From owner-software@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!newshub.tc.umn.edu!newsstand.tc.umn.edu!biosci!horton From: horton@biosci.cbs.umn.edu (Robert Horton) Newsgroups: bionet.software Subject: Applescript woes Date: 2 Aug 1996 03:42:22 GMT Organization: University of Minnesota Lines: 24 Message-ID: <4trteu$c3e@epx.cis.umn.edu> NNTP-Posting-Host: biosci.cbs.umn.edu X-Newsreader: TIN [version 1.2 PL2] Dear Netters; I just got a new powermac 8500, and I've been experimenting with voice-activated control. I'd like to be able to use a voice command to tell the thing to capture a picture from my video camera to disk. (Specifically, I'd like to be able to tell it to take a picture of a fluorescent gel without having to touch, i.e., contaminate, the computer). The problem is, the "Apple Video Player" application won't launch when speech recognition is on, because they both want to use the microphone, and they don't share. So I thought I could write a script to shut off voice recognition from the "Speech" control panel, launch "Apple Video Player", take a picture, shut off "Apple Video Player", reactivate Voice Recognition, and tell me it had finished the job. No joy. Neither "Apple Video Player" nor the Speech control panel seem to be scriptable. Can it be? Any suggestions? TIA< Bob From owner-software@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!UCDAVIS.EDU!rmhorton From: rmhorton@UCDAVIS.EDU (Bob Horton) Newsgroups: bionet.software Subject: Applescripting Speech Recog and video player? Date: 1 Aug 1996 20:49:27 -0700 Organization: UC Davis, Dermatology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <32017B80.7DAA@ucdavis.edu> Reply-To: horton@biosci.cbs.umn.edu NNTP-Posting-Host: net.bio.net Dear Netters; Sorry if this is a duplication, but I'm not sure if my message really got out last time... I just got a new powermac 8500, and I've been experimenting with voice-activated control. I'd like to be able to use a voice command to tell the thing to capture a picture from my video camera to disk. (Specifically, I'd like to be able to tell it to take a picture of a fluorescent gel without having to touch, i.e., contaminate, the computer). The problem is, the "Apple Video Player" application won't launch when speech recognition is on, because they both want to use the microphone, and they don't share. So I thought I could write a script to shut off voice recognition from the "Speech" control panel, launch "Apple Video Player", take a picture, shut off "Apple Video Player", reactivate Voice Recognition, and tell me it had finished the job. No joy. Neither "Apple Video Player" nor the Speech control panel seem to be scriptable. Any suggestions? From owner-software@net.bio.net Thu Aug 01 23:00:00 1996 Date: 1 Aug 1996 16:12:02 +0300 Path: biosci!agate!news.ucdavis.edu!info.ucla.edu!newsfeed.internetmci.com!in3.uu.net!hst1us.satlink.com!satlink!un1.satlink.com!satlink!un3.satlink.com!giga.com.ar!lilio Newsgroups: bionet.software From: lilio@giga.com.ar (Lilio) Message-ID: <8389303227408@bbs.giga.com.ar> Organization: Giga System - Buenos Aires, Argentina Subject: zip to exe Lines: 11 Does anybody have a soft which allows me to convert .zip to .exe? Thank you -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GIGA SYSTEM BBS | Telnet: giga.com.ar (login: new) BUENOS AIRES - ARGENTINA | http://www.giga.com.ar From owner-software@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!EU.net!sun4nl!uva.nl!amc!eland!kuiken From: "Carla Kuiken (microbio)" Newsgroups: bionet.software Subject: Re: Help on programs for synonymous and nonsynonymous substitutions Date: Fri, 2 Aug 1996 13:13:53 +0200 Organization: Academic hospital of the University of Amsterdam Lines: 34 Message-ID: References: <3200962C.CE9@bbsrc.ac.uk> NNTP-Posting-Host: eland Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: kuiken@eland In-Reply-To: <3200962C.CE9@bbsrc.ac.uk> Hi Aengus, I don't know about Li93, but there's another program called MEGA, also by Li et al, that does syn/nonsyn substitutions. It can be obtained from Sudhir Kumar from Penn State University, email imeg@psuvm.psu.edu. It's for DOS. Carla On Thu, 1 Aug 1996, Aengus Stewart wrote: > I have a user that is looking at a group of tomato genes and > wants to do some work on synonymous and nonsynonymous > substitution. He has told me that there is a program Li93 > that a prof Li at the University of Texas has written. > > Does anyone know where I might get this or what similar > software is available. > > I tried look at the indiana ftp site but had no luck. > > Any help would be greatly appreciated. > > > Aengus > > ----------------------------------------------------------- > Aengus Stewart aengus.stewart@bbsrc.ac.uk > Computing Centre > Biotechnology and Biological Sciences Research Council > Harpenden, Herts, AL5 2JE, UK. > ----------------------------------------------------------- > > From owner-software@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!agate!spool.mu.edu!news.sgi.com!news-res.gsl.net!news.gsl.net!nntp.coast.net!nntp.primenet.com!news.cais.net!news.structured.net!empnet.com!jreese.dublclick.com!user From: josie@unboxed.com (Josie) Newsgroups: bionet.software Subject: Bolton Software Announces... Date: Fri, 02 Aug 1996 11:29:52 -0700 Organization: Software Unboxed Lines: 6 Message-ID: NNTP-Posting-Host: jreese.dublclick.com Bolton Software announces the release of Cleaver v3.6 for electronic download... Cleaver is a management and forecasting tool which runs on top of (and requires) Microsoft Excel v4.0 or later. Let Cleaver CUT business FAT so you can run leaner. For more information visit Software Unboxed on the internet at http://www.unboxed.com or on aol at keyword: Unboxed From owner-software@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!agate!spool.mu.edu!news.sgi.com!news-res.gsl.net!news.gsl.net!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!news.daimi.aau.dk!biobase!usenet From: Torben Gjetting Newsgroups: bionet.software Subject: Re: Simple helper software? Date: Thu, 01 Aug 1996 14:11:40 -0700 Organization: Kennedy Institute Lines: 28 Message-ID: <32011D8C.359C@biobase.dk> References: <31EE23F0.517D@biobase.dk> NNTP-Posting-Host: torpc.kennedy.dk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 2.01 (Win16; I) Marek Treiman wrote: > > -- > ************************************************************************> Marek Treiman, MD,DMS Associate Professor > Department of Medical Physiology, University of Copenhagen > The Panum Institute, Blegdamsvej 3C > DK-2200 Copenhagen N Fax +45-35327537 Tel. +45-35327510 > E-mail mat@biobase.dk > *********************************************************************** > > --------------------------------------------------------------- > > Hi netters! Does anyone know about a simple, inexpensive (or > shareware) software to help in the routine reading of your sequencing > films? I don’t mean optical scanning, extensive manipulations etc. - > just simply to enable one to supply as input the first few bases read > and to ask for an alignment with the previously supplied longer > reference sequence ( for inst. your standard sequence, or a homologous > sequence), to make it easy to orient yourself where you are? > > Many thanks for hints! The Danish Biobase offers access to the GCG package. In this collection of molecular biology tools you would be interested in the GELASSEMBLE program, which allows you to do the tricks you mention above. Best regards. Torben Gjetting. From owner-software@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!newsfeed.pitt.edu!newsflash.concordia.ca!news.mcgill.ca!bluejay.parasitology.mcgill.ca!user From: robin_beech@maclan.mcgill.ca (Robin Beech) Newsgroups: bionet.software Subject: Re: Applescripting Speech Recog and video player? Date: Fri, 02 Aug 1996 10:07:54 -0400 Organization: McGill University Lines: 17 Distribution: world Message-ID: References: <32017B80.7DAA@ucdavis.edu> NNTP-Posting-Host: bluejay.parasitology.mcgill.ca In article <32017B80.7DAA@ucdavis.edu>, horton@biosci.cbs.umn.edu wrote: >No joy. Neither "Apple Video Player" nor the Speech control panel >seem to be scriptable. > >Any suggestions? I can't say I have looked into whether this is possible but have you tried the free NIH Image software package? I believe there is a large community of users using Image for gel analysis and although I don't know if it is scriptable but it is possible to write your own macros in pascal for it. The NIH Image web page is Robin Beech Institute of Parasitology McGill University From owner-software@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!news.sgi.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: Prog that finds all possible synonymous mutations. Date: 2 Aug 1996 13:29:35 GMT Organization: Best Internet Communications Lines: 8 Message-ID: <4tsvrv$pir@nntp1.best.com> References: <4tmb3a$d7e@nntp3.u.washington.edu> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Greg Schaefer (gregs@u.washington.edu) wrote: : Hello, : I'm trying to do some domain swapping with several proteins that have unfortunate restriction sites. I wonder if anyone knows a program that can show all the places where synonomous mutations are possible, so I can PCR in new sites to stick th e pieces back together as unobtrusively as possible. Greg, PCGENE has just this function in a program called 'mutbase'. From owner-software@net.bio.net Thu Aug 01 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!interpath!news.sprintlink.net!news-fw-22.sprintlink.net!news.up.net!news.mtu.edu!msunews!mbi.org!deits From: deits@mbi.org (Tom Deits) Newsgroups: bionet.software Subject: Software for fermentation optimization Date: Fri, 2 Aug 1996 11:58:21 UNDEFINED Organization: Michigan Biotechnology Institute Lines: 8 Message-ID: NNTP-Posting-Host: ash.mbi.org X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] Can anyone offer recommendations for software tools which can be used for or are designed to guide the fermentation optimization process? Thanks for the help T.L. Deits deits@mbi.org From owner-software@net.bio.net Fri Aug 02 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!news-stk-200.sprintlink.net!news.sprintlink.net!news-stk-11.sprintlink.net!news2.insinc.net!roger.interlynx.net!news From: Lars Thomsen Newsgroups: bionet.software Subject: Free program that drawa a voltage profile a copies it to the clipboard (WIN95, 32bit) Date: Fri, 02 Aug 1996 04:59:14 -0400 Organization: McMaster University, Intestinal Research Disease Programme Lines: 30 Message-ID: <3201C362.E3D@interlynx.net> Reply-To: lthomsen@interlynx.net NNTP-Posting-Host: ppp05-max1.interlynx.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5a (Win95; I) Dear Reader I have made a program that generates a voltage profile as used when doing whole cell recordings. I made the program because PClamp6 is a DOS program and impossible with graphics. I then bought MicroCal Origin, but eventhough that this program has a PClamp module, it simply doesn't import the voltage profile and then you have to draw it yourself (that takes a lot of time) So you can get it from my homepage. Click on the label "PROGRAMS". The name of the program is "PROFILE" it is a true 32bit WIN95 program. Requires 800x600 as the minimum screen resolution. Whenever you change a setting the picture is updated and copied automatically to the clipboard. The cost of the program is your comments, otherwise there are no fees. So please send me line or two. DOWNLOAD (PROGRAM AVAILABLE AFTER 3.AUG 1996 8 AM) http://home.interlynx.net/~lthomsen/index.htm Have a nice time -- Lars Thomsen, MSc. PhD. 115 South Oval, Hamilton, L8S1R2 Ontario, Canada tel +1 905 777 0720 fax +1 905 777 0738 email : lthomsen@interlynx.net homepage : http://home.interlynx.net/~lthomsen/index.htm From owner-software@net.bio.net Fri Aug 02 23:00:00 1996 Path: biosci!agate!hpg30a.csc.cuhk.hk!news.cuhk.edu.hk!mailserv.cuhk.hk!b025703 From: b025703@mailserv.cuhk.hk (Leung Kwan Chi) Newsgroups: bionet.software Subject: promoter screening Date: Sat, 3 Aug 1996 14:26:34 Organization: The Chinese University of Hong Kong Lines: 11 Message-ID: NNTP-Posting-Host: @137.189.47.149 Keywords: promoter, transcription factors X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Dear All, Does anybody know what is the best method for screening the promoter of a gene to locate potential regions of transcriptional control? I would appreciate if you could E-mail your suggestion to me at: chkcheng@cuhk.edu.hk Thank you. Chris From owner-software@net.bio.net Fri Aug 02 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!news.sprintlink.net!news-stk-200.sprintlink.net!news.sprintlink.net!news-stk-11.sprintlink.net!news2.insinc.net!roger.interlynx.net!news From: Lars Thomsen Newsgroups: bionet.software Subject: Re: WARNING!! DON'T BUY COREL WEB.DESIGNER Date: Fri, 02 Aug 1996 05:01:28 -0400 Organization: McMaster University, Intestinal Research Disease Programme Lines: 20 Message-ID: <3201C3E8.3101@interlynx.net> References: <4tgjt9$adk@tigger.planet.eon.net> Reply-To: lthomsen@interlynx.net NNTP-Posting-Host: ppp05-max1.interlynx.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5a (Win95; I) Allan D. Lariviere wrote: > > This piece of expensive crap is supposed to help you design web pages. > All it gives you is 8000 images, a few templates, but not one word on > how everything is supposed to integrate together. No manual, no > tutorial. Much better programs out there like Hotdog etc. GET HOTMETAL PRO version 3. That is a excellent piece of software Check out my homepage. I did not know anything about the HTML language for 2 weeks ago. http://home.interlynx.net/~lthomsen/index.htm -- Lars Thomsen, MSc. PhD. 115 South Oval, Hamilton, L8S1R2 Ontario, Canada tel +1 905 777 0720 fax +1 905 777 0738 email : lthomsen@interlynx.net homepage : http://home.interlynx.net/~lthomsen/index.htm From owner-software@net.bio.net Sat Aug 03 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!bstsnews.kymtnnet.org!bnewsom From: Jeff Robinson Newsgroups: bionet.software Subject: Macroinvertebrate software Date: Sat, 03 Aug 1996 20:58:01 -0700 Organization: BSTS Lines: 7 Message-ID: <32041FC9.5B7C@kymtnnet.org> NNTP-Posting-Host: pm1-13.kymtnnet.