From owner-population-bio@net.bio.net Wed Sep 01 23:00:00 1993 Path: biosci!rutgers!cs.utexas.edu!uunet!pipex!zaphod.crihan.fr!univ-lyon1.fr!cri.ens-lyon.fr!ibcp.fr!deleage From: deleage@ibcp.fr (G.Delage) Newsgroups: bionet.population-bio Subject: ANTHEPROT: A package for protein sequence analysis Message-ID: <264uf0$fbm@cri.ens-lyon.fr> Date: 2 Sep 93 14:03:12 GMT Organization: Institut de Biologie et Chimie des Proteines. CNRS-Lyon Lines: 120 NNTP-Posting-Host: ibcp.fr X-Newsreader: TIN [version 1.1 PL8] -- ------------------------------------------------------------------------ # # # ####### # # ####### ###### ###### ####### ####### # # ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ####### ##### ###### ###### # # # ####### # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # ####### # # # ####### # ----------------------------------------------------------------------- by G.Deleage & C. Geourjon This is a general annoucement of the availability of ANTHEPROT to all academic researchers. ANTHEPROT (ANalyze THE PROTeins) is a package to make protein sequence analysis such as alignment, secondary structure predictions, sites & function detection, physico-chemical profiles, homology search and 3D display of protein structures. This program is now available either for IBM RISC 6000 workstations or IBM PC compatible microcomputers. The main feature of ANTHEPROT is that it is fully interactive within a graphical interface. No particular knowledge about computers is needed and any mole- cular biologist is able to use it. The main methods are: * Input, addition or modification of sequences (FASTA format). * Edition (graphic display of sequence, molecular weight,...). * Extraction of a sequence from databases (SWISSPROT). * Search for subsequences (with pattern matching approach). * Dot matrix plot (4 substitution matrix). * Secondary structure prediction (6 methods). * Profile analysis (Hydrophobicity, flexibility, solvant accessibility, membrane spanning regions, antigenicity,...). * Amphiphilicity of secondary structure. * Prediction of the cleavage site of signal peptide. * Helical wheel projection. * Protein digestion and RP-HPLC simulations. * Circular dichroism spectra analysis. * Search for pattern of biological sites and functions (PROSITE). * Matrix profile analysis of blocks (BLOCKS.DAT). * Multiple alignment methods. * Fasta graphical interface. IBM RISC 6000 version ===================== This version can be considered as a molecular graphic software that is very useful to those who want to play with molecular modelling of proteins. These graphic capabilities are combined with many powerful tools to analyze a protein sequence and structure. The ANTHEPROT package is made of more than 71 submenus which account for about 30 different methods of protein sequence analysis. The complete package represents: 50 000 lines of source code 500 subroutines 1 3000 000 octets of source code 2 6800 000 octets for the antheprot executable file Systems and materials --------------------- ANTHEPROT can run on all IBM Risc 6000 computer equipped with a 3 D graphic adapter (with or without Z buffer, 8 or 24 bits plane) with graPHIGS libraries installed (libgP.a). The perfect configuration : IBM Risc 6000 (any model of CPU from 220 to 580) with at least 32 Mo of RAM), valuators, LPFK, 3 D+ graphic adapter with 24 bits plane + Z buffer or GT4x and GTO graphic cards. About 160 Mo of disk place is needed since the SWISSPROT and the NBRF/PIR protein sequence databases are also included. Distribution support : 150Mo streamer cartridge. References: C. Geourjon, G. Deleage and B. Roux ANTHEPROT : An interactive graphic software for analyzing protein structures from sequences. J. Mol. Graph., 1991, 9, 188-190 Geourjon C., Deleage G. Interactive and graphic coupling between multiple alignments, secondary structure predictions and motif/pattern scanning into proteins. Comput. Appl. Biosci. 9:87-91(1993). G. Deleage and C. Geourjon An interactive graphic program for calculating secondary structures content of proteins from circular dichroism spectrum. CABIOS, 1993, 9, 197-199 IBM PC compatible version ========================= The methods are essentailly the same than in the RISC 6000 except for the 3D display module. ANTHEPROT works onto all 80x86 with x>=2 processors. Math coprocessor is fully supported. The total disk space needed is about 5Mo. It is supplied onto 2 HD (1.44Mo) disks. An automatic installation menu is available by typing A:install The maximal graphic resolution supported is VGA (640x480). The program can be fully mouse driven (Microsoft compatible). Distribution support : 2 MS-DOS fomatted HD disks (1.44Mo) References: G. Deleage, FF Clerc and B Roux ANTHEPROT: IBM PC and Apple Macintosh versions. CABIOS, (1989) 5, 159-160 G. Deleage, FF Clerc, B Roux and DC Gautheron ANTHEPROT: A package for protein sequence analysis using a microcomputer. CABIOS, (1988) 5, 159-160 ===================================================================== # Institut de Biologie et Chimie des Proteines. UPR 412-CNRS # # ***** ***** **** ***** Dr Gilbert Deleage # # # # # # # # # 7, passage du Vercors # # # ***** # # # 69367 Lyon Cedex 07 # # # # # # #**** Tel: (33) 72-72-26-47 # # # # # # # # Fax: (33) 72-72-26-01 # # ***** ****** **** # deleage@ibcp.fr # ===================================================================== From owner-population-bio@net.bio.net Thu Sep 02 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!math.ohio-state.edu!uwm.edu!psuvax1!psuvm!n8b From: N8B@psuvm.psu.edu Newsgroups: bionet.population-bio Subject: paternity testing Message-ID: <93246.112625N8B@psuvm.psu.edu> Date: 3 Sep 93 15:26:25 GMT Organization: Penn State University Lines: 9 Hello - we're looking for any information on paternity testing in amphibians (salamanders, specifically). Has anyone out there currently doing paternity research with amphibians found any useful molecular markers? Any references or suggestions would be greatly appreciated. Thanks in advance! Nancy Bowers Penn State University From owner-population-bio@net.bio.net Sun Sep 05 23:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!howland.reston.ans.net!xlink.net!math.fu-berlin.de!tertius.in-berlin.de!novell_achtman!Achtman From: Achtman@MPIMG-Berlin-Dahlem.MPG.DE (Mark Achtman) Newsgroups: bionet.population-bio Subject: MEGA address Message-ID: Date: 6 Sep 93 23:13:27 GMT Organization: Max Planck Institut fuer molekulare Genetik, Berlin Lines: 14 Nntp-Posting-Host: novell_achtman.rz-berlin.mpg.de Nntp-Posting-User: nntp_client X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I've been trying to send an E-mail to get MEGA and it keeps bouncing whether I send it to IMEG@psuvm.psu.edu ot to IMEG@psuvm. Could somebody please supply me with a correct address? Or a suggestion why E-mail to that address bounces. Thanks in advance Mark Achtman Achtman@MPIMG-Berlin-Dahlem.MPG.DE -------------------------------------------------------- Mark Achtman, Max-Planck Institut f|r molekulare Genetik Ihnestra_e 73, D-14169 Berlin, Germany e-mail: Achtman@MPIMG-Berlin-Dahlem.MPG.DE From