From owner-software@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!agate!spool.mu.edu!uwm.edu!daffy!uwvax!zazen!post.its.mcw.edu!not-for-mail From: dmeier@post.its.mcw.edu (Daniel Meier) Newsgroups: bionet.software Subject: Secondary Prot. Struct. Program?? Message-ID: <1kk8lkINNqa7@post.its.mcw.edu> Date: 1 Feb 93 22:36:36 GMT Organization: Medical College of Wisconsin (Milwaukee, WI) Lines: 10 NNTP-Posting-Host: post.its.mcw.edu X-Newsreader: TIN [version 1.1 PL7] Hello All, Can someone please point me to software for the Mac that will find secondary protein structures (alpha-helices, beta-sheets, beta-turns, etc.) using amino acid sequences? Thanks much! Dan Meier dmeier@post.its.mcw.edu From owner-software@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!agate!spool.mu.edu!yale.edu!nigel.msen.com!math.fu-berlin.de!news.belwue.de!news.uni-tuebingen.de!studserv!zxmkr08 From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Keywords: microcomputer microprocessor Intel 486 Message-ID: Date: 2 Feb 93 16:14:50 GMT References: <1993Jan25.090410.12066@gserv1.dl.ac.uk> <1993Jan25.170138.10928@welchgate.welch.jhu.edu> <1993Feb2.041849.14127@monu6.cc.monash.edu.au> Sender: news@softserv.zdv.uni-tuebingen.de (News Operator) Organization: Comp. Center (ZDV) U of Tuebingen, FRG Lines: 25 In kristoff@net.bio.net (David Kristofferson) writes: >parry@yoyo.cc.monash.edu.au (Tom J Parry) writes: >>I'll apologise in advance - but I'm geting a little disappointed at the volume >>of material wandering through bionet.software which has very little to do with >>biology other than that the author was probably a biologist. There are very >Tom actually is right. Undoubtedly many people participating via There are other advances of posting "ordinary" soft-/hardware requests to bionet.software. 1) You can be quite sure that you get an answer which you understand (that is, not too much technological terms). 2) You don't have to figure out which newsgroup might be the right one for your request (and possibly end up into flames since you posted into the wrong one). Just my $0.02. -- /* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen */ /* email: krasel@studserv.zdv.uni-tuebingen.de (Internet) HAS CHANGED!! */ /* NO WIN/X400 MAIL POSSIBLE AT THE MOMENT! */ /* "People are DNA's way of making more DNA." (R. Dawkins / anonymous) */ From owner-software@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!bcm!bcm!usenet From: steffen@mbcr.bcm.tmc.edu (David Steffen) Newsgroups: bionet.software Subject: Re: MOO??? Message-ID: <1km3noINNk6h@gazette.bcm.tmc.edu> Date: 2 Feb 93 15:24:40 GMT References: <9301300053.AA12864@net.bio.net> Distribution: bionet Organization: Baylor College of Medicine, Houston, Tx Lines: 39 NNTP-Posting-Host: mbcr.bcm.tmc.edu MCCAINKW@DUVM.BITNET (Kate McCain) writes: >OK -- I'll bite. what's a MOO. (Besides a good example for my pre-sophomore >information science students on the problems of acronyms, initialisms and >insider communication.) I posted a rather long review of the use of MOOs by biologists in bionet.general a couple of days ago, in which I defined the term. Also, Rob Harper posted an introduction to MOOs a few weeks earlier in bionet.users.addresses. If you are interested in the concept and its utility in addition to just the definition, you might like to look at these. Briefly: MOO == MUD, Object Oriented. MUD == Multi-User Dungeon Dungeon stands for a category of text games in which one moves around a virtual environment (a "dungeon"). Examples include the games produced for many home computers by Infocom, including Zork, and the ubiquitous game 'Adventure'. (I have seen 'Adventure' on a dedicated Wang word processing system listed as a diagnostic!). The 'Object Oriented' in MOO refers to the fact that the environment includes a built-in object oriented programming environment with which you can program the environment. (This is *NOT* the language the MOO is written in, but more like the macro language of Lotus 1,2,3). It is this programmability we are making use of to squeeze every last bit of fun out of the game environment to convert it into yet another tool for the most calvanist of scientists. If you cannot find my review, email me and I will email you a copy. -- David Steffen Department of Cell Biology, Baylor College of Medicine, Houston TX 77030 Telephone = (713) 798-6655, FAX = (713) 790-0545 Internet = steffen@bcm.tmc.edu From owner-software@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!paladin.american.edu!news.univie.ac.at!vm.univie.ac.at!A8471DAB From: A8471DAB@vm.univie.ac.at (Dr. Ch. Wawrosch/Prof.Dr. B. Kopp) Newsgroups: bionet.software Subject: Re: Windows interested people! Message-ID: <1993Feb2.150305.12641@newssrv.edvz.univie.ac.at> Date: 2 Feb 93 15:00:07 GMT Sender: news@newssrv.edvz.univie.ac.at (News System - Vienna University) Organization: University of Vienna Lines: 17 Nntp-Posting-Host: helios.edvz.univie.ac.at >If your interested in some opinions on various windows software, and >want my thoughts, just send my a note... maybe we could setup a mail >windows support group - sounds good to me :) > > D.P. Hi D.P., sounds good, please add me to your list: Chris Wawrosch Univ. of Vienna e-mail: a8471dab@awiuni11.edvz.univie.ac.at Thank you and Greetings from Ol'Europe, Chris. From owner-software@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Keywords: microcomputer microprocessor Intel 486 Message-ID: Date: 2 Feb 93 07:46:56 GMT References: <1993Jan25.090410.12066@gserv1.dl.ac.uk> <1993Jan25.170138.10928@welchgate.welch.jhu.edu> <1993Feb2.041849.14127@monu6.cc.monash.edu.au> Organization: BIOSCI International Newsgroups for Biology Lines: 26 parry@yoyo.cc.monash.edu.au (Tom J Parry) writes: >I'll apologise in advance - but I'm geting a little disappointed at the volume >of material wandering through bionet.software which has very little to do with >biology other than that the author was probably a biologist. There are very >good groups for discussing the relative merits of intel processors - you might >even find your answers in the FAQ. I personally don't follow them - because >I'm more interested in reading about bilogical software. No more said. >Flame me at will. >-- >Tom J Parry. >Your reality is a figment of my imagination. Tom actually is right. Undoubtedly many people participating via e-mail may not have access to the myriad of USENET computer newsgroups and therefore post to this forum. If you do have USENET access however, there is not much of an excuse to post non-biological software/hardware questions here. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-software@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!zaphod.mps.ohio-state.edu!malgudi.oar.net!caen!batcomputer!munnari.oz.au!bruce.cs.monash.edu.au!monu6!yoyo.cc.monash.edu.au!parry From: parry@yoyo.cc.monash.edu.au (Tom J Parry) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Keywords: microcomputer microprocessor Intel 486 Message-ID: <1993Feb2.041849.14127@monu6.cc.monash.edu.au> Date: 2 Feb 93 04:18:49 GMT References: <1993Jan25.090410.12066@gserv1.dl.ac.uk> <1993Jan25.170138.10928@welchgate.welch.jhu.edu> Sender: news@monu6.cc.monash.edu.au (Usenet system) Organization: Monash University, Melb., Australia. Lines: 11 Originator: parry@yoyo.cc.monash.edu.au I'll apologise in advance - but I'm geting a little disappointed at the volume of material wandering through bionet.software which has very little to do with biology other than that the author was probably a biologist. There are very good groups for discussing the relative merits of intel processors - you might even find your answers in the FAQ. I personally don't follow them - because I'm more interested in reading about bilogical software. No more said. Flame me at will. -- Tom J Parry. Your reality is a figment of my imagination. From owner-software@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!POST.ITS.MCW.EDU!fgarbrec From: fgarbrec@POST.ITS.MCW.EDU (Frederick Garbrecht) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Message-ID: Date: 2 Feb 93 23:05:47 GMT References: <9302020450.AA24230@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 27 Hear, hear!@ I agree; keep the non-biology stuff in other more appropriate places. F Garbrecht Medical College of Wisconsin On 2 Feb 1993, Tom J Parry wrote: > Date: 2 Feb 93 04:18:49 GMT > From: Tom J Parry > To: bio-soft@net.bio.net > Subject: Re: PC 80486 and bionet ? > > I'll apologise in advance - but I'm geting a little disappointed at the volume > of material wandering through bionet.software which has very little to do with > biology other than that the author was probably a biologist. There are very > good groups for discussing the relative merits of intel processors - you might > even find your answers in the FAQ. I personally don't follow them - because > I'm more interested in reading about bilogical software. No more said. > Flame me at will. > > -- > Tom J Parry. > Your reality is a figment of my imagination. > From owner-software@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!ub!acsu.buffalo.edu!ubvmsb.cc.buffalo.edu!caminak From: caminak@ubvmsb.cc.buffalo.edu (Ichiro Nakamura) Newsgroups: bionet.software Subject: Wanted:Oligo/Primer Shareware Keywords: Primer Oligo Message-ID: Date: 2 Feb 93 14:46:00 GMT Sender: nntp@acsu.buffalo.edu Organization: University at Buffalo Lines: 8 News-Software: VAX/VMS VNEWS 1.41 Nntp-Posting-Host: ubvmsb.cc.buffalo.edu To anyone: Our lab is looking for a program (Shareware if available) to find primers/oligos. We have looked at Hitachi's OLIGO program, but it is expensive and much more comprehensive than we need at this time. Any information would be appreciated. Please reply via e-mail- Caminak@ubvms.cc.buffalo.edu Thanks. From owner-software@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!news.cs.indiana.edu!usenet.ucs.indiana.edu!sol.ctr.columbia.edu!spool.mu.edu!olivea!charnel!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: Windows interested people! Message-ID: Date: 3 Feb 93 04:42:33 GMT References: <1993Feb2.150305.12641@newssrv.edvz.univie.ac.at> Sender: news@sifon.cc.mcgill.ca Organization: McGill University Lines: 69 Nntp-Posting-Host: monod.biol.mcgill.ca A8471DAB@vm.univie.ac.at (Dr. Ch. Wawrosch/Prof.Dr. B. Kopp) writes: >>If your interested in some opinions on various windows software, and >>want my thoughts, just send my a note... maybe we could setup a mail >>windows support group - sounds good to me :) >> >> D.P. >Hi D.P., >sounds good, please add me to your list: >Chris Wawrosch >Univ. of Vienna >e-mail: a8471dab@awiuni11.edvz.univie.ac.at before you people jump on the bandwagon of getting a window love_in group together, maybe you should look at what is already out there: if I grep my .newsrc file for windows, I get these groups: (OK, besides the first one :-) I am sure you can find something for your liking ... and if you don't have usenet access .... this would probably be a good reason to get it! alt.msdos.windows.hate.hate.hate: comp.os.ms-windows: 1-18 comp.os.ms-windows.advocacy: 1-3752 comp.os.ms-windows.announce: 1-111 comp.os.ms-windows.apps: 1-7738 comp.os.ms-windows.misc: 1-6673 comp.os.ms-windows.programmer: 1-32 comp.os.ms-windows.programmer.misc: 1-5655 comp.os.ms-windows.programmer.tools: 1-2297 comp.os.ms-windows.programmer.win32: 1-3268 comp.os.ms-windows.setup: 1-2932 comp.windows.interviews! 1-1093 comp.windows.m: comp.windows.misc: 1-891 comp.windows.ms: 1-3030 comp.windows.ms.programmer: 1-2293 comp.windows.news: 1-521 comp.windows.open-look: 1-2638 comp.windows.ws: comp.windows.x: 1-10094 comp.windows.x.announce: 1-237 comp.windows.x.apps: 1-1765 comp.windows.x.intrinsics: 1-833 comp.windows.x.motif: 1-12811 comp.windows.x.openlook: 1-40 comp.windows.x.pex: 1-394 fj.windows.gmw: fj.windows.misc: 1-14 fj.windows.x: 1-332 comp.ms.windows.advocacy: comp.windows.garnet: 1-174 ba.windows.x: comp.binaries.ms-windows: 1-65 regards, francis -- | B.F. Francis Ouellette | manager, yeast chromosome I & XVI sequencing project | dept of biology, McGill university, Montreal, Qc, Canada | francis@monod.biol.mcgill.ca From owner-software@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!howland.reston.ans.net!sol.ctr.columbia.edu!The-Star.honeywell.com!umn.edu!lenti.med.umn.edu!ernest From: ernest@lenti.med.umn.edu (Ernest Retzel (1535 49118)) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Summary: Why Not? Message-ID: Date: 3 Feb 93 02:22:28 GMT Sender: news@news2.cis.umn.edu (Usenet News Administration) Organization: University of Minnesota Lines: 10 Nntp-Posting-Host: lenti.med.umn.edu Sorry, I tend to agree with Krasel. If a biologist has a question, I can't really see a reason that it not be discussed. And for that query, I can think of no better bioforum to ask it in. The serious hardware groups flame people for asking basic things. Ernie Retzel ernest@lenti.med.umn.edu From owner-software@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!sgiblab!munnari.oz.au!bruce.cs.monash.edu.au!monu6!yoyo.cc.monash.edu.au!parry From: parry@yoyo.cc.monash.edu.au (Tom J Parry) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Keywords: microcomputer microprocessor Intel 486 Message-ID: <1993Feb3.022205.17656@monu6.cc.monash.edu.au> Date: 3 Feb 93 02:22:05 GMT References: <1993Jan25.090410.12066@gserv1.dl.ac.uk> <1993Jan25.170138.10928@welchgate.welch.jhu.edu> <1993Feb2.041849.14127@monu6.cc.monash.edu.au> Sender: news@monu6.cc.monash.edu.au (Usenet system) Organization: Monash University, Melb., Australia. Lines: 24 Originator: parry@yoyo.cc.monash.edu.au zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) writes: >1) You can be quite sure that you get an answer which you understand (that > is, not too much technological terms). The people who really know the answers to your questions probably aren't reading bionet.software. Those "technological terms" are the symptoms of the growing pains you experience whilst learning. For example you won't be able to appreciate the difference in Intel processors till you unserstand concepts like clock speed, bus size, pipe-lining. Most people aren't nasty about explaining these things. >2) You don't have to figure out which newsgroup might be the right one > for your request (and possibly end up into flames since you > posted into the wrong one). We could just have one big flat newsgroup space where everyone posts everything - that way noone would have to think or look before posting. >Just my $0.02. You're welcome, but I don't really agree. -- Tom J Parry. Your reality is a figment of my imagination. From owner-software@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!uwm.edu!rpi!usc.edu!howland.reston.ans.net!spool.mu.edu!yale.edu!ira.uka.de!math.fu-berlin.de!news.belwue.de!news.uni-tuebingen.de!studserv!zxmkr08 From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Keywords: microcomputer microprocessor Intel 486 Message-ID: Date: 3 Feb 93 15:50:45 GMT References: <1993Jan25.090410.12066@gserv1.dl.ac.uk> <1993Jan25.170138.10928@welchgate.welch.jhu.edu> <1993Feb2.041849.14127@monu6.cc.monash.edu.au> <1993Feb3.022205.17656@monu6.cc.monash.edu.au> Sender: news@softserv.zdv.uni-tuebingen.de (News Operator) Organization: Comp. Center (ZDV) U of Tuebingen, FRG Lines: 36 Sorry, maybe this is not the right place to discuss it :-) In <1993Feb3.022205.17656@monu6.cc.monash.edu.au> parry@yoyo.cc.monash.edu.au (Tom J Parry) writes: >zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) writes: >>1) You can be quite sure that you get an answer which you understand (that >> is, not too much technological terms). >The people who really know the answers to your questions probably aren't >reading bionet.software. Those "technological terms" are the symptoms of >the growing pains you experience whilst learning. For example you won't >be able to appreciate the difference in Intel processors till you unserstand >concepts like clock speed, bus size, pipe-lining. Most people aren't nasty >about explaining these things. Well, I asked rather technical questions several times in bionet.software and got always a satisfying answer. Don't think too bad of biologists and related folks :-) :-) :-) >>2) You don't have to figure out which newsgroup might be the right one >> for your request (and possibly end up into flames since you >> posted into the wrong one). >We could just have one big flat newsgroup space where everyone posts everything >- that way noone would have to think or look before posting. Well, at least at the moment this newsgroup does not suffer from too much traffic, does it? (Although it is one of the bionet.