From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!nwnews.wa.com!nwfocus.wa.com!krel.iea.com!e5.iea.com!user From: stevem@comtch.iea.com (Steve McGrew) Newsgroups: bionet.software Subject: Re: Seeking software for graphing and spreadsheet functions Date: 2 Feb 1996 14:21:59 GMT Organization: New Light Industries, Ltd. Lines: 14 Distribution: world Message-ID: References: NNTP-Posting-Host: e5.iea.com In article , lcl@porky.bu.edu (Lisa Caroline Lewis) wrote: > The company I work for is looking for software that can both handle > graphing and spreadsheet functions. We need to have programming > ability with it, so that we can write our own macros. The graphing > must be able to do sigmoidal plots on a semi-log scale [dose-response > curves]. Excel for Windows does all the things you want. In addition, "Generator" a genetic algorithm software package from New Light Industries, can work with Excel to do optimizations like curve fitting, model development, equation solving and lots more. If you're interested, check the NLI home page at www.iea.com/~nli. Or, e-mail at nli@comtch.iea.com. From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.uoregon.edu!news.rediris.es!power.ci.uv.es!usenet From: jose oviedo Newsgroups: bionet.software Subject: Re: want mac software sites Date: 2 Feb 1996 18:10:25 GMT Organization: dep. parasitology-university of valencia (spain) Lines: 12 Message-ID: <4etk2h$tbo@power.ci.uv.es> References: NNTP-Posting-Host: parasit.parasit.uv.es Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) To: jlepine@haverford.edu X-URL: news:jlepine-0202961003280001@s219.haverford.edu To: jlepine@haverford.edu You can obtained mac software in iluso.uv.es Jose A. Oviedo Parasitology University of Valencia Spain From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!COMPUSERVE.COM!76773.1171 From: 76773.1171@COMPUSERVE.COM (gus baydoun) Newsgroups: bionet.software Subject: joining group Date: 1 Feb 1996 19:08:33 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <960202025732_76773.1171_EHT158-1@CompuServe.COM> NNTP-Posting-Host: net.bio.net Could you send me information about your group.I am an independent software developer interested in this area of software. Ghassan Baydoun. Compuserve:76773,1171 From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.rediris.es!power.ci.uv.es!usenet From: jose oviedo Newsgroups: bionet.software Subject: Re: want mac software sites Date: 2 Feb 1996 17:40:41 GMT Organization: dep. parasitology-university of valencia (spain) Lines: 10 Message-ID: <4etiap$tbo@power.ci.uv.es> References: NNTP-Posting-Host: parasit.parasit.uv.es Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) To: jlepine@haverford.edu X-URL: news:jlepine-0202961003280001@s219.haverford.edu You can obtained mac software in iluso.uv.es Jose A. Oviedo Parasitology University of Valencia Spain From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.rediris.es!power.ci.uv.es!usenet From: jose oviedo Newsgroups: bionet.software Subject: Re: want mac software sites Date: 2 Feb 1996 17:41:14 GMT Organization: dep. parasitology-university of valencia (spain) Lines: 10 Message-ID: <4etibq$tbo@power.ci.uv.es> References: NNTP-Posting-Host: parasit.parasit.uv.es Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; 68K) To: jlepine@haverford.edu X-URL: news:jlepine-0202961003280001@s219.haverford.edu You can obtained mac software in iluso.uv.es Jose A. Oviedo Parasitology University of Valencia Spain From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!EU.net!sun4nl!uva.nl!amc!ka2-05.amc.uva.nl!user From: a337ard@horus.sara.nl (ard jonker) Newsgroups: bionet.software Subject: Re: Image analysis software? Date: Fri, 02 Feb 1996 09:52:06 +0100 Organization: University of Amsterdam (fac. med.) Lines: 21 Message-ID: References: <4eoiml$197@gwsun.medinf.mu-luebeck.de> NNTP-Posting-Host: ka2-05.amc.uva.nl In article <4eoiml$197@gwsun.medinf.mu-luebeck.de>, "Oliver Schmitt" wrote: > KONTRON in germany (KS System). > KHOROS (free). > >I would like to know if there is any image analysis software available > >for measuring fruit and vegetable shapes. > > Optimas Corporation's OPTIMAS image analysis software includes several > measurements for quantifying shape and texture. If you will e-mail me > with you physical mailing address (number, street, city, state, zip, etc.) > I will send you a brochure and demonstration disk for OPTIMAS. > > Best regards, > > Matt Davidson > Sales Manager USA/Canada > Optimas Corporation NIH-Image free ftp-able from zippy.nimh.nih.gov for macintosh. about 1 MB ard From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!lhc.nlm.nih.gov!gold!epstein From: epstein@gold.nlm.nih.gov (Jonathan Epstein) Newsgroups: bionet.software Subject: Re: [Q]:?how to run MAC SW on PC (Windows95) Date: 2 Feb 1996 16:08:28 GMT Organization: National Library of Medicine Lines: 21 Message-ID: <4etcts$a25@lhc.nlm.nih.gov> References: <4eprqm$kes@mserv1.dl.ac.uk> <31114385.41C6@rhapsody.stanford.edu> NNTP-Posting-Host: 130.14.25.47 X-Newsreader: TIN [version 1.2 PL2] Lionel Gilet (gilet@rhapsody.stanford.edu) wrote: > In article <4eprqm$kes@mserv1.dl.ac.uk>, Ivo Wiesner wrote: > > > >Hello Netters out there! > > > >Could anybody inform me: > > > >1. if there is any emulator for PC (Windows) platform > >which enables running MAC software? See comp.emulators.mac.executor. Good luck ... it doesn't look like a very comprehensive solution, but I believe that it's the best one out there. - Jonathan Jonathan Epstein epstein@ncbi.nlm.nih.gov National Center for Biotechnology Information Phone: (301)496-2477 x254 National Library of Medicine Building 38A, Room 8N805 National Institutes of Health 8600 Rockville Pike Bethesda, MD 20894 From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!newsxfer2.itd.umich.edu!newsxfer.itd.umich.edu!news.flint.umich.edu!news.gmi.edu!msunews!netnews.upenn.edu!news.cc.swarthmore.edu!news.haverford.edu!s219.haverford.edu!user From: jlepine@haverford.edu Newsgroups: bionet.software Subject: want mac software sites Date: Fri, 02 Feb 1996 10:03:28 -0500 Organization: Bryn Mawr and Haverford College NetNews Lines: 3 Message-ID: NNTP-Posting-Host: 165.82.1.219 X-Newsreader: Value-Added NewsWatcher 2.0b22.0+ I really need a www site where I can download MACINTOSH software. Everything I try to download turns out to be for other systems. jlepine@haverford.edu From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!news.ultranet.com!bigboote.WPI.EDU!news3.near.net!yale!news.ycc.yale.edu!news From: Danny Chamovitz Newsgroups: bionet.software Subject: boxshade or similar Date: 2 Feb 1996 18:21:48 GMT Organization: Yale University Lines: 25 Message-ID: <4etkns$n7g@news.ycc.yale.edu> NNTP-Posting-Host: peaplant.biology.yale.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; HP-UX A.09.03 9000/750) X-URL: news:bionet.software Does anyone know of a BOXSHADE type of program for Mac or UNIX? BOXSHADE is a freeware that foramts alignments with black and grey boxes showing sequence conservation. Thank Danny chamo@peaplant.biology.yale.edu ________________________________________________________________________________ Daniel Chamovitz tel: 203-432-8909 Department of Biology fax: 203-432-3854 Yale University http://peaplant.biology.yale.edu:8001/denglab.html P.O.Box 208104 home tel: 203-776-3474 New Haven, CT 06520-8104 "Let's not keep silent. Let our voices rise high to speak of our commitment to peace for all times to come, and let us tell those who live in darkness who are the enemies of life ... we are not ashamed, nor are we afraid, nor are we anything but determined to fulfill the legacy for which my friend fell..." King Hussein of Jordan, November 7, 1995 From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!sun4nl!uva.nl!amc!ka2-05.amc.uva.nl!user From: a337ard@horus.sara.nl (ard jonker) Newsgroups: bionet.software Subject: Re: [Q]:?how to run MAC SW on PC (Windows95) Date: Fri, 02 Feb 1996 14:04:31 +0100 Organization: University of Amsterdam (fac. med.) Lines: 26 Message-ID: References: <4eprqm$kes@mserv1.dl.ac.uk> <31114385.41C6@rhapsody.stanford.edu> NNTP-Posting-Host: ka2-05.amc.uva.nl In article <31114385.41C6@rhapsody.stanford.edu>, Lionel Gilet wrote: > In article <4eprqm$kes@mserv1.dl.ac.uk>, Ivo Wiesner wrote: > >Could anybody inform me: > >1. if there is any emulator for PC (Windows) platform > >which enables running MAC software? > >2.how difficult work represents to rewrite Mac software for Windows PC? > I have no idea concerning the first point. ... You can run Executor, demo ftp-able from ARDI. Basically, it resembles the speed of a Mac II under system 6 when used on a 66MHz 486. So you turn your PC into a '86 Mac. Don't ask me on how to set it up, I have no PC experience other than have tested Executor once ;-) It might do some jobs. Have a look from the other side (ie. the other way around, softwindows on a PPC runs a bit faster yet giving access to both platforms simultaneously) > As far as rewriting a Mac software for Windows PC, it really depends > on the language used, the size of the program and what it does. If I understand its docs correctly, the MetroWerks Code Warrior compiler is cross platform; you can develop both Windoze and Macintosh programs on a mac with the same compiler, which compiles Pascal, C and C++. ard From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: want mac software sites Date: 2 Feb 1996 21:52:08 GMT Organization: Biology, Indiana University - Bloomington Lines: 8 Message-ID: <4eu128$q56@usenet.ucs.indiana.edu> References: NNTP-Posting-Host: sunflower.bio.indiana.edu for molecular and other biology free/shareware for Macintoshes, take a look at IUBio archive, at iubio.bio.indiana.edu, using ftp, gopher, http internet protocols (e.g., http://iubio.bio.indiana.edu/ ) In the Software+Data section, look in folder molbio/mac/, or folder biology/mac/ . -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.crl.com!a104024.sfo4.as.crl.com!user From: sunger@a.crl.com (Stefan Unger) Newsgroups: bionet.software Subject: Re: Primer design software Date: 2 Feb 1996 17:16:48 GMT Organization: BioSoftware Marketing Lines: 22 Message-ID: References: <4eqnlg$j3f@news.ycc.yale.edu> NNTP-Posting-Host: a104024.sfo4.as.crl.com RightPrimer is a useful program. You can read about it and others at the BIO Online Store at www.bio.com. Hope this helps. In article <4eqnlg$j3f@news.ycc.yale.edu>, gary.rudnick@yale.edu (Gary Rudnick) wrote: > Does anyone know of a reasonably priced alternative to Oligo for > PC-based primer design. We have both Gene Runner and Primer Designer > and they both leave something to be desired, but Oligo is so > expensive. Any ideas? > > Gary Rudnick > rudnick@biomed.med.yale.edu -- Stefan Unger, Ph.D. BioSoftware Marketing 4151 Middlefield Rd, Ste 109 Palo Alto, CA 94303-4743 Full technical software marketing services; Product Manager, Scientific Software, Bio Online Store at www.bio.com From owner-software@net.bio.net Thu Feb 01 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!sun4nl!sci.kun.nl!usenet From: Friso Westerhuis Newsgroups: bionet.software Subject: Re: EEG (brainwave) analysis Date: 2 Feb 1996 13:09:04 GMT Organization: University of Nijmegen, The Netherlands Lines: 11 Message-ID: <4et2dg$nui@wn1.sci.kun.nl> References: <30FF00A4.7E6D@biosys.zynet.co.uk> <4dvhgv$26ts@hopper.acs.ryerson.ca> NNTP-Posting-Host: 131.174.200.197 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) A very good system is the new ACODAS system for Windows it contains software to display the signal online and offline a sofware development libary an AD conversion board (sorry for my English) all kinds of analysis methods like FFT etc. Friso From owner-software@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!biosci!not-for-mail From: "David J. States" Newsgroups: bionet.general,comp.theory,comp.databases,comp.graphics,bionet.software,bionet.biophysics,,comp.ai,sci.bio.technology,sci.engr.biomed,wu.general Subject: CFP and extended deadline - Intelligent Systems for Molecular Biology '96 Conference Date: 2 Feb 1996 19:28:26 -0800 Organization: Institute for Biomedical Computing Lines: 102 Sender: daemon@net.bio.net Distribution: world Message-ID: <3111186F.1CBC@ibc.wustl.