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysqlhotcopy]<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>interactive-timeout<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Just in case I missed anything I decided to add a symbolic link
back to /var/lib/mysql – this turns out to be important because my
configuration file still has “basedir=/var/lib” which is a total mistake.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># cd /var/lib<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># ln -s
/usr/local/mysql-database/ ./mysql</span><span style='font-family:Arial;
mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Now we can start the MySQL datbase...<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>/etc/rc.d/init.d/mysql
start<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Important!</span></b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'> Protect your database by setting a root MySQL password:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># mysqladmin -u
root password 'xxxxxxx'<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>After installing, configuring, starting and enabling a root
password it should be possible to logoff as root and re-login as a ‘normal’
system user.<span style="mso-spacerun: yes">  </span><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>To test this I made the switch from root user to my normal 'dag'
user account and confirmed that I can login as root to the mysql instance:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3
scripts]$ mysql -u root -p<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Enter password:
<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Welcome to the
MySQL monitor.<span style="mso-spacerun: yes">  </span>Commands end with ; or
\g.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Your MySQL
connection id is 8 to server version: 3.23.41-log<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Type 'help;' or
'\h' for help. Type '\c' to clear the buffer.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt; exit<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Bye</span><span
style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Success! We now have a working MySQL instance.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Step 2 Install the perl interfaces to MySQL <o:p></o:p></span></b></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>In future steps we are going to use perl to help us talk to the
MySQL database. In order to do this we need some additional perl modules
installed. We need:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l13 level1 lfo7;
tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>DBI:: - The perl generic database interface<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l13 level1 lfo7;
tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>DBD::MySQL – The perl MySQL database driver module<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Given the lazy RPM install we previously did with the MySQL
database it makes sense to install the preconfigured RPM versions of these
modules that RedHat provides. The specific modules installed were:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l2 level1 lfo8;
tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
mso-fareast-font-family:"MS Mincho"'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style='mso-fareast-font-family:"MS Mincho"'>perl-DBI-1.18-1.i386.rpm<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l2 level1 lfo8;
tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style='mso-fareast-font-family:"MS Mincho"'>perl-DBD-MySQL-1.2216-4.i386.rpm</span><span
style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Installation of these modules went smoothly. This was a welcome
relief as given the still traumatic memories of spending days trying to get
DBD::Oracle to install and work cleanly on Compaq Alphaservers and HP-UX
machines.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Step 3 Install Bundle::BioPerl via CPAN.pm <o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Note: Skip this step if BioPerl is already on your system.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Some of the perl scripts needed to help load the database with
sequence data we will be using in future steps are themselves dependent on the
BioPerl distribution (<a href="http://bioperl.org/">http://bioperl.org/</a>)<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>for critical functions such as sequence parsing etc. <o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The BioPerl distribution itself has its own dependencies on Perl
modules and other programs that may or may not be found by default on a system.
These external dependencies are not required but if installed they will give
the BioPerl distribution additional functionality and features.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The BioPerl people have created a special CPAN package called
“Bundle::BioPerl” that can assist with downloading and automatically installing
all of the CPAN resident modules that BioPerl likes to use. By itself
Bundle::BioPerl is next to useless but when used with CPAN.pm it becomes very
convenient.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>For the purposes of building a BioSQL database we don’t really
care about all of the various external BioPerl dependencies enough to give
special attention to the issue. The proper ‘lazy’ way then is just to fire up
CPAN.pm and let it do all of the work. <o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>People unfamiliar with the CPAN.pm module can read its
documentation by issuing the system command ‘perldoc CPAN’.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>To fire up the CPAN module in shell mode issue the following
command as root:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'># perl –MCPAN –e shell<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>If this is the first time that CPAN.pm has been used there will be
an initial setup and configuration phase where CPAN configures itself to the
local network environment. The user is also prompted to select from a list of
available mirror sites.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>To install Bundle::BioPerl while in the CPAN shell environment:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>cpan&gt; install Bundle::BioPerl<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>That’s about it. The process may take some time depending on the
speed of the server and available network connection.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>NOTE:<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>When attempting this for the first time the installation of
Bundle::BioPerl completely failed because one of the perl modules<span
style="mso-spacerun: yes">  </span>implementing SOAP functionality listed in
the Bundle is apparently only distributed as a .ZIP archive rather than the
more traditional tar.gz format.<span style="mso-spacerun: yes">  </span>The
install process failed because CPAN.pm had not been configured to know where a
suitable ‘unzip’ utility could be found. The solution was to exit from the CPAN
shell, manually install the unzip rpm and then restart the CPAN shell.<span
style="mso-spacerun: yes">  </span>Within the restarted CPAN shell environment
the following command will make CPAN aware of the newly installed unzip
utility:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>cpan&gt; o conf unzip<span