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; U) Does anyone know of good software to calculate biological index, diversity, and other statistics for aquatic macroinvertebrate samples? Ever heard of Eco-Stat? Thanks, jeff@kymtnnet.org From owner-software@net.bio.net Sat Aug 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!in3.uu.net!news.gtn.com!RRZ.Uni-Koeln.DE!usenet From: cyrus.papan@uni-koeln.de (Cyrus Papan) Newsgroups: bionet.software Subject: Reconstuction Date: Sun, 04 Aug 1996 18:17:16 GMT Organization: Universitaet Koeln Lines: 12 Message-ID: <4u2pjo$4i3@news.rrz.uni-koeln.de> NNTP-Posting-Host: annexr3-5.slip.uni-koeln.de X-Newsreader: Forte Free Agent v0.55 Hi, My name is Cyrus Papan. I'm working at the Institute of Developmental Biology in Cologne/Germany. I don't know if this is the right place for this. Anyway, does somebody know about software for 3D reconstuction of anatomical structures from serial 2D sections? Win95/3,x, DOS or Apple Platform is preferred, Linux is also possible. Many thanks in advance Cyrus Papan. email: cyrus.papan@uni-koeln.de From owner-software@net.bio.net Sat Aug 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeed.internetmci.com!in2.uu.net!news.gtn.com!RRZ.Uni-Koeln.DE!usenet From: Hier Ihre Mailadresse (Hier Ihr Name) Newsgroups: bionet.software Subject: Reconstuction Date: Sun, 04 Aug 1996 17:01:01 GMT Organization: Regional Computing Center, University of Cologne Lines: 12 Message-ID: <4u2l4p$1e1@news.rrz.uni-koeln.de> NNTP-Posting-Host: annexr2-39.slip.uni-koeln.de X-Newsreader: Forte Free Agent v0.55 Hi, My name is Cyrus Papan. I'm working at the Institute of Developmental Biology in Cologne/Germany. I don't know if this is the right place for this. Anyway, does somebody know about software for 3D reconstuction of anatomical structures from serial 2D sections? Win95/3,x, DOS or Apple Platform is preferred, Linux is also possible. Many thanks in advance Cyrus Papan. email: cyrus.papan@uni-koeln.de From owner-software@net.bio.net Sat Aug 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!news From: cabot@bangs.gcg.com (Eric Cabot) Newsgroups: bionet.software Subject: Re: Alignement of sequences in PC Date: 04 Aug 1996 14:39:48 -0500 Organization: Genetics Computer Group, Madison, WI, USA Lines: 17 Sender: cabot@bangs.gcg.com Message-ID: References: <1996Jul26.124432@eucmax> <4tivqn$n5d@herald.concentric.net> NNTP-Posting-Host: din.gcg.com In-reply-to: Ketchup@cris.com's message of Mon, 29 Jul 1996 18:25:03 GMT X-Newsreader: Gnus v5.1 For manual alignments I invite you to try my multiple sequence editor Esee3 which is available via anonymous ftp from: trog.mbb.sfu.ca (directory pub/esee) or alanine.gcg.com (directory pub/msdos) the files of interest are: esee3zip.exe and xeseezip.exe Eric Cabot cabot@gcg.com -- Regards, Eric L. Cabot cabot@gcg.com From owner-software@net.bio.net Sun Aug 04 23:00:00 1996 Path: biosci!BACATA.USC.UNAL.EDU.CO!eramirez From: eramirez@BACATA.USC.UNAL.EDU.CO (EFRAIN RAMIREZ ZAPATA) Newsgroups: bionet.software Subject: Re: Reconstuction Date: 5 Aug 1996 14:43:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4u2l4p$1e1@news.rrz.uni-koeln.de> NNTP-Posting-Host: net.bio.net try at national inst of health, email them,, they have I think what u r looking for. bye hope this works for u. On Sun, 4 Aug 1996, Hier Ihr Name wrote: > Hi, > My name is Cyrus Papan. I'm working at the Institute of Developmental > Biology in Cologne/Germany. I don't know if this is the right place > for this. Anyway, does somebody know about software for 3D > reconstuction of anatomical structures from serial 2D sections? > Win95/3,x, DOS or Apple Platform is preferred, Linux is also > possible. > Many thanks in advance > Cyrus Papan. > email: cyrus.papan@uni-koeln.de > > > > From owner-software@net.bio.net Sun Aug 04 23:00:00 1996 Path: biosci!BACATA.USC.UNAL.EDU.CO!eramirez From: eramirez@BACATA.USC.UNAL.EDU.CO (EFRAIN RAMIREZ ZAPATA) Newsgroups: bionet.software Subject: Re: zip to exe Date: 5 Aug 1996 14:33:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <8389303227408@bbs.giga.com.ar> NNTP-Posting-Host: net.bio.net pkunzip!!!!!! On 1 Aug 1996, Lilio wrote: > > Does anybody have a soft which allows me to convert .zip to .exe? > > Thank you > > -- > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > GIGA SYSTEM BBS | Telnet: giga.com.ar (login: new) > BUENOS AIRES - ARGENTINA | http://www.giga.com.ar > > > From owner-software@net.bio.net Sun Aug 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!cpk-news-hub1.bbnplanet.com!snooze.ser.bbnplanet.com!tick.cs.wm.edu!library.vims.edu!news From: Mark Siddall Newsgroups: bionet.software Subject: TGARD - Windows Shell for Hennig86 Date: Mon, 05 Aug 1996 16:59:16 +0000 Organization: Va. Inst. of Marine Science, Gloucester Point Lines: 16 Message-ID: <32062864.4330@vims.edu> NNTP-Posting-Host: leech.fish.vims.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) Tiago Ramos has developed a Windows Shell for Hennig86 which will manage datasets, execute Hennig86 and visualize trees. He has made an early version of this available free of charge via the Willi Hennig Society's anonymous ftp site: ftp.vims.edu in the directory: pub/hennig as file: tgard.zip (a DOS zip file) Or from the Willi Hennig Society's software pages in the yet-to-be reviewed section: http://www.vims.edu/~mes/hennig/software.html#others but make sure in your browser Preferences' Helper Applications that files of extension type .zip are set to "SAVE". From owner-software@net.bio.net Sun Aug 04 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!usenet From: Harold Drabkin Newsgroups: bionet.software Subject: Re: zip to exe Date: Mon, 05 Aug 1996 18:14:34 -0400 Organization: Massachvsetts Institvte of Technology Lines: 7 Message-ID: <3206724A.4030@mit.edu> References: <8389303227408@bbs.giga.com.ar> NNTP-Posting-Host: methionine.mit.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Lilio wrote: > > Does anybody have a soft which allows me to convert .zip to .exe? > If you have the pkzip package, it came with a zip to exe utility to creat a self-extracting exe. From owner-software@net.bio.net Sun Aug 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!cpk-news-hub1.bbnplanet.com!snooze.ser.bbnplanet.com!tick.cs.wm.edu!library.vims.edu!news From: Mark Siddall Newsgroups: bionet.software Subject: NONA and PIWE - FREE! Date: Mon, 05 Aug 1996 16:57:15 +0000 Organization: Va. Inst. of Marine Science, Gloucester Point Lines: 20 Message-ID: <320627EB.4732@vims.edu> NNTP-Posting-Host: leech.fish.vims.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) Pablo Goloboff has generously made available the latest update of his phylogenetic software PIWE and NONA free of charge as demo versions. These versions are fully functional though they do require that you hit an extra key each time that you execute a command. The software and the documentation are available by anonymous ftp from the Willi Hennig Society anonymous ftp site: ftp.vims.edu in the directory: pub/hennig as file: pars-pag.exe (a self-extracting DOS zip file) Or from the Willi Hennig Society's software pages: http://www.vims.edu/~mes/hennig/software.html but make sure in your browser Preferences' Helper Applications that files of extension type .exe are set to "SAVE". From owner-software@net.bio.net Sun Aug 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: jmerelo@kal-el.ugr.es (J.J. Merelo Guervos) Newsgroups: bionet.software,bionet.molbio.proteins,comp.ai.neural-nets Subject: [Web]: protein 2ary structure from CD spectra using NNs Date: 5 Aug 1996 15:34:54 -0700 Organization: GeNeura Team Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <51raprl7l6.fsf@kal-el.ugr.es> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:16239 bionet.molbio.proteins:8444 comp.ai.neural-nets:23410 Dear usenetters: We announce the establishment of a web server for prediction of protein secondary structure percentages from UV circular dichroism spectra. You only need to submit 41 CD values ranging from 200 nm to 240 nm (given in deg cm^2 dmol^-1 multiplied by 0.001) and the server gives back the estimated percentages of helix, beta and rest of secondary structure of your protein plus an estimation of the accuracy of the prediction. The prediction is done using a Kohonen neural network with a 2-dimensional output layer. The algorithm has been published [1, 2] and possitively referenced in a recent review [3]. The program itself (k2d) can be retrieved by anonymous ftp (see the k2d home page for details). The http address of the k2d server is: http://kal-el.ugr.es/k2d/spectra.html The home page of the k2d program is at: http://kal-el.ugr.es/k2d/k2d.html or at http://www.embl-heidelberg.de/~andrade/k2d.html As the server just began we would be very grateful in receiving your feedback about it. J.J. Merelo M.A. Andrade References [1] Merelo, J.J., M.A. Andrade, A. Prieto and F. Moran. 1994. Neurocomputing. 6, 443-454 [2] Andrade, M.A., P. Chacon, J.J. Merelo and F. Moran. 1993. Prot. Eng. 6, 383-390 [3] Greenfield, N.J. 1996. Anal. Biochem., 235, 1-10 -- JJ Merelo | http://kal-el.ugr.es/htbin/jj-plex Grupo Geneura ---- Univ. Granada | http://kal-el.ugr.es/ From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in3.uu.net!nntp.inet.fi!news.funet.fi!news.eunet.fi!newsmaster From: Keijo Karvonen Newsgroups: bionet.software Subject: Re: zip to exe Date: Tue, 06 Aug 1996 07:52:46 +0300 Organization: Sysdeco Finland Oy Lines: 20 Message-ID: <3206CF9E.2114@sysdeco.fi> References: <8389303227408@bbs.giga.com.ar> Reply-To: keijo.karvonen@sysdeco.fi NNTP-Posting-Host: vuokko.sysdeco.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5a (Win95; I) EFRAIN RAMIREZ ZAPATA wrote: > > pkunzip!!!!!! ^^^^^^^ WRONG! You can not do that with PKUNZIP. However, you can do it with ZIP2EXE which is included in shareware distribution of PKZIP. Command syntax: ZIP2EXE filename.zip This creates a self extracting .zip compressed file named filename.exe > > On 1 Aug 1996, Lilio wrote: > > > > > Does anybody have a soft which allows me to convert .zip to .exe? > > > > Thank you > > Keijo From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in3.uu.net!ott.istar!istar.net!news.trytel.on.ca !usenet From: Dan Nedoborski Newsgroups: bionet.software Subject: CMB Announcement Date: Mon, 05 Aug 1996 19:55:02 -0500 Organization: Nedcore Enterprises Lines: 22 Message-ID: <320697E6.5BA2@ov-m.com> NNTP-Posting-Host: dan.trytel.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02Gold (Win95; I) Announcement and call for participation; Announcing the 2nd World Congress on Cellular and Molecular Biology http://www.cmb.org/ Look for; An exciting multidisciplinary program Listen to world experts report their findings Opportunity to present your research Creative environment to internationally network Professional development through 13 diverse workshops Visit exhibits and see new developments in instrumentation and equipment Please visit our Web Site at http://www.cmb.org/ for more information and online registrations. Please consider this an invitation to view our Web Site and attend our Conference! September 3rd - 6th, 1996. Ottawa, Ontario, Canada. From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in3.uu.net!news00.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!eagle.novo.dk!tshj.novo.dk!user From: tshj@novo.dk (Thomas Hoeg-Jensen) Newsgroups: bionet.software Subject: NMR data processing on a Mac Date: 5 Aug 1996 13:15:01 GMT Organization: Novo Nordisk A/S Lines: 17 Message-ID: NNTP-Posting-Host: tshj.novo.dk Hi. I wonder if anyone know of a package that will allow NMR processing on a Macintosh? The data comes from a Bruker apparatus. Thanks for any suggestions, Thomas -- Thomas Hoeg-Jensen, Ph.D. Insulin Research, Novo Nordisk A/S tshj@novo.dk -- Thomas Hoeg-Jensen, Ph.D. Insulin Research, Novo Nordisk A/S tshj@novo.dk From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!elroy.jpl.nasa.gov!lll-winken.llnl.gov!fnnews.fnal.gov!lakesis.fapesp.br!news.dcc.unicamp.br!bee.uspnet.usp.br!news From: Sergio Rosso Newsgroups: bionet.software Subject: Re: Reconstruction Date: Tue, 06 Aug 1996 17:33:26 -0300 Organization: DEG - IBUSP Lines: 29 Message-ID: <3207AC16.70F3@usp.br> References: <4u2l4p$1e1@news.rrz.uni-koeln.de> NNTP-Posting-Host: 143.107.244.68 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0b5aGold (Win95; I) Hier Ihr Name wrote: > > Hi, > My name is Cyrus Papan. I'm working at the Institute of Developmental > Biology in Cologne/Germany. I don't know if this is the right place > for this. Anyway, does somebody know about software for 3D > reconstuction of anatomical structures from serial 2D sections? > Win95/3,x, DOS or Apple Platform is preferred, Linux is also > possible. > Many thanks in advance > Cyrus Papan. > email: cyrus.papan@uni-koeln.de Your challenge is shared by my group in LabMar - Sao Paulo University - and also many other researchers. A solution is lasting too much to come! Is it possible to deal with the problem using some program like 3D-Studio? How to solve, then, the limitation to same number of vertices in all 2D Shapes? -- ********************** Sergio Rosso, Ph.D. Departamento de Ecologia Geral Instituto de Biociências Universidade de São Paulo, São Paulo (SP), Brasil. phone 55 (011) 8187529 / 55 (011) 8134151-fax [when calling internationally, local code=(11)] mailto:serrosso@usp.br; http://djsa.com/srosso/index.htm (in construction) From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!agate!news.Stanford.EDU!nntp-hub2.barrnet.net!newsfeed.internetmci.com!news.campus.mci.net!news.uky.edu!usenet From: "Michael W. Thompson" Newsgroups: bionet.software Subject: Re: Simple helper software? Date: 6 Aug 1996 21:21:12 GMT Organization: University of Kentucky Lines: 4 Message-ID: <4u8d08$bep@service3.uky.edu> References: <31EE23F0.517D@biobase.dk> <32011D8C.359C@biobase.dk> NNTP-Posting-Host: 128.163.70.124 