From mark.gerstein@yale.edu Thu Apr 1 16:26:11 1999 Received: from csbleu.csb.yale.edu (csbleu.csb.yale.edu [130.132.17.46]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id QAA25184 for ; Thu, 1 Apr 1999 16:26:11 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by csbleu.csb.yale.edu (8.9.1a/8.9.1) with ESMTP id QAA11018; Thu, 1 Apr 1999 16:25:49 -0500 (EST) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id QAA05670; Thu, 1 Apr 1999 16:25:43 -0500 Date: Thu, 1 Apr 1999 16:25:43 -0500 Message-Id: <199904012125.QAA05670@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@bofur.csb.yale.edu Subject: test #4 From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu test #4 From mark.gerstein@yale.edu Thu Apr 1 16:29:49 1999 Received: from csbleu.csb.yale.edu (csbleu.csb.yale.edu [130.132.17.46]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id QAA25208 for ; Thu, 1 Apr 1999 16:29:49 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by csbleu.csb.yale.edu (8.9.1a/8.9.1) with ESMTP id QAA11027; Thu, 1 Apr 1999 16:29:27 -0500 (EST) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id QAA05688; Thu, 1 Apr 1999 16:29:26 -0500 Date: Thu, 1 Apr 1999 16:29:26 -0500 Message-Id: <199904012129.QAA05688@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@bofur.csb.yale.edu Subject: test #5 From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu test #5 From mark.gerstein@yale.edu Thu Apr 1 16:32:46 1999 Received: from csbleu.csb.yale.edu (csbleu.csb.yale.edu [130.132.17.46]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id QAA25237 for ; Thu, 1 Apr 1999 16:32:45 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by csbleu.csb.yale.edu (8.9.1a/8.9.1) with ESMTP id QAA11040; Thu, 1 Apr 1999 16:32:23 -0500 (EST) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id QAA05749; Thu, 1 Apr 1999 16:32:22 -0500 Date: Thu, 1 Apr 1999 16:32:22 -0500 Message-Id: <199904012132.QAA05749@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@bofur.csb.yale.edu Subject: test #6 From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu test #6 From mark.gerstein@yale.edu Thu Apr 1 16:44:00 1999 Received: from csbleu.csb.yale.edu (csbleu.csb.yale.edu [130.132.17.46]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id QAA25351 for ; Thu, 1 Apr 1999 16:43:59 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by csbleu.csb.yale.edu (8.9.1a/8.9.1) with ESMTP id QAA11082; Thu, 1 Apr 1999 16:43:37 -0500 (EST) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id QAA05957; Thu, 1 Apr 1999 16:43:36 -0500 Date: Thu, 1 Apr 1999 16:43:36 -0500 Message-Id: <199904012143.QAA05957@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@bofur.csb.yale.edu Subject: test #11 From: Mark.Gerstein@yale.edu test #11 From mark.gerstein@yale.edu Thu Apr 1 16:45:06 1999 Received: from csbleu.csb.yale.edu (csbleu.csb.yale.edu [130.132.17.46]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id QAA25370 for ; Thu, 1 Apr 1999 16:45:06 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by csbleu.csb.yale.edu (8.9.1a/8.9.1) with ESMTP id QAA11087; Thu, 1 Apr 1999 16:44:44 -0500 (EST) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id QAA05989; Thu, 1 Apr 1999 16:44:43 -0500 Date: Thu, 1 Apr 1999 16:44:43 -0500 Message-Id: <199904012144.QAA05989@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@bofur.csb.yale.edu Subject: test #12 From: Mark.Gerstein@yale.edu test #12 From mark.gerstein@yale.edu Thu Apr 1 16:46:13 1999 Received: from csbleu.csb.yale.edu (csbleu.csb.yale.edu [130.132.17.46]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id QAA25382 for ; Thu, 1 Apr 1999 16:46:13 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by csbleu.csb.yale.edu (8.9.1a/8.9.1) with ESMTP id QAA11100; Thu, 1 Apr 1999 16:45:51 -0500 (EST) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id QAA06037; Thu, 1 Apr 1999 16:45:50 -0500 Date: Thu, 1 Apr 1999 16:45:50 -0500 Message-Id: <199904012145.QAA06037@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@bofur.csb.yale.edu Subject: test #13 From: Mark.Gerstein@yale.edu test #13 From mark.gerstein@yale.edu Thu Apr 1 16:46:54 1999 Received: from csbleu.csb.yale.edu (csbleu.csb.yale.edu [130.132.17.46]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id QAA25402 for ; Thu, 1 Apr 1999 16:46:54 