owner-population-bio@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!kuhub.cc.ukans.edu!jimdb From: jimdb@kuhub.cc.ukans.edu Newsgroups: bionet.announce,bionet.population-bio,bionet.molbio.evolution,sci.bio,sci.environment,sci.research,talk.environment Subject: 14TH MIDWESTERN CONFERENCE ON POPULATION BIOLOGY Message-ID: <1993Sep8.230149.53395@kuhub.cc.ukans.edu> Date: 9 Sep 93 04:01:49 GMT Sender: kristoff@net.bio.net Organization: University of Kansas Academic Computing Services Lines: 220 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.announce:691 bionet.population-bio:477 bionet.molbio.evolution:1058 sci.bio:4757 sci.environment:11447 sci.research:1259 talk.environment:6444 The 14th Annual MIDWEST CONFERENCE ON POPULATION BIOLOGY University of Kansas, Lawrence 12-14 November 1993 This year's Midwest Conference on Population Biology will take place at the University of Kansas on 12-14 November 1993. The MCPB provides an excellent opportunity for the exchange of ideas within the broad scope of population biology, including (but not limited to) genetics, ecology, evolution, and behavior, and from both empirical and theoretical perspectives. Besides the customary selection of outstanding speakers (see SCHEDULE OF EVENTS), this year's program will feature a contributed poster session (see POSTER SESSION for details) and a panel discussion on the topic: "Reconciling "Good" Science with Conservation Imperatives: Problems and Prospects." LOCATION: All talks will be held in Haworth Hall, room 1005. Posters will be displayed in the foyer. PARKING: Free parking begins after 4:00 PM on Friday in all Yellow Zones. We recommend the use of Lot 90, located just south of Haworth Hall; it has many spaces and is convenient to the meeting site. FRIDAY NIGHT RECEPTION: Conference participants and friends are invited to meet at the 2nd floor lobby of the Burge Union on Friday evening from 6:00 to 11:30 PM. Late registration will also be available. Please park in lot 72 on the east side of the building. MIXER, BANQUET, AND PLENARY ADDRESS: These Saturday evening events will be held at The American Bistro; all participants are encouraged to attend. Daniel Simberloff, Florida State University, will present the plenary address following the meal. LODGING: The following is a list of twelve Lawrence hotels (area code 913): Singl./dbl. 1. Best Western (800/528-1234, 841-6500) $29/$33 2. Bismark Inn (749-4040) $32/$38 3. College Motel (843-0131) 4. Days Inn (800/325-2525, 843-9100) $43/$46 5. Eldridge Hotel (800/527-0909, 749-5011) $66/$74 6. Holiday Inn (800/465-4329, 841-7077) $64/$70 7. Jayhawk Motel (843-4131) $22/$25 8. Quality Inn (842-7030) $46/$54 9. Super 8 Motel (800/800-8000, 842-5217) $34/$40 10. Travelodge (842-5100) $39/$43 11. Virginia Inn (800/468-8979, 843-6611) $33/$40 12. Westminister Inn (841-8410) $34/$42 We encourage you to make reservations early to ensure room availability, but please note that hotels are not within easy walking distance of Haworth Hall. For those willing to bring their own sleeping bag, floor space will be available at no cost, although space is limited. Contact Barbara Hayford at 913/842-4776 for further information. POSTER SESSION: Abstracts of posters should be sent to Jim Danoff-Burg (see address below) by 31 October 1993 and _must_ be submitted on diskette Macintosh format) to be included in the MCPB program. Please also enhardcopy and a note explaining what software was uand tape to mount your poster (1.2 x 2.4 m). Posters will be onday Saturday, although authors will be available for questions during a period immediately following lunch. NB: A prize will be awarded. SCHEDULE OF EVENTS Friday, 12 November 6:00 - 11:30 PM Reception and late registration (2nd floor lobby, Burge Union). Saturday, 13 November Morning Session (1005 Haworth Hall): "Population Ecology" 8:45 - 9:00 AM Welcome and Introductory Remarks. 9:00 - 9:40 Jane H. Bock, University of Colorado. Soil seed banks: Records of the past and predictors of the future. 9:40 - 10:20 Victoria L. Sork, University of Missouri -- St. Louis. Impact of natural selection and gene flow on genetic differentiation among local subpopulations of temperate forest oaks. 10:40 - 11:20 Carl E. Bock, University of Colorado. Effects of ungulate grazing on grassland ecosystems: Evidence from the Great Plains and American Southwest. 11:20 - 12:00 Andrew Sih, University of Kentucky. Ecological factors influencing the 'battle between the sexes': Experimental studies on water strider mating dynamics. Afternoon Session (1005 Haworth Hall): Posters, "The Genetics and Evolution of Sociality," and Panel Discussion 1:00 - 1:40 PM Poster presentations. 1:40 - 2:20 Deborah R. Smith, University of Kansas. Population genetics in cooperative spiders. 2:20 - 3:00 Zuleyma Tang-Martinez, University of Missouri -- St. Louis. Inclusive fitness and the evolution of sociality: Cause or consequence? 3:20 - 4:00 Diana Wheeler, University of Arizona. Castes in social insects as alternative phenotypes. 4:00 - 5:00 Panel Discussion: Reconciling "Good" Science with Conservation Imperatives: Problems and Prospects. Evening Session (The American Bistro, 1st floor of the Eldridge Hotel) 5:00 - 6:30 PM Mixer. 6:30 - 8:00 Banquet. 8:00 - 9:00 Plenary Address: Daniel Simberloff, Florida State University. Sunday, 14 November Morning Session (1005 Haworth Hall): "Evolutionary Biology" 9:00 - 9:40 AM Michael Ryan, University of Texas. Historical and sensory aspects of sexual selection. 9:40 - 10:20 Richard Gomulkiewicz, University of Kansas. The evolution of age-dependent sexually selected traits. 10:40 - 11:20 Ruth Shaw, University of Minnesota. Evolutionary genetics of plant interactions. 11:20 - 12:00 Mark Kirkpatrick, University of Texas. Constraint and adaptation in the evolution of growth. 12:00 - 12:30 Closing Remarks and Business Meeting. - - - - - - - - - - - - - - - - - (cut here) - - - - - - - - - - - - - - - - - REGISTRATION FORM: Please return this form and a check by 31 October 1993 to Jim Danoff-Burg, MCPB, Snow Entomological Museum, University of Kansas, Lawrence, KS 66045. Late registrants will be charged an additional $10. REGISTRATION (Students $15.00, Professionals $25.00): $______________ BANQUET ($17.50): $______________ Menu preference (circle one): SPINACH MANICOTTI or CHICKEN DIJON. The delicious buffet will also include a full salad bar, two vegetables, dessert, and coffee/tea. TOTAL AMOUNT ENCLOSED: $______________ (Make checks payable to the _Division of Biological Sciences_.) NAME: I plan to present a poster _______ (yes/no) INSTITUTION: ADDRESS: PHONE: EMAIL: - - - - - - - - - - - - - - - - - (cut here) - - - - - - - - - - - - - - - - - FOR ADDITIONAL INFORMATION: Contact Jim Danoff-Burg, 913/749-1034. (Email: jimdb@kuhub.cc.ukans.edu). $ -- ---------------------------------------------------------------------- Jim Danoff-Burg (Snow Museum, Univ. of Kansas, Lawrence, KS 66045) Bitnet: JIMDB@UKANVAX Internet:jimdb@kuhub.cc.ukans.edu "Myrmecophiles-R-Us" From owner-population-bio@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!caen!kuhub.cc.ukans.edu!jimdb