From owner-software@net.bio.net Fri Apr 01 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!munnari.oz.au!foxhound.dsto.gov.au!fang.dsto.gov.au!vail.levels.unisa.edu.au!levels.unisa.edu.au!ntx.City.UniSA.edu.au!yoyo.aarnet.edu.au!news.adelaide.edu.au!news.cs.su.oz.au!metro!news Newsgroups: bionet.software Subject: Re: mac drawing (mixed text and boxes problem) Message-ID: From: Mark Smith Date: Fri, 25 Mar 1994 02:57:00 GMT Sender: news@ucc.su.OZ.AU Organization: Sydney Uni Nntp-Posting-Host: mtspc.biochem.su.oz.au X-Newsreader: Lines: 29 In article <1994Mar23.180814.1793@news.gdb.org> cporter@indy.gdb.org (Chris Porter) writes: >[I don't know who wrote this because I don't have the original yet...] > >>> Having used Mac Draw II, Mac Draw Pro, Claris Works (versions 1&2) >>> Claris Impact and Cricket Draw (version 2), all these programs seem to >>> give the same result, i.e. that a drawn object aligned with some >>> characters on the screen does not print in the same relative position, >> > >I've often found that when using MacDraw, doing the allignments at a >higher magnification (800 or 1600%) means the printed result more precisely >matches what is seen on screen (at the high resolution). Some things >seem to be shifted to some degree when viewing at 100%, so it may look >wrong when you're viewing the full page. I don't know whether this will >work with your problem, but it may be worth a try... > >Chris We have found problem with presenting aligned biological sequences eg DNA or protein sequences and then try to box regions of homology This occurs in most of the mac porgrams you cite. We have found that SuperPaint does a better doing these type of things. It's not always perfect but is better than others. The drawback is that SuperPaint is harder to use than these other programs. Mark Smith Dept Biochemistry University of Sydney Sydney, Austrailia mts@biochem.su.oz.au From owner-software@net.bio.net Fri Apr 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!news.cso.uiuc.edu!lwalsh From: lwalsh@nemo.life.uiuc.edu (Laura L. Walsh) Newsgroups: bionet.software Subject: Re: PDB CONTENTS -please decipher! Date: 2 Apr 94 03:47:33 GMT Organization: University of Illinois at Urbana Lines: 35 Distribution: bionet Message-ID: References: <9404010100.AA04391@sun1> <1994Apr1.211508.4614@alw.nih.gov> NNTP-Posting-Host: nemo.life.uiuc.edu bernard@elsie.nci.nih.gov (Bernard Murray) writes: >Hello there, > Laura Lynn Walsh has done all the work for us and put together an >annotated listing of all the PDB files. I believe I collected my copy from >nemo.life.uiuc.edu but I will have to check this (correction gratefully >welcomed as I want to collect an updated version). > This file is wonderful and saves hunting through all those headers >individually. The file is also only about 200 k in size. > I hope that this is what you are looking for, > Bernard >Bernard Murray, Ph.D. >bernard@elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA) Thanks for the good word. I really appreciate it. Yes, I am working on an update. It should be available soon. I have finished around 2100 of the files and have only around 227 to go ;-) Yes, the January, 1994 release of the database has around 2327 files. I am also working on a paper about the file, so sometime soon, there may actually be a more comprehensive description of the file contents and methodology. The file is a bit too large now to email easily, so try to ftp it if you can. The new version contains annotations for all of the lysozyme files as well as all of the DNA files, plus some extra info about fold classes, which is, unfortunately, not quite complete, but still may be useful. Let me know. A beta release of the file will be put on nemo.life.uiuc.edu as soon as I can transfer it from a computer which is temporarily out of commission. Again, thanks. Maybe now they will let me get my Ph.D. ;-) Laura Lynn Walsh lwalsh@nemo.life.uiuc.edu lwalsh@silibio.ncsa.uiuc.edu From owner-software@net.bio.net Fri Apr 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!news.tamu.edu!bioch.tamu.edu!erich From: erich@bioch.tamu.edu (Eric Hebert) Newsgroups: bionet.software Subject: Re: PDB CONTENTS -please decipher! Date: 1 Apr 1994 19:12 CST Organization: Texas A&M University, Academic Computing Services Lines: 49 Distribution: bionet Message-ID: <1APR199419125566@bioch.tamu.edu> References: <9404010100.AA04391@sun1> NNTP-Posting-Host: bioch.tamu.edu News-Software: VAX/VMS VNEWS 1.41 In article , g3421101@MUCC.MAHIDOL.AC.TH (Enrique Jose Labadan Frio - SCBC - 3421101) writes... > > I just downloaded the CONTENTS.LIS from the PDB Protein Database >(pdb.pdb.bnl.gov), in order to find the protein names of the entry codes >and info on several proteins of interest to my research..... > > Does anybody have a complete list of entry names and their >corresponding protein names?... > ... >Querix Querix I may have a quick answer for you. The easiest way I can think of is to do a veronica search on the PDB gopher system. Although I haven't attempted a search for some time now the procedure is quite simple. Youe entry a keys word to be searched for... staphylococcal nuclease and the gopher search returns all the pdb*****.ent file names that contain this key word. Once you have the name of the file (files) you want. ftp into PDB and login under anonymous Type cd fullrelease Type cd uncompressed_files Type ls */pdb9rnt.ent obviously pdb9rnt.ent is the name from the search this gives yout he tape number then Type get tape8/pdb9rnt.ent and give the local file name and your done. As before, I haven't done this in awhile, so maybe someone else in Netter-Land could confirm whether this still works. Good luck and happy hunting. E. From owner-software@net.bio.net Sat Apr 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!netmbx.de!zib-berlin.de!fauern!winx03!wrzx14!bot2008 From: bot2008@wrzx14.rz.uni-wuerzburg.de (Andreas Weber) Newsgroups: bionet.software Subject: plasmid drawing program? Date: 2 Apr 1994 10:58:23 GMT Organization: University of Wuerzburg, Germany Lines: 9 Message-ID: <2njj4f$5n6@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: wrzx14 X-Newsreader: TIN [version 1.2 PL2] Hi netters, I'm looking for a good, publishing quality plasmid drawing program, if possible it should run under MS Windows. Where can I find this? Many thanks in advance Andreas From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!phibred.com!news From: Scott Nichols Subject: Re: Gene Jockey? Message-ID: X-Xxdate: Mon, 4 Apr 94 14:25:56 GMT Sender: news@phibred.com (USENET News System) Organization: Pioneer Hi-Bred International X-Useragent: Version 1.1.3 References: <9403161909.AA22981@phage.cshl.org> Date: Mon, 4 Apr 1994 20:27:10 GMT Lines: 13 In article <9403161909.AA22981@phage.cshl.org> Bobbie Peters in Grace Computer Center, peters@CSHL.ORG writes: >I am told there is a program "Gene Jockey" from a company named Biosoft >in England. Does anyone have any information about the company? Slight >preference for contacts in the USA. They are located at: PO Box 10938 Ferguson MO 63135 ph 314-524-8029 I have not used Gene Jockey but have used UltraFit by the same authors and found it both useful and easy to use. From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!wupost!ukma!seqanal.mi.uky.edu!mpm From: mpm@seqanal.mi.uky.edu (Mark Mattson) Newsgroups: bionet.software Subject: Mac downloading Date: 4 Apr 1994 14:31:50 GMT Organization: University of Kentucky, Dept. of Math Sciences Lines: 9 Message-ID: <2np8cm$8aa@s.ms.uky.edu> NNTP-Posting-Host: seqanal.mi.uky.edu X-Newsreader: TIN [version 1.1 PL9] Okay, so I've downloaded a self-converting text file to a Mac -- now what? I have experience with DOS: one simply edits the file, renames with an EXE or .COM extention, and runs. But how do you do the equivalent with a Mac? I don't even know how to access the operating system in this "user friendly" environment. Thanks for any help. Steve Barger From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!EU.net!howland.reston.ans.net!darwin.sura.net!news-feed-1.peachnet.edu!ukma!seqanal.mi.uky.edu!mpm From: mpm@seqanal.mi.uky.edu (Mark Mattson) Newsgroups: bionet.software Subject: Re: Mac downloading Date: 4 Apr 1994 17:53:57 GMT Organization: University of Kentucky, Dept. of Math Sciences Lines: 29 Distribution: world Message-ID: <2npk7l$pis@s.ms.uky.edu> References: <2npbmr$hbt@columba.udac.uu.se> NNTP-Posting-Host: seqanal.mi.uky.edu X-Newsreader: TIN [version 1.1 PL9] Gerard Kleijwegt (gerard@rigel.bmc.uu.se) wrote: : you mean a self-extracting archive file ? : how about simply double-clicking on it ? : --Gerard : ****************************************************************** : Gerard J. Kleywegt ___ : Department of Molecular Biology | | /\ : Biomedical Centre /\ -- || : Uppsala University || || || : Box 590, S-751 24 || || || : Uppsala, SWEDEN || \/ -- : -- |__| : E-mail: gerard@xray.bmc.uu.se : ****************************************************************** : "He's probably pining for the fiords ..." : ****************************************************************** : The opinions in this mail/post are fictional. Any similarity : to actual opinions, living or dead, is purely coincidental. : (Nevertheless, they're mine, mine, MINE !) : ****************************************************************** Yeah, I tried double-clicking, but the finder just tried to open it as a text document (using TeachText or something). Does this mean something's wrong with the file? Steve Barge From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!ihnp4.ucsd.edu!news.service.uci.edu!NewsWatcher!user From: myirwin@uci.edu (Mike) Newsgroups: bionet.software Subject: Re: Mac downloading Followup-To: bionet.software Date: 4 Apr 1994 20:22:04 GMT Organization: UC Irvine, Dpt Microbio Lines: 15 Distribution: world Message-ID: References: <2npbmr$hbt@columba.udac.uu.se> <2npk7l$pis@s.ms.uky.edu> NNTP-Posting-Host: 128.200.5.58 > Yeah, I tried double-clicking, but the finder just tried to open it as > a text document (using TeachText or something). Does this mean something's > wrong with the file? No, there is nothing wrong with the file. This just means that it is a generic text file. By default the Mac asks you if you want to open it with TeachText. But, TeachText is mostly good for brief messages since it has a 32k size limit. Go into your favorite word processing program (like Word) or another text editor (like Alpha) and open it from within the program...Open the program. Select Open from the file menu and navigate through the subsequent menu to locate and open you file. And jeez, you don't have to rename it or anything...what kinda primitives do you think we are? From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!columba.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.software Subject: Re: Mac downloading Date: 4 Apr 1994 15:28:27 GMT Organization: Uppsala University Lines: 33 Distribution: world Message-ID: <2npbmr$hbt@columba.udac.uu.se> References: <2np8cm$8aa@s.ms.uky.edu> NNTP-Posting-Host: rigel.bmc.uu.se In article <2np8cm$8aa@s.ms.uky.edu>, mpm@seqanal.mi.uky.edu (Mark Mattson) writes: |> Okay, so I've downloaded a self-converting text file to a Mac -- now what? |> I have experience with DOS: one simply edits the file, renames with an |> EXE or .COM extention, and runs. But how do you do the equivalent with |> a Mac? I don't even know how to access the operating system in this |> "user friendly" environment. |> |> Thanks for any help. |> |> Steve Barger you mean a self-extracting archive file ? how about simply double-clicking on it ? --Gerard ****************************************************************** Gerard J. Kleywegt ___ Department of Molecular Biology | | /\ Biomedical Centre /\ -- || Uppsala University || || || Box 590, S-751 24 || || || Uppsala, SWEDEN || \/ -- -- |__| E-mail: gerard@xray.bmc.uu.se ****************************************************************** "He's probably pining for the fiords ..." ****************************************************************** The opinions in this mail/post are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. (Nevertheless, they're mine, mine, MINE !) ****************************************************************** From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!gatech!usenet.ufl.edu!gnv.ifas.ufl.edu!glind From: glind@gnv.ifas.ufl.edu Newsgroups: bionet.software Subject: Image analysis software for IBM Message-ID: <1994Apr4.153947.4127@tower> Date: 4 Apr 94 15:39:47 -0500 Lines: 13 I am interested in any programs that are capable of doing image analysis on scanned images of transparencies (ie northern blots, sequencing gels etc) on an IBM compatible computer. Does anyone know of any software packages that are available? Any replies would be appreciated ASAP as we are under a time constraint to spend some equipment money. We have a scanner capable of scanning transparencies; all we need is the right software. Thanks in advance, ******************************************************************************** |Graeme Lindbeck (Aussie in exile) | _--_|\ | Citrus Res. & Edu. Center | |GLIND@gnv.ifas.ufl.edu | / \ | 700 Experiment Station Road | |Phone:(813) 956-1151 | \_.--._/ | Lake Alfred, Florida 33850 | |FAX: (813) 956-4631 | v | U.S.A. | ******************************************************************************** From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!newsserver.jvnc.net!netnews.upenn.edu!rudnitzk From: rudnitzk@mail.sas.upenn.edu (Ned I Rudnitzky) Newsgroups: bionet.software Subject: Origin Graphing Software Advice? Date: 4 Apr 1994 17:24:52 GMT Organization: University of Pennsylvania, School of Arts and Sciences Lines: 7 Distribution: world Message-ID: <2npih4$p6g@netnews.upenn.edu> NNTP-Posting-Host: mail.sas.upenn.edu Our lab is thinking of buying a new graphing software package called Origin , sold by MicroCal Inc. I would be interested to hear from anyone with experience with this program, specifically if there are any good reasons _NOT_ to buy it. Thank you From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!ciens.ula.ve!alejo From: alejo@ciens.ula.ve (ALEJANDRO MUJICA) Newsgroups: bionet.software Subject: Some help Date: 4 Apr 1994 15:58:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404042258.AA10692@merlin.ciens.ula.ve> NNTP-Posting-Host: net.bio.net Hello everybody, We are beginers using computer based molecular modelling software at the Universidad de Los Andes, in Venezuela for protein analysis and drugs design. At the moment we are using Hypercube's (reciently Autodesk's) Hyperchem R3 for Windows, and we found it pretty easy_to_use. We are using Hyperchem in basic protein modelling and we would like to go further... Few weeks ago, we get subscribed to some BIOSCI forums so we would like to know: 1) Is there any expierience among you using Hyperchem in homology problems? 2) Where may I found a list (or lists) of the most popular molecular modelling software, their capabilities, dealers, prices, ftp sites, etc. Any information may be useful, thanks in advance. Yours, Alejandro ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Alejandro Mujica e-mail: alejo@ula.ve Departamento de Biologia Facultad de Ciencias Universidad de Los Andes Tel: (58 74) 401284 Merida - Venezuela Fax: (58 74) 401286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!news.intercon.com!panix!zip.eecs.umich.edu!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!alberta!quartz.ucs.ualberta.ca!acs.ucalgary.ca!pc22.mid.ucalgary.ca!user From: macklon@acs.ucalgary.ca (PMacklon) Subject: Image and video printers Message-ID: Date: Mon, 4 Apr 1994 23:35:02 GMT Nntp-Posting-Host: pc22.mid.ucalgary.ca Organization: u. of c. Followup-To: bionet.software Lines: 5 Can anyone provide any comparative information or recommendations for a video (thermal or other) printer which could be used to produce hard-copy from video images captured with NIH Image software? Greyscale output only required. What about cost per print? Many thanks. From owner-software@net.bio.net Sun Apr 03 23:00:00 1994 Path: biosci!MEDINFO.AB.UMD.EDU!hlai From: hlai@MEDINFO.AB.UMD.EDU (Alexandra) Newsgroups: bionet.software Subject: Re: mac drawing (mixed text and boxes problem) Re: mac drawing (mixed text and boxes problem) Re: mac drawing (mixed text and boxes problem) Re: mac drawing (mixed text and boxes problem) Date: 4 Apr 1994 15:42:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404042244.AA25323@medinfo.medinfo.ab.umd.edu> NNTP-Posting-Host: net.bio.net This might be another option and do a better job for it is supplied by a sequence specialist. Use "EXCEL" I have not had the chance to try it myself so do not count on me. Good luck! Hsing-Tsu Lai hlai@cosy.ab.umd.edu pathology, UMAB From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!swrinde!sgiblab!darwin.sura.net!gatekeeper.es.dupont.com!esds01.es.dupont.com!MILLERTJ@esvx17.es.dupont.com From: millertj@esvx17.es.dupont.com (Thomas Miller, Dupont, Wilm, DE) Subject: Re: Mac downloading Message-ID: <1994Apr4.234853.1588@es.dupont.com> Sender: news@es.dupont.com (USENET News System) Nntp-Posting-Host: esvx17.es.dupont.com Reply-To: millertj@esvx17.es.dupont.com Organization: DuPont (Opinions are those of the writer only) References: <2np8cm$8aa@s.ms.uky.edu> Date: Mon, 4 Apr 1994 23:48:53 GMT Lines: 20 In article <2np8cm$8aa@s.ms.uky.edu>, mpm@seqanal.mi.uky.edu (Mark Mattson) writes: >Okay, so I've downloaded a self-converting text file to a Mac -- now what? >I have experience with DOS: one simply edits the file, renames with an >EXE or .COM extention, and runs. But how do you do the equivalent with >a Mac? I don't even know how to access the operating system in this >"user friendly" environment. > >Thanks for any help. > >Steve Barger * Is it a BinHex file? * Try StuffIt Expander? * Did you download it as a Binary or Text? * Or could be a corrupt file to begin with? Just my 2 cents... Regards, Tom. From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news Newsgroups: bionet.software Subject: Re: MacMosaic Message-ID: <1994Apr5.121532.115@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 5 Apr 94 12:15:31 +0100 References: <9404050946.AA04906@pclsp2> Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24In-Reply-To: mihara@PCLSP2.KUICR.KYOTO-U.AC.JP's message of 5 Apr 1994 02:43:30 -0700Lines: 29 Lines: 29 In <9404050946.AA04906@pclsp2> mihara@PCLSP2.KUICR.KYOTO-U.AC.JP writes: > I got Mosaic software for Mac ver.103. > It required MacTCP 2.0.2 or later. But I have only ver.1.1.1. > > Does anyone know how I can get MacTCP ver2.0.2? > Is it commercial? Long time ago it was public domain but meanwhile it's commercial. But in general you don't need to buy it because most of the commercially available programs dealing with TCP/IP on the mac contain MacTCP. If you have none of them, then of course you must buy it. It's sold by Apple itself. Regards Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!usenet.ins.cwru.edu!news.ecn.bgu.