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  11 <title>MyGENBANK with mySQL: Rolling your own relational sequence database</title>
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 562 -->
 563 </style>
 564 </head>
 565
 566 <body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
 567
 568 <div class=Section1>
 569
 570 <div style='border:none;border-bottom:solid windowtext 1.5pt;padding:0in 0in 1.0pt 0in'>
 571
 572 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 573 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
 574
 575 </div>
 576
 577 <h3 style='margin-left:0in'>BioTeam.Net HOWTO #1</h3>
 578
 579 <h3 style='margin-left:0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></h3>
 580
 581 <h3 align=center style='margin-left:0in;text-align:center'>“BioSQL with
 582 MySQL: </h3>
 583
 584 <h3 align=center style='margin-left:0in;text-align:center'>Rolling your own
 585 relational sequence database”</h3>
 586
 587 <p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 588
 589 <p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
 590 color:black'>Additional titles considered:<o:p></o:p></span></b></p>
 591
 592 <p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 593
 594 <ul style='margin-top:0in' type=disc>
 595  <li class=MsoNormal style='color:black;mso-list:l12 level1 lfo6;tab-stops:
 596      list .5in'><span style='font-size:10.0pt;font-family:Arial'>“Oracle DBA
 597      not required :)”</span><span style='font-family:Arial'><o:p></o:p></span></li>
 598  <li class=MsoNormal style='color:black;mso-list:l12 level1 lfo6;tab-stops:
 599      list .5in'><span style='font-size:10.0pt;font-family:Arial'>“Escape from
 600      flatfile hell?” </span><span style='font-family:Arial'><o:p></o:p></span></li>
 601 </ul>
 602
 603 <p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 604
 605 <p class=MsoNormal><b><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
 606 font-family:Arial;color:black'>Summary:<o:p></o:p></span></b></p>
 607
 608 <p class=MsoBodyText>A step-by-step diary written by a database novice
 609 describing how to use freely available tools and schemas from the Open
 610 Bioinformatics Foundation to create a MySQL-based relational database
 611 repository for biological sequence and annotation data.</p>
 612
 613 <p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 614
 615 <p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
 616 color:black'>Author:</span></b><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
 617
 618 <p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'>Chris
 619 Dagdigian, <a href="mailto:dag@sonsorol.org">dag@sonsorol.org</a> </span><span
 620 style='font-family:Arial;color:black'><o:p></o:p></span></p>
 621
 622 <p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'><a
 623 href="http://bioteam.net/">http://BioTeam.net</a><o:p></o:p></span></p>
 624
 625 <p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 626
 627 <p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
 628 color:black'>Version:</span></b><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
 629
 630 <p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'>1.1
 631 - Last updated May 30, 2002 <o:p></o:p></span></p>
 632
 633 <p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 634
 635 <p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
 636 color:black'>Revision History:<o:p></o:p></span></b></p>
 637
 638 <p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'>1.0;
 639 Original version – May 2002<o:p></o:p></span></p>
 640
 641 <p class=MsoNormal><span style='font-size:10.0pt;font-family:Arial;color:black'>1.1;
 642 Reader feedback and error corrections; first ‘complete’ revision – May 2002<o:p></o:p></span></p>
 643
 644 <p class=MsoNormal><span style='font-family:Arial;color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 645
 646 <p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
 647 color:black'>Acknowledgements:<o:p></o:p></span></b></p>
 648
 649 <ul style='margin-top:0in' type=disc>
 650  <li class=MsoNormal style='color:black;mso-list:l16 level1 lfo17;tab-stops:
 651      list .5in'><span style='font-size:10.0pt;font-family:Arial'>Open
 652      Bioinformatics Foundation, <a href="http://www.open-bio.org/">http://www.open-bio.org</a><o:p></o:p></span></li>
 653  <li class=MsoNormal style='color:black;mso-list:l16 level1 lfo17;tab-stops:
 654      list .5in'><span style='font-size:10.0pt;font-family:Arial'>Bauer Center
 655      for Genomics Research, Harvard University, <a
 656      href="http://cgr.harvard.edu/">http://cgr.harvard.edu</a><o:p></o:p></span></li>
 657 </ul>
 658
 659 <p class=MsoBodyText style='margin-left:.5in;text-indent:-.25in;mso-list:l16 level1 lfo17;
 660 tab-stops:list .5in'><![if !supportLists]><span style='mso-bidi-font-size:10.0pt;
 661 font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 662 </span></span><![endif]><span style='mso-bidi-font-size:10.0pt'>Keith Allen,
 663 PhD, Paradigm Genetics, USA<o:p></o:p></span></p>
 664
 665 <p class=MsoBodyText style='margin-left:.5in;text-indent:-.25in;mso-list:l16 level1 lfo17;
 666 tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol'>·<span
 667 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 668 </span></span><![endif]><span style='mso-bidi-font-size:10.0pt'>Mark </span>Lambrecht,
 669 PhD - University of Leuven, Centre of Microbial and Plant Genetics, Belgium</p>
 670
 671 <p class=MsoBodyText style='margin-left:.5in;text-indent:-.25in;mso-list:l16 level1 lfo17;
 672 tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol'>·<span
 673 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 674 </span></span><![endif]>Adam Witney, St. George’s Hospital Medical School,
 675 University of London, UK</p>
 676
 677 <p class=MsoNormal style='margin-left:14.45pt'><span style='mso-fareast-font-family:
 678 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 679
 680 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
 681 "MS Mincho"'>Additional Resources:<o:p></o:p></span></b></p>
 682
 683 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
 684 "MS Mincho"'>Open Bio Database Access website, <a
 685 href="http://obda.open-bio.org/">http://obda.open-bio.org</a><o:p></o:p></span></p>
 686
 687 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
 688 "MS Mincho"'>Open-bio-l mailing list, <a
 689 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>
 690
 691 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
 692 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 693
 694 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
 695 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
 696
 697 <p class=MsoNormal><b><span style='font-size:10.0pt;font-family:Arial;
 698 color:black'>Contents:</span></b><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
 699
 700 <p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
 701 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;
 702 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 703 color:black'>Background &amp; purpose</span><span style='font-family:Arial;
 704 color:black'><o:p></o:p></span></p>
 705
 706 <p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
 707 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;
 708 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 709 color:black'>Assumptions</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
 710
 711 <p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
 712 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;
 713 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 714 color:black'>About the OBDA effort</span><span style='font-family:Arial;
 715 color:black'><o:p></o:p></span></p>
 716
 717 <p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
 718 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;
 719 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 720 color:black'>About BioSQL</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
 721
 722 <p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
 723 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;
 724 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 725 color:black'>About Bioperl-db</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
 726
 727 <p class=MsoNormal style='margin-left:.5in;text-indent:-21.55pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
 728 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;
 729 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 730 color:black'>Step-by-step guide</span><span style='font-family:Arial;
 731 color:black'><o:p></o:p></span></p>
 732
 733 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 734 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 735 color:black'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
 736 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 737 color:black'>Installing MySQL the lazy way (via RPM) and configuring</span><span
 738 style='font-family:Arial;color:black'><o:p></o:p></span></p>
 739
 740 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 741 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 742 color:black'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
 743 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 744 color:black'>Installing perl interfaces to MySQL</span><span style='font-family:
 745 Arial;color:black'><o:p></o:p></span></p>
 746
 747 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 748 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 749 color:black'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
 750 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 751 color:black'>Installing Bundle::BioPerl via CPAN.pm</span><span
 752 style='font-family:Arial;color:black'><o:p></o:p></span></p>
 753
 754 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 755 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 756 color:black'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
 757 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 758 color:black'>Installing BioPerl via CPAN.pm</span><span style='font-family:
 759 Arial;color:black'><o:p></o:p></span></p>
 760
 761 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 762 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 763 color:black'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
 764 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 765 color:black'>Downloading &amp; installing bioperl-db directly from the OBF CVS
 766 repository</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
 767
 768 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 769 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 770 color:black'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
 771 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 772 color:black'>Downloading biosql-schema directly from the OBF CVS repository</span><span
 773 style='font-family:Arial;color:black'><o:p></o:p></span></p>
 774
 775 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 776 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 777 color:black'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
 778 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 779 color:black'>Putting it all together: creating a biosql instance within MySQL</span><span
 780 style='font-family:Arial;color:black'><o:p></o:p></span></p>
 781
 782 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 783 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 784 color:black'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
 785 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 786 color:black'>Loading a test protein dataset: SwissProt release 40</span><span
 787 style='font-family:Arial;color:black'><o:p></o:p></span></p>
 788
 789 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 790 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 791 color:black'>9.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