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:19719 comp.theory:9049 comp.databases:33501 bionet.software:14616 bionet.biophysics:1669 comp.ai:21862 sci.bio.technology:4701 sci.engr.biomed:5390 The Fourth International Conference on Computational Biology Intelligent Systems for Molecular Biology '96 June 12-15, 1996 Washington University, St. Louis, Missouri, USA http://ibc.wustl.edu/ismb96 Call For Papers An electronic mailing list can be joined by sending a message to ismb96@ibc.wustl.edu with the word "subscribe" as the body of the message. Key Dates Meeting: June 12-15, 1996 Paper Submissions Papers due: Feb 6, 1996 *** note extended date *** Replies to authors: Mar 15, 1996 Revised papers due: Apr 1, 1996 Open Poster Submissions Abstracts due: Apr 1, 1996 Tutorial Proposals Full proposals due: March 18, 1996 Replies to authors: April 1, 1996 Draft handouts due: April 15, 1996 Final handouts due: May 13, 1996 Tutorials presented: June 12, 1996 The purpose of the ISMB conference is to disseminate the latest developments in computational molecular biology and biophysics and to stimulate new work on the application of intelligent computational systems to problems in molecular biology. ISMB is a multidisciplinary conference bringing together scientists from computer science, mathematics, statistics, and molecular biology. Its scope extends to any computational method or system supporting a biological task that is algorithmically, cognitively, or conceptually challenging, involves a synthesis of heterogeneous information, or exhibits the emergent properties of an "intelligent system." From a computational perspective, areas of interest include adaptive systems, intelligent experimental control, data modeling, machine learning, artificial intelligence, combinatorics, stochastic optimization, string and graph algorithms, linguistic methods, and parallel computer technologies. Biological areas of interest include molecular structure, genomics, molecular sequence analysis, evolution and phylogenetics, adaptive experimental systems, and molecular biology. Emphasis is placed on the validation of methods using real data sets and on practical application in the biological sciences. The ISMB conference has attracted a large and enthusiastic audience comprising scientists involved in application areas such as artificial intelligence, structural biology, DNA, RNA and protein sequence analysis and structure prediction, genome mapping, gene identification, molecular biology data and knowledge bases, and the modeling of biochemical processes. We are continuing the tradition of soliciting original papers, which will be rigorously refereed and published (by AAAI Press and the MIT Press) in proceedings available at the conference. The conference proceedings are indexed in the Medline database. The previous ISMB meetings were 1993: National Library of Medicine, USA 1994: Stanford University, USA 1995: Cambridge University, UK The four-day conference will feature introductory and advanced tutorials on June 12th and presentations of original refereed papers, posters, and invited talks (June 13-15). There will be special sessions at the conference on "Whole Genomes: Challenges and Implications," and on the "Interconnection of Molecular Biology Databases (MIMBD)." A test suite of raw data will be set aside to evaluate base-calling and gene-finding programs. A job fair and a vendor fair are also being organized. Organizing committee David States (states@ibc.wustl.edu) Terry Gaasterland (gaasterl@mcs.anl.gov) Randall Smith (rsmith@imgen.bcm.tmc.edu) Keynote Speakers Robert Waterston, Washington Univ., St. Louis David Haussler, Univ. of California, Santa Cruz Russell Doolittle, Univ. of California, San Diego Chris Sander, EMBL, Heidelberg Contact address ISMB '96 Institute for Biomedical Computing Washington University 700 South Euclid Avenue St. Louis, MO 63110-1012 USA Phone: (314) 362-2134 FAX: (314) 362-0234 -- David J. States Institute for Biomedical Computing / Washington University in St. Louis From owner-software@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.bctel.net!kryten.awinc.com!uucp105!bryan.webster From: bryan.webster@pcc.awinc.com (Bryan Webster) Newsgroups: bionet.software Subject: Re: want mac software sites Date: Sat, 3 Feb 1996 07:28:45 GMT Message-ID: <96020308175880@pcc.awinc.com> Organization: Peace Country Computers Distribution: world References: Lines: 8 -> From: jlepine@haverford.edu -> Subject: want mac software sites -> -> I really need a www site where I can download MACINTOSH software. -> Everything I try to download turns out to be for other systems. -> jlepine@haverford.edu When you are on the www next, try using one of the search systems such as YAHOO to locate sites with MAC software. From owner-software@net.bio.net Fri Feb 02 22:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!harbinger.cc.monash.edu.au!news.cs.su.oz.au!tmx!news.tmx.com.au!news From: pajell@midcoast.com.au Subject: software to predict lake stratification Message-ID: Nntp-Posting-Host: pajell.midcoast.com.au Sender: news@online.tmx.com.au (System Administrator) Organization: The Message eXchange Pty Ltd Date: Sat, 3 Feb 1996 19:53:37 GMT X-Newsreader: Forte Free Agent 1.0.82 Lines: 8 Does anyone know of a reasonably simple model for predicting the behaviour of the thermocline (ie lake stratification) in impounded freshwaters? I am studying the potential for a proposed manmade lake system to stratify and turnover. Peter Jelliffie 4 Gordon St Coffs Harbour NSW 2450 Australia e-mail pajell@midcoast.com.au From owner-software@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!angis.su.OZ.AU!tim From: tim@angis.su.OZ.AU (Tim Littlejohn) Newsgroups: bionet.software Subject: Re: want mac software sites Date: 3 Feb 1996 03:30:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4eu128$q56@usenet.ucs.indiana.edu> NNTP-Posting-Host: net.bio.net On 2 Feb 1996, Don Gilbert wrote: > for molecular and other biology free/shareware for Macintoshes, > take a look at IUBio archive, at iubio.bio.indiana.edu, using > ftp, gopher, http internet protocols (e.g., http://iubio.bio.indiana.edu/ ) > In the Software+Data section, look in folder molbio/mac/, or > folder biology/mac/ . And for those of you in Australia or close by in net terms, have a look at the ANGIS archive at: ftp://www.angis.su.oz.au/pub/mac/ Tim Littlejohn -------------------------------------------------------------------------- | ANGIS- The Australian National Genomic Information Service | | http://www.angis.su.oz.au | | email: tim@angis.su.oz.au Phone/FAX: 61-2-351 2948 | -------------------------------------------------------------------------- From owner-software@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!sierra.net!bigchief-d15 From: drr@sierra.net (Denis Renard) Newsgroups: bionet.software Subject: Re: want mac software sites Date: Sat, 03 Feb 96 04:09:21 GMT Organization: Sierra-Net Lines: 15 Message-ID: <4eun5h$fn8_001@bigchief-d15.sierra.net> References: NNTP-Posting-Host: bigchief-d15.sierra.net X-Newsreader: News Xpress Version 1.0 Beta #4 In article , jlepine@haverford.edu wrote: >I really need a www site where I can download MACINTOSH software. >Everything I try to download turns out to be for other systems. >jlepine@haverford.edu My main entry point for Mac stuff is: http://macfaq.com For an all purpose site (you can select Mac only): http://www.shareware.com (aka CNet Virtual Software Library) I'm not sure that they have much Biology programs but Biology is not my forte. Hope this helps, Denis From owner-software@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.exodus.net!aimnet.com!ns2.mainstreet.net!sloth.swcp.com!tesuque.cs.sandia.gov!lynx.unm.edu!bubba.NMSU.Edu!dkim From: dkim@nmsu.edu (DANIEL Y KIM) Newsgroups: bionet.software Subject: MOLSCRIPT compiled for MSDOS or WINDOWS? Date: 31 Jan 1996 18:55:52 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 11 Message-ID: <4eodvo$n1j@bubba.NMSU.Edu> NNTP-Posting-Host: verdi.nmsu.edu Hello: I am looking for a compiled .EXE of MOLSCRIPT that can run in DOS or WINDOWS. Does anyone have such a thing? Per Kraulis states that he has heard of such ports, but has no details. Thank you. Daniel Kim dkim@nmsu.edu From owner-software@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!newsrelay.netins.net!news.netins.net!news.dordt.edu!jnthnrks From: jnthnrks@dordt.edu (Jonathan Eerkes) Newsgroups: bionet.software Subject: Re: Biology Education Software FAQ Date: 3 Feb 1996 19:26:00 GMT Organization: Dordt College, Sioux Center, IA Lines: 24 Distribution: world Message-ID: <4f0cs8$k7p@bbs.dordt.edu> References: <4ep0h8$lqn@nntp3.u.washington.edu> NNTP-Posting-Host: cc.dordt.edu X-Newsreader: TIN [version 1.2 PL2] : http://www.zoology.washington.edu/biosoft/ : Hope that's useful to some of you. : Eli Meir : Dept of Zoology, Univ of Washington : meir@zoology.washington.edu Thanks! I've been looking at this topic for a while now, since I am doing an Individual Studies trying to write some educational software in Visual Basic (it's the only language I know). Is there any other good sites/sources I could use to find out what type of programs are out there? I don't want to write a program thats been done a billion times before. -- If your parents didn't have any children, There is a good chance you won't have any. Jonathan Eerkes (jnthnrks@cc.dordt.edu) From owner-software@net.bio.net Fri Feb 02 22:00:00 1996 Path: biosci!PCLSP2.KUICR.KYOTO-U.AC.JP!kissy From: kissy@PCLSP2.KUICR.KYOTO-U.AC.JP (kissy) Newsgroups: bionet.software Subject: (no subject) Date: 3 Feb 1996 04:50:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9602031250.AA11719@pclsp2.kuicr.kyoto-u.ac.jp> NNTP-Posting-Host: net.bio.net Hello, my friends!! I am losing my time to find the PDBViewer. Please tell me how to get it. Sincerely yours. From owner-software@net.bio.net Sat Feb 03 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!demon!asheep.demon.co.uk From: Robert@Asheep.Demon.CO.Uk (Robert Shell) Newsgroups: bionet.software Subject: Re: Structure conversion software Date: Sun, 04 Feb 1996 23:09:44 GMT Lines: 44 Message-ID: <823476203.7787@asheep.demon.co.uk> References: <4eknof$635@netserver.univ-lille1.fr> NNTP-Posting-Host: asheep.demon.co.uk X-NNTP-Posting-Host: asheep.demon.co.uk X-Newsreader: Forte Free Agent 1.0.82 philippe@ICPL2.UNIV-LILLE2.FR (Philippe CHAVATTE) wrote: >>I look for a software which can convert structures 2D or 3D in SMILES chemical >>notation line. There are a large number of methods for handling the convertion of between 1D line notations like SMILES , 2D depictions for papers and documents and 3D molecular configurations for modelling and property calculations. One of the best source of these utilitiies is the Daylight with their Programming tool-kits and applications. For quick creation of 3D configurations for 3D chemical database searching and starting points for MOPAC and other calculations are are a number of commerical tools :- Concord Tripos USA Rubicon Daylight see http://www.daylight.com Chem-X Chemical Design limited UK CACTVS see http://schiele.organik.uni-erlangen.de/cactvs (free convertion service for a small number of structures via the WWW) There creation of smiles codes from 2D depictions is handled by ChemDraw, ChemWindows and many other chemical drawing programme. There CACTVS system contains a good free graphical editor for creations of smiles on some common unix platforms. The ability to convertion of Smiles to 2D depictions is less common. There Daylight WWW page http://www.daylight.com provides a simple Web page for this. The following tools are also available for the PC environment. Consisant Exographics USA Accord Synopics UK Unity Tripos USA Depict-Toolkit Daylight The Best utility I have found for the general conversion between the various 2D formats Babel released by the Dept. of Chemistry, University of Arizona,Tucson, AZ 85721 babel@mercury.aichem.arizona.edu (source code is available) Yours Robert Shell Research Computing, Dagenham Research Centre Rhone Poulenc Rorer UK From owner-software@net.bio.net Sat Feb 03 22:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!warwick!bham!bhamcs!news.ox.ac.uk!news From: Ewan Birney Newsgroups: bionet.software,bionet.software.gcg Subject: PairWise and SearchWise 1.5 beta release Date: Sun, 04 Feb 1996 18:14:21 +0000 Organization: Oxford University Lines: 80 Message-ID: <3114F77C.41C6@molbiol.ox.ac.uk> NNTP-Posting-Host: nmrd.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b6a (X11; I; IRIX 5.3 IP22) CC: birney@molbiol.ox.ac.uk Xref: biosci bionet.software:14626 bionet.software.gcg:1606 **** PairWise and SearchWise 1.5 Release **** *** *** This is to announce the beta release of PairWise and SearchWise. The programs PairWise and SearchWise are based around an algorithm which compares a Protein Profile to a DNA sequence, *allowing* for frameshifts and introns in the DNA sequence. As a protein profile can be trivially made from a protein sequence, both PairWise and SearchWise can use a protein sequence as a query. This is the first proper beta release for PairWise and SearchWise. Although there are a variety of bugs to be worked out, and many aspects to improve, the core of PairWise and SearchWise is probably robust enough to be used on additional sites with not too much work :) PairWise also comes with Profileweight code in-built, which has many options for the optimisation of profile production. More information on PairWise and SearchWise can be found at http://www.ocms.ox.ac.uk/~birney/wise/topwise.html which includes a WWW based server for you to try out PairWise queries at http://www.ocms.ox.ac.uk/~birney/wise/hwise.html and binaries can be found at the ftp site nmrz.ocms.ox.ac.uk in /pub/wise but I would read the hypertext help first! See the README file on the ftp site or any of the source code files for copyright (it is also on the WWW site). It is free for both academic and commerical users, but commerical users must register first. As a teaser, in one SearchWise run we discovered around 40% of the ESTs with a PH domain to contain frameshifts, almost certainly due to seqeuncing errors. These sequences were unlikely to be seen without SearchWise - although the GCG Framesearch program can cope with frame shifts it cannot use the more sensitive profile methods which can find distantly related sequences. PairWise and SearchWise are designed to work either as stand-alone programs or in the GCG sequence analysis enviroment. PairWise can be linked to GCG8 at compile time. SearchWise can read GCG databases (ascii or binary), fasta databases or EMBL databases. PairWise and SearchWise are written in ANSI C and developped concurrently on SunOS, IRIX and AXP VMS platforms. Digital UNIX seems to require no changes. It is likely that programs are easily ported to any platform with an ANSI C compiler. The front ends (PairWise and SearchWise) have been tweaked with to make sure that novice users can easily grasp what to do and not to make (too many) mistakes early on. However the user is given complete control over as many aspects as possible and can reset virtually all options through a run time configuration system. There are a few bugs in: In these cases they are documented if at all possible in both output and log files. I respond quite quickly to bugs: any suggestions are also very wellcome. I hope you find the package as useful as we have over the years. Author/Programmers: Ewan Birney (Oxford) Julie Thompson (EMBL) Author/Developper/Guru and Lead Bug tester ;) Toby Gibson (EMBL) From owner-software@net.bio.net Sat Feb 03 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!nntp.coast.net!oleane!jussieu.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!cs.tu-berlin.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: boxshade or similar Date: 4 Feb 1996 14:18:03 GMT Organization: University of Wuerzburg, Germany Lines: 14 Message-ID: <4f2f6r$elm@winx03.informatik.uni-wuerzburg.de> References: <4etkns$n7g@news.ycc.yale.edu> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Danny Chamovitz (chamo) wrote: > Does anyone know of a BOXSHADE type of program for Mac or UNIX? BOXSHADE is a > freeware that foramts alignments with black and grey boxes showing sequence > conservation. Boxshade is apparently available for unix. Check out bionet.software.gcg for a recent thread. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Sat Feb 03 22:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!uchinews!woodlawn!sjchmura From: sjchmura@woodlawn.uchicago.edu (steven joseph chmura) Subject: Re: [Q]:?how to run MAC SW on PC (Windows95) X-Nntp-Posting-Host: midway.uchicago.edu Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Reply-To: sjchmura@midway.uchicago.edu Organization: The University of Chicago References: <4eprqm$kes@mserv1.dl.ac.uk> <31114385.41C6@rhapsody.stanford.edu> Date: Sun, 4 Feb 1996 20:26:45 GMT Lines: 30 In article , ard jonker wrote: >In article <31114385.41C6@rhapsody.stanford.edu>, Lionel Gilet > wrote: > >> In article <4eprqm$kes@mserv1.dl.ac.uk>, Ivo Wiesner wrote: >> >Could anybody inform me: >> >1. if there is any emulator for PC (Windows) platform >> >which enables running MAC software? >> >2.how difficult work represents to rewrite Mac software for Windows PC? >> I have no idea concerning the first point. >... >You can run Executor, demo ftp-able from ARDI. Basically, it resembles the >speed of a Mac II under system 6 when used on a 66MHz 486. So you turn >your PC into a '86 Mac. Don't ask me on how to set it up, I have no PC >experience other than have tested Executor once ;-) It might do some jobs. >Have a look from the other side (ie. the other way around, softwindows on >a PPC runs a bit faster yet giving access to both platforms >simultaneously) > Well, this is just plain wrong. The registered version is far faster. And with a P5-133 costing $350 (yes, you can buy a motherboard and P5-133 for $500) the "exectutor" runs 680x0 apps as fast as a $1000 PowerMac. Apple is in deep deep trouble - face it. The Amiga of the '90s. Softwindows is horrible and requires 16megs of RAM. -- ________________________________________________________________________________Steven Chmura MuDPhud4 TEAM APACHE: To hell with jets From owner-software@net.bio.net Sun Feb 04 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.cais.net!xara.net!SoNet!innotts.co.uk!usenet From: mikeb@innotts.co.uk (mike) Newsgroups: bionet.software Subject: enhance software --- NEW !!!! Date: Mon, 05 Feb 1996 22:58:25 GMT Organization: The Bridge Lines: 8 Message-ID: <4f6219$4o8@mapperley.innotts.co.uk> NNTP-Posting-Host: seriald0b.innotts.co.uk X-Newsreader: Forte Agent .99c/32.126 http://www.innotts.co.uk/enhance/software/software.htm enhance@innotts.co.uk Internet Applications For Windows FTP.IRC.E-MAIL. HTML.ARCHIE.NEWS.WEB.TERMINAL.FINGER.VRML.TALK. PLUG-IN.GRAPHICS.ART.AUDIO.GOPHER. From owner-software@net.bio.net Sun Feb 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!newsfeed.internetmci.com!primus.ac.net!news.cais.net!xara.net!peer-news.britain.eu.net!lyra.csx.cam.ac.uk!warwick!bham!bhamcs!news.ox.ac.uk!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk (Mad Dan Eccles) Newsgroups: bionet.software Subject: Re: [Q]:?how to run MAC SW on PC (Windows95) Date: 5 Feb 96 08:42:30 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 40 Message-ID: <1996Feb5.084230@molbiol.ox.ac.uk> References: <4eprqm$kes@mserv1.dl.ac.uk> <31114385.41C6@rhapsody.stanford.edu> NNTP-Posting-Host: ania.path.ox.ac.uk sjchmura@woodlawn.uchicago.edu (steven joseph chmura) writes: >> > Well, this is just plain wrong. The registered version is far faster. And > with a P5-133 costing $350 (yes, you can buy a motherboard and P5-133 for > $500) the "exectutor" runs 680x0 apps as fast as a $1000 PowerMac. Well, I don't know about that, but I do know you can buy a PowerMac with 486 DOS card for GBP1300 - and probably cheaper in the US. If I was buying, I'd get a PMac w/ 486 card, maybe a P5 card. Two more points: One: for $$/computing power, PowerMacs are far faster than P5s, which is not surprising because of the RISC technology. I mean, who wants two 486s soldered back to back?? At least it keeps the room warm in winter. :) Two: To make a P5 costs TWICE as much as making a PowerPC chip. Again, the technology accounts for this. > Apple is in deep deep trouble - face it. The Amiga of the '90s. Bull. Go tell that to 20 million happy users. They shifted more units last quarter than ever before, and over a million PowerMacs. OK, they made a $70 million loss which is bad news but that was a forecasting problem (they overestimated demand, which cancelled out the underestimation of earlier last year when they had backorders totalling 1 _billion_ US$). Cf with a $122 million _profit_ for the same quarter the previous year, I don't think they're struggling. Spindler's gone, so they _shouldn't_ make the same mistakes again. They've licensed the MacOS and now well respected companies such as UMAX (btw, they make a MEAN colour scanner, fantastic) are making Mac-compatibles - so we should see even more real computers around. > Softwindows is horrible and requires 16megs of RAM. Hm, just like Win95? ;-) Happy computing, Richard From owner-software@net.bio.net Sun Feb 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!swrinde!howland.reston.ans.net!nntp.coast.net!torn!nott!crc-news.doc.ca!netfs.dnd.ca!coyote.dres.dnd.ca!news From: Reno Pontarollo Newsgroups: bionet.software Subject: Wanted: public DNA alignment/primer design software Date: 5 Feb 1996 17:05:23 GMT Organization: DRES Lines: 5 Message-ID: <4f5dcj$670@coyote.dres.dnd.ca> NNTP-Posting-Host: bg1.dres.dnd.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) I already use MACAW 2.05 for DNA alignment, but could use some more software. I have access to a UNIX system and was wondering what the CLUSTAL and FASTA packages are capable of and how easy they are to use. From owner-software@net.bio.net Sun Feb 04 22:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: (Ken INUI) Newsgroups: bionet.software Subject: Re: boxshade or similar Date: 5 Feb 1996 14:03:37 GMT Organization: IAH Pirbright Lines: 23 Message-ID: <4f52np$ikg@is.bbsrc.ac.uk> References: <4etkns$n7g@news.ycc.yale.edu> Reply-To: michael.baron@bbsrc.ac.uk NNTP-Posting-Host: pc0258.avri.bbsrc.ac.uk X-Newsreader: WinVN 0.91.6 In article <4etkns$n7g@news.ycc.yale.edu>, Danny Chamovitz says: > >Does anyone know of a BOXSHADE type of program for Mac or UNIX? BOXSHADE is a >freeware that foramts alignments with black and grey boxes showing sequence >conservation. > The BOXSHADE distribution contains the full source code, including OSF1 makefile. You will need to have your own PASCAL compiler. If it does not compile on your particular flavour of UNIX, please tell me what the offending code is, and I'll try and work something out. You can get the distribution from the EMBL software archive in the VMS directory. I'm (_very slowly_) working on a MAC version, but it's just a hobby. The latest version of BOXSHADE, which I'll put in the EMBL archive when I get the time, writes PICT files. regards, Michael D. Baron michael.baron@bbsrc.ac.uk From owner-software@net.bio.net Sun Feb 04 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!gwen.pcug.co.uk!kate.ibmpcug.co.uk!phoretix!nonlin Newsgroups: bionet.software Message-ID: <241@phoretix.win-uk.net> References: Reply-To: nonlin@phoretix.win-uk.net (Will Dracup) From: nonlin@phoretix.win-uk.net (Will Dracup) Date: Mon, 05 Feb 1996 11:30:43 GMT Subject: Re: Information on DNA Analysis Software Lines: 51 In article , Graham Casey (GCasey@EM.AGR.CA) writes: >Hello everyone: > >We are considering implementing an image capture system to store the >data generated in our gels in digital form. We have been given some >advice regarding the types of software that we can use to "clean up the >image" (ie., adjust contrast etc), but we do not have much information on >software to do some of the actual data analysis. > >Generally, we would be interested in the basic functions of molecular >weight/ fragment length determination, DNA sequence reading, sequence >alignment, RFLP and RAPD fragment analysis running on a 486 and or >Pentium PC. (We're not asking for much, are we :)!) We would >appreciate it if any of you can suggest some software packages, >companies or web sites we could look at; or even some of your own >experiences with a given software package(s). > >Thanks in advance for any help or advice. > >Graham Casey >Cereal Research Centre >Agriculture Agri-Foods Canada >gcasey@em.agr.ca > Phoretix International is British company who have been developing electrophoresis image analysis software for PC’s since 1989. Both our 1D and 2D software packages are specifically designed for the in depth analysis of electrophoresis gels. We can import images in 8, 12 or 16 bit formats from many forms of image capture device, such as commercial document scanners, CCD cameras, phosphor imagers and laser densitometers. For visualisation purposes, the image can then be "enhanced" using contrast stretching, false colours, negative images or zooming in to look at a very few pixels. However the image data itself is never altered since the software was developed to operate within the confines of Good Laboratory Practice. Spots or bands can be automatically detected and measured, and quantity, MW, and many othermeasurements calculated. Histograms, dendrograms, comparison tables and other forms of displaying the data make the results easily assessable in a clear and instantly recognisable way. I am afraid our web site is currently under construction but do e-mail me with any questions you may have, or send me your address so that I can forward you further information and a demo disk. James Sykes From owner-software@net.bio.net Sun Feb 04 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: nolan@cyberlearn.com (Ron S. Nolan) Newsgroups: bionet.software Subject: FS: Marine Life Investigations Date: 5 Feb 1996 11:21:34 -0000 Lines: 260 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4f4p7u$6np@mserv1.dl.ac.uk> X-Sender: nolan@scruznet.com Original-To: bio-software@dl.ac.uk Coral Kingdom 1.1 Announcing a new CD-ROM for Macintosh and Windows that offers an exciting venture into the marine world of the coral reef. Why Study Coral Reefs? Coral reefs are well defined ecosystems that provide concise examples of energy flow and materials recycling as well as the complex interrelationships between organisms and the environment. Since coral reef plants and animals have developed specialized adaptations for feeding, reproduction and predator avoidance that permit very high biodiversity in a limited geographic area, the study of the coral reef is ideally suited for units on adaptations, biodiversity and competition. =46inally, coral reefs and their inhabitants are strikingly interesting, beautiful and exotic. They are wild, colorful places that excite the imagination. The software has been carefully crafted to challenge students to use critical thinking about nature and the environment. To paraphrase one reviewer's comment, "Coral Kingdom is not a game. It is a serious academic program." The Coral Kingdom package offers you many ways to incorporate the software into your curriculum. The extensive, 179 page Teachers Guide is packed with ideas and activities. Transcripts of the program content allow you to turn off the sound and provide your own expert commentary. And since the topics are thematically arranged, you may select assignments that will illustrate some of the most important concepts in biology and ecology. "Coral Kingdom is a serious academic program. It asks students to do some real scientific thinking." Technology and Learning. "If...you are looking for thematic units in science, then you should examine Coral Kingdom." The Computing Teacher. "Stunning visuals, detailed narration and excellent supplemental reference materials guide exploration of a coral reef, its biology and its ecology. MacUser "The Ultimate Guide to Children's Software" 4 mice. =46eel free to request a flyer or copies of educational journal reviews by calling Digital Studios at (800) 499-3322 or by sending e-mail with your address to nolan@cyberlearn.com You may preview Coral Kingdom and download a demo version at our Web Site. http://www.netins.net/showcase/macintosh/cyblearn.htm Special Note to California Educators Coral Kingdom has recently been awarded a "Desirable" rating by the State of California Software Clearinghouse. The program has also been certified as in compliance with social content requirements of Education Code sections 60040=3D66044. Placement on this list notifies school personnel that Coral Kingdom is approved for purchase with up to 30% of their state Instructional Materials Fund (IMF) monies or through petitions requested through the California Department of Education. CORAL KINGDOM FEATURES -------------------------------------- Thematic Approach to Biology and Ecology: Created by a marine ecologist, the software incorporates a tremendous collection of original underwater photography to illustrate a thematic approach to the study of reef biology and ecology. The software is ideally suited for units on the coral reef or to demonstrate the concepts of form and function in adaptations, interrelationships between organisms and habitat, competition, predator avoidance, energy and materials cycles and human impacts in general biology or introductory environmental science or ecology classes. Missions: Each of the four units incorporates a hands-on activity to be completed by students--either in small groups or individually. Each mission consists of an exploratory microworld intended to stimulate the curiosity of students and to engage their interest in the natural world. The methods used by the students at the computer are much like those actually employed by a field ecologist. Each of the four missions takes the user on a research SCUBA dive in which he or she controls the direction and pace of the investigation. The procedures to be followed and mission objectives are described in detail within the unit sections of the teachers guide and can be accessed by clicking the "?" button during a mission. An on-line notebook is provided in which