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!ts5-53.upenn.edu!user From: gustilo@pobox.upenn.edu () Newsgroups: bionet.software Subject: Contig Assembler Followup-To: bionet.software Date: Mon, 04 Apr 1994 22:36:08 -0400 Organization: University of Pennsylvania Lines: 17 Message-ID: NNTP-Posting-Host: ts5-53.upenn.edu greetings, Is there a public domain contig assembler for the mac or a publicly accessible machine (sort of like the BLAST server) that will do contigs? I have access to CAP2 and also IBI's AssemblyLIGN but would like to double check the contigs I get from these software. thanks in advance for any pointers -- Standard Disclaimer: I am not responsible for comments that I make after 3:00 A.M. or after 5 cups of double espresso, whichever comes first. gustilo@pobox.upenn.edu From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!PCLSP2.KUICR.KYOTO-U.AC.JP!mihara From: mihara@PCLSP2.KUICR.KYOTO-U.AC.JP (Mihara Hisaaki) Newsgroups: bionet.software Subject: MacMosaic Date: 5 Apr 1994 02:43:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404050946.AA04906@pclsp2> NNTP-Posting-Host: net.bio.net Dear bioNetters. I got Mosaic software for Mac ver.103. It required MacTCP 2.0.2 or later. But I have only ver.1.1.1. Does anyone know how I can get MacTCP ver2.0.2? Is it commercial? Thanx. From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!niftyserve.or.jp!HGF02633 From: HGF02633@niftyserve.or.jp (=?ISO-2022-JP?B?GyRAQFBETT1TPCMbKEo=?=) Newsgroups: bionet.software Subject: free cation calculation program for Mac Date: 5 Apr 1994 04:17:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199404051117.UAA07010@inetnif.niftyserve.or.jp> NNTP-Posting-Host: net.bio.net FROM:HGF02633@niftyserve.or.jp Does anybody know the program for calculating free cation concentration in solution? The solution includes several kinds of chelating agents. The dissociation constant and concentration of each chelator are knwon. Any program is Ok, but preferably for Mac. Please teach me. Sincerely yours, ========================================================================= Dr.Toshiharu Ishizuka Department of Biochemistry, Chiba University, School of Medicine 1-8-1, Inohana, Chuo-ku, Chiba, 260 JAPAN FAX +81-43-226-2041 E-mail QFH03407@niftyserve.or.jp tishizuk@twics.com ========================================================================= From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!library.ucla.edu!csulb.edu!csus.edu!netcom.com!biodata.slip.netcom.com!vern From: Vernon Keenan Subject: SUMMARY: Pharmacokinetics Software Message-ID: X-Xxmessage-Id: X-Xxdate: Tue, 5 Apr 94 23:33:19 GMT Sender: netnews@netcom.com (USENET Administration) Organization: BioData, Inc. X-Useragent: Version 1.1.3 Date: Tue, 5 Apr 1994 22:34:57 GMT Lines: 367 Here's a summary of responses I've received to my "what's the best pharmacokentics software out there" posting. Many thanks to all who took the time to respond! Summary: There aren't many programs out there for PK novices -- most seem to require some expertise in nonlinear regression techniques and the ability to code models in FORTRAN. I'll keep this summary up to date if anyone sends me any corrections or updates. I'll repost to bionet.software periodically. Vernon Keenan BioData, Inc. Internet: vern@biodata.com 1825 South Grant Street, Suite 620 San Mateo, CA 94402 Voice: 415-513-8950 ----------------------------------------- From: mhamiltn%dres.dnd.ca (Dr. Murray G. Hamilton) >Software For Science catalog (SciTech >International - call 1-800-622-3345 for a free copy of the catalog) of a >product called MINSQ and MINSQ Pharmacokinetic Library. This number does not work from Canada. Could you please E-mail a "real" number to me. Thanks in advance. Murray ************************************************************************* **** The non-800 number for SciTech International is +1 312-472-0444 **** ************************************************************************* - Vern ----------------------------------------- From: christo1@fmi.ch (Christen Tobias) I would highly appreciate a summary! Thanks! In wuarchive.wustl.edu there is kinsim a tool for the mac (rather low level but flexible..) it is in the directory /packages/kinsim Cheers and thank you for the summary Toby ----------------------------------------- From: GEXFABRY@cmu.unige.ch (Marianne Gex-Fabry) I recently made a survey of software packages available for analysis of pharmacokinetic data. More than 40 products have been cited to me, mostly for IBM compatible PCs. A complete list of these products, together with information about how to obtain them, is being sent to you by normal mail. Please note that the list together with a general discussion of features and requirements of the different products will be part of a chapter entitled "Considerations on data analysis using computer methods and currently available software for personal computers" by M. Gex-Fabry and L.P. Balant, to be published soon in "Handbook of Experimental Pharmacology", volume 110 "Pharmacokinetics of drugs" (Welling and Balant, eds), Springer, Berlin. With best regards, Marianne Gex-Fabry ----------------------------------------- From: ahb@gene.com (Ann Benninger) We use NONLIN84 from SCI Software in Lexington KY. It is available on IBM compatibles and in 2 source (fortran) versions; for VMS and a 'portable' version. I'm using the VMS specific version on our UNIX machines because the portable version is pretty lean. NONLIN84 is inexpensive and it is standard. Check out BIOPAK from the same vendor. A less standard program is available from USC and is called ADAPT. It is also in fortran and distributed in source. I think there's a SUN version in addition to the VMS version. C D. Z. D'Argenio, Biomedical Simulations Resource (BMSR) * C University of Southern California * C Los Angeles, California 90089-1451 * Note: to use ADAPT, the PK group needs to have at least one person who's comfortable writing fortran subroutines to describe the PK models. - Ann ----------------------------------------- From: DOSIO@silver.ch.unito.it (Franco Dosio) Dear Vernon, to obtain a (complete) list of available pharmacokinetic software, try to NISS bbs. At sun.nsf.ac.uk (pass. janet) host: uk.ac.niss.bb In the directory P8B7. To analize the pharmacokinetic data of MAb, toxin and drugs I'm using Pcnonlin 4.0 (SCI software, Lexington, Kentuky, tel 606-224-2438) and it works fine, but it runs only on PC or Vax. Regards Franco Dosio Ist. Chim.Farm.Applicata University of Turin, Italy DOSIO@silver.ch.unito.it U196CFA@csivms.csi.it ************************************************************************* **** Here is the catalog Franco was talking about! **** ************************************************************************* To get access to this bulletin board do this: telnet sun.nsf.ac.uk user janet pass janet Hostname: uk.ac.niss.bb - Vern PHARMACOKINETICS SOFTWARE CATALOGUE Title: Boomer and MultiForte Subject Area: Pharmacokinetics Description: Non-linear regression programs for the Macintosh and IBM PC. Weighted non-linear regression, simulations, Bayesian analysis, and Iteratively Reweighed Least Squares analyses are possible. In MultiForte models are specified by modifying model definition subroutines in FORTRAN. In Boomer the model is defined by the selection of parameters such as dose, first-order rate constant, volume etc. Integrated and differential equation type models are possible. Fitting algorithms include Gauss-Newton, Marquardt, and simplex. Numerical integration routines include Runge-Kutta, Runge-Kutta-Fehlberg, and Gears Section P8B7 Page 2 of 14 Hardware: Macintosh and IBM PC Contact: David Bourne OU HSC College of Pharmacy, 1110 N Oklahoma City, OK 73117-1223, USA Tel (405) 271-6471 david-bourne@uokhsc.edu Cost:40 dollars for Mac version Source: D. Bourne Section P8B7 Page 3 of 14 Title: Pharmacokinetics Simulation Subject Area: Pharmacokinetics Description: Simulation software written for the Apple II computer. Students select model type, input plot descriptions input parameter values and the computer presents a linear or semi-log plot of the calculated values. With appropriate printer hard copy is available. Written in AppleSoft BASIC. Models include one or two compartment pharmacokinetic models, single and mutiple dose. Only integrated equation models are included in the Apple II version Section P8B7 Page 4 of 14 Hardware: Apple IIe being ported to the