 792 </span></span><![endif]><span style='font-size:10.0pt;font-family:Arial;
 793 color:black'>Observations</span><span style='font-family:Arial;color:black'><o:p></o:p></span></p>
 794
 795 <p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l14 level1 lfo4;
 796 tab-stops:list 1.0in'><![if !supportLists]><span style='font-family:Arial;
 797 color:black'>10.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]><span
 798 style='font-size:10.0pt;font-family:Arial;color:black'><span
 799 style="mso-spacerun: yes"> </span>Next steps…</span><span style='font-family:
 800 Arial;color:black'><o:p></o:p></span></p>
 801
 802 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:Arial;
 803 color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 804
 805 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:Arial;
 806 color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 807
 808 <p class=MsoNormal style='margin-left:.5in'><span style='font-family:Arial;
 809 color:black'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 810
 811 <div style='border:none;border-bottom:solid windowtext 1.5pt;padding:0in 0in 1.0pt 0in'>
 812
 813 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 814 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
 815
 816 </div>
 817
 818 <p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
 819 font-family:Arial'>Background &amp; purpose<o:p></o:p></span></b></p>
 820
 821 <div style='border:none;border-bottom:solid windowtext 1.5pt;padding:0in 0in 1.0pt 0in'>
 822
 823 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 824 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 825 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 826
 827 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 828 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 829 mso-bidi-font-size:12.0pt;font-family:Arial'>While working on an
 830 informatics/Bio-IT project at Harvard University’s new Bauer Center for
 831 Genomics Research (<a href="http://cgr.harvard.edu/">http://cgr.harvard.edu</a>)
 832 I met some people who were interested in storing sequence data into a
 833 relational database so they could avoid having to parse or index big flat text
 834 files.<o:p></o:p></span></p>
 835
 836 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 837 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 838 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 839
 840 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 841 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 842 mso-bidi-font-size:12.0pt;font-family:Arial'>Knowing that (a) The Open
 843 Bioinformatics Foundation had started work on solution and (b) I am a complete
 844 and utter moron when it comes to relational databases I thought that it would
 845 be a fun experiment to document my efforts at building such a server starting
 846 with a bare-bones RedHat Linux 7.2 server.<o:p></o:p></span></p>
 847
 848 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 849 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 850 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 851
 852 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 853 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 854 mso-bidi-font-size:12.0pt;font-family:Arial'>This document is essentially a
 855 diary of my experiences. It took me roughly a day to get to the point where I
 856 could load Swissprot into a biosql database via Jason Stajich’s
 857 load_seqdatabase.pl script.<o:p></o:p></span></p>
 858
 859 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 860 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 861 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 862
 863 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 864 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 865 mso-bidi-font-size:12.0pt;font-family:Arial'>Another reason I wrote this is
 866 that as a member of the Open Bioinformatics Foundation board of directors I am
 867 well aware that our website(s) are horrific and that our documentation often
 868 lags behind the functionality of our code base. <o:p></o:p></span></p>
 869
 870 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 871 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 872 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 873
 874 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 875 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 876 mso-bidi-font-size:12.0pt;font-family:Arial'>In particular the bioperl website
 877 gives little or no mention to “bioperl-db” and the related obda.open-bio.org
 878 website is totally devoid of any real information.<o:p></o:p></span></p>
 879
 880 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 881 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 882 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 883
 884 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 885 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 886 mso-bidi-font-size:12.0pt;font-family:Arial'>In fact- one practically needs to
 887 be an existing developer on one of our existing projects to even know that this
 888 stuff exists.<o:p></o:p></span></p>
 889
 890 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 891 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 892 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 893
 894 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 895 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 896 mso-bidi-font-size:12.0pt;font-family:Arial'>So- besides being a fun way to
 897 spend a day this is also a way for me to get myself more up to speed with the
 898 OBDA website and related work so that I can eventually help contribute to the
 899 website and project documentation efforts.<o:p></o:p></span></p>
 900
 901 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 902 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 903 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 904
 905 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 906 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 907 mso-bidi-font-size:12.0pt;font-family:Arial'>Comments/corrections/additions/flames
 908 regarding this document are welcome. Just send them along to me at <a
 909 href="mailto:dag@sonsorol.org">dag@sonsorol.org</a><o:p></o:p></span></p>
 910
 911 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 912 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 913 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 914
 915 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 916 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
 917 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 918
 919 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 920 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
 921
 922 </div>
 923
 924 <p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
 925 font-family:Arial'>Assumptions<o:p></o:p></span></b></p>
 926
 927 <p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
 928 font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
 929
 930 <p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
 931 l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
 932 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;
 933 </span></span><![endif]><span style='font-family:Arial'>This document describes
 934 installing a biosql-compliant database on an x86-based server running RedHat
 935 7.2. <o:p></o:p></span></p>
 936
 937 <p class=MsoPlainText><span style='font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 938
 939 <p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
 940 l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
 941 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;
 942 </span></span><![endif]><span style='font-family:Arial'>Different hardware
 943 architectures or OS’s may require different install procedures. Specifically
 944 the server used for this process was a Dell PowerEdge 6450 system with dual
 945 Xeon CPUs, 4GB physical memory and the 2.4.18 linux kernel.<o:p></o:p></span></p>
 946
 947 <p class=MsoPlainText><span style='font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 948
 949 <p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
 950 l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
 951 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;
 952 </span></span><![endif]><span style='font-family:Arial'>This document assumes
 953 the user has root access to the server system for the purposes of installing
 954 software and perl modules.<o:p></o:p></span></p>
 955
 956 <p class=MsoPlainText><span style='font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 957
 958 <p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
 959 l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
 960 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;
 961 </span></span><![endif]><span style='font-family:Arial'>This document assumes
 962 at least basic knowledge of RPM packages and how to install them<o:p></o:p></span></p>
 963
 964 <p class=MsoPlainText><span style='font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
 965
 966 <p class=MsoPlainText style='margin-left:.25in;text-indent:-.25in;mso-list:
 967 l15 level1 lfo5;tab-stops:list .25in'><![if !supportLists]><span
 968 style='font-size:12.0pt;mso-bidi-font-size:10.0pt;font-family:Symbol;
 969 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;
 970 </span></span><![endif]><span style='font-family:Arial'>The process described
 971 here includes downloading code from the internet via anonymous CVS which some
 972 firewalls may not allow. Explaining the use of CVS-over-SSH is not within the
 973 scope of this document.</span><b><span style='font-size:12.0pt;mso-bidi-font-size:
 974 10.0pt;font-family:Arial'> <o:p></o:p></span></b></p>
 975
 976 <p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
 977 font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
 978
 979 <div style='border:none;border-bottom:solid windowtext 1.5pt;padding:0in 0in 1.0pt 0in'>
 980
 981 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
 982 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
 983
 984 </div>
 985
 986 <p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
 987 font-family:Arial'>About the Open Bio Database Access (OBDA) effort<o:p></o:p></span></b></p>
 988
 989 <p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
 990
 991 <p class=MsoBodyText>OBDA is standard developed by the <a
 992 href="http://www.open-bio.org/">Open Bioinformatics Foundation</a> to
 993 standardize the way all of the OBF-affiliated projects access sequence data
 994 resources. This includes local sequence resources (indexed flatfiles), remote
 995 databases (web accessible sequence resources), CORBA servers (implementing the <a
 996 href="http://www.biocorba.org/">BioCORBA/BSANE</a> specification) and
 997 relational databases using the <a
 998 href="http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/?cvsroot=biosql">BioSQL</a>
 999 schema.</p>
1000
1001 <p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1002
1003 <p class=MsoBodyText>The website for the OBDA effort will eventually be <a
1004 href="http://obda.open-bio.org/">http://obda.open-bio.org/</a> . At this time
1005 though the site is only online in template form. The OBF is actively soliciting
1006 people to take over the website and OBDA documentation efforts. </p>
1007
1008 <p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1009
1010 <p class=MsoBodyText>The primary discussion forum for the OBDA effort is the
1011 “open-bio-l” mailing list. The list signup page is located at: <a
1012 href="http://open-bio.org/mailman/listinfo/open-bio-l">http://open-bio.org/mailman/listinfo/open-bio-l</a>
1013 . The list archives are online at <a
1014 href="http://open-bio.org/pipermail/open-bio-l/">http://open-bio.org/pipermail/open-bio-l/</a>.