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12(Macintosh; I; PPC) X-URL: news:32011D8C.359C@biobase.dk I'm not exactly sure, but I believe that DNA Star can be customized to read sequencing gels with the right hardware. The URL is : http://www.dnastar.com/lasergen/lasergen.htm From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!BACATA.USC.UNAL.EDU.CO!eramirez From: eramirez@BACATA.USC.UNAL.EDU.CO (EFRAIN RAMIREZ ZAPATA) Newsgroups: bionet.software Subject: help Date: 6 Aug 1996 13:44:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net can anyone tell me how can I get mopac, or molgra, or amber, or some shareware software like this? From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!in3.uu.net!hearst.acc.Virginia.EDU!newslink.runet.edu!burden.psych.runet.edu!user From: jwillner@runet.edu (Jeff Willner) Newsgroups: bionet.software Subject: Re: Applescript woes Date: Tue, 06 Aug 1996 16:08:31 -0400 Organization: Radford University Lines: 55 Message-ID: References: <4trteu$c3e@epx.cis.umn.edu> NNTP-Posting-Host: burden.psych.runet.edu In article <4trteu$c3e@epx.cis.umn.edu>, horton@biosci.cbs.umn.edu (Robert Horton) wrote: > Dear Netters; > > I just got a new powermac 8500, and I've been experimenting with > voice-activated control. I'd like to be able to use a voice command to > tell the thing to capture a picture from my video camera to disk. > (Specifically, I'd like to be able to tell it to take a picture of a > fluorescent gel without having to touch, i.e., contaminate, the > computer). The problem is, the "Apple Video Player" application won't > launch when speech recognition is on, because they both want to use the > microphone, and they don't share. > > So I thought I could write a script to shut off voice recognition from > the "Speech" control panel, launch "Apple Video Player", take a > picture, shut off "Apple Video Player", reactivate Voice Recognition, > and tell me it had finished the job. > > No joy. Neither "Apple Video Player" nor the Speech control panel seem > to be scriptable. Can it be? > > Any suggestions? > > TIA< > > Bob Bob, I've not tried to do what you're doing, so take this with the requisite grains of salt. 1. Use Quickeys from CE software. You can use it to open the requisite control panels, change their status, etc. It can be controlled from within Applescript, or you can set up macros so that they can be activated from the speech recognizer. As far as I know, Quickeys is still the best way to control applications that can't be scripted through Applescript. 2. Dump the Apple Video Player and use other software (e.g., NIH Image to capture your video. Image supports a number of video boards, plug-in digitizers, etc., and may be able to do what you want. The web site for Image is Subject: ELISA software X-Nntp-Posting-Host: neph-pc51.bsd.uchicago.edu Content-Type: text/plain; charset=us-ascii Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Content-Transfer-Encoding: 7bit Organization: Department of Medicine Mime-Version: 1.0 Date: Tue, 6 Aug 1996 16:41:04 GMT X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Lines: 12 Hi! I was wondering if anyone could refer me to software that aids in ELISA data interpretation; i.e. a program in which you can plug in your standard values and have your unknowns spit out to you. I know it sounds quite basic, but we are in need of such a program. Thanks in advance, Alice alim@medicine.bsd.uchicago.edu From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.eecs.nwu.edu!newsfeed.acns.nwu.edu!news.acns.nwu.edu!elvex38.nuts.nwu.edu!user From: rkhurana@merle.acns.nwu.edu (RK) Newsgroups: bionet.software Subject: * SURVEY * Date: Tue, 06 Aug 1996 10:47:49 -0600 Organization: none Lines: 26 Message-ID: NNTP-Posting-Host: elvex38.nuts.nwu.edu Hi out there.... E-mail your response if you have time..... Qs1: Which beverage do you like: A. Coca Cola B. Pepsi C. Other (please specify) _____________ Qs2: What age group are you in: A. Younger than 18 B. 18-29 C. 30-49 D. 50+ Qs3: Your gender: A. Male B. Female C. Other Just curious....... thats all, just curious...... Thanx for your time -- RK -- RK From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.uwa.edu.au!styx.uwa.edu.au!cs.uwa.edu.au!cpudney From: cpudney@cs.uwa.edu.au (Chris Pudney) Newsgroups: bionet.software Subject: Re: Reconstuction Date: 6 Aug 96 00:55:47 GMT Organization: The University of Western Australia Lines: 23 Message-ID: References: <4u2l4p$1e1@news.rrz.uni-koeln.de> NNTP-Posting-Host: alphapharm.pharm.uwa.edu.au X-Newsreader: NN version 6.5.0 #3 (NOV) G'day, In <4u2l4p$1e1@news.rrz.uni-koeln.de> Hier Ihre Mailadresse (Hier Ihr Name) writes: >My name is Cyrus Papan. I'm working at the Institute of Developmental >Biology in Cologne/Germany. I don't know if this is the right place >for this. Anyway, does somebody know about software for 3D >reconstuction of anatomical structures from serial 2D sections? >Win95/3,x, DOS or Apple Platform is preferred, Linux is also >possible. A good place to start is the 3D reconstruction home page: http://biocomp.arc.nasa.gov:80/3dreconstruction/ Follow links from here to such packages as IMOD and nuages. Regards, ______________________________________________________________________________ Chris Pudney Biomedical Confocal Microscopy Research Centre cpudney@alphapharm.pharm.uwa.edu.au Department of Pharmacology http://www.cs.uwa.edu.au/~chrisp The University of Western Australia PH: (+61 9) 346 4571 FAX: (+61 9) 346 3469 Nedlands, WA 6907, AUSTRALIA From owner-software@net.bio.net Mon Aug 05 23:00:00 1996 Path: biosci!biosci!not-for-mail From: andy@rag3.RZ-Berlin.MPG.DE (Andrei Grigoriev) Newsgroups: bionet.software Subject: physical mapping calculators - update Date: 6 Aug 1996 16:20:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <4u7pap$bbk@fu-berlin.de> NNTP-Posting-Host: net.bio.net I've added a calculator which uses the model of Roach (1995) for random fingerprinting to the set of physical mapping calculators. You'll need a Java-enabled browser to view these at http://www.mpimg-berlin-dahlem.mpg.de/~andy/calc/mapcalc.html Andrei Grigoriev From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in3.uu.net!ott.istar!istar.net!n3ott.istar!infoshare!passport.ca!news2.insinc.net!roger.interlynx.net!news From: Lars Thomsen Newsgroups: bionet.software Subject: Recipe program for WIN95 -get it here for free Date: Tue, 06 Aug 1996 01:36:09 -0400 Organization: McMaster University, Intestinal Research Disease Programme Lines: 50 Message-ID: <3206D9C9.7F@interlynx.net> Reply-To: lthomsen@interlynx.net NNTP-Posting-Host: ppp22-max2.interlynx.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5a (Win95; I) Dear Reader I have made a program for Windows95 that basically is a recipe program. The program has two major parts. A chemical database and a solution database. By clicking on the toolbar you can jump from one to another. When you are in the chemical database you can transfer chemicals from a spreedsheet to the current solution, by pressing the right mouse button and chosing "transfer". In the solution window you can add the desired concentration of the chemical and the program will calculate the amount of grams (mg or ml) that you need to make e.g. 1000 ml of the solution. Changing the volume will also change the calculation. The printouts are really nice and they stamped with date and time for the printout. At the printout you will also find the Chemical name, chemical formula and the location of the chemical. This is very useful because I often find myself walking back and forth to the chemical database to find the location of a drug that I forgot where is. This version is freeware, but I would like your comments and ideas for improvement. DOWNLOAD FROM : http://home.interlynx.net/~lthomsen/index.htm Click on the image map for PROGRAMS Program name : CHEMBASE 0.1 Zipped file : CHEM.ZIP contains installation program Requirements : WIN95 and a screen resolution of minimum 800x600 (best viewed in 1024x768) NB The current version must be installed in the directory C:\CHEMBASE to work. The installation program (SETUP.EXE) will by default try to install in C:\PROGRAM FILES\CHEMBASE, but then the program can't find the database. Enjoy it Lars Thomsen -- Lars Thomsen, MSc. PhD. 115 South Oval, Hamilton, L8S1R2 Ontario, Canada tel +1 905 777 0720 fax +1 905 777 0738 email : lthomsen@interlynx.net homepage : http://home.interlynx.net/~lthomsen/index.htm From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!hunter.premier.net!news.cais.net!mr.net!newshub.tc.umn.edu!fu-berlin.de!news.th-darmstadt.de!uni-erlangen.de!uni-regensburg.de!lrz-muenchen.de!news From: Klaus Salger Newsgroups: bionet.software Subject: Re: ELISA software Date: Tue, 06 Aug 1996 22:46:29 +0200 Organization: Zoologisches Institut der Uni Muenchen Lines: 31 Distribution: world Message-ID: <3207AF25.167E@zi.biologie.uni-muenchen.de> References: NNTP-Posting-Host: wap4.zi.biologie.uni-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; AIX 2) Alice Lim wrote: > > Hi! > > I was wondering if anyone could refer me to software that aids in ELISA data interpretation; > i.e. a program in which you can plug in your standard values and have your unknowns spit out to > you. I know it sounds quite basic, but we are in need of such a program. Hi Alice, every spreadsheet program (Excel etc.) should do what you want. You could type in your standard values, calculate a standard curve by regression or fitting, enter the formulas to handle your data and save it as a template. Each time you want to analyze your data you would just copy the template and type in your data to have them calculated automaticly. Hope this helps Klaus -- Klaus Salger phone : +49 (0)89 5902 -502 Zoologisches Institut FAX : -450 AG Wetterauer e-mail: salger@zi.biologie.uni-muenchen.de Luisenstr. 14 80333 Muenchen Germany BioLinks: http://www.zi.biologie.uni-muenchen.de/~salger/salger.html From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!ames!enews.sgi.com!decwrl!lll-winken.llnl.gov!fnnews.fnal.gov!lakesis.fapesp.br!bee.uspnet.usp.br!news From: Sergio Rosso Newsgroups: bionet.software Subject: Re: Reconstruction Date: Wed, 07 Aug 1996 02:49:16 -0300 Organization: DEG - IBUSP Lines: 12 Message-ID: <32082E5C.521E@usp.br> References: <4u2l4p$1e1@news.rrz.uni-koeln.de> NNTP-Posting-Host: 143.107.244.68 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0b5aGold (Win95; I) Well, fellows! That's it. See http://biocomp.arc.nasa.gov/3dreconstruction Let's work. -- ********************** Sergio Rosso, Ph.D. Departamento de Ecologia Geral Instituto de Biociências Universidade de São Paulo, São Paulo (SP), Brasil. phone 55 (011) 8187529 / 55 (011) 8134151-fax [when calling internationally, local code=(11)] mailto:serrosso@usp.br; http://djsa.com/srosso/index.htm From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!ames!enews.sgi.com!news.sgi.com!news.msfc.nasa.gov!info.uah.edu!maze.dpo.uab.edu!usenet From: Vince Nguyen Newsgroups: bionet.software Subject: HP reader Date: Wed, 07 Aug 1996 12:03:59 +0000 Organization: UAB- Department of Cell Biology Lines: 9 Message-ID: <3208862F.2BC2@uabdpo.dpo.uab.edu> Reply-To: Cba0101@uabdpo.dpo.uab.edu NNTP-Posting-Host: cba110.cmc.uab.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) Does anyone know programs or drivers for PC (Win 3.1/Win95/DOS or Mac) that can read HP formated floppy. Flow cytometry data are saved on a HP interface machine. You can post it here or email me at Cba0101@uabdpo.dpo.uab.edu Thanks in advance, Vince From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.cftnet.com!ns2.mainstreet.net!sloth.swcp.com!tesuque.cs.sandia.gov!lynx.unm.edu!bubba.NMSU.Edu!dkim From: dkim@nmsu.edu (D. KIM) Newsgroups: bionet.software Subject: Re: zip to exe Date: 5 Aug 1996 16:52:25 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 10 Message-ID: <4u58s9$ci4@bubba.NMSU.Edu> References: <8389303227408@bbs.giga.com.ar> NNTP-Posting-Host: verdi.nmsu.edu In article <8389303227408@bbs.giga.com.ar> lilio@giga.com.ar (Lilio) writes: > >Does anybody have a soft which allows me to convert .zip to .exe? > >Thank you > I think you can get zip2exe.exe from the pkware WWW site. Daniel Kim From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!ames!enews.sgi.com!EU.net!main.Germany.EU.net!fu-berlin.de!news.th-darmstadt.de!c4.hrz.uni-giessen.de!usenet From: Magnus Mueller Newsgroups: bionet.software Subject: build-up a herbarium-database ? Date: Wed, 07 Aug 1996 15:59:35 +0200 Organization: Institute for Biochemistry and Endocrinology Lines: 12 Message-ID: <3208A147.7517@vetmed.uni-giessen.de> NNTP-Posting-Host: biofrac3.vetmed.uni-giessen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win95; I) Does anyone have any tips for me concerning available software, database structure, internet pointers ... for the build-up of a catalog of a big (say 10000 sheets) herbarium of vascular plants. Thanks in advance -- Magnus Mueller ******************************************* Justus-Liebig-Universitaet Giessen EMail: magnus.mueller@vetmed.uni-giessen.de http: http://www.uni-giessen.de/~gi04/MM/ From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!demos!news.spb.su!arcom.rcom.spb.su!nfss.iephb.ru!usenet From: Alex Spirov Newsgroups: bionet.software Subject: Re: promoter screening Date: 7 Aug 1996 10:46:05 GMT Organization: Institute of Evolutionary Physiology and Biochemistry Lines: 24 Message-ID: <4u9s5d$l9n@nfss.iephb.ru> NNTP-Posting-Host: avs.iephb.ru b025703@mailserv.cuhk.hk (Leung Kwan Chi) writes: > Dear All, > > Does anybody know what is the best method for screening the promoter of a gene > to locate potential regions of transcriptional control? > > I would appreciate if you could E-mail your suggestion to me at: > chkcheng@cuhk.edu.hk > > Thank you. > Dear Chris: Try TESS on-line http://agave.humgen.upenn.edu/tess/index.html and see also TRANSFAC pages http://transfac.gbf-braunschweig.de/ Regards, Alex. From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!news-feed-1.peachnet.edu!usenet.eel.ufl.edu!news-res.gsl.net!news.gsl.net!