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by csbleu.csb.yale.edu (8.9.1a/8.9.1) with ESMTP id QAA11104; Thu, 1 Apr 1999 16:46:32 -0500 (EST) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id QAA06049; Thu, 1 Apr 1999 16:46:31 -0500 Date: Thu, 1 Apr 1999 16:46:31 -0500 Message-Id: <199904012146.QAA06049@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@bofur.csb.yale.edu Subject: test #14 From: Mark.Gerstein@yale.edu test #14 From mark.gerstein@yale.edu Thu Apr 1 16:48:17 1999 Received: from csbleu.csb.yale.edu (csbleu.csb.yale.edu [130.132.17.46]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id QAA25421 for ; Thu, 1 Apr 1999 16:48:17 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by csbleu.csb.yale.edu (8.9.1a/8.9.1) with ESMTP id QAA11108; Thu, 1 Apr 1999 16:47:55 -0500 (EST) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id QAA06065; Thu, 1 Apr 1999 16:47:54 -0500 Date: Thu, 1 Apr 1999 16:47:54 -0500 Message-Id: <199904012147.QAA06065@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@bofur.csb.yale.edu Subject: test #15 (spam) From: Mark.Gerstein@yale.edu This is a test. Please ignore. [ test #15 (spam) ] From shoshanna.pearlman@yale.edu Thu Apr 1 23:10:24 1999 Received: from pantheon-po02.its.yale.edu (pantheon-po02.its.yale.edu [130.132.143.33]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id XAA25748 for ; Thu, 1 Apr 1999 23:10:23 -0500 Received: from minerva.cis.yale.edu (sap29@minerva.cis.yale.edu [130.132.143.250]) by pantheon-po02.its.yale.edu (8.8.8/8.8.8) with ESMTP id XAA14780; Thu, 1 Apr 1999 23:10:01 -0500 (EST) Received: from localhost (sap29@localhost) by minerva.cis.yale.edu (8.8.8/8.8.8) with SMTP id XAA14069; Thu, 1 Apr 1999 23:10:01 -0500 (EST) X-Authentication-Warning: minerva.cis.yale.edu: sap29 owned process doing -bs Date: Thu, 1 Apr 1999 23:10:00 -0500 (EST) From: Shoshanna Pearlman X-Sender: sap29@minerva.cis.yale.edu To: "Mark B. Gerstein" cc: course@bofur.csb.yale.edu Subject: Re: Don't Meet 4/2, Meet 4/9, Meet 4/26, 1st talk 4/12 In-Reply-To: <37038002.47D01869@yale.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This looks perfect for me. When you say, "we will be meeting for a normal class next on Friday April 9," I assume you don't mean that we're skipping Mon. and Wed. classes until then? > Hello All, > > After studying the schedule, processing the comments people had in > class on Wednesday, and finally (!) looking at the completed web > enrollment list, I have decided on the following plan: > > 1 -- Meet once in READING PERIOD, probably on Monday 26 April. > > 2 -- CANCEL class on Friday. (Upon reflection, if we are going to substitute > one reading period day for a Friday, this is the best Friday to substitute > as it is a holiday and not that convenient for a number of people in class.) > > 3 -- SHIFT the student talks, so that they commence on Monday 12 April > (with ALIGNMENT) instead of Friday 9 April. > > We will be meeting for a normal class next on Friday 9 April. > > Please acknowledge receiving this message. > > cheers, > > Mark Gerstein > > -- > Mark.Gerstein@yale.edu * 203 432-6105 * http://bioinfo.mbb.yale.edu > -Shoshannah From mark.gerstein@yale.edu Sat Apr 3 23:42:06 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id XAA27921 for ; Sat, 3 Apr 1999 23:42:06 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id XAA09433 for ; Sat, 3 Apr 1999 23:41:45 -0500 (EST) Received: from MA.csb.yale.edu (net186-44.its.yale.edu [130.132.186.44]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id XAA03808; Sat, 3 Apr 1999 23:41:36 -0500 Message-Id: <199904040441.XAA03808@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@aragorn.csb.yale.edu Subject: RESEND class list From: Mark.Gerstein@yale.edu Date: Sat, 3 Apr 1999 22:05:27 -0500 (EST) Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu Hi All, I am resending the class list. marK . _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. first last cred fr2 email fruit URL Raghav Gorur Y A raghav.gorur@yale.edu mango ??NA?? Vadim Alexandrov Y C vadim.alexandrov@yale.edu blueberry N/A AYMAN EL-GUINDY Y B ayman.el-guindy@yale.edu ??NA?? ??NA?? Shoshannah Pearlman Y A shoshanna.pearlman@yale.edu banana none Paul Bertone Y C paul.bertone@yale.edu ??NA?? ??NA?? Daqi Tu Y A daqi.tu@yale.edu orange ??NA?? Amy Seila Y S amy.seila@yale.edu strawberries none Amar Drawid Y A amar.drawid@yale.edu apple http://zoo.cs.yale.edu/~amd33/ Parag Vora Y C parag.vora@yale.edu mango http://pantheon.yale.edu/~parag Bill Russ N B russ@paradigm.csb.yale.edu Pears _ Dita Gratzinger N A dita.gratzinger@yale.edu apricot ??NA?? Koji Sonoda N B koji@pantheon.yale.edu banana _ Rajdeep Das N B rajdeep.das@yale.edu orange http://bioinfo.mbb.yale.edu/~das Michael Kosowsky N C michael.kosowsky@yale.edu apple ??NA?? suganthi balasubramanian N B suganthi@csb.yale.edu grapes ??NA?? Michael Reifler N S michael.reifler@yale.edu Kiwi ??NA?? Soumitra Basu N C basu@csb.yale.edu cherry ??NA?? Jun Li N C jli@bi-pharm.com ??NA?? _ Diane Bilodeau N C diane.bilodeau@yale.edu not yet but d'like to tamara shaw N B shawtz@biomed.med.yale.edu banana ??NA?? Jennifer Chao N S chaojr@biomed.med.yale.edu Orange or grapefruit ??NA?? From mark.gerstein@yale.edu Sat Apr 3 23:49:18 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id XAA27942 for ; Sat, 3 Apr 1999 23:49:18 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id XAA09449 for ; Sat, 3 Apr 1999 23:48:58 -0500 (EST) Received: from MA.csb.yale.edu (net186-44.its.yale.edu [130.132.186.44]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id XAA03882; Sat, 3 Apr 1999 23:48:49 -0500 Date: Sat, 3 Apr 1999 23:48:49 -0500 Message-Id: <199904040448.XAA03882@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@aragorn.csb.yale.edu Subject: readings from Kate in 336 From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu CC: kathleen.tatham@yale.edu The next class will meet on Friday 4/9. We are not meeting next Monday or Wednesday. A big packet with readings will be available from Monday onwards from Kate Tatham in Bass 336. From mark.gerstein@yale.edu Sun Apr 4 00:20:45 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id AAA27991 for ; Sun, 4 Apr 1999 00:20:45 -0500 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id AAA09498 for ; Sun, 4 Apr 1999 00:20:22 -0500 (EST) Received: from MA.csb.yale.edu (net186-44.its.yale.edu [130.132.186.44]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id AAA04576; Sun, 4 Apr 1999 00:20:17 -0500 Date: Sun, 4 Apr 1999 00:20:17 -0500 Message-Id: <199904040520.AAA04576@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@aragorn.csb.yale.edu Subject: schedule of talks From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu Hi All, Based on various people's requests, I have slightly jiggled the talk schedule again. Hopefully, everyone can be accommodated by this. Please get to me if otherwise. marK . _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. _ .. .. _ .. first last talk day date Paul Bertone Alignment M 12-Apr Daqi Tu Alignment M 12-Apr Vadim Alexandrov Statistics F 16-Apr AYMAN EL-GUINDY Statistics F 16-Apr Amy Seila Databases M 26-Apr Amar Drawid Databases M 26-Apr Shoshannah Pearlman Genomics-10 M 26-Apr Raghav Gorur Geometry M 26-Apr Parag Vora Geometry M 26-Apr From Mark.Gerstein@yale.edu Sun Apr 4 17:23:15 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id RAA28651 for ; Sun, 4 Apr 1999 17:23:14 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id RAA10496 for ; Sun, 4 Apr 1999 17:22:51 -0400 (EDT) Received: from yale.edu (net186-44.its.yale.edu [130.132.186.44]) by mail.csb.yale.edu (8.6.11/8.6.11) with ESMTP id RAA11237; Sun, 4 Apr 1999 17:22:47 -0400 Message-ID: <3707D63F.81565084@yale.edu> Date: Sun, 04 Apr 1999 17:14:39 -0400 From: "Mark B. Gerstein" Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: course@aragorn.csb.yale.edu Subject: Current schedule is now on-line. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Current schedule is now on-line. -- Mark.Gerstein@yale.edu * 203 432-6105 * http://bioinfo.mbb.yale.edu From Mark.Gerstein@yale.edu Sun Apr 4 17:24:01 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id RAA28691 for ; Sun, 4 Apr 1999 17:24:01 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id RAA10512 for ; Sun, 4 Apr 1999 17:23:37 -0400 (EDT) Received: from yale.edu (net186-44.its.yale.edu [130.132.186.44]) by mail.csb.yale.edu (8.6.11/8.6.11) with ESMTP id RAA11329; Sun, 4 Apr 1999 17:23:33 -0400 Message-ID: <3707D7F5.4A82A440@yale.edu> Date: Sun, 04 Apr 1999 17:21:57 -0400 From: "Mark