style="mso-spacerun: yes">  </span>/usr/bin/unzip<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>cpan&gt; install Bundle::BioPerl</span><span
style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Step 4 Install BioPerl via CPAN.pm<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Note: Skip this step if BioPerl is already on your system.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Now that the various helper modules and external dependencies of
BioPerl have been installed it should now be possible to use the same CPAN.pm
shortcut to automatically download and install the full BioPerl distribution.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Asking CPAN to install the ‘Bio::Seq’ module is enough to get it
to download and install the full distribution:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>cpan&gt; install Bio::Seq<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>BioPerl is a very large distribution (possibly the single largest
collection of related perl modules in the entire CPAN repository) – you may
wish to download and manually install the full BioPerl distribution directly
from <a href="http://bioperl.org/">http://bioperl.org/</a>.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Step 5 Download and install bioperl-db directly from the OBF CVS
repository<o:p></o:p></span></b></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Getting the latest and greatest version of the bioperl-db
distribution involves downloading straight from the public source code server
located at <a href="http://cvs.open-bio.org/">http://cvs.open-bio.org/</a><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Instructions for downloading code via anonymous CVS are available
on the cvs.open-bio.org website. Your firewall or local network configuration
may not allow anonymous CVS connections to occur. See below for a workaround:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>How to use the web and avoid anonymous CVS altogether:<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>If a firewall or network gateway device blocks CVS connection
attempts it should be possible to download code and full distributions directly
from the <a href="http://cvs.open-bio.org/">http://cvs.open-bio.org/</a>
website. The CGI gateway to the CVS repository has a nice feature entitled
“Download Tarball”. When clicked the server will generate a fresh code checkout
and will send it to your browser as a .tar.gz archive file which can be saved
locally to disk. The files may all be named “cvs_root.tar.gz” so beware of
potential file overwrite issues when downloading multiple files or codebases.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>How to checkout via anonymous:<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The anonymous CVS password is ‘cvs’<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Full instructions are available at <a
href="http://cvs.open-bio.org/">http://cvs.open-bio.org</a><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Example session with output:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># cvs
-d:pserver:cvs@cvs.open-bio.org:/home/repository/bioperl login<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>CVS password: <o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># <o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># cvs
-d:pserver:cvs@cvs.open-bio.org:/home/repository/bioperl co bioperl-db <o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
Updating bioperl-db<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
bioperl-db/BUGS<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
bioperl-db/Changes<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
bioperl-db/LICENSE<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
bioperl-db/MANIFEST<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
bioperl-db/MANIFEST.SKIP<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
bioperl-db/Makefile.PL<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
bioperl-db/README<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
Updating bioperl-db/Bio<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
Updating bioperl-db/Bio/DB<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
bioperl-db/Bio/DB/Annotation.pm<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><b><i><span style='font-family:
Courier;mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>&lt;FULL
OUTPUT CUT FOR BREVITY&gt;<o:p></o:p></span></i></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Installing bioperl-db<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The bioperl-db distribution is in the standard CPAN-style format
so installation is similar to any other external perl module:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Once the distribution is uncompressed and unpacked there are only
three commands necessary:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'># perl Makefile.PL<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'># make<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'># make install</span><span
style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>NOTE: This install will fail if the DBD:: and DBI::Mysql modules
cannot be found.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Step 6 Download and install biosql-schema directly from the OBF
CVS repository<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Reference the above discussion on anonymous CVS, firewalls and the
ability to download tar archives directly from the <a
href="http://cvs.open-bio.org/">http://cvs.open-bio.org/</a> website.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The OBDA schema for BioSQL databases lives in its own CVS code
repository because its use spans many of the Open Bio projects and coding
efforts.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The repository is called “biosql”, the module is called
“biosql-schema”. The CVS root for the respository can be found at
“/home/repository/biosql”.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Example anonymous CVS checkout session:<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[root@pe3]# cvs
-d :pserver:cvs@cvs.open-bio.org:/home/repository/biosql login<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Logging in to
:pserver:cvs@cvs.open-bio.org:2401/home/repository/biosql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>CVS password: <o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[root@pe3
biosql]# cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biosql checkout
biosql-schema<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
Updating biosql-schema<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
Updating biosql-schema/doc<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/doc/README<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/doc/biosql-ERD.pdf<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/doc/biosql.html<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
Updating biosql-schema/scripts<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/scripts/create_mysql_db.pl<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/scripts/transform_sql.pl<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