Macintosh (68020+) Contact: David Bourne, OU HSC College of Pharmacy, 1110 N Oklahoma City, OK 73117-1223 USA Tel:(405) 271-6471 david-bourne@uokhsc.edu Cost: Distribution Only Source: D. Bourne Section P8B7 Page 5 of 14 Title: Kinetics Workshops Subject Area: Pharmacokinetics Description: Workshops to compliment pharmacokinetics undergraduate course self assesment style. Hardware: BBC Software Contact: Dr H Crystyn Pharm Technology School of Pharmacy Bradford University Bradford UK Tel 0279 733466 Extn 558 Cost: 50 pounds Source: DIT Section P8B7 Page 6 of 14 Title: Pharmod Subject Area: Pharmacokinetics Description: Powerful but very friendly pharmacokinetic modeling program. Models 2 different pharmacokinetic situations including linear and non linear elimination. Sample tutorial and demonstration disc available. Hardware: IBM compatable PC Contact: Dr P H Rowe Health Sciences Liverpoll Poly Byrom Street Liverpool UK Tel 051 207 3581 Ext 2069 Cost 200 pounds Source: DIT Section P8B7 Page 7 of 14 Title: Maxsim Subject Area: Pharmacokinetics Description: Pharmacokinetics simulation Hardware: IBM-compatable PC Contact: Gabrielsson Biopharmaceutics & Pharmacokinetics Box 580, BMC S-75123 Uppsala Sweden Cost: 70 pounds Source: DIT Section P8B7 Page 8 of 14 Title: Mupharm - Human Drug Kinetics Subject Area: Pharmacokinetics Description: Simulation program in Pharmacokinetics Hardware: IBM-compatable PC Contact: IRL Press Oxford University Press Eynsham Oxford Cost: 100 pounds approx Source: DIT Section P8B7 Page 9 of 14 Title: MacDope Subject Area: Pharmacokinetics Description: Computer simulation of pharmacokinetics which enables patient factors and drug factors to be changed. Changes are reflected in drug concs. in biological fluids. Hardware: Mainframe computer Contact: Dr D Ingram Dept of Medicine St Bartholomews West Smithfield London UK Cost: Source: DIT Section P8B7 Page 10 of 14 Title: ADAPT II Subject Area: Pharmacokinetics Description: Non-linear regression programs for the VAX/VMS, DOS, or SUN/UNIX. Models are specified using FORTRAN statements. Requires a FORTRAN compiler as each model is recompiled before use. Simulation can be error free of with noise or based on population values. Uses the LSODA method for numerical integration (which is suitable for non- stiff and stiff problems). The program will perform simplex optimization, maximum likelihood and Bayesian fitting or will develop optimal sampling designs. Hardware: VAX/VMS, DOS, or SUN/UNIX Contact: David Z. D'Argenio, Biomedical Simulations Resource, University of Southern California, Los Angeles CA 90089-1451, USA Tel (213) 740-0839 Cost: Free (in U.S.) Source: D. Bourne Section P8B7 Page 12 of 14 Title: NONMEM Subject Area: Pharmacokinetics Description: Computer prgram for fitting nonlinear mixed effects (statistical regression-type) models. These techniques are particularly useful where the data are population pharmacokinetic data and when there are few measurements from each subject and/or the variation between subjects is considerable. Hardware: Computer capable of compiling FORTRAN77 code, but workstation, mainframe recommended. Contact: Dr Stuart Beal, The NONMEM Project Group, Clinic-255, University of California, CA 94143 USA Cost: Academic US$150 per year Source: D. Bourne Section P8B7 Page 13 of 14 Title: SAAM30 and CONSAM Subject Area: Pharmacokinetics Description: Computer programs for performing non- linear regression analysis. Models are specified by means of various parameters or free-form equations. SAAM30 is operated in batch mode while CONSAM is more interactive. Numerical integration routines are available non-stiff and stiff systems. Hardware: VAX/VMS and DOS Contact: Loren A. Zech, M.D., N.I.H./NCI, Laboratory of Mathematical Biology, MD 20892 USA Tel (301) 496-8914 Cost: Free (in U.S.) Source: D. Bourne Section P8B7 Page 14 of 14 Title: Pharmacokinetics Subject Area: Pharmacokinetics Description: CAL porgrams in pharmacokinetics Hardware: (1) BBC (2) IBM-compatable PC Contact: (1) Alan Kensley (2) Dr Foster, Dept of Pharmacy Manchester University Manchester UK Tel: 061 2752340 Cost: Source: DIT *************************************************************** | Vernon Keenan | Voice: 415-513-8940 | | President | Fax: 415-312-8086 | | BioData, Inc. | Internet: vern@BioData.COM | | 1826 S. Grant St. Suite 620 | | | San Mateo, California 94402 | | *************************************************************** From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!eunet.no!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!nih-csl!bernard From: bernard@elsie.nci.nih.gov (Bernard Murray) Subject: Re: free cation calculation program for Mac Message-ID: <1994Apr5.215106.12395@alw.nih.gov> Summary: CaBuffer for PC Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: National Institutes of Health References: <199404051117.UAA07010@inetnif.niftyserve.or.jp> Distribution: bionet Date: Tue, 5 Apr 1994 21:51:06 GMT Lines: 30 In article <199404051117.UAA07010@inetnif.niftyserve.or.jp>, HGF02633@niftyserve.or.jp (=?ISO-2022-JP?B?GyRAQFBETT1TPCMbKEo=?=) writes: > FROM:HGF02633@niftyserve.or.jp > Does anybody know the program for calculating free cation concentration > in solution? The solution includes several kinds of chelating agents. > The dissociation constant and concentration of each chelator are > knwon. Any program is Ok, but preferably for Mac. Please teach me. > > Sincerely yours, > > ========================================================================= > Dr.Toshiharu Ishizuka > Department of Biochemistry, Chiba University, School of Medicine > 1-8-1, Inohana, Chuo-ku, Chiba, 260 JAPAN > FAX +81-43-226-2041 > E-mail > QFH03407@niftyserve.or.jp > tishizuk@twics.com > ========================================================================= I don't know about programs for the Mac but I am aware of a program called CaBuffer for the PC. This is written in Turbo BASIC (just text mode) so can probably be transported to the Mac. I think I collected my copy from wuarchive (I'll check and confirm, if this sounds okay to you). Bernard Bernard Murray, Ph.D. bernard@elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA) From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.software Subject: COMPMED 94 FINAL SCHEDULE Date: 5 Apr 1994 12:39:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404051939.AA08455@morpheus> NNTP-Posting-Host: net.bio.net FINAL PROGRAM ANNOUNCEMENT FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE AND PUBLIC HEALTH 24-28 April 1994 Hyatt on the Lake, Austin, Texas The final program for the First World Congress On Computational Medicine and Public Health has now been set. Over 200 speakers will be presenting work in a variety of applications areas related to medicine and public health. Registration is still open for attendees. Registration details and/or a copy of the schedule at a glance, schedule-in-detail may be requested by sending an email request to compmed94@chpc.utexas.edu or by calling 512-471-2472 or by faxing 512-471-2445 There is no ftp form of the conference schedule due to the size of the file. We will be happy to fax/send a copy to anyone who requests it. The conference proceedings will appear as a series of volumes published by World Scientific. If you are interested in possibly submitting a paper for the proceedings, please contact mwitten@chpc.utexas.edu or call 512-471-2457 The overwhelming response to this congress has already justified having a second world congress in the future. The tentative schedule is to have in in 3 years. If you are interested in participating at the 2nd World Congress On Computational Medicine and Public Health, please contact Dr. Matthew Witten Congress Chair mwitten@chpc.utexas.edu From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.software Subject: COMPMED 94 FINAL SCHEDULE Date: 5 Apr 1994 12:38:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404051939.AA08449@morpheus> NNTP-Posting-Host: net.bio.net FINAL PROGRAM ANNOUNCEMENT FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE AND PUBLIC HEALTH 24-28 April 1994 Hyatt on the Lake, Austin, Texas The final program for the First World Congress On Computational Medicine and Public Health has now been set. Over 200 speakers will be presenting work in a variety of applications areas related to medicine and public health. Registration is still open for attendees. Registration details and/or a copy of the schedule at a glance, schedule-in-detail may be requested by sending an email request to compmed94@chpc.utexas.edu or by calling 512-471-2472 or by faxing 512-471-2445 There is no ftp form of the conference schedule due to the size of the file. We will be happy to fax/send a copy to anyone who requests it. The conference proceedings will appear as a series of volumes published by World Scientific. If you are interested in possibly submitting a paper for the proceedings, please contact mwitten@chpc.utexas.edu or call 512-471-2457 The overwhelming response to this congress has already justified having a second world congress in the future. The tentative schedule is to have in in 3 years. If you are interested in participating