B. Gerstein" Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: course@aragorn.csb.yale.edu Subject: http://bioinfo2.csb.yale.edu/cgi-bin/messages?list=mbb447b4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit All course mailing list correspondence now on-line in an archive. See course web page or http://bioinfo2.csb.yale.edu/cgi-bin/messages?list=mbb447b4. -- Mark.Gerstein@yale.edu * 203 432-6105 * http://bioinfo.mbb.yale.edu From Mark.Gerstein@yale.edu Sun Apr 4 17:24:40 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id RAA28705; Sun, 4 Apr 1999 17:24:40 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id RAA10520; Sun, 4 Apr 1999 17:24:17 -0400 (EDT) Received: from yale.edu (net186-44.its.yale.edu [130.132.186.44]) by mail.csb.yale.edu (8.6.11/8.6.11) with ESMTP id RAA11404; Sun, 4 Apr 1999 17:24:12 -0400 Message-ID: <3707D840.63BC0619@yale.edu> Date: Sun, 04 Apr 1999 17:23:12 -0400 From: "Mark B. Gerstein" Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: "all@bioinfo" CC: course@aragorn.csb.yale.edu Subject: Classical Molecular Dynamics: Three-dimensional billiards. [url] Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit cool movies! http://udel.edu/~rakov/md_expl6.htm From kathleen.tatham@yale.edu Mon Apr 5 07:26:27 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id HAA29377 for ; Mon, 5 Apr 1999 07:26:27 -0400 Received: from BIOMED.MED.YALE.EDU (biomed.med.yale.edu [130.132.19.48]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with ESMTP id HAA11398 for ; Mon, 5 Apr 1999 07:26:03 -0400 (EDT) Received: from yale.edu (ktatham.mbb.yale.edu) by biomed.med.yale.edu (PMDF V5.1-10 #20971) with ESMTP id <01J9NZET0R4A00QDZK@biomed.med.yale.edu> for course@aragorn.csb.yale.edu; Mon, 5 Apr 1999 07:23:53 EST Date: Mon, 05 Apr 1999 07:33:57 -0700 From: Kathleen Tatham Subject: reading packet for Bioinformatics To: "course@aragorn.csb.yale.edu" Message-id: <3708C9D5.5467BBCF@yale.edu> MIME-version: 1.0 X-Mailer: Mozilla 4.07 [en] (Win16; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Please let me know when you take your reading packet. If there are none on my door (Bass 336) I have more on a chair in my office. Thanks, kate From kathleen.tatham@yale.edu Wed Apr 7 08:14:43 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id IAA00381 for ; Wed, 7 Apr 1999 08:14:43 -0400 Received: from BIOMED.MED.YALE.EDU (biomed.med.yale.edu [130.132.19.48]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with ESMTP id IAA16425 for ; Wed, 7 Apr 1999 08:14:14 -0400 (EDT) Received: from yale.edu (ktatham.mbb.yale.edu) by biomed.med.yale.edu (PMDF V5.1-10 #20971) with ESMTP id <01J9QTNLPV8W00QPGZ@biomed.med.yale.edu> for course@aragorn.csb.yale.edu; Wed, 7 Apr 1999 08:11:33 EST Date: Wed, 07 Apr 1999 08:21:40 -0700 From: Kathleen Tatham Subject: reading -- Bioinformatics To: "course@aragorn.csb.yale.edu" Message-id: <370B7804.ABE14EF5@yale.edu> MIME-version: 1.0 X-Mailer: Mozilla 4.07 [en] (Win16; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit To whom it may concedrn: There are fourteen members of the Bioinformatics class who have picked up the reading material. If your name appears below and you have pickup your reading please let me know immediately. And as before, e-mail/notify me when you do get the packet. Thanks, Kate raghav.gorur@yale.edu vadim.alexandrov@yale.edu ayman.el-guindy@yale.edu paul.bertone@yale.edu daqi.tu@yale.edu amar.drawid@yale.edu russ@paradigm.csb.yale.edu dita.gratzinger@yale.edu rajdeep.das@yale.edu suganthi@csb.yale.edu michael.reifler@yale.edu basu@csb.yale.edu jli@bi-pharm.com shawtz@biomed.med.yale.edu chaojr@biomed.med.yale.edu From mark.gerstein@yale.edu Thu Apr 8 21:14:07 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id VAA02342 for ; Thu, 8 Apr 1999 21:14:07 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id VAA20623 for ; Thu, 8 Apr 1999 21:13:35 -0400 (EDT) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id VAA00668; Thu, 8 Apr 1999 21:13:32 -0400 Date: Thu, 8 Apr 1999 21:13:32 -0400 Message-Id: <199904090113.VAA00668@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@aragorn.csb.yale.edu Subject: 9 AM on 4/30 From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu Final assignment due in my mailbox (in printout form) on the 4th floor of Bass at end of reading period. Provisionally