* groups which are used rather frequently.) Anyways, I would object if anybody wanted to discuss cloning here (but this is more unrelated to the topic of this group as is the pros and cons of Intel CPUs). -- /* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen */ /* email: krasel@studserv.zdv.uni-tuebingen.de (Internet) HAS CHANGED!! */ /* NO WIN/X400 MAIL POSSIBLE AT THE MOMENT! */ /* "People are DNA's way of making more DNA." (R. Dawkins / anonymous) */ From owner-software@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!spool.mu.edu!olivea!charnel!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: Windows interested people! Message-ID: Date: 3 Feb 93 22:10:45 GMT References: <1993Feb2.150305.12641@newssrv.edvz.univie.ac.at> Sender: news@sifon.cc.mcgill.ca Organization: McGill University Lines: 70 Nntp-Posting-Host: monod.biol.mcgill.ca francis@monod.Biol.McGill.CA (Francis Ouellette) writes: >A8471DAB@vm.univie.ac.at (Dr. Ch. Wawrosch/Prof.Dr. B. Kopp) writes: >>>If your interested in some opinions on various windows software, and >>>want my thoughts, just send my a note... maybe we could setup a mail >>>windows support group - sounds good to me :) >>> >>> D.P. >>Hi D.P., >>sounds good, please add me to your list: >>Chris Wawrosch >>Univ. of Vienna >>e-mail: a8471dab@awiuni11.edvz.univie.ac.at >before you people jump on the bandwagon of getting a window love_in >group together, maybe you should look at what is already out there: Here is a copy of a message I sent to David Salt, who does not have usenet access: From francis Wed Feb 3 17:08:11 1993 Date: Wed, 3 Feb 93 17:08:10 EST From: francis (Francis Ouellette) To: BOTSALT@vm.uoguelph.ca Subject: Re: Windows interested people! Cc: francis Content-Length: 1257 X-Lines: 37 Dear David, > Unfortunatly for me I only have access to internet through our large, old > CMS machine which does not provide me with access to usenet, thus a > windows bulletin board which is avalible to me via Email would be of > interest to me. I didn't want to sound condensending, although I may have. "Windows" has a way of bringing that out in me! Even though I use it quite a bit. I did a search of the windows groups which are available by a listservers, and I came up with a few of them: WFW-L WFW-L@UMDD Microsoft Windows for Workgroups WIN-VAX WIN-VAX@UMDD MS-Windows interfaces to VAX-Rdb WIN3-L WIN3-L@UICVM Microsoft Windows Version 3 Forum WKSH-L WKSH-L@UCSFVM Windowing Korn Shell Discussion List. WPWIN-L WPWIN-L@UBVM WordPerfect For Windows Discussion List So if you want to subscribe to any of these, send a message to "listserv@uicvm.bitnet" which would read: sub win3-l David Salt if you wanted to subscribe to the "Microsoft Windows Version 3 Forum" regards, francis -- | B.F. Francis Ouellette | manager, yeast chromosome I & XVI sequencing project | dept of biology, McGill university, Montreal, Qc, Canada | francis@monod.biol.mcgill.ca From owner-software@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!olivea!charnel!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: Windows interested people! Message-ID: Date: 3 Feb 93 21:37:16 GMT References: <1993Feb2.150305.12641@newssrv.edvz.univie.ac.at> <1993Feb3.123815.84@ntet.nctr.fda.gov> Sender: news@sifon.cc.mcgill.ca Organization: McGill University Lines: 35 Nntp-Posting-Host: monod.biol.mcgill.ca wmelchior@ntet.nctr.fda.gov writes: >> before you people jump on the bandwagon of getting a window love_in >> group together, maybe you should look at what is already out there: >... >> fj.windows.gmw: >> fj.windows.misc: 1-14 >> fj.windows.x: 1-332 >... >> ba.windows.x: >francis- >We have only partial usenet access: biosci, comp, and sci. What are the fj >and ba groups? Bill, fj is from japan, and ba is "bay area" I must admit these groups rarely get read by this user! The policy here seems to be:"we get it all" and the reader writes a good init file. regards, francis -- | B.F. Francis Ouellette | manager, yeast chromosome I & XVI sequencing project | dept of biology, McGill university, Montreal, Qc, Canada | francis@monod.biol.mcgill.ca From owner-software@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!fconvx.ncifcrf.gov!ntet.nctr.fda.gov!wmelchior From: wmelchior@ntet.nctr.fda.gov Newsgroups: bionet.software Subject: Re: Windows interested people! Message-ID: <1993Feb3.123815.84@ntet.nctr.fda.gov> Date: 3 Feb 93 18:38:15 GMT References: <1993Feb2.150305.12641@newssrv.edvz.univie.ac.at> Organization: NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH Lines: 24 > before you people jump on the bandwagon of getting a window love_in > group together, maybe you should look at what is already out there: ... > fj.windows.gmw: > fj.windows.misc: 1-14 > fj.windows.x: 1-332 ... > ba.windows.x: francis- We have only partial usenet access: biosci, comp, and sci. What are the fj and ba groups? ________________________________________________________________________________ Views expressed are not necessarily those of NCTR, its sponsoring agencies, or the United States government. Bill Melchior || MISSING LINK National Center for Toxicological Research || Man's a kind Jefferson, AR 72079 || of Missing Link, (501) 543-7206 || fondly thinking || he can think. WMELCHIOR@NTET.NCTR.FDA.GOV || from Grooks, by Piet Hein From owner-software@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.methds-reagnts,bionet.software,bionet.immunology Subject: Gopher search Kabat Database of Sequences of Immunological Interest Message-ID: <1993Feb3.163843.29871@welchgate.welch.jhu.edu> Date: 3 Feb 93 16:38:43 GMT Organization: Johns Hopkins Univ. Welch Medical Library Lines: 153 Xref: biosci bionet.molbio.methds-reagnts:4140 bionet.software:4101 bionet.immunology:234 The Kabat Database - Sequences of Proteins of Immunological Interest is now available for searching by Gopher. If you have a gopher client just point it at merlot.welch.jhu.edu and go to the --> 12. Search Databases at Welchlab (Vectors, Promoters, NRL-3D,...) directory. Once there you will see - --> 6. Kabat Database of Proteins of Immunological Interest You may search this database using booleans (and, or, not), wildcards (*), and phrase searches (" ") as the search is running off of Don Gilbert's modified Wais code. If you don't know about gopher - just write me a note and I'll send you all the information you need to get started (gopher is free and on net). From the maintainers of the Kabat Database (slightly modified): We have had a couple of questions about our 'family' designations. These families do not and are not meant to correspond to families cited in the literature. They are purely something generated at our end for the purpose of combining sequences of high AMINO ACID homology within the variable region together to help us and others locate sequences that seem to belong with each other more than with other sequences. Each family is composed of sequences that differ from one another by 12 amino acids or less. These amino acid differences do not take into consideration the codons that generated them. It is a division based on amino acid sequence only. (A glance over the codon sequences though indicates that the codons are quite similar too). Each family has a 'miscellaneous' family associated with it. For example, HUMAN HEAVY CHAINS FAMILY I is associated with the HUMAN HEAVY CHAINS FAMILY I MISCELLANEOUS. These 'miscellaneous' sequences are not complete through the V-region but that do share a great similarity with sequences in HUMAN HEAVY CHAINS FAMILY I. Because they are incomplete, these sequences cannot be unambigously assigned to family I. Also, there are two large groups associated with each CLASS of sequences, a 'miscellaneous unknown' and a 'miscellaneous fragment' group. The unknown group contains sequences which do not fit into a family and are mostly complete. The fragment group contains sequences which are incomplete throughout most of the V-region. Please keep in mind that the family designation is for our purposes and for purposes of locating similar sequences. There is no relationship between our families and everyone else's families that we know of. Entry Format ================ Here is an example of one of the entries you would find in an entry: AA TABLE : MOUSE HEAVY CHAIN FAMILY I NUC TABLE : CODONS OF MOUSE HEAVY CHAINS FAMILY I AMINO NAME: TF5-139'CL CODON NAME: TF5-139 REFERENCE : RILEY,S.C.,CONNORS,S.J.,KLINMAN,N.R. & OGATA,R.T. (1986) PROC.NAT.ACAD.SCI.USA,83,2589-2593. (CHECKED BY AUTHOR 08/19/87) AB SPECIFI: SPECIES : MOUSE CLASS : IGA-KAPPA STRAIN : SOURCE : NEONATAL SPLEEN CELL HYBRIDOMA INSERTSAA : INSERTSNUC: NOTES AA : FROM BALB/c NEONATAL SPLEEN CELL HYBRIDOMA. NOTES NUC : KABAT NUM : 0|1|2|3|4|5|6|7|8|9|10|11|12|13|14|15|16|17|18|19|20|21|22|23|24|25|26|27|28|29|30|31|32|33|34|35|35A|35B|36|37|38|39|40|41|42|43|44|45|46|47|48|49|50|51|52|52A|52B|52C|53|54|55|56|57|58|59|60|61|62|63|64|65|66|67|68|69|70|71|72|73|74|75|76|77|78|79|80|81|82|82A|82B|82C|83|84|85|86|87|88|89|90|91|92|93|94|95|96|97|98|99|100|100A|100B|100C|100D|100E|100F|100G|100H|100I|100J|100K|101|102|103|104|105|106|107|108|109|110|111|112|113 AA SEQUEN : ---|GLU|VAL|GLN|LEU|GLN|GLU|SER|GLY|PRO|SER|LEU|VAL|LYS|PRO|SER|GLN|THR|LEU|SER|LEU|THR|CYS|SER|VAL|THR|GLY|ASP|SER|ILE|THR|SER|GLY|TYR|TRP|ASN|---|---|TRP|ILE|ARG|LYS|PHE|PRO|GLY|ASN|LYS|LEU|GLU|TYR|MET|GLY|TYR|ILE|SER|---|---|---|TYR|SER|GLY|SER|THR|TYR|TYR|ASN|PRO|SER|LEU|LYS|SER|ARG|ILE|SER|ILE|THR|ARG|ASP|THR|SER|LYS|ASN|GLN|TYR|TYR|LEU|GLN|LEU|ASN|SER|VAL|THR|THR|GLU|ASP|THR|ALA|THR|TYR|TYR|CYS|ALA|ARG|TRP|ASP|VAL|---|---|---|---|---|---|---|---|---|---|---|TRP|TYR|PHE|ASP|VAL|TRP| A|GLY|THR|THR|VAL|THR|VAL|SER|SER NUC SEQ : ---|gag|gtg|cag|ctt|cag|gag|tca|gga|cct|agc|ctc|gtg|aaa|cct|tct|cag|act|ctg|tcc|ctc|acc|tgt|tct|gtc|act|ggc|gac|tcc|atc|acc|agt|ggt|tac|tgg|aac|---|---|tgg|atc|cgg|aaa|ttc|cca|ggg|aat|aaa|ctt|gag|tac|atg|ggg|tac|ata|agc|---|---|---|tac|agt|ggt|agc|act|tac|tac|aat|cca|tct|ctc|aaa|agt|cga|atc|tcc|atc|act|cga|gac|aca|tcc|aag|aac|cag|tac|tac|ctg|cag|ttg|aat|tct|gtg|act|act|gag|gac|aca|gcc|aca|tat|tac|tgt|gca|aga|tgg|gac|gtc|---|---|---|---|---|---|---|---|---|---|---|tgg|tac|ttc|gat|gtc|tgg| // Some things to note right off: 1. The lines are variable length, ended by a line feed (\n). 2. Some fields are empty; they only have a line feed. 3. Each field name is the same length (13 characters) 4. The sequences are aligned. 5. Each codon or amino acid is separated by a |. This is useful if you have a procedure that can read in text and make an array out of it using a deliminator like the | to indicate each index value. Some descriptions AA TABLE-- A simple description of where the sequence came from in our database. Mouse heavy chains family I means that this sequence is a mouse immunoglobulin heavy chain which belongs to family I. A family, by our definition, is a collection of sequences which differ from one another by less than twelve amino acid residues. NUC TABLE-- Nucleotide sequence table name (see AA TABLE) AMINO NAME- The amino acid sequence name CODON NAME- The nucleotide sequence name REFERENCE-- The reference of the paper(s) that these sequences came from. SPECIES, CLASS, NOTES -- Annotations INSERTS AA, INSERTS NUC- For alignment, sometimes codons and amino acids must be removed from the sequence. When this is done, a # sign is placed in the sequence where the removal occurred. The sequence that was removed is placed in these rows. KABAT NUM-- Kabat's numbering system. --------- The format is loose. Some of the different types of sequences have different annotation fields. All entries have AA TABLE, NUC TABLE, AMINO NAME, CODON NAME, NOTES AA, NOTES NUC, KABAT NUM, NUC SEQ, and AA SEQUEN. Problems and Suggestions ======================== If you have problems with these files or constructive suggestions, please e-mail the project at: George Johnson tt@immuno.esam.nwu.edu. For questions about the gopherized version write: Dan Jacobson danj@welchgate.welch.jhu.edu Happy searching, Dan Jacobson danj@welchgate.welch.jhu.edu Johns Hopkins University From owner-software@net.bio.net Tue Feb 02 22:00:00 1993 Path: biosci!news.cs.indiana.edu!sgiblab!spool.mu.edu!olivea!charnel!