1015 </p>
1016
1017 <div style='border:none;border-bottom:solid windowtext 1.5pt;padding:0in 0in 1.0pt 0in'>
1018
1019 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
1020 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><span style='font-size:10.0pt;
1021 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1022
1023 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
1024 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1025
1026 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
1027 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1028
1029 </div>
1030
1031 <p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
1032 font-family:Arial'>About BioSQL<o:p></o:p></span></b></p>
1033
1034 <p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1035
1036 <p class=MsoBodyText>The website and primary email discussion list for all
1037 things BioSQL related will be the ones listed above in the OBDA section.</p>
1038
1039 <p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1040
1041 <p class=MsoBodyText>A BioSQL ER diagram in PDF form can be <a
1042 href="http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/biosql-schema/doc/biosql-ERD.pdf?rev=HEAD&amp;cvsroot=biosql">downloaded
1043 directly</a> (PDF) from the OBF anonymous CVS server. A formatted listing of
1044 the tables described in the schema can be <a
1045 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
1046 online directly</a> (HTML) from the same server.</p>
1047
1048 <div style='border:none;border-bottom:solid windowtext 1.5pt;padding:0in 0in 1.0pt 0in'>
1049
1050 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
1051 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1052
1053 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
1054 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1055
1056 </div>
1057
1058 <p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
1059 font-family:Arial'>About BioPerl-db<o:p></o:p></span></b></p>
1060
1061 <p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
1062 font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
1063
1064 <p class=MsoBodyText>The bioperl-db project was started by Ewan Birney with
1065 major work contributed by Elia Stupka and continued support coming from the
1066 bioperl community.<span style="mso-spacerun: yes">  </span>Its purpose is a
1067 standalone sequence database with little external dependencies and tight
1068 integration with the bioperl distribution.<span style="mso-spacerun: yes">
1069 </span>Support for more databases and bindings in java and python by Biojava
1070 and Biopython projects are welcomed and encouraged.<span style="mso-spacerun:
1071 yes">  </span>All questions and comments should be directed to the bioperl list
1072 &lt;<a href="mailto:bioperl-l@bioperl.org">bioperl-l@bioperl.org</a>&gt; and
1073 more information can be found about the related projects at <a
1074 href="http://bio.perl.org">http://bio.perl.org</a> and <a
1075 href="http://www.open-bio.org.">http://www.open-bio.org.</a></p>
1076
1077 <p class=MsoBodyText><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1078
1079 <p class=MsoBodyText>Bioperl-db is a standalone module located within the CVS
1080 code repository operated by the BioPerl Project. Anonymous CVS access and
1081 tarball downloads are available at <a href="http://cvs.bioperl.org/">http://cvs.bioperl.org</a>.
1082 Look in the bioperl repository for the “bioperl-db” module.</p>
1083
1084 <span style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
1085 "Times New Roman";mso-ansi-language:EN-US;mso-fareast-language:EN-US;
1086 mso-bidi-language:AR-SA'><br clear=all style='mso-special-character:line-break;
1087 page-break-before:always'>
1088 </span>
1089
1090 <div style='border:none;border-bottom:solid windowtext 1.5pt;padding:0in 0in 1.0pt 0in'>
1091
1092 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
1093 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1094
1095 <p class=MsoNormal style='border:none;mso-border-bottom-alt:solid windowtext 1.5pt;
1096 padding:0in;mso-padding-alt:0in 0in 1.0pt 0in'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></p>
1097
1098 </div>
1099
1100 <p class=MsoPlainText><b><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
1101 font-family:Arial'>Step by step guide</span></b><b><span style='font-size:12.0pt;
1102 mso-bidi-font-size:10.0pt;font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></b></p>
1103
1104 <p class=MsoPlainText><span style='mso-fareast-font-family:"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1105
1106 <p class=MsoPlainText><span style='mso-fareast-font-family:"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1107
1108 <p class=MsoPlainText><b><span style='font-size:11.0pt;mso-bidi-font-size:10.0pt;
1109 font-family:Arial;mso-fareast-font-family:"MS Mincho"'>Step 1 Install MySQL the
1110 lazy way (via RPM) and configure<o:p></o:p></span></b></p>
1111
1112 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1113 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
1114
1115 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1116 "MS Mincho"'>While logged in as root I installed the following RedHat RPMS:<o:p></o:p></span></p>
1117
1118 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1119 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1120
1121 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1122 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysqlclient9-3.23.22-6<o:p></o:p></span></p>
1123
1124 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1125 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-3.23.41-1<o:p></o:p></span></p>
1126
1127 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1128 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-server-3.23.41-1<o:p></o:p></span></p>
1129
1130 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1131 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-devel-3.23.41-1<o:p></o:p></span></p>
1132
1133 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Arial;
1134 mso-fareast-font-family:"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1135
1136 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1137 "MS Mincho"'>The install was verified by issuing the following command:<o:p></o:p></span></p>
1138
1139 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1140 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1141
1142 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1143 "MS Mincho"'><span style='mso-tab-count:1'>            </span># rpm –qa | grep
1144 mysql<o:p></o:p></span></p>
1145
1146 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1147 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysqlclient9-3.23.22-6<o:p></o:p></span></p>
1148
1149 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1150 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-3.23.41-1<o:p></o:p></span></p>
1151
1152 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1153 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-server-3.23.41-1<o:p></o:p></span></p>
1154
1155 <p class=MsoPlainText style='text-indent:.5in'><span style='font-family:Courier;
1156 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql-devel-3.23.41-1</span><span
1157 style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
1158
1159 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1160 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1161
1162 <p class=MsoBodyText><b><span style='mso-fareast-font-family:"MS Mincho"'>MySQL
1163 version warning:</span></b><span style='mso-fareast-font-family:"MS Mincho"'>
1164 Mark Lambrecht recommends the use of MySQL version 3.23 or later. When trying
1165 to install version 3.22 on an Alpha-based system he received errors relating to
1166 the creation of the “</span><span style='font-family:"Courier New"'>fattribute_to_feature</span>”
1167 table. <span style='mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
1168
1169 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1170 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1171
1172 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1173 "MS Mincho"'>By default the RPM MySQL install puts sample configuration files
1174 into /usr/share/mysql/<o:p></o:p></span></p>
1175
1176 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1177 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1178
1179 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1180 "MS Mincho"'>The base directory that the RPM MySQL install uses is
1181 /var/lib/mysql<o:p></o:p></span></p>
1182
1183 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1184 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1185
1186 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1187 "MS Mincho"'>The global configuration file is kept at /etc/my.cnf<o:p></o:p></span></p>
1188
1189 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1190 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1191
1192 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1193 "MS Mincho"'>It is important to edit the configuration file at /etc/my.conf <b>BEFORE</b>
1194 starting the database for the first time particularly if you want (like me) to
1195 have the MySQL data files live somewhere other than /var/lib/mysql.<o:p></o:p></span></p>
1196
1197 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1198 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1199
1200 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1201 "MS Mincho"'>In my case I wanted to do two main things to the global config
1202 file, (a) change the default location to the much larger /usr/local/ partition
1203 and (b) incorporate some of the config suggestions found in /usr/share/mysql/
1204 specific to large dedicated database servers. <o:p></o:p></span></p>
1205
1206 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1207 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1208
1209 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1210 "MS Mincho"'>WARNING</span></b><span style='font-family:Arial;mso-fareast-font-family:
1211 "MS Mincho"'>; BioSQL databases can be very large. It may be wise to double
1212 check the size of your /var partition before continuing on with a totally
1213 default RPM-based install. The 1GB /var partition present on the Dell 6450
1214 server is far too small. As an example:<span style="mso-spacerun: yes">
1215 </span>The swissprot40 database is 307MB in size. When this dataset was loaded
1216 into MySQL the resulting database files and indices consumed roughly 399MB of
1217 disk space. <o:p></o:p></span></p>
1218
1219 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1220 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1221
1222 <p class=MsoBodyText><b><span style='mso-fareast-font-family:"MS Mincho"'>NOTE</span></b><span
1223 style='mso-fareast-font-family:"MS Mincho"'>: Several BioSQL users have found
1224 that very large sequence records will greatly exceed some of the default
1225 settings that MySQL uses. In particular one may need to set the configuration
1226 value “</span><span style='font-family:"Courier New";mso-fareast-font-family:
1227 "MS Mincho"'>max_allowed_packet</span><span style='mso-fareast-font-family:
1228 "MS Mincho"'>” to a fairly high value (several megabytes at least). If you
1229 encounter any error messages that are similar to: “</span><span
1230 style='font-family:"Courier New"'>DBD::mysql::st execute failed: MySQL server
1231 has gone away…</span>” than it is likely that <span style='font-family:"Courier New"'>max_allowed_packet</span>
1232 needs to be set to a larger value. In an email post to the bioperl-l (<a
1233 href="http://bioperl.org/mailman/listinfo/bioperl-l">http://bioperl.org/mailman/listinfo/bioperl-l</a>)
1234 mailing list Keith Allen covers his experience with this problem in excellent
1235 detail. The full email message can be read at the following URL: <a
1236 href="http://bioperl.org/pipermail/bioperl-l/2002-May/007987.html">http://bioperl.org/pipermail/bioperl-l/2002-May/007987.html</a>
1237 </p>
1238
1239 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1240 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1241
1242 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1243 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1244
1245 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1246 "MS Mincho"'>After revising the value of max_allowed_packet to ‘3M’ due to
1247 feedback from Keith Allen (see above Note) the global configuration file
1248 /etc/my.conf now looks like this:<o:p></o:p></span></p>
1249
1250 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1251 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1252
1253 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1254 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysqld]<o:p></o:p></span></p>
1255
1256 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1257 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>port=3306<o:p></o:p></span></p>
1258
1259 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1260 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>datadir=/usr/local/mysql-database<o:p></o:p></span></p>
1261
1262 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1263 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>socket=/usr/local/mysql-database/mysql.sock<o:p></o:p></span></p>
1264
1265 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1266 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>skip-locking<o:p></o:p></span></p>
1267
1268 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1269 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable= key_buffer=256M<o:p></o:p></span></p>
1270
1271 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1272 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
1273 max_allowed_packet=3M<o:p></o:p></span></p>
1274
1275 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1276 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
1277 table_cache=256<o:p></o:p></span></p>
1278
1279 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1280 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
1281 sort_buffer=1M<o:p></o:p></span></p>
1282
1283 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1284 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
1285 record_buffer=1M<o:p></o:p></span></p>
1286
1287 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1288 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
1289 myisam_sort_buffer_size=64M<o:p></o:p></span></p>
1290
1291 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1292 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
1293 thread_cache=8<o:p></o:p></span></p>
1294
1295 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1296 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
1297 thread_concurrency=4<o:p></o:p></span></p>
1298
1299 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1300 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>server-id= 1<o:p></o:p></span></p>
1301
1302 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1303 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>tmpdir= /tmp/<span
1304 style='mso-tab-count:1'> </span><span style='mso-tab-count:1'>      </span><o:p></o:p></span></p>
1305
1306 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1307 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1308
1309 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1310 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><span
1311 style="mso-spacerun: yes">     </span><o:p></o:p></span></p>
1312
1313 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1314 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysql.server]<o:p></o:p></span></p>
1315