at the 2nd World Congress On Computational Medicine and Public Health, please contact Dr. Matthew Witten Congress Chair mwitten@chpc.utexas.edu From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: ptaylor@crc.ac.uk (Dr. P.L. Taylor) Newsgroups: bionet.software Subject: Mac downloading Date: 5 Apr 1994 10:20:39 +0100 Lines: 34 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2nrah7$amu@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk >> Yeah, I tried double-clicking, but the finder just tried to open it as >> a text document (using TeachText or something). Does this mean something's >> wrong with the file? >No, there is nothing wrong with the file. This just means that it is a >generic text file. By default the Mac asks you if you want to open it with >TeachText. But, TeachText is mostly good for brief messages since it has a >32k size limit. >Go into your favorite word processing program (like Word) or another text >editor (like Alpha) and open it from within the program...Open the program. >Select Open from the file menu and navigate through the subsequent menu to >locate and open you file. And jeez, you don't have to rename it or >anything...what kinda primitives do you think we are? No, I think you are missing the point here. The file is text, but there's no point trying to read it with a word processor; it will just look like gibberish apart perhaps from a short comment at the beginning. The text contains encoded binary information, and you have to use a program to decode it. You will probably find that the file name ends in the extension '.hqx'. This means that it has been encoded using BinHex, and you will need BinHex, or Stuffit (any version) to decode it. Run the program, open the file, save the resulting new file somewhere. This will be given the extension '.sea' for Self Extracting Archive. Now double- click on this, and it will unpack itself. Phil Taylor | MRC Reproductive Biology Unit | Centre for Reproductive Biology | 37 Chalmers Street ptaylor@hgmp.mrc.ac.uk | Edinburgh EH3 9EW mbplt@seqnet.dl.ac.uk | Scotland. From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!rutgers!cis.ohio-state.edu!news.sei.cmu.edu!bb3.andrew.cmu.edu!cantaloupe.srv.cs.cmu.edu!fs7.ece.cmu.edu!europa.eng.gtefsd.com!howland.reston.ans.net!darwin.sura.net!lhc!lhc!hunter From: hunter@work.nlm.nih.gov (Larry Hunter) Newsgroups: bionet.software Subject: HICSS-28 Biotechnology Computing Track call for papers Message-ID: Date: 31 Mar 94 18:07:21 GMT Sender: news@nlm.nih.gov Reply-To: Hunter@nlm.nih.gov Organization: National Library of Medicine Lines: 152 Call for Papers Biotechnology Computing Track Hawaii International Conference on System Sciences 28 Maui, Hawaii --- January 3-6, 1995 The twenty-eighth annual Hawaii International Conference on System Sciences (HICSS) will include a three day conference track on Biotechnology Computing. The Biotechnology Computing Track provides a forum for the interchange of ideas, research results, and system building activities in all areas of computation related to biology. It includes presentations of original research, tutorials, advanced seminars and a distinguished guest lecture. The conference is sponsored by the University of Hawaii in cooperation with the Association for Computing Machinery (ACM), the IEEE Computer Society, and the Pacific Research Institute for Information Systems and Management (PRIISM). Advances in biotechnology generally and in the international Human Genome Project are creating an explosion of fundamental biological data underlying all life processes. The computational problems in gathering, managing and analyzing this explosion are daunting, but the challenges are exciting and the potential payoff is very high. Every aspect of computer science is involved, from algorithm development, systems integration and advanced database management to image analysis, parallel computing, artificial intelligence and robotics. The Biotechnology Computing Track presents the leading edge of this research in five minitracks, each focused on a rapidly evolving research area. Relevant papers are solicited for each of the minitrack areas listed below. Papers must be previously unpublished, and should be from 22-26 double spaced pages in length, including figures. Submitted papers are subject to a rigorous peer review process with written reviews from at least five referees. Accepted papers will be published in the conference proceedings which is also made generally available by the IEEE Computer Society Press. Prospective authors are urged to contact the appropriate minitrack chair as early as possible. Please leave adequate time for international mail, as all deadlines are firm. For general information, or proposals for tutorials, advanced seminars and review papers, contact the track chair: Lawrence Hunter (hunter@nlm.nih.gov) National Library of Medicine Building 38A, Mail Stop 54 Bethesda, MD 20894 USA +1 (301) 496-9300 +1 (301) 496-0673 (fax) The other members of the Track steering committee are: * Tom Marr, Cold Spring Harbor Laboratory, USA * John Wootton, National Center for Biotechnology Information, USA * Minoru Kanehisa, Kyoto University, Japan * Peter Edwards, Aberdeen University, Scotland DEADLINES: Full manuscripts must be RECEIVED by June 15, 1994 Notification of accepted papers will be sent by August 31, 1994 Accepted camera ready copy must be RECEIVED by October 1, 1994 International mail can be slow. We recommend use of courier services to international destinations. BIOTECHNOLOGY COMPUTING MINITRACKS AND CHAIRS. Please contact the relevant minitrack chair as soon as possible for further information on the requirements and deadlines for that minitrack. * Project-Oriented Databases and Knowledge Bases in Genome Research: Database and knowledge base tools and technologies that support the management of specific research groups or purposes, e.g. community databases for specialized research groups, laboratory notebooks, data management system supporting experiments, links between different databases, biological function knowledge bases, knowledge representation for biological functions and data models and structures for genome data. Toshihisa Takagi (takagi@ims.u-tokyo.ac.jp) Human Genome Center, The Institute of Medical Science, The University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108 JAPAN Tel. +81-3-3443-8111 ex.613 Fax: +81-3-3440-6173 * Parallel Computing for Computational Biology: The use of parallel and distributed computer systems and software in computational biology, including for molecular modeling, protein folding, sequence analysis, linkage analysis and other problems in the biological sciences. Timothy G. Mattson (tgm@ssd.intel.com) L. Ridgway Scott (scott@uh.edu) Intel Corp., Supercomputer Systems Division Mail Stop CO6-09 14924 N.W. Greenbrier Pkwy Beaverton, Oregon 97229 USA phone: +1 (503) 531-5627 fax: +1 (503) 531-5501 * Stochastic Models and Grammars for Bioinformatics: including hidden Markov models, regular grammar, context-free grammar, stochastic grammars and other stochastic approaches to recognize or analyze genetic/protein sequences and their structures. Kiyoshi Asai (asai@etl.go.jp) Hidetoshi Tanaka (htanaka@icot.or.jp) Institute for New Generation Computer Technology Mita Kokusai Bldg. 21F, 1-4-28, Mita, Minato-ku, Tokyo 108 Japan FAX : +81-3-3456-1618 * Computer Tools for Molecular Modeling: current research in computer algorithms and systems for molecular modeling and drug design. Teri E. Klein (klein@cgl.ucsf.edu) Mark C. Surles (surles@sdsc.edu) University of California, San Francisco 513 Parnassus Avenue, Box 0446 San Francisco, California 94143 USA phone: +1 (415) 476-0663 fax: +1 (415) 502-1755 * Protein Structure Prediction: Novel computational advances relevant to protein structure prediction from the primary sequence, including direct and "inverse" folding, homology-derived, statistical, machine learning, analytic, modeling, pattern-based, and related methods. Richard Lathrop (rickl@ai.mit.edu) Keith Dunker (dunker@bobcat.csc.wsu.edu) MIT AI Laboratory NE43-795 545 Technology Square Cambridge, MA 02139 USA +1 (617) 253-8833 +1 (617) 258-8682 (fax) -- Lawrence Hunter, PhD. National Library of Medicine Bldg. 38A, MS-54 Bethesda. MD 20894 USA tel: +1 (301) 496-9300 fax: +1 (301) 496-0673 internet: hunter@nlm.nih.gov encryption: public key via RIPEM server or "finger hunter@work.nlm.nih.gov" From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!BCH.UMontreal.CA!nick From: nick@BCH.UMontreal.CA (Nick Blom) Newsgroups: bionet.software Subject: Fourier transformation Date: 5 Apr 1994 06:31:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404051329.AA12896@crysbio1.BCH.UMontreal.CA> NNTP-Posting-Host: net.bio.net In his letter Jason Smith wrote : > I am working on a dental histology project for which I must create >the optical diffraction pattern for a series of micrographs of enamel >microwear. I have heard of the technique of using a Fourier transform to >accomplish this. Does anyone know of any software for an IBM system that >can do this? > > Jason Smith > University of Pennsylvania This depends on what you have? I assume