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: Wanted:Oligo/Primer Shareware Keywords: Primer Oligo Message-ID: Date: 3 Feb 93 04:35:25 GMT References: Sender: news@sifon.cc.mcgill.ca Organization: McGill University Lines: 190 Nntp-Posting-Host: monod.biol.mcgill.ca caminak@ubvmsb.cc.buffalo.edu (Ichiro Nakamura) writes: >To anyone: Our lab is looking for a program (Shareware if available) >to find primers/oligos. We have looked at Hitachi's OLIGO program, but >it is expensive and much more comprehensive than we need at this time. >Any information would be appreciated. from the methods_and_reagents FAQ (Frequently Asked Questions): ******************************************************************* * * * Frequently Asked Question (FAQ) list * * for bionet.molbio.methds-reagnts * * * * Last update was on 29 January 1993 * * * ******************************************************************* My intention for creating this FAQ list is not to attempt a comprehensive review of the subjects discussed within the newsgroup bionet.molbio.methds-reagnts, but rather to provide a quick resource for first time users. Many of the questions answered below are asked by people new to the group on a recurring basis. This FAQ list is available by anonymous ftp to ncifcrf.gov Simply get the file pub/methods/FAQlist If anyone would like to make additions or corrections to the FAQ list, please send the information to: Paul N. Hengen National Cancer Institute Frederick Cancer Research and Development Center Frederick, Maryland 21702-1201 USA e-mail: pnh@ncifcrf.gov ================================================================================ 12. What kinds of programs are available for designing PCR primers? What kinds of programs are available for designing PCR primers? There are four programs which deal with pcr primer construction which one can obtain by anonymous ftp and one which will be mailed to you by the author. The programs are: 1. Pgen - for DOS only PrimerGen searches strings of amino acid residues in order to reverse-translate oligonucletide primers of a desired range of lengths and maximum number of degeneracies. PrimerGen only works on IBM-PC(TM), XT, AT, PS/2 and compatibles with EGA or VGA graphics adaptors. It will not work on computers with CGA or Hercules(TM) graphics cards. A hard drive is NOT required and PrimerGen will fit on a 360K 5.25" floppy disk. PrimerGen contains a sequence editor where amino acid residues are entered. The amino acid sequence must be ONE fragment and cannot be longer than 70 residues. The sequence must be in the ONE LETTER CODE and cannot contain any UNKNOWNS. After the desired amino acid sequence has been entered have the option of saving the sequence to a disk. PrimerGen will also accept and re-edit previously saved sequence files, and also contains a codon preference table editor. You can get this program by anonymous ftp at ftp.bio.indiana.edu. It is found in the molbio/ibmpc directory. 2. Primer - Stanford - Sun Sparcstations only The program 'primer' is written by Don Faulkner. It helps to find potential mispriming sites (primer sequences should be designed before running the program!). The program gives higher weights to matches at the 3' end of the primer, linearly decreasing them towards the 5' end (the default is weight=10 for 3' nucleotide decreasing to 1 at nucleotide # 8 from the 3' end). The program can be used when amplifying *long* fragments from a known sequence. The program is written in "C" and runs on Sun workstation (Unix). You can get the program by anonymous ftp at 36.45.0.126 or contact James Mullins jmullins.stanford.edu (415) 723-0668. 3. Primer - Whitehead -Unix, Vms (and DOS and Mac if you can compile it) PRIMER is a computer program for automatically selecting PCR primers written by Steve Lincoln, Mark Daly, and Eric Lander. PRIMER will run on just about anything which supports a standard C language compiler. - IBM PC and compatibles. A PC/AT (286) class machine or better with 640K of - Apple Macintosh computers. A Mac II series or SE/30 with a math coprocessor - Most Unix workstations including Sun SPARCStation and DEC DECStation systems - DEC VAX/VMS computers under VMS Version 5 with VAX C. PRIMER is available from a number of sources: - You can get PRIMER from another user, provided you strictly follow the terms - You can download the most recent version off the Internet via anonymous FTP - You can send a request to: PRIMER c/o The Lander Lab, Whitehead Institute/MIT 9 Cambridge Center, Cambridge, MA 02142. E-mail to "primer@genome.wi.edu" (Internet), or FAX to 617-258-6505 You can also get PRIMER by anonymous ftp from genome.wi.edu in the distribution/primer.0.4 directory. 4. Amplify - MAC only This software is for use in designing, analyzing, and simulating experiments involving the polymerase chain reaction (PCR). PCR is a technique used by molecular biologists to amplify highly selected segments of DNA. You can obtain a copy of Amplify from sumex-aim.stanford.edu via anonymous ftp. Look for the file: /info-mac/app/amplify-10.hqx The author, Bill Engels, can be reached at WREngels@wisc.macc.edu 5. OSP - Unix, X-windows, Vms, DOS, Mac - by snail-mail only. OSP is available for free, but the university lawyers require that you sign a licensing agreement. The legal document is not for the paperwork faint-at-heart. It is quite long and daunting. If you're waiting for the legal stuff before starting your experiment, you may be better off working out a primer by hand. Here is the abstract from the paper describing OSP, which appeared in PCR Methods and Applications 1, 124-128 (1991), along with information on how to get the program. ABSTRACT OSP (Oligonucleotide Selection Program) selects oligonucleotide primers for DNA sequencing and the polymerase chain reaction (PCR). The user can specify (or use default) constraints for primer and amplified product lengths, %(G+C), (absolute or relative) melting temperatures, and primer 3' nucleotides. To help minimize non-specific priming and primer secondary structure, OSP screens candidate primer sequences, using user-specifiable cutoffs, against potential base pairing with a variety of sequences present in the reaction, including the primer itself, the other primer (for PCR), the amplified product, and any other sequences desired (e.g., repetitive element sequences in genomic templates, vector sequence in cloned templates, or other primer pair sequences in multiplexed PCR reactions). Base pairing involving the primer 3' end is considered separately from base pairing involving internal sequences. Primers meeting all constraints are ranked by a ``combined score'', a user-definable weighted sum of any of the above parameters. OSP is being routinely and extensively used to select sequencing primers for the C. elegans genome sequencing project, and human genomic PCR primer pairs for the Washington University Genome Center mapping project, with success rates exceeding 96% and 81% respectively. It is available for research purposes from the authors, at no cost, in both text output and interactive graphics (X windows) versions. AVAILABILITY C language source code for OSP is available (for research purposes only) at no cost from the authors, in either the text output version (tested for VAX/VMS, PC, MAC, and SUN Sparcstations), or interactive X windows graphics version (tested for SUN Sparcstations). To obtain OSP please send your postal address either to Phil Green by email, (pg@genome.wustl.edu) or (preferably) by FAX to (314) 362-2985 c/o Paula, the secretary handling OSP requests. You must provide a signed licensing agreement (which she will send you) and a stamped addressed mailer with diskette before the program can be sent to you. Sorry for the formalities. ========================================================================= regards to all, francis -- | B.F. Francis Ouellette | manager, yeast chromosome I & XVI sequencing project | dept of biology, McGill university, Montreal, Qc, Canada | francis@monod.biol.mcgill.ca From owner-software@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!news.cs.indiana.edu!sgiblab!spool.mu.edu!hri.com!noc.near.net!news.cs.brandeis.edu!binah.cc.brandeis.edu!BRANHAM From: branham@binah.cc.brandeis.edu Newsgroups: bionet.software Subject: PDB C++ Classes Message-ID: <1993Feb4.030615.7649@news.cs.brandeis.edu> Date: 4 Feb 93 03:06:15 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Reply-To: branham@binah.cc.brandeis.edu Organization: Brandeis University Lines: 22 I have been toying with the idea of a public domain set of standards for a set of classes for the last two years, and I think several things need to be settled by means of public discussion first. I would propose that a standard set of objects needs to be extensible not just in terms of additional objects, but in the real ability to extend the functionality Along with the ability to curb those extensions so that an individual task does not wildly overwhelm the systems capability. For example, good objects for such a system might be able to be used for a program simply looking at the structure, in which case knowing ribbon structures and secondary structure information might be quite valuable, whereas individual charge distributions for the residues might not be so valuable, but would be critical for any energy calculations one might want from another application. Another point I would forward for discussion is that it might make sense to build the objects from a set of base classes that are not specific to a single implementation of a container class, but rather at a lower level such that the objects are highly portable between C++ implementations. Ah, if I had 6 months free I would swim in this project, but grad school goes on and it slowly percolates in some small backwater of my mind :^) Tom Branham branham@binah.cc.brandeis.edu From owner-software@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!news.cs.indiana.edu!usenet.ucs.indiana.edu!sol.ctr.columbia.edu!spool.mu.edu!agate!doc.ic.ac.uk!daresbury!bioftp.unibas.ch!rc1!waverheu From: waverheu@vub.ac.be (Willy A Verheulpen) Newsgroups: bionet.software Subject: Re: Windows interested people! Message-ID: <1138@rc1.vub.ac.be> Date: 2 Feb 93 16:33:35 GMT References: <1993Feb2.150305.12641@newssrv.edvz.univie.ac.at> Sender: news@rc1.vub.ac.be Reply-To: waverheu@vub.ac.be Followup-To: poster Organization: Vrije Universiteit Brussel, Belgium Instit. Molec. Biol. Lines: 32 In article <1993Feb2.150305.12641@newssrv.edvz.univie.ac.at> A8471DAB@vm.univie.ac.at (Dr. Ch. Wawrosch/Prof.Dr. B. Kopp) writes: > >>If your interested in some opinions on various windows software, and >>want my thoughts, just send my a note... maybe we could setup a mail >>windows support group - sounds good to me :) >> >> D.P. > >Hi D.P., >sounds good, please add me to your list: > >Chris Wawrosch >Univ. of Vienna >e-mail: a8471dab@awiuni11.edvz.univie.ac.at > >Thank you and Greetings from Ol'Europe, > >Chris. I'm also interested but there are already a number of windows support & discussion groups. Isn't this too much of the good life ? :-) #################################################################### # # # Willy A Verheulpen Systems Coordination # # Brussels Free University Institute Molecular Biology # # e-mail : waverheu@vub.ac.be # # # #################################################################### From owner-software@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!sdd.hp.com!swrinde!zaphod.mps.ohio-state.edu!howland.reston.ans.net!sol.ctr.columbia.edu!The-Star.honeywell.com!umn.edu!lenti.med.umn.edu!ernest From: ernest@lenti.med.umn.edu (Ernest Retzel (1535 49118)) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Message-ID: Date: 4 Feb 93 15:24:23 GMT Sender: news@news2.cis.umn.edu (Usenet News Administration) Organization: University of Minnesota Lines: 36 Nntp-Posting-Host: lenti.med.umn.edu > Ok, agreeably, there is more to a "software" group than just discussion of > software development, or its use or its installation - but it's a standing > joke around here that about the only thing you don't see in bionet software > is things related to the problems associated with writing and using software > in the biological field. [stuff deleted] > I get > more amusement from reading the list of subject lines in here than I get from > rec.humour.funny on a typical day. Then you must be sorely in need of amusement that you bother to read it. Consider a pet. > I believe in orthogonality - we have groups for discussing pure hardware > problems and we have groups for discussion of purely biological problems, > and the things which can't be resolved in either belong to that blissful > area in the middle which is the fascinating interaction between disciplines. > I just get annoyed that I can't see the discussion in that interface for > all the noise coming from both sides. Spare me/us the arrogance of pseudo-intellectual purity. Expending this much effort to quell a discussion, particularly one that was started by a question, is basically immature. > Why can't we have a decent discussion on something like "What issues are > involved in the automation of mapping procedures for a project like > the Human Genome Mapping". Perhaps you should begin one; that would be constructive. > I will keep my mouth shut now maybe. Please. Ernie Retzel ernest@lenti.med.umn.edu From owner-software@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: embnet@comp.bioz.unibas.ch (EMBnet Switzerland [BASEL]) Newsgroups: bionet.software Subject: SUPER 2.0 Message-ID: <1993Feb4.132846.4162@comp.bioz.unibas.ch> Date: 4 Feb 93 13:28:46 GMT Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: embnet@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 273 Nntp-Posting-Host: biox.embnet.unibas.ch Did you always want to ask your user community on your computer on how they rate your services? Did you write command files, or any other probe for this? Then the program SUPER is for you: S implified U ser P oll and E xperience R eport language SUPER is a program which is written in C, and tested on Silicon Graphics, DEC Ultrix, and VAX/VMS. It reads a template file which describes the questions to be asked, and puts the answers into a file. Help and the backstep option are provided at any step, and can be adapted to national languages easily. The software is extensively documented. As from Version 2.0 (available now), the SUPER program can also have the evaluation of results made by SUPER by automatically writing a C program which in turn takes all the input and makes statistics on the numerical fields of your poll. The SUPER script language is used at the Biocomputing Basel facility to poll users on-site. If the users need to reply off-line,the program SUPER can act as 'compiler' and generate (UNIX) csh and (VMS) com files which can be requested from the mail server. In this case, after execution, the user must send back the generated output file. As contributed by the Finnish node of EMBnet, SUPER also runs on SUN com- puters. They've further made it run as a 'telnet hole' by making entries in /etc/services and /usr/etc/inetd.conf accordingly. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ BIOFTP BASEL SOFTWARE DISTRIBUTION +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ SUPER is available from bioftp.unibas.ch in the programs/bioftp-sw directory and can be retrieved as compressed tar file (for UNIX) or as MFTU-encoded VAX/VMS backup save set. The program SUPER is also available from the EMBL servers: 1) by anonymous ftp from FTP.EMBL-Heidelberg.DE (/pub/software/unix/super.tar.Z) (/pub/software/vax/super.uue) 2) by electronic mail from NetServ@EMBL-Heidelberg.DE (get unix_software:super.uaa) (get vax_software:super.uue) Full credits go to the Author (Lukas Rosenthaler) and the Swiss National Science Foundation (NF) for funding the EMBnet SWITZERLAND project. Thanks to Rob Harper and the Team there for contributing the changes on the SUN, and the inetd hack. DETAILED DESCRIPTION. Guess you want to know the satisfaction of people with the computers they use (This is a very primitive example). The dialogue the user will see is as follows: What are Your personal experiences with computers ? 