From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!reuter.cse.ogi.edu!netnews.cc.wwu.edu!netnews.nwnet.net!news.u.washington.edu!hobbes!sanjay From: "Sanjaya N. Joshi" Newsgroups: bionet.molbio.proteins,bionet.software Subject: Re: Programs for schematic drawings of proteins? Date: Thu, 1 Jun 1995 16:31:57 -0700 Organization: University of Washington Lines: 82 Message-ID: References: <3goein$e5i@helka.iif.hu> <3qhv1v$de1@winx03.informatik.uni-wuerzburg.de> <1995May31.212051.16977@ucl.ac.uk> NNTP-Posting-Host: nntp4.u.washington.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: sanjay@hobbes In-Reply-To: <1995May31.212051.16977@ucl.ac.uk> Xref: biosci bionet.molbio.proteins:4702 bionet.software:12238 OOPS!! I mistakenly replied to the "Re: Protein adsorption" message. Sorry!! I will repeat the message: I think "rasmol" ftp forte.mathematik.uni-bremen.de /pub/unix/visualization/rasmol OR ftp ftp.uni-stuttgart.de /pub/scivi/chemie/rasmol will do that (at least the ribbon or ball-stick model of the H bond). It will also convert the pseudo 3D image from the "pdb" structure data file to a GIF image format, which can then be printed (color/grayscale) _________ _________ ____sanjay@hobbes.chmc.org_________ / /| / /| / / | / / | Sanjaya Joshi /--------/ | /--------/ | Department of Radiology, CH-69 | | <|------| | | Children's Hospital & Med. Ctr. | A |--/----->| B | / Seattle, Washington 98105 | | / | | / (206) 528-2744 |________|/ |________|/ And networks for all ................................................ On Wed, 31 May 1995, Rob Miller wrote: > Geier Gerhard (b049@mail.fh-wuerzburg.de) wrote: > : In article <3goein$e5i@helka.iif.hu>, szia@enzim.hu says... > : > > : >I am looking for programs that can draw schematic drawings of protein > : >structures. I am interested in the following two types of drawings: > : > > : > (1) schematic representation of the [main chain] hydrogen bonding > : >pattern (based on known 3D structure) > : > > : > (2) schematic representation of the domain structure and > : >disulfide bonding pattern, using a chain of several circles, each circle > : >representing a residue, and the type of the residue written in the > : >circle. This chain of circles is folded in 2D to approximately represent > : >the domain structure and the disulfide bonding pattern. > : > > : >Such drawings often appear in journals but I don't know any program that > : >can easily draw such things. (As to the hydrogen bonding pattern, I heard > : >of a program called HERA but I have no idea how to get it.) > : > > : >Anyone can help? > : > > : >Andras Szilagyi (szia@enzim.hu) > : >Institute of Enzymology, Hungarian Academy of Sciences > : > > > : If you have found a program who is able to draw that, pleas sent me seh name > : of the program and the name of the server > : Thanks in forward > : Gerhard Geier > > > I think Gail Hutchinson's PROMOTIF is what you are interested in. It is > available by anonymous ftp on 128.40.46.11, but you will need to sign > a confidentiality agreement. See pages on it and our other bioinformatics > software at http://www.biochem.ucl.ac.uk/bsm/index.html > > > rob. > > > > > -- > ------------------------------------------------------- > Rob Miller, Ph.D. > > Biomolecular Structure and Modelling Unit (BSM), > Department of Biochemistry and Molecular Biology, > University College / Gower Street / London WC1E 6BT. > United Kingdom. > > Tel: 44 171380 7777 x3896 > Fax: 44 171380 7193 > > Internet: rmiller@bsm.bioc.ucl.ac.uk > http://www.biochem.ucl.ac.uk/~rmiller > ------------------------------------------------------- > > From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!news.clark.net!NewsWatcher!user From: douglas@clark.net (Douglas Hale) Newsgroups: bionet.software Subject: Power Date: Thu, 01 Jun 1995 21:34:11 -0400 Organization: Clark Internet Services, Inc. Lines: 2 Message-ID: NNTP-Posting-Host: douglas-ppp.clark.net Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Is anyone aware of any mac software that can do power analysis/sample size determination. Thank you. From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!CORNELL.EDU!gma2 From: gma2@CORNELL.EDU (Gregory M. Acland) Newsgroups: bionet.software Subject: Re: Mac PostScript converter/viewer Date: 2 Jun 1995 05:18:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Re: 1.lpss@unixg.ubc.ca (Alex Chang) wrote: > I am looking for a Mac PostScript converter or viewer 2. Andy.Law @ bbsrc.ac.uk wrote > There is a rather flaky Mac version of Ghostscript around Ghostscript is huge (10 Mb?) slow and awful, not practically useful. Showpages is around at most sites and is a great print only utility, supports drag and drop. Gregory M. Acland (607) 256-5684 [phone] Center for Canine Genetics & Reproduction (607) 256-5689 [fax] James A. Baker Institute for Animal Health gma2@cornell.edu College of Veterinary Medicine Cornell University Hungerford Hill Rd, Ithaca, New York 14853 From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!news.sprintlink.net!demon!uknet!gdt!bsspak From: bsspak@bath.ac.uk (P A Keller) Subject: Re: General Bio Software Message-ID: Reply-To: P.A.Keller@bath.ac.uk Organization: Collaborative Computational Project 4, Daresbury Laboratory, UK References: Date: Fri, 2 Jun 1995 14:09:13 GMT Lines: 28 In the referenced article, wmcqueen@infolane.com (Will McQueen) writes: >Hello, all! > [snip] > Any ideas? This is the only newsgroup I could find where this type of >posting would be appropriate. Do you know of any others? WWW sites, >perhaps? FTP? Anything. Thanks! > I don't know this package in any detail, but the Pharmacy School here at Bath has developed software for computer-aided distance learning. Try the URL http://www.bath.ac.uk/PCCAL/ . Have fun, Peter. ======================================================================== Peter Keller. \ Dept. of Biology and \ "Not even the greatest nonsense is beyond Biochemistry, \ the reach of human invention." University of Bath, \ Bath, BA2 7AY, UK. \ --- Ryszard Kapuscinski ------------------------------\----------------------------------------- Tel. (+44/0)1225 826826 x 4302 | Email: P.A.Keller@bath.ac.uk (Internet) Fax. (+44/0)1225 826449 | P.A.Keller%bath.ac.uk@UKACRL (BITNET) ======================================================================== From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.starnet.net!wupost!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!osi-east2.es.net!oracle.pnl.gov!mica.inel.gov!cwis.isu.edu!news.cc.utah.edu!zifi.genetics.utah.edu!zinc From: zinc@zifi.genetics.utah.edu (zinc) Newsgroups: bionet.software Subject: Re: PGP software Date: 1 Jun 1995 15:12:05 GMT Organization: assorted dsRNAs and lotsa zinc Lines: 49 Message-ID: <3qklc5$ek6@news.cc.utah.edu> References: <3qj3ev$oqg@ixnews4.ix.netcom.com> NNTP-Posting-Host: zifi.genetics.utah.edu -----BEGIN PGP SIGNED MESSAGE----- In article <3qj3ev$oqg@ixnews4.ix.netcom.com>, Craig Franklin wrote: >I am looking for a software package called PGP. I stands for Pretty >Good Protection. It would be an incredible help to me if someone has >it and could get back to me on it. I am willing to trade other >software. Thanks a lot. >cfrank@ix.netcom.com > pgp is available to us and canadian citizens under the laws/rules of ITAR. it may be found at net-dist.mit.edu (i believe that is the correct site). here's what you have to do: telnet to net-dist.mit.edu log on as getpgp and answer the questions if you answer all of the questions correctly you will be told the name of the hidden directory where pgp is kept. after you get that name, ftp to net-dist.mit.edu, log on as anonymous, cd to the appropriate dir and d/l the appropriate version of pgp. there is a newsgroup dedicated to pgp, alt.security.pgp as well as several www pages. write if you need more info. - -zinc -----BEGIN PGP SIGNATURE----- Version: 2.6.2 iQCVAwUBL83Zkk3Qo/lG0AH5AQH5AwP9GsarLfUwCe2vzvaAQnyHisz/iARBLc/R HxYYukueURDn8bMTLyV5O6t+qmZ8UQSoKamIqSfo3/WsnR0IuDaJsB14rgOiwI5D DbNJk234KBgZWBeHCciYk5kHoA5Gh1ZXSLPSYBq1bTJKcJ9haiud5ffztOxuPdnj ArxZzsKN7jc= =9e7a -----END PGP SIGNATURE----- -- patrick finerty -- finerty@msscc.med.utah.edu pfinerty@nyx10.cs.du.edu U of Utah biochem grad student/slave in the Bass lab easily found at (801) 585-3110 almost anytime. rm 207 wintrobe. From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!demon!uknet!sunsite.doc.ic.ac.uk!daresbury!is.bbsrc.ac.uk!pc0519.ri.bbsrc.ac.uk!user From: Andy.Law@bbsrc.ac.uk (Andy Law (Big Nose)) Newsgroups: bionet.software Subject: Re: Mac PostScript converter/viewer Date: Fri, 02 Jun 1995 09:40:37 +0000 Organization: Roslin Institute Lines: 19 Message-ID: References: <3qlcd7$1us@nnrp.ucs.ubc.ca> NNTP-Posting-Host: pc0519.ri.bbsrc.ac.uk X-Newsreader: Value-Added NewsWatcher 2.0b24.0+ In article <3qlcd7$1us@nnrp.ucs.ubc.ca>, lpss@unixg.ubc.ca (Alex Chang) wrote: > Dear netter: > > I am looking for a Mac PostScript converter or viewer, in order to read > PostScript files using Mac computer. I'll appreciate if someone could > provide that information, esp. a noncommercial program. > > There is a rather flaky Mac version of Ghostscript around on the info-mac archives somewhere I think. It is free, but it's not that good. I can't remember offhand if it is called GhostScript or GhostView. Try an archie search for both and see what it spits out. -- Andy Law ( Andy.Law @ bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!news.primenet.com!ip168.phx.primenet.com!llward From: llward@primenet.com (larry ward) Newsgroups: bionet.software Subject: need multivariate analysis software Date: Thu, 1 Jun 1995 22:43:05 MST Organization: Primenet Lines: 4 Message-ID: NNTP-Posting-Host: ip168.phx.primenet.com X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] if you know of a statistical package that does multivariate, logistic regression, please email with details. fyi i have data in excel & paradox for windows, can import/export to ascii etc. Thanks. -Larry Ward, MD From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!sunserver.insinc.net!news.Direct.CA!scipio.cyberstore.ca!vanbc.wimsey.com!unixg.ubc.ca!news.bc.net!rover.ucs.ualberta.ca!news.sas.ab.ca!freenet.edmonton.ab.ca!hbestman From: hbestman@freenet.edmonton.ab.ca () Newsgroups: bionet.software Subject: Image analysis software for PC Date: 2 Jun 1995 05:01:12 GMT Organization: Edmonton Freenet, Edmonton, Alberta, Canada Lines: 13 Message-ID: <3qm5uo$8q9@news.sas.ab.ca> NNTP-Posting-Host: freenet.edmonton.ab.ca X-Newsreader: TIN [version 1.2 PL2.2E] I am in the process of acquiring frame grabbing and image analysis software. The two systems that I have been looking at is the MOCHA software and the CONCEPT V.i from Graftek. The latter can be integrated with LABVIEW (which we have already). My particular application requires that the image be displayed on the computer screen, and then be captured, and analyzed. Does anyone have any experience with these two systems, or any other ones. I sure would appreciate some help. Please email me at: hbestman@kingsu.ab.ca Thanks. -- HANK BESTMAN email: hbestman@freenet.edmonton.ab.ca From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!helium.gas.uug.arizona.edu!bear From: bear@helium.gas.uug.arizona.edu (Soaring Bear) Newsgroups: bionet.software Subject: Re: helical wheel program Date: 2 Jun 1995 22:42:02 GMT Organization: University of Arizona, Unix Users Group Lines: 18 Message-ID: <3qo43q$d3m@news.ccit.arizona.edu> References: NNTP-Posting-Host: helium.gas.uug.arizona.edu In article , Nik Veldhoen wrote: > In discussions of amino acid positioning and function along an alpha >helix, a helical wheel diagram is sometimes desirable. Unfortunately, I >and my collegues have not been able to find a simple Mac program that >creates and positions an amino acid sequence along a helical wheel. If >anyone has or knows of Mac freeware or shareware that can create these >schematic diagrams, please let me know at nveldhoe@sol.uvic.ca. Thanks. >Nik Veldhoen In the same vein, how about a unix version, please? -- topo-O O-topo URL http://copsg2.pharm.arizona.edu/~bear/top/top 5'**. : : .***. ___ __ Cyber-Chemist: cancer drug design | | *. .* | | |* (___ l .) Molecular & Nutritional Biochemist | | | *. * | | | * ___)OARING |__)EAR Herbs, Nutrition, Natural Dentistry From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!news From: dalehn@facstaff.wisc.edu (Donald A. Lehn, Ph.D.) Newsgroups: bionet.software Subject: Re: "The Scientist" is looking for the best freeware and shareware Date: 2 Jun 1995 20:26:05 GMT Organization: University of Wisconsin Medical School Lines: 19 Message-ID: <3qns4t$7io@news.doit.wisc.edu> References: NNTP-Posting-Host: islet.medsch.wisc.edu X-Newsreader: WinVN 0.99.3 In article , finn@netcom.com says... > > I would nominate MACAW (Multiple Alignment Construction and Analysis Workbench) by Greg Schuler at NCBI/NLM/NIH It is a great program for sequence alignments and is available in Windows, WindowsNT and Mac versions. Don -- Donald A. Lehn, Ph.D. Phone: (608) 263-7668 Medical Sciences Center / 3415 Fax: (608) 262-9300 University of Wisconsin Medical School Email: dalehn@facstaff.wisc.edu 1300 University Avenue Home: (608) 277-1025 Madison, WI 53706-1532 Diabetes Knowledgebase: http://www.biostat.wisc.edu/diaknow/index.htm From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Newsgroups: bionet.software Path: biosci!rutgers!utcsri!info.physics.utoronto.ca!utzoo!mes From: mes@zoo.toronto.edu (Mark Siddall) Subject: Re: PAUP Message-ID: Date: Fri, 2 Jun 1995 05:21:30 GMT References: <3qfcbr$sd6@portal.gmu.edu> Organization: U of Toronto Zoology Lines: 30 In article <3qfcbr$sd6@portal.gmu.edu> herwin@osf1.gmu.edu (HARRY R. ERWIN) writes: >Any sign yet of the commercial version of PAUP? I understand Sinauer will >handle the marketing. > Yes indeed. Swofford is presenttly in the pre-beta-test stage of version 4 of PAUP. I am participating in this testing and can give you the following: 1) it is likely to be available in the late summer or early fall but there is no date yet. Anything can happen. Dave is working very very hard. 2) it will be distributed by Sinauer (if the welcome screen is any indication). 3) there is a Mac version, a PowerPC(PowerMac) version and a DOS version. (I believe the latter will be compilable on a SUN but I am not certain of this). 4) it includes parsimony, maximum likelihood, and Neibor Joining algorithms. 