students store information acquired by clicking objects on the screen during the underwater expedition. The content of the notebook may be saved as a text file, then edited or printed using a word processor program. Sea Life Catalog: Students have access to an extensive data base which is available for reference at all times. Problems to be solved in the missions require students to conduct library research using the data base. Species entries in the Sea Life Catalog are accessed by scientific or common names. Each Sea Life Catalog entry provides information about an organism's structure, coloration, relationship to the environment, behavior, specializations and human impact. The catalog may be accessed from any map or from the slide shows by clicking on the "SLC" button. In a mission, the SLC button lights after the user has clicked on a subject on the screen. Clicking the highlighted SLC button during a mission takes the user directly to information about the organism on the screen. Study Units: The program content is thematically presented and organized into four major units. Each unit consists of a series of multimedia slides shows and is accompanied by a research activity. Unit 1: Discovering Adaptations introduces the theme that structure matches function and presents an overview of the diversity of sizes, shapes, colors and lifestyles found on a coral reef. In this unit we explore the relationship of species to the environment--in particular adaptations in feeding and coloration. In Mission: Kohala Coast, the user makes underwater observations, then uses the Sea Life Catalog to find the unique adaptations of the selected organisms. In Unit 2: The Coral Reef Ecosystem, we look at how reefs are formed and the vertical distribution of organisms on the reef face. We also seek to understand the living and non-living forces that build reefs and break them down. Finally we explore how solar energy is captured and transmitted through the ecosystem. The activity for this unit, Mission: Marshall Islands, challenges students to make underwater observations in order to develop a species list, then fit the organisms into a food web. Unit 3: Investigating Interrelationships examines the ways in which organisms interact with the biotic and abiotic environment. We explore competition for food and habitat and the concept of the Competitive Exclusion Principle--as well as symbiotic relationships. Finally, we examine structural and behavioral adaptations and the survival strategies employed by a wide diversity of organisms. In the activity, Mission: South Point, students speculate about how superficially similar species of butterflyfishes are able to live in close proximity. In Unit 4: Exploring Human Impacts, we examine the environmental impacts of development, fishing and diving. We also survey the present status of reef ecosystems in the Pacific and Atlantic and learn why reefs are important to the planet and the human species. Finally we offer suggestions on what can be done to protect imperiled coral reefs. In Mission: Reef Preservation, students discover human activities that may negatively impact coral reef ecosystems. Incorporation into Existing Curricula: CORAL KINGDOM 1.1 was designed for flexible incorporation into existing academic programs. Ranging from straight forward activities (discovering the relationship of structure and function in adaptations) to the complex (investigating how butterflyfishes avoid competition), the teacher may pick and choose from twenty hours of suggested activities. The materials may be used to introduce a unit on ecology in general biology classes or as a case study in environmental science and ecology courses. The hypermedia format of the program allows instructors to select topics of particular interest for either classroom presentation or individual study. As part of the design enabling flexible application, teachers may use a special feature to turn off the audio when presenting the slide shows in group settings. To support this feature, transcripts of the narration are provided in the teachers guide providing a valuable source for lectures. When used in this fashion, the slide shows serve as an extensive visual database of underwater imagery which may be quickly accessed during the lecture. Students who fully explore the slide shows and participate in the research missions will gain a solid understanding of some of the most important themes of ecology This experience will, hopefully, lead them to the conclusion that coral reefs are precious resources worthy of our protection. Product Information CD-ROM for Macintosh and Windows from the CyberLearning Collection=81 Age Level: middle through first year college Developer/Publisher: Digital Studios=81 Product Orders: (800) 499-3322 Pricing: CD-ROM for Mac or Windows with 179 page Teachers Guide--$79.95; Multiple Lab Pack Discounts are Available Availability: Now More Information: Digital Studios * 209 Santa Clara Avenue * Aptos * CA 95003 * (408) 688-3158 Save with Special Lab Pack Pricing Options Unit Price Shipping FEDEX** A. Single Edition* 79.00 5.58 11.00 B. Lab Pack (5)* 158.00 5.74 12.65 5 CD-ROMs C. Lab Pack (10)* 237.00 5.86 15.45 10 CD-ROMs D. Lab Pack (20)* 315.00 6.00 19.80 20 CD-ROMs E. Lab Pack (35)* 395.00 6.25 25.05 35 CD-ROMs =46. Extra guides 20.00 5.58 11.00 * Each Option is accompanied by a Teachers Guide. **FEDEX rate is for next day standard. FEDEX orders must be received by 2 PM PST for next day delivery. Sales in California please add 8.25% to total price. Hawaii orders, please call to discuss the fastest and most cost effective way to get Coral Kingdom back to Hawaii. ------------------------------------------------------------------ Evaluation by the California Software Clearinghouse 1995 Rated "Desirable" TITLE: Coral Kingdom 1.1 DESCRIPTION: The goal of this simulation is to explore the principle themes of marine ecology and the environmental impact of human activities. The program tour provides a clear introduction to information that is organized logically by traditional pathways (kinds of organisms), major concepts (ecological themes), and projected learning pathways (way students are most likely to want to move from section to section and back again). Logistically the program is easy to navigate. It can be adapted for whole class use, small group investigations using the missions, or as an independent resource for individuals. Slide shows present information around major concepts and themes: adaptations, interactions, ecological systems, human impact. Missions stimulate scientific observations and are organized around "diving" at investigation sites in Hawaii and Micronesia. Students view slides with hot spots to focus on important ecological information. They collect information about the inhabitants offshore in shallow to deep waters. A student notebook facilitates systematic information gathering and notes can be incorporated in a complete scientific report. The fourth mission involves identifying and solving problems related to human impact and reef preservation. As a logistics aid, dives are limited to "twenty minutes of air time" each. A Sea Life catalog provides a database of nearly one hundred organisms listed by common and scientific name with information on habitat, ecological niche, impact on/by humans, behaviors and other interesting details. One drawback is that progression through the slide show is linear and it is difficult to access specific slides out of sequence. SUPPORT MATERIALS: There is a CD-ROM and a teacher's manual with guides to the slide shows and missions, suggested classroom uses, report form, scripts, and suggested readings. SYSTEM REQUIREMENTS: IBM: 4MB with 386 or better processor, Windows, sound capability, VGA graphics, hard drive, and CD-ROM drive. Macintosh: 4MB, CD-ROM drive, and color monitor. CURRICULUM APPLICATIONS: This would be an excellent resource in a library media center or science lab. It supports the thematic approach of the California science framework. Activities offer hands-on experience in gathering and analyzing scientific data. The program is very text-dependent and requires a prior understanding of biological terms. Students who love details would absorb it all, while others can appreciate the big ideas that are reinforced by example throughout. Consistency of format allows individual comparisons to be made, and the photos provide a wealth of pictorial examples for the embedded tasks as well as other uses the instructor might have when connecting this program with other students of varying verbal abilities. Teachers can use the program for direct assignments, independent resource material, or presentation of specific information. The control can be given to students with excellent results. It fits nicely in a constructivist learning environment. From owner-software@net.bio.net Sun Feb 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!rice!cs.rice.edu!schaffer From: schaffer@cs.rice.edu (Alex Schaffer) Newsgroups: bionet.molbio.gene-linkage,bionet.software Subject: FASTLINK 3.0P available Date: 5 Feb 1996 22:26:02 GMT Organization: Rice University Lines: 112 Message-ID: <4f605q$83a@larry.rice.edu> NNTP-Posting-Host: cs.rice.edu Xref: biosci bionet.molbio.gene-linkage:962 bionet.software:14634 I am pleased to announce that FASTLINK 3.0P is now available. FASTLINK is an improved version of the linkage analysis package LINKAGE 5.1, which is --faster sequentially than LINKAGE, --runs well in parallel, --is more robust against errors, and --includes substantial new documentation The initial improvements that led to FASTLINK 1.0 are described in: 1. R. W. Cottingham Jr., R. M. Idury, and A.A. Schaffer, Faster Sequential Genetic Linkage Computations, American Journal of Human Genetics, 53(1993), pp. 252-263. (available as paper1.ps in the distribution) The improvements that led to FASTLINK 2.0 are described in: 2. A.A. Schaffer, S. K. Gupta, K. Shriram, and R. W. Cottingham, Jr., Avoiding Recomputation in Linkage Analysis, Human Heredity, 44(1994), pp. 225-237. (available as paper2.ps in the distribution) The improvements that led to FASTLINK 3.0 are described in: 3. A. A. Schaffer, Faster Linkage Analysis Computations for Pedigrees with Loops or Unused Alleles, Human Heredity, to appear. (available as paper5.ps in the distribution) We ask that you cite papers 1 and 2, as well as at least one paper about LINKAGE, if you use FASTLINK in a published experiment. paper3.ps and paper4.ps in the distribution describe how FASTLINK runs in parallel. As with previous versions, the code is available by ftp from: softlib.cs.rice.edu Login as anonymous, leave full e-mail address as password. cd pub/fastlink If you are a UNIX user: get fastlink.tar.Z If you are a DOS user: cd dos If you are a VMS user: get README get README.VMS and follow the instructions there for what you need Retrievers in Europe may find it more convenient to retrieve from the mirror site at: ftp.ebi.ac.uk The instructions are similar, but instead of: cd pub/fastlink (for softlib) do cd pub/software/linkage_and_mapping/FASTLINK/fastlink (for ebi) It takes up to 24 hours for the contents of the Rice site to get updated at the U.K. mirror site. Among the improvements in FASTLINK 3.0P (compared to 2.3P) are: -- The code runs faster on data sets that have loops or unused alleles If you used FASTLINK 2.3P, you may have noticed that it printed diagnostics when a data set had unused alleles, but it did not take advantage of the situation. -- UNKNOWN now detects violations of Mendelian rules of inheritance in looped pedigrees. It never did this before. -- maxhap and maxfem are no longer in the code as constants, except in UNKNOWN. If you were resetting maxhap each time and recompiling, you won't have to do that any more. If you were setting maxhap unnecessarily high to avoid recompiling, you may perceive some speedup. -- The code can now handle more than 31 alleles at a numbered allele locus. It still can't handle more than 31 alleles at a binary factors locus. More than 31 liability classes or quantitative trait classes have not been a problem. -- The parallel code can now handle data sets with an arbitrary number of loops. -- The constant MAXWORKINGSET was eliminated from the parallel code. The net effect is to save space in most cases, and reduce the need for recompilation in some. See the file README.updates for more details on recent code changes in FASTLINK. There are many people to thank for their recent help in the FASTLINK project. Thanks to: Dylan Cooper, Christopher Hoelscher, and Christopher Hyams for programming assistance. Lucien Bachner, Les Biesecker, Anita Destefano, Lynn Goldin, Ramana Idury, Kimmo Kallio, Cathryn Lewis, Ken Morgan, Scot Stenroos, Jim Tomlin, Gerard Tromp for beta testing version 3.0P. Jeff O'Connell and Joe Terwilliger for pointing out the 31-allele limitation. Lucien Bachner for pointing out that UNKNOWN did not detect errors in looped pedigrees. Please address any comments or questions about FASTLINK to me at: schaffer@nchgr.nih.gov. From owner-software@net.bio.net Mon Feb 05 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!psgrain!iafrica.com!slipper12253.iafrica.com!tjones From: tjones@iafrica.com (Tim Jones) Newsgroups: bionet.software Subject: COPYIIPC - or equivalent for Stiffies? Date: Tue, 6 Feb 1996 15:05:13 Organization: Internet Africa Lines: 7 Message-ID: NNTP-Posting-Host: slipper12253.iafrica.com X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hi, Does anybody remember copyiipc - a disk copying programme ? Well I need one with similar capabilties but for 1.4 Stiffies. Any suggestions? The software I am trying to backup, won't with diskcopy etc. Thanks, Tim From owner-software@net.bio.net Mon Feb 05 22:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!rome.netwide.net!not-for-mail From: Michael Banditt Subject: GCK Message-ID: <3115CA70.2F64@cell.biol.ethz.ch> Date: Mon, 05 Feb 1996 10:14:24 +0100 Organization: IZB ETH Zurich X-Mailer: Mozilla 2.0b6a (Macintosh; I; PPC) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 11 Hello! Does anybody have some experience with the "Gene Construction Kit" for the MacIntosh? We are currently evaluating this program and would like to hear some other opinions. -- Michael Banditt Phone: +41-1-633-3345 Institute for cell biology Fax: +41-1-633-1069 Swiss Institute of Technology Email: banditt@cell.biol.ethz.ch From owner-software@net.bio.net Mon Feb 05 22:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!hookup!news.nstn.ca!news.cs.indiana.edu!umn.edu!dialup-16-a-15.gw.umn.edu!user From: velaz001@maroon.tc.umn.edu (Ruben A. Velazquez) Subject: Re: want mac software sites Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: dialup-16-a-15.gw.umn.edu Organization: UMN References: <96020308175880@pcc.awinc.com> Date: Tue, 6 Feb 1996 06:09:23 GMT Lines: 14 In article <96020308175880@pcc.awinc.com>, bryan.webster@pcc.awinc.com (Bryan Webster) wrote: > -> From: jlepine@haverford.edu > -> Subject: want mac software sites > -> > -> I really need a www site where I can download MACINTOSH software. > -> Everything I try to download turns out to be for other systems. > -> jlepine@haverford.edu > When you are on the www next, try using one of the search systems > such as YAHOO to locate sites with MAC software. Try http://www.shareware.com/ From owner-software@net.bio.net Mon Feb 05 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!gatech!