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!demos!Gamma.RU!srcc!news1.relcom.ru!news.spb.su!arcom.rcom.spb.su!nfss.iephb.ru!usenet From: Alex Spirov Newsgroups: bionet.software Subject: Signal sequence in promoter regions? Date: 7 Aug 1996 10:36:29 GMT Organization: Institute of Evolutionary Physiology and Biochemistry Lines: 15 Message-ID: <4u9rjd$l9n@nfss.iephb.ru> NNTP-Posting-Host: avs.iephb.ru Dear Netters, Would you be so kind as to outline me briefly what algorithms and programs are commonly used for the search of promoters and transcriptional signals? Where can I get the description of programs Consindex and Sitevideo? Thank you Maria Samsonova Inst. of High-Performance Computing St.Petersburg Russia e-mail: samson@genet.lgu.spb.su From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!hpg30a.csc.cuhk.hk!news.cuhk.edu.hk!hkusuc.hku.hk!hkucc.hku.hk!h9090086 From: h9090086@hkucc.hku.hk Newsgroups: bionet.software Subject: ANybody using Reference Manager - Help! Date: 8 Aug 96 02:50:41 +0800 Organization: The University of Hong Kong Lines: 13 Message-ID: <1996Aug8.025041.1@hkucc.hku.hk> NNTP-Posting-Host: hkucc.hku.hk Anybody using Reference Manager for windows ver 6 or 7. I would like to purchase my own copy through sombody who is about to upgrade to ver 7 or who has already done so. The co. has a special deal. Please contact me -- urgent. Danny in Hong kong From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: ANybody using Reference Manager - Help! Date: 7 Aug 1996 19:54:41 GMT Organization: University of Cambridge Lines: 21 Message-ID: <4uasa1$bne@lyra.csx.cam.ac.uk> References: <1996Aug8.025041.1@hkucc.hku.hk> NNTP-Posting-Host: mole.bio.cam.ac.uk In article <1996Aug8.025041.1@hkucc.hku.hk>, wrote: >Anybody using Reference Manager for windows > >ver 6 or 7. > >I would like to purchase my own copy through sombody >who is about to upgrade to ver 7 or who has already done so. > >The co. has a special deal. > >Please contact me -- urgent. Buying upgraded copies is piracy. If you buy an upgrade, rather than an new licence, you usually lose the licence to own the old version, and cannot therefore sell it on. Check the licence that comes with your software. Tim. From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!DEKALB.COM!rramadha From: rramadha@DEKALB.COM (Ravindra Ramadhar) Newsgroups: bionet.software Subject: A Vector DataBase Date: 7 Aug 1996 12:35:20 -0700 Organization: DeKalb Genetics Corporation Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <30A7A13001431B00@smtp.dekalb.com> NNTP-Posting-Host: net.bio.net Cheers Fellow CompuBiologists, Does anyone know of a good software package that can be used to set up a sequenced based vector database? Or if that does not exist, does anyone have any suggestions on setting up a sequenced based vector database? Thanks, In advance Ravi From owner-software@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!munnari.OZ.AU!harbinger.cc.monash.edu.au!usenet From: Jeff Dyason Newsgroups: bionet.software Subject: Re: NMR data processing on a Mac Date: Wed, 07 Aug 1996 12:32:55 -0700 Organization: Victorian College of Pharmacy Lines: 21 Message-ID: <3208EF67.41C6@vcp.monash.edu.au> References: NNTP-Posting-Host: fucose.vcp.monash.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01S (X11; I; IRIX64 6.1 IP26) Thomas Hoeg-Jensen wrote: > > Hi. > > I wonder if anyone know of a package that will allow NMR processing on a > Macintosh? > The data comes from a Bruker apparatus. > There is a package called SwaN-MR which does all this. It can be downloaded from sfdzuma.usc.es, in the directory /pub/NMR. I think you need a license from the author (Dr. Balacco) for it to work at its full capability, but the information is available on the above site. Bye Jeff. -- Jeff Dyason Department of Medicinal Chemistry, Victorian College of Pharmacy, Ph: 61 3 9903-9110 Monash University, Parkville, Fax: 61 3 9903-9582 Melbourne Victoria Australia e-mail: jeff.dyason@vcp.monash.edu.au From owner-software@net.bio.net Wed Aug 07 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news-stk-200.sprintlink.net!news-stock.gsl.net!news.gsl.net!news-penn.gsl.net!news.gsl.net!news-dc.gsl.net!news.gsl.net!news.NetVision.net.il!news From: robi Newsgroups: bionet.software Subject: analyses of rhythmic processes Date: Thu, 08 Aug 96 04:07:27 PDT Organization: NetVision LTD. Lines: 6 Message-ID: NNTP-Posting-Host: ts011p12.pop4a.netvision.net.il Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage Hi friends, Does anybody know about a good software for analyzing rhythmic processes (power spectra, cosinor analysis, mesor, amplitude, acrophase...)? thanks, Robi Guttman From owner-software@net.bio.net Wed Aug 07 23:00:00 1996 Path: biosci!agate!spool.mu.edu!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in3.uu.net!ott.istar!istar.net!n3ott.istar!infoshare!passport.ca!news2.insinc.net!roger.interlynx.net!news From: Lars Thomsen Newsgroups: bionet.software Subject: Chemibase version 01 and 02 (no charge) Date: Wed, 07 Aug 1996 03:50:22 -0400 Organization: McMaster University, Intestinal Research Disease Programme Lines: 25 Message-ID: <32084ABE.76F3@interlynx.net> Reply-To: lthomsen@interlynx.net NNTP-Posting-Host: ppp16-max1.interlynx.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5a (Win95; I) Dear Reader I have made a recipe program that is called Chemibase. The program has excellent printouts and it is possible to transfer chemicals from the database to your recipe by using the right mousebutton. The program also calculates Nerst potentials. The first version 0.1 and can be downloaded from my web site (3.4 MB) The upgrade to version 0.2 (34 KB) fixes following : ) Printouts now available for the chemical database aswell 2) Calc button error message fixed. The button now loads the windows calculator 3) Scrollbars added in the main window so that the program can be viewed under any conditions -- Lars Thomsen, MSc. PhD. 115 South Oval, Hamilton, L8S1R2 Ontario, Canada tel +1 905 777 0720 fax +1 905 777 0738 email : lthomsen@interlynx.net homepage : http://home.interlynx.net/~lthomsen/index.htm From owner-software@net.bio.net Wed Aug 07 23:00:00 1996 Newsgroups: bionet.software Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in3.uu.net!news.biu.ac.il!news.huji.ac.il!wisipc.weizmann.ac.il!news From: Eitan Rubin Subject: Re: Databases of less than N% similar proteins (or portable Smith Waterman) Content-Type: text/plain; charset=us-ascii Message-ID: <3209CB15.5874@dapsas1.weizmann.ac.il> Sender: news@wisipc.weizmann.ac.il (News User) Content-Transfer-Encoding: 7bit Organization: Weizmann Inst of Science, Rehovot, Isreal References: <4tmbqg$jet@staff.cs.su.oz.au> <4to5ji$1rp@lyra.csx.cam.ac.uk> Mime-Version: 1.0 Date: Thu, 8 Aug 1996 11:10:13 GMT X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Lines: 73 Are you familiar with the following? I don't have a personal experiance with it yet. asset.note (gcguser) Wed Feb 14 11:49:12 1996 /* ================================================================== ======== = * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software is freely available to the * public for use. The National Library of Medicine and the U.S. Government * have not placed any restriction on its use or reproduction. * * Although reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite * * A. F. Neuwald and P. Green (1994) "Detecting Patterns in Protein * Sequences", J. Mol. Biol. 239:698-712. * * in any work or product based on this material. * * The data structures used in this program are part of a package * of object oriented C code for molecular biological applications * being developed by A. F. Neuwald. * * =================================================================== ======* ASSET (Aligned Segment Statistical Evaluation Tool) version 1.0 Include 3 programs: asset, purge and scan. Each of these programs require fasta formated input files. The PURGE program removes closely related sequences from an input file prior to running asset. This is important in order to reduce input sequence redundancy. The command syntax for purge is: purge where determines the maximum blosum62 relatedness score between any two sequences in the output file (the output file is created with the name .b). A score between 100 and 200 is recommended. The scan program scans a database for sequences that contain motifs detected by asset. A paper describing the details of the scan and purge programs is in preparation. The ASSET program will produce a "scan file" of the locally aligned segment blocks by using the -f option; specifies the percentage of sequences in the input file that are required to contain a motif before the corresponding motif block can be included in the scan file. The scan file is given the name .sn. From owner-software@net.bio.net Wed Aug 07 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!Andy.Law From: Andy.Law@bbsrc.ac.uk (Andy Law) Newsgroups: bionet.software Subject: Re: ANybody using Reference Manager - Help! Date: Thu, 08 Aug 1996 09:36:52 +0100 Organization: Roslin Institute Lines: 34 Message-ID: References: <1996Aug8.025041.1@hkucc.hku.hk> <4uasa1$bne@lyra.csx.cam.ac.uk> NNTP-Posting-Host: pc0734.ri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b13 In article <4uasa1$bne@lyra.csx.cam.ac.uk>, tjrc1@mole.bio.cam.ac.uk (Tim Cutts) wrote: > In article <1996Aug8.025041.1@hkucc.hku.hk>, wrote: > >Anybody using Reference Manager for windows > > > >ver 6 or 7. > > > >I would like to purchase my own copy through sombody > >who is about to upgrade to ver 7 or who has already done so. > > > >The co. has a special deal. > > > >Please contact me -- urgent. > > Buying upgraded copies is piracy. If you buy an upgrade, rather than > an new licence, you usually lose the licence to own the old version, > and cannot therefore sell it on. Check the licence that comes with > your software. > If this is what I think it is, then it is not piracy. I believe RIS were offering extra, reduced cost copies of the new version if you upgraded an existing copy. i.e. if you have version 6 and shared it with your colleague, when you upgraded to version 7, your colleague could also get a copy of version 7 at the reduced rate. I think it was something to do with RIS altering the way databases could be shared. I may be wrong - it has been known to happen in the past. Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Wed Aug 07 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!scanner.worldgate.com!ppp23.worldgate.com!user From: info@Falconar.com (Geoff Falconar) Newsgroups: bionet.software Subject: Marketing Help for Software Developers Date: Thu, 08 Aug 1996 10:26:02 -0700 Organization: WorldGate Inc. Lines: 54 Message-ID: NNTP-Posting-Host: ppp23.worldgate.com ...You have developed a viable, leading edge technology product that needs a boost into the marketplace... ...Your company is currently almost 100% dedicated to product development and engineering and you realize that this orientation won't do wonders for sales... ...You want to take your product / service international, as that is where the real big numbers are for your product... ...You need to exhibit at a major trade show and are worried about the tremendous cost and if it will pay for itself... ...Your company can benefit from expert, hands-on help in developing its marketing... ...You know there's potential to do a lot of business with large corporations but you really are not sure how to start off going about it... A company called FALCONAR MARKETING SERVICES can help you in affordable, bite-sized pieces of marketing consulting and management project work. the Web site for Falconar Marketing Services at: http://www.falconar.com and see how we can help you get the maximum potential investment . Then you can your mind of marketing stuff and get back to doing what you really do best while your company grows. If you don't have a Web browser, there is an way of contact us for more information: _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ FALCONAR MARKETING SERVICES _/ _/ Phone: 403 448-9100 _/_/_/_/ _/_/_/_/_/ _/_/_/_/ _/ _/ Fax: 479-2093 _/ _/ _/ _/ _/ _/ _/ 11930 - 76 ST _/_/_/ _/ _/ _/ _/_/_/_/ _/ _/ Edmonton AB T5B 2C7 _/ _/ _/ _/ _/ _/ Canada _/ _/ _/ _/_/_/_/ _/ _/ E-mail: Info@Falconar.com _/ _/ Web Site: www.Falconar.com _/ _/ _/ _/ Marketing consulting and project management specializing in: _/ _/ -> International Marketing & Sales _/ _/ -> Trade Show Exhibiting Management _/ _/ -> Dealer Network Development _/ _/ -> Transition from Development to Marketing Orientation _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From owner-software@net.bio.net Wed Aug 07 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.bctel.net!news.island.net!usenet From: Gordon B. Hutchinson Newsgroups: bionet.software Subject: Re:promoter screening Date: 8 Aug 1996 18:34:20 GMT Organization: RabbitHutch Biotechnology Corporation Lines: 38 Message-ID: <4udbvc$45n@cliff.island.net> References: NNTP-Posting-Host: 100mile-15.netshop.net Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: PROCOMM PLUS 3.0 for Windows Hi I have developed a program to scan vertebrate DNA sequence for promoter regions. It is available (as an IBM-PC executable program) at: ftp://iubio.bio.indiana.edu/molbio/ibmpc as file PROFIN11.EXE. A paper describing the algorithm is in press: Hutchinson, G.B. The prediction of vertebrate promoter regions using differential hexamer frequency analysis. (1996) CABIOS. Cheers, Gord Hutchinson In article b025703.6.000E71D5@mailserv.cuhk.hk, b025703@mailserv.cuhk.hk (Leung Kwan Chi) said: > >Dear All, > >Does anybody know what is the best method for screening the >promoter of a gene >to locate potential regions of transcriptional control? > >I would appreciate if you could E-mail your suggestion to me at: >chkcheng@cuhk.edu.hk > >Thank you. > >Chris > > From owner-software@net.bio.net Wed Aug 07 23:00:00 1996 Newsgroups: bionet.software,bionet.software.gcg,embnet.general,embnet.info Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!surfnet.nl!sun4nl!sci.kun.nl!caos.kun.nl!root From: "Jack A.M. Leunissen" Subject: EMBnet course: "Mastering The Bioccelerator" Message-ID: <01bb851a.e55c5ca0$844cae83@jackleun> Sender: root@caos.kun.nl (System PRIVILEGED Account) Nntp-Posting-Host: 131.174.76.132 Organization: CAOS/CAMM Center X-Newsreader: Microsoft Internet News 4.70.1085 Date: Thu, 8 Aug 1996 11:15:24 GMT Lines: 40 Xref: biosci bionet.software:16267 bionet.software.gcg:1945 CAOS/CAMM (EMBnet the Netherlands), INN (EMBnet Israel), and Compugen Ltd. organise the EMBnet sponsored course MASTERING THE BIOCCELERATOR on 18-19 Sepember, 1996 This two-day course will cover all facets of understanding of the setup and operation of the BIOCCELERATOR, search methods, and API programming. The course aims primarily at managers of bioinformatics facilities running (or intending to run) a BIOCCELERATOR for fast database searches. Location: CAOS/CAMM Center, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands Registration: Via e-mail to "bic@caos.kun.nl", stating the reason why you would benefit from this course, accompanied by a short CV. Fee: There is no registration fee. There is a limited possibility for (partial) reimbursement of the traveling costs. Deadline: Registration should be received before September 1th. The number of participants will be limited to 14. Information: Dr. Jack Leunissen, CAOS/CAMM (jackl@caos.kun.nl), or Dr. Leon Esterman, INN (lsestern@weizmann.weizmann.ac.il) +--------------------------------------------------------------+ Jack A.M. Leunissen, PhD | CAOS/CAMM Center Email: jackl@caos.kun.nl | University of Nijmegen Tel. : +31 24 365 22 48 | Toernooiveld 1 Fax : +31 24 365 29 77 | 6525 ED Nijmegen, The Netherlands | URL=http://www.caos.kun.nl/ +------- CAOS/CAMM is the Dutch National Node in EMBnet -------+ From owner-software@net.bio.net Wed Aug 07 23:00:00 1996 Newsgroups: bionet.software Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!bshomer From: bshomer@ebi.ac.uk (Benny Shomer) Subject: Re: promoter screening Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Wed, 7 Aug 1996 14:05:36 GMT References: Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 29 Leung Kwan Chi (b025703@mailserv.cuhk.hk) wrote: : Dear All, : Does anybody know what is the best method for screening the promoter of a gene : to locate potential regions of transcriptional control? : I would appreciate if you could E-mail your suggestion to me at: : chkcheng@cuhk.edu.hk Hi Chris, Use the signal scan program. Versions for Mac DOS and Unix can be found on the EBI server at: ftp://ftp.ebi.ac.uk/pub/software/mac/signalscan/ ftp://ftp.ebi.ac.uk/pub/software/dos/signalscan/ ftp://ftp.ebi.ac.uk/pub/software/unix/signalscan/ I hope it helps, Benny. -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Benny Shomer, Ph.D. Biological User Support EMBL outstation - The EBI, Tel: +44-223-494437 Hinxton Hall, Hinxton, Fax: +44-223-494468 Cambridge CB10 1RQ, UK Email: bshomer@EBI.ac.uk ~~~~~~~http://www.ebi.ac.uk/ebi_docs/staff/benny.html~~~~~~~ From owner-software@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!cdc2.cdc.net!news.texas.net!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (Ketchup) Newsgroups: bionet.software Subject: GeneDoc 1.1.4 Release (Shading and Alignment Utility for PC/Windows) Date: Fri, 09 Aug 1996 03:54:06 GMT Organization: Concentric Internet Services Lines: 59 Message-ID: <4ued21$sdd@herald.concentric.net> NNTP-Posting-Host: cnc500128.concentric.net X-Newsreader: Forte Free Agent 1.0.82 Please be informed that GeneDoc 1.1.4 has been released onto GeneDoc's web site. http://www.cris.com/~ketchup/genedoc.shtml The biggest reasons for this release are Bug Fixes and Phylogenetic Tree support. 1.1.004 CHANGES: Added Phylogenetic Scoring support. Added ability to read directly Phylips or Nexus style tree description files. Added show current score table values. Added Scoring Information output for Phylogenetic scoring. Fixed Deleting the last sequence in the tree special case bug. Fixed DNA File open and set correct score table problem. Fixed DNA Score Table values being in error. Fixed Fasta file import. Fixed Import from Sequence Edit. Fixed Attempting to open Tree View, Score View or Stat view after File New. Fixed Copy to Clipboard as a BitMap. Fixed Cursor doesn't show on first opening of stat or score view. Fixed PictFile cuts half of Lower Consensus line off. Fixed Print Preview with Child window not maximized. ======================================================= GeneDoc's Purpose and Features. GeneDoc is a full featured Multiple Sequence Alignment Editor and Shading Utility with Phylogenetic tree support. GeneDoc is also intended to help you bring your genetics research work to publication with lots of shading, page and font layout features. This is a utility that reads either .MSF multiple Sequence alignment files or can Import Fasta Format files to be saved as a .MSF file project. GeneDoc provides a comprehensive range of shading modes, functions and capabilities. These functions give flexible ways to look at the data and to show important concepts. Shading can even be done manually! GeneDoc provides output many different ways. You can print directly to the printer, export BitMaps, Text or MAC style Pict files. GeneDoc is an alignment editor, that is it allows you to Edit the alignment so that different residues from each sequence are lined up with each other. This is accomplished by moving the residues in one or all but one) sequence relative to the other sequences by inserting or deleting gaps. GeneDoc also features the exclusive Grab and Drag mode, arranging residues like beads on a string. A residue editing mode is available to allow you to change the residues values themselves. Built in DayHoff and BlockSum scoring functions allow you to be sure your alignment changes are improving the score. Scores can be determined either by a Sum of Pairs method or with the Phylogenetic tree support. GUI implimentation makes it all so easy to use! From owner-software@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!ukrv.de!jea From: jea@ukrv.de Newsgroups: bionet.software Subject: Haplotyping Date: 9 Aug 1996 05:14:01 -0700 Organization: dhzb Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608091213.AA11004@postamt1.ukrv.de> NNTP-Posting-Host: net.bio.net I want to do haplotyping and I know that several programs exist to do it. One program (HAPLO) is written in FORTRAN. Does anybody knows where I can get a version for DOS. I know that Dr. Slatkin and Dr. Excoffier from Switzerland wrote a program in DOS, but I have no telephone number or e-mail adress to contact them. I hope someone can help me. Jeanette From owner-software@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!agate!howland.erols.net!news1.erols.com!hunter.premier.net!news.cais.net!nntp.uio.no!aloechen From: aloechen@bioslave.uio.no (Ole Andreas L|chen \kstad) Newsgroups: bionet.software Subject: TOPPRED program for MS Windows? Date: 9 Aug 1996 14:39:57 GMT Organization: University of Oslo, Norway Lines: 15 Message-ID: <4ufijt$9qm@ratatosk.uio.no> NNTP-Posting-Host: bioslave.uio.no X-Newsreader: TIN [version 1.2 PL2] Does anybody know if the TOPPRED program (von Heijne G. (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive inside rule. J Mol Biol 225: 487-494) is available for PC (MS Windows)? I know that it is for MacIntosh, but ..... As far as I understand this is the best program for making secondary structure predictions of membrane proteins (?). If it is available, I would appreciate info on where and how to get tha program (maybe it is possible to get it on the Web?). Any answer will be greatly appreciated! Ole Andreas Oekstad PhD student Biotechnology Centre of Oslo Norway From owner-software@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!agate!news.ucdavis.edu!info.ucla.edu!csulb.edu!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!act.news.telstra.net!nsw.news.telstra.net!asstdc.scgt.oz.au!metro!metro!news.cs.su.oz.au!news.cs.su.oz.au!not-for-mail From: michaelw@cs.su.oz.au (Michael Wise) Newsgroups: bionet.software Subject: Bioinformatics Courses and Courseware (even of the paper kind!) Date: 9 Aug 1996 14:56:30 +1000 Organization: Basser Dept of Computer Science, Uni of Sydney, Australia Lines: 50 Message-ID: <4uegdu$c5r@staff.cs.su.oz.au> NNTP-Posting-Host: staff.cs.su.oz.au I am currently two lists relating to the teaching of Bioinformatics. Firstly, to help with some local politics, I would like to put together a list of Bioinformatics courses been offered around the world. The sort of information I require is: *) Title of course and where offered *) Level of couse ug (which year)/pg *) duration *) assumed knowledge/client population *) (if possible) rough list of topics covered The second list I am trying to compile is a list of bioinformatics teaching resources. Obvious choices here include the various ISMB and HICSS-Bio/PSB conferences, ``Sequence Analysis Primer'', but then what? Of course, I'd also include Web-based resources, but in this case I'm really only interested in course-materials sites rather than sites with tools, or sites which mainly point to other sites, which point to other sites, which .... I plan to place the latter list on the Web, but if there's sufficient interest, I can do the same with the first list. Finally, perhahaps I have simply missed it, but cannot see a bionet.software subgroup interested in bioinformatics education. Perhaps there is one somewhere else in the bionet heirarchy? Cheers (and thanks) MichaelW Dr Michael J. Wise Basser Department of Computer Science, F09 Sydney University, N.S.W. 2006 Australia Telephone: +61 2 9351 4156 FAX: +61 2 9351 3838 Internet: michaelw@cs.su.oz.au URL: http://www.cs.su.oz.au/~michaelw -- "If I'm not for myself, who is for me? But if I am only for myself, what am I? AND IF NOT NOW, WHEN?" - Sayings of the Fathers (Hillel) (emphasis my own) From owner-software@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Petar_Stojadinovic@sequana.com (Petar Stojadinovic) Newsgroups: bionet.biophysics,bionet.genome.chromosomes,bionet.neuroscience,bionet.protista,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software.srs,bionet.software.staden,bionet.software.x-plor,bionet.structural-nmr,bionet.toxicology,bionet.users.addresses,bionet.women-in-bio,bionet.xtallography Subject: Clinical Lab Automation & Development, Computational Biology,Biotech Engineering Date: 8 Aug 1996 22:36:25 -0700 Organization: Sequana Therapeutics, Inc. Lines: 13 Sender: biohelp@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:2205 bionet.genome.chromosomes:1303 bionet.neuroscience:15213 bionet.protista:584 bionet.software:16272 bionet.software.acedb:956 bionet.software.gcg:1948 bionet.software.srs:286 bionet.software.staden:221 bionet.software.x-plor:680 bionet.structural-nmr:1434 bionet.toxicology:849 bionet.users.addresses:3079 bionet.women-in-bio:5326 bionet.xtallography:2789 Wanted: Abstracts, Interested members to Join Engineers in Biotechnology Subchapter of Assoc. of Laboratory Automation (ALA) or ICAR in Europe. please send email to : petar@sequana.com PS: Do you know how I may enter a new newsgroup in alt as alt.biotech.engineers? Thank you. Petar Stojadinovic Sequana Therapeutics Inc. Engineering Dept. Phone: 619-6468263 email: petar@sequana.com From owner-software@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!homer.alpha.net!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.msfc.nasa.gov!info.uah.edu!maze.dpo.uab.edu!usenet From: Vince Nguyen Newsgroups: bionet.software Subject: Re: HP reader Date: Fri, 09 Aug 1996 11:26:02 -0500 Organization: University of Alabama at Birmingham Lines: 7 Message-ID: <320B669A.22B@uabdpo.dpo.uab.edu> References: <3208862F.2BC2@uabdpo.dpo.uab.edu> <4uf04h$ocd@arcturus.ciril.fr> Reply-To: Cba0101@uabdpo.dpo.uab.edu NNTP-Posting-Host: cba111.cmc.uab.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; 68K) I have obtained a the program HP2PC at http://facs.scripps.edu/software.html but the catch is that the floppy has to be formatted with MEDIAINI 16 option. My FACS facility personnel doesn't seem to be able to do that. Vince From owner-software@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!Norway.EU.net!usenet From: john.norheim@login.eunet.no (John Norheim) Newsgroups: bionet.software Subject: need help converting tiff - files - color.doc [1/1] Date: 9 Aug 1996 21:39:51 GMT Organization: Privat Lines: 15 Message-ID: <4ugb77$10r@elle.eunet.no> NNTP-Posting-Host: pc13.pm2-3.eunet.no Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.5 Converting *.tif - files Problem: Converting all *.tif - files in a directory from color to black-white. I have a large number (about 2000) of tif-files (produced with Canon ION-camera and software) that have been stored as color-photographs. Editing and converting each file seperately will take too much time. I am therefore looking for a graphics application with a macro/batch file that, one by one, will convert all files in the directory from color to a new black/white tif-file. I tanks evryone who gives me hint's, e-mail to: johnno@loging.eunet.no From owner-software@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!news.sgi.com!sdd.hp.com!night.primate.wisc.edu!newsspool.doit.wisc.edu!wiscnews.wiscnet.net!post.its.mcw.edu!simont From: simont@post.its.mcw.edu (Simon Twigger) Newsgroups: bionet.software Subject: Ambis densitometry softwar- importing files Date: 9 Aug 1996 16:33:54 GMT Organization: Medical College of Wisconsin - Milwaukee, WI Lines: 23 Message-ID: <4ufp9i$hs0@wiscnews.wiscnet.net> NNTP-Posting-Host: post.its.mcw.edu X-Newsreader: TIN [version 1.2 PL2] Hi there, We have the Ambis densitometry software and I would like to import files so that I can use the software for basic densitometry. If I need to do accurate measurements we have the scanner but it is miles away in another department, so I would like to be able to scan in autorads as TIF files, convert them to RAW format and pop them into Ambis to get some readings. I accept that they wont be as accurate as they could be, but that isnt a problem. I have tried taking tif files and converting them to RAW using Adobe Photoshop, however, when I come to load them up into Ambis, it fails to display the picture. When I save the file as RAW it asks for 'header size' the default being '0' and it may be that this is the wrong number in this case. Has anyone managed to import files into Ambis in this way, and if so, how did you manage it! :) Thanks in advance, Simon. From owner-software@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!jussieu.fr!univ-angers.fr!ciril.fr!usenet From: jgaraud@faust.u-strasbg.fr (Jean-Claude GARAUD) Newsgroups: bionet.software Subject: Re: HP reader Date: Fri, 09 Aug 1996 09:21:59 GMT Organization: CIRIL, Nancy, France Lines: 29 Message-ID: <4uf04h$ocd@arcturus.ciril.fr> References: <3208862F.2BC2@uabdpo.dpo.uab.edu> NNTP-Posting-Host: myrte.