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Date: Mon, 02 Dec 1996 15:32:54 GMTServer: NCSA/1.4.2Content-type: text/html<html> <head><title>CSE 590BI Bboard/Mail Log</title></head><body><h1>CSE 590BI <br> Algorithms in Molecular Biology <br> Bboard/Mail Log<br> Winter 1996</h1>This page contains a log of all email sent to the CSE590BI classmailing list <tt>cse590bi@cs</tt>. Please feel free to use it to ask questions, post information, orinitiate discussions of general interest to the class. Of course,questions or comments that don't seem of general interest can bedirected to the instructors(<tt>karp@cs, ruzzo@cs,</tt> or <tt>tompa@cs</tt>), instead. <p> Administrative requestsconcerning the mailing list itself, such as add/delete/addresschange requests, should be addressed to <tt>cse590bi-request@cs</tt>.<h2>Index of Messages</h2>(Latest message Tuesday, 06-Aug-96 19:53:23 PDT.)<p><ul><li><a href=#821343917001><tt> 5 Jan 96 tompa@cs ______ CSE 590 BI distrib list; variable credits</tt></a><li><a href=#821343917002><tt>10 Jan 96 roach@u _______ textbooks</tt></a><li><a href=#821417184001><tt>11 Jan 96 ruzzo@cs ______ extra handouts</tt></a><li><a href=#821477697001><tt>12 Jan 96 tompa@cs ______ Do we have your 590bi plans?</tt></a><li><a href=#821819285001><tt>16 Jan 96 tompa@cs ______ notetakers needed</tt></a><li><a href=#821846259001><tt>16 Jan 96 tompa@cs ______ lineup of notetakers</tt></a><li><a href=#822340283001><tt>22 Jan 96 tompa@cs ______ Lecture 6 available on the web</tt></a><li><a href=#822520024001><tt>24 Jan 96 tompa@cs ______ lineup of notetakers completed</tt></a><li><a href=#822693690001><tt>26 Jan 96 tompa@cs ______ Assignment 1, problem 3</tt></a><li><a href=#822779387001><tt>27 Jan 96 ruzzo@cs ______ Pevzner talks</tt></a><li><a href=#823825729001><tt> 8 Feb 96 tompa@cs ______ CSE 590 BI projects</tt></a><li><a href=#823891483001><tt> 9 Feb 96 tompa@cs ______ some course project suggestions</tt></a><li><a href=#824921569001><tt>21 Feb 96 tompa@cs ______ student and postdoc financial support to</tt></a><li><a href=#824922066001><tt>21 Feb 96 tompa@cs ______ lecture notes drafts</tt></a><li><a href=#825465060001><tt>27 Feb 96 tompa@cs ______ sequel to CSE 590BI</tt></a><li><a href=#827189986001><tt>18 Mar 96 joe@genetics __ Phylogeny course Sprinq Quarter</tt></a><li><a href=#827367172001><tt>20 Mar 96 ruzzo@cs ______ CSE 590BI continues...</tt></a><li><a href=#827539407001><tt>22 Mar 96 tompa@cs ______ course on Protein Stucture Prediction</tt></a><li><a href=#827948936001><tt>27 Mar 96 ruzzo@cs ______ CSE590BI schedule change</tt></a><li><a href=#829077850001><tt> 9 Apr 96 tompa@cs ______ University of Pennsylvania Conference on</tt></a><li><a href=#829441831001><tt>13 Apr 96 tompa@cs ______ Graduate Research Position in Theoretica</tt></a><li><a href=#830217242001><tt>22 Apr 96 ruzzo@cs ______ CSE 590BI Comp. Bio. Seminar Restarts</tt></a><li><a href=#831525714001><tt> 7 May 96 ruzzo@cs ______ cse590bi ROOM CHANGE</tt></a><li><a href=#831576080001><tt> 8 May 96 jiang@cs ______ CSE590bi May 9 lecture</tt></a><li><a href=#831681083001><tt> 9 May 96 ruzzo@cs ______ Haussler Talk.</tt></a><li><a href=#832228312001><tt>15 May 96 ruzzo@cs ______ NO CSE590BI THIS WEEK</tt></a><li><a href=#833424288001><tt>29 May 96 brendan@willow tomorrow's seminar</tt></a><li><a href=#839111871001><tt> 3 Aug 96 phg@u _________ course on Genome Sequence Analysis</tt></a><li><a href=#839386376001><tt> 6 Aug 96 phg@u _________ 599C, AU 1996 (fwd)</tt></a></ul><pre></pre><h2>Messages</h2><pre><hr size=4><a name="821343917001">To: cse590bi@csSubject: <b>CSE 590 BI distrib. list, and variable credits</b>Date: Fri, 05 Jan 1996 13:54:07 PSTFrom: <b>Martin Tompa <tompa@geoduck.cs.washington.edu></b></a>1. We have created a mail distribution list cse590bi@cs.washington.edu fromthe electronic addresses you supplied in the first week. This can be usedfor announcements, discussion outside of class, etc.2. As Dick mentioned, we very much want to encourage you to sign up for creditif at all possible. To accomodate this, we have changed to variable credit(anywhere between 1 and 3), with the following scheme:a. 1 credit for attending faithfully and serving as notetaker when it is yourturn,b. 1 credit for homework plus the take-home final, if there is one,c. 1-2 credits for the project, depending on its magnitude, up to a maximum of 3 credits. Please choose your level of involvement andsign up for the appropriate number of credits. Monday is the last day to makesuch changes without penalty, I believe. Signing up for credits is good forthe department and, if you're anything like me when it comes to goodintentions, good for the student as well. If you have questions about the credits or would like to discuss your plan forthe course, feel free to talk with any of us. If (or when) you aresigned up for credit, please also send mail to Tompa saying how you intend tosatisfy the number of credits you chose, so that we know who are thenotetakers, who is doing a project, etc.<hr size=4><a name="821343917002">Date: Wed, 10 Jan 1996 14:23:44 -0800 (PST)From: <b>Jared Roach <roach@u.washington.edu></b>To: cse590bi@cs.washington.eduSubject: <b>textbooks</b></a>From: Martin Tompa <tompa@cs.washington.edu>To: Jared Roach <roach@u.washington.edu>Thanks for the great pointers. Would it be o.k. for either you or me to sendthis to the class list, cse590bi@cs? I think they'd appreciate it. Let meknow if you'd like me to do it. OK, I'll forward it.From: Jared Roach <roach@u.washington.edu>To: tompa@cs.washington.eduSubject: Algorithms notesMartin, I just wanted to alert the class to a couple of topical books.1) Calculating the Secrets of Life Lander and Waterman, eds. 1995 National academy Press This has several good chapters, including one on yesterday and tomorrow's lectures by Gene Myers. At the end of this chapter, Gene states that the lowest bound on comparing two sequences yet found is O(NlogN), which addresses a question raised at the end of class yesterday. He claims that the fastest algorithm to date is O(N^2/log^2N) (Masek and Paterson, 1980), leaving a gap between the fastest algorithm and the highest lowest theoretical bound for algorithms, and thus an open problem. Other good chapters include one on statistical significance of comparisons by Waterman, probabilistic gene mapping by Lander, and molecular clock rates by Tavare. The book also includes four chapters on conformational computation. The UW library's copy is checked out by me and currently has a hold on it by someone else. The bookstore should have one or more copies.2) Introduction to Computational Biology Waterman 1995 Chapman and Hall This book just came out. I ordered my copy through the bookstore and it took many weeks for it to arrive. I haven't had a chance to read it yet, but it covers many of the above areas. It is about 50% on mapping, 30% on sequence alignment and assembly, and has a chapter on RNA secondary structure and one on tree assembly. It has a 50 page chapter on the dynamic programming of yesterday and tomorrow's lectures.- -Jared- ---------------------------------------------------Jared RoachDepartment of Molecular BiotechnologyUniversity of Washington, Room K354Box 357730Seattle, WA 98195phone 616-4536FAX 685-7301roach@u.washington.edubtw, dangling modifiers are not intentional, they just came out of my head that way.