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!harbinger.cc.monash.edu.au!news.mel.connect.com.au!munnari.OZ.AU!metro!metro!dchamber From: dchamber@extro.ucc.su.oz.au (Dianne Chambers) Newsgroups: bionet.software Subject: Re: Biology Education Software FAQ Date: 6 Feb 1996 04:21:53 GMT Organization: The University of Sydney Lines: 30 Sender: dchamber@linnaeus.bio.usyd.edu.au. Distribution: inet Message-ID: <4f6l11$aom@metro.usyd.edu.au> References: <4ep0h8$lqn@nntp3.u.washington.edu> <4f0cs8$k7p@bbs.dordt.edu> NNTP-Posting-Host: ntbt.bio.usyd.edu.au X-Posted-From: InterNews 1.0@0.0.0.0.in-addr.arpa. I am part of UniServe*Science which is an Australian group whose role includes finding and evaluating software packages that could be used in undergraduate science teaching. I look after biology, biochemistry, and psychology. Thus, I too have been tracking down software for teaching undergraduate biology. Our database can be searched at http://129.78.153.144/ROFM_CGI/search.html or visit our site at http://www.usyd.edu.au.su/SCH I'd love to hear about any other software (or videodiscs) for teaching undergraduate science, in particlular if it is a package you have used and would recommend. Cheers, Dianne Chambers --------------------------------------------------------------------- Contact details: Dr Dianne Chambers UniServe*Science (F07) The University of Sydney NSW 2006 AUSTRALIA Tel: 61 2 351 2960 Fax: 61 2 351 2175 email: dchamber@extro.ucc.su.oz.au From owner-software@net.bio.net Mon Feb 05 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!uwm.edu!usenet From: youngmin@csd4.fsu.edu Newsgroups: bionet.software Subject: REQ: Reference Manager for Windows Date: Tue, 06 Feb 1996 23:12:46 GMT Organization: University of Wisconsin - Milwaukee Lines: 3 Message-ID: <4f8g42$s81@uwm.edu> NNTP-Posting-Host: 129.89.8.202 X-Newsreader: Forte Free Agent 1.0.82 I am a bio student. I badly need RF for windows. I will have something in return. From owner-software@net.bio.net Mon Feb 05 22:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!primus.ac.net!news.cais.net!xara.net!peer-news.britain.eu.net!strath-cs!bradford.ac.uk!leeds.ac.uk!news From: bmb5meb@bmb.leeds.ac.uk (Michael Beck) Subject: Re: MS-Dos or Windows 95 software Message-ID: <1996Feb6.121419.23735@leeds.ac.uk> Reply-To: bmb5meb@bmb.leeds.ac.uk NNTP-Posting-Host: bmbaxp.leeds.ac.uk Organization: The University of Leeds, UK Date: Tue, 6 Feb 1996 12:14:19 +0000 (GMT) References: <1996Feb6.121149.21976@leeds.ac.uk> Lines: 16 In article <1996Feb6.121149.21976@leeds.ac.uk>, bmb5meb@bmb.leeds.ac.uk (Michael Beck) writes: >Hi, > >I'm trying to locate some software which I can run either under MS-Dos or >Windows 95. The software I need is a UUencoder/decoder and a C compiler. If >anyone can give me pointers to FTP sites where either of these are available >I'd appreciate it. > >Mike. Sorry, I forgot my .sig with e-mail address. Michael Beck (Leeds University Archery Team) : ___ Protein Database Group, : <*,*> Home of the OWL University of Leeds : [`_'] protein database. e-mail : bmb5meb@bmb.leeds.ac.uk : _"_"_ From owner-software@net.bio.net Mon Feb 05 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!metro!metro!dchamber From: dchamber@extro.ucc.su.oz.au (Dianne Chambers) Newsgroups: bionet.software Subject: Re: Biology Education Software FAQ Date: 6 Feb 1996 22:35:02 GMT Organization: The University of Sydney Lines: 15 Sender: dchamber@linnaeus.bio.usyd.edu.au. Distribution: inet Message-ID: <4f8l2m$h3h@metro.usyd.edu.au> References: <4ep0h8$lqn@nntp3.u.washington.edu> <4f0cs8$k7p@bbs.dordt.edu> <4f6l11$aom@metro.usyd.edu.au> NNTP-Posting-Host: ntbt.bio.usyd.edu.au X-Posted-From: InterNews 1.0@metro.ucc.su.oz.au. Sorry, the second URL should have been http://www.usyd.edu.au/su/SCH --------------------------------------------------------------------- Contact details: Dr Dianne Chambers UniServe*Science (F07) The University of Sydney NSW 2006 AUSTRALIA Tel: 61 2 351 2960 Fax: 61 2 351 2175 email: dchamber@extro.ucc.su.oz.au From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!gatech!newsfeed.internetmci.com!news.sprintlink.net!ralph.vnet.net!islpub.vnet.net!user From: islpub@vnet.com (TeeMo) Newsgroups: bionet.software Subject: SOFTER WEAR!!!! Date: 7 Feb 1996 00:25:38 GMT Organization: Vnet Internet Access, Charlotte, NC - info@char.vnet.net Lines: 16 Message-ID: NNTP-Posting-Host: islpub.vnet.net You're gonna be GLAD you been HAD, when you visit this site! Sysop Softwear! http://www.hiltonheadisland.com/sysop.htm T-Shirts€ T-Shirts€T-Shirts€ T-Shirts€ T-Shirts€ T-Shirts€ T-Shirts made just for that special part of you that most people refer to as: prefix:Computer-SPAZ! GEEK! or WIERDO! Join The Worldwide Coalition of Systems Operators While It's on an underground level. and Check out my little slice of the American dream. It's well worth the 30 seconds it takes to get there. Questions?: islpub@vnet.net From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!milo.mcs.anl.gov!jadoube.mcs.anl.gov!levine From: levine@jadoube.mcs.anl.gov (David Levine) Newsgroups: bionet.software Subject: PGAPack V1.0, Parallel GA Software Date: Wed, 7 Feb 1996 2:29:32 GMT Organization: Math and Computer Science, Argonne National Laboratory Lines: 25 Distribution: world Message-ID: <82366017219610@jadoube.mcs.anl.gov> NNTP-Posting-Host: jadoube.mcs.anl.gov PGAPack is a general-purpose, data-structure-neutral, parallel genetic algorithm library. It is intended to provide most capabilities desired in a genetic algorithm library, in an integrated, seamless, and portable manner. Key features include: * Callable from Fortran or C. * Runs on uniprocessors, parallel computers, and workstation networks. * Binary-, integer-, real-, and character-valued native data types. * Full extensibility to support custom operators and new data types. * Easy-to-use interface for novice and application users. * Multiple levels of access for expert users. * Parameterized population replacement. * Multiple crossover, mutation, and selection operators * Easy integration of hill-climbing heuristics. * Extensive debugging facilities. * Large set of example problems. * Detailed users guide PGAPack is available: -- via anonymous ftp from ftp.mcs.anl.gov in file pub/pgapack/pgapack.tar.Z -- via the web at http://www.mcs.anl.gov/pgapack.html David Levine levine@mcs.anl.gov http://www.mcs.anl.gov/home/levine MCS 221 C-216 Argonne National Laboratory Argonne, Illinois 60439 (708)-252-6735 Fax: (708)-252-5986 From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.tamu.edu!news.utdallas.edu!geraldo.cc.utexas.edu!netnews.uthscsa.edu!netnews!garrisonp From: garrisonp@uthscsa.edu (Preston Garrison) Newsgroups: bionet.software Subject: Re: boxshade or similar Date: Wed, 7 Feb 96 03:43:16 GMT Organization: Uthscsa Lines: 15 Message-ID: References: <4etkns$n7g@news.ycc.yale.edu> NNTP-Posting-Host: bioc04.uthscsa.edu X-Newsreader: VersaTerm Link v1.1.1 In Article <4etkns$n7g@news.ycc.yale.edu>, Danny Chamovitz wrote: >Does anyone know of a BOXSHADE type of program for Mac or UNIX? BOXSHADE is a >freeware that foramts alignments with black and grey boxes showing sequence >conservation. >.... You might try SeqVu for Mac. It's $10 shareware available at: http://iubio.bio.indiana.edu:80/1/IUBio-Software%2bData/molbio/mac Preston Garrison garrisonp@uthscsa.edu Biochem. Dept. Univ of Texas Health Sci Ctr San Antonio, Tx 78284-7760 USA 210-567-3702 From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!wizard.pn.com!brighton.openmarket.com!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!news From: Brian Fristensky Newsgroups: bionet.software Subject: Re: Wanted: public DNA alignment/primer design software Date: 7 Feb 1996 18:59:00 GMT Organization: University of Manitoba Lines: 35 Message-ID: <4faspk$7mu@canopus.cc.umanitoba.ca> References: <4f5dcj$670@coyote.dres.dnd.ca> NNTP-Posting-Host: vogt.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12 (X11; I; SunOS 5.4 sun4m) X-URL: news:4f5dcj$670@coyote.dres.dnd.ca Reno Pontarollo wrote: >I already use MACAW 2.05 for DNA alignment, but could use some more software. > >I have access to a UNIX system and was wondering what the CLUSTAL and FASTA packages are >capable of and how easy they are to use. > I have built a comprehensive sequence analysis facility on our Sun/Unix system using only freely-available software. I have written two packages: FSAP - general sequence analysis tasks XYLEM - sequence database creation and manipulation These programs run from the command line, but can also be run from Steven Smith's GDE (Genetic Data Environment). I have written a very extensive set of GDE menus for running FSAP and XYLEM programs, as well as other freeware programs (FASTA, PHYLIP, CLUSTAL, PIMA...) from GDE. For more information and to download software see: http://home.cc.umanitoba.ca/~psgendb/ -- =============================================================================== Brian Fristensky | We've heard 3 or 4 times this morning that, Department of Plant Science | out of 85,000 works funded by the NEA, University of Manitoba | only 20 were controversial. I don't know Winnipeg, MB R3T 2N2 CANADA | why anyone would cite that as something to frist@cc.umanitoba.ca | be proud of. Office phone: 204-474-6085 | FAX: 204-261-5732 | Garrison Keillor, testimony to Congress in http://home.cc.umanitoba.ca/~frist/ defense of Natl. Endowment for the Arts =============================================================================== From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!col.hp.com!csn!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!oitnews.harvard.edu!ionchann!marty From: marty@ionchann (Marty Gallagher) Newsgroups: bionet.software Subject: Re: [Q]:?how to run MAC SW on PC (Windows95) Date: 7 Feb 1996 15:55:09 GMT Organization: Harvard University Office of Information Technology Lines: 20 Distribution: bionet Message-ID: <4fai0t$2hr@netope.harvard.edu> References: <4eprqm$kes@mserv1.dl.ac.uk> NNTP-Posting-Host: ionchannel.med.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Search the net for a program called "executor." There is a free demo available. -- Marty Ivo Wiesner (nfix@jcu.cz) wrote: : Hello Netters out there! : Could anybody inform me: : 1. if there is any emulator for PC (Windows) platform : which enables running MAC software? : 2.how difficult work represents to rewrite Mac software for Windows PC? : Any info much appreciated. : Ivo Wiesner From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news From: timc@chiark.chu.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: REQ: Reference Manager for Windows Date: 07 Feb 1996 09:24:18 +0000 (GMT) Organization: Linux Unlimited Lines: 16 Message-ID: References: <4f8g42$s81@uwm.edu> NNTP-Posting-Host: myrddin.chu.cam.ac.uk Originator: timc@chiark.chu.cam.ac.uk (UNIX:@[131.111.131.114]) In article <4f8g42$s81@uwm.edu>, wrote: >I am a bio student. I badly need RF for windows. >I will have something in return. I hope you're not advocating software piracy... There are lots of reference management programs about. There are no free ones, but there are one or two in the $50 price range. And if you're telling me you can't afford that much, I won't believe you!!! :-) There's a good summary at: http://www.peinet.pe.ca:2080/Chorus/Mega/m001.html Regards, Tim. From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!howland.reston.ans.net!nntp.coast.net!torn!news.unb.ca!coranto.ucs.mun.ca!usenet From: username@terra.nlnet.nf.ca (Full name) Newsgroups: bionet.software Subject: Need help running WIN.95-help!!! Date: 7 Feb 1996 07:34:45 GMT Organization: Memorial University of Newfoundland Lines: 7 Message-ID: <4f9kml$n36@coranto.ucs.mun.ca> NNTP-Posting-Host: n104h081.nlnet.nf.ca X-Newsreader: WinVN 0.92.6+ I recently downloaded some files needed to finish installing the net. Now when I start my computer I get a message saying that a windows registary or System ini.file can no longer be found. If by mistake, I erased this file, how can I get it back? ps. I tried installing win.95 again with same results. And also not in the Recycle Bin. NEED HELP From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!newsroom.utas.edu.au!dslip6.its.utas.edu.au!user From: tim.barlow@lib.utas.edu.au (Tim Barlow) Newsgroups: bionet.software Subject: Beta Testers Required - Electronic Forms for the Mac Date: Wed, 07 Feb 1996 18:43:45 +1100 Organization: Barlow & Bond Enterprises Lines: 78 Message-ID: NNTP-Posting-Host: dslip6.its.utas.edu.au Abstract -------- Form is a suite of applications that implements electronic forms for the Macintosh; it has three components. The first application, the 'Generator' has a dual purpose. Firstly, it provides facilities for the creation, storage and testing of electronic forms. Secondly, when one or more forms have been created and tested the application may then be used to generate a 