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Forte Free Agent 1.0.82 Vince Nguyen wrote: Have a look at http://facs.scripps.edu/software.html. The HP2PC utility by Pierluigi Lollini is what you are looking for. Works very well for me. Regards, Jean-Claude _________________________________________________________________________ Jean-Claude GARAUD Institut de Chimie Biologique Tel: 88 37 12 55 11, rue Humann Fax: 88 24 01 90 67085 STRASBOURG Cedex FRANCE _________________________________________________________________________ >Does anyone know programs or drivers for PC (Win 3.1/Win95/DOS or >Mac) that can read HP formated floppy. Flow cytometry data are >saved on a HP interface machine. >You can post it here or email me at Cba0101@uabdpo.dpo.uab.edu >Thanks in advance, >Vince From owner-software@net.bio.net Fri Aug 09 23:00:00 1996 Path: biosci!agate!howland.erols.net!news2.digex.net!lynx.unm.edu!bubba.NMSU.Edu!dkim From: dkim@nmsu.edu (D. KIM) Newsgroups: bionet.software Subject: printing a .ps file on a macintosh Date: 7 Aug 1996 17:52:18 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 14 Message-ID: <4ual4i$qn2@bubba.NMSU.Edu> NNTP-Posting-Host: verdi.nmsu.edu Hello: I would like to print a .ps file (raw postscript, NOT EPS) from a Macintosh. This is accomplished on an IBM PC compatible using the DOS copy/b command, but on a Mac, there seems to be no easy way to do it. Users of Tektronix Phaser II printers are given a nice postscript driver called SendFile PS. I don't know how to get a copy for myself however. Thanks Daniel Kim From owner-software@net.bio.net Fri Aug 09 23:00:00 1996 Path: biosci!agate!howland.erols.net!cs.utexas.edu!swrinde!news.sgi.com!nntp.coast.net!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: printing a .ps file on a macintosh Date: 10 Aug 1996 13:08:19 GMT Organization: University of Wuerzburg, Germany Lines: 15 Message-ID: <4ui1k3$rr6@winx03.informatik.uni-wuerzburg.de> References: <4ual4i$qn2@bubba.NMSU.Edu> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] D. KIM (dkim@nmsu.edu) wrote: > I would like to print a .ps file (raw postscript, NOT EPS) from a > Macintosh. This is accomplished on an IBM PC compatible using the DOS > copy/b command, but on a Mac, there seems to be no easy way to do it. Check out the LaserWriter Utilities. They allow downloading of raw postscript files directly to the printer circumventing the whole printer driver stuff. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Fri Aug 09 23:00:00 1996 Path: biosci!agate!howland.erols.net!news2.digex.net!lynx.unm.edu!bubba.NMSU.Edu!dkim From: dkim@nmsu.edu (D. KIM) Newsgroups: bionet.software Subject: Re: ELISA software Date: 7 Aug 1996 17:49:58 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 11 Message-ID: <4ual06$qk3@bubba.NMSU.Edu> References: NNTP-Posting-Host: verdi.nmsu.edu In article Alice Lim writes: >Hi! > >I was wondering if anyone could refer me to software that aids in ELISA data interpretation; >i.e. a program in which you can plug in your standard values and have your unknowns spit out to >you. I know it sounds quite basic, but we are in need of such a program. I would think that any simple spreadsheet program can be coaxed to do this. There is no need for custom software for such an application. Daniel Kim From owner-software@net.bio.net Fri Aug 09 23:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.ac.net!news.bconnex.net!news2.insinc.net!roger.interlynx.net!news From: lthomsen@interlynx.net (Lars Thomsen) Newsgroups: bionet.software Subject: Re: Outcomes Software for Medical Device Date: Fri, 09 Aug 1996 13:33:40 GMT Organization: Interlynx Lines: 31 Message-ID: <4uigj0$ef7@roger.interlynx.net> References: <4sedno$jgm@dfw-ixnews3.ix.netcom.com> NNTP-Posting-Host: ppp23-max2.interlynx.net X-Newsreader: Forte Free Agent 1.0.82 nccrsrch@ix.netcom.com(Nemours Research) wrote: This is a very simple tast so any programmer should be able to make a small program like that within two weeks. If the programmer is using Visual Basic then the database routines are really advanced and very (I mean very) easy to use. He will need a aquisition card from e.g. National Instruments (many of them supports Visual Basic). NB The program could be made in any language. I just prefer VB because it is so easy to use. I'm sorry that I do not have the time to help you. >Is anyone aware of outcomes software or companies that do this type of >programming: I need to monitor the effectiveness of a medical device, >and would like to link hospital cost accounting to such measures as >time on device, incidence of adverse effects, so that each site may see >their own results. >Is the best way to manage this through a central database and allow >access? I would like to distribute such software with each device so >that sites may monitor the effectiveness of the device themselves. Lars Thomsen, MSc. PhD. 115 South Oval, Hamilton L8S1R2 Ontario Canada tlf : +1 905 777 0720 fax : +1 905 777 0738 email : lthomsen@interlynx.net homepage : http://home.interlynx.net/~lthomsen/index.htm McMaster University, Intestinal Disease Research Program From owner-software@net.bio.net Fri Aug 09 23:00:00 1996 Path: biosci!SDSC.EDU!bourne From: bourne@SDSC.EDU (Philip Bourne) Newsgroups: bionet.software Subject: QuickPDB - A Lightweight Java Applet for Sequence/Structure Search Date: 10 Aug 1996 08:55:52 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net QuickPDB - A Sequence/Structure Search and Display Java Applet http://xtal1.sdsc.edu/misha/QuickPDB.html Ilya Shindyalov and Phil Bourne We are pleased to announce the availability of the Java applet QuickPDB. QuickPDB is a lightweight applet with two major functions: (i) Find a structure in the PDB based upon a text or sequence search. (ii) Render that structure with ability to mark up fragments in sequence and see them accordingly in structure view. QuickPDB accesses the most current (nightly updated) version of the PDB database located on San Diego Supercomputer Center (SDSC) servers and uses the new index-based database structure for fast search and retrieval which was developed at SDSC (see Bourne P.E., Shindyalov I.N. "LOCAL MACROMOLECULAR STRUCTURE DATABASE FOR CRYSTALLOGRAPHIC LABORATORIES", XVII Congress and General Assembly of the International Union of Crystallography, http://www.bmsc.washington.edu/cgi-bin/mfs/01/abstracts/abstracts/E0478.html). QuickPDB is the first of a series of applets for the analysis of macromolecules which we hope to release. The applets will rely on the generic class structure developed by the authors which implements API's to a variety of biological databases. Comments are welcome. Send comments to bourne@sdsc.edu. This work is supported by National Science Foundation through grants BIR-9507625 and ASC 8902825. From owner-software@net.bio.net Fri Aug 09 23:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.ac.net!news.bconnex.net!news2.insinc.net!roger.interlynx.net!news From: lthomsen@interlynx.net (Lars Thomsen) Newsgroups: bionet.software Subject: PClamp file format - how do I read them manually Date: Fri, 09 Aug 1996 13:27:13 GMT Organization: Interlynx Lines: 27 Message-ID: <4uig6t$eeb@roger.interlynx.net> NNTP-Posting-Host: ppp23-max2.interlynx.net X-Newsreader: Forte Free Agent 1.0.82 Dear Reader I am trying to access my PClamp files. I have used all the information available from Axon, however it is not possible to find any meaning in the way the data are stored. I just want to read my data directly from the binary files. The Axon help files explains where the binary offsets are and what the numbers are stored as (float, integers ect). However, using a hexeditor at the specified offsets shows that the information that was supposed to be in that specified location simply either doesn't exist or is totally different from what is specified. I am a big ? Any help will be greatly appreciated Lars Thomsen, MSc. PhD. 115 South Oval, Hamilton L8S1R2 Ontario Canada tlf : +1 905 777 0720 fax : +1 905 777 0738 email : lthomsen@interlynx.net homepage : http://home.interlynx.net/~lthomsen/index.htm McMaster University, Intestinal Disease Research Program From owner-software@net.bio.net Sat Aug 10 23:00:00 1996 Path: biosci!SUN.NANKAI.EDU.CN!liuy From: liuy@SUN.NANKAI.EDU.CN (liu ying) Newsgroups: bionet.software Subject: Does anyone know how to download images from internet Date: 11 Aug 1996 05:48:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608111143.AA14347@SUN.nankai.edu.cn> NNTP-Posting-Host: net.bio.net Dear netters, I am medical student of nankai unviersity. Now I am planning to collect some important images on cardiology from internet. However, I can only copy the text file to my harddisk, and cannot copy the images. Can anyone give me some advices on how to download the images via WWW browser software. Please sent your email at: liuy@sun.nankai.edu.cn Thanks a lot in advance. yingliu medical school Nankai unviersity Tianjin 300071 P.R.China From owner-software@net.bio.net Sat Aug 10 23:00:00 1996 Path: biosci!MICRO.MED.CORNELL.EDU!greg From: greg@MICRO.MED.CORNELL.EDU ("Dr. Greg Quinn") Newsgroups: bionet.software Subject: Java class consensus? Date: 11 Aug 1996 07:30:52 -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 Just checked out Ilya Shindyalov and Phil Bourne's excellent QuickPDB java applet, (see previous post in this newsgroup), and it occurred to me that it would be really cool if a standard set of biological java classes could be agreed upon (for base functions) which could be distributed and loaded onto the local machine running the java apps, which would reduce the overall download time for a bio-app. In fact, all it would really require is acentral 'registry' where one could upload a particular class which would be included in the '.zip' distribution of the bio-app classes, and likely in time, the most useful of these classes would be dominant and other classes that performed similar functions would be removed from this distribution (by the person who originally wrote them.). The latest facility of Netscape (beta7) to read a zip'd file of classes will certainly speed up java app download, but with some real big classes, it would be good if these were locally accessed. Maybe I am jumping the gun, and it's too early yet to do this, but hey, you have to start somewhere! Anyone feel like offering to act as a depository for this zipped file, where people could upload their bio-classes with a short description of what it does, and these would be added to the main zip file? Excuse me if this already exists, but it's not very well publicized if it does! From owner-software@net.bio.net Sat Aug 10 23:00:00 1996 Path: biosci!FMI.CH!plikat From: plikat@FMI.CH Newsgroups: bionet.software Subject: translation source code Date: 11 Aug 1996 10:53:02 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <320B78D5.6A78@fmi.ch> NNTP-Posting-Host: net.bio.net Help! Is there a source code available in C for the translation of a given DNA sequence? Thanks. From owner-software@net.bio.net Sat Aug 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Java class consensus? Date: 11 Aug 1996 17:04:11 GMT Organization: Biology, Indiana University - Bloomington Lines: 23 Message-ID: <4ul3qb$ess@usenet.ucs.indiana.edu> References: NNTP-Posting-Host: chipmunk.bio.indiana.edu one of the promises of java, which hasn't been fulfilled yet, is that applets, java classes, etc., would be fetched only once, or whenever updated. the current java browsers don't do this - they fetch a java applet each time you reconnect to a java html page. this is a big waste of everyone's time. having a local cache for applets is the only reasonable thing to do. there are beginnings of "standard" biology java classes out there. but i don't expect to see any more standardization with java than we have seen with c, c++, fortran, etc. there are many useful ways to skin cats; don't expect to see cat skinning be locked in a single mold. once the browser boys get their act together, expect to see applets that persist on your local computer. hopefully, they will do this in a way that individual class files can be cached and reused (thus a set of "standard" classes would speed up functions). - don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Sat Aug 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.erols.net!newsxfer2.itd.umich.edu!uunet!in2.uu.net!news.mindspring.com!usenet From: jpryan@balt.mindspring.com (Joseph P. Ryan) Newsgroups: bionet.software Subject: looking for upgrade for PFS: PROFESSIONAL FILE v1.0 database Date: Sun, 11 Aug 1996 15:44:39 GMT Organization: Joseph P. Ryan Enterprises Lines: 21 Message-ID: <4ukv53$12fg@mule1.mindspring.com> Reply-To: jpryan@balt.mindspring.com NNTP-Posting-Host: user-168-121-189-218.dialup.mindspring.com X-Newsreader: Forte Free Agent 1.0.82 Joseph P. Ryan Enterprises 12360 Glynowings Drive, P.O. Box 776 Reisterstown, MD 21136-0776 Phone: (410) 833-8741 Internet: http://www.mindspring.com/~jpryan E-Mail: jpryan@balt.mindspring.com Dear News Reader, I am looking for an upgrade for PFS: Professional File. I have version 1.0, which is a dos based program. I understand that there was a windows based version, but is now unavailable. PFS was bought out by Softkey International who will no longer sell the program. Since all my files are in this