1) I had only the best experiences, no troubles at all 2) I like computers, but sometimes they drive me crazy 3) I hate computers, but sometimes they help a little 4) I work only with computers because my boss want's it Now if the user does not have any idea he might enter ?>help and, stupidly, the answer will be Input error: You should enter menu option between 1 and 4 ! ?>? "?" gives help, "!" repeats last question. Please enter menu option between 1 and 4 ! Let us assume that the user achieved to type in "3", then the next question is: ?>3 Was in Your opinion the training sufficient You received? 1) yes 2) no 3) don't know Our dummy user might answer ?>3 and gets finally adressed with the fllowing questions: Personal info ============= Do You want to enter Your name and address or do You prefer to be anonymous ? 1) I'm giving name and address 2) I want to stay anonymous Certainly (2) is a good option, and the program ends: ?>2 Thank You very much for this interesting information. I hope that You will be a frequent user of SUPER Good Bye This dialog will create the following data file, one per user: SUPER: demo experience : 3 very_bad_exp : 3 all_users : 2 The program to generate this dialog is called SUPER, and can run either on VAX/VMS or on various flavours of UNIX. If you prefer to send it around via eMail, you can prepare DCL or csh shell scripts by invoking SUPER with the appropriate flag as documented in the program description. The output evaluation will be easy if you have only numerical fields (as in this case). Each menu can have up to 10 options, and one of which must be choosen. Multiple choice selection is scheduled to be in the next release of SUPER. Other data fields can be one line or several lines of free text. Let us assume that you have mostly ststistical interest, and need to evaluate the fields. You do this by Rwriting a C program with SUPER, because SUPER accepts a flag (-rep for 'report) which reads the dialogue and writes a C program for its evaluation. You compile the program and feed each of the output files sequentially. Let us assume , further, that we had 8 results. Then, output looks like: 1: experience -> options: 0="invalid" (0), 1="I had only the best experiences, no troubles at all" (2), 2="I like computers, but sometimes they drive me crazy" (1), 3="I hate computers, but sometimes they help a little" (2), 4="I work only with computers because my boss want's it" (3), 2: very_bad_exp -> options: 0="invalid" (3), 1="yes" (1), 2="no" (2), 3="don't know" (2), 3: good_exp 4: best_exp 5: all_users -> options: 0="invalid" (0), 1="I'm giving name and address" (7), 2="I want to stay anonymous" (1), 6: name 7: street 8: city 9: tele The non-numerical fields are just listed as blanks. However, the C program also writes an output file which is in tab-separated format which you can directly import in spreadsheet - like programs. The basic functionality of SUPER is to interpret the script which determines the dialogue. Branching and reevaluation of choices is possible. The script for the dialog above, therefore, had also a script which is printing as follows: //============================================================================= // This is a simple demo program written in the SUPER script language //============================================================================= // // first question // LABEL experience Experiences about Computer What are Your personal experiences with computers ? MENU I had only the best experiences, no troubles at all I like computers, but sometimes they drive me crazy I hate computers, but sometimes they help a little I work only with computers because my boss want's it GET MENU ON (1) GOTO best_exp // we will ask some different questions, depending ON (2) GOTO good_exp // on the experiences of the user // option 3 and 4 are treated equally // here's the question for the very unlucky user LABEL very_bad_exp Was in Your opinion the training sufficient You received? MENU yes no don't know GET MENU GOTO all_users // heres the question for the "normal" user LABEL good_exp What was Your most frustrating experience? Please describe Your frustrating experience. You may use several lines, enter an empty line to proceed to the next question: GET FREETEXT GOTO all_users // heres the question for the lucky user LABEL best_exp So far You had only very good experiences (We hope that this will not change...). What was Your best experience so far, the highlight? Please describe Your highlight by entering text. You may use several lines, an empty line will get You to the next answer. GET FREETEXT LABEL all_users Personal info Do You want to enter Your name and address or do You prefer to be anonymous ? MENU I'm giving name and address I want to stay anonymous GET MENU ON (2) GOTO stop // Ask personal question WRITE WRITE Personal Information WRITE LABEL name Please enter name: GET TEXT LABEL street Please enter the street You live: GET TEXT LABEL city Please enter the city: GET TEXT LABEL tele Please enter Your telephone number: GET TEXT LABEL stop Thank You very much for this interesting information. I hope that You will be a frequent user of SUPER . Good Bye Hope you like it. Suggestions welcome to embnet@comp.bioz.unibas.ch - thanks. -- +----------------------------------+-------------------------------------+ | Dr From owner-software@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!news.cs.indiana.edu!usenet.ucs.indiana.edu!sol.ctr.columbia.edu!howland.reston.ans.net!bogus.sura.net!darwin.sura.net!sgiblab!munnari.oz.au!bruce.cs.monash.edu.au!monu6!yoyo.cc.monash.edu.au!parry From: parry@yoyo.cc.monash.edu.au (Tom J Parry) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Message-ID: <1993Feb4.051201.12026@monu6.cc.monash.edu.au> Date: 4 Feb 93 05:12:01 GMT References: Sender: news@monu6.cc.monash.edu.au (Usenet system) Organization: Monash University, Melb., Australia. Lines: 41 Originator: parry@yoyo.cc.monash.edu.au ernest@lenti.med.umn.edu (Ernest Retzel (1535 49118)) writes: >Sorry, I tend to agree with Krasel. >If a biologist has a question, I can't really see a reason that it not >be discussed. And for that query, I can think of no better bioforum to >ask it in. The serious hardware groups flame people for asking basic >things. Ok, agreeably, there is more to a "software" group than just discussion of software development, or its use or its installation - but it's a standing joke around here that about the only thing you don't see in bionet software is things related to the problems associated with writing and using software in the biological field. We've had rambling discussions on the up arrow key in GCG that had nothing to do with biology, we've had in depth discussions on the difficulty of connecting apple laser writers to ethernets - I get more amusement from reading the list of subject lines in here than I get from rec.humour.funny on a typical day. You'd be really amused if I started posting bug reports for the g++ compiler in here just because I'm using to write software for biologists - or started a rambling discussion on why the xor operator in c++ can't be usefully overloaded to implement exponentiation. I believe in orthogonality - we have groups for discussing pure hardware problems and we have groups for discussion of purely biological problems, and the things which can't be resolved in either belong to that blissful area in the middle which is the fascinating interaction between disciplines. I just get annoyed that I can't see the discussion in that interface for all the noise coming from both sides. Why can't we have a decent discussion on something like "What issues are involved in the automation of mapping procedures for a project like the Human Genome Mapping". For the rest of you, there is a discussion in comp.sys.intel going on about the various processors right now as we speak. enough said - I will keep my mouth shut now maybe. -- Tom J Parry. Your reality is a figment of my imagination. From owner-software@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!spool.mu.edu!hri.com!noc.near.net!news.cs.brandeis.edu!binah.cc.brandeis.edu!BRANHAM From: branham@binah.cc.brandeis.edu Newsgroups: bionet.software Subject: PDB C++ Message-ID: <1993Feb4.152414.17180@news.cs.brandeis.edu> Date: 4 Feb 93 15:24:14 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Reply-To: branham@binah.cc.brandeis.edu Organization: Brandeis University Lines: 16 I have been thinking about putting together a good set of objects for dealing with molecular structures for about two years now. Grad school has not left me the time I would like to work on it though (Get to see my wife about 5th weekend or so). There are some ideas I would like to discuss though before I force time into my schedule. I propose that a publicly available set of objects should be extensible, so that widely varying purposes could be met, but at the same time a mechanism for limiting the extensions for certain purposes. For example, someone wanting to look at a protein structure would like the code to know about helix and beta sheet conformations and would probably not worry about the individual atomic masses, whereas doing certain typpes of calculations one might need the reverse. Should separate objects e developed that could be associated with one another, or should a control mechanism be established, along with guidelines for making extensions to the standard? Tom Branham branham@binah.cc.brandeis.edu From owner-software@net.bio.net Thu Feb 04 22:00:00 1993 Path: biosci!SALK-SC2.SDSC.EDU!mangalam From: mangalam@SALK-SC2.SDSC.EDU (Harry Mangalam) Newsgroups: bionet.software Subject: Re: postscript viewer for DOS Message-ID: <9302052224.AA25897@salk-sgi.sdsc.edu> Date: 5 Feb 93 22:24:48 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 47 David Salt Writes: >Well I am rather apprehensive about asking this question now as it is >not directly related to computers in biology (re the extensine moanings >about intel chips on this group!) other than to help a biologist produce >better presentations of his work. Pay no attention to those plaintive cries of gloom/doom! While in-depth discussion of die masks and superscalar instruction sets may be a bit off-topic, any wombat that follows the group can read the header and skip it if it offends their delicate sensibilities. > >Well the question is simple does anyone know of a program for mswindows that >would allow me to view a postscript file and that is ftp'able (OK and buy'able) >The reason I ask is that my department is thinking of buying a slide maker >from polaroid which works through windows and to make it usable by alot of >people it would be nice just to print to disc as postscript, go to the machine >look at the files in windows and then send them to the slide maker (it works >like a windows printer driver). If the WinDoze restriction isn't set in stone, and you're somewhat compu-tent, you can ftp GHOSTSCRIPT (386 version also available - may require a certain amount of futzing to get the 32-bit addressing set up correctly) from any of a number of FTP (ie - oak.oakland.edu in /pub/msdos/postscript - file is ps252386.zip, I believe) sites (and the related fonts - free, but in a separate file), and then use it as an extremely good PS previewer. Alternatively, I just recently got a mailing for Hijaak for Windows that seems to do a number of useful image conversion/viewing routines including viewing PS output. !!!On sale NOW for ONLY $99!!! .....8)...... It does come with a 30 day money back and I've heard from a couple of people that if you need to do lots of image bashing, it's one of the better pkgs to do it with, but I've never used it and so this is not a personal rec. Nuf said, Good Hunting Harry Harry Mangalam (Piled quite high 'n' deep) Vox:(619) 453-4100, x250 Dept of Biocomputing Fax:(619) 552-1546 The Salk Institute 1' mangalam@salk-sc2.sdsc.edu 10010 N Torrey Pines Rd 2' hjm@salk-sgi.sdsc.edu La Jolla CA 92037 3' mangalam@salk.bitnet From owner-software@net.bio.net Thu Feb 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!elroy.jpl.nasa.gov!usc!sol.ctr.columbia.edu!caen!batcomputer!munnari.oz.au!hp9000.csc.cuhk.hk!hkuxb.hku.hk!hkucc.hku.hk!vldnaseq From: vldnaseq@hkucc.hku.hk Newsgroups: bionet.software Subject: Oligonucleotide Tm prediction Message-ID: <1993Feb5.122833.1@hkucc.hku.hk> Date: 5 Feb 93 04:28:33 GMT Sender: usenet@hkuxb.hku.hk (USENET News System) Organization: The University of Hong Kong Lines: 8 Nntp-Posting-Host: hkucc.hku.hk Dear netters, I am optimizing the hybridization and washing conditions for single base mismatch oligonucleotide hybridization experiments. This is used as a means to detect mutations. Is there any software that can predict accurately the Tm of a complete match / single mismatch under different ionic strengths ? Wai Ming From owner-software@net.bio.net Thu Feb 04 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!sol.ctr.columbia.edu!emory!gatech!udel!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: Oligonucleotide Tm prediction Message-ID: <1993Feb5.194338.24075@welchgate.welch.jhu.edu> Date: 5 Feb 93 19:43:38 GMT References: <1993Feb5.122833.1@hkucc.hku.hk> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 21 In article <1993Feb5.122833.1@hkucc.hku.hk> vldnaseq@hkucc.hku.hk writes: >Dear netters, > >I am optimizing the hybridization and washing conditions for single base >mismatch oligonucleotide hybridization experiments. This is used as a means >to detect mutations. Is there any software that can predict accurately the >Tm of a complete match / single mismatch under different ionic strengths ? > >Wai Ming A quick Gopher seacrh tells me that there is a program for the PC called Melt (by John Nash) which may be what you're looking for. You can obtain melt.uue by gopher or by anonymous ftp at felix.embl-heidelberg.de. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Thu Feb 04 22:00:00 1993 Path: biosci!CUHHCA.HHMI.COLUMBIA.EDU!system From: system@CUHHCA.HHMI.COLUMBIA.EDU (Phil Bourne) Newsgroups: bionet.software Subject: subscribe Message-ID: <9302051727.AA26358@cuhhca.hhmi.columbia.EDU> Date: 5 Feb 93 17:27:06 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 subscribe From owner-software@net.bio.net Thu Feb 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!caen!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc.harvard.edu!