'Sender' application. This application may be configured with one or more of the stored forms and is essentially a cut-down version of the Generator without any of the form creation or editing capabilities. The second program of the suite is the 'Sender' application, created in the manner described above. The application is intended to be an easy to use tool for office staff, that enables the direct filling in, and immediate transmission of forms. The application may be configured with any number of forms and provides facilities for the completion, validation and submission of the forms. The manner in which a form is dispatched to its intended recipient is by embedding the form data within an eMail message. The Sender application does not send the eMail message itself but hands over responsibility to a separate eMail application, referred to as its eMail 'helper'. The third application, the 'Receiver' provides facilities for processing received forms, ie. forms that have arrived at their destination embedded in eMail messages. It does not receive eMail messages itself, it instead relies upon a separate eMail application, its eMail helper. It scans the mailboxes of its helper recognising and reading only those messages that contain embedded form data about which it knows, ie. for which it has been configured. The extracted messages are then processed. A message is firstly scanned and the form data is extracted. The extracted data may then, optionally be written to a database. This is achieved by handing the data over to a separate database application, referred to as the database 'helper'. The data may also be written to a text file. An automatic reply may be sent and the message transferred to another mailbox. Requirements ------------ a) System 7.5 or later. b) AppleScript 1.1 or later. c) Geneva and Monaco 9 point fonts. d) Courier 12 point Application Helpers ------------------- All eForm applications require the specification of an eMail Œhelper¹ application. An eMail helper is an application that is used by the host to perform all of its eMail operations, such as sending and receiving mail. An initialisation process involves the specification of the eMail helper application to be used. This is done by selecting the appropriate eMail helper library from the folder of libraries supplied with the package. Each library contains the necessary AppleScripts to enable the host to communicate with its eMail helper. The Receiver application may also optionally require the services of a database application. This too, is provided via means of a helper library of AppleScripts. In this initial release of the product only Eudora and FileMaker Pro are supported as eMail and database helper applications. It is hoped to add support for further applications as demand requires. Eudora Light may be downloaded from the following url - ftp://ftp.qualcomm.com/quest/mac/eudora/1.5/eudora154.hqx Beta Testers ------------ The package may be downloaded from the following url - ftp://ftp.utas.edu.au/mac/eform/eForm_1.0b4_Installer.hqx If, after looking at the package, you would like to become a beta tester then contact me for a free 5 form license. Tim Barlow - tim.barlow@its.utas.edu.au -- Tim Barlow tim.barlow@lib.utas.edu.au GPO Box 607 Sandy Bay Tasmania 7005 Australia From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!news.rrz.uni-hamburg.de!news From: Reinhard Windoffer Newsgroups: bionet.software Subject: QE: GDE on DEC Alpha or IBM? Date: Wed, 07 Feb 1996 16:59:24 -0800 Organization: University of Hamburg -- Germany Lines: 6 Message-ID: <31194AEC.198B@zoologie.uni-hamburg.de> NNTP-Posting-Host: windoffer.zoologie.uni-hamburg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b5 (Win16; I) Hi Has anybody ported GDE (Genetic Data Environment) on the DEC alpha or IBM? Reinhard From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!news.internetMCI.com!darwin.sura.net!blaze.cs.jhu.edu!news.jhu.edu!news From: jiyun kim Newsgroups: bionet.software Subject: DNA analysis program for PC Date: 7 Feb 1996 21:14:18 GMT Organization: johns hopkins university school of medicine Lines: 8 Message-ID: <4fb4na$7l5@news.jhu.edu> NNTP-Posting-Host: 128.220.138.178 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 32bit) Hello, I am trying to find a PC DNA analysis that has similar features as mac version of DNA strider. It would be nice if it is windows version. Thanks for help. From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: PESTFIND program available Date: 7 Feb 1996 21:06:31 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 578 Message-ID: <4fb48n$iif@gap.cco.caltech.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu Interested in PEST sequences? The PESTFIND program (from M. Rechsteiner's laboratory) has been ported from BASICA to ANSI C. The new version should be very portable, it is known to compiles and run on both OpenVMS and Irix and should function on any machine with an ANSI C compiler (provided that the compiler is actually run in the ANSI C mode, which is not usually the default). One major change between the BASICA and ANSI C versions - the former would process a series of sequences in a special format. The new one will only process one sequence at a time, and the input file must consist of only protein sequence (no comments, or numbers). Both versions prompt for all needed information, there are no command line switches available. Following my signature you will find: PESTFIND.C ANSI C version, includes all of original program as a comment. PESTFIND.COM DCL procedure for OpenVMS systems - a wrapper around PESTFIND so that GCG formatted sequences and database entries may be fed transparently to the program. Please report any bugs to me or to greg_pratt@medschool.med.utah.edu (in Rechsteiner's lab). David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech ****pestfind.c******************************************************** /*pestfind.c 1-NOV-1995, David Mathog, Biology Division, Caltech Find PEST sequences from a single protein sequence. REQUIRED Input format for sequence: plain sequence on one or more lines. No numbers or spaces should be present. Sequences longer than 10000 amino acids will not run correctly. A terminal "*" is allowed, but not required. The only allowed Amino Acid designations are: ARNDCQEGHILKMFPSTWYV Ambiguous residues, such as 'X' will cause the program to abort. This is an ANSI C version, translated from the original Basic program provided by Martin Rechsteiner, and incorporating the corrections provided to him by Bob Stellwagen. It should be quite portable. (It compiles without errors or warnings in DECC 4.1 for /standard=ansi89 and /standard=portable.) Compilation/Use on OpenVMS: $ cc/standard=ansi89/prefix=all pestfind $ link pestfind $ run pestfind Compilation/Use on Unix (Irix 5.3, anyway): $ cc -xansi -o pestfind pestfind.c % pestfind For reference purposes, here is the original program: 1 REM PESTFIND 100 ON ERROR GOTO 485 105 CLS:WIDTH 40:KEY OFF:GOTO 330 110 CNT=0:HLD=1 115 FOR Q = HLD TO X 120 IF Q=1 THEN 130 ELSE 125 125 IF A$(Q)="R" OR A$(Q)="K" OR A$(Q)="H" THEN 130 ELSE 320 130 CNT=0: HND=Q :HLD=Q 135 FOR B = 1 TO 23 : R(B) = 0 :NEXT 140 TFD(21) = 0 145 FOR I = (Q+1) TO X 150 IF A$(I)="H" OR A$(I)="K" OR A$(I)="R" THEN 165 ELSE 155 155 CNT = CNT + 1 160 NEXT I 165 IF CNT < WS THEN 170 ELSE 175 170 HLD = I : GOTO 320 175 FOR K = HLD+1 TO I-1 180 FOR N = 1 TO 20 185 IF L$(N) = A$(K) THEN 195 ELSE 190 190 NEXT N 195 R(N)=R(N)+T(N) 200 NEXT K 205 IF R(15) = 0 OR R(4)+R(7) = 0 OR R(16)+R(17) = 0 THEN 210 ELSE 235 210 IF R$ = "N" THEN 230 ELSE 215 215 LPRINT "INVALID PEST SEQUENCE: ";N$;" ";Q;"-";I;" (WS=";WS;")" 220 FOR B=HND TO I: LPRINT A$(B);:NEXT 225 LPRINT:LPRINT "--------------------------------------------------": LPRINT 230 HLD = I : GOTO 320 235 FOR J = 1 TO 20 : R(21)=R(21)+R(J):NEXT 240 R(22)=(((R(7)+R(15)+R(16)+R(17))-(T(7)+T(15)+T(17)))/R(21))*100 245 R(23)=(((R(4)+R(7)+R(15)+R(16)+R(17))-(T(7)+T(15)+T(17)))/R(21))*100 250 FOR J = 1 TO 20 :TFD(21) = TFD(21)+(TFD(J)*(R(J)/R(21))):NEXT 255 DSC2 = -1*((-.55*R(23))+(.5*TFD(21))) 260 IF DSC2 >0 THEN 265 ELSE 300 265 LPRINT "POTENTIAL PEST SEQUENCE: ";N$;" ";Q;"-";I;" (WS=";WS;")" 270 FOR B= HND TO I: LPRINT A$(B);" ";:NEXT B 275 LPRINT:LPRINT:LPRINT "THE MOLE FRACTION OF PEDST IS: ";R(23) 280 LPRINT "THE HYDROPHOBICITY INDEX IS ";TFD(21) 285 LPRINT:LPRINT "THE PEST-FIND SCORE IS ";: LPRINT CHR$(14) DSC2 290 LPRINT:LPRINT CHR$(14) "POSSIBLE PEST SEQUENCE":LPRINT "-------------------------------------------------":LPRINT 295 GOTO 315 300 LPRINT "POOR PEST SEQUENCE: ";N$;" ";Q;"-";I;" (WS=";WS;")" 305 FOR B= HND TO I: LPRINT A$(B);" ";:NEXT B 310 LPRINT:LPRINT "THE PEST-FIND SCORE IS ";: LPRINT CHR$(14) DSC2 :LPRINT "-------------------------------------------------" 315 HLD = HLD + I 320 NEXT Q 325 CLS:LPRINT:LPRINT "END PEST SEARCH OF ";N$:LPRINT:LPRINT:LPRINT: IF D$ = "P" GOTO 435 ELSE RUN 330 DIM R(24): DIM T(22):DIM TFD(23):DIM L$(23): DIM A$(1500) 335 FOR I = 1 TO 20 : READ L$(I):NEXT I 340 FOR I = 1 TO 20 : READ T(I):NEXT I 345 FOR I = 1 TO 20 : READ TFD(I):NEXT 350 PRINT "************** PEST FIND ***************":PRINT:PRINT 355 INPUT "ENTER PROTEIN NAME: ",N$ 360 CLS:LOCATE 10,5:INPUT "PRINT INVALID PEST SEQUENCES";R$ 365 CLS:PRINT:PRINT:INPUT "WHAT IS THE MINIMUM NUMBER OF AAs BETWEEN POSITIVE FLANKS";WS 370 PRINT:PRINT:INPUT "ENTRY FROM SCREEN(S) OR FROM PROGRAM(P)";D$ 375 IF D$="S" THEN 380 ELSE 435 380 CLS:PRINT:PRINT:PRINT"ENTER ONE LETTER AMINO ACID CODE FOR SEQUENCE (* TO END)":PRINT:PRINT:PRINT 385 FOR X = 1 TO 1500 390 PRINT"AMINO ACID ";X;" : ";:INPUT A$(X) 395 IF A$(X)="*" THEN GOTO 405 ELSE 400 400 NEXT 405 LPRINT CHR$(14) "PEST SEARCH: ",N$ 410 LPRINT "--------------------------------------------------" 415 LET X = X-1:GOTO 110 420 DATA A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y,V 425 DATA 71,156,114,115,103,128,129,57,137,113,113,128,131,147,97,87,101,186,163,99 430 DATA 63,0,10,10,70,10,10,41,13,90,82,6,64,72,29,36,38,36,32,87 435 READ N$ 440 CLS:PRINT:PRINT:PRINT:PRINT:PRINT"READING ",N$ 445 FOR B=1 TO 1500 450 READ A$(B) 455 IF A$(B)= "*" THEN GOTO 465 ELSE 460 460 NEXT B 465 X = B-1 470 LPRINT CHR$(14) "PEST SEARCH: ",N$ 475 LPRINT "--------------------------------------------------" 480 GOTO 110 485 IF ERR=4 THEN RUN */ #include #include #include #ifdef __VMS #include #endif /* __VMS */ #include int main(){ /* references to "was something" indicate the corresponding BASIC variable */ int i,j,k,n; /* assorted loop variables */ int query; /* loop variable, marks the beginning of a query, was q*/ int last; /* loop variable, marks the end of a query, was i*/ int piece; /* length of individual line read from input sequence */ int remaining; /* bytes free in buffer for input sequence */ int seqlen; /* length of AA sequence being searched */ int flank_dist; /* distance between positive flanks, was WS*/ int aanum[256]; /* lookup table, aa_name -> position */ float score[20]; /* pest score, was array R() */ float sum_score; /* score summation, was R(21) */ float weight_percent; /* weight percent of PEDST, was R(23) */ float pf_score; /* PESTfind score, was DSC2 */ float weight[20]; /* weight in grams of 1 mole of this amino acid, was T() */ float phobe[20]; /* normalized hydrophobicity value for this amino acid, was TFD()*/ float phobe_index; /* hydrophobicity index, was TFD(21) */ char invalid; /* if 'y' then print invalid PEST sequences, else no, was N$*/ char aa_name[20]; /* single letter name for this amino acid, was L$() */ char sequence[10000]; /* a protein sequence in single letter code, was A$() */ char line[1000]; /* a place to format output lines */ char infile[1000]; /* input file name */ char outfile[1000]; /* output file name */ FILE *ifile,*ofile; /* file pointer for input file */ /* Initialize the arrays. Use this long form because it's easier to check the value at a given position than in more compact forms. Note that the hydrophobicity value for tyrosine used here is 58, not 32 as in the original program - following a correction from Bob Stellwagen (USC). */ for(i=0;i<256;i++)aanum[i] = -1; i = 0; aa_name[i]='A'; aanum[(int) 'A']=i; weight[i]= 71; phobe[i]=63; i = 1; aa_name[i]='R'; aanum[(int) 'R']=i; weight[i]=156; phobe[i]= 0; i = 2; aa_name[i]='N'; aanum[(int) 'N']=i; weight[i]=114; phobe[i]=10; i = 3; aa_name[i]='D'; aanum[(int) 'D']=i; weight[i]=115; phobe[i]=10; i = 4; aa_name[i]='C'; aanum[(int) 'C']=i; weight[i]=103; phobe[i]=70; i = 5; aa_name[i]='Q'; aanum[(int) 'Q']=i; weight[i]=128; phobe[i]=10; i = 6; aa_name[i]='E'; aanum[(int) 'E']=i; weight[i]=129; phobe[i]=10; i = 7; aa_name[i]='G'; aanum[(int) 'G']=i; weight[i]= 57; phobe[i]=41; i = 8; aa_name[i]='H'; aanum[(int) 'H']=i; weight[i]=137; phobe[i]=13; i = 9; aa_name[i]='I'; aanum[(int) 'I']=i; weight[i]=113; phobe[i]=90; i =10; aa_name[i]='L'; aanum[(int) 'L']=i; weight[i]=113; phobe[i]=82; i =11; aa_name[i]='K'; aanum[(int) 'K']=i; weight[i]=128; phobe[i]= 6; i =12; aa_name[i]='M'; aanum[(int) 'M']=i; weight[i]=131; phobe[i]=64; i =13; aa_name[i]='F'; aanum[(int) 'F']=i; weight[i]=147; phobe[i]=72; i =14; aa_name[i]='P'; aanum[(int) 'P']=i; weight[i]= 97; phobe[i]=29; i =15; aa_name[i]='S'; aanum[(int) 'S']=i; weight[i]= 87; phobe[i]=36; i =16; aa_name[i]='T'; aanum[(int) 'T']=i; weight[i]=101; phobe[i]=38; i =17; aa_name[i]='W'; aanum[(int) 'W']=i; weight[i]=186; phobe[i]=36; i =18; aa_name[i]='Y'; aanum[(int) 'Y']=i; weight[i]=163; phobe[i]=58; i =19; aa_name[i]='V'; aanum[(int) 'V']=i; weight[i]= 99; phobe[i]=87; fprintf(stdout,"************** PEST FIND ***************\n\n\n"); fprintf(stdout,"Enter the name of the amino acid sequence file to process: "); scanf("%s",&infile[0]); fprintf(stdout,"Enter the minimum number of AAs between positive flanks: "); scanf("%d",&flank_dist); fprintf(stdout,"Print invalid pest sequences (y/n): "); scanf("%s",&invalid); invalid=tolower(invalid); fprintf(stdout,"Enter a name for the output file: "); scanf("%s",&outfile[0]); fprintf(stdout,"\n\n"); /* Read in the sequence file, if possible. Put an "^" on each end - that will be used to enforce the PEST definition that N and C termini act as begin/end for PEST sequences. */ ofile = fopen(outfile,"w"); if(!ofile){ fprintf(stderr,"Fatal error: the file >%s< could not be created!