we'll set this time as 9 AM on Friday 30 April. I open to feed back on this tomorrow. From mark.gerstein@yale.edu Thu Apr 8 21:15:26 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id VAA02364 for ; Thu, 8 Apr 1999 21:15:26 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id VAA20632 for ; Thu, 8 Apr 1999 21:14:55 -0400 (EDT) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id VAA00682; Thu, 8 Apr 1999 21:14:51 -0400 Date: Thu, 8 Apr 1999 21:14:51 -0400 Message-Id: <199904090114.VAA00682@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@aragorn.csb.yale.edu Subject: class tomorrow + notes From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu * Reminder -- class tomorrow!! I'll try to arrive in class a few minutes early if there are any questions. * Updated web pages updated http://bioinfo.mbb.yale.edu/mbb447-99/lectures.htm check out http://bioinfo.mbb.yale.edu/mbb447b-99/todo.htm * Interesting lecture tomorrow by Bill Joy Friday 9 April 11:30 AM Auditorium 101, Luce Hall (34 Hillhouse) Bill Joy java and jini: towards reliable distributed computing From shoshanna.pearlman@yale.edu Mon Apr 12 04:19:09 1999 Received: from pantheon-po04.its.yale.edu (pantheon-po04.its.yale.edu [130.132.143.35]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id EAA05557 for ; Mon, 12 Apr 1999 04:19:08 -0400 Received: from minerva.cis.yale.edu (sap29@minerva.cis.yale.edu [130.132.143.250]) by pantheon-po04.its.yale.edu (8.8.8/8.8.8) with ESMTP id EAA25783 for ; Mon, 12 Apr 1999 04:18:30 -0400 (EDT) Received: from localhost (sap29@localhost) by minerva.cis.yale.edu (8.8.8/8.8.8) with SMTP id EAA06039 for ; Mon, 12 Apr 1999 04:18:29 -0400 (EDT) X-Authentication-Warning: minerva.cis.yale.edu: sap29 owned process doing -bs Date: Mon, 12 Apr 1999 04:18:29 -0400 (EDT) From: Shoshanna Pearlman X-Sender: sap29@minerva.cis.yale.edu To: course@bofur.csb.yale.edu Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, all, If you'r having trouble making the html file on your pantheon account accessible from the web,you might want to try the advice Cyrus Wilson gave me : >From your home directory, do a chmod go+x public_html to make sure your public_html directory is world-executable (so that files in the directory can be accessed). The files in the directory should be world-readable, so cd public_html and do chmod go+r * If it still doesn't work, it might be that you need to make your home-directory world-executable for public_html to be accessible in the first place. So cd ~ and do chmod go+x . It worked for me. -Shoshannah From mark.gerstein@yale.edu Wed Apr 14 19:50:43 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id TAA08648 for ; Wed, 14 Apr 1999 19:50:42 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id TAA10684 for ; Wed, 14 Apr 1999 19:50:01 -0400 (EDT) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id TAA17135; Wed, 14 Apr 1999 19:49:56 -0400 Date: Wed, 14 Apr 1999 19:49:56 -0400 Message-Id: <199904142349.TAA17135@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@aragorn.csb.yale.edu Subject: Remember class on Friday From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu Remember class on Friday From mark.gerstein@yale.edu Wed Apr 14 19:52:05 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id TAA08662 for ; Wed, 14 Apr 1999 19:52:04 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id TAA10692 for ; Wed, 14 Apr 1999 19:51:23 -0400 (EDT) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id TAA17189; Wed, 14 Apr 1999 19:51:18 -0400 Date: Wed, 14 Apr 1999 19:51:18 -0400 Message-Id: <199904142351.TAA17189@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@aragorn.csb.yale.edu Subject: NB: Final project topic is completely up to you. From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu NB: Final project topic is completely up to you. It doesn't have to do anything with talk topic. Final project is NOT done with a partner. From mark.gerstein@yale.edu Wed Apr 14 19:53:07 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id TAA08684 for ; Wed, 14 Apr 1999 19:53:07 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id TAA10700 for ; Wed, 14 Apr 1999 19:52:26 -0400 (EDT) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id TAA17243; Wed, 14 Apr 1999 19:52:20 -0400 Date: Wed, 14 Apr 1999 19:52:20 -0400 