------- End of Forwarded Message<hr size=4><a name="821417184001">Date: 11 Jan 1996 19:23 PSTFrom: <b>Larry Ruzzo <ruzzo@quinault.cs.washington.edu></b>To: cse590bi@csSubject: <b>extra handouts</b></a>In general, Martin Tompa (Sieg 426E) will keep extras of all thehandouts, in case you missed some. Handouts can also be printed from the course web pages:http://www.cs.washington.edu/education/courses/590bi<hr size=4><a name="821477697001">To: cse590bi@geoduckSubject: <b>Do we have your 590bi plans?</b>Date: Fri, 12 Jan 1996 12:14:48 PSTFrom: <b>Martin Tompa <tompa@geoduck.cs.washington.edu></b></a>If you have signed up for credit and haven't yet sent me the followinginformation, please do so now:1. How many credits? 2. Which of the options from my earlier message are you planning in order tosatisfy those credits?<hr size=4><a name="821819285001">To: cse590bi@geoduckSubject: <b>notetakers needed</b>Date: Tue, 16 Jan 1996 11:07:48 PSTFrom: <b>Martin Tompa <tompa@geoduck.cs.washington.edu></b></a>We have a notetaker for today (1/16) but need volunteers starting Thursday(1/18). If you are signed up for credit with notetaking as part of the plan,and haven't yet taken notes, please send me mail saying which of the nextseveral dates you can take notes. I'll then come up with a schedule. <hr size=4><a name="821846259001">To: cse590bi@geoduckSubject: <b>lineup of notetakers</b>Date: Tue, 16 Jan 1996 18:37:32 PSTFrom: <b>Martin Tompa <tompa@geoduck.cs.washington.edu></b></a>Thanks for the many volunteers. We've got enough for the time being again. Here's the lineup. Let me know if there are any conflicts.1/18: Mock1/23: Fulgham1/25: Fasulo1/30: Mumey2/1 : Madani2/6 : VanVleet2/8 : Jackson<hr size=4><a name="822340283001">To: cse590bi@geoduckSubject: <b>Lecture 6 available on the web</b>Date: Mon, 22 Jan 1996 11:50:58 PSTFrom: <b>Martin Tompa <tompa@geoduck.cs.washington.edu></b></a>For those of you anxious to work on the multiple string alignment homeworkproblems, Lecture 6 is now available on the course web. We will hand outpaper versions of it in Tuesday's lecture.<hr size=4><a name="822520024001">To: cse590bi@geoduckSubject: <b>lineup of notetakers completed</b>Date: Wed, 24 Jan 1996 13:46:52 PSTFrom: <b>Martin Tompa <tompa@geoduck.cs.washington.edu></b></a>Here's the final lineup for the remaining notetakers. If you are on thislist, please check below to make sure we've agreed on the date.1/25: Fasulo1/30: Mumey2/1 : Madani2/6 : Graham2/8 : Jackson2/13: VanVleet2/15: Thathachar2/20: Adams2/22: Chan2/27: Fix2/29: Lee3/5 : Hong3/7 : Adams<hr size=4><a name="822693690001">To: cse590bi@geoduckSubject: <b>Assignment 1, problem 3</b>Date: Fri, 26 Jan 1996 14:01:00 PSTFrom: <b>Martin Tompa <tompa@geoduck.cs.washington.edu></b></a>My instructions led you down a slightly wrong path on problem 3. You shouldassume that n is a power of 2, rather than one more than a power of 2, forsimplicity. A small bonus is that it means you can ignore all the ceilingnotation in the problem. A big bonus is that it means you won't have the samemisconception about how the algorithm works that I had until a few minutes ago.Sorry for misleading you.<hr size=4><a name="822779387001">Date: 27 Jan 1996 13:46 PSTFrom: <b>Larry Ruzzo <ruzzo@quinault.cs.washington.edu></b>To: cse590bi@csSubject: <b>Pevzner talks</b></a>here are abstracts of the two Pevzner talks mentioned in classrecently: > Date: Thu, 25 Jan 1996 14:51:02 -0800 (PST) > Subject: UW-CSE Colloq / 2-5-96 / Pevzner / USC / Genome Rearrangements, or, What Dobzhansky and Sturtevant Did Not Tell Us > > > UNIVERSITY OF WASHINGTON > Seattle, Washington 98195 > > Department of Computer Science and Engineering > Box 352350 > (206) 543-1695⌨️ 快捷键说明
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