\n",outfile); fprintf(stderr,"PESTFIND run aborted\n"); exit(0); } ifile = fopen(infile,"r"); if(!ifile){ fprintf(stderr,"Fatal error: the file >%s< does not exist or is unreadable!\n" ,infile); fprintf(stderr,"PESTFIND run aborted\n"); exit(0); } else{ remaining=9999; seqlen=1; sequence[0]='^'; while(fgets(&sequence[seqlen],remaining,ifile)){ piece = strlen(&sequence[seqlen]); seqlen = seqlen + piece - 1; remaining = remaining - piece; } } /* Remove trailing "*" and any spaces after it, if present. Add a trailing '^' to enforce the N/C rule. */ for(i=0;i%s< is invalid!\n",infile); fprintf(stderr,"Reason: >%c< is not in the single letter AA code\n" ,sequence[i]); fprintf(stderr,"PESTFIND run aborted\n"); exit(0); } } /* Time for the actual calculation */ /* First find the beginning of the possible PEST region, defined as the N terminus or an R, K, or H amino acid. The beginning will be marked by the variable "query" */ query=0; while(query 0){ fprintf(ofile,"Potential PEST sequence %d-%d (flank_dist=%d)\n", query,last,last-query-1); strncpy(line,&sequence[query],last-query+1); line[last-query+1] = '\0'; fprintf(ofile," %s\n",line); fprintf(ofile," The weight percent of PEDST is: %f\n",weight_percent); fprintf(ofile," The hydrophobicity index is: %f\n",phobe_index); fprintf(ofile," The PEST-FIND score is: %f\n",pf_score); fprintf(ofile,"---------------------------------\n\n"); } else { fprintf(ofile,"Poor PEST sequence %d-%d (flank_dist=%d)\n", query,last,last-query-1); strncpy(line,&sequence[query],last-query+1); line[last-query+1] = '\0'; fprintf(ofile," %s\n",line); fprintf(ofile," The best PEST-FIND score is: %f\n",pf_score); fprintf(ofile,"---------------------------------\n\n"); } query = last; continue; /* to bottom of query loop */ } query++; } } /* loop on query */ fprintf(stderr,"PESTFIND run completed normally\n"); } ****pestfind.com****************************************************** $!Pestfind.com $! 4-NOV-1995, David Mathog, biology division, Caltech $! $! This procedure is a wrapper for the actual PestFind program, it $! allows it to act on one or more GCG formatted files. $! This uses the TOSEQ program, if you don't have that, you may $! have the EGCG TOTEXT, which does the same thing. This wrapper isn't $! terribly robust, so files of file names must consist of ONLY entries $! and filenames; comments,"..", stuff after the filename, etc, any of these $! will break this procedure!!! $! $! All files are processed with a window of 9 and no invalid PEST sequences. $! $! A logical PESTFIND must point to the location of the PESTFIND program $! $! invoke with $! $! @pestfind filename (either a file or a GCG entry) $! or $! @pestfind @filename (a file of file names) $! $! $ if(P1 .eqs. "") $ then $ type sys$input Find PEST sequences in proteins. This will accept as input one of: 1. The name of a GCG formatted peptide file: filename.pep 2. The name of a GCG peptide database entry: sw:1433_HORVU 3. A GCG file of filenames (containing either of the above but nothing else) @filelist.fil Note 1: If any sequence contains an ambiguous residue, such as B,X, or Z, pestfind will not process that sequence. It will issue an error message and stop. Note 2: Default Parameters: minimum pest sequence (window) size =9 no invalid PEST sequences shown outfile = pestfind.out To change one or more of thse parameters, hit a ^Y NOW and issue one or more of these commands before running PESTFIND again: $ pestfind_window :== 10 (or whatever value you want) $ pestfind_invalid :== Y (to see invalid ones) $ pestfind_out :== filename (valid VMS filename) $ inquire acton "Enter file, entry, or file of filenames = " $ else $ acton = P1 $ endif $! $! make up a root for temporary file names $! $ now = f$time() $ username = f$getjpi("","USERNAME") $ username = f$edit(username,"COLLAPSE") $ tempname = "kill_" + username + "_" - + f$cvtime(now,,"MONTH") - + f$cvtime(now,,"DAY") - + f$cvtime(now,,"HOUR") - + f$cvtime(now,,"MINUTE") - + f$cvtime(now,,"HUNDREDTH") $! $! does it begin with an "@"? $! $ on control_c then goto $ if(f$extract(0,1,acton) .eqs. "@") $ then $ loop = 1 $ namelen = f$length(acton) - 1 $ open/read/error=oops tfil: 'f$extract(1,namelen,acton) $ read tfil: file $ else $ loop = 0 $ file = acton $ endif $! $! $ if("''pestfind_window'" .nes. "") $ then $ window = pestfind_window $ else $ window = 9 $ endif $! $ if("''pestfind_invalid'" .nes. "Y") $ then $ invalid = "N" $ else $ invalid = "Y" $ endif $! $ if("''pestfind_out'" .nes. "") $ then $ pout = pestfind_out $ else $ pout := pestfind.out $ endif $! $open/write rfil: 'tempname'.accum $write rfil: "Pestfind analysis of ''acton'" $write rfil: "Processing began at ''now'" $write rfil: " " $write rfil: "Results on: ''file'" $write rfil: "====================================================" $close rfil: $! $ on error then goto oops $top: $ write sys$output "Now processing: ''file'" $ toseq/infile='file'/out='tempname'.pep/line=50/protein/default $ open/write cfil: 'tempname'.com $ write cfil: "define/user sys$output nla0:" $ write cfil: "define/user sys$error ''tempname'.error" $ write cfil: "$run pestfind:pestfind" $ write cfil: "''tempname'.pep" $ write cfil: window $ write cfil: invalid $ write cfil: "''tempname'.tmp" $ close cfil: $ @'tempname'.com $ define/user sys$output nla0: $ define/user sys$error nla0: $ search 'tempname'.error "PESTFIND run completed normally" $ if($STATUS .ne. 1) $ then $! $! error during run, put the error message in instead $! $ convert/fdl=sys$input 'tempname'.error 'tempname'.tmp2 RECORD BLOCK_SPAN yes CARRIAGE_CONTROL print FORMAT vfc SIZE 0 CONTROL_FIELD_SIZE 2 $ else $! $! Run completed ok, so tack the results on $! $! Convert file type so that append will work properly. streamlf $! strikes again :-(. $! $ convert/fdl=sys$input 'tempname'.tmp 'tempname'.tmp2 RECORD BLOCK_SPAN yes CARRIAGE_CONTROL print FORMAT vfc SIZE 0 CONTROL_FIELD_SIZE 2 $ endif $ append 'tempname'.tmp2 'tempname'.accum $ delete 'tempname'.tmp2; $ delete 'tempname'.error; $ delete 'tempname'.pep; $ delete 'tempname'.com; $ delete 'tempname'.tmp; $ if(loop .eq. 1) $ then $ read/end=done tfil: file $ open/append rfil: 'tempname'.accum $ write rfil: "Results on: ''file'" $ write rfil: "====================================================" $ close rfil: $ goto top $ endif $ goto cleanup $! $done: $ close tfil: $! $cleanup: $ rename 'tempname'.accum 'pout' $ write sys$output "Run completed, results are in ''pout'" $ exit $! $oops: $ write sys$output "--------------------------" $ write sys$output "FATAL ERROR!!!!!" $ write sys$output "something went wrong when processing ''acton'" $ if(loop .eq. 1)then close tfil: $ exit $oops2: $ write sys$output "--------------------------" $ write sys$output "Run aborted by ^C or ^Y" $ delete 'tempname'.*.* $ exit From owner-software@net.bio.net Tue Feb 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!howland.reston.ans.net!plug.news.pipex.net!pipex!tube.news.pipex.net!pipex!lade.news.pipex.net!pipex!news.ftech.net!news From: psiber@ftech.co.uk (Alan) Newsgroups: bionet.software Subject: Re: [Q]:?how to run MAC SW on PC (Windows95) Date: Wed, 07 Feb 1996 02:24:26 GMT Organization: Visionaries.co.uk Lines: 39 Message-ID: <4f92f5$ku0@alpha.ftech.net> References: <4eprqm$kes@mserv1.dl.ac.uk> <31114385.41C6@rhapsody.stanford.edu> Reply-To: psiber@ftech.co.uk NNTP-Posting-Host: psiber.ftech.co.uk X-Newsreader: Forte Free Agent 1.0.82 Hi, I'm Alan Sorry to butt in likr this, but there is something of great interest to me here. Lionel Gilet wrote: >I did that once. The Mac software was written in object-oriented c/c++ >with Symantec librairies. It was basicallly reading a file generated by >Excell, doing some calculation and displaying a bunch of graphic windows with >a floating window that would display the coordinates of the point you click >on. So my question is, does anyone here now of some shareware or freeware that can map coordnates clicked into a plain text file? This is, I know completely irrelevant to this thread, but I guessed that some peple in this field may have had use for such a tool at some time. Greateful if anyone can help. Alan By the way, I'm mapping bitmapped celtic knots to vector's for raytracing. I'll need something to smooth the lines of my shaky hand too! Visionaries T-shirts & Gifts London: Don't miss it @ http://www.visionaries.co.uk/ or visit The Hotlist http://www.visionaries.co.uk/zine/hots/hotindex.hts#index |\ .-. | \ / \ .-. .-. _ +--\--p--/--s--\--i--/-b-\-e-/-r-\---/-\--- | \ / \ / '-' '-' | '-' '-' Email: psiber@ftech.co.uk From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!plug.news.pipex.net!pipex!tube.news.pipex.net!pipex!lade.news.pipex.net!pipex!news.ftech.net!news From: psiber@ftech.co.uk (Alan) Newsgroups: bionet.software Subject: Re: SOFTER WEAR!!!! Date: Thu, 08 Feb 1996 00:45:07 GMT Organization: Visionaries.co.uk Lines: 32 Message-ID: <4fbh0p$v4q@alpha.ftech.net> References: Reply-To: psiber@ftech.co.uk NNTP-Posting-Host: psiber.ftech.co.uk X-Newsreader: Forte Free Agent 1.0.82 islpub@vnet.com (TeeMo) wrote: >You're gonna be GLAD you been HAD, when you visit this site! I have to say, that I wasn't impressed >Sysop Softwear! Softop Syswear? >T-Shirts€ T-Shirts€T-Shirts€ T-Shirts€ T-Shirts€ T-Shirts€ >Questions?: islpub@vnet.net Yes. What have T-shirts to do with bionet software? BTW thanks to all posters. This group is highly informative, relaxed, and a pleasure to read! Alan Visionaries T-shirts & Gifts London: http://www.visionaries.co.uk/ The Hotlists http://www.visionaries.co.uk/zine/hots/hotindex.hts#index |\ .-. | \ / \ .-. .-. _ +--\--p--/--s--\--i--/-b-\-e-/-r-\---/-\--- | \ / \ / '-' '-' | '-' '-' Email: psiber@ftech.co.uk From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!plug.news.pipex.net!pipex!tube.news.pipex.net!pipex!lade.news.pipex.net!pipex!news.ftech.net!news From: psiber@ftech.co.uk (Alan) Newsgroups: bionet.software Subject: Re: Need help running WIN.95-help!!! Date: Thu, 08 Feb 1996 00:45:10 GMT Organization: Visionaries.co.uk Lines: 42 Message-ID: <4fbh0t$v4q@alpha.ftech.net> References: <4f9kml$n36@coranto.ucs.mun.ca> Reply-To: psiber@ftech.co.uk NNTP-Posting-Host: psiber.ftech.co.uk X-Newsreader: Forte Free Agent 1.0.82 I think that if youread a little closer, you may see that the message actually says something about A system device or driver _Reffered to in_ the registry or system.ini cannot be found. Read the name of the offending file (proably something.drv .dll .386 or .vxd. Locate this file! If it is not on your disk/bin you must remove the offending system.ini, or registry entry. This may or may not affect some installed software. The reg or ini entry should indicate the program that wants to find or use the missing file. You may have deleted the main program but not fully cleaned your system's references to it. Good Luck. let me know if you have problems. username@terra.nlnet.nf.ca (Full name) wrote: >I recently downloaded some files needed to finish installing the net. >Now when I start my computer I get a message saying that a windows registary >or System ini.file can no longer be found. >If by mistake, I erased this file, how can I get it back? > ps. I tried installing win.95 again with same results. > And also not in the Recycle Bin. > NEED HELP "..my God..*. it's full of stars...*..*.............*. ...*....*....* http://www.visionaries.co.uk/ ........ *..*.Raylist * .........*..Add......*Your..*....Link....*.*. **.. http://www.visionaries.co.uk/zine/hots/hotrays.hts .* Email: *...*......*... psiber@ftech.co.uk ..*...*.*. From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!newsfeed.internetmci.com!primus.ac.net!news.cais.net!xara.net!peer-news.britain.eu.net!liv!news From: P.W.Gould@liverpool.ac.uk (Paul Gould) Subject: Re: Biology Education Software FAQ Message-ID: Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: ctibiol2.bioc.liv.ac.uk Organization: The University of Liverpool X-Newsreader: RadicalNews (TM) v0.8.1 Beta References: <4ep0h8$lqn@nntp3.u.washington.edu> <4f0cs8$k7p@bbs.dordt.edu> <4f6l11$aom@metro.usyd.edu.au> Distribution: inet Date: Thu, 8 Feb 1996 12:10:58 GMT Lines: 21 In <4f6l11$aom@metro.usyd.edu.au> Dianne Chambers wrote: > I am part of UniServe*Science which is an Australian group whose role > includes finding and evaluating software packages that could be used in > undergraduate science teaching. I look after biology, biochemistry, > and psychology. A third alternative is the CTI Biology Resource Directory, which is available from our home page at . This is in the process of being updated, and holds information on a wide range of courseware, videodiscs, books etc. useful for teaching biology at university level. Regards, Paul -- Paul Gould, Network Support Officer +44 151-794 5118 (Tel) CTI Biology, Donnan Laboratories +44 151-794 4401 (Fax) University of Liverpool, PO Box 147 P.W.Gould@liv.ac.uk Liverpool L69 3BX, UK (MIME/NeXTmail OK) From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!peer-news.britain.eu.net!lyra.csx.cam.ac.uk!warwick!news.nott.ac.uk!griffin.nott.ac.uk!wpbfd.biochem.nottingham.ac.uk!user From: mbxfd@unix.ccc.nottingham.ac.uk (Fergus Doherty) Newsgroups: bionet.software Subject: Intracellular calcium movies? Followup-To: bionet.software Date: 5 Feb 1996 17:36:27 GMT Organization: Nottingham University, UK. Lines: 11 Distribution: world Message-ID: NNTP-Posting-Host: wpbfd.biochem.nottingham.ac.uk Does anyone know of any QuickTime or MPEG movies showing intracellular calcium changes in response to ligand binding? Is their anything on the WWW I can download. I can translate Video for Windows to QT if necessary. Fergus Doherty, dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH Tel: (0)115 970 9366 FAX (0)115 942 2225 Internet: Fergus.Doherty@nottingham.ac.uk From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!howland.reston.ans.net!nntp.coast.net!torn!news.ccs.queensu.ca!news From: "Eric B. Carstens" Newsgroups: bionet.software Subject: Re: GCK Date: Thu, 08 Feb 1996 09:59:05 +0000 Organization: Queen's University Lines: 5 Message-ID: <3119C969.3F7C@post.queensu.ca> References: <3115CA70.2F64@cell.biol.ethz.ch> NNTP-Posting-Host: u133.n148.queensu.