format, I would deeply appreciate any help. Thank you, Joe Ryan From owner-software@net.bio.net Sat Aug 10 23:00:00 1996 Path: biosci!BIOBASE.DK!mnm From: mnm@BIOBASE.DK (Mads Noerregaard-Madsen) Newsgroups: bionet.software Subject: Re: TOPPRED Date: 11 Aug 1996 08:21:04 -0700 Organization: Department of Molecular Biology, Odense University, Denmark Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <320D51D1.167E@biobase.dk> NNTP-Posting-Host: net.bio.net oops, something got lost in the mail - sorry. I don't know about TOPPRED, but the PredictProtein server at EMBL can perhaps be of help to you. http://www.embl-heidelberg.de/predictprotein/predictprotein.html The following was copied from their server. Refined prediction of transmembrane helices and topology (PHDtopology; examples for: request; and output) The neural network prediction of transmembrane helices (PHDhtm) is refined by a dynamic programming-like algorithm. This method resulted in correct predictions of all transmembrane helices for 89% of the 131 proteins used in a cross-validation test; more than 98% of the transmembrane helices were correctly predicted. The output of this method is used to predict topology, i.e., the orientation of the N-term with respect to the membrane. The expected accuracy of the topology prediction is > 86%. Prediction accuracy is higher than average for eukaryotic proteins and lower than average for prokaryotes. PHDtopology is more accurate than all other methods tested on identical data sets (Rost, Casadio & Fariselli, 1996a and 1996b; evaluation of accuracy). Hope this can be of any help. Mads Noerregaard-Madsen Dept. Mol. Biol. Odense University Denmark From owner-software@net.bio.net Sat Aug 10 23:00:00 1996 Path: biosci!BIOBASE.DK!mnm From: mnm@BIOBASE.DK (Mads Noerregaard-Madsen) Newsgroups: bionet.software Subject: Re: TOPPRED Date: 11 Aug 1996 07:34:08 -0700 Organization: Department of Molecular Biology, Odense University, Denmark Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: <320D46CD.41C6@biobase.dk> NNTP-Posting-Host: net.bio.net I don't know about TOPPRED, but the PredictProtein server at EMBL can perhaps be of help to you. http://www.embl-heidelberg.de/predictprotein/predictprotein.html The follwing was copied from their server. . . . Refined prediction of transmembrane helices and topology (PHDtopology; examples for: request; and output) The neural network prediction of transmembrane helices (PHDhtm) is refined by a dynamic programming-like algorithm. This method resulted in correct predictions of all transmembrane helices for 89% of the 131 proteins used in a cross-validation test; more than 98% of the transmembrane helices were correctly predicted. The output of this method is used to predict topology, i.e., the orientation of the N-term with respect to the membrane. The expected accuracy of the topology prediction is > 86%. Prediction accuracy is higher than average for eukaryotic proteins and lower than average for prokaryotes. PHDtopology is more accurate than all other methods tested on identical data sets (Rost, Casadio & Fariselli, 1996a and 1996b; evaluation of accuracy). . . . Hope this can be of any help. Mads Noerregaard-Madsen Dept. Mol. Biol. Odense University Denmark From owner-software@net.bio.net Sat Aug 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in3.uu.net!munnari.OZ.AU!harbinger.cc.monash.edu.au!usenet From: Jeff Dyason Newsgroups: bionet.software Subject: Re: printing a .ps file on a macintosh Date: Sun, 11 Aug 1996 16:02:19 -0700 Organization: Victorian College of Pharmacy Lines: 24 Message-ID: <320E667B.41C6@vcp.monash.edu.au> References: <4ual4i$qn2@bubba.NMSU.Edu> NNTP-Posting-Host: fucose.vcp.monash.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01S (X11; I; IRIX64 6.1 IP26) D. KIM wrote: > > Hello: > > I would like to print a .ps file (raw postscript, NOT EPS) from a > Macintosh. This is accomplished on an IBM PC compatible using the DOS > copy/b command, but on a Mac, there seems to be no easy way to do it. > > Users of Tektronix Phaser II printers are given a nice postscript driver > called SendFile PS. I don't know how to get a copy for myself however. There is a program called DropPS, which should be available on the info-mac archives and it will send off a postscript file to a postscript printer using a Appletalk connection. I believe that on the disks that ship with Apple laser printers there is also a program called Apple Printer Utility which will also do what you want. Bye Jeff. -- Jeff Dyason Department of Medicinal Chemistry, Victorian College of Pharmacy, Ph: 61 3 9903-9110 Monash University, Parkville, Fax: 61 3 9903-9582 Melbourne Victoria Australia e-mail: jeff.dyason@vcp.monash.edu.au From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!rockyd!cmcl2!panix!news1.erols.com!hunter.premier.net!news-res.gsl.net!news.gsl.net!swrinde!cs.utexas.edu!howland.erols.net!newsxfer2.itd.umich.edu!netnews.worldnet.att.net!news.u.washington.edu!roach From: roach@u.washington.edu (Jared Roach) Newsgroups: bionet.software Subject: Re: translation source code Date: 11 Aug 1996 23:20:04 GMT Organization: University of Washington, Seattle Lines: 328 Message-ID: <4ulpr4$l5s@nntp3.u.washington.edu> References: <320B78D5.6A78@fmi.ch> NNTP-Posting-Host: saul3.u.washington.edu NNTP-Posting-User: roach Well, here's C translation source code I wrote as an XFCN for HyperCard for the Macintosh, so you would be able to dispense with most of it for whatever you wanted it for, most likely. I include the whole code just to put it into context. Please don't hesitate to ask for clarification. Note that my elegance and experience in programming C probably falls somewhere in the middle of the lowest percentile, so be warned! The XFCN parts of the code are shareware by Mark Hanrek. // DNA2Prot XFCN by Jared Roach © August 1996 // This program translates DNA sequences // The XFCN shell was downloaded form the Web and is © 1992 Mark Hanrek //*************************************************************************************** // Hanrek XCMD Shell 1.2 // // ©1992 Mark Hanrek & The Information Workshop. All Rights Reserved. // // Note: Do all your programming between the bold black lines below. // Put additional functions you create into the "Support Functions" // section below that. Put function prototypes into ExampleXFCN.h. // /******************************************************************* Includes ********/ #include "SetUpA4.h" #include "HyperXCmd.h" #include "SuperCard.h" #include "StandardFunctions.h" #include "string.h" /******************************************************************* Main Entry ******/ pascal void main( XCmdPtr paramPtr ) // No need to ever change any of this... { RememberA0(); SetUpA4(); InitializeReturnInfo( paramPtr ); ExternalHandler( paramPtr ); RestoreA4(); } //¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥ // // DNA2ProtXFCN HyperTalk Syntax: // put 1 into frame (should be 1,2, or 3) // put 1 into flag // // put cd fld "Sequence" into seq // // put DNA2ProtXFCN( seq, frame, flag ) into cd fld "output" // // #include "DNA2ProtXFCN.h" void ExternalHandler( XCmdPtr paramPtr ) { short i=0; short k=0; short q=0; short p=0; short nFrame; short nProtLength; char pBase; char pResidue; char pSeq[3000]; char pProtSeq[1000]; size_t nSeqLength; short nFlagVariable = 0; ParamToCString( 0, pSeq ); // the first parameter is the sequence ParamToShort( 1, &nFrame ); ParamToShort( 2, &nFlagVariable ); nSeqLength=strlen(pSeq); nProtLength = (nSeqLength-nFrame+1)/3; if ( nSeqLength < 1 ) return; k = nFrame-1; q = nProtLength*3+k; for (i=k; i < q; ++i) { pBase = pSeq[i]; if ( pBase == 'A' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pResidue = 'K'; } else if ( pBase == 'C' ) { pResidue = 'N'; } else if ( pBase == 'G' ) { pResidue = 'K'; } else if ( pBase == 'T' ) { pResidue = 'N'; } else { // case of N or other character 3rd base pResidue = 'X'; } } else if ( pBase == 'C' ) { ++i; pResidue = 'T'; //all codons starting with AC are threonine } else if ( pBase == 'G' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pResidue = 'R'; } else if ( pBase == 'C' ) { pResidue = 'S'; } else if ( pBase == 'G' ) { pResidue = 'R'; } else if ( pBase == 'T' ) { pResidue = 'S'; } else { // case of N or other character 3rd base pResidue = 'X'; } } else if ( pBase == 'T' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pResidue = 'I'; } else if ( pBase == 'C' ) { pResidue = 'I'; } else if ( pBase == 'G' ) { pResidue = 'M'; } else if ( pBase == 'T' ) { pResidue = 'I'; } else { // case of N or other character 3rd base pResidue = 'X'; } } else { // case of N or other character 2nd base ++i; pResidue = 'X'; } } else if ( pBase == 'C' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pResidue = 'Q'; } else if ( pBase == 'C' ) { pResidue = 'H'; } else if ( pBase == 'G' ) { pResidue = 'Q'; } else if ( pBase == 'T' ) { pResidue = 'H'; } else { // case of N or other character 3rd base pResidue = 'X'; } } else if ( pBase == 'C' ) { ++i; pResidue = 'P'; //all codons starting with CC are proline } else if ( pBase == 'G' ) { ++i; pResidue = 'R'; //all codons starting with CG are arginine } else if ( pBase == 'T' ) { ++i; pResidue = 'L'; //all codons starting with CT are leucine } else { // case of N or other character 2nd base ++i; pResidue = 'X'; } } else if ( pBase == 'G' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pResidue = 'E'; } else if ( pBase == 'C' ) { pResidue = 'D'; } else if ( pBase == 'G' ) { pResidue = 'E'; } else if ( pBase == 'T' ) { pResidue = 'D'; } else { // case of N or other character 3rd base pResidue = 'X'; } } else if ( pBase == 'C' ) { ++i; pResidue = 'A'; //all codons starting with GC are alanine } else if ( pBase == 'G' ) { ++i; pResidue = 'G'; //all codons starting with GG are glycine } else if ( pBase == 'T' ) { ++i; pResidue = 'V'; //all codons starting with GT are valine } else { // case of N or other character 2nd base ++i; pResidue = 'X'; } } else if ( pBase == 'T' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pResidue = ' '; } else if ( pBase == 'C' ) { pResidue = 'Y'; } else if ( pBase == 'G' ) { pResidue = ' '; } else if ( pBase == 'T' ) { pResidue = 'Y'; } else { // case of N or other character 3rd base pResidue = 'Y'; // I call uncertainty between tyrosine and stop: tyrosine } } else if ( pBase == 'C' ) { ++i; pResidue = 'S'; //all codons starting with TC are serine } else if ( pBase == 'G' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pResidue = ' '; } else if ( pBase == 'C' ) { pResidue = 'C'; } else if ( pBase == 'G' ) { pResidue = 'W'; } else if ( pBase == 'T' ) { pResidue = 'C'; } else { // case of N or other character 3rd base pResidue = 'X'; } } else if ( pBase == 'T' ) { pBase = pSeq[++i]; if ( pBase == 'A' ) { pResidue = 'L'; } else if ( pBase == 'C' ) { pResidue = 'F'; } else if ( pBase == 'G' ) { pResidue = 'L'; } else if ( pBase == 'T' ) { pResidue = 'F'; } else { // case of N or other character 3rd base pResidue = 'X'; } } else { // case of N or other character 2nd base ++i; pResidue = 'X'; } } else { // case of N or other character 1st base ++i; ++i; pResidue = 'X'; } pProtSeq[p++]=pResidue; } //Return Result for (i=0; i < p; ++i) AppendReturnInfo( kResult, "|b", pProtSeq[i] ); AppendReturnInfo( kResult, "\r"); if (nFlagVariable == 1) AppendReturnInfo( kResult, "\r DNA2Prot XFCN copyright Jared Roach 8/8/96 v0.01"); } From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!gatech!news.jsums.edu!news.uoregon.edu!news-res.gsl.net!news.gsl.net!news.sprintlink.net!news-dc-5.sprintlink.net!news.sprintlink.net!news-dc-9.sprintlink.net!hermes.is.co.za!dodo.global.co.za!news From: "Warren Larkan" Newsgroups: bionet.software Subject: Screen Saver Date: 11 Aug 1996 23:37:00 GMT Organization: Global Internet access Lines: 1 Message-ID: <01bb87ce$33b91180$0ea603c4@warrenl.global.co.za> Reply-To: "Warren Larkan" NNTP-Posting-Host: 196.3.166.14 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet News 4.70.1132 Where can I get scrantic screen saver? From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!gatech!news.jsums.edu!news.uoregon.edu!arclight.uoregon.edu!enews.sgi.com!news.sgi.com!news.msfc.nasa.gov!info.uah.edu!maze.dpo.uab.edu!usenet From: Vince Nguyen Newsgroups: bionet.software Subject: Re: cuuter restriction enzyme tool Date: Mon, 12 Aug 1996 03:15:47 -0500 Organization: University of Alabama at Birmingham Lines: 8 Message-ID: <320EE833.39CD@uabdpo.dpo.uab.edu> References: <320E1569.3333@eosc.osshe.edu> Reply-To: Cba0101@uabdpo.dpo.uab.edu NNTP-Posting-Host: tty22.maze.ppp.uab.