5) it is much faster than versions 3 and earlier. Hope this helps. I am sure there will be an appropriate announcement in this and relevant newsgroups when it is available. Mark -- Mark E. Siddall "I don't mind a parasite... mes@vims.edu I object to a cut-rate one" Virginia Inst. Marine Sci. - Rick Gloucester Point, VA, 23062 From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!demon!uknet!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: PGP software Message-ID: <1995Jun2.173225.16636@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <3qj3ev$oqg@ixnews4.ix.netcom.com> <3qklc5$ek6@news.cc.utah.edu> Date: Fri, 2 Jun 1995 17:32:25 GMT Lines: 33 zinc (zinc@zifi.genetics.utah.edu) wrote: : In article <3qj3ev$oqg@ixnews4.ix.netcom.com>, : Craig Franklin wrote: : >I am looking for a software package called PGP. I stands for Pretty : >Good Protection. It would be an incredible help to me if someone has : >it and could get back to me on it. I am willing to trade other : >software. Thanks a lot. : >cfrank@ix.netcom.com : > PGP stands for Pretty Good Privacy. : pgp is available to us and canadian citizens under the laws/rules of : ITAR. it may be found at net-dist.mit.edu (i believe that is the : correct site). To my information, this is not entirely correct. "PGP is completely legal to use everywhere in the world, as long as you get it from the right place and as long as your nation does not outlaw the use of strong crypto. You can't export it from the United States or Canada, but it's available from places all over the world. " quote from http://draco.centerline.com:8080/~franl/pgp/ Regards Reinhard Doelz EMBnet Switzerland -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!howland.reston.ans.net!sol.ctr.columbia.edu!news.mindlink.net!vanbc.wimsey.com!unixg.ubc.ca!hochac From: hochac@bcu.ubc.ca (Wesley "Hoocher" Hochachka) Newsgroups: bionet.software Subject: Re: Power Date: 2 Jun 1995 17:16:20 GMT Organization: The University of British Columbia Lines: 12 Message-ID: <3qnh14$9qc@nntp.ucs.ubc.ca> References: NNTP-Posting-Host: light.bcu.ubc.ca X-Newsreader: TIN [version 1.2 PL2] Douglas Hale (douglas@clark.net) wrote: : Is anyone aware of any mac software that can do power analysis/sample size : determination. Thank you. Have a look at JMP from the nice people who brought you SAS. It's a really nice conventional/exploratory data analysis package, with a heavy emphasis on graphical presentation of results and analyses. It also does power analysis for t-tests, ANOVAs of various sorts, and (I think) contingency tables. The power analyses tell you statistical power for a given data set, as well as sample sizes needed to obtain reasonable power from a given data set. AND the whole package is a lot less user-hostile than SAS. Wesley Hochachka From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!lamarck.sura.net!sprout.nalusda.gov!usenet From: Doug Bigwood Newsgroups: bionet.software Subject: Re: "The Scientist" is looking for the best freeware and shareware Date: 2 Jun 1995 15:45:43 GMT Organization: Genome Informatics Group Lines: 20 Message-ID: <3qnbn7$haq@sprout.nalusda.gov> References: NNTP-Posting-Host: locus.nalusda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3_U1 sun4m) To: finn@netcom.com X-URL: news:finnD93Jnz.4Ey@netcom.com Dear Robert: I would like to suggest that ACeDB is perhaps the best freeware available for those working in genome analysis. We use this software extensively in making genome data available on the Internet. We have extensive documentation on ACeDB on our WWW server (http://probe.nalusda.gov:8000/acedocs/index.html). I hope this is helpful information for your article. Doug -------------------------------------------------------------------------- Douglas W. Bigwood, Ph.D. Manager, Genome Informatics Group USDA, NAL, ISD Voice: 301-504-6813 10301 Baltmore Blvd. Fax: 301-504-7473 Beltsville, MD 20705 Internet: dbigwood@nalusda.gov -------------------------------------------------------------------------- From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news2.near.net!das-news2.harvard.edu!fas-news.harvard.edu!lipid!robison From: robison@lipid.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: Re: Mac PostScript converter/viewer Date: 2 Jun 1995 13:53:03 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 25 Message-ID: <3qn53v$g7e@decaxp.harvard.edu> References: <3qlcd7$1us@nnrp.ucs.ubc.ca> NNTP-Posting-Host: lipid.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Alex Chang (lpss@unixg.ubc.ca) wrote: : Dear netter: : I am looking for a Mac PostScript converter or viewer, in order to read : PostScript files using Mac computer. I'll appreciate if someone could : provide that information, esp. a noncommercial program. Adobe Distiller & Acrobat is one solution, though its probably not quite what you are looking for. Distiller converts your PostScript file into something called Portable Document Format (PDF). Distiller is not free -- but the Acrobat viewer is (in fact, you can get the viewer from ftp.adobe.com). So, if your need is to distribute PostScript documents to multiple Macs for viewing, this might be a reasonable solution. For general PostScript viewing, it probably isn't. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@mito.harvard.edu From owner-software@net.bio.net Thu Jun 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!osi-east2.es.net!oracle.pnl.gov!mica.inel.gov!cwis.isu.edu!news.cc.utah.edu!zifi.genetics.utah.edu!zinc From: zinc@zifi.genetics.utah.edu (zinc) Newsgroups: bionet.software Subject: Re: Mac PostScript converter/viewer Date: 2 Jun 1995 03:03:34 GMT Organization: assorted dsRNAs and lotsa zinc Lines: 36 Message-ID: <3qlv26$1vi@news.cc.utah.edu> References: <3qlcd7$1us@nnrp.ucs.ubc.ca> NNTP-Posting-Host: zifi.genetics.utah.edu -----BEGIN PGP SIGNED MESSAGE----- In article <3qlcd7$1us@nnrp.ucs.ubc.ca>, Alex Chang wrote: >Dear netter: > >I am looking for a Mac PostScript converter or viewer, in order to read >PostScript files using Mac computer. I'll appreciate if someone could >provide that information, esp. a noncommercial program. Alex Chang, ghostscript is available for the mac and allows viewing of all sorts of postscript files. sorry, i don't know the location but i'm sure an archie or gopher search will turn it up. if not, write me and i'll send it your way or make it avail via ftp. ciao, - -pjf -----BEGIN PGP SIGNATURE----- Version: 2.6.2 iQCVAwUBL86AaE3Qo/lG0AH5AQEimAP/cfm9t17RhBvjU40kpVYI0haukpeT1vRo lmgMub6ev81RHV6ok1YzZoBJVCbqNBand4miC3Eq2CReZuIub+SpbPmsuHTZparH S8yici8zqZHesJA6jf1EwjC9jnt+hG/nTsKSsPwVooPlioJyPuUTywKSFxLq7UOb 6DBVCDJawPE= =eEyU -----END PGP SIGNATURE----- -- patrick finerty -- finerty@msscc.med.utah.edu pfinerty@nyx10.cs.du.edu U of Utah biochem grad student/slave in the Bass lab easily found at (801) 585-3110 almost anytime. rm 207 wintrobe. From owner-software@net.bio.net Fri Jun 02 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!cs.utexas.edu!geraldo.cc.utexas.edu!netnews.uthscsa.edu!usenet From: griess@uthscsa.edu (Gary Griess) Newsgroups: bionet.software Subject: Re: Mac PostScript converter/viewer Date: 3 Jun 1995 20:34:23 GMT Organization: U.T.Health Science Center Lines: 7 Sender: Griess@thorin.uthscsa.edu Message-ID: <3qqh0f$bev@cosmos.uthscsa.edu> References: <3qlcd7$1us@nnrp.ucs.ubc.ca> NNTP-Posting-Host: phage.uthscsa.edu X-Posted-From: InterNews 1.0.5@phage.uthscsa.edu X-Authenticated: Griess on POP host thorin.uthscsa.edu MacLPR is a nifty drag-and-drop application for Macs that converts and sends Postscript files to your printer. Gary A. Griess Biochemistry Dept. U.T. Health Science Center San Antonio, TX 78284 From owner-software@net.bio.net Sat Jun 03 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sun2!sun1.iusb.edu!kchaudhr From: kchaudhr@sun1.iusb.edu ("Akoona Matata") Subject: Re: Help with Runtime [toolbook] Message-ID: Sender: usenet@sun2.iusb.indiana.edu (USENET poster) Nntp-Posting-Host: sun1.iusb.indiana.edu Organization: Indiana University South Bend Date: Sun, 4 Jun 1995 03:54:26 GMT Lines: 16 Hi, I am trying to run the runtime.exe which will play or read tbk files but, when ever I install runtime and try to run it through file mangaer I get the following messge "Cannot run without a book. A book must be specified" Could any one please help me out and tell me what I need to do to get this thing going. You can leave me mail at kchaudhr@sun1.iusb.indiana.edu Any responce will be greatly appreciated Regards From owner-software@net.bio.net Sat Jun 03 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!univ-lyon1.fr!jussieu.fr!oleane!pipex!sunic!sunic.sunet.se!news.funet.fi!ousrvr.oulu.fi!ppc.oulu.fi!user From: mhaveri@cc.oulu.fi (Matti Haveri) Newsgroups: bionet.software Subject: Re: Mac PostScript converter/viewer Date: Sun, 04 Jun 1995 20:40:17 +0200 Organization: University of Oulu Lines: 13 Message-ID: References: <3qlcd7$1us@nnrp.ucs.ubc.ca> NNTP-Posting-Host: ppc.oulu.fi Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit :I am looking for a Mac PostScript converter or viewer, in order to read :PostScript files using Mac computer. I'll appreciate if someone could :provide that information, esp. a noncommercial program. For viewing this is the best at the moment. It doesn't support printing yet. For printing: -Matti Haveri From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Newsgroups: bionet.software,bionet.general Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!newsserver.jvnc.net!newsserver2.jvnc.net!netnews.upenn.edu!msunews!harbinger.cc.monash.edu.au!news.cs.su.oz.au!inferno.mpx.com.au!metro!news From: sfletche@extro.ucc.su.OZ.AU Subject: Re: Refman vs Endnote Content-Type: TEXT/PLAIN; charset=US-ASCII Message-ID: Lines: 63 Sender: news@ucc.su.OZ.AU Nntp-Posting-Host: ts-h08-15-47.ucc.su.oz.au Organization: Information Services, Sydney University, Sydney, NSW, Australia X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage References: <3q3ulq$gq3@lyra.csx.cam.ac.uk> Mime-Version: 1.0 Date: Tue, 30 May 1995 07:36:08 GMT Xref: biosci bionet.software:12258 bionet.general:15583 > > >For you diehard Windows users, I got the latest newsletter and they saw that > >the Windows version is in the last phase of testing. They don't give a > >release date, but say that upgrades will be $49 + shipping for users of the > >DOS version and suggested list price of the new version $299. > > Alternatively Refs and WinRefer together will give you almost the same > functionality and cost you only $47.99 or 29.99 UKP. These packages > are both available for ftp from: > > ftp://cyclin.zoo.cam.ac.uk/pub/refs/refs772.zip > ftp://cyclin.zoo.cam.ac.uk/pub/refs/extra/wr30.zip > > There is a WWW page with screen shots of Refs so you don't even have > to try it out to see what the interface is like: > > http://cyclin.zoo.cam.ac.uk/refs/refs.html > > Refs is available in four languages: English, German, Spanish and > Japanese. > > Regards, > > Tim. > Yes I am a die hard windows user. I almost decided to bugger the stuffing around, and just get endnote today, as people have given the best response regarding this product, but I found out it wasn't windows. I stood at the counter, money in hand, saying "NOT WINDOWS?????...NO WINDOWS VERSION??????" and the guy said, "You like Windoze?"... "YEAH!!!".... "Yeah, I guess it's more user friendly than dos".... then I was about to start up a discussion on the advantages of multitasking but thought, bugger it. Basically Refs seems great. From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!gatech!sdd.hp.com!spool.mu.edu!uwm.edu!msunews!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!chuynh From: chuynh@morgan.angis.su.oz.au (Camson Huynh) Subject: ANNOUNCEMENT: ShadyBox version 2.0.1 Message-ID: Sender: news@ucc.su.OZ.AU Nntp-Posting-Host: morgan.angis.su.oz.au Organization: ANGIS X-Newsreader: xrn 7.00 (Motif) Date: Mon, 5 Jun 1995 02:37:57 GMT Lines: 98 ShadyBox Version 2.0.1 ---------------------- ShadyBox is a drawing program which enables you to box and shade regular and irregular shaped segments of aligned multiple sequences. It was designed with the intention of producing PostScript output suitable for use in publications. Version 2.0.1 was implemented with colour features. It is now possible to colour regions of sequences, individual residues or residues of specified frequency. Regions may be shaded with colour or the residues themselves may be coloured. GreyScale is available for those wishing to use it. ShadyBox accepts either an MSF (Multiple Sequence File), a Pretty or a Macaw formats. MSF files are produced by the GCG program Pileup or by ClustalW. Pretty files are produced by the GCG program Pretty and may include a consensus sequence. Macaw files are produced by the Macintosh multiple sequence alignment program, Macaw. ShadyBox allows you to generate a PostScript file in which you can display and print the box and shade regions. NEW FEATURES AND FIXES ---------------------- * scrolling fixed, also scrollbars now is static. * resize events, expose events of drawing area fixed. * redisplay of sequences after expose or resize events fixed. * undo a clear function fixed. * bug in boxall fixed. * bug in load saved file fixed. * bug in load previously saved boxall figures fixed. * some of the memory problems fixed. * lots of minor bug fixes. New Features in version 2.0.1: * ShadyBox now supports colour shades, colour residues, etc.... * New functions added. For a list of new functions, see shadyboxes.txt help. * Uses a DYNAMIC COLOUR SCALE supplied by libXG.a enhancement version. * Uses SHADYBOX_HLPDIR environment variable to track shadyboxes.txt help. * Uses SHADYBOX_ALSDIR environment variable to track alscript programs. * Uses SHADYBOX_PS environment variable for external postscript viewer. It's default is ghostview. COPYRIGHT --------- ShadyBox Version 2.0.1 (c) Copyright 1995 Camson Huynh, ANGIS (Australian National Genomic Information Service ) Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. This software is provided "AS IS" without express or implied warranty. REQUIREMENTS ------------ Motif 1.X. X11 R4 or later. libXG enhanced version. ( Tarred together within this version ) Information on libXG can be found in the libxg directory when untarred ShadyBox. Alscript. ( Tarred together within this version ) Information on alscript can be found in the alscript145 directory when untarred ShadyBox. ShadyBox has been tested and run successfully on SunOS 4.1.3 and Sun Solaris 2.X. It may run on other platforms aswell. WHERE TO GET IT --------------- ftp://morgan.angis.su.oz.au/pub/unix Solaris platform : ShadyBox-2.0.1.README ShadyBox-2.0.1.sol.tar.gz or ShadyBox-2.0.1.sol.tar.Z Other platforms : ShadyBox-2.0.1.README ShadyBox-2.0.1.tar.gz or ShadyBox-2.0.1.tar.Z ----------------------------------------------------------------------------- ANGIS (The Australian National Genomic Information Service) University of Sydney, Australia. General Enquiries email : help@angis.su.oz.au WWW URL : http://morgan.angis.su.oz.au From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!news.sprintlink.net!noc.netcom.net!netcom.com!csus.edu!csulb.edu!paris.ics.uci.