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: Re: PC 80486 and bionet ? Message-ID: Date: 5 Feb 93 06:05:36 GMT References: Lines: 21 Nntp-Posting-Host: husc10.harvard.edu ernest@lenti.med.umn.edu (Ernest Retzel (1535 49118)) writes: >> Why can't we have a decent discussion on something like "What issues are >> involved in the automation of mapping procedures for a project like >> the Human Genome Mapping". >Perhaps you should begin one; that would be constructive. Better yet, put in in the computational biology group, which has little traffic and is the appropriate place. For better or worse, .software has evolved into a "user's group" rather than a "developer's group" (I'd vote better -- it's always nice to have a place to turn too before going bald through manual extraction). Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@ribo.harvard.edu From owner-software@net.bio.net Thu Feb 04 22:00:00 1993 Path: biosci!VM.UOGUELPH.CA!BOTSALT From: BOTSALT@VM.UOGUELPH.CA (david salt) Newsgroups: bionet.software Subject: postscript viewer for DOS Message-ID: <9302052034.AA13431@net.bio.net> Date: 5 Feb 93 20:25:40 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 Well I am rarther apprehensive about asking this question now as it is not directly related to computers in biology (re the extensine moanings about intel chips on this group!) other than to help a biologist produce better presentations of his work. Well the question is simple does anyone know of a program for mswindows that would allow me to view a postscript file and that is ftp'able (OK and buy'able) The reason I ask is that my department is thinking of buying a slide maker from polaroid which works through windows and to make it usable by alot of people it would be nice just to print to disc as postscript, go to the machine look at the files in windows and then send them to the slide maker (it works like a windows printer driver). Well heres hoping David Salt From owner-software@net.bio.net Fri Feb 05 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!howland.reston.ans.net!usc!sol.ctr.columbia.edu!destroyer!news.iastate.edu!rjhoffma From: rjhoffma@iastate.edu (Richard J. Hoffmann) Newsgroups: bionet.software Subject: Re: postscript viewer for DOS Message-ID: Date: 5 Feb 93 23:12:48 GMT References: <9302052224.AA25897@salk-sgi.sdsc.edu> Sender: news@news.iastate.edu (USENET News System) Distribution: bionet Organization: Iowa State University, Ames, IA Lines: 36 In article <9302052224.AA25897@salk-sgi.sdsc.edu> mangalam@SALK-SC2.SDSC.EDU (Harry Mangalam) writes: >David Salt Writes: >>Well the question is simple does anyone know of a program for mswindows that >>would allow me to view a postscript file and that is ftp'able (OK and buy'able) > If the WinDoze restriction isn't set in stone, and you're somewhat >compu-tent, you can ftp GHOSTSCRIPT (386 version also available - may >require a certain amount of futzing to get the 32-bit addressing set up >correctly) from any of a number of FTP (ie - oak.oakland.edu in >/pub/msdos/postscript - file is ps252386.zip, I believe) sites (and the ^ >related fonts - free, but in a separate file), and then use it as an >extremely good PS previewer. Actually, the file is called gs252386.zip; it contains 386-specific files. Also present is gs252286.zip, which is for 286's. There is a Windows version too, called gs252win.zip, which works under Windows, but lacks much of a Windows interface. In any case, you must also retrieve gs252ini.zip, which contains files required byall of the above. I've found that I prefer using the 386 DOS version, even though I launch it through Windows. It shows an entire slide on one screen, where as the Windows version requires scrolling. The Windows version is also slower. Either works, and both require command line execution commands. All are free. They work fine for me to just what you want to do. Dick Hoffmann -- Richard J. Hoffmann Internet: rjhoffma@iastate.edu Department of Zoology & Genetics Bitnet: rjhoffma%iastate.edu@isumvs Iowa State University Voice: (515) 294-8075 Ames, Iowa 50011 From owner-software@net.bio.net Fri Feb 05 22:00:00 1993 Path: biosci!agate!spool.mu.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: X on PC 386? Message-ID: <1993Feb6.174237.9576@welchgate.welch.jhu.edu> Date: 6 Feb 93 17:42:37 GMT References: <9302052337.AA06448@ingen.cu> Distribution: bionet Organization: Johns Hopkins Univ. Welch Medical Library Lines: 34 In article <9302052337.AA06448@ingen.cu> web!ingen.cu!carmas@NET.BIO.NET (Carlos Israel Armas) writes: >hi there! >I apologize for asking it here, but I have no other way to know. >does anybody knows of a discussion list for Xwindows on 386 PCs? >the fact is that xpert list at MIT is too wide and advanced for beginners. >thanks a lot. >--- >carlos armas carmas%ingen@web.apc.org >network manager center of genetic engng. & biotech >havana, cuba There is a Usenet group just for this - it's called comp.windows.x.i386unix You can get the FAQ (Frequently Asked Questions) for this newsgroup via Gopher at merlot.welch.jhu.edu - just go through the following subdirectories: --> 16. Usenet News and FAQs/ --> 2. All FAQs (Frequently Asked Questions) Searches and Archives/ --> 1. FAQs - Archives/ --> 242. comp.windows.x.i386unix/ Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Fri Feb 05 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!gatech!emory!sol.ctr.columbia.edu!news.columbia.edu!psinntp!psinntp!alsys1!leper1!zucker From: zucker@ksksun.bioc.aecom.yu.edu (Thomas Zucker-Scharff x3513) Newsgroups: bionet.software Subject: gcgmenu Message-ID: <1368@alsys1.aecom.yu.edu> Date: 4 Feb 93 21:27:55 GMT Sender: news@alsys1.aecom.yu.edu Reply-To: zucker@ksksun.bioc.aecom.yu.edu Organization: Sun Microsystems, Inc. Lines: 23 Nntp-Posting-Host: leper1.ca.aecom.yu.edu After reading a number of postings here, I ventured out into the cold cruel world of FTP. My purpose: obtain gcgmenu program for bedraggled users. I have been only somewhat successful (or not successful at all, depending how one views it). I have all the required files on my disk, but when I edit then cat the five gcgmenu files from the netserver then try to run them as a command file to obtain either a zip or mftu file, I only get errors. I know earlier postings said how to do this, but there is something I must have missed. Could someone please reiterate the instructions for me. Thanks, tom /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ | Tom Zucker-Scharff | | | Director Scientific Computing Facility | phone : 212-430-3512 | | Albert Einstein College of Medicine | beeper: 212-419-6984 | | 1300 Morris Park Avenue, Chanin 333 | fax : 212-822-6538 | | Bronx, New York 10461 USA | e-mail: zucker@aecom.yu.edu | \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From owner-software@net.bio.net Fri Feb 05 22:00:00 1993 Path: biosci!NET.BIO.NET!web!ingen.cu!carmas From: web!ingen.cu!carmas@NET.BIO.NET (Carlos Israel Armas) Newsgroups: bionet.software Subject: X on PC 386? Message-ID: <9302052337.AA06448@ingen.cu> Date: 5 Feb 93 23:37:43 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 hi there! I apologize for asking it here, but I have no other way to know. does anybody knows of a discussion list for Xwindows on 386 PCs? the fact is that xpert list at MIT is too wide and advanced for beginners. thanks a lot. --- carlos armas carmas%ingen@web.apc.org network manager center of genetic engng. & biotech havana, cuba From owner-software@net.bio.net Sat Feb 06 22:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!howland.reston.ans.net!paladin.american.edu!gatech!concert!rock!stanford.edu!hsdndev!nmr-z!OPAL.MGH.HARVARD.EDU!CHERRY From: cherry@OPAL.MGH.HARVARD.EDU Newsgroups: bionet.software Subject: Re: Oligonucleotide Tm prediction Message-ID: <1993Feb7.140555.10592@nmr-z.mgh.harvard.edu> Date: 7 Feb 93 14:05:55 GMT References: <1993Feb5.122833.1@hkucc.hku.hk>,<1993Feb5.194338.24075@welchgate.welch.jhu.edu> Sender: usenet@nmr-z.mgh.harvard.edu (User for USENET news postings) Reply-To: cherry@OPAL.MGH.HARVARD.EDU Organization: Molecular Biology - Mass Gen Hospital Lines: 18 Nntp-Posting-Host: opal.mgh.harvard.edu In article <1993Feb5.122833.1@hkucc.hku.hk> vldnaseq@hkucc.hku.hk writes: >I am optimizing the hybridization and washing conditions for single base >mismatch oligonucleotide hybridization experiments. This is used as a means >to detect mutations. Is there any software that can predict accurately the >Tm of a complete match / single mismatch under different ionic strengths ? > >Wai Ming The PRIMER program by Steve Lincoln and Mark Daly at the Whitehead can be used to calculate oligo Tm. Use the manual mode to enter the oligo sequences and PRIMER will report the Tm. The C source to PRIMER is available from genome.wi.mit.edu (this is a new address). Look in the /distribution/primer.0.4 directory. A DOS executable is available in this directory. Makefiles for DOS, VMS, and Unix are also available. Mike From owner-software@net.bio.net Sat Feb 06 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: gartmann@VMS.MPIIB-FREIBURG.MPG.dbp.de (Christoph Gartmann) Newsgroups: bionet.software Subject: RE: GCG-menu Message-ID: <1993Feb7.134157.4970@gserv1.dl.ac.uk> Date: 7 Feb 93 15:41:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 46 Content-Identifier: 12 Original-To: bio-software@uk.ac.daresbury Conversion: Prohibited Tom Zucker-Scharff ("zucker@aecom.yu.edu") wrote: > After reading a number of postings here, I ventured out into the cold cruel > world of FTP. My purpose: obtain gcgmenu program for bedraggled users. I > have been only somewhat successful (or not successful at all, depending how > one views it). I have all the required files on my disk, but when I edit > then cat the five gcgmenu files from the netserver then try to run them as > a command file to obtain either a zip or mftu file, I only get errors. What you actually got from the EMBL-fileserver is already the MFTU-file. MFTU does a 7-bit encoding, you don't need to make a VMS-share archive out of it. Provided that you got GCGMENU.MFT by mail, you have five parts. Remove all mail-header information and concatenate all the parts into one single file. Next, decode it using MFTU. To get a copy of MFTU do the following: Send a message to FILESERV@WKUVX1.BITNET containing the line SEND FILESERV_TOOLS When you receive the result (five parts), extract it from VMS-Mail and store and concatenate all parts in one file (e.g. TOOLS.COM). Finally execute the procedure @TOOLS This file is a VMS-Share archive and is self-extracting. You'll get executables for LZDCMP, UnZip and MFTU. To decode GCGMENU.MFT define a symbol for MFTU MFTU :== $disk:[directory]MFTU Then type MFTU DECODE GCGMENU.MFT and you will retrieve two files, GCG-MENU021.A and README.TXT . Install the backup saveset GCG-MENU021.A as described in README.TXT using @SYS$UPDATE:VMSINSTAL (You need SYSTEM privileges to do that) Happy unpacking... Christoph Gartmann +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%026245050160374::GARTMANN | | Immunbiologie X400 : S=gartmann;OU=vms;O=mpiib-freiburg; | | Stuebeweg 51 P=mpg;A=dbp;C=de | | D-7800 Freiburg RFC : gartmann@vms.mpiib-freiburg.mpg.dbp.de | | FRG will change to: gartmann@immunbio.mpg.de | +------------- Do you know MENUE, the user environment for VMS? -------------+ From owner-software@net.bio.net Sun Feb 07 22:00:00 1993 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!usc!rpi!ghost.dsi.unimi.it!univ-lyon1.fr!scsing.switch.ch!bernina!neptune!cbrg From: cbrg@inf.ethz.ch (CompBioResGrp) Newsgroups: bionet.software Subject: Searching proteins by their digested mass profile Message-ID: <1993Feb8.115510.4888@neptune.inf.ethz.ch> Date: 8 Feb 93 11:55:10 GMT Sender: news@neptune.inf.ethz.ch (Mr News) Organization: Dept. Informatik, Swiss Federal Institute of Technology (ETH), Zurich, CH Lines: 153 Nntp-Posting-Host: rutishauser-gw.inf.ethz.ch A new server is available from the CBRG in Zurich. A description of the server follows. This description can be obtained by sending e-mail to cbrg@inf.ethz.ch with one line "help MassSearch". For a description of other servers at the CBRG, send an e-mail with the line: "help all" ------------------------------------------------------------------ In some cases, recognition of proteins can be done by fragmenting the protein according to certain pattern and using the molecular weights of the fragments as a trace. This method is not effective to find the composition of an unknown protein, but it is effective in locating an unknown sample if its sequence is recorded in a protein database. One of the ways of breaking a protein into smaller pieces according to a certain pattern is by using enzymes which digest the protein. For example, trypsin breaks a protein after every Arginine (R) or after every Lysine (K) not followed by a Proline (P). AspN breaks a protein before every Aspartic acid (D). A table of recognized enzymes and their cleavage rules is given below. The molecular weight of fragments can be found experimentally by mass spectrometry methods to a good level of accuracy. More importantly, these methods typically require very small samples in the order of fractions of pico-moles. The problem of identifying a sampled protein can be reduced to digesting the protein with an enzyme, finding the molecular weights of each of the pieces and then comparing this set of weights to what would be obtained from the digestion of each protein in the database. The process can be repeated with several different enzymes to increase its selectivity. The function MassSearch locates the best candidates in a protein database (SwissProt at this time) that would fit the given weights once digested by the given enzyme. This type of searching has been found particularly useful in the following circumstances: o To identify proteins when the amount available is very small, for example as can be separated by 2D gels. o To determine whether an unknown protein is already known in the database before spending a significant effort in sequencing. o To identify more than one protein which cannot be separated by other means (this method has been successfully used to identify two proteins which were digested together). The template of the body of the message to be sent to cbrg@inf.ethz.ch is (between but not including the dashed lines): --------------------------------------------------------------------- MassSearch Trypsin: 1524.0, 1509.7, 1387.5, 1169.4, 1014.4, 842.5, 836.4, 743.2, 717.2, 563.1, 511.3 --------------------------------------------------------------------- The token "MassSearch" indicates the operation to be run. The following lines contain the name of the digester enzyme followed by the weights. The weights can be separated by spaces, commas, tabs or newlines as convenient, but no other extraneous characters. Many different searches can be requested in a single command, each request must be identified by the name of the enzyme and followed by the weights. The output of the above request is: Searching on SwissProt version 23. For each set of weights, the matching sequences are printed in decreasing order of significance. Scores lower than 70 are generally not significant. Searching the weights 1524, 1509.7000, 1387.5000, 1169.4000, 1014.4000, 842.5000 , 836.4000, 743.2000, 717.2000, 563.1000, 511.3000 as digested by Trypsin Score n k AC DE OS 159.4 15 9 P80049; FATTY ACID-BINDING PROTEIN, LIVER (FABP). GINGLYMOSTOMA CIRRATUM (NURSE SHARK). 