1316 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1317 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>user=mysql<o:p></o:p></span></p>
1318
1319 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1320 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>basedir=/usr/lib<o:p></o:p></span></p>
1321
1322 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1323 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1324
1325 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1326 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[safe_mysqld]<o:p></o:p></span></p>
1327
1328 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1329 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>err-log=/var/log/mysqld.log<o:p></o:p></span></p>
1330
1331 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1332 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>pid-file=/var/run/mysqld/mysqld.pid<o:p></o:p></span></p>
1333
1334 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1335 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1336
1337 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1338 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1339
1340 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1341 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysqldump]<o:p></o:p></span></p>
1342
1343 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1344 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>quick<o:p></o:p></span></p>
1345
1346 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1347 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable=
1348 max_allowed_packet=16M<o:p></o:p></span></p>
1349
1350 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1351 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1352
1353 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1354 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysql]<o:p></o:p></span></p>
1355
1356 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1357 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>no-auto-rehash<o:p></o:p></span></p>
1358
1359 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1360 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>safe-updates<o:p></o:p></span></p>
1361
1362 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1363 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1364
1365 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1366 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[isamchk]<o:p></o:p></span></p>
1367
1368 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1369 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
1370 style='mso-tab-count:1'>      </span>= key_buffer=128M<o:p></o:p></span></p>
1371
1372 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1373 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
1374 style='mso-tab-count:1'>      </span>= sort_buffer=128M<o:p></o:p></span></p>
1375
1376 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1377 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
1378 style='mso-tab-count:1'>      </span>= read_buffer=2M<o:p></o:p></span></p>
1379
1380 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1381 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
1382 style='mso-tab-count:1'>      </span>= write_buffer=2M<o:p></o:p></span></p>
1383
1384 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1385 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1386
1387 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1388 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[myisamchk]<o:p></o:p></span></p>
1389
1390 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1391 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
1392 style='mso-tab-count:1'>      </span>= key_buffer=128M<o:p></o:p></span></p>
1393
1394 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1395 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
1396 style='mso-tab-count:1'>      </span>= sort_buffer=128M<o:p></o:p></span></p>
1397
1398 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1399 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
1400 style='mso-tab-count:1'>      </span>= read_buffer=2M<o:p></o:p></span></p>
1401
1402 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1403 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>set-variable<span
1404 style='mso-tab-count:1'>      </span>= write_buffer=2M<o:p></o:p></span></p>
1405
1406 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1407 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1408
1409 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1410 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[mysqlhotcopy]<o:p></o:p></span></p>
1411
1412 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1413 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>interactive-timeout<o:p></o:p></span></p>
1414
1415 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1416 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1417
1418 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1419 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1420
1421 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1422 "MS Mincho"'>Just in case I missed anything I decided to add a symbolic link
1423 back to /var/lib/mysql – this turns out to be important because my
1424 configuration file still has “basedir=/var/lib” which is a total mistake.<o:p></o:p></span></p>
1425
1426 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1427 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1428
1429 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1430 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1431
1432 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1433 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># cd /var/lib<o:p></o:p></span></p>
1434
1435 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1436 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># ln -s
1437 /usr/local/mysql-database/ ./mysql</span><span style='font-family:Arial;
1438 mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
1439
1440 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1441 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1442
1443 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1444 "MS Mincho"'>Now we can start the MySQL datbase...<o:p></o:p></span></p>
1445
1446 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1447 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1448
1449 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1450 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>/etc/rc.d/init.d/mysql
1451 start<o:p></o:p></span></p>
1452
1453 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1454 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1455
1456 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1457 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1458
1459 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1460 "MS Mincho"'>Important!</span></b><span style='font-family:Arial;mso-fareast-font-family:
1461 "MS Mincho"'> Protect your database by setting a root MySQL password:<o:p></o:p></span></p>
1462
1463 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1464 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1465
1466 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1467 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># mysqladmin -u
1468 root password 'xxxxxxx'<o:p></o:p></span></p>
1469
1470 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1471 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1472
1473 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1474 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1475
1476 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1477 "MS Mincho"'>After installing, configuring, starting and enabling a root
1478 password it should be possible to logoff as root and re-login as a ‘normal’
1479 system user.<span style="mso-spacerun: yes">  </span><o:p></o:p></span></p>
1480
1481 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1482 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1483
1484 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1485 "MS Mincho"'>To test this I made the switch from root user to my normal 'dag'
1486 user account and confirmed that I can login as root to the mysql instance:<o:p></o:p></span></p>
1487
1488 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1489 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1490
1491 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1492 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3
1493 scripts]$ mysql -u root -p<o:p></o:p></span></p>
1494
1495 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1496 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Enter password:
1497 <o:p></o:p></span></p>
1498
1499 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1500 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Welcome to the
1501 MySQL monitor.<span style="mso-spacerun: yes">  </span>Commands end with ; or
1502 \g.<o:p></o:p></span></p>
1503
1504 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1505 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Your MySQL
1506 connection id is 8 to server version: 3.23.41-log<o:p></o:p></span></p>
1507
1508 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1509 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1510
1511 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1512 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Type 'help;' or
1513 '\h' for help. Type '\c' to clear the buffer.<o:p></o:p></span></p>
1514
1515 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1516 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1517
1518 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1519 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt; exit<o:p></o:p></span></p>
1520
1521 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
1522 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Bye</span><span
1523 style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
1524
1525 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1526 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1527
1528 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1529 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1530
1531 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1532 "MS Mincho"'>Success! We now have a working MySQL instance.<o:p></o:p></span></p>
1533
1534 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1535 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1536
1537 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1538 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1539
1540 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1541 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1542
1543 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1544 "MS Mincho"'>Step 2 Install the perl interfaces to MySQL <o:p></o:p></span></b></p>
1545
1546 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1547 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
1548
1549 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1550 "MS Mincho"'>In future steps we are going to use perl to help us talk to the
1551 MySQL database. In order to do this we need some additional perl modules
1552 installed. We need:<o:p></o:p></span></p>
1553
1554 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1555 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1556
1557 <p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l13 level1 lfo7;
1558 tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
1559 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
1560 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1561 </span></span><![endif]><span style='font-family:Arial;mso-fareast-font-family:
1562 "MS Mincho"'>DBI:: - The perl generic database interface<o:p></o:p></span></p>
1563
1564 <p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l13 level1 lfo7;
1565 tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
1566 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
1567 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1568 </span></span><![endif]><span style='font-family:Arial;mso-fareast-font-family:
1569 "MS Mincho"'>DBD::MySQL – The perl MySQL database driver module<o:p></o:p></span></p>
1570
1571 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1572 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1573
1574 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1575 "MS Mincho"'>Given the lazy RPM install we previously did with the MySQL
1576 database it makes sense to install the preconfigured RPM versions of these
1577 modules that RedHat provides. The specific modules installed were:<o:p></o:p></span></p>
1578
1579 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1580 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1581
1582 <p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l2 level1 lfo8;
1583 tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
1584 mso-fareast-font-family:"MS Mincho"'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1585 </span></span><![endif]><span style='mso-fareast-font-family:"MS Mincho"'>perl-DBI-1.18-1.i386.rpm<o:p></o:p></span></p>
1586
1587 <p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l2 level1 lfo8;
1588 tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
1589 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
1590 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1591 </span></span><![endif]><span style='mso-fareast-font-family:"MS Mincho"'>perl-DBD-MySQL-1.2216-4.i386.rpm</span><span
1592 style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
1593
1594 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1595 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
1596
1597 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1598 "MS Mincho"'>Installation of these modules went smoothly. This was a welcome
1599 relief as given the still traumatic memories of spending days trying to get
1600 DBD::Oracle to install and work cleanly on Compaq Alphaservers and HP-UX
1601 machines.<o:p></o:p></span></p>
1602
1603 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1604 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1605
1606 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1607 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1608
1609 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1610 "MS Mincho"'>Step 3 Install Bundle::BioPerl via CPAN.pm <o:p></o:p></span></b></p>
1611
1612 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1613 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1614
1615 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1616 "MS Mincho"'>Note: Skip this step if BioPerl is already on your system.<o:p></o:p></span></p>
1617
1618 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1619 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1620
1621 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1622 "MS Mincho"'>Some of the perl scripts needed to help load the database with
1623 sequence data we will be using in future steps are themselves dependent on the
1624 BioPerl distribution (<a href="http://bioperl.org/">http://bioperl.org/</a>)<o:p></o:p></span></p>
1625
1626 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1627 "MS Mincho"'>for critical functions such as sequence parsing etc. <o:p></o:p></span></p>
1628
1629 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1630 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1631
1632 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1633 "MS Mincho"'>The BioPerl distribution itself has its own dependencies on Perl
1634 modules and other programs that may or may not be found by default on a system.