From: jimdb@kuhub.cc.ukans.edu Newsgroups: bionet.biology.tropical,bionet.population-bio Subject: 14TH MIDWESTERN CONFERENCE ON POPULATION BIOLOGY Message-ID: <1993Sep8.231048.53397@kuhub.cc.ukans.edu> Date: 9 Sep 93 04:10:48 GMT Organization: University of Kansas Academic Computing Services Lines: 203 Xref: biosci bionet.biology.tropical:256 bionet.population-bio:478 The 14th Annual MIDWEST CONFERENCE ON POPULATION BIOLOGY University of Kansas, Lawrence 12-14 November 1993 This year's Midwest Conference on Population Biology will take place at the University of Kansas on 12-14 November 1993. The MCPB provides an excellent opportunity for the exchange of ideas within the broad scope of population biology, including (but not limited to) genetics, ecology, evolution, and behavior, and from both empirical and theoretical perspectives. Besides the customary selection of outstanding speakers (see SCHEDULE OF EVENTS), this year's program will feature a contributed poster session (see POSTER SESSION for details) and a panel discussion on the topic: "Reconciling "Good" Science with Conservation Imperatives: Problems and Prospects." LOCATION: All talks will be held in Haworth Hall, room 1005. Posters will be displayed in the foyer. PARKING: Free parking begins after 4:00 PM on Friday in all Yellow Zones. We recommend the use of Lot 90, located just south of Haworth Hall; it has many spaces and is convenient to the meeting site. FRIDAY NIGHT RECEPTION: Conference participants and friends are invited to meet at the 2nd floor lobby of the Burge Union on Friday evening from 6:00 to 11:30 PM. Late registration will also be available. Please park in lot 72 on the east side of the building. MIXER, BANQUET, AND PLENARY ADDRESS: These Saturday evening events will be held at The American Bistro; all participants are encouraged to attend. Daniel Simberloff, Florida State University, will present the plenary address following the meal. LODGING: The following is a list of twelve Lawrence hotels (area code 913): Singl./dbl. 1. Best Western (800/528-1234, 841-6500) $29/$33 2. Bismark Inn (749-4040) $32/$38 3. College Motel (843-0131) 4. Days Inn (800/325-2525, 843-9100) $43/$46 5. Eldridge Hotel (800/527-0909, 749-5011) $66/$74 6. Holiday Inn (800/465-4329, 841-7077) $64/$70 7. Jayhawk Motel (843-4131) $22/$25 8. Quality Inn (842-7030) $46/$54 9. Super 8 Motel (800/800-8000, 842-5217) $34/$40 10. Travelodge (842-5100) $39/$43 11. Virginia Inn (800/468-8979, 843-6611) $33/$40 12. Westminister Inn (841-8410) $34/$42 We encourage you to make reservations early to ensure room availability, but please note that hotels are not within easy walking distance of Haworth Hall. For those willing to bring their own sleeping bag, floor space will be available at no cost, although space is limited. Contact Barbara Hayford at 913/842-4776 for further information. POSTER SESSION: Abstracts of posters should be sent to Jim Danoff-Burg (see address below) by 31 October 1993 and _must_ be submitted on diskette (IBM or Macintosh format) to be included in the MCPB program. Please also enclose a hardcopy and a note explaining what software was used. Bring both thumb tacks and tape to mount your poster (1.2 x 2.4 m). Posters will be on display all day Saturday, although authors will be available for questions during a period immediately following lunch. NB: A prize will be awarded. SCHEDULE OF EVENTS Friday, 12 November 6:00 - 11:30 PM Reception and late registration (2nd floor lobby, Burge Union). Saturday, 13 November Morning Session (1005 Haworth Hall): "Population Ecology" 8:45 - 9:00 AM Welcome and Introductory Remarks. 9:00 - 9:40 Jane H. Bock, University of Colorado. Soil seed banks: Records of the past and predictors of the differentiation am temperate forest oaks. 10:40 - 11:20 Carl E. Bock, University of Colorado. Effects of ungulate grazing on grassland ecosystems: Evidence from the Great Plains and American Southwest. 11:20 - 12:00 Andrew Sih, University of Kentucky. Ecological factors influencing the 'battle between the sexes': Experimental studies on water strider mating dynamics. Afternoon Session (1005 Haworth Hall): Posters, "The Genetics and Evolution of Sociality," and Panel Discussion 1:00 - 1:40 PM Poster presentations. 1:40 - 2:20 Deborah R. Smith, University of Kansas. Population 4:00 - 5:00 Panel Discussion: Reconciling "Good" Science with Conservation Imperatives: Problems and Prospects. Evening Session (The American Bistro, 1st floor of the Eldridge Hotel) 5:00 - 6:30 PM Mixer. 6:30 - 8:00 Banquet. 8:00 - 9:00 Plenary Address: Daniel Simberloff, Florida State University. Sunday, 14 November Morning Session (1005 Haworth Hall): "Evolutionary Biology" 9:00 - 9:40 AM Michael Ryan, University of Texas. Historical and sensory aspects of sexual selection. 9:40 - 10:20 Richard Gomulkiewicz, University of Kansas. The evolution of age-dependent sexually selected traits. 10:40 - 11:20 Ruth Shaw, University of Minnesota. Evolutionary genetics of plant interactions. 11:20 - 12:00 Mark Kirkpatrick, University of Texas. Constraint and adaptation in the evolution of growth. 12:00 - 12:30 Closing Remarks and Business Meeting. - - - - - - - - - - - - - - - - - (cut here) - - - - - - - - - - - - - - - - - REGISTRATION FORM: Please return this form and a check by 31 October 1993 toBANQUET ($17.50): $______________ Menu preference (circle one): SPINACH MANICOTTI or CHICKEN DIJON. The delicious buffet will also include a full salad bar, two vegetables, dessert, and coffee/tea. TOTAL AMOUNT ENCLOSED: $______________ (Make checks payable to the _Division of Biological Sciences_.) NAME: I plan to present a poster _______ (yes/no) INSTITUTION: ADDRESS: PHONE: EMAIL: - - - - - - - - - - - - - - - - - (cut here) - - - - - - - - - - - - - - - - - FOR ADDITIONAL INFORMATION: Contact Jim Danoff-Burg, 913/749-1034. (Email: jimdb@kuhub.cc.ukans.edu). $ -- ---------------------------------------------------------------------- Jim Danoff-Burg (Snow Museum, Univ. of Kansas, Lawrence, KS 66045) Bitnet: JIMDB@UKANVAX Internet:jimdb@kuhub.cc.ukans.edu "Myrmecophiles-R-Us" From owner-population-bio@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!olivea!pagesat!ukma!widener!dsinc!netnews.upenn.edu!barkdoll From: barkdoll@lepomis.psych.upenn.edu (Edwin Barkdoll) Newsgroups: sci.bio.ecology,bionet.population-bio Subject: Kaibab deer herd eruption question Message-ID: <146027@netnews.upenn.edu> Date: 9 Sep 93 21:53:29 GMT Sender: news@netnews.upenn.edu Followup-To: sci.bio.ecology Organization: University of Pennsylvania Lines: 26 Xref: biosci sci.bio.ecology:345 bionet.population-bio:479 Nntp-Posting-Host: lepomis.psych.upenn.edu Graeme Caughley [Eruption of ungulate populations, with emphasis on Himalayan Thar in New Zealand. _Ecology_ 1970 51(1)] discusses the unreliability of data regarding the alleged eruption of the Kaibab deer herd 1906-1924 and concludes, "...the factors that may have resulted in an upsurge of deer are hopelessly confounded. The study is unlikely to teach us much about eruption of unngulate populations." I find his arguments reasonably convincing - although many of the source articles are difficult to obtain he reproduces graphs and data from important ones - yet many texts (e.g. Peek's 1986 _A Review of Wildlife Management_; Belanger's 1988 _Managing American Wildlife_) still refer to the explosion of deer numbers to 100,000 from 4,000 and subsequent crash to 40,000 over 2 winters as though the data were unequivocal and the conclusions were obvious. Is there some reason that Caughley's conclusions are not accepted generally (some texts _do_ accept them), are they not widely known (I find it impossible to believe that Peek is not aware of them)...? -- Edwin Barkdoll barkdoll@lepomis.psych.upenn.edu eb3@world.std.com From owner-population-bio@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!agate!news.ucdavis.edu!josquin.!john From: john@josquin.ucdavis.edu (John Gillespie) Newsgroups: bionet.population-bio Subject: Postdoc available Keywords: postdoc Message-ID: Date: 10 Sep 93 22:47:28 GMT Sender: usenet@ucdavis.edu (News Administrator) Organization: University of California, Davis Lines: 16 X-Newsreader: TIN [version 1.2 PL1] Post Doctoral Fellowship in Theoretical Population Genetics Michael Turelli and John Gillespie have funds for a one-year postdoctoral fellow effective immediately. If you are interested in pushing back the frontiers of human knowledge concerning theoretical analyses of molecular evolution or quantitative genetics, this may be for you! Send inquiries to: John Gillespie Section of Evolution and Ecology University of California Davis CA 95616 jhgillespie@ucdavis.edu From owner-population-bio@net.bio.net Fri Sep 10 23:00:00 1993 Path: biosci!rutgers!uwm.edu!wupost!kuhub.cc.ukans.edu!jimdb From: jimdb@kuhub.cc.ukans.edu Newsgroups: bionet.biology.tropical,bionet.population-bio,bionet.general,bionet.jobs,bionet.agroforestry,bionet.molbio.evolution,sci.bio,sci.environment,sci.research,talk.environment Subject: REPOST: 14th Midwest Conf. Population Biology at KU Message-ID: <1993Sep11.035224.53504@kuhub.cc.ukans.edu> Date: 11 Sep 93 08:52:24 GMT Organization: University of Kansas Academic Computing Services Lines: 208 Xref: biosci bionet.biology.tropical:258 bionet.population-bio:481 bionet.general:6025 bionet.jobs:2262 bionet.agroforestry:376 bionet.molbio.evolution:1065 sci.bio:4798 sci.environment:11524 sci.research:1300 talk.environment:6462 Howdy folks, sorry about the mess up with the previous posting (if you read it), all of the margins were far too wide and it came out looking barely legible. Anyway, I hope that this is more legible. BTW: Please do consider coming to our little rendezvous, as I think it will be a very stimulating and fascinating experience. If you have any questions, feel free to contact me directly. =============================Begin Repost============================= The 14th Annual MIDWEST CONFERENCE ON POPULATION BIOLOGY University of Kansas, Lawrence 12-14 November 1993 This year's Midwest Conference on Population Biology will take place at the University of Kansas on 12-14 November 1993. The MCPB provides an excellent opportunity for the exchange of ideas within the broad scope of population biology, including (but not limited to) genetics, ecology, evolution, and behavior, and from both empirical and theoretical perspectives. Besides the customary selection of outstanding speakers (see SCHEDULE OF EVENTS), this year's program will feature a contributed poster session (see POSTER SESSION for details) and a panel discussion on the topic: "Reconciling "Good" Science with Conservation Imperatives: Problems and Prospects." LOCATION: All talks will be held in Haworth Hall, room 1005. Posters will be displayed in the foyer. PARKING: Free parking begins after 4:00 PM on Friday in all Yellow Zones. We recommend the use of Lot 90, located just south of Haworth Hall; it has many spaces and is convenient to the meeting site. FRIDAY NIGHT RECEPTION: Conference participants and friends are invited to meet at the 2nd floor lobby of the Burge Union on Friday evening from 6:00 to 11:30 PM. Late registration will also be available. Please park in lot 72 on the east side of the building. MIXER, BANQUET, AND PLENARY ADDRESS: These Saturday evening events will be held at The American Bistro; all participants are encouraged to attend. Daniel Simberloff from Florida State University will present the plenary address following the meal. LODGING: The following is a list of twelve Lawrence hotels (area code 913): Singl./dbl. 1. Best Western (800/528-1234, 841-6500) $29/$33 2. Bismark Inn (749-4040) $32/$38 3. College Motel (843-0131) 4. Days Inn (800/325-2525, 843-9100) $43/$46 5. Eldridge Hotel (800/527-0909, 749-5011) $66/$74 6. Holiday Inn (800/465-4329, 841-7077) $64/$70 7. Jayhawk Motel (843-4131) $22/$25 8. Quality Inn (842-7030) $46/$54 9. Super 8 Motel (800/800-8000, 842-5217) $34/$40 10. Travelodge (842-5100) $39/$43 11. Virginia Inn (800/468-8979, 843-6611) $33/$40 12. Westminister Inn (841-8410) $34/$42 We encourage you to make reservations early to ensure room availability, but please note that hotels are not within easy walking distance of Haworth Hall. For those willing to bring their own sleeping bag, floor space will be available at no cost, although space is limited. Contact Barbara Hayford at 913/842-4776 for further information. POSTER SESSION: Abstracts of posters should be sent to Jim Danoff-Burg (see address below) by 31 October 1993 and _must_ be submitted on diskette (IBM or Macintosh format) to be included in the MCPB program. Please also enclose a hardcopy and a note explaining what software was used. Bring both thumb tacks and tape to mount your poster (1.2 x 2.4 m). Posters will be on display all day Saturday, although authors will be available for questions during a period immediately following lunch. NB: A prize will be awarded. SCHEDULE OF EVENTS Friday, 12 November 6:00-11:30 PM Reception and late registration (2nd floor lobby, Burge Union). Saturday, 13 November MORNING SESSION (1005 Haworth Hall): "Population Ecology" 8:45-9:00 AM Welcome and Introductory Remarks. 9:00-9:40 AM Jane H. Bock, University of Colorado. "Soil seed banks: Records of the past and predictors of the future." 9:40-10:20 AM Victor 10:40-11:20 AM Carl E. Bock, University of Colorado. "Effects of ungulate grazing on grassland ecosystems: Evidence from the Great Plains and American Southwest." 11:20-12:00 AM Andrew Sih, University of Kentucky. "Ecological factors influencing the 'battle between the sexes': Experimental studies on water strider mating dynamics." POSTER SESSION (Haworth Hall foyer) 1:00-1:40 PM Poster presentations. AFTERNOON SESSION (1005 Haworth Hall): "The Genetics and Evolution of Sociality" 1:40-2:20 PM Deborah R. Smith, University of Kansas. "Population genetics in cooperative spiders." 2:20-3:00 PM Zuleyma Tang-Martinez, University of Missouri, St. Louis. "Inclusive fitness and the evolution of sociality: Cause or consequence?" 3:20-4:00 PM Diana Wheeler, University of Arizona. "Castes in social insects as alternative phenotypes." PANEL DISCUSSION (1005 Haworth Hall) 4:00-5:00 PM Discussion topic: "Reconciling 'Good' Science with Conservation Imperatives: Problems and Prospects." EVENING SESSION (The American Bistro, 1st floor of the Eldridge Hotel) 5:00-6:30 PM Mixer. 