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: Simple text editor for mac wanted. Date: Mon, 05 Jun 1995 11:44:41 -0700 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 31 Distribution: bionet Message-ID: References: <3qhbf3$3bt@mserv1.dl.ac.uk> NNTP-Posting-Host: buggus.mmg.uci.edu In article , weix@netcom.com (Patrick Weix) wrote: > (Dave Johnston) writes: > > >Hi, > >I am looking for a basic (freeware) text editor for the Mac with cut, copy, > >paste, find, exchange etc type functions but it must be (a) 100% > >reliable) and (b) capable of handling very big data files (too large for > >simpletext/teachtext). We have Word6 but would prefer something less > >lumbering. Any suggestions. Another Vote for Alpha!! Alpha - Pete Keleher. Now *$30* shareware (and cheap at twice the price). Also comes with Power Mac native form. A text editor based on Ousterhout's tcl scripting language that comes with custom setups for just about any kind of file (HTML, TeX, Perl, C/C++, Fortran, Pascal, tcl, you name it, and is further almost infinitely customizable via tcl. Huge number of predefined keybindings, can define your own. Also has keyboard macros, many unixy tools (grep, diff, sort), can be used as the external editor for MacPerl, Think C, Metrowerks, etc. Carried in many Mac Archives, but home is: http://www.cs.umd.edu/~keleher/alpha.html Harry -- Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 --- knowledge is fractal --- http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!newsxfer.itd.umich.edu!gatech!newsfeed.pitt.edu!godot.cc.duq.edu!usenet From: "Frank R. Gorga" Newsgroups: bionet.software Subject: Re: Help with Runtime [toolbook] Date: 5 Jun 1995 14:25:43 GMT Organization: Duquesne University Lines: 20 Message-ID: <3qv457$8jj@godot.cc.duq.edu> References: NNTP-Posting-Host: phosphorus.chemistry.duq.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: kchaudhr@sun1.iusb.edu You probably need to make an icon for your application. The command line for the icon should read something like: \runtime.exe \book.tbk. In other words you need to force the toolbook run time to load a file as it loads itself. --- F.R. Gorga *********************************** Frank R. Gorga, Ph.D. Dept. of Chemistry & Biochemistry Duquesne University Pittsburgh, PA 15282 412-396-5858 / 412-396-5683 (fax) gorga@next.duq.edu From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!gatech!newsfeed.pitt.edu!godot.cc.duq.edu!usenet From: "Frank R. Gorga" Newsgroups: bionet.software Subject: Re: Help with Runtime [toolbook] Date: 5 Jun 1995 14:27:12 GMT Organization: Duquesne University Lines: 20 Message-ID: <3qv480$8jj@godot.cc.duq.edu> References: NNTP-Posting-Host: phosphorus.chemistry.duq.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: kchaudhr@sun1.iusb.edu You probably need to make an icon for your application. The command line for the icon should read something like: \runtime.exe \book.tbk. In other words you need to force the toolbook run time to load a file as it loads itself. --- F.R. Gorga *********************************** Frank R. Gorga, Ph.D. Dept. of Chemistry & Biochemistry Duquesne University Pittsburgh, PA 15282 412-396-5858 / 412-396-5683 (fax) gorga@next.duq.edu From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: (Russell Stothard) Newsgroups: bionet.software Subject: RESTSITE or REAP Date: 5 Jun 1995 13:01:28 +0100 Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3qurmo$7jj@mserv1.dl.ac.uk> X-POPmail-Charset: English Original-To: bio-software@dl.ac.uk Hi Does anyone have a copy of either j.c.miller's RESTSITE or d.McElroy's REAP. The programs are freeware and I have been unable to find a copy on the net. Thanks Russ Stothard Russ Stothard@nhm.ac.uk Dept Zoology Natural History Museum London From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!network.ucsd.edu!risaacso.extern.ucsd.edu!risaacson From: risaacson@ucsd.edu (Roger Isaacson) Newsgroups: bionet.software Subject: PDB importing to AutoCad 12 Date: Sun, 4 Jun 1995 07:35:39 Organization: UCSD Physics Lines: 11 Message-ID: NNTP-Posting-Host: risaacso.extern.ucsd.edu Summary: AutoCad Lisp routine for importing AutoCad files Keywords: xyz X-ray coordinates X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I have just had the first version of a LISP routine programmed so we can import Protein Data Bank files into AutoCad for 3D editing and doing fancier publication drawing than is usually possible with most low end 3D molecular graphics programs such as RasMol. We would be interested in your comments and are willing to share the routine with anyone interested. Roger Isaacson Physics Dept University of Calif. San Diego risaacson@ucsd.edu FAX 619 534-0173 From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!usc!nic-nac.CSU.net!deernisse.fullerton.edu!user From: DEernisse@fullerton.edu (Doug Eernisse) Newsgroups: bionet.software Subject: Re: Mac PostScript converter/viewer Date: Mon, 05 Jun 1995 15:27:50 -0700 Organization: CSUF Lines: 27 Message-ID: References: <3qlcd7$1us@nnrp.ucs.ubc.ca> NNTP-Posting-Host: deernisse.fullerton.edu In article , mhaveri@cc.oulu.fi (Matti Haveri) wrote: > :I am looking for a Mac PostScript converter or viewer, in order to read > :PostScript files using Mac computer. [ ... ] > For printing: > > > -Matti Haveri I second the suggestion for drop-ps for printing. Another available program that is useful in conjunction with its use is Lizzie Borden for those situations when you have a huge ps file that doesn't seem to print from drop-ps, no matter how much RAM you throw at it. Lizzie Borden converts it to a format that then prints with drop-ps just fine. This really saved me on April 15 when I was trying to complete my taxes with on-line ps forms. Available at the usual sites. -- Doug Eernisse Dept. Biological Science MH282 California State University Fullerton, CA 92634 From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!noc.netcom.net!ix.netcom.com!netnews From: hlthways@ix.netcom.com (Jerome Smith) Newsgroups: bionet.software Subject: re: refman/endnotes/PROCITE Date: 5 Jun 1995 22:43:24 GMT Organization: Netcom Lines: 19 Distribution: world Message-ID: <3r01ac$re4@ixnews3.ix.netcom.com> NNTP-Posting-Host: ix-rnwk1-24.ix.netcom.com Personal Bibliographics software, Inc. distributes PROCITE and BIBLIOLINK. phone 313-996-1580, fax 313-996-4672. I don't have either one yet but two of my key pharmaceutical clients do. They seem to love it. Procite is a windows based - full featured bibliographic reference management database. Imports comma delimited or tab delim. records. Exports to ascii or a word processor. I think you need to get Biblio link as well however. It seems to be the best (only) way to transfer downloaded records (from CD or online database services). Total costs runs under $600...and they have a 30 day money back guarantee. I think the rep told me they just came out with a new version too. From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!CLONTECH.COM!DAVIDK From: DAVIDK@CLONTECH.COM Newsgroups: bionet.software Subject: Data Acquisition software Date: 5 Jun 1995 13:59:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Netters: I do not use the network regularly and would like to know if there are any freeware/shareware programs for data acquisition, i.e. multichannel temperature recording to Mac or PC. Thanks, David Kellogg davidk@clontech From owner-software@net.bio.net Sun Jun 04 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!gatech!newsfeed.pitt.edu!godot.cc.duq.edu!usenet From: "Frank R. Gorga" Newsgroups: bionet.software Subject: Re: Help with Runtime [toolbook] Date: 5 Jun 1995 14:24:49 GMT Organization: Duquesne University Lines: 20 Message-ID: <3qv43h$8jj@godot.cc.duq.edu> References: NNTP-Posting-Host: phosphorus.chemistry.duq.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: kchaudhr@sun1.iusb.edu You probably need to make an icon for your application. The command line for the icon should read something like: \runtime.exe \book.tbk. In other words you need to force the toolbook run time to load a file as it loads itself. --- F.R. Gorga *********************************** Frank R. Gorga, Ph.D. Dept. of Chemistry & Biochemistry Duquesne University Pittsburgh, PA 15282 412-396-5858 / 412-396-5683 (fax) gorga@next.duq.edu From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!sol.ctr.columbia.edu!news.mindlink.net!vanbc.wimsey.com!unixg.ubc.ca!lpss From: lpss@unixg.ubc.ca (Alex Chang) Newsgroups: bionet.software Subject: Mac Postscript converter/viewer Date: 6 Jun 1995 00:54:36 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 10 Message-ID: <3r090c$n89@nnrp.ucs.ubc.ca> NNTP-Posting-Host: interchg.ubc.ca X-Newsreader: TIN [version 1.2 PL2] Thanks for those who responded to my question. I tried various programs recommeded by those netters and found out the Gostscript program is the one I really need. -- Alex Chang Pathology University of British Columbia achang@hivnet.ubc.ca From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!gatech!news.sprintlink.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!serra.unipi.it!king.ifc.pi.cnr.it!user From: king@po.ifc.pi.cnr.it (Giuliano Kraft) Newsgroups: bionet.software Subject: Genetic linkage software for Mac Date: Tue, 06 Jun 1995 17:04:03 +0100 Organization: CNR Inst. of Clinical Physiology Pisa Lines: 10 Message-ID: NNTP-Posting-Host: king.ifc.pi.cnr.it I am looking for a free Macintosh software package for genetic linkage analysis. It would be an incredible help to me if someone knows an ftp site to find it. Thanks a lot. Giuliano Kraft CNR Inst. of Clinical Physiology Via Savi, 8 I-56100 Pisa e-mail: king@po.ifc.pi.cnr.it From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!vector.nsk.su!eroshkin From: eroshkin@vector.nsk.su (Alexy Eroshkin) Newsgroups: bionet.software Subject: (none) Date: 6 Jun 1995 03:15:01 -0700 Organization: NPO Vector Lines: 89 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net To: BIO-SOFT@net.bio.net From: eroshkin@vector.nsk.su Subject: Protein Structure-Activity Analyzing Software Available PROANAL version 2.0 ------------------- New software package PROANAL version 2 is freely available thru: IuBio archive, EBI ftp and email server, NIG (Japan) ftp server. How to get it: 1. From IuBio archive as ftp://iubio.bio.indiana.edu/molbio/ibmpc/proanal2.exe (and proanal2.readme) IUBio archive files are now all available by e-mail to users. This is thru a network Gopher to Email gateway. To start, send mail to gophermail@iubio.bio.indiana.edu 2. From EBI ftp and email server: ftp.ebi.ac.uk /pub/software/dos/proanal$.exe This is the self-extracting archive, so it should before transferring, ftp should be set to binary transfer. Or by sending an email message containing: GET DOS_SOFTWARE:PROANAL.UAA to netserv@ebi.ac.uk Which will return the 6 files. Running UUDECODE you'll get self-extracting archive with the program. 3. From NIG (Japan) ftp server ftp.nig.ac.jp directory: /pub/dos/proanal file: proanal$.exe URL: gopher://gopher.nig.ac.jp:70/59/pub/dos/proanal/proanal$ ftp://ftp.nig.ac.jp/pub/dos/proanal/proanal$.exe ----------------------------------------------------------------- PROANAL ver 2.0 description: Enhanced version of the program PROANAL (CABIOS, 9, 491-497, 1993) Purpose: * investigation of relationships between structure and activity in a family of evolutionary related (or/and artificially mutated) proteins/peptides (searching relations between data on activity and various physico- chemical characteristics of different regions in primary structures); * analysis of multiple protein alignments; * studying protein structure-function relationships; * comparative analysis of sequences; * protein-engineering experiment planning. PROANAL may be used to predict protein secondary structures, functionally or structurally important regions, antigenic determinants (B- and T-call epitopes), transmembrane regions. Input data: * aligned protein amino acid sequences with data of their activity (pK, Km, ED50 or any other, if available). New options: * converts alignments from CLUSTAL output files to PROANAL input files; * plots individual and average profiles (10 different profiles, including alpha-helical and beta-strand moments) for entire protein family; * searching physico-chemically variable and conservative regions (e.g., regions with low dispersion of alpha-helical moments of hydrophobicity); * searching sites with high and low physico-chemical properties; * database of about 100 amino acid physico-chemical properties; * examples, extensive manual and help system. Requirements: DOS 3.30 or later, EGA/VGA video card, 500 KB RAM. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Alexey Eroshkin Research Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7 (3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!demon!uknet!bhamcs!news.ox.ac.uk!oxpath!enriquez From: enriquez@molbiol.ox.ac.uk (PITA ENRIQUEZ HARRIS) Newsgroups: bionet.software Subject: GCK for PCs??? Date: 6 Jun 95 11:49:11 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 7 Message-ID: <1995Jun6.114911@ania.path.ox.ac.uk> NNTP-Posting-Host: ania.path.ox.ac.uk Dioes anyone know if there are any plans to do a version of Gene Construction Kit for PCs? Its a terrific Mac program, but I have a PC at home. Thanks , Pita From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!news.primenet.com!ssmith From: ssmith@primenet.com (Program World Services) Newsgroups: bionet.software Subject: q Date: 6 Jun 1995 06:39:53 GMT Organization: Primenet Services for the Internet (602)395-1010 Lines: 18 Message-ID: <3r0t7p$30a@news4.primenet.com> NNTP-Posting-Host: usr4.primenet.com X-Newsreader: TIN [version 1.2 PL2] -- ------------------------------------------------------------------------------- For Private Full Year Automotive Information for $39.95 Contact myself below. For anymore or future technical support contact ssmith@primenet.com directly. Scott Smith Program World Services __ __ ____ ___ ___ ____ ssmith@primenet.com BBS:(209) 255-9110 /__)/__) / / / / /_ /\ / /_ / Compuserve 74441,2713, Aol[SCOTT93727] / / \ / / / / /__ / \/ /___ / Professional Automotive Repair Information, Professional Job Placement Professional Internet Advertising, Shareware Program Development Complete Professional Chiltons Manual Specifications from 1955-1995 for Domestic and Import Cars of almost all makes and models. ------------------------------------------------------------------------------- From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!news.primenet.com!ssmith From: ssmith@primenet.com (Program World Services) Newsgroups: bionet.software Subject: Very Professional shop software Date: 6 Jun 1995 06:39:18 GMT Organization: Primenet Services for the Internet (602)395-1010 Lines: 64 Message-ID: <3r0t6m$30a@news4.primenet.com> NNTP-Posting-Host: usr4.primenet.com X-Newsreader: TIN [version 1.2 PL2] *********************************************************** S H O P M A N V E R S I O N 2 . 