<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Sorry, I don't know why I didn't send that the mailing list! Here is it again.<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Susan<BR><DIV><BR><DIV>Begin forwarded message:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="4" color="#000000" style="font: 14.0px Helvetica; color: #000000"><B>From: </B></FONT><FONT face="Helvetica" size="4" style="font: 14.0px Helvetica">Susan Alberts <<A href="mailto:alberts@duke.edu">alberts@duke.edu</A>></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="4" color="#000000" style="font: 14.0px Helvetica; color: #000000"><B>Date: </B></FONT><FONT face="Helvetica" size="4" style="font: 14.0px Helvetica">September 12, 2006 5:24:13 PM EDT</FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="4" color="#000000" style="font: 14.0px Helvetica; color: #000000"><B>To: </B></FONT><FONT face="Helvetica" size="4" style="font: 14.0px Helvetica">"Karl O. Pinc" <<A href="mailto:kop@meme.com">kop@meme.com</A>>, Jeanne Altmann <<A href="mailto:altj@Princeton.EDU">altj@Princeton.EDU</A>>, KETHERINE FENN <<A href="mailto:kfenn@Princeton.EDU">kfenn@Princeton.EDU</A>>, Leah Gerber <<A href="mailto:lgerber@duke.edu">lgerber@duke.edu</A>>, Catherine_Markham Markham <<A href="mailto:amarkham@princeton.edu">amarkham@princeton.edu</A>></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="4" color="#000000" style="font: 14.0px Helvetica; color: #000000"><B>Subject: </B></FONT><FONT face="Helvetica" size="4" style="font: 14.0px Helvetica"><B>babase update and conf call</B></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> Dear all,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Karl is about to reach a solid end point and we are excited about this. There are some loose ends that will need to be tied up, and we think that a babase conference call for Thursday would be a good thing. We would really love Catherine to be involved if at all possible becuase of her relatively long history with babase (and as a future user), but I realize her schedule is now quite different.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Jeanne and I have a different conf call at 11. We could do our babase conf call before that, at 10 am, or we could do it bewtween 2:30 and 3:30. That is about all the time that I have free that day. If that can't work out then let me know and we will discuss another time after Karl is back in Chi, but it seems like it would be good to do it before he leaves here (but not absolutely necessary).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Here is the update and agenda for our call:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV class="MsoNormal">Here are the things that still need to be done before Karl leaves.</DIV><DIV class="MsoNormal"> <O:P></O:P></DIV><OL style="margin-top:0in" start="1" type="1"><LI class="MsoNormal" style="mso-list:l1 level1 lfo1;tab-stops:list .5in">Cycgaps validation and assigning cycles.series AND automatic cycgaps updateing. This is in progress now.</LI><LI class="MsoNormal" style="mso-list:l1 level1 lfo1;tab-stops:list .5in">Reconversion using the new automatic updates.</LI><LI class="MsoNormal" style="mso-list:l1 level1 lfo1;tab-stops:list .5in">Update Ranks documentation (is this the last table for which the documentation reflects the old foxpro system?)</LI></OL><DIV class="MsoNormal"> <O:P></O:P></DIV><DIV class="MsoNormal">At that point, the conversion is done, except for then debugging to deal with conversion errors that are programming errors (if any).</DIV><DIV class="MsoNormal"> <O:P></O:P></DIV><DIV class="MsoNormal">After this final conversion, there are some things that we will need to do and decisions we need to make that affect how we use the database (I am NOT including in this list the things that we all know are outstanding, such a developing the data entry procedures, adding new tables, creating new ranker, and fixing the front end).</DIV><DIV class="MsoNormal"> <O:P></O:P></DIV><OL style="margin-top:0in" start="1" type="1"><LI class="MsoNormal" style="mso-list:l0 level1 lfo2;tab-stops:list .5in"><B>Non-trigger error checks.