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5aGold (Win95; I) It is at http://firstmarket.com/firstmarket/cutter/ but currently there is some problem at the site. The mirror sites is http://www.medkem.gu.se/cutter Have fun, Vince Nguyen UAB From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!news.sgi.com!csulb.edu!news.uoregon.edu!newsfeed.orst.edu!osshe.edu!eaglecap!news From: "J. Rinehart" Newsgroups: bionet.software Subject: cutter restriction analysis tool Date: Sun, 11 Aug 1996 10:24:42 -0700 Organization: Eastern Oregon State College Lines: 8 Message-ID: <320E175A.79F9@eosc.osshe.edu> NNTP-Posting-Host: drusilla Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win16; I) CC: J., Rinehart Can anyone direct me to a web-based service called "Cutter"? It analyzes a given sequence for restriction enzyme sites and gives an easy-to follow analysis. I had this site bookmarked but my web-browser crashed and I was forced to re-install, losing my bookmarks in the process. Thanks in advance for your assistance! J. Rinehart Eastern Oregon State College From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!news.sgi.com!news-res.gsl.net!news.gsl.net!news.uoregon.edu!newsfeed.orst.edu!osshe.edu!eaglecap!news From: "J. Rinehart" Newsgroups: bionet.software Subject: cuuter restriction enzyme tool Date: Sun, 11 Aug 1996 10:16:25 -0700 Organization: Eastern Oregon State College Lines: 8 Message-ID: <320E1569.3333@eosc.osshe.edu> NNTP-Posting-Host: drusilla Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win16; I) CC: J., Rinehart Can anyone direct me to a web-based service called "Cutter"? It analyzes a given sequence for restriction enzyme sites and gives an easy-to follow analysis. I had this site bookmarked but my web-browser crashed and I was forced to re-install, losing my bookmarks in the process. Thanks in advance for your assistance! J. Rinehart Eastern Oregon State College From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!mcrcr6!cmcl2!news.nyu.edu!mcrcr1.med.nyu.edu!user Newsgroups: bionet.software Subject: Re: printing a .ps file on a macintosh Message-ID: From: browns02@mcrcr.med.nyu.edu (Stuart M. Brown) Date: Mon, 12 Aug 1996 15:46:12 -0500 References: <4ual4i$qn2@bubba.NMSU.Edu> <320E667B.41C6@vcp.monash.edu.au> Organization: NYU-MC Research Computing Resource NNTP-Posting-Host: mcrcr1.med.nyu.edu Lines: 29 In article <320E667B.41C6@vcp.monash.edu.au>, Jeff Dyason wrote: > D. KIM wrote: > > > > Hello: > > > > I would like to print a .ps file (raw postscript, NOT EPS) from a > > Macintosh. This is accomplished on an IBM PC compatible using the DOS > > copy/b command, but on a Mac, there seems to be no easy way to do it. > > > > Users of Tektronix Phaser II printers are given a nice postscript driver > > called SendFile PS. I don't know how to get a copy for myself however. > > There is a program called DropPS, which should be available on the info-mac > archives and it will send off a postscript file to a postscript printer using a > Appletalk connection. I believe that on the disks that ship with Apple laser > printers there is also a program called Apple Printer Utility which will also > do what you want. If you want to preview and manipulate a postcript file on a Mac, get the shareware utility program "Ghostscript". -- Stuart M. Brown, Molecular Biology Consultant NYU-MC Research Computing Resource, Dept. of Cell Biology 550 First Ave, New York, NY 10016 Phone: (212)263-7689 FAX: (212)263-8139 From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!oitnews.harvard.edu!news.dfci.harvard.edu!usenet From: "Matthew P. Frosch, M.D., Ph.D." Newsgroups: bionet.software Subject: Re: cutter restriction analysis tool Date: Mon, 12 Aug 1996 09:27:10 +0000 Organization: Brigham and Women's Hospital Lines: 2 Message-ID: <320EF8EE.1942@dsg.harvard.edu> References: <4ul4ns$1cj@eaglecap.eosc.osshe.edu> NNTP-Posting-Host: 134.174.88.158 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b6 (Macintosh; I; PPC) Try: http://www.ccsi.com/firstmarket/cutter/cutter%2b.html From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: translation source code Date: 12 Aug 1996 05:57:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 380 Sender: daemon@net.bio.net Distribution: world Message-ID: <199608121257.IAA11301@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net A problem with this code is that it does not take into account the various genetic codes which exist. The Standard Code The Vertebrate Mitochondrial Code The Yeast Mitochondrial Code The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code The Invertebrate Mitochondrial Code The Ciliate, Dasycladacean and Hexamita Nuclear Code The Echinoderm Mitochondrial Code The Euplotid Nuclear Code The Bacterial "Code" The Alternative Yeast Nuclear Code The Ascidian Mitochondrial Code The Flatworm Mitochondrial Code The Blepharisma Nuclear Code To see a description of these codes, have a look at: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c We have something in our toolkit for translations (using the various genetic codes as an argument), but I will need to look into it a little, and tweese out what you may want. On the other hand, the code below may be all you need as far as translations are concerned, if you don't care or worry about alternative codes. cheers, f. -- | B.F. Francis Ouellette | GenBank | | francis@ncbi.nlm.nih.gov > From roach@u.washington.edu Mon Aug 12 05:04:21 1996 > To: bio-soft@net.bio.net > From: roach@u.washington.edu (Jared Roach) > Subject: Re: translation source code > Date: 11 Aug 1996 23:20:04 GMT > NNTP-Posting-Host: saul3.u.washington.edu > NNTP-Posting-User: roach > > Well, here's C translation source code I wrote as an XFCN for HyperCard > for the Macintosh, so you would be able to dispense with most of it for > whatever you wanted it for, most likely. I include the whole code just to > put it into context. Please don't hesitate to ask for clarification. > Note that my elegance and experience in programming C probably falls > somewhere in the middle of the lowest percentile, so be warned! > The XFCN parts of the code are shareware by Mark Hanrek. > > // DNA2Prot XFCN by Jared Roach © August 1996 > // This program translates DNA sequences > // The XFCN shell was downloaded form the Web and is © 1992 Mark Hanrek > > > //*************************************************************************************** > // Hanrek XCMD Shell 1.2 > // > // ©1992 Mark Hanrek & The Information Workshop. All Rights Reserved. > // > // Note: Do all your programming between the bold black lines below. > // Put additional functions you create into the "Support Functions" > // section below that. Put function prototypes into ExampleXFCN.h. > // > > /******************************************************************* Includes ********/ > > #include "SetUpA4.h" > #include "HyperXCmd.h" > #include "SuperCard.h" > #include "StandardFunctions.h" > #include "string.h" > > /******************************************************************* Main Entry ******/ > > pascal void main( XCmdPtr paramPtr ) // No need to ever change any of this... > { > RememberA0(); > SetUpA4(); > InitializeReturnInfo( paramPtr ); > ExternalHandler( paramPtr ); > RestoreA4(); > } > > > > > //¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥¥ > // > // DNA2ProtXFCN HyperTalk Syntax: > // put 1 into frame (should be 1,2, or 3) > // put 1 into flag > // > // put cd fld "Sequence" into seq > // > // put DNA2ProtXFCN( seq, frame, flag ) into cd fld "output" > // > // > > #include "DNA2ProtXFCN.h" > > void ExternalHandler( XCmdPtr paramPtr ) > { > short i=0; > short k=0; > short q=0; > short p=0; > short nFrame; > short nProtLength; > > > char pBase; > char pResidue; > char pSeq[3000]; > char pProtSeq[1000]; > > > size_t nSeqLength; > short nFlagVariable = 0; > > > ParamToCString( 0, pSeq ); // the first parameter is the sequence > ParamToShort( 1, &nFrame ); > ParamToShort( 2, &nFlagVariable ); > > nSeqLength=strlen(pSeq); > nProtLength = (nSeqLength-nFrame+1)/3; > > > > if ( nSeqLength < 1 ) > return; > > k = nFrame-1; > q = nProtLength*3+k; > > for (i=k; i < q; ++i) { > pBase = pSeq[i]; > if ( pBase == 'A' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pResidue = 'K'; > } > else if ( pBase == 'C' ) { > pResidue = 'N'; > } > else if ( pBase == 'G' ) { > pResidue = 'K'; > } > else if ( pBase == 'T' ) { > pResidue = 'N'; > } > else { // case of N or other character 3rd base > pResidue = 'X'; > } > } > else if ( pBase == 'C' ) { > ++i; > pResidue = 'T'; //all codons starting with AC are threonine > } > else if ( pBase == 'G' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pResidue = 'R'; > } > else if ( pBase == 'C' ) { > pResidue = 'S'; > } > else if ( pBase == 'G' ) { > pResidue = 'R'; > } > else if ( pBase == 'T' ) { > pResidue = 'S'; > } > else { // case of N or other character 3rd base > pResidue = 'X'; > } > } > else if ( pBase == 'T' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pResidue = 'I'; > } > else if ( pBase == 'C' ) { > pResidue = 'I'; > } > else if ( pBase == 'G' ) { > pResidue = 'M'; > } > else if ( pBase == 'T' ) { > pResidue = 'I'; > } > else { // case of N or other character 3rd base > pResidue = 'X'; > } > } > else { // case of N or other character 2nd base > ++i; > pResidue = 'X'; > } > } > else if ( pBase == 'C' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pResidue = 'Q'; > } > else if ( pBase == 'C' ) { > pResidue = 'H'; > } > else if ( pBase == 'G' ) { > pResidue = 'Q'; > } > else if ( pBase == 'T' ) { > pResidue = 'H'; > } > else { // case of N or other character 3rd base > pResidue = 'X'; > } > } > else if ( pBase == 'C' ) { > ++i; > pResidue = 'P'; //all codons starting with CC are proline > } > else if ( pBase == 'G' ) { > ++i; > pResidue = 'R'; //all codons starting with CG are arginine > } > else if ( pBase == 'T' ) { > ++i; > pResidue = 'L'; //all codons starting with CT are leucine > } > else { // case of N or other character 2nd base > ++i; > pResidue = 'X'; > } > } > else if ( pBase == 'G' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pResidue = 'E'; > } > else if ( pBase == 'C' ) { > pResidue = 'D'; > } > else if ( pBase == 'G' ) { > pResidue = 'E'; > } > else if ( pBase == 'T' ) { > pResidue = 'D'; > } > else { // case of N or other character 3rd base > pResidue = 'X'; > } > } > else if ( pBase == 'C' ) { > ++i; > pResidue = 'A'; //all codons starting with GC are alanine > } > else if ( pBase == 'G' ) { > ++i; > pResidue = 'G'; //all codons starting with GG are glycine > } > else if ( pBase == 'T' ) { > ++i; > pResidue = 'V'; //all codons starting with GT are valine > } > else { // case of N or other character 2nd base > ++i; > pResidue = 'X'; > } > } > else if ( pBase == 'T' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pResidue = ' '; > } > else if ( pBase == 'C' ) { > pResidue = 'Y'; > } > else if ( pBase == 'G' ) { > pResidue = ' '; > } > else if ( pBase == 'T' ) { > pResidue = 'Y'; > } > else { // case of N or other character 3rd base > pResidue = 'Y'; // I call uncertainty between tyrosine and stop: tyrosine > } > } > else if ( pBase == 'C' ) { > ++i; > pResidue = 'S'; //all codons starting with TC are serine > } > else if ( pBase == 'G' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pResidue = ' '; > } > else if ( pBase == 'C' ) { > pResidue = 'C'; > } > else if ( pBase == 'G' ) { > pResidue = 'W'; > } > else if ( pBase == 'T' ) { > pResidue = 'C'; > } > else { // case of N or other character 3rd base > pResidue = 'X'; > } > } > else if ( pBase == 'T' ) { > pBase = pSeq[++i]; > if ( pBase == 'A' ) { > pResidue = 'L'; > } > else if ( pBase == 'C' ) { > pResidue = 'F'; > } > else if ( pBase == 'G' ) { > pResidue = 'L'; > } > else if ( pBase == 'T' ) { > pResidue = 'F'; > } > else { // case of N or other character 3rd base > pResidue = 'X'; > } > } > else { // case of N or other character 2nd base > ++i; > pResidue = 'X'; > } > } > else { // case of N or other character 1st base > ++i; > ++i; > pResidue = 'X'; > } > pProtSeq[p++]=pResidue; > } > > > > > > > //Return Result > for (i=0; i < p; ++i) > AppendReturnInfo( kResult, "|b", pProtSeq[i] ); > AppendReturnInfo( kResult, "\r"); > > > > if (nFlagVariable == 1) > AppendReturnInfo( kResult, "\r DNA2Prot XFCN copyright Jared Roach 8/8/96 v0.01"); > } > > > > > > > From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Newsgroups: bionet.software Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!news.eecs.nwu.edu!news.cse.psu.edu!uwm.edu!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in3.uu.net!hearst.acc.Virginia.EDU!murdoch!slip-3-14.acc.virginia.edu!user From: gregs@u.washington.edu (Greg Schaefer) Subject: protein structure prediction X-Nntp-Posting-Host: slip-3-14.acc.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Washington Date: Mon, 12 Aug 1996 00:26:38 GMT Lines: 10 Hello, Is anyone familiar with a program that can predict the structure of closely related proteins based on the known structure of one of the family members? Thanks for any suggestions. Greg Schaefer From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!carbon!night.primate.wisc.edu!sdd.hp.com!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in3.uu.net!nntp04.primenet.com!news.shkoo.com!nntp.primenet.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: protein structure prediction Date: 12 Aug 1996 01:56:12 GMT Organization: Best Internet Communications Lines: 24 Message-ID: <4um2vs$dts@nntp1.best.com> References: NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Greg Schaefer (gregs@u.washington.edu) wrote: : Hello, : Is anyone familiar with a program that can predict the structure of : closely related proteins based on the known structure of one of the family : members? Yeah, what about Promod (check out :http://www-isrec.unil.ch/PROMOD.html) There is also a web interface to this program somewhere too. COMPOSER was written at Birbeck college (UK) and they used to allow access to the first-generation version (non-commercial, it's now part of the BioSym SYBYL modelling package). Also, some guy at Rockefeller wrote a similar type of package (sorry, can't be more specific). Also, most all major commercial molecular modelling packages now have modelling-by-homology modules Hope this helps From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!CYSTEINE.NCSA.UIUC.EDU!gpappas From: gpappas@CYSTEINE.NCSA.UIUC.EDU ("Georgios Pappas Jr.") Newsgroups: bionet.software Subject: Sequence Aligment Date: 12 Aug 1996 15:01:20 -0700 Organization: University of Illinois at Urbana-Champaign Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <320F6BB0.41C6@cysteine.ncsa.uiuc.edu> NNTP-Posting-Host: net.bio.net Hi all, I'm looking for a simple routine (in C or C++) that performs a Needleman-Wunsch aligment between two sequences and returns the similarity score. Could you point me where to find that? thanks in advance. Georgios Pappas University of Illinois From owner-software@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!news.sgi.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: Java class consensus? Date: 11 Aug 1996 19:10:29 GMT Organization: Best Internet Communications Lines: 31 Message-ID: <4ulb75$qvh@nntp1.best.com> References: <4ul3qb$ess@usenet.ucs.indiana.edu> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Don Gilbert (gilbertd@bio.indiana.edu) wrote: : one of the promises of java, which hasn't been fulfilled yet, : is that applets, java classes, etc., would be fetched only once, or : whenever updated. : the current java browsers don't do this - they fetch a java : applet each time you reconnect to a java html page. this is a big : waste of ever