0 0 ----------------------------------------------------------- Shopman is the latest Windows release for complete Very Professional automotive Shop Management Software, (May also be used for services other then automotive), Some of its options are as follows: 1) Databases: Vendor, Stock, Non-stock, Repair Order (RO), Calender and Alarm, Vehicle, Customer, Payroll Accounts Payable, Accounts Receivable, Type Work, plus More. 2) Edit: Orders, Accounts, Quotes, Invoices, Repair Orders, Stock Needs, Payroll, Calender, Plus more. 3) Search: By History, Name, Model, Part, Item #, Vin #, License, Payroll, Employer Name, Date, Plus More. 4) Accounts: Accounts Payable, Accounts Receive, Checkbook, Payroll, Tech Paid, Inventory Cost, Etc. 5) Built-in Utilities: Searchable Help, Back-up Database, Customization, Terminal, Editor, Clock, Programable Calender, Calculator, Plus More. 6) ALLDATA Terminal for rapid download into database of complex repair information and service bulletin updates, To make your repairs much easier. 7) Better then a lot of commercial programs at hundreds below there cost. 8) Shopman works within Windows for DLL Access and requires about 2 Meg to install. 9) Shopman can be download for evaluation from my BBS at 209-255-9110 for a timed evaluation copy, the cost for shopman is $249.00, and its about $350.00 below its comercial competitor and its better software !!!! *********************************************************** -- ------------------------------------------------------------------------------- For Private Full Year Automotive Information for $39.95 Contact myself below. For anymore or future technical support contact ssmith@primenet.com directly. Scott Smith Program World Services __ __ ____ ___ ___ ____ ssmith@primenet.com BBS:(209) 255-9110 /__)/__) / / / / /_ /\ / /_ / Compuserve 74441,2713, Aol[SCOTT93727] / / \ / / / / /__ / \/ /___ / Professional Automotive Repair Information, Professional Job Placement Professional Internet Advertising, Shareware Program Development Complete Professional Chiltons Manual Specifications from 1955-1995 for Domestic and Import Cars of almost all makes and models. ------------------------------------------------------------------------------- From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!biosci!not-for-mail From: richardg@Ne.Chem.LSA.UMich.Edu (Richard Goldstein) Newsgroups: bionet.general,bionet.biology.computational,bionet.biophysics,bionet.info-theory,bionet.molbio.evolution,bionet.molec-model,bionet.software,sci.bio.evolution,bionet.molbio.bio-matrix Subject: Call For Papers: Evolution and Structure of Biomolecules Date: 5 Jun 1995 18:53:00 -0700 Organization: University of Michigan Chemistry Department, Ann Arbor Lines: 73 Sender: biohelp@net.bio.net Approved: comp-bio-moderator@net.bio.net Distribution: world Message-ID: <3qshir$dgp@srvr1.engin.umich.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:15613 bionet.biology.computational:665 bionet.biophysics:967 bionet.info-theory:3407 bionet.molbio.evolution:2954 bionet.molec-model:418 bionet.software:12271 sci.bio.evolution:3035 bionet.molbio.bio-matrix:585 Announcement and Call for Papers THE EVOLUTION OF BIOMOLECULAR STRUCTURES AND THE STRUCTURE OF BIOMOLECULAR EVOLUTION A Seminar Track in the Pacific Symposium on Biocomputing January 3-6, 1996 Ritz Carlton Hotel, Hawaii All biological macromolecules have an evolutionary origin that is manifested in essentially every aspect of their biological and physico-chemical properties. In order to understand these macromolecules, it is necessary to understand the relationship between these properties and the evolutionary pressures that determined form and function. Information about the evolutionary history can be used to help predict the characteristics of these macromolecules. Conversely, these macromolecules encode this evolutionary heritage, and can provide insight into the process of molecular evolution. Possible topics include: - Role of natural selection and self-organization in biomolecular evolution - The relationship between sequence and structure evolution - Structure-based evolutionary reconstruction - Definition, significance, and evolution of protein cores, loops, and other conserved motifs - Evolutionary interpretations of multiple sequence or structure alignments, including their use in biomolecular structure prediction - The exon theory of protein structural organization We welcome papers describing results from a wide range of possible methodologies, including analyses of the databases of biomolecular sequences and structures, simple conceptual and computational evolutionary models, and experimental results. Current plans are for electronic publication of the papers by the MIT Press, in both HTML and postscript. People wishing to present posters without publishing a full paper may submit an abstract. Preregistration for the conference is required for the inclusion of a paper in the conference proceedings. Paper submission deadline: July 27, 1995 Notice to authors: September 11, 1995 Final paper and preregistration deadline: October 2, 1995 Richard A. Goldstein Chemistry Department Biophysics Research Division University of Michigan Ann Arbor, MI 48109-1055 (313) 763-8013 fax: (313) 747-4865 email: richardg@chem.lsa.umich.edu Russ B. Altman Section on Medical Informatics Stanford University Medical Center, MSOB X-215 Stanford, CA 94305-5479 (415) 723-6979 fax: (415) 725-7944 email: altman@camis.stanford.edu From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!howland.reston.ans.net!ix.netcom.com!netnews From: mrbrian@ix.netcom.com (brian sefton) Newsgroups: bionet.jobs,bionet.software,comp.databases.oracle.comp.databases.informix,comp.databases.sysbase Subject: Wanted: Prgrammers/applications for LIMS/Modeling Date: 6 Jun 1995 22:37:20 GMT Organization: Netcom Lines: 13 Distribution: world Message-ID: <3r2lb0$q09@ixnews2.ix.netcom.com> NNTP-Posting-Host: ix-sj9-25.ix.netcom.com Xref: biosci bionet.jobs:10127 bionet.software:12284 Inmartech is currently looking for programmers experienced in biological/pharm research database work, including data aquisition a/d conversion etc, on UNIX platforms. We are also interested in prgrammers who have written molecular modeling software, or other types of graphical simulation. Please respond to this email if you are interested in learning more about what we are doing. Sincerely B. Sefton Inmartech From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!sol.ctr.columbia.edu!news.mindlink.net!vanbc.wimsey.com!scipio.cyberstore.ca!news.Direct.CA!usenet From: p1d@Direct.CA (M. J. P.) Newsgroups: bionet.software Subject: Typing TUTOR NEEDED! Date: 6 Jun 1995 20:53:08 GMT Organization: Internet Direct Inc. Lines: 7 Message-ID: <3r2f7k$bv5@stud.Direct.CA> NNTP-Posting-Host: dyn-310.direct.ca X-Newsreader: WinVN 0.92.6+ If anyone out there knows how I can get a program that will help improve my typing speed and accuracy via the Internet, please let me know! THANK YOU IN ADVANCE email" p1d@Direct.Ca From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!pipex!oleane!jussieu.fr!nef.ens.fr!news!claros From: claros@biologie.ens.fr (Manuel .G CLAROS) Newsgroups: bionet.software Subject: Re: helical wheel program Date: Tue, 6 Jun 95 18:13:29 GMT Organization: Dpt Biologie, Ecole Normale Superieure Lines: 18 Message-ID: References: <3qo43q$d3m@news.ccit.arizona.edu> NNTP-Posting-Host: lgmmac0.ens.fr X-Newsreader: VersaTerm Link v1.1.1 bear@helium.gas.uug.arizona.edu (Soaring Bear) wrote: >> If >>anyone has or knows of Mac freeware or shareware that can create these >>schematic diagrams, please let me know > In the same vein, how about a unix version, please? MitoProt can easily do helical wheels (more information in an older post in this group) even if this is not the final goal of this program. We'll always have Paris (Rick Blaine, Casablanca) // \\ // \\ // \\ Un amigo es uno Manuel G. CLAROS \': | \\ // | :,\\': | \\ que lo sabe todo Ecole Normale Superieure \\ | | \\ // | | // \\ | | \\ sobre ti y a Genetique Moleculaire \\ | :,\\': | // \\ | :,\\ pesar de ello 46 rue d'Ulm \\ // \\ // \\ // te quiere. 75230 Paris Cedex 05 claros@biologie.ens.fr E. Hubbard From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!sunic.sunet.se!umdac!news From: peterl@umdix.umdc.umu.se (Peter Lundberg) Newsgroups: bionet.software Subject: Re: helical wheel program Date: 6 Jun 1995 16:46:16 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 249 Sender: -Not-Authenticated-[5799] Message-ID: <3r20oo$91o@studium.student.umu.se> References: NNTP-Posting-Host: spinup.chem.umu.se X-Posted-From: InterNews 1.0.6@spinup.chem.umu.se Xdisclaimer: No attempt was made to authenticate the sender's name. There is one for mac. It is one of several protein programs collectively called MacProt or Plot.A. You can probably get it from umich etc. Hope this helps. 73, Peter Ps. Here is the readme file: "From:ORANGE::GOLD::WINS%"JMILLER%VXBIO.SPAN@STAR.STANFORD.EDU" 17-AUG-1990 13:30 To:GILBERTD Subj:plota.readme file Return-Path: <@STAR.STANFORD.EDU:JMILLER@VXBIO.SPAN> Received: from STAR.STANFORD.EDU by gold.ucs.indiana.edu with SMTP ; Fri, 17 Aug 90 13:36:34 EST Received: from VXBIO by STAR.STANFORD.EDU via MAIL-11 with DECnet; Fri, 17 Aug 90 11:24:25-PST Date: Fri 17 Aug 90 11:24:24-PST From: JMILLER%VXBIO.SPAN@STAR.STANFORD.EDU Subject: plota.readme file To: "24986::""GilbertD@Gold.Bacs.Indiana.edu"""@VXBIO.SPAN Notes on the compiled versions of the MacPROT package (Peter Markiewicz, 1990) MACPROT MACProt consists of a set of programs for analyzing protein sequences for secondary structure, chain flexibility, hydropathy, helical wheels, and so on. Each program is supplied in a separate archive file. A list of the programs is given below. These notes on the MacPROT package (compiled) are adapted from the original instructions for the interpreted MS basic versions. Changes have been made to reflect the differences between the compiled and interpreted versions. A reference list will be given in a later version of this document. Each compiled version is supplied with the portion of the original manual which covers it, and the general descriptions in this document. A complete list of the programs (June 1990) is given below. Differences Between Complied and Interpreted versions: The compiled versions are for 512k mac and up models. Note that the programs may have problems with unenhanced (64k ROM) 512k macs. To run (simpler) versions of the programs on an "classic" 512k mac, you need to get the interpreted versions of the programs from Angela Luttke, as well as the Microsoft Basic interpreter. The compiled versions are (1)faster, (2)handle several input file types, (3) Allow printing of larger output pictures (up to 11", (4) allow user control of output file type, (5)allow user control of output colors, which will work with color output devices even if the mac has a black and white screen, and (6) improved mac interface and behavior under MultiFinder. Compiled versions run about 5-10 times faster than the interpreted versions. Using 6-point Monaco The Plot/A programs will use 6-point Monaco to output, if it is available in the System Folder. The font is supplied for installation. Using the smaller font makes the output charts easier to read. Adding to the output picture The user may add to the output drawing by clicking on it with the mouse. If a peak on a hydropathy plot is clicked, for example, the program will list the position in the protein that was clicked. This is very useful for finding interesting stretches in the peptide sequence. The numbers are added to output ONLY until the user saves the output to the Clipboard, or prints the result. After that, the user cannot add to the existing picture. The numbers are drawn in Monaco 9-point font UNLESS you have installed Monaco 6-point in your system folder. The font is provided for installation with the MacPROT package with the compiled versions. Input File Formats The interpreted versions of the programs recognize a specific format, and have file errors if any other sequence file format (including plain sequence is used). The compiled versions are more flexible, and can handle the following formats: the original MacPRot format, plain sequence (no comments or numbers), Pearson format, EMBL format, GenBank format, and IntelliGenetics format. If the file contains more than one sequence in these formats, only the first sequence is loaded. In theory, files up to 32,000 amino acids could be loaded, but the practical limit is about 1000 amino acids. All programs were tested for function with up to 1000 amino acid files. The program uses TEXT or DNA Strider protein files only. If you type in your sequences with a word processor or other program, you will need to save your sequences in TEXT ONLY format. If you don't do this, you won't see your sequence when you press the "load file" button! Consult the manual for your favorite word processor on how to save a sequence as a TEXT ONLY file. You CAN read protein files made with DNA Strider. However, this format is tricky, and if you write comments in Strider, the PLOT/A programs won't be able to tell where the sequence ends and the comments begin! If you must use Strider files, either remove all comments. MacPROT and MacDraw/MacPaint The programs in the MacPROT package work create useful output plots which may be printed, or copied to the Clipboard using File menu commands. Once the output is copied to the Clipboard, you may start either MacDraw or MacPaint (or similar programs), and paste the output graph into a document. You can also paste directly into your word processor, but you will probably want to edit the output chart somewhat before doing this. In MacDraw, the object