6:30-8:00 PM Banquet. 8:00-9:00 PM Plenary Address: Daniel Simberloff, MORNING SESSION (1005 Haworth Hall): "Evolutionary Biology" 9:00-9:40 AM Michael Ryan, University of Texas. "Historical and sensory aspects of sexual selection." 9:40-10:20 AM Richard Gomulkiewicz, University of Kansas. "The evolution of age-dependent sexually selected traits." 10:40-11:20 AM Ruth Shaw, University of Minnesota. "Evolutionary genetics of plant interactions." 11:20-12:00 AM Mark Kirkpatrick, University of Texas. "Constraint and adaptation in the evolution of growth." 12:00-12:30 PM Closing Remarks and Business Meeting. - - - - - - - - - - - - - - (cut here) - - - - - - - - - - - - - REGISTRATION FORM: Please return this form and a check by 31 October 1993 to Jim Danoff-Burg, MCPB, Snow Entomological Museum, University of Kansas, Lawrence, KS 66045. Late registrants will be charged an additional $10. REGISTRATION FEE: $__________ Students $15.00, Professionals $25.00; Late fee +$10.00. BANQUET: $__________ Cost $17.50. Menu preference (circle one): SPINACH MANICOTTI or CHICKEN DIJON. The delicious buffet will also include a full salad bar, two vegetables, Biological Sciences. NAME: INSTITUTION: ADDRESS: PHONE: EMAIL: I plan to present a poster _______ (yes/no). - - - - - - - - - - - - - - (cut here) - - - - - - - - - - - - - FOR ADDITI-- ---------------------------------------------------------------------- Jim Danoff-Burg (Snow Museum, Univ. of Kansas, Lawrence, KS 66045) Bitnet: JIMDB@UKANVAX Internet:jimdb@kuhub.cc.ukans.edu "Myrmecophiles-R-Us" From owner-population-bio@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!news.ecn.bgu.edu!wupost!gumby!yale!yale.edu!news.yale.edu!minerva!una From: una@minerva.cis.yale.edu (Una Smith) Newsgroups: sci.bio.ecology,sci.bio,bionet.population-bio Subject: Populus on sunsite.unc.edu Keywords: population biology simulation software PC sunsite Message-ID: <1993Sep14.162932.21562@news.yale.edu> Date: 14 Sep 93 16:29:32 GMT References: <9309132320.AA29751@umailsrv0.UMD.EDU> Sender: smith-una@yale.edu Followup-To: sci.bio Organization: Department of Biology, Yale University Lines: 34 Xref: biosci sci.bio.ecology:411 sci.bio:4848 bionet.population-bio:482 Nntp-Posting-Host: minerva.cis.yale.edu Donald Alstad wrote: >I have just posted a new version of Populus (v.3.2) for anonymous FTP on >the Minnesota Ecology Server, ecology.ecology.umn.edu, in the directory >/pub/populus. As I have the old version on the Ecology and Evolution gopher/anonymous FTP server on sunsite.unc.edu, I will update it to this version, for the convenience of gopher users. Gopher to sunsite.unc.edu, and choose this sequence of menu items: Sunsite Archives Ecology and Evolution Contributed research papers and tools PC software and files Or, from any gopher offering other biology gophers by topic, look for the menu item "Ecology and Evolution [at UNC and Yale]" and so on. If you have telnet, but not gopher, you can telnet to sunsite.unc.edu and log in to the public gopher server, no password required. You can also use anonymous FTP to sunsite.unc.edu, where the directory path is pub/academic/biology/ecology+evolution/contrib/pc/ There are other new programs available in the ...contrib/mac/ directory. My thanks to Jean Thioulouse for his Macintosh programs for multivariate data analysis. -- Una Smith Department of Biology smith-una@yale.edu Yale University New Haven, CT 06511 From owner-population-bio@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!uknet!pipex!sunic!corax.udac.uu.se!zeta.bmc.uu.se!daresbury!daresbury!news From: szsdawsn@uk.ac.reading (Colin Dawson) Newsgroups: bionet.population-bio Subject: Population Genetics Group Annual Meeting Message-ID: <1993Sep14.164935.21665@gserv1.dl.ac.uk> Date: 14 Sep 93 16:26:52 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 26 Content-Type: TEXT/PLAIN; charset=US-ASCII Precedence: first-class Original-To: pop-bio@uk.ac.daresbury Mime-Version: 1.0 The 27th annual Population Genetics Group meeting will be held between 16-18th December, 1993 at Reading University, UK. If you would like to present a paper or a poster please contact me before 1st October, 1993 with details. This year there is a fine collection of invited speakers including David Balding on population genetics of DNA fingerprinting; Nick Barton on gene flow in heterogeneous environments; Esteban Domingo on the molecular evolution of viruses; Tom Kirkwood on molecular evolution; Mark MacNair on trade-offs in plants and Monty Slatkin on the population genetics of microsatellite loci. For further information please contact Mrs Gill Bogue School of Animal and Microbial Sciences University of Reading Whiteknights, P.O. Box 228 Reading RG6 2AJ UK Fax: (0734) 310180 Phone: (0734) 875123 ext.7068 Or contact me (Colin Dawson) via E-Mail on szsdawsn@reading.ac.uk From owner-population-bio@net.bio.net Wed Sep 15 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uunet!bloom-beacon.mit.edu!ai-lab!news.cs.umb.edu!casim.bio.umb.edu!etter From: etter@umbsky.cc.umb.edu (Ron Etter) Newsgroups: bionet.population-bio Subject: Text for Population Biology course? Message-ID: <27a8cm$200@cs.umb.edu> Date: 16 Sep 93 17:39:34 GMT Organization: UMass/Boston Lines: 33 NNTP-Posting-Host: casim.bio.umb.edu X-UserAgent: Nuntius v1.1.1d17 X-XXMessage-ID: X-XXDate: Thu, 16 Sep 93 13:40:02 GMT I am planning to teach a required course in Population Biology next semester and would appreciate any suggestions people may have as to a good textbook. The course is for biology majors that have completed 1 year of Intro Biology and Genetics. The previous instructor for this course used 2 textbooks, Ayala!s Population and Evolutionary Genetics: A Primer (Sinauer) and Kormondy!s Concepts of Ecology (Prentice-Hall). I would like to find something a bit more integrated, though a good combination of books would be fine too. So far the books I have considered are: Solbrig & Solbrig 1982 An Introduction to Population Biology and Evolution (out of print though) Hedrick 1984 Population Biology Wilson & Bossert 1971 (A classic) A Primer of Population Biology Begon & Mortimer 1986 Population Ecology Pianka 1988 Evolutionary Ecology I am leaning towards Hedrick!s book because it covers population genetics, evolution and population ecology at about the right level of sophistication and depth. Please send suggestions to me etter@umbsky.cc.umb.edu and I will post a summary for any others who might be interested. Thanks in advance for any suggestions. Ron Etter etter@umbsky.cc.umb.edu From owner-population-bio@net.bio.net Wed Sep 15 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uknet!pipex!uunet!olivea!news.bu.edu!pfoster From: pfoster@bu.edu (Patricia Foster) Newsgroups: bionet.population-bio Subject: bacterial growth curve Message-ID: <27ans9$ju7@news.bu.edu> Date: 16 Sep 93 22:03:52 GMT Organization: Boston University Lines: 15 NNTP-Posting-Host: acs.bu.edu X-Newsreader: TIN [version 1.2 