76.2 28 5 P22966; ANGIOTENSIN-CONVERTING ENZYME PRECURSOR, TESTIS-SPECIFIC (EC 3.4.15.1) (ACE) (DIPEPTIDYL CARBOXYPEPTIDASE I) (KININASE II). HOMO SAPIENS (HUMAN). 72.4 11 4 P16291; COAGULATION FACTOR IX (EC 3.4.21.22) (CHRISTMAS FACTOR) (FRAGMENT). OVIS ARIES (SHEEP). 72.3 25 2 P18416; TRANSPOSASE (TRANSPOSON TN552) (ORF 480). STAPHYLOCOCCUS AUREUS. 71.0 5 6 P08821; DNA-BINDING PROTEIN II (HB) (HU). BACILLUS SUBTILIS, AND BACILLUS GLOBIGII. 66.9 23 7 P13214; ANNEXIN IV (LIPOCORTIN IV) (ENDONEXIN I) (CHROMOBINDIN 4) (PROTEIN II) (P32.5) (PLACENTAL ANTICOAGULANT PROTEIN II) (PAP-II) (PP4-X) (35-BETA CALCIMEDIN). BOS TAURUS (BOVINE). . . . . . The first column measures the quality of the match between the given weights and a protein sequence in the database. The higher the score, the better the match. The hits are listed in decreasing scoring order. The second column, identified by n, indicates the number of fragments that will result from the digestion of the found protein. The third column, identified with k, indicates the number of given weights which were successfully matched against the theoretical digestion. The score is calculated from the total number of fragments, the number of given weights matched, and from how closely these weights could be matched. The fourth column indicates the accession number of the sequence in SwissProt. The rest of each line contains the description and species of the sequence which serve as a quick guide to identify the protein. A complete description of the algorithm and the probability foundations can be found in chapter 20 of "A tutorial introduction to computational biochemistry using the Darwin system" by G.H. Gonnet. The boundary between insignificant and significant matches is around 70. Scores less than 70 are not very significant, while scores greater than 70 are significant. The enzymes which are presently recognized, and the names to be used, are the following (courtesy of Amos Bairoch) Enzyme name cuts between except for ########### ############ ########## Armillaria Xaa-Cys,Xaa-Lys ArmillariaMellea Xaa-Lys BNPS_NCS Trp-Xaa Chymotrypsin Trp-Xaa,Phe-Xaa,Tyr-Xaa, Trp-Pro,Phe-Pro,Tyr-Pro, Met-Xaa,Leu-Xaa, Met-Pro,Leu-Pro Clostripain Arg-Xaa CNBr_Cys Met-Xaa,Xaa-Cys CNBr Met-Xaa AspN Xaa-Asp LysC Lys-Xaa Hydroxylamine Asn-Gly MildAcidHydrolysis Asp-Pro NBS_long Trp-Xaa,Tyr-Xaa,His-Xaa NBS_short Trp-Xaa,Tyr-Xaa NTCB Xaa-Cys PancreaticElastase Ala-Xaa,Gly-Xaa,Ser-Xaa,Val-Xaa PapayaProteinaseIV Gly-Xaa PostProline Pro-Xaa Pro-Pro Thermolysin Xaa-Leu,Xaa-Ile,Xaa-Met, Xaa-Phe,Xaa-Trp,Xaa-Val TrypsinArgBlocked Lys-Xaa Lys-Pro TrypsinCysModified Arg-Xaa,Lys-Xaa,Cys-Xaa Arg-Pro,Lys-Pro,Cys-Pro TrypsinLysBlocked Arg-Xaa Arg-Pro Trypsin Arg-Xaa,Lys-Xaa Lys-Pro V8AmmoniumAcetate Glu-Xaa Glu-Pro V8PhosphateBuffer Asp-Xaa,Glu-Xaa Asp-Pro,Glu-Pro Please report any problems with the server to knecht@inf.ethz.ch From owner-software@net.bio.net Sun Feb 07 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!news From: jlogsdon@bio.indiana.edu (John Logsdon) Newsgroups: bionet.software Subject: Re: Sequencher address Message-ID: Date: 8 Feb 93 01:07:02 GMT References: <1993Feb7.225333.3474@news.cs.brandeis.edu> Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Department of Biology / Indiana University Lines: 22 X-Xxdate: Sun, 7 Feb 93 15:06:24 GMT Nntp-Posting-Host: woodchuck.bio.indiana.edu X-Useragent: Nuntius v1.1.1d7 Gene Codes Corporation P.O. Box 3369 Ann Arbor, MI 48106 Tel: 313-769-7249 Fax: 313-662-3379 America Online (they don't give an internet address): Gene Codes Disclaimer: I don't work for these folks I just am demoing their product! John ___________________________________________________________ John Logsdon Department of Biology Indiana University Bloomington, IN 47405 (812) 855-2549 (812) 855-6705 fax jlogsdon@bio.indiana.edu ____________________________________________________________ From owner-software@net.bio.net Sun Feb 07 22:00:00 1993 Path: biosci!agate!ames!saimiri.primate.wisc.edu!hp9000.csc.cuhk.hk!hkuxb.hku.hk!hkucc.hku.hk!vldnaseq From: vldnaseq@hkucc.hku.hk Newsgroups: bionet.software Subject: Tm prediction : more Message-ID: <1993Feb8.190445.1@hkucc.hku.hk> Date: 8 Feb 93 11:04:45 GMT Sender: usenet@hkuxb.hku.hk (USENET News System) Organization: The University of Hong Kong Lines: 15 Nntp-Posting-Host: hkucc.hku.hk Dear netters, I recently enquired a program for Tm calculation in oligonucleotide hybridization experiments, and received pointers to the "Primer" by Whitehead and "Oligo" from a commercial source. Naturally, Tm is DNA concentration dependent. But ......., in washing, the DNA concentration is negligible, and the situation is not an equilibrium condition. It is only a transient state. Equilibrium may require days or years to attend. Thus the Tm predicted by both programs cannot be applied to the real washing step. So, is there any better solution to this (excluding emperical determination)? Wai Ming From owner-software@net.bio.net Sun Feb 07 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!spool.mu.edu!sgiblab!munnari.oz.au!bunyip.cc.uq.oz.au!marlin.jcu.edu.au!solwarra.gbrmpa.gov.au!jamieo From: jamieo@gbrmpa.gov.au (Jamie Oliver) Newsgroups: bionet.software Subject: image analysis, morphometric software for PC ? Message-ID: <1993Feb7.234758.21780@gbrmpa.gov.au> Date: 7 Feb 93 23:47:58 GMT Organization: Great Barrier Reef Marine Park Authority Lines: 31 I am looking for a program (preferably for Windows) running on a IBM PC which will input an image (usually from a video camera, put sometimes scanned in) and which will enable me to carry out some sort of crude classification and then give me statisstics on the diameter, area, etc on individual and grouped entities in the image. I would also want to simply get dimensions and areas for entities defined interactively by myself. I gather there are a few packages for the Mac that do this type of thing (one is even public domain) but I haven't seen anything for the PC other than a rather limited package called TIM, which comes close but doesn,t calculate areas. Any help or advice would be appreciated. ------------------------------------------------------------------------- Jamie Oliver | Great Barrier Reef | Managing Australia's Marine Park Authority | Great Barrier Reef | email(internet): jamieo@gbrmpa.gov.au | "Ours to Use Wisely" ------------------------------------------------------------------------- -- ------------------------------------------------------------------------------- Jamie Oliver Managing Australia's Great Barrier Reef From owner-software@net.bio.net Sun Feb 07 22:00:00 1993 Path: biosci!VM.UOGUELPH.CA!BOTSALT From: BOTSALT@VM.UOGUELPH.CA (david salt) Newsgroups: bionet.software Subject: GhostScript Message-ID: <9302081754.AA21539@net.bio.net> Date: 8 Feb 93 17:50:11 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Thanks for all the responses to my request for a postscript file viewer GhostScript seems to work well enough but unfortunately the windows version does not implement a full windows interface which means that I cannot use it to view a postscript file and then print it to my polaroid slide maker....which is what I want to do. A possible way round this would be to view the postscript file with ghostscript and then copy to the clipboard (which is implemented) and then paste to an application which will let me print the image.....but I am trying to set up a system which will be easy to use by everybody in the department and that seems rarther a long winded way to go. I will continue my search! David Salt, University of Guelph Guelph, Ontario, Canada. From owner-software@net.bio.net Sun Feb 07 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!spool.mu.edu!hri.com!noc.near.net!news.cs.brandeis.edu!news From: ahouse@hydra.rose.brandeis.edu (Jeremy John Ahouse) Newsgroups: bionet.software Subject: Sequencher address Message-ID: <1993Feb7.225333.3474@news.cs.brandeis.edu> Date: 7 Feb 93 22:53:33 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Organization: Center for Complex Systems Lines: 7 X-Xxdate: Sun, 7 Feb 93 22: 57:33 GMT X-Useragent: Nuntius v1.1.1d17 I am looking for the ph # or email for the folks who make Sequencher. Thank you in advance... Jeremy Ahouse Biology - Brandeis Univ ahouse@hydra.rose.brandeis.edu From owner-software@net.bio.net Sun Feb 07 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: lobsterman@edvz.uni-graz.ada.at (Robert Huber) Newsgroups: bionet.software Subject: mac software for the neurosciences - hints needed Message-ID: <1993Feb8.181434.10540@gserv1.dl.ac.uk> Date: 8 Feb 93 17:45:23 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 18 Content-Identifier: 230 Original-To: bio-soft Conversion: Prohibited Howdy ya'll, Would anybody please be so kind to point me to software running on Macs which is suitable for the teaching of undergrads and grads in various topics of neuroscience. There must be programs out there that model the membrane of neurons, the behavior of networks, or the tuning of receptors. Any hints would be greatly appreciated. Much oblidged, Lobsterman (= Robert Huber) Snail: Inst. Zoology / Div. Neuroethology Universitaetsplatz 2 A-8010 Graz AUSTRIA Tel: (316) 380-5281 Fax: (316) 381-255 EMail: lobsterman@edvz.uni-graz.ada.at From owner-software@net.bio.net Sun Feb 07 22:00:00 1993 Path: biosci!agate!dog.ee.lbl.gov!hellgate.utah.edu!cs.utexas.edu!usc!howland.reston.ans.net!bogus.sura.net!darwin.sura.net!haven.umd.edu!purdue!mentor.cc.purdue.edu!sage.cc.purdue.edu!sabeard From: sabeard@sage.cc.purdue.edu (Scott Beard) Newsgroups: bionet.software Subject: POLO Keywords: polo Message-ID: Date: 8 Feb 93 22:33:13 GMT Sender: sabeard@sage.cc.purdue.edu Organization: Purdue University Computing Center Lines: 11 Does anyone know where to obtain the latest version of this program w/documentation for DOS? The latest version may be POLO II. And is there a version for the Macintosh? Please mail responses to zhlb@mace.cc.purdue.edu thanks -- ****************************************************************** Scott Beard Eagle class 91 Alpha Phi Omega sabeard@sage.cc.purdue.edu AFROTC ****************************************************************** From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!agate!ames!saimiri.primate.wisc.edu!caen!nic.umass.edu!noc.near.net!saturn.caps.maine.edu!dartvax!Robert.H.Gross From: Robert.H.Gross@dartmouth.edu (Bob Gross) Newsgroups: bionet.software Subject: Re: Tm prediction : more Message-ID: Date: 8 Feb 93 22:50:32 GMT References: <1993Feb8.190445.1@hkucc.hku.hk> Sender: news@dartvax.dartmouth.edu (The News Manager) Organization: Dartmouth College, Hanover, NH Lines: 14 X-Posted-From: InterNews1.0b9@newshost.dartmouth.edu In article <1993Feb8.190445.1@hkucc.hku.hk> vldnaseq@hkucc.hku.hk writes: > Naturally, Tm is DNA concentration dependent Shouldn't Tm be DNA concentration INdependent? It just represents the energy needed to pull the two strands of DNA apart - that is independent of how many molecules of DNA there are. Reassociation of the two strands obviously is concentration dependent. Bob Gross Dept. of Biology, Dartmouth College bob.gross@dartmouth.edu From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: gartmann@VMS.MPIIB-FREIBURG.MPG.dbp.de (Christoph Gartmann) Newsgroups: bionet.software Subject: GCG-menu (decoding, more...) Message-ID: <1993Feb9.092758.14670@gserv1.dl.ac.uk> Date: 9 Feb 93 10:51:47 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 19 Content-Identifier: 12 Original-To: bio-software@uk.ac.daresbury Conversion: Prohibited Hi, I forgot to say that you should use ASCII transfer mode for 'ftp'ing GCGMENU.MFT . MFTU encoded files contain only printable characters and are suitable for mail exchange. Thanks to David Mathog for the hint. Christoph Gartmann +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%026245050160374::GARTMANN | | Immunbiologie X400 : S=gartmann;OU=vms;O=mpiib-freiburg; | | Stuebeweg 51 P=mpg;A=dbp;C=de | | D-7800 Freiburg RFC : gartmann@vms.mpiib-freiburg.mpg.dbp.de | | FRG will change to: gartmann@immunbio.mpg.de | +------------- Do you know MENUE, the user environment for VMS? -------------+ From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!agate!spool.mu.edu!darwin.sura.net!newsserver.jvnc.net!jvnc.net!news From: mrl775@tigger.jvnc.net Newsgroups: bionet.software Subject: Beads on a String drawings - software Message-ID: <1993Feb9.203222.28069@tigger.jvnc.net> Date: 9 Feb 93 20:32:22 GMT Sender: news@tigger.jvnc.net (Zee News Genie) Reply-To: mrl775@tigger.jvnc.net Organization: TheNews Lines: 17 Nntp-Posting-Host: mrl775.jvnc.net Geez... I hate when I post empty notes.... Folks I am looking for a program that will facilitate the drawing of those protein "Beads on a String" figures. The ones where you "schematize" the secondary structure of a protein, with each amino acid being a bead. Does anyone know of a program that will do this? Sounds like a really good problem for a Macitosh solution... draw a string of amino acids beads, and place them on the page and let the user move them around. Anyone got any info??? Thanks Keith Elliston mrl775@tigger.jvnc.net From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!howland.reston.ans.net!usc!sol.ctr.columbia.edu!ira.uka.de!math.fu-berlin.de!news.netmbx.de!Germany.EU.net!mcsun!fuug!funic!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.software Subject: Re: SUPER 2.0 Message-ID: <1993Feb9.110044.29656@nic.funet.fi> Date: 9 Feb 93 11:00:44 GMT References: <1993Feb4.132846.4162@comp.bioz.unibas.ch> Sender: usenet@nic.funet.fi Organization: Finnish Academic and Research Network Project - FUNET Lines: 41 Nntp-Posting-Host: convex.csc.fi In <1993Feb4.132846.4162@comp.bioz.unibas.ch> embnet@comp.bioz.unibas.ch (EMBnet Switzerland [BASEL]) writes: >As contributed by the Finnish node of EMBnet, SUPER also runs on SUN com- >puters. They've further made it run as a 'telnet hole' by making entries >in /etc/services and /usr/etc/inetd.conf accordingly. There are a couple of ways to try this out at the moment You can give the following command telnet finsun.csc.fi 2001 or you can fire up gopher and point it at the Finnish EMBnet BioBox and have a look in the FAQ files directory. Under SUPER-GCG. I guess this is a first for using gopher for collecting data. I made up a simple script to ask questions about GCG, but SUPER will allow you to design questionaires just about anything. You are only limited by your own imagination. FAQ Files 1. EMBnet: Information. 2. EMBnet: Internet resources guide. 