Message-Id: <199904142352.TAA17243@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@aragorn.csb.yale.edu Subject: Rajdeep Das will be helping out with getting From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu Rajdeep Das will be helping out with getting your talks and projects up on the web. From m@kosowsky.net Sun Apr 18 15:34:38 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id PAA13060 for ; Sun, 18 Apr 1999 15:34:38 -0400 Received: from daimler.ivy69.net (mail@net244-108.its.yale.edu [130.132.244.108]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with ESMTP id PAA19865 for ; Sun, 18 Apr 1999 15:33:46 -0400 (EDT) Received: from mrk by daimler.ivy69.net with local (Exim 2.05 #1 (Debian)) id 10YxJH-0006og-00; Sun, 18 Apr 1999 15:32:55 -0400 From: Michael Kosowsky Date: 18 Apr 1999 14:40:09 -0400 To: course@aragorn.csb.yale.edu Subject: Dynamic Programming References: <3.0.3.32.19990415220143.0069b984> Message-Id: The question is what does "dynamic programming" mean. As a computer programmer I can't come up with a way of defining the phrase that would apply to any of the algorithms we discussed in class. A modern definition, taken from Robert Sedgewick, Algorithms, Addison-Wesley, 1983. (EAS QA76.6 S345 1983, also CCL) is: The principle of divide and conquer has guided the design of many of the algorithms we've studied: to solve a large problem, break it up into smaller problems which can be solved independently. In dynamic programming this principle is carried to an extreme: when we don't know exactly which smaller problems to solve, we simply solve them all, then store the answers away to be used later in solving larger problems. ... These problems involve looking for the "best" way to do something, and they have the general property that any decision involved in finding the best way to do a small subproblem remains a good decision even when that subproblem is included as a piece of some larger problem. (p. 483) This definition indeed highlights some of the features of the SW algorithm. But it gives no rationale for the name; none of the attributes of this class of algorithms suggests "dynamic." I've found an historical derivation. Turns out there's a 1957 work titled Richard Bellman, Dynamic Programming, A Rand Corporation Research Study, Princeton University Press, 1957. (available at Kline QA264 B44 1957, also CCL and EAS) In the introduction to the book, Bellman takes an epistomological look at mathematical modeling, and rails against the then current practice of changing problems that involve multiple stages into a single stage, multiple dimension problem (see below for stuff I started to write about that). When a problem is solved that way, ... the mathematician has not discharged his responsibilities. The problem is not to be considered solved in the mathematical sense until the structure of the optimal policy is understood. (p. ix) The rest of the book are techniques for explicitly thinking of problems in terms of their step by step nature, and indeed "dynamic programming" is coined to emphasize this approach: The title is also derived this way. The problems we treat are programming problems, to use a terminology now popular. The adjective "dynamic," however, indicates that we are interested in processes in which time plays a significant role, and in which the order of operations may be crucial. (p. xi) The phrase "to use a terminology now popular" refers to the use of "programming" to mean "tabulation method." (Credit to Amar -- forgive me if I got your name wrong.) It's the third definition of programming in the Oxford English Dictionary at http://jeeves.library.yale.edu/oed/, and predates the omnipresence of computers: 3. Planning carried out for purposes of control, management, or administration, esp. in economics. 1943 Sun (Baltimore) 1 July 14/2 The President transferred from Mr. Jones' RFC to Mr. Wallace's BEW full control over the programming of imported strategic materials. 