PL0] Hi Netters, Can someone give me an equation describing the growth of bacteria that are running out of a nutrient. i.e. the growth rate starts out high and then smoothly decreases with time until it falls to 0. I know this would be a logistic equation, but I can't find or derive one describing exponential growth. Thanks, pat -- Patricia L. Foster Boston University School of Medicine Boston, MA USA pfoster@bu.edu From owner-population-bio@net.bio.net Thu Sep 16 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!dziuxsolim.rutgers.edu!gandalf.rutgers.edu!schaffnr From: schaffnr@gandalf.rutgers.edu (Donald Schaffner) Newsgroups: bionet.population-bio Subject: Re: bacterial growth curve Message-ID: Date: 17 Sep 93 16:36:19 GMT References: <27ans9$ju7@news.bu.edu> Organization: Rutgers Univ., New Brunswick, N.J. Lines: 23 > Can someone give me an equation describing the growth >of bacteria that are running out of a nutrient. i.e. the >growth rate starts out high and then smoothly decreases with >time until it falls to 0. We routinely use the Gompertz function for describing the whole curve (lag, exponential and stationary phases). y = a + c * exp(-exp(-b * (x-m))) where y = log number CFU/ml x = time a,c,b,m = regression parameters does this help? ================================================================= Don Schaffner Schaffner@Daemon.Rutgers.Edu Food Science Building, POB 231 Schaffner@Zodiac.Rutgers.Edu Extension Specialist in Food Science Don@CAFT1.Rutgers.Edu Rutgers - The State University of New Jersey (908) 932-9661 New Brunswick, NJ 08903 FAX (908) 932-6776 ================================================================= From owner-population-bio@net.bio.net Sun Sep 19 23:00:00 1993 Path: biosci!rutgers!gatech!howland.reston.ans.net!xlink.net!scsing.switch.ch!aristo.tau.ac.il!pc386 From: pc386@ccsg.tau.ac.il (BENNY SHOMER 9238) Newsgroups: bionet.population-bio Subject: Primers database through gopher. Message-ID: <1993Sep20.174902.25062@aristo.tau.ac.il> Date: 20 Sep 93 17:49:02 GMT Sender: usenet@aristo.tau.ac.il (USENET) Organization: Tel-Aviv University Computation Center Lines: 163 X-Newsreader: TIN [version 1.2 PL1] Hello Bionetters. It has been recently suggested that a searchable database of primers for PCR will be set. The basic idea behind this database is that only ___TESTED_&_WORKING___ (!!!) primers should be contained. This may save many valuable planning and working hours, as well as money. We all know that even carefully planned primers fail to operate when it comes down to the tubes... Dan Jacobson from the Johns Hopkins Univ. GDB, and your humble servant, are now working on the establishment of this database as a gopher server. Cited below is the suggested basic form for this database. We now open a discussion regarding the suggested data fields. We are interested in hearing your opinions regarding this form. Please pay attention to the following: 1. This message has been cross posted to several bionet.xxxx groups. It is suggested however, that the thread will be maintained in bionet.molbio. methds-reagnts . This will make it easier to read and respond to everyone's followups. 2. A followup to the newsgroup is prefferred over direct responses in the Email, so as to keep the thread open. If, for any reason you want to contact us directly, Dan's address is: danj@gdb.org, my @ is: pc386@ccsg.tau.ac.il We hope that this thread will be constructive, and that the database will be 'on the air' as soon as possible. Greetings, Dan Jacobson, Benny Shomer. This is the suggested form: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Primer Name: ______________________________ Target Gene: ______________________________________________________________ Species: ___________________________ Direction: { FOR / REV } Matching Primer(s) in this database: _________________________________ Sequence (5' --> 3'): ___________________________ Length: __ Flanking bases ______ to _____ on the target sequence. Product Length (cDNA):_______ Product Length (genomic):_______ {Lengths are in bp, or 0 for inverse PCR, where length is unknown} Restriction Site Added: _____________ Mutation presented at base: __ Special Applications: { Inverse/ RT-PCR/ Sequencing/ Cloning/ Mutation/ / Ligation Mediated} __________________________________________________________________________ __________________________________________________________________________ ******************** Cycle Conditions ********************************* Hot Start: {Yes/No} Initial Denaturation- Temp: __ Time: ____ Denaturation - Temp: __ Time: ____ Annealing - Temp: __ Time: ____ Extension - Temp: __ Time: ____ Number Of Cycles: __ Final Extension - Temp: __ Time: ____ ********************** Buffer Constituents **************************** (This section basically regards non-standard buffer constituents) Reaction Volume (ul): __ Used Standard Buffer Supplied By: _______________ MgCl2 Concentration (mM): __ DMSO Concentration (%): __ Formamide Concentration (%): __ Gelatin Concentration (%): __ dNTP's Concentration (uM): __ Primers Concentration (uM): __ Polymerase Type: ___________ Polymerase Concentration (U/Rxn.): ___ Make: _____________ ************************************************************************** Submitting Author. Name: __________________________________ Institution: ______________________________________________________________ __________________________________________________________________________ Address: _________________________________________________________________ __________________________________________________________________________ E-mail : ________________________________ Fax# : ______________________ References: __________________________________________________________________________ __________________________________________________________________________ __________________________________________________________________________ Remarks: __________________________________________________________________________ __________________________________________________________________________ __________________________________________________________________________ __________________________________________________________________________ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ************************************************************** * Benny Shomer * * Tel-Aviv University * * Sackler School of Medicine, Dept.of Embryology and Teratology* *--------------------------------------------------------------* * Snail: Ramat-Aviv , Tel-Aviv 69978 , Israel. * * E-mail : pc386@ccsg.tau.ac.il * * Tel : 972-3-640-9238 FAX : 972-3-642-2046 * * * %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % So Many Computers , So Little Time ... % % % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-population-bio@net.bio.net Sun Sep 19 23:00:00 1993 Path: biosci!SDSC.EDU!sulzbach From: sulzbach@SDSC.EDU (Dan Sulzbach) Newsgroups: bionet.population-bio Subject: Computational Ecology Position Opening Message-ID: <9309202030.AB10618@mailserver.sdsc.edu> Date: 20 Sep 93 20:30:10 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 