3. All FAQs (Frequently Asked Questions) Searches and Archives/ 4. EMBnet nodes FAQ/ 5. GCG_Projects/ 6. Help files from E-mail servers in biology./ 7. Important Documents from Bionet/ --> 8. SUPER-GCG (questionaire) 9. The BIOSCI FAQ I/ 10. The BIOSCI FAQ II/ 11. The BioBit Collection./ 12. The Materials and Methods FAQ/ RGDS -=ROB=- -- ~ Rob Harper ~ E-mail: harper@convex.csc.fi ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi ~ P.O. Box 40 ~ Telephone: +358 0 457 2076 ~ SF-02101 Espoo Finland ~ Fax: +358 0 457 2302 From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!uwm.edu!caen!saimiri.primate.wisc.edu!zazen!post.its.mcw.edu!not-for-mail From: gordin@post.its.mcw.edu (Erez Gordin) Newsgroups: bionet.software Subject: Wright's Inbreeding Coefficient Message-ID: <1l8ma1INNpub@post.its.mcw.edu> Date: 9 Feb 93 16:32:01 GMT Sender: gordin@post.its.mcw.edu Organization: Medical College of Wisconsin (Milwaukee, WI) Lines: 13 NNTP-Posting-Host: post.its.mcw.edu Does anyone know of a program to calculate Wright's Inbreeding coefficient for a medium to large fairly inbred population? Please respond here or to: Erez Gordin Dept. of Physiology Medical College of Wisconsin E-mail: gordin@post.its.mcw.edu Phone : (414) 257-8727 Fax : (414) 257-8570 From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!usc!howland.reston.ans.net!spool.mu.edu!yale.edu!newsserver.jvnc.net!jvnc.net!news From: mrl775@tigger.jvnc.net Newsgroups: bionet.software Subject: Beads on a Strings drawings - software Message-ID: <1993Feb9.202859.27851@tigger.jvnc.net> Date: 9 Feb 93 20:28:59 GMT Sender: news@tigger.jvnc.net (Zee News Genie) Reply-To: mrl775@tigger.jvnc.net Organization: TheNews Lines: 2 Nntp-Posting-Host: mrl775.jvnc.net From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!ub!acsu.buffalo.edu!ubvmsb.cc.buffalo.edu!camdna From: camdna@ubvmsb.cc.buffalo.edu (Darren Natale) Newsgroups: bionet.software Subject: Re: Tm prediction : more Message-ID: Date: 9 Feb 93 15:07:00 GMT References: <1993Feb8.190445.1@hkucc.hku.hk> Sender: nntp@acsu.buffalo.edu Organization: University at Buffalo Lines: 31 News-Software: VAX/VMS VNEWS 1.41 Nntp-Posting-Host: ubvmsb.cc.buffalo.edu In article , Robert.H.Gross@dartmouth.edu (Bob Gross) writes... >In article <1993Feb8.190445.1@hkucc.hku.hk> >vldnaseq@hkucc.hku.hk writes: > >> Naturally, Tm is DNA concentration dependent > >Shouldn't Tm be DNA concentration INdependent? It just represents the >energy needed to pull the two strands of DNA apart - that is >independent of how many molecules of DNA there are. Reassociation of >the two strands obviously is concentration dependent. > Tm is defined as the temperature at which 50% of the DNA molecules are single-stranded. The strand separation/strand annealing steps are both reversible processes. Therefore, the ability of a single stranded molecule to become annealed to its complement will depend on the likelihood of "finding" that complement--thus it is concentration dependant. Contrary to your supposition, Tm does not represent the energy needed to pull the strands apart. In fact, at the Tm, the energy released by the annealing of strands equals the energy required to separate them (since it is at equilibrium) and therefore no _extra_ energy input is required. The Tm of a DNA molecule depends on such factors as the primary sequence and the salt concentration. Tm is also defined as the temperature at which delta H (heat of enthalpy) equals delta S (heat of entropy). The deltas H and S values for all possible dinucleotide pairs (GA,AT,TT, etc.) are known (Breslauer et. al. PNAS 83:3746-3750) as is the effect of salt on the Tm. The programs that calculate Tm use these values (at least I know some do--others may simply use base composition). DN From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!yale.edu!ira.uka.de!scsing.switch.ch!news.unige.ch!ugsc2a!excoffie From: excoffie@sc2a.unige.ch (Laurent Excoffier) Newsgroups: bionet.software Subject: POPULATION GENETICS SOFTWARE Message-ID: <1993Feb9.144415.1@sc2a.unige.ch> Date: 9 Feb 93 12:44:15 GMT Sender: usenet@news.unige.ch Organization: University of Geneva, Switzerland Lines: 34 Hi, does anyone know of a good population genetics software able to compute ============================ different statistics like : - gene and haplotype frequencies - linkage disequilibrium between loci - molecular diversity, within and/or among populations - population structure indices etc... and carry out several test useful in the area of population genetics and ecology like : - Hardy-Weinberg equilibrium - neutrality tests (one or several loci) - population sub-structuring - genetic variance heterogeneity among populations etc... I would appreciate receiving comments on the existing softwares in this field, and to know on which platform they are developped (Mac, PC, Sun, etc...). The goal of these questions is that if such a software does not yet exist, we may develop it ourselves. So comments are also welcome on what should be included in the "ideal" population genetics package... Many thanks ----- Laurent Excoffier(*NT*) / Genetics and Biometry Lab / Dept. of Anthropology U. of Geneva / 12, rue G. Revilliod / 1227 Carouge / Switzerland Voice +41-22 343 6930 / Fax +41-22 300 0351 / Email: excoffie@sc2a.unige.ch From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!POST.ITS.MCW.EDU!fgarbrec From: fgarbrec@POST.ITS.MCW.EDU (Frederick Garbrecht) Newsgroups: bionet.software Subject: Re: TurboTAX Message-ID: Date: 9 Feb 93 23:03:20 GMT References: <9302092108.AA25952@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 20 TurboTax is a COMMERCIAL program. You have to pay for it. Try any software vendor for your personal copy. On 9 Feb 1993 6nguyen_p@spcvxb.spc.edu wrote: > Date: 9 Feb 93 20:30:23 GMT > From:6nguyen_p@spcvxb.spc.edu > To: bio-soft@net.bio.net > Subject: TurboTAX > > To All Readers of Software: > > I was wondering if anybody could help me look for a software called > Turbo Tax under windows or any tax forms software that I could used. > The more recent software is the more appreciated I am. > > Thankyou. > Michael > From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!UVVM.UVIC.CA!JCOWARD From: JCOWARD@UVVM.UVIC.CA Newsgroups: bionet.software Subject: ITCH'94 - CALL FOR PAPERS Message-ID: <9302092229.AA02285@net.bio.net> Date: 9 Feb 93 22:22:20 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 ITCH'94 "INFORMATION TECHNOLOGY IN COMMUNITY HEALTH" CONFERENCE HAS NOW BEEN SCHEDULED FOR OCTOBER 16 TO 19,1994. THIS INTERNATIONAL CONFERENCE ON COMMUNITY HEALTH AND INFORMATION SYSTEMS, WILL BE HELD AGAIN IN VICTORIA, B.C. CANADA. A "CALL FOR PAPERS" WILL BE SENT OUT SOON... AS WILL A "CALL FOR STUDENT POSTERS".... IN '92 A GRADUATE STUDENT FROM THE UNVIERSITY OF ALBERTA IN EDMONTON, CANADA, WON THE $500 PRIZE AND FREE CONFERENCE REGISTRATION. FOR MORE INFORMATION PLEASE CONTACT DR. PAUL FISHER, SCHOOL OF HEALTH INFORMATION SCIENCE AT THE UNIVERSITY OF VICTORIA. (604) 721-8575 OR SEND E-MAIL IN C/O JCOWARD@UVVM.UVIC.CA From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!uwm.edu!daffy!uwvax!zazen!post.its.mcw.edu!not-for-mail From: dmeier@post.its.mcw.edu (Daniel Meier) Newsgroups: bionet.software Subject: digitizing film needs? Keywords: tiff, gif files, x-ray film Message-ID: <1l8l25INNp7s@post.its.mcw.edu> Date: 9 Feb 93 16:10:45 GMT Organization: Medical College of Wisconsin (Milwaukee, WI) Lines: 11 NNTP-Posting-Host: post.its.mcw.edu X-Newsreader: TIN [version 1.1 PL7] Hello all, We are considering purchasing some sort of a scanner such as ThunderScan to digitize bands on x-film. Can you please recommend software and hardware that we need to purchase. Our laboratory has an SE/30. In addition to a scanner and software, do we need to purchase a video card? All replies gratefully received. Dan Meier dmeier@post.its.mcw.edu From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!KARL.ACC.IIT.EDU!CMSWALTERS From: CMSWALTERS@KARL.ACC.IIT.EDU Newsgroups: bionet.software Subject: Re: Beads on a String drawings - software Message-ID: <01GUIT5721DY8Y5SHV@minna.acc.iit.edu> Date: 9 Feb 93 21:14:31 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 32 >Folks > >I am looking for a program that will facilitate the drawing of those protein >"Beads on a String" figures. The ones where you "schematize" the secondary >structure of a protein, with each amino acid being a bead. Does anyone know of >a program that will do this? Sounds like a really good problem for a Macitosh >solution... draw a string of amino acids beads, and place them on the page and >let the user move them around. > >Anyone got any info??? > >Thanks > >Keith Elliston >mrl775@tigger.jvnc.net This question comes up about every two months on this list (I know--I've asked it myself). When is some clever Macprogrammer going to do the job? Eric =========================================================================== | D. Eric Walters, Ph.D. | | Associate Professor, Biological Chemistry | | Chicago Medical School phone: 708-578-3000, ext 498 | | 3333 Green Bay Road fax: 708-578-3240 | | North Chicago, IL 60064 email: cmswalters@minna.iit.edu | | | | "We have no money, therefore we must think" --Sir Ernest Rutherford | =========================================================================== From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!agate!spool.mu.edu!yale.edu!newsserver.jvnc.net!rutgers!spcvxb!6nguyen_p From: 6nguyen_p@spcvxb.spc.edu Newsgroups: bionet.software Subject: TurboTAX Message-ID: <1993Feb9.153023.5144@spcvxb.spc.edu> Date: 9 Feb 93 20:30:23 GMT Organization: St. Peter's College, US Lines: 8 To All Readers of Software: I was wondering if anybody could help me look for a software called Turbo Tax under windows or any tax forms software that I could used. The more recent software is the more appreciated I am. Thankyou. Michael From owner-software@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!agate!spool.mu.edu!uwm.edu!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!fly.bio.indiana.edu!gilbertd From: gilbertd@fly.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: IUBio Archive update Message-ID: Date: 9 Feb 93 21:22:22 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 64 Nntp-Posting-Host: fly.bio.indiana.edu The IUBio Archive is getting back to normal after a disk crash several days ago. The Drosophila Stock Center has replaced the dead disk with a new one. Here is a partial list of new information available at IUBio archive, either thru anonymous ftp or using Internet Gopher to ftp.bio.indiana.edu. New files in the IUBio-Software+Data section (or the ftp section) ...size...date.....path/name................ 326771 Dec 11 ./biology/ibmpc/ml.zip 4735 Feb 9 ./flybase/... 1828 Jan 19 ./molbio/codon/anopheles.codons 31413 Feb 3 ./molbio/data/rebase 306637 Jan 24 ./molbio/ibmpc/win-blast.zip 309633 Jan 24 ./molbio/ibmpc/win-irx.zip 60715 Dec 13 ./molbio/ibmpc/bed100.zip 81130 Dec 19 ./molbio/ibmpc/dprel3-0.zip 347703 Dec 4 ./molbio/loopdloop/loopdloop-update.hqx 1243157 Dec 31 ./molbio/mac/genconkit-demo/... 54027 Dec 1 ./molbio/mac/human-chromosomes.hqx 112664 Jan 25 ./molbio/mac/yeaststrain.hqx 105073 Jan 10 ./molbio/mac/digispeak122.hqx 172665 Feb 2 ./molbio/readseq/readseq.shar 41835 Dec 13 ./molbio/search/prosearch2.1.shar.Z 319 Feb 4 ./molbio/other/yeast-email.doc 226648 Jan 24 ./util/vms/vms-fileutils.uue Also, many of you have pledged funds to purchase an additional disk drive for this archive. I very much appreciate your support for this expansion. Enough money has been pledged to purchase an added gigabyte disk drive. As well, people at NSF and NIH have suggested I could seek funds thru supplements to existing grants here. There has been a very positive response from individuals and organizations around the world, to this request for funds to improve this archive. A disk drive purchased from your contributions will belong to the IUBio archive, for the first time, rather than to another project. These contributions are coming in now, and I hope to have enough to purchase the drive in the next few weeks. Until now IUBio Archive has lived in the goodwill part of cyberspace, finding its home in under-utilized portions of equipment. But it is now using a significant chunk of real resources, and those many of you who have pledged support for its new disk drive can be pleased to know you will provide this archive with a first real home of its own. If the archive should move to another computer (as it has moved 4 times in the past 4 years), then it will now be able to move with its own disk. Thank you, Don Gilbert -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!UM.CC.UMICH.EDU!Doug.Eernisse From: Doug.Eernisse@UM.CC.UMICH.EDU Newsgroups: bionet.software Subject: Re: PAUP and other software Message-ID: <19842055@um.cc.umich.edu> Date: 10 Feb 93 18:24:34 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 54 Because a few potentially misleading responses to "where to get PAUP" were posted recently, I will lift the following from a previous answer to this FAQ by Jochen Kleinschmidt: How to get PAUP (Phylogenetic Analysis Using Parsimony): > > The only up-to-date version of PAUP presently available is version 3.0s for > the Mac (dated Dec. 1991). I understand that David Swofford is also > working on an updated version for PC-DOS machines (under Windows?) as well > as on a universal graphical interface which will first be implemented in a > Unix version. > > Version 3.0s of PAUP for the Mac can be obtained from: > > David L. Swofford > c/o Mary Lou Williamson > Illinois Natural History Survey > 607 E. Peabody Drive > Champaign, ILL 61820, USA > Phone: 217-333-6846 > > Send to Mary Lou Williamson at the address above: (1) a check for $50.00 > ($60 outside North America) drawn on a U.S. bank and made out to the > University of Illinois/IHNS, or an International Money Order, (2) a note > stating that you understand that the present version of the User's Manual > is a draft that is incomplete in many parts, and that this is acceptable to > you. You will receive the program with manual within 2-3 weeks. A final > version of the manual will be sent to you once it is finished. > > PAUP is an excellent program that is quite usable even with the present > incomplete manual. It runs even on classic Macs. For $50, it is a > bargain. If you're in the habit of ripping off software companies by using > illegal copies of their products, DON'T do this with PAUP! David Swofford > provides a tremendous service to molecular phylogenists with this program, > and the amount he charges goes into a Univ. of Ill. account and is used > only to cover costs and pay for some upgrades in hardware and software that > make his life as a program developer easier. You wouldn't want the man to > get disgruntled and stop improving his program, an activity to which he > devotes a good amount of his time (undoubtedly too much, from his > perspective). The PAUP production is a one-man operation, and the reason > why it is somewhat inconvenient to obtain the program is simply because > David's use of a simple "cash sales" account keeps the price of the program > to a minimum. Overseas