1959 Listener 21 May 884/2 The design of controls, the programming of production methods, and so forth. ... So, the name was created to highlight an aspect of an approach that no longer differentiates that approach from other similar approaches. In other words, it was coined to point out what is isn't, but what it wasn't is no longer really what it isn't. Seems like a good time to hold a naming contest ... MK ------------------------------------------------------------ [Here's more detail about the introduction to Bellman's book, where I realized I was getting too far off point, but someone may find it interesting anyway:] Consider a multi-stage problem, e.g. the "raise-counter-raise system of poker with its delicate overtones of bluffing" (a favorite of theoreticians). How does a mathematician approach this problem? One approach is to turn the multiple stages into multiple dimensions of a single stage problem, and then apply any of a plethora of techniques to the new problem. Let's analyze a round of poker which allows only one raise. Then "I bet $10 then you raise $5 then I call" might correspond to the point in three dimensional space with coordinates (x=10, y=15, z=15). The analyst then places all of sorts of constraints on the possible coordinates. For example, z must be greater than or equal to y which must be greater than or equal to x, except we allow a zero in any position to mean the player folds. Another example is that there must be complex relationships imposed indicating how likely you are to call my bet given the amount I raise and the cards you hold and what you think I hold. The analyst then finds the coordinates that give the maximum value of the appropriate function -- in this case a function representing how much I win -- subject to the constraints. Not only can these problems can be difficult to solve tbis way, but Bellman is also concerned that when we solve them analytically, we may not be left with any understanding of the answer: Assume, however, that we have circumvented all these difficulties and have attained a certain computational nirvana. Withal, the the mathematician has not discharged his responsibilities. The problem is not to be considered solved in the mathematical sense until the structure of the optimal policy is understood. (p. ix) Continuing in this vein: Put another way, in place of determining the optimal sequence of decisions from some FIXED state of the system, we wish to determine the optimal decision to be made at ANY state of the system. Only if we know the latter, do we understand the intrinsic structure of the solution. (p. xi) To illustrate, if we return to our round of poker, he demands an analysis that, given the current state of the system -- the cards in the player's hands, the betting history, ... -- yields the best next move. And then here's the derivation of "dynamic programming": The title is also derived this way. The problems we treat are programming problems, to use a terminology now popular. The adjective "dynamic," however, indicates that we are interested in processes in which time plays a siginificant role, and in which the order of operations may be crucial. From amar.drawid@yale.edu Sun Apr 18 16:06:30 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id QAA13088 for ; Sun, 18 Apr 1999 16:06:30 -0400 Received: from pantheon-po03.its.yale.edu (pantheon-po03.its.yale.edu [130.132.143.34]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with ESMTP id QAA19900 for ; Sun, 18 Apr 1999 16:05:43 -0400 (EDT) Received: from mars.its.yale.edu (amd33@mars.its.yale.edu [130.132.143.37]) by pantheon-po03.its.yale.edu (8.8.8/8.8.8) with ESMTP id QAA16847 for ; Sun, 18 Apr 1999 16:05:41 -0400 (EDT) Received: from localhost (amd33@localhost) by mars.its.yale.edu (8.8.8/8.8.8) with SMTP id QAA06453 for ; Sun, 18 Apr 1999 16:05:39 -0400 (EDT) X-Authentication-Warning: mars.its.yale.edu: amd33 owned process doing -bs Date: Sun, 18 Apr 1999 16:05:39 -0400 (EDT) From: Amar Drawid X-Sender: amd33@mars.its.yale.edu To: course@aragorn.csb.yale.edu Subject: Re: Dynamic Programming In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I found some more interesting things about dynamic programming that I would like to add to Mike's message. They are from the book "Intorduction to Algorithms" by Cormen, Leiserson, Rivest (The MIT Press, McGraw-Hill Book Company, 1990): ""Programming" in this context refers to a tabular method, not to writing computer code.... Divide-and-conquer algorithms partition the problem into independent subproblems, solve the subproblems recursively, and then combine their solutions to solve the