your images are all base-2 sized (64*64, 128*128, 256*256, 512*512....). If you have a C, Pascal or FORTRAN compiler on your machine the cheapest way is to take the algorithm's from Numerical Recipes. You can find those in any Math, Chemistry or Physics Library. The next option is to get NIH Images 1.52 from the network. There are a number of sites where you can get it. Use or to look for one. If that doesn't help try the fancy one. Buy a Mac and put Digital Micrograph on it. Digital Micrograph has been developed specifically for High Resolution Electron Microscopy images, but its functionality is also be suitable for other types of miscoscopes. Digital Micrograph is a product of GATAN R&D in Pleasanton (CA). Good luck, Nick ================================================================== Dr. Nick Blom Tel : +1-514-3436111 ext 5352 Departement de Biochimie Fax : +1-514-3432210 Universite de Montreal Email: nick@bch.umontreal.ca C.P. 6128, Station Centre-Ville Montreal, PQ, H3C 3J7 Canada ****************************************************************** to be is to do --- Aristotle to do is to be --- Sartre do be do be do --- Sinatra de do do do de da da da --- Sting ================================================================== From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!lerc.nasa.gov!purdue!news.bu.edu!koskq From: koskq@bu.edu (Kosuke Kawakyu) Newsgroups: bionet.software Subject: dna -> protein Date: 5 Apr 1994 03:17:41 GMT Organization: Boston University Lines: 7 Message-ID: <2nql8l$g43@news.bu.edu> NNTP-Posting-Host: acs4.bu.edu X-Newsreader: TIN [version 1.2 PL0] anybody know where i can get access to a program that does dna -> protein? ftp site? anybody have this program and can send to me? thanks a million koskq@acs.bu.edu live long and prosper From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.software Subject: COMPMED 94 FINAL SCHEDULE Date: 5 Apr 1994 12:30:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 50 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404051931.AA07505@morpheus> NNTP-Posting-Host: net.bio.net FINAL PROGRAM ANNOUNCEMENT FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE AND PUBLIC HEALTH 24-28 April 1994 Hyatt on the Lake, Austin, Texas The final program for the First World Congress On Computational Medicine and Public Health has now been set. Over 200 speakers will be presenting work in a variety of applications areas related to medicine and public health. Registration is still open for attendees. Registration details and/or a copy of the schedule at a glance, schedule-in-detail may be requested by sending an email request to compmed94@chpc.utexas.edu or by calling 512-471-2472 or by faxing 512-471-2445 There is no ftp form of the conference schedule due to the size of the file. We will be happy to fax/send a copy to anyone who requests it. The conference proceedings will appear as a series of volumes published by World Scientific. If you are interested in possibly submitting a paper for the proceedings, please contact mwitten@chpc.utexas.edu or call 512-471-2457 The overwhelming response to this congress has already justified having a second world congress in the future. The tentative schedule is to have in in 3 years. If you are interested in participating at the 2nd World Congress On Computational Medicine and Public Health, please contact Dr. Matthew Witten Congress Chair mwitten@chpc.utexas.edu From owner-software@net.bio.net Mon Apr 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!ee.und.ac.za!inet.up.ac.za!ovisun.ovi.ac.za!ovisun.ovi.ac.za!not-for-mail From: basil@ovisun.ovi.ac.za (Basil Allsopp) Newsgroups: bionet.software Subject: Re: Software for sequence alignment? Date: 5 Apr 1994 10:47:02 +0200 Organization: Onderstepoort Veterinary Institute Lines: 26 Message-ID: <2nr8i6$i61@ovisun.ovi.ac.za> References: NNTP-Posting-Host: ovisun.ovi.ac.za Paul Davis writes: >... is working on the mammalian D-loop of mitochondrial DNA and is looking >for a program that finds optimal sequence alignment and assigns gaps. >It would be good if the software also does multiple alignments of both >closely and distantly related species. >If anyone out there has any suggestions, please email me at >karyn@connect.com.au >I will post a summary. >karyn@connect.com.au We use CLUSTALV which is distributed as C source code and which can be installed on DOS, Mac, Unix and VMS systems. You can get the package by anonymous ftp at the Indiana, Houston, and EMBL molecular biology distribution sites. Their network addresses are respectively: ftp.bio.indiana.edu ftp.bchs.uh.edu ftp.embl-heidelberg.de In the Indiana archive one must enter directory molbio/align. In the Houston archive it is in directory pub/gene-server in all of the four sub directories dos, Mac, unix, and vms. On the EMBL archive it is in pub/software/unix or pub/software/vax. You can play with the aligment parameters of CLUSTALV to get what you want. You would need to align the closely related seqs first using one set of parameters and then do a profile alignment (which does not alter the alignment already made) with the more distantly related seqs using different parameters. Another package which you will find very useful is called GDE. It allows (among many other things) the user to edit computer aligned seqs by hand. You will find this 'tidying up' to be essential. The GDE system runs under Unix and employs Xwindows. The latest version is GDE2.2a and it is available by anonymous ftp from megasun.bch.umontreal.ca or golgi.harvard.edu From owner-software@net.bio.net Tue Apr 05 23:00:00 1994 Path: biosci!dc.uba.edu.ar!bd4a From: bd4a@dc.uba.edu.ar (Diego M.Burrieza LU 674/90) Newsgroups: bionet.software Subject: SIMTEL20 Mirrors Date: 6 Apr 1994 10:27:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net Hi, is SIMTEL or any of his mirrors working?. I tried to connect using ftpmail, but it was impossible. Can you ask my question please ? Thanks Diego M. Burrieza bd4a@zorzal.edu.ar From owner-software@net.bio.net Tue Apr 05 23:00:00 1994 Path: biosci!rnisd0.DNET.roche.com!delisior From: delisior@rnisd0.DNET.roche.com (Bob DeLisio) Newsgroups: bionet.software Subject: Re: Mac downloading Date: 6 Apr 1994 07:40:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404061424.AA27434@mailgate.roche.com> NNTP-Posting-Host: net.bio.net Steve, May I recommend running the "text" file through BinHex 5.0. This sometimes corrects problems in the header of the file that occured during transfer even though the file may not have been compressed by this program. BTW are you transfering through a Local Area Network modem? Regards, Bob DeLisio ======================================================================= _/ _/ Robert DeLisio _/ _/ Roche Institute of Molecular Biology _/ Roche Research Center _/ _/ Nutley, New Jersey 07110-1199 _/ _/ _/ _/ Voice: (201) 235-3728 _/ Fax: (201) 235-2318 _/ _/ Internet: robert.delisior@roche.com _/ _/ CompuServe: 73517,2616 ======================================================================= In the article "myirwin@uci.edu" "Mike" writes: >> Yeah, I tried double-clicking, but the finder just tried to open it as >> a text document (using TeachText or something). Does this mean something's >> wrong with the file? > >No, there is nothing wrong with the file. This just means that it is a >generic text file. By default the Mac asks you if you want to open it with >TeachText. But, TeachText is mostly good for brief messages since it has a >32k size limit. > >Go into your favorite word processing program (like Word) or another text >Go into your favorite word processing program (like Word) or another text >editor (like Alpha) and open it from within the program...Open the program. >Select Open from the file menu and navigate through the subsequent menu to >locate and open you file. And jeez, you don't have to rename it or >anything...what kinda primitives do you think we are? From owner-software@net.bio.net Tue Apr 05 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!ihnp4.ucsd.edu!news.cerf.net!nic.cerf.net!strand From: strand@nic.cerf.net (Parallel Performance Group) Newsgroups: bionet.software,sci.comp-aided,comp.robotics Subject: DSP Graphical Programming Date: 6 Apr 1994 19:34:05 GMT Organization: CERFnet Dial n' CERF Customer Lines: 150 Message-ID: <2nv2rd$bpe@news.cerf.net> NNTP-Posting-Host: nic.cerf.net Xref: biosci bionet.software:7816 sci.comp-aided:325 comp.robotics:6412 DSP GRAPHICAL PROGRAMMING NEWSLETTER PARALLEL PERFORMANCE GROUP, INC. Volume #1, Issue #1 April, 1994 This is the first issue of Parallel Performance Group's free monthly E-Mail DSP Graphical Programming Newsletter, a publication on Graphical Programming for Signal and Image Processing. DSP Graphical Programming is illustrated via the DataFlo visual software development facility and runtime environment for signal and image processing applications. DataFlo operates on UNIX-based workstations and supports both OPEN LOOK and Motif standards. A multiprocessing version for CSP and VxWorks multiprocessing boards using a Sun workstation as a host is also available. For more in- formation on DSP Graphical Programming and