</B><SPAN style=""> There are a set of error checks that we can run to check the integrity and accuracy of the database. The errors that this would find are not errors that could or should be coded as automatic triggers, hence we will describe these as non-trigger error checks. They are things like checking that every animal present in the group has a rank assigned (as opposed to checking that no one is assigned a rank unless they are in the group – this latter one is a trigger, the former cannot be because before ranks are assigned, no one has a rank).<SPAN style="mso-spacerun: yes"> </SPAN>Karl notes that we have always had these non-trigger error checks available to run in foxpro, but that no one has every really run them or used them to identify and correct errors. Hence, they are effectively optional error checks. The code has been written for these error checks, but not debugged and hence not run before. Our options are:</SPAN></LI><OL style="margin-top:0in" start="1" type="a"><LI class="MsoNormal" style="mso-list:l0 level2 lfo2;tab-stops:list 1.0in">Take the error checks that Karl has written and debug and run them ourselves, one by one as needed. They are sql queries, so this is highly feasible but laborious.</LI><LI class="MsoNormal" style="mso-list:l0 level2 lfo2;tab-stops:list 1.0in">Have Karl debug and concatenate them into a single program that would be run whenever we wanted it to be, probably automatically on a regular basis.</LI><LI class="MsoNormal" style="mso-list:l0 level2 lfo2;tab-stops:list 1.0in">Outsource this project to someone else – i.e., hire someone to concatenate and debug these programs into a single program that would be run automatically.</LI></OL><LI class="MsoNormal" style="mso-list:l0 level1 lfo2;tab-stops:list .5in"><B>Testing and pushing the system.</B><SPAN style=""> Karl’s concern as a professional programmer is that we find the worst bugs early on and fix them. He points out that of course there will be bugs. To find them, we need to push the system – do a lot of manipulation of the tables using babase_test. Update rows, delete rows, make illegal and legal changes and see how the system performs. Ideally this should be done for all tables, all columns. The sexual cycles tables should have special attention here because there are so many “analyzed” tables. This kind of testing will also reveal performance issues that might come up that we haven’t anticipated or found yet.<SPAN style="mso-spacerun: yes"> </SPAN>One approach would be to just devote a certain amount of time in Leah’s and Tabby’s week, some week, to doing this. Another option would be contracting Karl or someone else to do this. It might be a couple of days work, hard for me to say.</SPAN></LI><LI class="MsoNormal" style="mso-list:l0 level1 lfo2;tab-stops:list .5in"><B>Dealing with warnings and unwanted error messages.</B><SPAN style=""> Every night, the program will run the triggers, and these automatic checks will produce a list of error messages and warnings related to data “errors” in the database. Specifically, anytime a rule is violated (rules outlined in the documentation) a message will appear. Some of these we will want to ignore forever or for the time being, and we will not want to be revisited with them every day. So, Karl proposes a program that will defer or eliminate unwanted error messages and warnings. This is optional, but would be a great convenience. It is not really something that I think is feasible for us to do without professional help, unless Leah or Tabby have insight into this. What to do?</SPAN></LI><LI class="MsoNormal" style="mso-list:l0 level1 lfo2;tab-stops:list .5in"><B>Checking cycle ids?</B><SPAN style=""> Karl points out that in creating the new cycle files in the new babase system, cycles have different cids in many cases than they did in the old babase system. He wants to know whether we want a program that maps old onto new, so that we can find particular cycles that we analyzed in foxpro. </SPAN></LI></OL><DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>-----------------------------------------------</DIV><DIV>Susan Alberts, Dept. Biology, Duke University, Durham NC 27708. Phone 919-660-7272, Fax 919-660-7293. <A href="mailto:alberts@duke.edu">alberts@duke.edu</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN> </DIV><BR></DIV></BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>-----------------------------------------------</DIV><DIV>Susan Alberts, Dept. Biology, Duke University, Durham NC 27708. Phone 919-660-7272, Fax 919-660-7293. <A href="mailto:alberts@duke.edu">alberts@duke.edu</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN> </DIV><BR></DIV></BODY></HTML>