original problem. In contrast, dynamic programming is applicable when the subproblems are not independent, that is, when subproblems share subsubproblems. In this context a divide-and-conquer algorithm does more work than necessary, repeatedly solving the common subsubproblems. A dynamic-programming algorithm solves every subsubproblem just once and then saves its answer in a table..." This first made me more confused than before. But when I thought of a combinatorial problem (like the one we did in class), and tried to apply the normal divide-and-conquer method to it, I realized how dyn.prog. would work in it but div-n-conq would fail. Dynamic programming rules :) Amar From mark.gerstein@yale.edu Mon Apr 19 10:12:44 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id KAA15094 for ; Mon, 19 Apr 1999 10:12:44 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id KAA21858 for ; Mon, 19 Apr 1999 10:11:57 -0400 (EDT) Received: from BIFUR.csb.yale.edu (bifur.csb.yale.edu [130.132.17.175]) by mail.csb.yale.edu (8.6.11/8.6.11) with SMTP id KAA06355; Mon, 19 Apr 1999 10:11:54 -0400 Date: Mon, 19 Apr 1999 10:11:54 -0400 Message-Id: <199904191411.KAA06355@mail.csb.yale.edu> X-Mailer: emacs 19.34.1 (via feedmail 3 I) To: course@aragorn.csb.yale.edu Subject: Reminder: class today and attendence counts! From: Mark.Gerstein@yale.edu Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) Reply-to: Mark.Gerstein@yale.edu Reminder: class today and attendence counts! From Mark.Gerstein@yale.edu Tue Apr 20 07:58:58 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id HAA17434; Tue, 20 Apr 1999 07:58:58 -0400 Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with SMTP id HAA24903; Tue, 20 Apr 1999 07:58:08 -0400 (EDT) Received: from yale.edu (net231-177.its.yale.edu [130.132.231.177]) by mail.csb.yale.edu (8.6.11/8.6.11) with ESMTP id HAA17498; Tue, 20 Apr 1999 07:58:05 -0400 Message-ID: <371C44DF.193050CF@yale.edu> Date: Tue, 20 Apr 1999 05:11:59 -0400 From: "Mark B. Gerstein" Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: course@aragorn.csb.yale.edu CC: David.Gonda.B@bayer.com, mleach@curagen.com Subject: final class, industry speakers Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Final class meeting on Monday 4/26. Bioinformatics in industry went pretty well. Our speakers were: Martin Leach David Gonda -- Mark.Gerstein@yale.edu * 203 432-6105 * http://bioinfo.mbb.yale.edu From Mark.Gerstein@yale.edu Wed Apr 28 19:22:55 1999 Received: from aragorn.csb.yale.edu (aragorn.csb.yale.edu [130.132.17.179]) by bofur.csb.yale.edu (8.8.7/8.8.5) with ESMTP id TAA26307 for ; Wed, 28 Apr 1999 19:22:55 -0400 Received: from csbleu.csb.yale.edu (csbleu.csb.yale.edu [130.132.17.46]) by aragorn.csb.yale.edu (8.9.1/8.9.1) with ESMTP id TAA00856 for ; Wed, 28 Apr 1999 19:26:12 -0400 (EDT) Received: from mail.csb.yale.edu (csbmet.csb.yale.edu [130.132.17.44]) by csbleu.csb.yale.edu (8.9.1a/8.9.1) with ESMTP id SAA28897 for ; Tue, 27 Apr 1999 18:05:49 -0400 (EDT) Received: from yale.edu (net245-243.its.yale.edu [130.132.245.243]) by mail.csb.yale.edu (8.6.11/8.6.11) with ESMTP id FAA15333; Tue, 27 Apr 1999 05:20:12 -0400 Message-ID: <37258161.EC78022@yale.edu> Date: Tue, 27 Apr 1999 05:20:33 -0400 From: "Mark B. Gerstein" Organization: Yale MB&B Bioinformatics (http://bioinfo.mbb.yale.edu) X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 To: course@bioinfo.mbb.yale.edu CC: Kathleen Tatham Subject: final projects will be due by 9 AM on 5.3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit As we discussed in class, final projects will be due by 9 AM on 5.3. Please hand them in to Kate Tatham in Bass 336. She will be in at 9 AM and date stamp them, so it will be apparent if your project is late. At that time, also send an e-mail to me, with the link to the on-line version of your paper (html, pdf, ps, or rtf). If you want to hand in the project early, you can put it in Kate's mailbox on the 3rd floor of Bass, clearly indicating that it is for me and MB&B 447b. Good luck! I've enjoyed the class. -- Mark.Gerstein@yale.edu * 203 432-6105 * http://bioinfo.mbb.yale.edu +---------------------------< < AWAY > >--------------------------+ Will probably not be reading e-mail until 4.30. +-------------------------------------------------------------------+