1635 These external dependencies are not required but if installed they will give
1636 the BioPerl distribution additional functionality and features.<o:p></o:p></span></p>
1637
1638 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1639 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1640
1641 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1642 "MS Mincho"'>The BioPerl people have created a special CPAN package called
1643 “Bundle::BioPerl” that can assist with downloading and automatically installing
1644 all of the CPAN resident modules that BioPerl likes to use. By itself
1645 Bundle::BioPerl is next to useless but when used with CPAN.pm it becomes very
1646 convenient.<o:p></o:p></span></p>
1647
1648 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1649 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1650
1651 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1652 "MS Mincho"'>For the purposes of building a BioSQL database we don’t really
1653 care about all of the various external BioPerl dependencies enough to give
1654 special attention to the issue. The proper ‘lazy’ way then is just to fire up
1655 CPAN.pm and let it do all of the work. <o:p></o:p></span></p>
1656
1657 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1658 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1659
1660 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1661 "MS Mincho"'>People unfamiliar with the CPAN.pm module can read its
1662 documentation by issuing the system command ‘perldoc CPAN’.<o:p></o:p></span></p>
1663
1664 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1665 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1666
1667 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1668 "MS Mincho"'>To fire up the CPAN module in shell mode issue the following
1669 command as root:<o:p></o:p></span></p>
1670
1671 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1672 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1673
1674 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
1675 "MS Mincho";mso-bidi-font-family:Arial'># perl –MCPAN –e shell<o:p></o:p></span></p>
1676
1677 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1678 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1679
1680 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1681 "MS Mincho"'>If this is the first time that CPAN.pm has been used there will be
1682 an initial setup and configuration phase where CPAN configures itself to the
1683 local network environment. The user is also prompted to select from a list of
1684 available mirror sites.<o:p></o:p></span></p>
1685
1686 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1687 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1688
1689 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1690 "MS Mincho"'>To install Bundle::BioPerl while in the CPAN shell environment:<o:p></o:p></span></p>
1691
1692 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1693 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1694
1695 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
1696 "MS Mincho";mso-bidi-font-family:Arial'>cpan&gt; install Bundle::BioPerl<o:p></o:p></span></p>
1697
1698 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1699 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1700
1701 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1702 "MS Mincho"'>That’s about it. The process may take some time depending on the
1703 speed of the server and available network connection.<o:p></o:p></span></p>
1704
1705 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1706 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1707
1708 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1709 "MS Mincho"'>NOTE:<o:p></o:p></span></b></p>
1710
1711 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1712 "MS Mincho"'>When attempting this for the first time the installation of
1713 Bundle::BioPerl completely failed because one of the perl modules<span
1714 style="mso-spacerun: yes">  </span>implementing SOAP functionality listed in
1715 the Bundle is apparently only distributed as a .ZIP archive rather than the
1716 more traditional tar.gz format.<span style="mso-spacerun: yes">  </span>The
1717 install process failed because CPAN.pm had not been configured to know where a
1718 suitable ‘unzip’ utility could be found. The solution was to exit from the CPAN
1719 shell, manually install the unzip rpm and then restart the CPAN shell.<span
1720 style="mso-spacerun: yes">  </span>Within the restarted CPAN shell environment
1721 the following command will make CPAN aware of the newly installed unzip
1722 utility:<o:p></o:p></span></p>
1723
1724 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1725 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1726
1727 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
1728 "MS Mincho";mso-bidi-font-family:Arial'>cpan&gt; o conf unzip<span
1729 style="mso-spacerun: yes">  </span>/usr/bin/unzip<o:p></o:p></span></p>
1730
1731 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
1732 "MS Mincho";mso-bidi-font-family:Arial'>cpan&gt; install Bundle::BioPerl</span><span
1733 style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
1734
1735 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1736 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1737
1738 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1739 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1740
1741 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1742 "MS Mincho"'>Step 4 Install BioPerl via CPAN.pm<o:p></o:p></span></b></p>
1743
1744 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1745 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1746
1747 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1748 "MS Mincho"'>Note: Skip this step if BioPerl is already on your system.<o:p></o:p></span></p>
1749
1750 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1751 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1752
1753 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1754 "MS Mincho"'>Now that the various helper modules and external dependencies of
1755 BioPerl have been installed it should now be possible to use the same CPAN.pm
1756 shortcut to automatically download and install the full BioPerl distribution.<o:p></o:p></span></p>
1757
1758 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1759 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1760
1761 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1762 "MS Mincho"'>Asking CPAN to install the ‘Bio::Seq’ module is enough to get it
1763 to download and install the full distribution:<o:p></o:p></span></p>
1764
1765 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1766 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1767
1768 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
1769 "MS Mincho";mso-bidi-font-family:Arial'>cpan&gt; install Bio::Seq<o:p></o:p></span></p>
1770
1771 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1772 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1773
1774 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1775 "MS Mincho"'>BioPerl is a very large distribution (possibly the single largest
1776 collection of related perl modules in the entire CPAN repository) – you may
1777 wish to download and manually install the full BioPerl distribution directly
1778 from <a href="http://bioperl.org/">http://bioperl.org/</a>.<o:p></o:p></span></p>
1779
1780 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1781 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1782
1783 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1784 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1785
1786 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1787 "MS Mincho"'>Step 5 Download and install bioperl-db directly from the OBF CVS
1788 repository<o:p></o:p></span></b></p>
1789
1790 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1791 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
1792
1793 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1794 "MS Mincho"'>Getting the latest and greatest version of the bioperl-db
1795 distribution involves downloading straight from the public source code server
1796 located at <a href="http://cvs.open-bio.org/">http://cvs.open-bio.org/</a><o:p></o:p></span></p>
1797
1798 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1799 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1800
1801 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1802 "MS Mincho"'>Instructions for downloading code via anonymous CVS are available
1803 on the cvs.open-bio.org website. Your firewall or local network configuration
1804 may not allow anonymous CVS connections to occur. See below for a workaround:<o:p></o:p></span></p>
1805
1806 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1807 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1808
1809 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1810 "MS Mincho"'>How to use the web and avoid anonymous CVS altogether:<o:p></o:p></span></b></p>
1811
1812 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1813 "MS Mincho"'>If a firewall or network gateway device blocks CVS connection
1814 attempts it should be possible to download code and full distributions directly
1815 from the <a href="http://cvs.open-bio.org/">http://cvs.open-bio.org/</a>
1816 website. The CGI gateway to the CVS repository has a nice feature entitled
1817 “Download Tarball”. When clicked the server will generate a fresh code checkout
1818 and will send it to your browser as a .tar.gz archive file which can be saved
1819 locally to disk. The files may all be named “cvs_root.tar.gz” so beware of
1820 potential file overwrite issues when downloading multiple files or codebases.<o:p></o:p></span></p>
1821
1822 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1823 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1824
1825 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1826 "MS Mincho"'>How to checkout via anonymous:<o:p></o:p></span></b></p>
1827
1828 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1829 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1830
1831 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1832 "MS Mincho"'>The anonymous CVS password is ‘cvs’<o:p></o:p></span></p>
1833
1834 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1835 "MS Mincho"'>Full instructions are available at <a
1836 href="http://cvs.open-bio.org/">http://cvs.open-bio.org</a><o:p></o:p></span></p>
1837
1838 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1839 "MS Mincho"'>Example session with output:<o:p></o:p></span></p>
1840
1841 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1842 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1843
1844 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1845 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1846 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># cvs
1847 -d:pserver:cvs@cvs.open-bio.org:/home/repository/bioperl login<o:p></o:p></span></p>
1848
1849 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1850 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1851 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>CVS password: <o:p></o:p></span></p>
1852
1853 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1854 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1855 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># <o:p></o:p></span></p>
1856
1857 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1858 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1859 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'># cvs
1860 -d:pserver:cvs@cvs.open-bio.org:/home/repository/bioperl co bioperl-db <o:p></o:p></span></p>
1861
1862 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1863 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1864 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
1865 Updating bioperl-db<o:p></o:p></span></p>
1866
1867 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1868 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1869 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
1870 bioperl-db/BUGS<o:p></o:p></span></p>
1871
1872 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1873 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1874 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
1875 bioperl-db/Changes<o:p></o:p></span></p>
1876
1877 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1878 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1879 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
1880 bioperl-db/LICENSE<o:p></o:p></span></p>
1881
1882 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1883 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1884 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
1885 bioperl-db/MANIFEST<o:p></o:p></span></p>
1886
1887 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1888 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1889 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
1890 bioperl-db/MANIFEST.SKIP<o:p></o:p></span></p>
1891
1892 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1893 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1894 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
1895 bioperl-db/Makefile.PL<o:p></o:p></span></p>
1896
1897 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1898 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1899 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
1900 bioperl-db/README<o:p></o:p></span></p>
1901
1902 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1903 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1904 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