is pasted as a true collection of draw objects, rather than a bitmap, which allows you to customize it by color, font sizes, etc. MacDraw output prints at the resolution of your printer, 300dpi (dots per inch resolution) for a laserprinter, and 72 dpi for an ImageWriter. You can also paste into a paint-type program, which will create a bitmap at 72dpi, and print at 72dpi (even with a LaserWriter!) Note that this copy/paste routine works with ALL Mac programs. That is, is you select "Copy" in any Mac program, load a new program, and select "Paste", the Copied result is pasted. This is an excellent way to move data between drawing programs and word processors. For example, after "cleaning up" a plot in MacDraw, you could select it, copy it, start MacWrite or MS word, and select Paste. The chart would become part of your word processing document. Note that very large protein sequences (>500-600 amino acids) may exceed the maximum allowed output picture size in some of the programs. If this happens, an alert warns the user to reduce the size of the sequence plotted. If this occurs, the best thing is to analyze several portions, copy the results, and paste each segment's results in turn into a single draw or paint document. This works especially well with MultiFinder. The complete set of programs are listed below. MacPROT programs listed under the menu 'Programs' in the given order. MENUPROT (NOT IN THE COMPILED VERSIONS!!!!) gives an overview on the individual programs and their tasks (not under programs, but opened either from the finder or from within the programs by using 'CANCEL' or 'Exit' in all other programs; see below). It is a reminder on what the programs are doing and helps in deciding which program needs be opened for a certain analysis. It is useful for the starting user, who is not yet familiar with what the programs' names stand for. AA.DATAis for storing and revising a protein sequence. The program puts the sequence in the format, which is later used by the analysing programs. It can also be used for editing an already stored sequence. In addition to storing the plain sequence, an optional comment as well as data on amino acid frequency and molecular weights are calculated and written to the same file. PLOT.A/HYDanalyses the hydropathy (hydrophobicity/ hydrophilicity) according to four published hydropathy scales of any sequence stored in AA.DATA file format. The plot can be printed or saved to the clipboard for pasting it into a picture accepting program. After the plot is completed the same sequence can be analysed using different parameters and/or a different hydropathy scale. PLOT.A/HYD5analyses the hydropathy of a given sequence. It calculates and plots the hydropathy for five increasing moving averages (spans) simultaneously. The first span and the step for the increase is chosen by the user. Saving and printing is done as in PLOT.A/HYD. PLOT.A/SUMprovides three hydropathy plots for a single sequence simultaneously using three different hydropathy scales. Saving and printing is done as in PLOT.A/HYD. PLOT.A/H3calculates and plots the hydropathy of up to three sequences simultaneously. It can be chosen among four hydropathy scales. Saving and printing is done as in PLOT.A/HYD. PLOT.A/TMHcalculates and plots the hydropathy. In addition each value for the chosen span is evaluated for its coordinates in a 'hydrophobic moment' plot and the corresponding assignment to the helix type shown. The assignment is also written to a disk file in ASCII format. Saving and printing is done as in PLOT.A/HYD. PLOT.A/HELdraws a helical wheel of a user selected span of amino acids, plots the hydropathy, and calculates the mean hydropathy using two scales. Saving and printing is done as in PLOT.A/HYD. PLOT.A/DOTplots two sequences (the same or different ones) against each other in a dot matrix. Two methods are used, which either search for perfect matches (identities) or for similarities according to five different score matrices based on (a) accepted point mutations, (b) genetic and structural similarities, (c) conformational state, and (d) observed substitutions. Saving and printing is done as in PLOT.A/HYD. PLOT.A/GORcalculates and plots the preference of each residue for four conformations (helix, extended, coil, turn) along the sequence. The sequence is written to a file in coded letters according to the most likely preference. Saving and printing is done as in PLOT.A/HYD. PLOT.A/GGRsimilarly calculates and plots the preference for three conformations (helix, extended, coil) along the sequence and writes the evaluation to a disk file. Saving and printing is done as in PLOT.A/HYD. PLOT.A/STRsearches for up to ten user selected stretches of amino acids within a given sequence and plots the respective positions found along the sequence. Saving and printing is done as in PLOT.A/HYD. PLOT.A/FOTsuggests regions likely to be amphipathic. Two disk files are created (1) to specify the residue starting an amphipathic segment, and (2) to write the sequence in coded format. Saving and printing is done as in PLOT.A/HYD. PLOT.A/POWplots the power spectrum of a user selected stretch. Saving and printing is done as in PLOT.A/HYD. PLOT.A/KASdetermines main chain flexibility and in turn antigenic determinants. PLOT.A/TSLtranslates a DNA sequence. Paths among programs Each program can be opened from the finder by double-clicking on the respective icon or by starting MENUPROT and then choosing the respective program from the menu bar under the 'Programs' menu. From within the programs a different/same program can be chosen at any time during the run by pulling down the 'Programs' menu. A 'CANCEL' button in the first window provides the option to leave the program and go to 'MENUPROT'. There are two other ways of leaving a program during program execution, 'Exit' and 'Quit', via the 'File' menu (see sketch above), which also contains the options for saving a plot to the clipboard or printing it on a dot matrix printer. A "Help" button in the input window summarizes program use (briefly). The 'File' menu Note that the File menu commands for Open and Save are handled differently in the MacPROT package. The standard Open command for an input file is provided by the "load file" button, and the programs prompt for the name of an output file to Save if necessary. Save to Clipsaves a plot to the clipboard for pasting it into a picture accepting program (graphs created by programs for this manual were saved to FullPaint). This option is available only after the the plot is finished. It is otherwise identical to the "Copy" command found under the Edit menu of most mac programs. At other times during program execution (loading a file, choosing parameters, analysis) the option is dimmed. If a plot is saved to the Clipboard, you should quit the program (Finder), or switch to the program you want to paste to (MultiFinder), and select Paste. It may take several seconds, since some of the plots are very complex for the mac to draw! Rerunning the program immediately with the same or different parameters erases the current plot and creates a new one. Print Pictureprints the plot to any printer. As with 'Save to ...' the option is available only after the plot is finished. The common two commands on paper size and printing options need be answered before printing starts. Note that MacPROT program can only draw a singel page of output, meaning the plot can't be more than 10 inches to print. To print a long plot, select the sideways "landscape" print mode in the Page Setup Window. QuickPrintNOTE:THIS WORKS ONLY WITH AN APPLE IMAGEWRITER!!!! prints an instant hardcopy of the screen on the dot matrix printer (printer must be on!) in 'Standard' quality. Though similar to the 'Print Picture' option in 'Standard', it's a quick print facility omitting the selection windows for paper format and print quality. Exit closes all files in memory (the running program as well as textfiles created by some programs) and goes to 'MENUPROT'. The option is available all the time during program execution. It is particularly useful, if by mistake the 'wrong' program was opened and explanations about the label for the 'right' program are required (or a cup of coffee/tea is needed in between?). Quit also closes all open files, but goes back to the Finder (done for the day!). The Options Menu The compiled versions of MacPROT have an Options menu, where the user may change the colors used in creating the output graph, and the output file type. Colors being currently used are listed in the input window. The color information is recorded even if you have a black and white mac. You can print in color to (1)an ImageWriter II with a color ribbon, (2)a HP PaintJet or other color inkjet printer with a mac interface, or (3)a color laserprinter. The file type option sets the output file format used in creating text output of the calculations. When the output file is clicked (it may be necessary to open and close its volume/folder first), the mac will use the specified word processor to open it. MacWrite,WriteNow, MS Word,EDIT, and FORMAT are currently supported. Access to Programs Compiled versions of these programs will will become available in 1990. They may be downloaded from the following databases using electronic mail or FTP over bitnet, internet, or your local net if it has a gateway. EMBL: NETSERV@EMBL GET MAC_SOFTWARE:filename.ext IUBIO: IuBio.Bio.Indiana.Edu (IP name) 129.79.1.101 (IP address) U Houston: genbank-server@bchs.uh.edu (INTERNET/ARPANET) uhnix2!genbank-server (usenet won't work for much longer) SEND MAC hqx-encoded-file-name America Online: New service summer 1990, consult your manual for details send HELP messages to find out how to download the programs. from the various servers listed above. They are also available on floppies as part of a larger set of public domain programs for sequence analysis on the Macintosh from the following address: Peter Markiewicz Dept. Microbiology, MBI, UCLA Los Angeles, CA 90024 To get them on floppy, you must (1)send 15 800k initialized floppies with blank labels. (2)Include a return enveloped, addressed to you, with $2.40 postage (US). If one of the above is lacking, the programs won't be sent. It normally takes me 2-4 months to process requests. Note that you can get the programs MUCH faster by using electronic mail and/or online databases listed above. A tutorial on how to use electronic mail and online databases is available as a HyperCard stack from the above address. " O==O ================================== O==O O==O Peter Lundberg O==O O==O Email: peterl@umdix.umdc.umu.se O==O O==O ============761.91141============= O==O From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!xlink.net!rz.uni-karlsruhe.de!news.uni-stuttgart.de!news.belwue.de!news.belwue.de!newsserv.zdv.uni-tuebingen.de!local!uwe.schueler From: uwe.schueler@uni-tuebingen.de (Uwe Schueler) Newsgroups: bionet.software Subject: KEITHLEY TESTPOINT FILES WANTED Date: Tue, 6 Jun 1995 16:02:54 Organization: Elektroniklabor Physiologie Lines: 4 Message-ID: NNTP-Posting-Host: elab.physiologie.medizin.uni-tuebingen.de X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I'm looking for the files TP11D1.zip TP11D2.zip TP12947.zip does a KEITHLEY FTP-server exist or could somebody email them uuencoded ? From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!ief.spb.su!spin From: spin@ief.spb.su (Alexandr Spirov) Newsgroups: bionet.software Subject: Re: Promoter region sequence analysis Date: 6 Jun 1995 08:51:39 -0700 Organization: Inst. of Evolutionary Physiology & Biochemistry, St.Petersburg Lines: 80 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net This is news-message from my archive (Newsgroups: bionet.molbio.genome-program). To my mind, Brian Foley's comments is good illustration of situation in the field under discussion. In other word, if you have unique newly sequencised gene (especially if by your own hands), then we will do all the work with enthusiasm. But if you interesting in treatment and comparisons of multigene (multiKB) DNA blocks, then such preferably hand-made search & analysis became impracticable. Alexander Spirov. --------------------------------------------------------------------------- >Date: Wed, 23 Nov 1994 03:48:03 GMT >From: brianf@med.uvm.edu (Brian Foley) >Message-Id: <1994Nov23.034803.21069@emba.uvm.edu> >Organization: EMBA Computer Facility, University of Vermont >Newsgroups: bionet.molbio.genome-program >Subject: [NEWS] Re: sequence comparison >Status: O >Giltsu Choi (tchoi@binah.cc.brandeis.edu) wrote: >: I have 2kb upstream of A gene from two related species >: and 2kb upstream of B gene from a species. B gene is >: coordinately regulated with A gene in terms of >: expression pattern. Now I want to do some sequence >: comparisons to extract information such as >: possible sequence elements for the regulation of these genes. > Are we talking eukaryotic or prokaryotic? If eukaryotic: > First look at the Eukaryotic Promoter Database to see if >any previously desribed promoter elements are present in the >upstream regions of gene A and gene B. > This will also show you the types of sequences that have >been found to have regulatory activity. You will find that >such promoter elements as the glucocoricoid response element (GRE) >are quite short sequences of 6-12 bases, often palindromic >or semi-palindromic but sometimes asymetrical. > This tells you that you will not be looking for big regions >of 20 to 50 bp of similarity in the promoters of A and B, so when you >do an alignment of the two promoters, you want to use an algorithm that >will find short segments of similarity among a lot of background "noise" >of non-similar sequence. A dot-plot type of program is good for this >a small window size, but perhaps a high stringency (like use a window >of 5 and only plot a point when 4 or 5 bases in the window are >perfect match between A and B). > Also dot-plot each against itself, because many promoter elements >turn up in repeated arrays in promoters. > None of this is going to PROVE that the sequences you find >in common between A and B are actually involved in promoter activity. >You will have to do some deletions or site-directed mutations of each >promoter, linked to a reporter gene to prove that the elements >you identify have biological function. > On the other hand, if you have good evidence already that >these two genes are activated by a common signal, and you find >copies of previously reported promoter elements that also appear >in other genes which respond to that signal, you have a