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) We have been using GCK for a number of years now. It has proven very useful in a number of different ways. We especially like cloning by computer so that predictions about REN sites, size of fragments, etc can be easily made. The parent company Textco has also proven to be very helpful and continues to support the program with free updates. From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!DALI.MATHEMATIK.UNI-BIELEFELD.DE!fuellen From: fuellen@DALI.MATHEMATIK.UNI-BIELEFELD.DE (Georg Fuellen) Newsgroups: bionet.software Subject: Join the Bioperl Development List Now ! Date: 8 Feb 1996 08:19:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: <9602081615.AA13606@dali.Mathematik.Uni-Bielefeld.DE> NNTP-Posting-Host: net.bio.net Dear fellow Bionetters, The Bioperl Development List has been established recently, to coordinate development of a set of modules to manage molecular biology information in Perl. A few days ago, a proposal for Perl5 Objects for Sequences, Alignments, and Phylogenies has been posted to the list, and we hope to get discussion going really soon. The more feedback you provide now, the better Bioperl modules can serve you at a future date ! The URL of the proposal is http://www.techfak.uni-bielefeld.de/bcd/Tec/Bioperl/welcome.html To join the Bioperl Development List, send a "subscribe BIOPERL" message to bioperl-request@mole.bio.cam.ac.uk You will be sent further information, and instructions on how you can unsubscribe. The URL of the list is http://scop.mrc-lmb.cam.ac.uk/pub/bioperl/ About Perl: Perl5 (a significant improvement of former Perl versions) is a high-level scripting language with facilities for modular, object-oriented programming; productivity gains can be significant without compromising high standards in maintainabilty and readabilty. Applications that require very high speed can be integrated from a C library; a Perl compiler is under development. ----------- best wishes, georg fuellen@dali.Mathematik.Uni-Bielefeld.DE, fuellen@MIT.EDU http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/georgF.html From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.software Subject: ANNOUCING PRANA - NEW PROTEIN STRUCTURE-ACTIVITY ANALYSIS SOFTWARE Date: 8 Feb 1996 11:50:48 -0000 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 100 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4fco2o$f2a@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk To: bio-software@dl.ac.uk From: eroshkin@vector.nsk.su Subject: ANNOUNCING PRANA - NEW PROTEIN STRUCTURE-ACTIVITY ANALYSIS SOFTWARE ------------------------------------------------------------------- PRANA : PC-based program for studying the relationships between structure and activity in protein/peptide families ------------------------------------------------------------------- by I.Pika, V.Ivanisenko & A.Eroshkin State Research Center of Virology and Biotechnology "Vector" Koltsovo, Novosibirsk Region, 633159 Russia E.mail: eroshkin@vector.nsk.su, Tel: +7 (3832) - 647774, Fax: +7 (3832) - 328831 ------------------------------------------------------------------- The State Research Center of Virology and Biotechnology "VECTOR" is pleased to announce the availability of PRANA v1.0. PRANA is an easy-to-use, state-of-the-art MSDOS application for studying the relationships between structure and activity in protein/peptide families divided in two groups (by activity, property, evolution, etc.). The program examines the relationships between protein grouping and physico-chemical characteristics (e.g., mean Hydrophobicity, Charge, or Volume, alpha-helical or beta-strand moments of Hydrophobicity, etc.) of different regions in their primary structures and delineates the sites and characteristics describing the given grouping. PRANA is based on the program PROANAL (A. Eroshkin, V.Fomin, P.Zhilkin, CABIOS, 1993, 9, 491-497) and designed to provide analysis of additional data. PROANAL looks for correlations between quantitative data on protein activity and physico-chemical characteristics of the regions in the primary structures. In case of PRANA the analysis is based on aligned amino acid sequences and data on protein grouping (qualitative activity data). The program searches activity-modulating regions in aligned proteins that have different structure characteristics for two groups (biophore or pharmacophore). Student's or Kolmogorov - Smirnov's criteria are used to compare the distributions of the characteristics in two protein groups. The results - found sites and their physico-chemical characteristics as well as all necessary statistical evaluations - are presented in the form of text and histograms that can be saved or printed as required. PRANA CAN BE USED: - to find sites and site characteristics that may be responsible for the difference in proteins activity or property; - to classify newly sequenced proteins/peptides; - to assist in simulation of protein engineering experiments. EXAMPLES OF DATA TYPES TO BE ANALYZED - 15 variants of human alpha-interferons can be divided into two groups of high and low antiviral activity. The task is to find amino acid residues in IFN-alpha related with this difference in activity; - influenza A virus M(2) proteins from virus strain resistant or sensitive to amantadine. The task: to find amino acid residues in M(2) involved in amantadine binding and amino acid physico-chemical properties important for this interaction. - peptides inserted into VP1 protein of poliovirus type 1. Some of mutant viruses were viable, other - not. The task: to find the physico-chemical characteristics of the peptide inserts, that are important for mutant virus viability. PRANA HAS * converter from SWISS-PROT, CLUSTAL, GCG, PHYLIP formats to PRANA input files; * data files with about 100 amino acid physico-chemical properties; * examples, manual and help system. REQUIREMENTS: DOS 3.30 or later, EGA/VGA video card, 400 KB RAM. PRANA AVAILABILITY PRANA v1.0 is freely available for academic users through EBI ftp server ftp.ebi.ac.uk (directory /pub/software/dos/prana). For companies inquire to: Alexey Eroshkin SRC VB "Vector" Koltsovo, Novosibirsk Region 633159 Russia E.mail: eroshkin@vector.nsk.su Tel: +7 (3832) - 647774 Fax: +7 (3832) - 328831 PRANA USERS Don't hesitate to contact us in case of problems, bugs or suggestions. Could you send us your address (Email is preferred) and your feelings about your PRANA experience? From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!info.ucla.edu!news.ucdavis.edu!quad!knight From: knight@quad.cs.ucdavis.edu (James Knight) Newsgroups: bionet.software Subject: ANNOUNCE: SEQIO - A C Package for Reading and Writing Sequences Date: 8 Feb 1996 03:09:24 GMT Organization: University of California, Davis Lines: 88 Message-ID: <4fbph4$31@mark.ucdavis.edu> NNTP-Posting-Host: quad.cs.ucdavis.edu X-Newsreader: TIN [version 1.2 PL2] This is the initial release of the SEQIO package, a set of C functions which can read and write biological sequence files formatted using various file formats and which can be used to perform efficient database searches on biological databases. It's essentially a successor to the "readseq" program, but geared more toward being used in programs than just as a file conversion program (although it can do that too. The package currently supports the following file formats: GenBank Flat File, PIR/CODATA, EMBL/Swiss-Prot, FASTA, NBRF, IG/Stanford, ASN.1 text files. More formats will be included as I can find out the details about them. The package is freely available to anyone and can be ftp'ed from the following FTP site: ftp://ftp.cs.ucdavis.edu/pub/strings/seqio.tar.gz It is a gzip'ed, tar file containing the package code and documentation files. I don't have a Web site up yet, but it's coming soon. What I'm looking for now are four things, 1) Users to begin writing programs with the package (see below for an example program). 2) People who have examples and/or descriptions of other file formats so I can include them (it takes me on average about a hour per file format). High on my list of formats to include are the Phylip formats, FASTA/BLAST output and any multiple sequence alignment formats. A more complete list is given in the documentation. 3) Information about the organization and file formats used by any databases out there (if you look at the documentation to the package, you'll see what I mean). 4) Folks who are interested enough in getting the package to run on their machine that they would help me port it. It currently is Unix-specific software and has been tested under SunOS, Ultrix and IRIX, because they are the only machines I have access to. I'm willing to do as much as I can to get it to work on any and all machines. The main goal of the package was to make reading and writing sequences as easy as reading and writing normal files, as well as being able to handle large databases like GenBank. As an example, this complete program takes a keyword and database name, checks all of the sequences in the database and outputs the entries whose sequences match a keyword: #include #include #include "seqio.h" int main(int argc, char *argv[]) { int len; char *seq, *entry; SEQFILE *sfp; if (argc != 3) { fprintf(stderr, "match keyword database\n"); exit(1); } if ((sfp = seqfopendb(argv[2])) == NULL) exit(1); while ((seq = seqfgetseq(sfp, &len, 0)) != NULL) { if (len > 0 && strstr(seq, argv[1])) { entry = seqfentry(sfp, NULL, 0); fputs(entry, stdout); } } seqfclose(sfp); return 0; } This program scanned all of the GenBank database, Flat File Release 87.0 (about 800MB characters, 249MB of sequence), for a randomly generated 20 character sequence in under 8 minutes on a DEC 5000/240 (not an Alpha). From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.uoregon.edu!news.rediris.es!news.belnet.be!news.fundp.ac.be!st10.info.fundp.ac.be!van From: van@info.fundp.ac.be Newsgroups: bionet.software Subject: Help. I need a driver for my scanner Date: Thu, 8 Feb 1996 14:42:39 Organization: Institut d'Informatique (FUNDP - Namur), Belgium Lines: 6 Message-ID: NNTP-Posting-Host: st10.info.fundp.ac.be Summary: Help. I need a driver for my scanner Keywords: scanner X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Does anyone have a driver for a Proscan 256 Gray scale scanner model PS-4001G ? If not, where could I get it ? Thanks in advance From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!netnews.nwnet.net!mule.fhcrc.org!hal-quadra.fhcrc.org!user From: dturner@fred.fhcrc.org (Dave Turner) Newsgroups: bionet.software Subject: Re: DNA Alignment Software Date: 8 Feb 1996 19:53:35 GMT Organization: FHCRC Lines: 14 Message-ID: References: NNTP-Posting-Host: hal-quadra.fhcrc.org X-Newsreader: Yet Another NewsWatcher 2.1.2 In article , yasuhito@m.ehime-u.ac.jp (Yasuhito Abe) wrote: >Dear Netters, >I would like to get information on the alignment software for DNA >using MacOS. Would someone please tell me the best ones? >Of course, I prefer free ones. Another NOT FREE program is DNASTAR About 1 1/2 years ago I reveiwaed all the commercial packages and DNASTAR had the best multiple sequence alignment (by far). It has great options for displaying the alignments and highlighting what you want. Unfortunately it is not cheep. From owner-software@net.bio.net Wed Feb 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!vixen.cso.uiuc.edu!milo.mcs.anl.gov!jadoube.mcs.anl.gov!levine From: levine@jadoube.mcs.anl.gov (David Levine) Newsgroups: bionet.software Subject: PGAPack V1.0, Parallel GA Software Date: Thu, 8 Feb 1996 18:7:58 GMT Organization: Math and Computer Science, Argonne National Laboratory Lines: 27 Distribution: world Message-ID: <82380287821309@jadoube.mcs.anl.gov> NNTP-Posting-Host: jadoube.mcs.anl.gov The following freely-distributed software is now available... PGAPack is a general-purpose, data-structure-neutral, parallel genetic algorithm library. It is intended to provide most capabilities desired in a genetic algorithm library, in an integrated, seamless, and portable manner. Key features include: * Callable from Fortran or C. * Runs on uniprocessors, parallel computers, and workstation networks. * Binary-, integer-, real-, and character-valued native data types. * Full extensibility to support custom operators and new data types. * Easy-to-use interface for novice and application users. * Multiple levels of access for expert users. * Parameterized population replacement. * Multiple crossover, mutation, and selection operators * Easy integration of hill-climbing heuristics. * Extensive debugging facilities. * Large set of example problems. * Detailed users guide PGAPack is available: -- via anonymous ftp from ftp.mcs.anl.gov in file pub/pgapack/pgapack.tar.Z -- via the web at http://www.mcs.anl.gov/pgapack.html David Levine levine@mcs.anl.gov http://www.mcs.anl.gov/home/levine MCS 221 C-216 Argonne National Laboratory Argonne, Illinois 60439 (708)-252-6735 Fax: (708)-252-5986 From owner-software@net.bio.net Thu Feb 08 22:00:00 1996 Path: biosci!news.Stanford.EDU!nntp-hub2.barrnet.net!news1.digital.com!ames!usenet.kornet.nm.kr!news.kreonet.re.kr!news.dacom.co.kr!nntp.coast.net!howland.reston.ans.net!ix.netcom.com!netnews From: rcq@ix.netcom.com(RONALDO QUISPE ) Newsgroups: bionet.software Subject: 3-D molecule representation software NEEDED Date: 9 Feb 1996 02:42:15 GMT Organization: Netcom Lines: 11 Message-ID: <4feca7$cnu@reader2.ix.netcom.com> NNTP-Posting-Host: ix-pat3-16.ix.netcom.com X-NETCOM-Date: Thu Feb 08 6:42:16 PM PST 1996 Hello, I need software that can represent molecules in a 3-D format. I need to be able to modify and create other molecules. I have seen CAD programs that can do this but are rather expensive. Anything out there at a reasonable price? Ron Q. E-mail: rcq@ix.netcom.com From owner-software@net.bio.net Thu Feb 08 22:00:00 1996 Path: biosci!bcm.tmc.edu!newshost.convex.com!news.duke.edu!news.mathworks.com!news.kei.com!nntp.coast.net!harbinger.cc.monash.edu.au!news.bhp.com.au!mel.dit.csiro.au!actcsiro!news From: m.ballard@chem.csiro.au (Mat Ballard) Newsgroups: bionet.software,