1905 Updating bioperl-db/Bio<o:p></o:p></span></p>
1906
1907 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1908 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1909 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
1910 Updating bioperl-db/Bio/DB<o:p></o:p></span></p>
1911
1912 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1913 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1914 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
1915 bioperl-db/Bio/DB/Annotation.pm<o:p></o:p></span></p>
1916
1917 <p class=MsoPlainText style='margin-top:0in;margin-right:-.5in;margin-bottom:
1918 0in;margin-left:.5in;margin-bottom:.0001pt'><span style='font-family:Courier;
1919 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1920
1921 <p class=MsoPlainText style='margin-left:.5in'><b><i><span style='font-family:
1922 Courier;mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>&lt;FULL
1923 OUTPUT CUT FOR BREVITY&gt;<o:p></o:p></span></i></b></p>
1924
1925 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1926 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1927
1928 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1929 "MS Mincho"'>Installing bioperl-db<o:p></o:p></span></b></p>
1930
1931 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1932 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1933
1934 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1935 "MS Mincho"'>The bioperl-db distribution is in the standard CPAN-style format
1936 so installation is similar to any other external perl module:<o:p></o:p></span></p>
1937
1938 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1939 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1940
1941 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1942 "MS Mincho"'>Once the distribution is uncompressed and unpacked there are only
1943 three commands necessary:<o:p></o:p></span></p>
1944
1945 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1946 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1947
1948 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
1949 "MS Mincho";mso-bidi-font-family:Arial'># perl Makefile.PL<o:p></o:p></span></p>
1950
1951 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
1952 "MS Mincho";mso-bidi-font-family:Arial'># make<o:p></o:p></span></p>
1953
1954 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
1955 "MS Mincho";mso-bidi-font-family:Arial'># make install</span><span
1956 style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
1957
1958 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1959 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1960
1961 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1962 "MS Mincho"'>NOTE: This install will fail if the DBD:: and DBI::Mysql modules
1963 cannot be found.<o:p></o:p></span></p>
1964
1965 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1966 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1967
1968 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1969 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1970
1971 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
1972 "MS Mincho"'>Step 6 Download and install biosql-schema directly from the OBF
1973 CVS repository<o:p></o:p></span></b></p>
1974
1975 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1976 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1977
1978 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1979 "MS Mincho"'>Reference the above discussion on anonymous CVS, firewalls and the
1980 ability to download tar archives directly from the <a
1981 href="http://cvs.open-bio.org/">http://cvs.open-bio.org/</a> website.<o:p></o:p></span></p>
1982
1983 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1984 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1985
1986 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1987 "MS Mincho"'>The OBDA schema for BioSQL databases lives in its own CVS code
1988 repository because its use spans many of the Open Bio projects and coding
1989 efforts.<o:p></o:p></span></p>
1990
1991 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1992 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
1993
1994 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
1995 "MS Mincho"'>The repository is called “biosql”, the module is called
1996 “biosql-schema”. The CVS root for the respository can be found at
1997 “/home/repository/biosql”.<o:p></o:p></span></p>
1998
1999 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2000 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2001
2002 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2003 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2004
2005 <p class=MsoPlainText><b><span style='font-family:Arial;mso-fareast-font-family:
2006 "MS Mincho"'>Example anonymous CVS checkout session:<o:p></o:p></span></b></p>
2007
2008 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2009 "MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2010
2011 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2012 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[root@pe3]# cvs
2013 -d :pserver:cvs@cvs.open-bio.org:/home/repository/biosql login<o:p></o:p></span></p>
2014
2015 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2016 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Logging in to
2017 :pserver:cvs@cvs.open-bio.org:2401/home/repository/biosql<o:p></o:p></span></p>
2018
2019 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2020 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>CVS password: <o:p></o:p></span></p>
2021
2022 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2023 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[root@pe3
2024 biosql]# cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biosql checkout
2025 biosql-schema<o:p></o:p></span></p>
2026
2027 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2028 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
2029 Updating biosql-schema<o:p></o:p></span></p>
2030
2031 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2032 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
2033 Updating biosql-schema/doc<o:p></o:p></span></p>
2034
2035 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2036 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2037 biosql-schema/doc/README<o:p></o:p></span></p>
2038
2039 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2040 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2041 biosql-schema/doc/biosql-ERD.pdf<o:p></o:p></span></p>
2042
2043 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2044 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2045 biosql-schema/doc/biosql.html<o:p></o:p></span></p>
2046
2047 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2048 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
2049 Updating biosql-schema/scripts<o:p></o:p></span></p>
2050
2051 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2052 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2053 biosql-schema/scripts/create_mysql_db.pl<o:p></o:p></span></p>
2054
2055 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2056 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2057 biosql-schema/scripts/transform_sql.pl<o:p></o:p></span></p>
2058
2059 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2060 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
2061 Updating biosql-schema/sql<o:p></o:p></span></p>
2062
2063 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2064 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2065 biosql-schema/sql/README<o:p></o:p></span></p>
2066
2067 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2068 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2069 biosql-schema/sql/biopipelinedb-mysql.sql<o:p></o:p></span></p>
2070
2071 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2072 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2073 biosql-schema/sql/biosql-accelerators-pg.sql<o:p></o:p></span></p>
2074
2075 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2076 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2077 biosql-schema/sql/biosqldb-mysql.sql<o:p></o:p></span></p>
2078
2079 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2080 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2081 biosql-schema/sql/biosqldb-pg.sql<o:p></o:p></span></p>
2082
2083 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2084 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2085 biosql-schema/sql/biosqldb-views-pg.sql<o:p></o:p></span></p>
2086
2087 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2088 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2089 biosql-schema/sql/makefile<o:p></o:p></span></p>
2090
2091 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2092 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server: Updating
2093 biosql-schema/sql/ontology<o:p></o:p></span></p>
2094
2095 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2096 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2097 biosql-schema/sql/ontology/biosqldb-ontology-mysql.sql<o:p></o:p></span></p>
2098
2099 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2100 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>U
2101 biosql-schema/sql/ontology/biosqldb-ontology-pg.sql<o:p></o:p></span></p>
2102
2103 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2104 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>cvs server:
2105 Updating biosql-schema/t<o:p></o:p></span></p>
2106
2107 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2108 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[root@pe3
2109 biosql]# <o:p></o:p></span></p>
2110
2111 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2112 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2113
2114 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2115 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2116
2117 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2118 "MS Mincho"'>The files found in the biosql-schema do not need to be installed
2119 or otherwise processed. We are going to use the scripts and documents found in
2120 this module directly.<o:p></o:p></span></p>
2121
2122 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2123 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2124
2125 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2126 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2127
2128 <p class=MsoPlainText><b><span style='font-size:11.0pt;mso-bidi-font-size:10.0pt;
2129 font-family:Arial;mso-fareast-font-family:"MS Mincho"'>Step 7 – Putting it all
2130 together: creating a biosql instance within MySQL<o:p></o:p></span></b></p>
2131
2132 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2133 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2134
2135 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2136 "MS Mincho"'>Inside the biosql-schema/scripts folder there is a perl script called
2137 &quot;create_mysqldb.pl&quot;. This script is just a helper script that
2138 automates the process of connecting to the datbase and issuing<span
2139 style="mso-spacerun: yes">  </span>the SQL statements that cause the proper
2140 database tables to be created. The script reads the actual SQL commands from
2141 the file found in biosql-schema/sql/biosql-mysqldb.sql<o:p></o:p></span></p>
2142
2143 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2144 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2145
2146 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2147 "MS Mincho"'>After looking at how simple this script is I felt the need to
2148 bypass it completely and just perform the steps manually for curiosity sake.<o:p></o:p></span></p>
2149
2150 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2151 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2152
2153 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2154 "MS Mincho"'>Here is the output from creating an initial database named ‘biosql’:<o:p></o:p></span></p>
2155
2156 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2157 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2158
2159 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2160 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2161
2162 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2163 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3]$
2164 mysql -u root -p<o:p></o:p></span></p>
2165
2166 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2167 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Enter password:
2168 <o:p></o:p></span></p>
2169
2170 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2171 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Welcome to the
2172 MySQL monitor.<span style="mso-spacerun: yes">  </span>Commands end with ; or
2173 \g.<o:p></o:p></span></p>
2174
2175 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2176 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Your MySQL
2177 connection id is 9 to server version: 3.23.41-log<o:p></o:p></span></p>
2178
2179 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2180 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2181
2182 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2183 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Type 'help;' or
2184 '\h' for help. Type '\c' to clear the buffer.<o:p></o:p></span></p>
2185
2186 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2187 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2188
2189 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2190 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt;
2191 create database biosql;<o:p></o:p></span></p>
2192