pretty good >bet that you have identified significant elements. > Protein sequence similarities often span large regions and >are highly conserved throughout whole kingdoms. But promoter elements >are much more difficult to identify. They are short regions. They can >be variable distances from the start codon. They can have variable >spacing between repeats. Some genes are tightly regulated and have >highly conserved promoters, but others do not. > Let us know what you find. >******************************************************************** >* Brian Foley * If we knew what we were doing * >* Molecular Genetics Dept. * it wouldn't be called research * >* University of Vermont * * >******************************************************************** > From owner-software@net.bio.net Mon Jun 05 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!news.sprintlink.net!demon!uknet!strath-cs!st-and!Aberdeen!gen125 From: gen125@abdn.ac.uk (p.metcalfe) Newsgroups: bionet.software Subject: Wanted: DGGE Software Date: 6 Jun 1995 06:49:14 GMT Organization: University of Aberdeen, Scotland Lines: 16 Message-ID: <3r0tpa$qgf@nof.abdn.ac.uk> NNTP-Posting-Host: bio.if2.abdn.ac.uk X-Newsreader: TIN [version 1.2 PL2] Does anyone know where I can get hold of sofware for predicting melting domains during Denaturing Gradient Gel Electrophoresis (DGGE), knowing the sequence of the duplex to be analysed. I know of a programme called MELT, is there an FTP site for this software ?? Please reply by email. Paul Metcalfe Department of Molecular and Cell Biology University of Aberdeen Scotland UK Email: gen125@abdn.ac.uk From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!Germany.EU.net!EU.net!news.sprintlink.net!uunet!in1.uu.net!svc.portal.com!portal.com!cup.portal.com!Zekeman From: Zekeman@cup.portal.com (Enrico Ami-tox gilberti) Newsgroups: bionet.software Subject: ImageCalc location ? Date: 6 Jun 1995 20:20:04 -0700 Organization: The Portal System (TM) Lines: 2 Sender: pccop@unix.portal.com Message-ID: <139990@cup.portal.com> NNTP-Posting-Host: news1.unix.portal.com I am looking for a site where i can get the shareware program called ImageCalc. Anyone help ? From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!spool.mu.edu!uwm.edu!msunews!thomashaw-at.css.msu.edu From: bloksber@pilot.msu.edu (Leonard N. Bloksberg) Newsgroups: bionet.software Subject: Programming language querry Date: Tue, 06 Jun 1995 23:51 EDT Organization: Michigan State U., Crop & Soils Dept. Lines: 13 Distribution: world Message-ID: <19950606235137.bloksber@thomashaw-at.css.msu.edu> NNTP-Posting-Host: thomashaw-at.css.msu.edu X-Newsreader: FTPNuz (DOS) v1.0 I'm getting sick of waiting for some specialized applications to be written for me, so I'm entertaining the idea of writing my own programs. I am comfortable in DOS and UNIX, but I only have access to DOS and Windows machines right now. I'm leaning toward a C language because I understand that programs can be compiled for UNIX, DOS, or MAC from the same code. Is "Borland C++ 4.5 visual" a good language to dive into? Can anyone recomend something that will be both easy to pick up, and powerfull enough to bother spending time to learn? Thanks. . Lenny Bloksberg bloksber@pilot.msu.edu . . From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!msunews!thomashaw-at.css.msu.edu From: bloksber@pilot.msu.edu (Leonard N. Bloksberg) Newsgroups: bionet.software Subject: Re: GCK for PCs??? Date: Tue, 06 Jun 1995 23:42 EDT Organization: Michigan State U., Crop & Soils Dept. Lines: 20 Distribution: world Message-ID: <19950606234237.bloksber@thomashaw-at.css.msu.edu> References: <1995Jun6.114911@ania.path.ox.ac.uk> NNTP-Posting-Host: thomashaw-at.css.msu.edu X-Newsreader: FTPNuz (DOS) v1.0 In Article <1995Jun6.114911@ania.path.ox.ac.uk> "enriquez@molbiol.ox.ac.uk (PITA ENRIQUEZ HARRIS)" says: > Dioes anyone know if there are any plans to do a version of Gene Construction > Kit for PCs? Its a terrific Mac program, but I have a PC at home. > > Thanks , > > Pita > > Clone is a very similar program that runs on PC. Both GCK and Clone are nearly identicle, both have minor pros/cons against the other, and both are radically overpriced at around $1000- to $1500-. Neither program allows any file conversion to trade files between programs on the same machine, never mind different platforms. All this was correct as far as I could tell, about a year ago when I last looked the 2 programs over. I know of no other programs that come close to these 2. Lenny Bloksberg bloksber@pilot.msu.edu . . From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!msunews!harbinger.cc.monash.edu.au!newshost.anu.edu.au!newsmaster From: johna@rsbs-central.anu.edu.au Newsgroups: bionet.software Subject: RAPD data analysis - software Date: 7 Jun 1995 02:08:52 GMT Organization: rsbs - anu - Australia Lines: 20 Message-ID: <3r31nk$j0o@manuel.anu.edu.au> NNTP-Posting-Host: 150.203.38.97 X-Newsreader: RAPDistance Package A group at the Research School of Biological Sciences, Australian National University, Canberra under the direction of Prof. Adrian Gibbs has developed a software package called RAPDistance for the analysis of RAPD data. It has a comprehensive range of options for creating data files, editing them and using application programs to analyse them. The third version has just been released on the Internet. The first version was made available in October 1994. It is intended to maintain and extend the package as resources allow. The following files are available :- 1) README.DOC Getting started. 2) INTRO.DOC Brief details of scope of package and modifications. 3) RAPD103.EXE Self extracting archive file containing the package. Accessed from the Internet via :- 1) Anonymous ftp ftp://life.anu.edu.au/pub/RAPDistance or 2) WWW http://life.anu.edu.au/molecular/software/rapd.html Please register with me if you use the package so that I can keep you informed of new versions, bugs etc. Regards. John Armstrong From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!swrinde!pipex!oleane!jussieu.fr!jouy.inra.fr!butler From: butler@jouy.inra.fr (Philip Butler) Newsgroups: bionet.software Subject: Re: Programming language querry Date: 7 Jun 1995 11:56:24 GMT Organization: INRA Lines: 17 Message-ID: <3r4458$mom@saphir.jouy.inra.fr> References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> <3r3m5v$jpn@saphir.jouy.inra.fr> <1995Jun7.111611.66218@ucl.ac.uk> NNTP-Posting-Host: diamant.jouy.inra.fr X-Newsreader: TIN [version 1.2 PL2] Rob Miller (rmiller@bsm.bioc.ucl.ac.uk) wrote: : I suggest you also take a look at Tcl/Tk, a script language with ... Thanks for correcting the omission on my part. : If you run into anything that's too : numerically intensive, it's trivial to extend the interpreter with new : commands written in C or C++. APL simply provides a fine efficient way of extending the scripting approach to many number crunching problems. What I like about Unix is that you can pick the language that is best adapted to each specific task and then combine all the pieces of software together. This is extremely difficult to do with DOS (as I found out the hard way...). -- /WWW\ Philip BUTLER e-mail: butler@jouy.inra.fr |o,o| INRA/UCD/Service Linguistique tel: (33.1) 34.65.24.54 \_=_/ F-78352 Jouy-en-Josas Cedex fax: (33.1) 34.65.22.72 From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Newsgroups: bionet.software Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!uknet!bcc.ac.uk!rmiller From: rmiller@bsm.bioc.ucl.ac.uk (Rob Miller) Subject: Re: Programming language querry Message-ID: <1995Jun7.111611.66218@ucl.ac.uk> Date: Wed, 7 Jun 1995 11:16:11 GMT References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> <3r3m5v$jpn@saphir.jouy.inra.fr> Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Lines: 49 Leonard N. Bloksberg (bloksber@pilot.msu.edu) wrote: : I'm getting sick of waiting for some specialized applications to be written : for me, so I'm entertaining the idea of writing my own programs. I am : comfortable in DOS and UNIX, but I only have access to DOS and Windows : machines right now. I'm leaning toward a C language because I understand : that programs can be compiled for UNIX, DOS, or MAC from the same code. : Is "Borland C++ 4.5 visual" a good language to dive into? Can anyone recomend : something that will be both easy to pick up, and powerfull enough to bother : spending time to learn? Thanks. I suggest you also take a look at Tcl/Tk, a script language with interpreters available for Unix (where it started), Windows, maybe DOS, and probably MAC (I just do the Unix stuff, sometimes see notes about interpreters for other systems and comments about it being the `language of the internet' because of it's portability). It's quick to learn, powerful enough to do most things, very rapid for generating complete applications, and the Tk toolkit makes all the graphics and GUI stuff *very* easy and straightforward. If you run into anything that's too numerically intensive, it's trivial to extend the interpreter with new commands written in C or C++. There's a tcl newsgroup, comp.lang.tcl, and at least one book, _Tcl and the Tk Toolkit_ by John Ousterhout (isbn 0-201-63337-X), and it is public domain. rob. -- ------------------------------------------------------- Rob Miller, Ph.D. Biomolecular Structure and Modelling Unit (BSM), Department of Biochemistry and Molecular Biology, University College / Gower Street / London WC1E 6BT. United Kingdom. Tel: +44 171419 3896 Fax: +44 171380 7193 Internet: rmiller@bsm.bioc.ucl.ac.uk http://www.biochem.ucl.ac.uk/~rmiller ------------------------------------------------------- From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Newsgroups: bionet.software Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!pipex!uknet!bcc.ac.uk!dac159!dcurtis From: dcurtis@hgmp.mrc.ac.uk (David Curtis) Subject: Re: Programming language querry Sender: news@ucl.ac.uk (Usenet News System) Message-ID: Date: Wed, 7 Jun 1995 10:48:59 GMT References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> <3r3j7a$fge@lyra.csx.cam.ac.uk> Organization: Institute of Psychiatry X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 45 Wow, great! Now we can have language flames in bionet.software. Just to say: In article <3r3j7a$fge@lyra.csx.cam.ac.uk> tjrc1@mole.bio.cam.ac.uk (Tim Cutts (Zoology)) writes:>Path: bcc.ac.uk!uknet!plug.news.pipex.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk !tjrc1>From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts (Zoology))>Newsgroups: bionet.software>Subject: Re: Programming language querry >Date: 7 Jun 1995 07:07:22 GMT > >Consider carefully what sort of program you wish to write. Are you >going to be dealing with large memory structures (>64k)? >If so, you will find that DOS and Windows are a pain to develop on, >since even in 386 Enhanced mode, Windows deals with memory in 64k >chunks, which is a pain to work around. DOS is even worse, although >there are now 32bit DOS extenders, but I can't speak for these at all. I can speak for 32bit DOS extenders and they work fine. I've got the Symantec compiler and one can allocate big chunks of memory using the 32bit memory model, but you can't debug these applications. Windows is better than DOS use to be because you get access to virtual memory, so needing lots of memory isn't a problem provided you only want not-huge chunks. And the free C++ compiler, g++, is available for 32bit DOS as well as OS/2 and Unix and again this works fine.The FASTLINK linkage programs for DOS have been compiled with this and they use large memory structures and run perfectly well and quite quickly. So, if you like DOS/Windows then I think they offer a perfectly reasonable development environment for many applications. PS I agree with the choice of languages: go for C/C++. Try to avoid using the Borland-specific extensions if you want to ever be able to port your software to another system, and remember that if you want other people to be able use it then you should really consider Unix as a target as well. Personally, I do all my development work with DOS/Windows but aim to produce code I will be able to port to Unix. For progs with GUIs I use the (free) wxWindows library which produces applications that run under Windows and X. I expect this would be slightly harder to get started with than visual C++ though. It just depends whether portability is an issue for you. Good luck anyway. Dave Curtis (dcurtis@hgmp.mrc.ac.uk) http://www.iop.bpmf.ac.uk/home/depts/psychmed/general/dcurtis/dcurtis.htm From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.rhrz.uni-bonn.de!news.uni-stuttgart.de!news.belwue.de!news.belwue.de!News.Uni-Marburg.DE!news.th-darmstadt.de!fauern!winx03!wrzx15!phak004 From: phak004@wrzx15.rz.