Updating biosql-schema/sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/sql/README<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/sql/biopipelinedb-mysql.sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/sql/biosql-accelerators-pg.sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/sql/biosqldb-mysql.sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/sql/biosqldb-pg.sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/sql/biosqldb-views-pg.sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/sql/makefile<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server: Updating
biosql-schema/sql/ontology<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/sql/ontology/biosqldb-ontology-mysql.sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
biosql-schema/sql/ontology/biosqldb-ontology-pg.sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
Updating biosql-schema/t<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[root@pe3
biosql]# <o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The files found in the biosql-schema do not need to be installed
or otherwise processed. We are going to use the scripts and documents found in
this module directly.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-size:11.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial;mso-fareast-font-family:"MS Mincho"'>Step 7 – Putting it all
together: creating a biosql instance within MySQL<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Inside the biosql-schema/scripts folder there is a perl script called
&quot;create_mysqldb.pl&quot;. This script is just a helper script that
automates the process of connecting to the datbase and issuing<span
style="mso-spacerun: yes">  </span>the SQL statements that cause the proper
database tables to be created. The script reads the actual SQL commands from
the file found in biosql-schema/sql/biosql-mysqldb.sql<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>After looking at how simple this script is I felt the need to
bypass it completely and just perform the steps manually for curiosity sake.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Here is the output from creating an initial database named ‘biosql’:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3]$
mysql -u root -p<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Enter password:
<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Welcome to the
MySQL monitor.<span style="mso-spacerun: yes">  </span>Commands end with ; or
\g.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Your MySQL
connection id is 9 to server version: 3.23.41-log<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Type 'help;' or
'\h' for help. Type '\c' to clear the buffer.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt;
create database biosql;<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt; exit<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Bye</span><span
style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Now that the database is created we need to connect to the
database and issue the SQL commands contained in
biosql-scheme/sql/biosqldb-mysql.sql file:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Within the mysql client interface we can use the command
&quot;source&quot; to read in SQL statements from a file.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Here is the output from that process:<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3]$
mysql -u root -p biosql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Enter password:
<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Welcome to the
MySQL monitor.<span style="mso-spacerun: yes">  </span>Commands end with ; or
\g.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Your MySQL
connection id is 11 to server version: 3.23.41-log<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Type 'help;' or
'\h' for help. Type '\c' to clear the buffer.<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt;
source sql/biosqldb-mysql.sql<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 0
rows affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Records: 0<span
style="mso-spacerun: yes">  </span>Duplicates: 0<span style="mso-spacerun:
yes">  </span>Warnings: <o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><i><span style='font-family:
Arial;mso-fareast-font-family:"MS Mincho"'>&lt;snip - lots of boring output cut
here...&gt; <o:p></o:p></span></i></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 0
rows affected (0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt;<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Now that we are still connected to datbase ‘biosql’ let us see
what we created by issuing the command &quot;show tables;&quot;<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt; show
tables;<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>+----------------------------+<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
Tables_in_biosql<span style="mso-spacerun: yes">           </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>+----------------------------+<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
biodatabase<span style="mso-spacerun: yes">                </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| bioentry<span
style="mso-spacerun: yes">                   </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
bioentry_direct_links<span style="mso-spacerun: yes">      </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
bioentry_qualifier_value<span style="mso-spacerun: yes">   </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
bioentry_reference<span style="mso-spacerun: yes">         </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| bioentry_taxa<span
style="mso-spacerun: yes">              </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
biosequence<span style="mso-spacerun: yes">                </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
cache_corba_support<span style="mso-spacerun: yes">        </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| comment<span
style="mso-spacerun: yes">                    </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| dbxref<span
style="mso-spacerun: yes">                     </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
dbxref_qualifier_value<span style="mso-spacerun: yes">     </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
location_qualifier_value<span style="mso-spacerun: yes">   </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
ontology_term<span style="mso-spacerun: yes">              </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
reference<span style="mso-spacerun: yes">            </span><span
style="mso-spacerun: yes">      </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
remote_seqfeature_name<span style="mso-spacerun: yes">     </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
seqfeature<span style="mso-spacerun: yes">                 </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
seqfeature_location<span style="mso-spacerun: yes">        </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
seqfeature_qualifier_value |<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
seqfeature_relationship<span style="mso-spacerun: yes">    </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
seqfeature_source<span style="mso-spacerun: yes">          </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| taxa<span
style="mso-spacerun: yes">                       </span>|<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>+----------------------------+<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>21 rows in set
(0.00 sec)<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt; exit<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Bye</span><span