2193 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2194 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2195 affected (0.00 sec)<o:p></o:p></span></p>
2196
2197 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2198 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt; exit<o:p></o:p></span></p>
2199
2200 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2201 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Bye</span><span
2202 style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
2203
2204 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2205 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2206
2207 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2208 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2209
2210 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2211 "MS Mincho"'>Now that the database is created we need to connect to the
2212 database and issue the SQL commands contained in
2213 biosql-scheme/sql/biosqldb-mysql.sql file:<o:p></o:p></span></p>
2214
2215 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2216 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2217
2218 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2219 "MS Mincho"'>Within the mysql client interface we can use the command
2220 &quot;source&quot; to read in SQL statements from a file.<o:p></o:p></span></p>
2221
2222 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2223 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2224
2225 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2226 "MS Mincho"'>Here is the output from that process:<o:p></o:p></span></p>
2227
2228 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2229 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2230
2231 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2232 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3]$
2233 mysql -u root -p biosql<o:p></o:p></span></p>
2234
2235 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2236 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Enter password:
2237 <o:p></o:p></span></p>
2238
2239 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2240 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Welcome to the
2241 MySQL monitor.<span style="mso-spacerun: yes">  </span>Commands end with ; or
2242 \g.<o:p></o:p></span></p>
2243
2244 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2245 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Your MySQL
2246 connection id is 11 to server version: 3.23.41-log<o:p></o:p></span></p>
2247
2248 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2249 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2250
2251 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2252 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Type 'help;' or
2253 '\h' for help. Type '\c' to clear the buffer.<o:p></o:p></span></p>
2254
2255 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2256 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2257
2258 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2259 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt;
2260 source sql/biosqldb-mysql.sql<o:p></o:p></span></p>
2261
2262 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2263 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2264
2265 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2266 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 0
2267 rows affected (0.00 sec)<o:p></o:p></span></p>
2268
2269 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2270 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Records: 0<span
2271 style="mso-spacerun: yes">  </span>Duplicates: 0<span style="mso-spacerun:
2272 yes">  </span>Warnings: <o:p></o:p></span></p>
2273
2274 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2275 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2276
2277 <p class=MsoPlainText style='margin-left:1.0in'><i><span style='font-family:
2278 Arial;mso-fareast-font-family:"MS Mincho"'>&lt;snip - lots of boring output cut
2279 here...&gt; <o:p></o:p></span></i></p>
2280
2281 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2282 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2283
2284 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2285 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2286 affected (0.00 sec)<o:p></o:p></span></p>
2287
2288 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2289 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2290
2291 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2292 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2293 affected (0.00 sec)<o:p></o:p></span></p>
2294
2295 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2296 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2297
2298 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2299 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2300 affected (0.00 sec)<o:p></o:p></span></p>
2301
2302 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2303 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2304
2305 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2306 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2307 affected (0.00 sec)<o:p></o:p></span></p>
2308
2309 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2310 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2311
2312 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2313 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2314 affected (0.00 sec)<o:p></o:p></span></p>
2315
2316 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2317 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2318
2319 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2320 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2321 affected (0.00 sec)<o:p></o:p></span></p>
2322
2323 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2324 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2325
2326 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2327 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2328 affected (0.00 sec)<o:p></o:p></span></p>
2329
2330 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2331 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2332
2333 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2334 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2335 affected (0.00 sec)<o:p></o:p></span></p>
2336
2337 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2338 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2339
2340 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2341 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 1 row
2342 affected (0.00 sec)<o:p></o:p></span></p>
2343
2344 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2345 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2346
2347 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2348 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Query OK, 0
2349 rows affected (0.00 sec)<o:p></o:p></span></p>
2350
2351 <p class=MsoPlainText style='margin-left:1.0in'><span style='font-family:Courier;
2352 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt;<o:p></o:p></span></p>
2353
2354 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2355 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2356
2357 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2358 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2359
2360 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2361 "MS Mincho"'>Now that we are still connected to datbase ‘biosql’ let us see
2362 what we created by issuing the command &quot;show tables;&quot;<o:p></o:p></span></p>
2363
2364 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2365 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2366
2367 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2368 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2369
2370 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2371 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt; show
2372 tables;<o:p></o:p></span></p>
2373
2374 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2375 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>+----------------------------+<o:p></o:p></span></p>
2376
2377 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2378 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2379 Tables_in_biosql<span style="mso-spacerun: yes">           </span>|<o:p></o:p></span></p>
2380
2381 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2382 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>+----------------------------+<o:p></o:p></span></p>
2383
2384 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2385 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2386 biodatabase<span style="mso-spacerun: yes">                </span>|<o:p></o:p></span></p>
2387
2388 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2389 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| bioentry<span
2390 style="mso-spacerun: yes">                   </span>|<o:p></o:p></span></p>
2391
2392 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2393 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2394 bioentry_direct_links<span style="mso-spacerun: yes">      </span>|<o:p></o:p></span></p>
2395
2396 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2397 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2398 bioentry_qualifier_value<span style="mso-spacerun: yes">   </span>|<o:p></o:p></span></p>
2399
2400 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2401 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2402 bioentry_reference<span style="mso-spacerun: yes">         </span>|<o:p></o:p></span></p>
2403
2404 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2405 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| bioentry_taxa<span
2406 style="mso-spacerun: yes">              </span>|<o:p></o:p></span></p>
2407
2408 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2409 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2410 biosequence<span style="mso-spacerun: yes">                </span>|<o:p></o:p></span></p>
2411
2412 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2413 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2414 cache_corba_support<span style="mso-spacerun: yes">        </span>|<o:p></o:p></span></p>
2415
2416 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2417 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| comment<span
2418 style="mso-spacerun: yes">                    </span>|<o:p></o:p></span></p>
2419
2420 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2421 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| dbxref<span
2422 style="mso-spacerun: yes">                     </span>|<o:p></o:p></span></p>
2423
2424 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2425 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2426 dbxref_qualifier_value<span style="mso-spacerun: yes">     </span>|<o:p></o:p></span></p>
2427
2428 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2429 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2430 location_qualifier_value<span style="mso-spacerun: yes">   </span>|<o:p></o:p></span></p>
2431
2432 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2433 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2434 ontology_term<span style="mso-spacerun: yes">              </span>|<o:p></o:p></span></p>
2435
2436 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2437 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2438 reference<span style="mso-spacerun: yes">            </span><span
2439 style="mso-spacerun: yes">      </span>|<o:p></o:p></span></p>
2440
2441 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2442 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2443 remote_seqfeature_name<span style="mso-spacerun: yes">     </span>|<o:p></o:p></span></p>
2444
2445 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2446 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2447 seqfeature<span style="mso-spacerun: yes">                 </span>|<o:p></o:p></span></p>
2448
2449 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2450 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2451 seqfeature_location<span style="mso-spacerun: yes">        </span>|<o:p></o:p></span></p>
2452
2453 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2454 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2455 seqfeature_qualifier_value |<o:p></o:p></span></p>
2456
2457 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2458 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2459 seqfeature_relationship<span style="mso-spacerun: yes">    </span>|<o:p></o:p></span></p>
2460
2461 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2462 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>|
2463 seqfeature_source<span style="mso-spacerun: yes">          </span>|<o:p></o:p></span></p>
2464
2465 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2466 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>| taxa<span
2467 style="mso-spacerun: yes">                       </span>|<o:p></o:p></span></p>
2468
2469 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2470 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>+----------------------------+<o:p></o:p></span></p>
2471
2472 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2473 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>21 rows in set
2474 (0.00 sec)<o:p></o:p></span></p>
2475
2476 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2477 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2478
2479 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2480 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>mysql&gt; exit<o:p></o:p></span></p>