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: Mac PostScript converter/viewer Date: 6 Jun 1995 19:01:57 GMT Organization: University of Wuerzburg, Germany Lines: 33 Message-ID: <3r28n5$5pf@winx03.informatik.uni-wuerzburg.de> References: <3qlcd7$1us@nnrp.ucs.ubc.ca> NNTP-Posting-Host: wrzx15.rz.uni-wuerzburg.de X-Newsreader: TIN [version 1.2 PL2] Alex Chang (lpss@unixg.ubc.ca) wrote: > I am looking for a Mac PostScript converter or viewer, in order to read > PostScript files using Mac computer. I'll appreciate if someone could > provide that information, esp. a noncommercial program. There are several possibilities: You can print Postscript files directly on a LaserWriter if you have the LaserWriter Utility available. This works for all Postscript laser printers; I am not sure if it is also possible with non-laser printers like a style writer. The LaserWriter Utility comes with every Apple Laser Writer. If you have another printer, like an HP Laserjet, the company should provide some equivalent software (as HP does). You can use Ghostscript. I have no experience with it on a Mac. Several drawing programs are able to display Postscript and let you even manipulate it. These are all programs which are able to read Adobe Illustrator files. Adobe Illustrator format seems to be a "light" version of Postscript. There is a program called EPSconverter (free- or shareware, can'€t remember) which converts "normal" Postscript in a format which is readable by Adobe Illustrator. (WARNING: even on a PowerMac it is no fun to work with a Postscript file with 1000+ objects.) AFAIK, some graphics converters are able to convert EPS to GIF or whatever pixel format you would like. --Cornelius. -- /* Cornelius Krasel, Institut f. Pharmakologie, Versbacher Str. 9, D-97078 */ /* Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de */ /* "Science is the game you play with God to find out what His rules are." */ From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!cs.utexas.edu!howland.reston.ans.net!pipex!oleane!jussieu.fr!jouy.inra.fr!butler From: butler@jouy.inra.fr (Philip Butler) Newsgroups: bionet.software Subject: Re: Programming language querry Date: 7 Jun 1995 07:57:51 GMT Organization: INRA Lines: 40 Distribution: world Message-ID: <3r3m5v$jpn@saphir.jouy.inra.fr> References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> NNTP-Posting-Host: diamant.jouy.inra.fr X-Newsreader: TIN [version 1.2 PL2] Leonard N. Bloksberg (bloksber@pilot.msu.edu) wrote: : I'm getting sick of waiting for some specialized applications to be written : for me, so I'm entertaining the idea of writing my own programs. I am : comfortable in DOS and UNIX, but I only have access to DOS and Windows : machines right now. I'm leaning toward a C language because I understand : that programs can be compiled for UNIX, DOS, or MAC from the same code. : Is "Borland C++ 4.5 visual" a good language to dive into? Can anyone recomend : something that will be both easy to pick up, and powerfull enough to bother : spending time to learn? Thanks. C and C++ are good for writing middleware, i.e. code that is worth spending a lot of time on because it will run very frequently and every clock cycle that you can save is worth saving. C and C++ can be considered as 'portable assembly language'. If you are an ordinary scientist, you probably want to program in problem-space (in terms of molecules, plants etc..) rather than cyber-space (bits and bytes). Among 3rd generation languages, Ada (and Oberon?) is much closer to problem-space than C++ is. Another language that I find extremely useful is APL. Computer illeterate people can start doing useful things with it within a day and it is perfect for power users. Unix shell scripts and APL have more or less the same philosophy and suit me fine. Check out in the 'APL Quote Quad' and 'Vector' journals whether APL will suit you. A good server for APL is ftp://wuvieai.wu-wien.ac.at The appropriate newsgroup to browse through is comp.lang.apl Other languages that may be worth considering are Smalltalk, Lisp and Forth, but I am less acquainted with these. Prolog is great for some specific problems. I suspect software vendors try and make all end users use C++ because it will never match their requirements and will always have to spend more money. Ada and APL have their own ISO standards and are as safe as you can get in terms of portability. Just trying to show that APL fans can be open-minded too! -- /WWW\ Philip BUTLER e-mail: butler@jouy.inra.fr |o,o| INRA/UCD/Service Linguistique tel: (33.1) 34.65.24.54 \_=_/ F-78352 Jouy-en-Josas Cedex fax: (33.1) 34.65.22.72 From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!elroy.jpl.nasa.gov!swrinde!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts (Zoology)) Newsgroups: bionet.software Subject: Re: Programming language querry Date: 7 Jun 1995 07:07:22 GMT Organization: University of Cambridge, England Lines: 54 Message-ID: <3r3j7a$fge@lyra.csx.cam.ac.uk> References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> NNTP-Posting-Host: mole.bio.cam.ac.uk bloksber@pilot.msu.edu (Leonard N. Bloksberg) writes: >I'm getting sick of waiting for some specialized applications to be written >for me, so I'm entertaining the idea of writing my own programs. I am >comfortable in DOS and UNIX, but I only have access to DOS and Windows >machines right now. I'm leaning toward a C language because I understand >that programs can be compiled for UNIX, DOS, or MAC from the same code. >Is "Borland C++ 4.5 visual" a good language to dive into? Can anyone recomend >something that will be both easy to pick up, and powerfull enough to bother >spending time to learn? Thanks. Yes, as long as you use it to compile DOS programs only. Windows programs will *not* be easily portable to anything else (and they're much harder to write anyway). Consider carefully what sort of program you wish to write. Are you going to be dealing with large memory structures (>64k)? If so, you will find that DOS and Windows are a pain to develop on, since even in 386 Enhanced mode, Windows deals with memory in 64k chunks, which is a pain to work around. DOS is even worse, although there are now 32bit DOS extenders, but I can't speak for these at all. If you will be needing large data structures, you are much better off using a 32bit operating system, where you can happily say 'give me 3Mb now' and it will (provided you have enough memory). At the moment this means Windows NT, OS/2 or Unix. In the case of OS/2 and Unix, there is a free C++ compiler available (gcc), which is perfectly serviceable. It is rather more stable (in my experience) under Unix than OS/2, which is hardly surprising, since Unix is where it came from. I understand gcc for NT is being developed but is not yet available. The advantage of gcc is that it is free. The disadvantage (in my opinion) is that although GNU software is pretty functional, it does not have the ease of use and excellent debugging tools that are found in commercial compilers like Borland C++. Incidentally, Borland C++ is also available for OS/2. Here's my advice in a nutshell: 1) Assess what sort of program you need to write. 2) If it's going to involve large amounts of data in memory, think seriously about using a 32bit OS - Unix may be a pain in the backside to use, but it's a joy to write programs for. 3) If compatibility is a major issue, NT is probably the OS, to go for, but development tools are expensive. 4) If compatibility with DOS/Windows is not an issue, setting up a small Linux system on one of your PCs with gcc is probably a better bet. Tim. From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!Germany.EU.net!EU.net!news.sprintlink.net!uunet!zib-berlin.de!news.rrz.uni-hamburg.de!news From: Reski@botanik.uni-hamburg.de (Sven Kruse) Newsgroups: bionet.software Subject: TrueType fonts Date: 6 Jun 1995 09:08:05 GMT Organization: Uni Hamburg Lines: 2 Distribution: world Message-ID: <3r15tl$lnd@rzsun02.rrz.uni-hamburg.de> NNTP-Posting-Host: moses.botanik.uni-hamburg.de X-Newsreader: I am looking for Windows TrueType fonts with signs for "male" and "female". Thanks in advance Sven From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!elroy.jpl.nasa.gov!swrinde!pipex!news.sprintlink.net!sjuvm!zhltphs Nntp-Posting-Host: 149.68.2.20 Date: Tue, 6 Jun 1995 16:21:07 -0400 From: "Trombetta, Louis D" Newsgroups: bionet.software Subject: imagecalc Message-ID: <06JUN95.17649728.0122@sjumusic.stjohns.edu> Sender: usenet@sjumusic.stjohns.edu Organization: St. John's University Lines: 16 hi Does anyone have access to Imagecalc. Are there any sites where it can be found? Thanks ******************************************* | Louis D. Trombetta, Ph.D. | | Professor | | Department of Pharmaceutical Sciences | | St. John's University | | 8000 Utopia Parkway | | Jamaica, N.Y. 11439 | | 718 990 6025 | | zhltphs@stjohns.edu | ******************************************* From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!agate!msunews!netnews.upenn.edu!hmivax!bailey From: bailey@genetics.upenn.edu (Charles Bailey) Newsgroups: bionet.software Subject: Re: Programming language querry Date: 7 Jun 95 11:32:03 EDT Organization: HHMI/Human Genetics, Univ of Pa. Lines: 42 Distribution: world Message-ID: <1995Jun7.113203@hmivax> References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> NNTP-Posting-Host: hmivax.humgen.upenn.edu In article <19950606235137.bloksber@thomashaw-at.css.msu.edu>, bloksber@pilot.msu.edu (Leonard N. Bloksberg) writes: > machines right now. I'm leaning toward a C language because I understand > that programs can be compiled for UNIX, DOS, or MAC from the same code. > Is "Borland C++ 4.5 visual" a good language to dive into? Can anyone recomend > something that will be both easy to pick up, and powerfull enough to bother > spending time to learn? Thanks. If you're interested in writing fast code, and are willing to spend time developing it, then C is a reasonable choice. As long as you stick to ANSI-compatible constructs, your data-crunching code should be portable to wide variety of systems. If you want to perform I/O beyod simple byte-stream files (especially involving a terminal or window), then you'll probably have to use platform-specific extensions, but you can isolate these in a set of routines which change from machine to machine and insulate the underyling code from the environment. If you can afford it, I'd recommend getting a C compiler with a good debugger, since there's little that can replace actually tracing the execution of problem code (IMHO). As long as people are plugging their favorite "high-level" language, I'd suggest you have a look at Perl as well. Its control syntax is much like C, so it's relatively easy to switch back and forth. It has intrinsic numeric and string data types, and automatically handles type conversions, memory management, and many of the other 'housekeeping' activities you've got to code into a C program. It runs on a very broad range of systems, so Perl programs are likely to port well (again assuming that you haven't made extensive use of calls out to the OS. It's slower than C -- it's a semi-interpreted language -- but is still quite efficient, and there's a nice interface to external C routines which allows you to implement the parts of your algorithm that need to fly in C and converse easily with Perl. It has a large community developing both the language itself and task-specific extensions. Finally, it's free. Sounds pretty nice, no? :-) It's not the solution to all your problems, but we've found it very good for general-use procedural programming. Regards, Charles Bailey -- !------------------------------------------------------------------------------- ! Computational Biology and Informatics Laboratory ! Dept. of Genetics, Univ. of Pennsylvania School of Medicine ! Philadelphia, PA USA 19104 Tel. (215) 573-3112 ! Internet: bailey@genetics.upenn.edu !------------------------------------------------------------------------------- From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!is.bbsrc.ac.uk!winskill From: winskill@bbsrc.ac.uk (Andy Winskill) Newsgroups: bionet.software Subject: Re: Programming language querry Date: 7 Jun 1995 15:34:24 GMT Organization: Biotechnology & Biological Sciences Research Council Lines: 13 Distribution: world Message-ID: <3r4gu0$a43@is.bbsrc.ac.uk> References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> <1995Jun7.124721.22510@emba.uvm.edu> Reply-To: andy.winskill@bbsrc.ac.uk NNTP-Posting-Host: arco7.cc.bbsrc.ac.uk X-Newsreader: mxrn 6.18-16 I would suggest C++. I my experience if you've not done any programming before then C++ is, possibly, much easier to pick up than C. It also gives you access to many publically avaiable class libraries. I'm pretty certain I've seen some molecular biology classes out there. Cheers, Andy -- Andy Winskill | Computing Centre ,Biotechnology & Biological Andy.Winskill@bbsrc.ac.uk | Sciences Research Council, Harpenden, Herts. UK _____________________________+_________________________________________________ "Diplomacy is the art of saying "nice doggy" until you can find a rock." From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!news.Stanford.EDU!nntp-hub2.barrnet.net!news3.near.net!emba-news.uvm.edu!muskrat.uvm.edu!mosier From: mosier@muskrat.uvm.edu (edo) Subject: Re: Programming language querry Message-ID: <1995Jun7.124721.22510@emba.uvm.edu> Sender: news@emba.uvm.edu Organization: EMBA Computer Facility, University of Vermont X-Newsreader: TIN [version 1.2 PL2] References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> Date: Wed, 7 Jun 1995 12:47:21 GMT Lines: 36 Leonard N. Bloksberg (bloksber@pilot.msu.edu) wrote: [..] : machines right now. I'm leaning toward a C language because I understand : that programs can be compiled for UNIX, DOS, or MAC from the same code. : Is "Borland C++ 4.5 visual" a good language to dive into? Can anyone recomend : something that will be both easy to pick up, and powerfull enough to bother : spending time to learn? Thanks. pretty much any version of C which will compile in an ANSI C mode would be quite portable...ANSI C++ is also portable, however, ANSI C compilers may get stuck on the code generated in C++ mode...in other words, ANSI C++ is an extension of ANSI C, and can compile ANSI C code in addition to its own grammer...ANSI C can not compile ANSI C++ specific code... given a choice of C implementations, I would chose Borland for general programming...if you have specific needs (such as 486 optimization), you will want to read the packaging/advertising carefully... C as a language is quite powerful, being what's known as a low level language...it's closer to the operating system than higher level languages, creating quick and powerful code... as for C being easy to pick up: if you've done any programming at all, C will be an easy transition...even if you haven't, C is an excellent language to start with...there is a large assortment of fine books on learning C, from many different perspectives (such as for the Pascal programmer, for the DOS user, for the Mac user, for the complete beginner, etc)...you will find no shortage of literature... good luck, and enjoy! Og ----- hiding backwards inside of me i feel so unafraid annie, hold a little tighter i might just slip away NIN From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Newsgroups: ebi.announce,ebi.servers,bionet.molbio.embldatabank,bionet.software Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: Changes to EBI-FTP database directories Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Wed, 7 Jun 1995 13:28:03 GMT Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 48 Xref: biosci bionet.molbio.embldatabank:514 bionet.software:12297 ********************************************************************** Between June 16th & 19th 1995, the subdirectories of /pub/databases/protein_extras/ will be reorganized on ftp.ebi.ac.uk (ftp.embl-ebi.ac.uk) ********************************************************************** On June 16th, a new entry will be created for all subdirectories that are currently located in /pub/databases/protein_extras/ These new directories will be located one level higher in the directory tree e.g. /pub/databases/protein_extras/hssp will become /pub/databases/hssp On June 19th, the old locations in /pub/databases/protein_extras/ will dissappear If you run a mirror