Dataflo, please contact Parallel Performance Group at (602)282-6300, at strand@ppg.strand.com, or at 450 Jordan Rd., Suite E, Sedona, AZ 86336. This Issue's Topic: Intro To Graphical Programming For DSP and Image Processing DataFlo is an extension of the syntax and standards proven over the years as part of the Processing Graph Method (PGM) software developed by the US Naval Research Laboratory. PGM is perhaps the best-documented dataflow software to date. DataFlo was designed to conform to PGM terminology while adding a visual programming dimension through the X Window standard. The DataFlo system provides graphical programming, debugging, and runtime analysis tools to be used by scientists, engineers, and analysts who want to focus on the application rather than the details of computer programming. Data is represented by waveforms and images, as well as text files. All development is done by selecting icons, filling in menus, and connecting process boxes by lines to form an I/O-oriented flowchart representing the complete application. Thus the application is constructed in a building-block manner by synthesizing and testing individual algorithms before connections are made to the next hierarchical level. Signal generators can be synthesized for testing algorithms and observing waveforms at intermediate points. The ability to visualize algorithms as they evolve in the development process provides an extremely efficient method for the selection and modification of parameters. An Algorithm of Primitives The graphical programming of an algorithm uses preprogrammed "primitives" from the DataFlo Library. A complete algorithm can itself become a subroutine for use as part of a higher level process, or for use in another application requiring the same function. This ability to reuse elements of the overall program is an extremely valuable object-oriented feature incorporated into the DataFlo environment, and can increase software development productivity for even the most complex applications. The DataFlo programming environment is robust and hierarchical, handles real, integer, and complex data, and is based on a dataflow input-output methodology represented by FIFO data queues existing between process blocks. DataFlo Methodolgy and Terminology Graphs, Nodes, and Queues A graph is a pictorial description of the application's algorithm, composed of basic signal processing building blocks called nodes, connected by FIFO data queues. A graph may be just a few nodes connected by queues, or a more complex stucture of many nodes and subgraphs integrated into a hierarchy of structure levels. Each node contains a primitive, connection ports, and an interface procesdure. A primitive is the signal processing entity within the node, selected from the DataFlo Primitive Library of some 140 functions grouped into 17 Functional Primitve Groups: Arithmetic Operations Comparison Operations FFT Operations Filter Operations Format Operations Function Operations Input Operations Logic Operations Matrix Operations Move Operations Output Operations Statistics Operations Synthesis Operations Trigonometric Operations Image Operations Communications Operations User Operations Optional libraries for specific signal processing disciplines are available. The user can design primitives offline and add them to the standard library. A Sample DataFlo Flowchart In issue #2, we will describe the DataFlo Editor and Run-Time system, and describe the design and simulation of a frequency-modulated signal generator represented by the DataFlo graph shown below: ________________________________________ | | | ________ _________ | | |Feedback| \ Accum \ | | |mov_v_r |--|REAL |________| | |1 | |1 | | |________| /_________/ | | | | | | | | ________ | ________ | ________ ________ ________ ________ |One \ | |Incrmnt | | |DivBySiz| |Square | |Multiply| |Sin_Gen | |REAL |---|add_vs_r|---|div_vs_r|---|sqr_v_r |---|mul_vs_r|---|sin_v_r | |1 | |1 | _|256 | |256 | | |256 | |256 |-- |________/ |________| | |BREAK | |BREAK | | |BREAK | |BREAK | | | |________| |________| | |________| |________| | | | | ________ | | _________ | |Size \ | | \ Result \ | |REAL |______________| | |RESULT | | |1 | | |256 |-- |________/ | /_________/ | | ________ ________ | |TwoPi \ |MulByN | | |REAL |----------------|mul_vs_r|-------------- |1 | __|1 | |________/ | |________| | | ________ | |N \ | |REAL |------------- |1 | |________/ From owner-software@net.bio.net Tue Apr 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!library.ucla.edu!csulb.edu!csus.edu!netcom.com!barbose.slip.netcom.com!barbose From: Jeffrey J Barbose Subject: Re: MacMosaic Message-ID: X-Xxmessage-Id: X-Xxdate: Tue, 5 Apr 94 03:09:45 GMT Sender: netnews@netcom.com (USENET Administration) Organization: HowLand Software X-Useragent: Version 1.1.3 References: <9404050946.AA04906@pclsp2> Date: Wed, 6 Apr 1994 03:15:27 GMT Lines: 35 In article <1994Apr5.121532.115@immunbio.mpg.de> Christoph Gartmann, GARTMANN@IMMUNBIO.MPG.DE writes: >> I got Mosaic software for Mac ver.103. >> It required MacTCP 2.0.2 or later. But I have only ver.1.1.1. >> >> Does anyone know how I can get MacTCP ver2.0.2? >> Is it commercial? > >Long time ago it was public domain but meanwhile it's commercial. But in >general you don't need to buy it because most of the commercially available >programs dealing with TCP/IP on the mac contain MacTCP. If you have none >of them, then of course you must buy it. It's sold by Apple itself. > >Regards > Christoph Gartmann From Apple Programmers and Developers Association (APDA), it's $59. But if you buy the Internet Starter Kit (a book plus diskette), you get MacTCP 2.0.4 and some other Macintosh internet software, all for about $30. Quite a deal. Jeff ----------------------------------------------------------------- "The Bible contains six admonishments to homosexuals and 362 admonishments to heterosexuals. That doesn't mean that God doesn't love heterosexuals. It's just that they need more supervision." -- Lynn Lavner ----------------------------------------------------------------- internet: barbose@netcom.com Jeffrey J Barbose, HowLand Software From owner-software@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!cleveland.Freenet.Edu!ee612 From: ee612@cleveland.Freenet.Edu (Dave Statson) Newsgroups: bionet.software Subject: Prodigy Date: 7 Apr 1994 15:55:47 GMT Organization: Case Western Reserve University, Cleveland, Ohio (USA) Lines: 12 Message-ID: <2o1ae3$ecu@usenet.INS.CWRU.Edu> NNTP-Posting-Host: roo.ins.cwru.edu Hello, there. I have just become a member of the PRODIGY network, but I have a slight problem. The program that they sent me to access the Prodigy services has one or more of its files screwed up. If anyone out there got this program please E-mail it to me. In reward for this I'll send you either a Mortal Kombat or a Wing Comander 2 game upon your request. Thanx alot... -------------------------------------------------------------------------------- .................Beware the ides of March....................................... --------------------------------------------------------------------------------### -- +++fO,g From owner-software@net.bio.net Wed Apr 06 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!darwin.sura.net!hearst.acc.Virginia.EDU!liberty!C.J.Hussussian,.MD From: cjh@helix.nih.gov (C.J. Hussussian, MD) Subject: New ABI Analysis Upgrade? Message-ID: <1994Apr7.204457.12523@liberty.uc.wlu.edu> Sender: -Not-Authenticated-[3942] X-Posted-From: InterNews 1.0@liberty.uc.wlu.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. Date: Thu, 7 Apr 1994 20:44:57 GMT Lines: 36 Nntp-Posting-Host: 165.112.60.4 Organization: NIH Our lab is currently running several sequence-dependent projects and we make heavy use of our ABI sequencer. We have found that for our work Sequencher (GeneCodes, Ann Arbor, MI) is far and away the best assembly program available. Much of is functionality comes from the ability to directly download the analysis files from the ABI and compare the chromatograms from the aligned sequences in an efficient and intuitive way. Recently we have become aware of a possible upgrade in the ABI analysis software that would compress the analysis files in such a way as to render them unreadable to third party sequence assembly software such as Sequencher. We became aware of this upgrade through our ABI applications specialist who had contacted us about beta-testing the new version. We explained that it was doubtful that we would be able to use it as the files it creates would most likely be incompatible with our assembly software and haven't heard from them since. We have been in contact with Howard Cash, the president of GeneCodes who verified that any change in the format of the analysis files would create compatibility problems with Sequencher as ABI refuses to divulge its encryption algorithm except at high price. Does anybody know the status of this software upgrade? Does anyone know the reason for the upgrade or any benefits of upgrading other than compressed analysis files? We have fully tested the current and next generation versions of the ABI Inherit software and have found it to be insufficient