users are probably best off sending in an > International Money Order. It is true that David Swofford has moved to the Smithsonian, but I PAUP is still distributed by Illinois Natural History Survey, and should continue to be distributed by them. I wouldn't be so optimistic about the 2-3 weeks quoted above, however. I believe that he may want to delay as much as he can until 3.1 is available, to cut down on postage and diskettes. I don't know this for a fact, though. Doug Eernisse Museum of Zoology, Univ. of Michigan From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!CSC.FI!Rob.Harper From: Rob.Harper@CSC.FI (Rob Harper) Newsgroups: bionet.software Subject: First release of Gopher+ clients and server Message-ID: <199302101349.AA12115@csc.fi> Date: 10 Feb 93 13:49:29 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 162 Dateline: Minneapolis, MN 9 Feb 1993 The University of Minnesota Internet Gopher Team is pleased to announce the availability of first beta release of gopher+ clients and server. Now available for anonymous ftp from boombox.micro.umn.edu are: TurboGopher1.6b1 --- A Gopher+ client for the Macintosh available as /pub/gopher/Macintosh-TurboGopher/TurboGopher.1.06b1.hqx and gopher+1.2beta.tar.Z --- A Gopher+ client and server for Unix systems available as /pub/gopher/Unix/gopher+1.12.tar.Z After spending most of January eating turnips we have our first test release of Gopher+ software. However, not all features have been implemented yet, and there is plenty of testing to be done. You probably don't want to give this to everyone on your campus.... yet :-) Please, *Please*, Please send bug reports to gopher@boombox.micro.umn.edu Features currently implemented for TurboGopher ---------------------------------------------- Supports Multiple views of documents. Fetches item attributes (administrator, modification date etc.) Supports access to "Admit1" gopher+ servers (Admit1 is an extension to Gopher+ that allows secure authentication on a per user basis to servers using a ticketing scheme) User selectable helper applications for displaying alternate views and images. Support for JPEG, GIF, PICT, and sundry other image/document formats. Intelligent Gopher+ error handling. File retrieval status is displayed in a separate window for each retrieval. This makes it easy to terminate file retrievals or obtain status when several concurrent retrievals are active. Rudimentary support for ASK queries from the server. Features currently implemented for the UNIX client -------------------------------------------------- Intelligent Gopher+ error handling. Fetches item attributes (administrator, modification date etc.) Supports Multiple views of documents. Gripe command allows the user to complain to the specific adminstrator of a document. Configurable helper applications for displaying alternate views and images. More than rudimentary support for ASK queries from the server. Features currently implemented for the UNIX server -------------------------------------------------- Supports ASK blocks. Allows answers to multiple queries to be retrieved from a gopher+ client. Supports multiple views via configurable filename extension mapping. Basic Gopher+ error responses. Item attributes (administrator, abstracts, etc.) Very little documentation, but a bunch of examples Replacement code for .cap files. Gopher+ attribute registry -------------------------- The Gopher+ attribute is available via gopher on host Host=boombox.micro.umn.edu Port=70 Path=0/gopher/gopher_protocol/Gopher+/Gopher+AttributeRegistry This is also available via ftp to boombox.micro.umn.edu Gopher+ example server ---------------------- We are also running an example gopher+ example server. Connect to gopher.tc.umn.edu and select: Information about Gopher Gopher+ example server Note that the machine this points to will be changing soon. We will update the link to be current.. (i.e. don't depend on it being on mudhoney.micro.umn.edu) -- ~ Rob Harper ~ E-mail: harper@convex.csc.fi ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi ~ P.O. Box 40 ~ Telephone: +358 0 457 2076 ~ SF-02101 Espoo Finland ~ Fax: +358 0 457 2302 From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!NETCOM.COM!wick From: wick@NETCOM.COM (Potter Wickware) Newsgroups: bionet.software Subject: Re: PAUP and other software (fwd) Message-ID: Date: 10 Feb 93 16:59:17 GMT References: <199302101304.AA09683@csc.fi> Sender: daemon@net.bio.net Reply-To: Potter Wickware Distribution: bionet Lines: 11 DL Swofford Illinois Natural History Survey 607 E Peabody Dr Champaign, IL 61820 Ver 3.0a date 1991. Dec, which we got in Oct 92, was for Mac only; at that time they were "still working on" a PC version. From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!CSC.FI!Rob.Harper From: Rob.Harper@CSC.FI (Rob Harper) Newsgroups: bionet.software Subject: PAUP and other software (fwd) Message-ID: <199302101304.AA09683@csc.fi> Date: 10 Feb 93 13:04:44 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 25 %%%%%%%%%%%%%%%%%%%%%%% THIS WAS THE QUESTION %%%%%%%%%%%%%%%%%%%%%%%%%% > I can't seem to find a dang thing in my office. > > Could anybody send me David Swofford's address so I can order a recent > version of PAUP? > > The last version I had only worked on a MAC, does anyone know whether there > is an updated PC version? Can anyone recommend alternative software? I'm > particularly interested in anything shareware or PD that I could give to > my students. If such exists, is it available by FTP? > > Thanks in advance! > > > Randy Skelton an_rrs@lewis.umt.edu > Assistant Professor, Department of Anthropology > University of Montana, Missoula, MT, USA 59812 > (406) 243-4245 or 243-2693 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ~ Rob Harper ~ E-mail: harper@convex.csc.fi ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi ~ P.O. Box 40 ~ Telephone: +358 0 457 2076 ~ SF-02101 Espoo Finland ~ Fax: +358 0 457 2302 From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!darwin.sura.net!paladin.american.edu!howland.reston.ans.net!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!usenet.coe.montana.edu!news.uoregon.edu!news.u.washington.edu!carson.u.washington.edu!henikoff From: henikoff@carson.u.washington.edu (Steven Henikoff) Newsgroups: bionet.software Subject: Blocks e-mail searcher is back up Message-ID: <1l9r0rINNqbf@shelley.u.washington.edu> Date: 10 Feb 93 02:58:35 GMT Distribution: bionet Organization: University of Washington, Seattle Lines: 10 NNTP-Posting-Host: carson.u.washington.edu Since yesterday afternoon (Feb 8 PST) the Blocks e-mail searcher has been unavailable because of an unfortunate problem that occurred when some systems software was upgraded. Anyone sending a request to blocks@howard. fhcrc.org would have received a "mail loop error". Since requests were never received by the server and logged, we cannot know who this affected. However, the problem appears to have finally been tracked down and the server has been back in operation since late this afternoon (Feb 9 PST). Steve Henikoff Supriano Agus From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!usenet.ins.cwru.edu!howland.reston.ans.net!usc!sdd.hp.com!caen!umeecs!yale!yale.edu!newsserver.jvnc.net!netnews.upenn.edu!duong From: duong@chestnut.chem.upenn.edu (Duc Duong) Newsgroups: bionet.software,bionet.molbio.proteins Subject: Software to display peptide planes structures? Message-ID: <108912@netnews.upenn.edu> Date: 10 Feb 93 15:16:00 GMT Sender: news@netnews.upenn.edu Followup-To: bionet.software Organization: NMR Biochemistry Graduate Research Lab Lines: 10 Xref: biosci bionet.software:4157 bionet.molbio.proteins:515 Nntp-Posting-Host: chestnut.chem.upenn.edu hi.. I am urgently looking for a software (PD or comercial) that read in the alpha, and beta angles of the peptide planes then display or print it out on the paper as retangular planes.. The structure of the peptides we have determined can of course be hand drawing but We have a punches of them and they are in 3Dimension.. So are there such a software? E-mail please. Thank you.. duc From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!s.u-tokyo!kuis!wnoc-kyo!icspub!oskgate0.mei!chorus.mei!adagio.panasonic.com!sgiblab!sdd.hp.com!cs.utexas.edu!usc!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!chipmunk.bio.indiana.edu!gilbertd From: gilbertd@chipmunk.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Gopher+ server at IUBio Archive Message-ID: Date: 10 Feb 93 15:52:06 GMT References: <199302101349.AA12115@csc.fi> Sender: news@usenet.ucs.indiana.edu (USENET News System) Distribution: bionet Organization: Biology, Indiana University - Bloomington Lines: 27 Nntp-Posting-Host: chipmunk.bio.indiana.edu Those of you who want to try out Gopher+ can do so now with one of the previously mentioned gopher clients pointed to the IUBio Gopher+ archive. This is available for testing on port 140 (instead of the standard port 70) at ftp.bio.indiana.edu. From the Unix gopher+ client: gopher ftp.bio.indiana.edu 140 In the Mac TurboGopher+ client: Choose File/Another Gopher... Server name: ftp.bio.indiana.edu Server port: 140 check is a gopher+ server The only gopher+ goodies available now are in the folder This-Gopher/Gopher+-Examples/. I'll be adding more Gopher+ features over the coming weeks here, and eventually will shift the Archive to all Gopher+ (also useable thru the older format clients) at port 70. -- Don -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!CSC.FI!Rob.Harper From: Rob.Harper@CSC.FI (Rob Harper) Newsgroups: bionet.software Subject: Re: PAUP and other software (fwd) Message-ID: <199302101306.AA09784@csc.fi> Date: 10 Feb 93 13:06:05 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 %%%%%%%%%%%%%%%%%%%%%%%%% THIS WAS THE REPLY %%%%%%%%%%%%%%%%%%%%%%%%%%%% > >Could anybody send me David Swofford's address so I can order a recent > >version of PAUP? > > If anybody else is looking for me, the new address, etc., is below. > > Dave > --------------------------------------------------------------------- > David L. Swofford Internet: swofford@onyx.si.edu > Laboratory of Molecular Systematics > MRC 534, MSC > Smithsonian Institution Voice: (301)238-3444 > Washington, D.C. 20560 USA FAX: (301)238-3059 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ~ Rob Harper ~ E-mail: harper@convex.csc.fi ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi ~ P.O. Box 40 ~ Telephone: +358 0 457 2076 ~ SF-02101 Espoo Finland ~ Fax: +358 0 457 2302 From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: zang@rz.uni-sb.de (Klaus Piontek) Newsgroups: bionet.software Subject: SLIP Software Message-ID: <1993Feb10.131024.19155@gserv1.dl.ac.uk> Date: 10 Feb 93 13:09:49 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 9 Original-To: bio-software@uk.ac.daresbury I'm looking for software (especially shareware) that supports SLIP (Serial Line IP). I heard about MacSlip and VersaTerm but i don't know exactly. If someomne knows a good software package please tell me. Klaus Piontek Institute of Human Gentics University of the Saar Germany Fax: 49 - 6841- 16 6600 e-mail: zang@rz.uni-sb.de From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: zang@rz.uni-sb.de (Klaus Piontek) Newsgroups: bionet.software Subject: SLIP Software Message-ID: <1993Feb10.130415.18839@gserv1.dl.ac.uk> Date: 10 Feb 93 13:02:45 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 1 Original-To: bio-software@uk.ac.daresbury I'm looking for any software (espiacelly[D From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: zang@rz.uni-sb.de (Klaus Piontek) Newsgroups: bionet.software Subject: SLIP Software Message-ID: <1993Feb10.115537.16107@gserv1.dl.ac.uk> Date: 10 Feb 93 11:53:23 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 1 Original-To: bio-software@uk.ac.daresbury I^m. From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!higgins From: higgins@embl-heidelberg.de Newsgroups: bionet.software Subject: ClustalV on Silicon Graphics machines Message-ID: <1993Feb10.155305.70186@embl-heidelberg.de> Date: 10 Feb 93 14:53:05 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 23 Some time back: ray@le.ac.uk asked how to make ClustalV run properly on SGI machines. I apologise for the delay in replying; the fix turned out to be very simple. All source files should be compiled with the switch: -signed This can be accomplished by changing the ultrix makefile (makefile.ult) as follows: The line: CFLAGS = -c should be changed to: CFLAGS = -c -signed and then make this with: make -f makefile.ult Again, I apologise to all disgruntled SGI owners for the core dumps. Des Higgins EMBL Heidelberg Germany. From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!zaphod.mps.ohio-state.edu!malgudi.oar.net!caen!nic.umass.edu!noc.near.net!saturn.caps.maine.edu!dartvax!Robert.H.Gross From: Robert.H.Gross@dartmouth.edu (Bob Gross) Newsgroups: bionet.software Subject: Re: Tm prediction : more Message-ID: Date: 10 Feb 93 18:38:25 GMT References: <1993Feb8.190445.1@hkucc.hku.hk> Sender: news@dartvax.dartmouth.edu (The News Manager) Organization: Dartmouth College, Hanover, NH Lines: 16 X-Posted-From: InterNews1.0b9@newshost.dartmouth.edu I stand corrected. Thanks Darren. I guess the definition of Tm can be a little fuzzy. For example, if I take a solution of specific DNA (eg pBR322) and follow hypochromicity (decrease in absorbance) as the temperature is gradually increased, I will get a curve, the midpoint of which is the Tm. This midpoint will be the same temperature no matter what my starting DNA concentration is. Isn't that true? In other words, at a given temperature, a certain fraction of the DNA is denatured. The reverse reaction of reannealing the single strands is concentration dependent since the frequency of collisions between DNA molecules will vary with concentration. But if Tm is the temparature at which 50% of the DNA molecules have denatured, is this concentration dependent? Bob Gross Dept. of Biology, Dartmouth College bob.gross@dartmouth.edu From owner-software@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!stanford.edu!rock!concert!gatech!udel!bogus.sura.net!howland.reston.ans.net!sol.ctr.columbia.edu!The-Star.honeywell.com!umn.edu!gaia.ucs.orst.edu!ucs.orst.edu!chend From: chend@ucs.orst.edu (Donald Chen - Microbiology) Newsgroups: bionet.software Subject: win-blast/win-irx files from IUBIO Keywords: win-blast, win-irx, pkzip files Message-ID: <1lbgvbINN55b@gaia.ucs.orst.edu> Date: 10 Feb 93 18:19:23 GMT Organization: University Computing Services - OSU Lines: 18 NNTP-Posting-Host: ucs.orst.edu Hi: I've tried to download the zip files win-blast.zip and win-irx.zip from the IUBIO archives. When I finally get them to my home computer and try to unzip them, I get a response which says that the files can't be unzipped and I should fix them with pkfix (which I gather is not available for downloading). I set all the binary types for both ftp and kermit so I don't