process on any of the following directories then change your scripts during the period 16-19 June Affected directories: /pub/databases/protein_extras/dssp /pub/databases/protein_extras/fssp /pub/databases/protein_extras/ftphelp.txt /pub/databases/protein_extras/hssp /pub/databases/protein_extras/misfolded /pub/databases/protein_extras/models /pub/databases/protein_extras/nrl3d /pub/databases/protein_extras/pdb /pub/databases/protein_extras/pdb_select /pub/databases/protein_extras/puu /pub/databases/protein_extras/ras If you need more information, contact nethelp@ebi.ac.uk Jeroen -- ============================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ============================================================== From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!cis.ohio-state.edu!magnus.acs.ohio-state.edu!freenet.columbus.oh.us!not-for-mail From: hcampbel@freenet.columbus.oh.us (H Campbell) Newsgroups: bionet.software Subject: Anatomy graphics Date: 7 Jun 1995 16:17:34 -0400 Organization: The Greater Columbus Freenet Lines: 13 Message-ID: <3r51gu$fmp@acme.freenet.columbus.oh.us> NNTP-Posting-Host: acme.freenet.columbus.oh.us Summary: How do I use raw graphics? X-Newsreader: TIN [version 1.2 PL2] I have downloaded what is termed raw graphic data from the Visible Human Data Set at the National Library of Medicine. It is located at the FTP site: vhp.nlm.nih.gov This material consists of digitized cross-sections of an actual human and CAT/MRI data as well. I haven't the slightest idea how to view the material. It isn't in any format that my viewing programs or other graphics manipulation programs can use, nor is it legible to a tutorial program I use. I would like to incorporate this material into tutorial programs for an anatomy course. Any suggestions? Lee Campbell From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Newsgroups: bionet.general,sci.bio,bionet.software Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!nac.no!Norway.EU.net!EU.net!news.sprintlink.net!uunet!in1.uu.net!pipex!swrinde!elroy.jpl.nasa.gov!usc!math.ohio-state.edu!uwm.edu!vixen.cso.uiuc.edu!uchinews!news From: rmoldwin@midway.uchicago.edu Subject: Re: mRNA/cDNA sequence sites? X-Nntp-Posting-Host: rmoldwin.bsd.uchicago.edu Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Organization: U. of Chicago Hospitals X-Newsreader: Date: Wed, 7 Jun 1995 18:33:23 GMT Lines: 34 Xref: biosci bionet.general:15646 sci.bio:17102 bionet.software:12306 In article <3r4ous$76d@vixen.cso.uiuc.edu>, don@meibm25.cen.uiuc.edu (Don A. Walthers) writes: >i'm trying to find a site that stores sequences without any spaces between >a certain number of nucleotides. when i search the owl database at >www.gbd.org and pick the appropriate match any sequences available have >spaces inserted every 10 NT for easier reading. i'd like to use a text >editor to search for restriction sites and other various sequences >but the spaces would interfere. thanks for any info > >-- >|----------------------------------------------------------------------------| >|Don Walthers | don@uiuc.edu | University of Illinois at UC - Microbiology | >|http://www.cen.uiuc.edu/~don/ | Engineering Workstations - Site Operator | >|____________________________________________________________________________| Hi Don: I wrote a small visual basic program to strip out spaces and numbers from GenBank and similar files. If you want, I can E-mail you a copy (that is if you use Window.) --Rich ^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^ Richard Moldwin, M.D., Ph.D. Section of Pediatric Hematology/Oncology University of Chicago Hospitals Wyler Room C408, MC 4060 5841 S. Maryland Ave., M/C 4060 Chicago, IL 60637 E-mail: rmoldwin@midway.uchicago.edu Phone 312-702-6808 Fax 312-702-988 From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!news.sprintlink.net!uunet!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Re: Programming language querry Message-ID: <1995Jun7.180314.14586@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: spasm.niddk.nih.gov Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> Date: Wed, 7 Jun 1995 18:03:14 GMT Lines: 42 In article <19950606235137.bloksber@thomashaw-at.css.msu.edu>, bloksber@pilot.msu.edu (Leonard N. Bloksberg) writes: |> I'm getting sick of waiting for some specialized applications to be written |> for me, so I'm entertaining the idea of writing my own programs. I am |> comfortable in DOS and UNIX, but I only have access to DOS and Windows |> machines right now. I'm leaning toward a C language because I understand |> that programs can be compiled for UNIX, DOS, or MAC from the same code. |> Is "Borland C++ 4.5 visual" a good language to dive into? Can anyone recomend |> something that will be both easy to pick up, and powerfull enough to bother |> spending time to learn? Thanks. Exactly what kind of custom program are you looking to write? A little utility (like a customized pocket calculator), or a molecular dynamics program? How important is having a good (graphic) user interface? How important is the PC/Mac/Unix portability? For writing little utility programs, Tcl (for PC and Unix, but probably not Macs) is OK. Visual Basic is *much* better, but only runs on PCs (Windows or DOS). For writing really big programs, I advise you to talk to an expert. Inexperienced people tend to do a poor job of the initial organizing of a very large program. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| "Biophysics has driven me to an attitude of apocalyptic doom" --Frank Delaglio From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!meibm25.cen.uiuc.edu!don From: don@meibm25.cen.uiuc.edu (Don A. Walthers) Newsgroups: bionet.general,sci.bio,bionet.software Subject: mRNA/cDNA sequence sites? Date: 7 Jun 1995 17:51:24 GMT Organization: University of Illinois at Urbana Lines: 12 Message-ID: <3r4ous$76d@vixen.cso.uiuc.edu> NNTP-Posting-Host: meibm25.cen.uiuc.edu Xref: biosci bionet.general:15645 sci.bio:17100 bionet.software:12304 i'm trying to find a site that stores sequences without any spaces between a certain number of nucleotides. when i search the owl database at www.gbd.org and pick the appropriate match any sequences available have spaces inserted every 10 NT for easier reading. i'd like to use a text editor to search for restriction sites and other various sequences but the spaces would interfere. thanks for any info -- |----------------------------------------------------------------------------| |Don Walthers | don@uiuc.edu | University of Illinois at UC - Microbiology | |http://www.cen.uiuc.edu/~don/ | Engineering Workstations - Site Operator | |____________________________________________________________________________| From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!uknet!bhamcs!news.ox.ac.uk!news From: Geoff Barton Newsgroups: bionet.software Subject: Re: Programming language querry Date: 7 Jun 1995 17:40:26 GMT Organization: Laboratory of Molecular Biophysics Lines: 34 Message-ID: <3r4oaa$lpm@news.ox.ac.uk> References: <19950606235137.bloksber@thomashaw-at.css.msu.edu> NNTP-Posting-Host: weevil.biop.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-URL: news:19950606235137.bloksber@thomashaw-at.css.msu.edu bloksber@pilot.msu.edu (Leonard N. Bloksberg) wrote: >I'm getting sick of waiting for some specialized applications to be written >for me, so I'm entertaining the idea of writing my own programs. I am >comfortable in DOS and UNIX, but I only have access to DOS and Windows >machines right now. I'm leaning toward a C language because I understand >that programs can be compiled for UNIX, DOS, or MAC from the same code. >Is "Borland C++ 4.5 visual" a good language to dive into? Can anyone recomend >something that will be both easy to pick up, and powerfull enough to bother >spending time to learn? Thanks. I'd stick with C/C++ and keep close to the ANSI standard (at least for C). You may not want to distribute your programs now, but doubtless a friend or colleague will want your code if it does something useful! Writing in ANSI C usually makes such portability easy. As to development under DOS/Windows I'd buy a compiler that includes a DOS extender. I've used the WATCOM 32 bit compiler. I just took some big C programs developed for Unix and recompiled under DOS without any problem. The Watcom compiler will also compile for OS/2 and NT and Windows. So you have some flexibility. I think it is cheaper than the Symantec compiler, at least it was a couple of years ago when I bought my copy. I wouldn't waste time trying to write code that will run on 16bit PCs. They are a dying breed. Geoff. ---------------------------------------------------------------------------- Geoffrey J. Barton Laboratory of Molecular Biophysics, University of Oxford Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K. email: gjb@bioch.ox.ac.uk Telephone: +44 1865 275368 Fax: +44 1865 510454 anonymous: ftp://geoff.biop.ox.ac.uk WWW: http://geoff.biop.ox.ac.uk ---------------------------------------------------------------------------- From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!nac.no!Norway.EU.net!EU.net!howland.reston.ans.net!news.moneng.mei.com!news.ecn.bgu.edu!willis.cis.uab.edu!news.lsu.edu!unix1.sncc.lsu.edu!unix1.sncc.lsu.edu!not-for-mail From: jtolan@tiger.lsu.edu (James Marvin Tolan) Newsgroups: bionet.software Subject: systat for windows Date: 7 Jun 1995 14:08:41 -0500 Organization: Louisiana State University Lines: 7 Message-ID: <3r4tfp$res@tiger2.ocs.lsu.edu> NNTP-Posting-Host: tiger2-t.ocs.lsu.edu X-Newsreader: TIN [version 1.2 PL2] Anybody use Systat for windows?? If so, please send me the companies mailing address or phone number. I used it at UT, but since leaving, I have caught hell trying to locate another copy of it. Thanks -JT From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!news-e1a.megaweb.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: medmult@aol.com (MedMult) Newsgroups: bionet.software Subject: Re: Anatomy Date: 7 Jun 1995 00:27:27 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 8 Sender: root@newsbf02.news.aol.com Message-ID: <3r39rf$j8i@newsbf02.news.aol.com> References: <3qjijb$t1m@galaxy.ucr.edu> Reply-To: medmult@aol.com (MedMult) NNTP-Posting-Host: newsbf02.mail.aol.com For neuroanatomy, check out Brainiac! at our Website: http://www.webcom.com/~medmult A demo is available through this site. Shari Frick Medical Multimedia Systems From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!xlink.net!rz.uni-karlsruhe.de!thorin!brewhq.swb.de!news.th-darmstadt.de!fauern!winx03!wrzx15!phak004 From: phak004@wrzx15.rz.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: PDB importing to AutoCad 12 Date: 7 Jun 1995 20:41:34 GMT Organization: University of Wuerzburg, Germany Lines: 21 Message-ID: <3r52tu$lh2@winx03.informatik.uni-wuerzburg.de> References: NNTP-Posting-Host: wrzx15.rz.uni-wuerzburg.de X-Newsreader: TIN [version 1.2 PL2] Roger Isaacson (risaacson@ucsd.edu) wrote: > I have just had the first version of a LISP routine programmed so we can > import Protein Data Bank files into AutoCad for 3D editing and doing fancier > publication drawing than is usually possible with most low end 3D molecular > graphics programs such as RasMol. We would be interested in your comments and > are willing to share the routine with anyone interested. I would be interested in some example output (since I don't have AutoCad available). Have you ever looked at the output of render programs such as the Raster3D suite? Maybe this pleases you more than RasMol drawings? (Sorry, I am not familiar with other rendering packages such as ribbons or setor due to the lack of an SGI and my lazyness to contact the authors of the respective programs.) --Cornelius. -- /* Cornelius Krasel, Institut f. Pharmakologie, Versbacher Str. 9, D-97078 */ /* Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de */ /* "Science is the game you play with God to find out what His rules are." */ From owner-software@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!news.mathworks.com!news.ultranet.com!news.sprintlink.net!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.general,sci.bio,bionet.software Subject: Re: mRNA/cDNA sequence sites? Date: 7 Jun 1995 22:46:15 GMT Organization: Biology, Indiana University - Bloomington Lines: 39 Message-ID: <3r5a7n$kc9@usenet.ucs.indiana.edu> References: <3r4ous$76d@vixen.cso.uiuc.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu Xref: biosci bionet.general:15655 sci.bio:17108 bionet.software:12310 IUBio Archive provides keyword searches of Genbank, PIR and SwissProtein databases. OWL is a non-redundant amalgam of these. Though I can't offer you OWL searching, I can offer you output of your searches in a variety of formats, including: biosequence/genbank biosequence/fasta biosequence/gcg biosequence/embl biosequence/msf biosequence/nbrf biosequence/phylip biosequence/paup biosequence/pir text/plain The caveat to this is that this server uses 'readseq' to convert to new formats, and this converter drops out the documentation from sequence entries. Your need might be served by choosing the biosequence/fasta format, which has no spaces, but has 50 bases per line. If you want all the documentation, choose the default or text/plain format. You can find this data server thru www clients, at http://iubio.bio.indiana.edu/, look in folder Genbank-Sequences/ or by gopher+ to iubio.bio.indiana.edu, in folder Genbank-Sequences/ P.S., you might also like to try the sequence retrieval service (SRS) at this site: Pick "SRS @ IUBio" from the main IUBio menu. In article <3r4ous$76d@vixen.cso.uiuc.edu> don@meibm25.cen.uiuc.edu (Don A. Walthers) writes: >i'm trying to find a site that stores sequences without any spaces between >a certain number of nucleotides. when i search the owl database at >www.gbd.org and pick the appropriate match any sequences available have >spaces inserted every 10 NT for easier reading. i'd like to use a text >editor to search for restriction sites and other various sequences >but the spaces would interfere. thanks for any info -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msunews!news From: none (Meagan Moore) Newsgroups: bionet.software Subject: Re: Anatomy graphics Date: 7 Jun 1995 23:19:50 GMT Organization: MSU Lines: 34 Message-ID: <3r5c6m$15fe@msunews.cl.msu.edu> References: <3r51gu$fmp@acme.freenet.columbus.oh.us> NNTP-Posting-Host: msf1.bch.msu.edu Mime-Version: 1.0 X-Newsreader: WinVN 0.93.10 In article <3r51gu$fmp@acme.freenet.columbus.oh.us>, hcampbel@freenet.columbus.oh.us says... > > I have downloaded wha