29 COMPUTATIONAL ECOLOGY postion at the San Diego Supercomputer Center ----------------------------- The San Diego Supercomputer Center is a National Computational Science Laboratory operated by General Atomics and the National Science Foundation. It serves the nationwide community of scientists and engineers. We are currently accepting applications for a Staff Scientist in computational ecology to join our team of computational scientists. Areas of interest include, but are not limited to, simulation and spatial ecology. Requirements include a Ph.D. plus postdoctoral experience. In addition, a willingness to initiate an outreach program in, and collaborative projects with, the research community is necessary. General Atomics offers comprehensive salary and benefit plans as well as an exciting, dynamic environment well suited to applicants who are highly motivated and flexible. Please submit your letter of application, curriculum vitae, list of publications and three references to General Atomics, Dept. 93-23, P.O. Box 85608, San Diego, CA 92186-9784. EEO/AAE If you want further information about this position, please contact Rozeanne Steckler (steckler@sdsc.edu, 619-534-5122) or Dan Sulzbach (sulzbach@sdsc.edu, 619-534-5125) at SDSC. From owner-population-bio@net.bio.net Tue Sep 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!munnari.oz.au!newsroom.utas.edu.au!medicalsc49h103.med.utas.edu.au!user From: Kath.Nesbitt@plant.utas.edu.au (Michle Sale) Newsgroups: bionet.population-bio Subject: RAPD analysis Message-ID: Date: 22 Sep 93 01:13:43 GMT Followup-To: bionet.population-bio Organization: University of Tasmania Lines: 8 NNTP-Posting-Host: medicalsc49h103.med.utas.edu.au Hi! This is my first posting to this group, so I hope it works. I am looking for a computer programme that will calculate genetic distance (not create maps or do cladistic analysis) and which will accept missing data. I have sent a similar message to the mol. biol. RAPDS group, but noone has come up with anything usefulas yet. Thank you Katherine Nesbitt. From owner-population-bio@net.bio.net Tue Sep 21 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!xlink.net!scsing.switch.ch!cisun20!jgoudet From: jgoudet@ulci20.unil.ch (Jerome GOUDET) Newsgroups: bionet.population-bio Subject: Re: RAPD analysis Message-ID: <1993Sep22.143923.19220@ulci20.unil.ch> Date: 22 Sep 93 14:39:23 GMT References: Organization: University of Lausanne CH (Switzerland) Lines: 20 X-Newsreader: TIN [version 1.1 PL8] Michle Sale (Kath.Nesbitt@plant.utas.edu.au) wrote: > Hi! This is my first posting to this group, so I hope it works. I am > looking for a computer programme that will calculate genetic distance (not > create maps or do cladistic analysis) and which will accept missing data. I > have sent a similar message to the mol. biol. RAPDS group, but noone has > come up with anything usefulas yet. What type of genetic distances? BIOSYS-1 will calculate for you a large number of them, some satisfying the triangular inequality, others not. If you want distance a la Reynolds (Reynolds \& al, 1983), I have a pascal version of Weir program that could be used, with some data transforms... Hope it helps. Jerome GOUDET (jerome.goudet@izea.unil.ch) > Thank you Katherine Nesbitt. -- +---------------------------------------------------------------------------+ | JEROME GOUDET Tel:(+4121) 692.24.58 | | Institut de Zoologie et (+4121) 692.24.63 (Secretariat) | | Ecologie Animale Fax:(+4121) 692.25.40 | From owner-population-bio@net.bio.net Tue Sep 21 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!news.claremont.edu!pomona!jnusser From: jnusser@pomona.claremont.edu (John Nusser) Newsgroups: bionet.population-bio Subject: DNA fingerprinting data analysis Message-ID: <1993Sep22.121120.1@pomona> Date: 22 Sep 93 19:11:20 GMT Sender: news@news.claremont.edu (The News System) Organization: Pomona College Lines: 12 Hi! I have two questions. One, could anyone suggest software that will analyze DNA fingerprints for Average band sharing, % polymorphic loci, and % heterozygosity? Two, If I have DNA fingerprints of birds that have been bred in captivity for many years, what kind of analysis can I do? Specifically, I would like to quantify the degree of genetic variability in these captive-bred populations. Can I do this is a statistically significant way? Please post your replies to Jnusser@pomona.claremont.edu. Thanks in advance, John Nusser From owner-population-bio@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.population-bio Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9309230900.AA09646@net.bio.net> Date: 23 Sep 93 09:00:03 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 243 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.welch.jhu.edu and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comme From owner-population-bio@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!library.ucla.edu!network.ucsd.edu!usenet From: andy@pooh.ucsd.edu Newsgroups: bionet.population-bio Subject: Re: RAPD analysis Message-ID: <27qmfnINN2ju@network.ucsd.edu> Date: 21 Sep 93 23:18:43 GMT References: Organization: University of California, San Diego Lines: 38 NNTP-Posting-Host: adizon.ucsd.edu MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In article , writes: > Path: network.ucsd.edu!munnari.oz.au!newsroom.utas.edu.au!medicalsc49h103.m ed.utas.edu.au!user > From: Kath.Nesbitt@plant.utas.edu.au (Michle Sale) > Newsgroups: bionet.population-bio > Subject: RAPD analysis > Followup-To: bionet.population-bio > Date: 22 Sep 1993 01:13:43 GMT > Organization: University of Tasmania > Lines: 8 > Distribution: world > Message-ID: > NNTP-Posting-Host: medicalsc49h103.med.utas.edu.au > > Hi! This is my first posting to this group, so I hope it works. I am > looking for a computer programme that will calculate genetic distance (not > create maps or do cladistic analysis) and which will accept missing data. I > have sent a similar message to the mol. biol. RAPDS group, but noone has > come up with anything usefulas yet. > > > Thank you Katherine Nesbitt. PAUP ver 3.1 by Swofford does it fine. It's available from the Center for Biodiversity. Check out how to order it via e-mail: younga@ux1.cso.uiuc.edu Andrew From owner-population-bio@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!uwm.edu!linac!att!princeton!phoenix.Princeton.EDU!dastratt From: dastratt@phoenix.Princeton.EDU (Donald A. Stratton) Newsgroups: bionet.population-bio Subject: Postdoc: Ecological genetics Message-ID: <1993Sep23.170521.6110@Princeton.EDU> Date: 23 Sep 93 17:05:21 GMT Sender: news@Princeton.EDU (USENET News System) Organization: Princeton University Lines: 32 Originator: news@nimaster Nntp-Posting-Host: phoenix.princeton.edu ECOLOGICAL GENETICS POSTDOC A postdoctoral position is available in my lab to study spatial and temporal variation in selection in oldfield populations of Erigeron annuus. The position is for two years starting in October. The salary range is $21,000 to $23,000. The Erigeron system has already yielded a lot of information about spatial variation in selection. My