2481
2482 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2483 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Bye</span><span
2484 style='font-family:Arial;mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
2485
2486 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2487 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2488
2489 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2490 "MS Mincho"'>Excellent! We have just created a BioSQL database within MySQL !<o:p></o:p></span></p>
2491
2492 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2493 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2494
2495 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2496 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2497
2498 <p class=MsoPlainText><b><span style='font-size:11.0pt;mso-bidi-font-size:10.0pt;
2499 font-family:Arial;mso-fareast-font-family:"MS Mincho"'>Step 8 - Loading a test
2500 protein dataset (Swissprot) into the database<o:p></o:p></span></b></p>
2501
2502 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2503 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2504
2505 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2506 "MS Mincho"'>Before tackling all of GenBank, a smaller dataset is probably a
2507 good idea as a test case to learn about the process of loading up the new
2508 biosql database with sequence data.<o:p></o:p></span></p>
2509
2510 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2511 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2512
2513 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2514 "MS Mincho"'>The dataset selected was SwissProt downloaded from <a
2515 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>
2516
2517 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2518 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2519
2520 <p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l9 level1 lfo11;
2521 tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
2522 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
2523 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2524 </span></span><![endif]><span style='font-family:Arial;mso-fareast-font-family:
2525 "MS Mincho"'>Total uncompressed size: 307MB<o:p></o:p></span></p>
2526
2527 <p class=MsoPlainText style='margin-left:.5in;text-indent:-.25in;mso-list:l9 level1 lfo11;
2528 tab-stops:list .5in'><![if !supportLists]><span style='font-family:Symbol;
2529 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>·<span
2530 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2531 </span></span><![endif]><span style='font-family:Arial;mso-fareast-font-family:
2532 "MS Mincho"'>Apparent number of sequence entries: 101,707 <o:p></o:p></span></p>
2533
2534 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2535 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2536
2537 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2538 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2539
2540 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2541 "MS Mincho"'>The database loader script used was the<span style="mso-spacerun:
2542 yes">  </span>&quot;load_seqdatabase.pl&quot; script from the /scripts/ folder
2543 inside the bioperl-db distribution.<o:p></o:p></span></p>
2544
2545 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2546 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2547
2548 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2549 "MS Mincho"'>The script is pretty basic. There are some internal configuration
2550 settings inside the script that can be manually configured. Each of the
2551 configurable options can also be overridden by command line arguments.<o:p></o:p></span></p>
2552
2553 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2554 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2555
2556 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2557 "MS Mincho"'>The basic syntax for the load_seqdatabase.pl script is as follows:<o:p></o:p></span></p>
2558
2559 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2560 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2561
2562 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2563 "MS Mincho";mso-bidi-font-family:Arial'>./load_seqdatabase.pl &lt;options&gt;
2564 &lt;dataset identifier&gt; /path/to/data/file(s)<o:p></o:p></span></p>
2565
2566 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2567 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2568
2569 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2570 "MS Mincho"'>Some of the more important options and arguments that can be
2571 hard-coded into the perl script or passed via the command line are:<o:p></o:p></span></p>
2572
2573 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2574 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2575
2576 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2577 "MS Mincho";mso-bidi-font-family:Arial'>-h <span style='mso-tab-count:1'>      </span>(hostname
2578 of the mysql server)<o:p></o:p></span></p>
2579
2580 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2581 "MS Mincho";mso-bidi-font-family:Arial'>-sqldb (the name of the biosql database
2582 instance that was created)<o:p></o:p></span></p>
2583
2584 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2585 "MS Mincho";mso-bidi-font-family:Arial'>-dbuser (username to connect to MySQL
2586 with)<o:p></o:p></span></p>
2587
2588 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2589 "MS Mincho";mso-bidi-font-family:Arial'>-dbpass (MySQL user password)<o:p></o:p></span></p>
2590
2591 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2592 "MS Mincho";mso-bidi-font-family:Arial'>-format (the format of the sequence
2593 datafile that is going to be read/loaded)</span><span style='font-family:Arial;
2594 mso-fareast-font-family:"MS Mincho"'><o:p></o:p></span></p>
2595
2596 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2597 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2598
2599 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2600 "MS Mincho"'>One of the key options needed is the “dataset identifier”. This
2601 identifier allows one to store many ‘biodatabases” inside the single BioSQL
2602 instance.<span style="mso-spacerun: yes">  </span><o:p></o:p></span></p>
2603
2604 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2605 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2606
2607 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2608 "MS Mincho"'>Given that we are trying to load release 40 of the Swissprot
2609 dataset a logical identifier could be something like “swiss”, “swissprot”,
2610 “sprot” or “swissprot40” etc.<o:p></o:p></span></p>
2611
2612 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2613 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2614
2615 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2616 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2617
2618 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2619 "MS Mincho"'>Here we go…<o:p></o:p></span></p>
2620
2621 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2622 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2623
2624 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2625 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3
2626 biosql]$ ./load_seqdatabase.pl -host localhost -sqldb biosql -dbuser root
2627 -dbpass XXX -format swiss swissprot40 /n/data/mirrors/swissprot/sprot40.dat<o:p></o:p></span></p>
2628
2629 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2630 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>Reading
2631 /n/data/mirrors/swissprot/sprot40.dat<o:p></o:p></span></p>
2632
2633 <p class=MsoPlainText style='margin-left:.5in'><span style='font-family:Courier;
2634 mso-fareast-font-family:"MS Mincho";mso-bidi-font-family:Arial'>[dag@pe3
2635 biosql]$<o:p></o:p></span></p>
2636
2637 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2638 "MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2639
2640 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2641 "MS Mincho";mso-bidi-font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2642
2643 <p class=MsoPlainText><span style='font-family:Courier;mso-fareast-font-family:
2644 "MS Mincho";mso-bidi-font-family:Arial'>Wow! It worked!<o:p></o:p></span></p>
2645
2646 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2647 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2648
2649 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2650 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2651
2652 <p class=MsoPlainText><span style='font-family:Arial;mso-fareast-font-family:
2653 "MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2654
2655 <h1>Step 9 – Observations</h1>
2656
2657 <p class=MsoNormal><b><span style='font-size:11.0pt;mso-bidi-font-size:12.0pt;
2658 font-family:Arial;mso-fareast-font-family:"MS Mincho"'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></b></p>
2659
2660 <ul style='margin-top:0in' type=disc>
2661  <li class=MsoNormal style='mso-list:l7 level1 lfo9;tab-stops:list .5in'><span
2662      style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Loading
2663      Swissprot into the MySQL database took 2 hours and 10 minutes. The slow
2664      speed is caused by the overhead of having to parse each entry into a
2665      BioPerl sequence object prior to inserting it into the database. There is
2666      much room for performance tuning; one approach may be to start an
2667      internet-accessible repository where people can download pre-built
2668      tab-delimited MySQL data files that can be bulk imported into a
2669      biosql-compliant database very quickly.<o:p></o:p></span></li>
2670 </ul>
2671
2672 <p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
2673 font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2674
2675 <ul style='margin-top:0in' type=disc>
2676  <li class=MsoNormal style='mso-list:l7 level1 lfo9;tab-stops:list .5in'><span
2677      style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>The
2678      size of sprot40.dat is 307MB <o:p></o:p></span></li>
2679 </ul>
2680
2681 <p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
2682 font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2683
2684 <ul style='margin-top:0in' type=disc>
2685  <li class=MsoNormal style='mso-list:l7 level1 lfo9;tab-stops:list .5in'><span
2686      style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>After
2687      swissprot was loaded the cumulative size of all the files inside
2688      /var/lib/mysql/biosql/ was 399MB<o:p></o:p></span></li>
2689 </ul>
2690
2691 <p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
2692 font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2693
2694 <p class=MsoNormal style='margin-left:.25in'><span style='font-size:11.0pt;
2695 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2696
2697 <h1><span style='mso-fareast-font-family:"Times New Roman"'>Step 10 – What
2698 next?</span><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;mso-fareast-font-family:
2699 "Times New Roman"'><o:p></o:p></span></h1>
2700
2701 <p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
2702 font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2703
2704 <p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
2705 font-family:Arial'>This document is a work in progress. Among the things I’d
2706 like to do next:<o:p></o:p></span></p>
2707
2708 <p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
2709 font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2710
2711 <ul style='margin-top:0in' type=disc>
2712  <li class=MsoNormal style='mso-list:l1 level1 lfo10;tab-stops:list .5in'><span
2713      style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Write
2714      perl scripts to validate the information that was loaded into the database<o:p></o:p></span></li>
2715 </ul>
2716
2717 <p class=MsoNormal style='margin-left:.25in'><span style='font-size:10.0pt;
2718 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2719
2720 <ul style='margin-top:0in' type=disc>
2721  <li class=MsoNormal style='mso-list:l1 level1 lfo10;tab-stops:list .5in'><span
2722      style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Figure
2723      out how to export/dump the database and see how quickly we can recreate
2724      the database with these raw files instead of laboriously using BioPerl to
2725      parse and load objects one at a time. Loading the database is slow and it
2726      may be cool to package up tab-delimited biosql exports so that others can
2727      load their own databases much faster.<o:p></o:p></span></li>
2728 </ul>
2729
2730 <p class=MsoNormal style='margin-left:.25in'><span style='font-size:10.0pt;
2731 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2732
2733 <ul style='margin-top:0in' type=disc>
2734  <li class=MsoNormal style='mso-list:l1 level1 lfo10;tab-stops:list .5in'><span
2735      style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Run
2736      more time tests to see where things can be made faster<o:p></o:p></span></li>
2737 </ul>
2738
2739 <p class=MsoNormal style='margin-left:.25in'><span style='font-size:10.0pt;
2740 mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2741
2742 <ul style='margin-top:0in' type=disc>
2743  <li class=MsoNormal style='mso-list:l1 level1 lfo10;tab-stops:list .5in'><span
2744      style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>Start
2745      trying to cram all of GenBank into a biosql database!<o:p></o:p></span></li>
2746 </ul>
2747
2748 <p class=MsoNormal><span style='font-size:10.0pt;mso-bidi-font-size:12.0pt;
2749 font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></p>
2750
2751 </div>
2752
2753 </body>
2754
2755 </html>