style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Excellent! We have just created a BioSQL database within MySQL !<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><b><span style='font-size:11.0pt;mso-bidi-font-size:10.0pt;
font-family:Arial;mso-fareast-font-family:"MS Mincho"'>Step 8 - Loading a test
protein dataset (Swissprot) into the database<o:p></o:p></span></b></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Before tackling all of GenBank, a smaller dataset is probably a
good idea as a test case to learn about the process of loading up the new
biosql database with sequence data.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The dataset selected was SwissProt downloaded from <a
href="ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release/sprot40.dat">ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release/sprot40.dat</a><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l9 level1 lfo11;
tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Total uncompressed size: 307MB<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l9 level1 lfo11;
tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Apparent number of sequence entries: 101,707 <o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The database loader script used was the<span style="mso-spacerun:
yes">  </span>&quot;load_seqdatabase.pl&quot; script from the /scripts/ folder
inside the bioperl-db distribution.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The script is pretty basic. There are some internal configuration
settings inside the script that can be manually configured. Each of the
configurable options can also be overridden by command line arguments.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>The basic syntax for the load_seqdatabase.pl script is as follows:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>./load_seqdatabase.pl &lt;options&gt;
&lt;dataset identifier&gt; /path/to/data/file(s)<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Some of the more important options and arguments that can be
hard-coded into the perl script or passed via the command line are:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>-h <span style='mso-tab-count:1'>      </span>(hostname
of the mysql server)<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>-sqldb (the name of the biosql database
instance that was created)<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>-dbuser (username to connect to MySQL
with)<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>-dbpass (MySQL user password)<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>-format (the format of the sequence
datafile that is going to be read/loaded)</span><span style='font-family:Arial;
mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>One of the key options needed is the “dataset identifier”. This
identifier allows one to store many ‘biodatabases” inside the single BioSQL
instance.<span style="mso-spacerun: yes">  </span><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Given that we are trying to load release 40 of the Swissprot
dataset a logical identifier could be something like “swiss”, “swissprot”,
“sprot” or “swissprot40” etc.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'>Here we go…<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3
biosql]$ ./load_seqdatabase.pl -host localhost -sqldb biosql -dbuser root
-dbpass XXX -format swiss swissprot40 /n/data/mirrors/swissprot/sprot40.dat<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Reading
/n/data/mirrors/swissprot/sprot40.dat<o:p></o:p></span></p>
<p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3
biosql]$<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
"MS Mincho";mso-bidi-font-family:Arial'>Wow! It worked!<o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<h1>Step 9 – Observations</h1>
<p class=MsoNormal><b><span style='font-size:11.0pt;mso-bidi-font-size:12.0pt;
font-family:Arial;mso-fareast-font-family:"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
<ul style='margin-top:0in' type=disc>
<li class=MsoNormal style='mso-list:l7 level1 lfo9;tab-stops:list .5in'><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Loading
Swissprot into the MySQL database took 2 hours and 10 minutes. The slow
speed is caused by the overhead of having to parse each entry into a
BioPerl sequence object prior to inserting it into the database. There is
much room for performance tuning; one approach may be to start an
internet-accessible repository where people can download pre-built
tab-delimited MySQL data files that can be bulk imported into a
biosql-compliant database very quickly.<o:p></o:p></span></li>
</ul>
<p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<ul style='margin-top:0in' type=disc>
<li class=MsoNormal style='mso-list:l7 level1 lfo9;tab-stops:list .5in'><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>The
size of sprot40.dat is 307MB <o:p></o:p></span></li>
</ul>
<p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<ul style='margin-top:0in' type=disc>
<li class=MsoNormal style='mso-list:l7 level1 lfo9;tab-stops:list .5in'><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>After
swissprot was loaded the cumulative size of all the files inside
/var/lib/mysql/biosql/ was 399MB<o:p></o:p></span></li>
</ul>
<p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.25in'><span style='font-size:11.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<h1><span style='mso-fareast-font-family:"Times New Roman"'>Step 10 – What
next?</span><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></h1>
<p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
font-family:Arial'>This document is a work in progress. Among the things I’d
like to do next:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<ul style='margin-top:0in' type=disc>
<li class=MsoNormal style='mso-list:l1 level1 lfo10;tab-stops:list .5in'><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Write
perl scripts to validate the information that was loaded into the database<o:p></o:p></span></li>
</ul>
<p class=MsoNormal style='margin-left:.25in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<ul style='margin-top:0in' type=disc>
<li class=MsoNormal style='mso-list:l1 level1 lfo10;tab-stops:list .5in'><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Figure
out how to export/dump the database and see how quickly we can recreate
the database with these raw files instead of laboriously using BioPerl to
parse and load objects one at a time. Loading the database is slow and it
may be cool to package up tab-delimited biosql exports so that others can
load their own databases much faster.<o:p></o:p></span></li>
</ul>
<p class=MsoNormal style='margin-left:.25in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<ul style='margin-top:0in' type=disc>
<li class=MsoNormal style='mso-list:l1 level1 lfo10;tab-stops:list .5in'><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Run
more time tests to see where things can be made faster<o:p></o:p></span></li>
</ul>
<p class=MsoNormal style='margin-left:.25in'><span style='font-size:10.0pt;
mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
<ul style='margin-top:0in' type=disc>
<li class=MsoNormal style='mso-list:l1 level1 lfo10;tab-stops:list .5in'><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Start
trying to cram all of GenBank into a biosql database!<o:p></o:p></span></li>
</ul>
<p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
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