previous work on Erigeron has shown that variation in relative fitness is extremely fine-grained: most of the genotype-environment interactions for lifetime fitness occur over distances of only 10-20 cm. Very little is currently known about the relative importance of spatial and temporal variation in selection in natural populations. The goals of the current research are 1) to compare patterns of spatial vs. temporal variation in fitness in experimental populations and 2) to test several ecological factors that may cause variation in relative fitness among genotypes. The postdoctoral associate will help direct the ongoing studies of temporal variation in selection and will have ample opportunity to develop independent aspects of this research. Applicants should send a CV, a statement of research interests, and the names, addresses, and phone numbers of three references by October 15, 1993 to: Don Stratton Department of Ecology and Evolutionary Biology Princeton University Princeton, NJ 08544 phone: 609-258-6133 email:dastratt@pucc.princeton.edu From owner-population-bio@net.bio.net Thu Sep 23 23:00:00 1993 Path: biosci!MENDEL.BERKELEY.EDU!jose From: jose@MENDEL.BERKELEY.EDU (Jose Gutierrez) Newsgroups: bionet.population-bio Subject: address D. Young Message-ID: <9309242024.AA00456@mendel.Berkeley.EDU> Date: 24 Sep 93 20:24:40 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 Can anyone give me the address of Prof. Young, David. Dpt. Zoology, Univ. of Melbourne, Australia. Thank you jose jose@mendel.berkeley.edu From owner-population-bio@net.bio.net Wed Sep 29 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!mcsun!sun4nl!star.cs.vu.nl!balaena!mac_vers.bio.vu.nl!verse From: verse@bio.vu.nl (Henk W van Verseveld) Newsgroups: bionet.population-bio Subject: Re: RAPD analysis Message-ID: <1993Sep30.131446.1913@bio.vu.nl> Date: 30 Sep 93 13:14:46 GMT References: Sender: news@bio.vu.nl Organization: Vrije Universiteit-Faculty Biology Lines: 8 X-Xxmessage-Id: X-Xxdate: Thu, 30 Sep 93 13: 14:40 GMT X-Useragent: Nuntius v1.1.1d16 In article MichUle Sale, Kath.Nesbitt@plant.utas.edu.au writes: >create maps or do cladistic analysis) and which will accept missing data. I You could try Gelcompar from Applied Maths, Kortrijk, Belgium. The program does normalization of scanned gels and cluster analysis Fax: +32 56 402145 From owner-population-bio@net.bio.net Wed Sep 29 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uunet!haven.umd.edu!cville-srv.wam.umd.edu!usenet From: asmarina@next03epsl.wam.umd.edu (Ghermay Araya) Newsgroups: bionet.population-bio Subject: RESAMPLING SOLUTIONS TO PROBLEMS Message-ID: <28fj95$1af@cville-srv.wam.umd.edu> Date: 30 Sep 93 21:32:21 GMT Reply-To: THE ACM BUT HEADS Organization: University of Maryland College Park Lines: 178 NNTP-Posting-Host: next02wor.wam.umd.edu SOLUTIONS AND PROBLEMS TO PREVIOUS POSTING: Resampling, (bootstrapping, etc.), is revolutionizing the practice of statistic, and the way it is taught. For articles, and information on software + books, results of classroom trails, and descriptions of pending projects in which teachers can become involved, contact the University of Maryland's Resampling Project. We are especially interested in class testers. Contact: Resampling Project, attn. P.G. Bruce College of Business University of Maryland, College Park, MD 20742. Phone: 703-522-2713 FAX 703-522-5846 email pcbruce@wam.umd.edu (mark attn. P. C. Bruce). please provide both postal and email address. SOLUTIONS: Solution, Puzzle 1: 1. Three urns - "0,0"; "0,1"; "1,1". 2. Choose an urn at random. [Can do this on the computer with random selection of urn numbers, and then "If"] 3. Choose the first element in the chosen urn's vector. If "1", stop trial and make no further record. If "0", continue. 4. Record the second element in the chosen urn's vector on the scoreboard. 5. Repeat (2 - 5), and calculate the proportion "0s" on scoreboard. (Answer should be 2/3.) NUMBERS (1 2 3) a '"1" denotes a selection of urn 1 (u1), '"2" urn 2, "3" urn 3 NUMBERS (6 6) u1 '"u1" has two pennies (6's) NUMBERS (7 7) u2 '"u2" has two nickels (7's) NUMBERS (6 7) u3 '"u3" has one penny & one nickel REPEAT 1000 SAMPLE 1 a b 'Select an urn at random IF b =1 'If urn selector says urn 1 SHUFFLE u1 u1 'shuffle urn 1 TAKE u1 1 c11 'take one coin from urn 1, call it c11 IF c11=6 'if the coin is a penny TAKE u1 2 c12 'take the second coin IF c12=6 'if the second coin is a penny SCORE 6 z 'keep track of the second coin result END 'end IF conditions END END IF b =2 'if urn selector says urn 2 SHUFFLE u2 u2 'etc. as above TAKE u2 1 c21 IF c21=6 TAKE u2 2 c22 IF c22=6 SCORE 6 z END END END IF b =3 SHUFFLE u3 u3 TAKE u3 1 c31 IF c31=6 TAKE u3 2 c32 IF c32=6 SCORE 6 z END END END END 'End the experiment, go back and 'repeat until 1000 repetitions 'are complete COUNT z = 6 k DIVIDE k 1000 kk PRINT kk Answer: KK = 0.34 Solution: Puzzle 2 1. Put a white ball (later have the computer call it "7" to avoid confusion) or black (call it "8") in the urn with probability .5. 2. Put in a white and shuffle the two balls. 3. Take out a ball. If black, stop and make no record. 4. (If result of (3) is white): Take out the remaining ball, examine, and record its color. 5. Repeat steps 1-4 (say) until 1000 trials (with 1000 recordings) have been completed. (Alternatively, one can divide the number of repetitions by the number of records in the scoreboard). 6. Count the number and compute the proportion of whites (7s) among the trials where the result of step (3) is white. Carroll gives the answer as 2/3 (p. 32). COPY (7 8) A '7=WHITE COUNTER, 8=BLACK COUNTER. REPEAT 1000 SHUFFLE A B 'SHUFFLE THE TWO COUNTERS TAKE B 1 C 'TAKE A COUNTER FOR THE BAG CONCAT C 7 D 'JOIN A WHITE COUNTER TO THE BAG SHUFFLE D E 'SHUFFLE THE BAG TAKE E 1 F 'TAKE OUT A COUNTER IF F =7 'IF THE COUNTER YOU TAKE OUT IS WHITE TAKE E 2 G 'TAKE THE OTHER ONE SCORE G Z 'RECORD THIS SECOND ONE'S COLOR END END 'END THE REPEAT LOOP, GO BACK AND REPEAT COUNT Z =7 K 'COUNT HOW MANY TIMES SECOND ONE WAS WHITE DIVIDE K ZZ KK 'EXPRESS AS A PROPORTION OF THE NUMBER OF 'TRIALS ON WHICH THE FIRST ONE WAS WHITE. PRINT KK Answer: KK = 0.66356 FROM PREVIOUS MESSAGE: PROBLEMS: Two Puzzles: Does your reasoning lead you astray on the following puzzles? Most people's does. Here are resampling (simulation) solutions that illustrate how such an approach, though less sophisticated than a formulaic one, yields correct answers and offers fewer opportunities to go wrong. 1) "Three identical boxes each contain two coins. In one box both are pennies, in the second both are nickels, and in the third there is one penny and one nickel. A man chooses a box at random and takes out a coin. If the coin is a penny, what is the probability that the other coin in the box is also a penny?" [from Goldberg, 1960, p. 99] 2) A bag contains one counter, known to be either white or black. A white counter is put in, the bag shaken, and a counter drawn out, which proves to be white. What is now the chance of drawing a white counter? From Lewis Carroll's PILLOW PROBLEMS (1895/1958) (p. 2, via Martin Gardner)