for our needs. In light of the fact that ABI does not currently offer a viable alternative to third party assembly software, it seems to me that they should be more lenient towards the producers of these needed programs. Changing the format of the ABI analysis output files would reduce our ablility to use their sequencer to rapidly obtain high quality assembled sequences in our lab and undoubtedly others as well. I'm not sure this would engender a great deal of customer satisfaction. I have no affiliation with ABI or GeneCodes except as a heavy user of their products. C.J. Hussussian, MD Ph: 301-402-2029 NIH/NCHGR e-mail: cjh@helix.nih.gov 49/4A83 Bethesda, MD 20892 From owner-software@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!veths.no!Adrian.Smith From: Adrian.Smith@veths.no (Adrian Smith, Adrian Smith) Newsgroups: bionet.software Subject: NORINA database of audiovisuals Date: 7 Apr 1994 05:45:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199404071245.FAA17324@net.bio.net> NNTP-Posting-Host: net.bio.net To members of the Biological Software Discussion Group: I would like to draw your attention to a database compiled at the Oslo Veterinary School, which you may be interested in. Please feel free to distribute the following, in whole or in part, wherever you feel appropriate. Best wishes, Adrian Smith. NORINA: A NORWEGIAN INVENTORY OF AUDIOVISUALS The Laboratory Animal Unit, Norwegian College of Veterinary Medicine, Oslo, has compiled an English-language database of audiovisuals for use in the biological sciences. The compilers are Karina and Adrian Smith, in collaboration with Richard Fosse, Laboratory Animal Services, University of Bergen. The primary purpose of the database is to offer an overview of possible alternatives or supplements to the use of animals in student teaching, at all levels from schools to university. The database consists at present of around 1300 entries, including computer programs, interactive video, films and more traditional teaching aids such as slide series, 3-D models and classroom charts. There is also a section for Contact Persons who are developing and/or using audiovisuals at their institution, and for suppliers of audiovisuals. We invite users, developers and suppliers of audiovisuals to send in details for future upgrades of the database. NORINA has been written in Filemaker Pro, originally for Macintosh, but now also available for IBM Windows. NORINA is also available as a "stand-alone" IBM version that will run on any PC with harddisc, with no additional software. Price: US$ 150 (for networks with up to 30 workstations: US$ 750). NORINA is a non-profit venture (none of the developers receive any commission on sales) and income from sales is used purely to offset wage expenses. A free demonstration floppy disc is available: it will run on a Windows or Macintosh computer where the program Filemaker Pro is installed. Alternatively, a representative sample of 10 entries printed from NORINA may be ordered free of charge. Three sample files are available by FTP from wuarchive.wustl.edu in the directory \doc\techreports\wustl.edu\compmed\mac; these are the demo version for machines with Filemaker Pro (norina.bin), a text file with information on NORINA (norina.txt) and a tab-delimited version of the demo version (norina.tab). Further details from: Professor Adrian Smith, Laboratory Animal Unit, Norwegian College of Veterinary Medicine, P.O. Box 8146 Dep., 0033 Oslo 1, Norway. Fax: +47 22 96 45 35. Phone: +47 22 96 45 74. email (Internet): adrian.smith@veths.no From owner-software@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!usc!nic-nac.CSU.net!csulb.edu!paris.ics.uci.edu!news.claremont.edu!kaiwan.com!wetware!spunky.RedBrick.COM!psinntp!psinntp!newsserver.tasc.com!newsserver.tasc.com!news From: dhsprogis@tasc.com (David Sprogis) Newsgroups: bionet.software,comp.lang.postscript Subject: Re: Postscript conversion. Date: 4 Apr 1994 22:58:06 GMT Organization: TASC Lines: 96 Message-ID: <2nq61uINNdhc@jumbo.read.tasc.com> References: NNTP-Posting-Host: dhsprogis.read.tasc.com Xref: biosci bionet.software:7818 comp.lang.postscript:8263 In article , pmiguel@bilbo.bio.purdue.edu says: > > What programs exist that (somewhat) intelligently convert a Postscript >or EPS file to TIFF or PICT (etc.) so that it can be modified with a >typical graphics program (e.g. MacDraw, Canvas, etc.)? > > By "intelligently" I mean in such a way that text remains text, not >an arbitrary assembly of graphics. > Tscript (Teletypesetting Company, Brookline, MA) can do the EPS to TIFF >or PICT conversion but the resulting file contains one big graphics image >-- no text. Microsoft Word can convert an EPS file to a lesser extent >in that it can print it okay but displays it only as a large grey >box. Canvas does essentially the same thing. > > The postscript file comes from the GCG program PRETTYPLOT. If GCG could >create TIFF or PICT graphics files there wouldn't be a problem -- but GCG >seems to be made to allow output to a printer or printer-formated file >only. > >Phillip Hey Phillip, I guess I don't know what exactly you want, but it sounds like you want to convert from PostScript to TIFF in such a way as to be able to edit the resulting TIFF - the edit mode you want being one where you can select and edit the text (embodied in the TIFF) in the same way you might edit text in a word processor. I'm not sure that there is any route to accomplishing this. My understanding of TIFF is that it is a raster-only file format. Thus any conversion of text into a TIFF file would have to be "rasterized" - turned into a picture. As a picture, it would not be editable in the same way that text is editable in a word processor - unless the paint-box were very smart (with OCR) and could recognize the text portions of the image. I have never seen a paint-box with this capability - however, there are many with a text entry feature which might lead one to believe that they do have this capability. Frequently, a paint-box will allow the user to enter text by clicking on the canvas (page) then typing the text. The text can be ignored for a while, then later selected and edited - like on a word processor. Then the page with text can be saved to a TIFF file. I think you will find that if you read the TIFF file back into the paint-box that you will no-longer be able to select the text again. -- I just checked the TIFF spec to confirm this and while I see no explicit ASCII text capabilities (TAGs) it is always possible that a paint- box manufacturer has customized TIFF with their own TAGs to store the text in ASCII as well as in a raster format. If this is the case, then I would be wrong concerning writing, reading back and then editing. However, this being the case, it is unlikely that another manufacturer's PostScript to TIFF converter would be able to utilize these custom TAGs in the same way that the paint-box manufacturer did. In summary, I think you are looking for something which may not exist. Perhaps you should consider using a paint-box which reads PostScript files - I think Corel Draw does and more than likely Adobe products do - they are respondsible for PostScript. Good luck in your search. Some additional products which you might want to be aware of are: I know and like: Freedom of Press PostScript interpreter for many platforms which outputs to many printers as well as to several file formats -- available from CAI in Billerica, MA (508) 667-8585 GhostScript PostScript interpreter for essentially any platform which outputs to some printers and to files/raster data -- available from Aladdin Ent. Menlo Park, CA (415) 322-0103 I've heard about: Opium converts PostScript to several raster image formats. It has several language extensions relating to image processing (alpha channel, ``forall'' for images etc.) and usability of PostScript as a general purpose script language (``system'', secure and non-secure modes, etc.) Converts to TIFF 5.0 (including RLE, LZW, fax3, fax4, and JPEG compressions), PBM, PGM, PPM, Sixel (VT240, LN03), Group 3 fax, ASCII, and HPGL (experimental). Interpreter, Converts-PostScript-to-ASCII, Converts PostScript-to-TIFF, Converts-Images, Level-2, Converts-PostScript-to-HPGL. Status: commercial. Platforms: UNIX, Sun, DECstation, AIX, NeXT, Alpha and VMS. Get-From: Stream Technologies Inc., Valkjarventie 2, SF-02130 Espoo, FINLAND, Tel: +358 0 43577340, Fax: +358 0 43577348, Email: info@sti.fi. Be well, Dave Sprogis dhsprogis@tasc.com From owner-software@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!usc!sdd.hp.com!saimiri.primate.wisc.edu!news.doit.wisc.edu!chih-che From: chih-che@cae.wisc.edu (Chih-Che Lin) Newsgroups: bionet.software Subject: Raster3D in IBM rs6000! HELP! Followup-To: bionet.software Date: 7 Apr 1994 00:59:56 GMT Organization: U of Wisconsin-Madison College of Engineering Lines: 15 Sender: chih-che@cae.wisc.edu (Gary C. Lin) Distribution: world Message-ID: <2nvluc$4se@news.doit.wisc.edu> NNTP-Posting-Host: sun-37.cae.wisc.edu Hi there, I am trying to install Raster3D software in our IBM rs6000 workstation ( version 3.2.0 ) and I have some error message from ribbon.f file after running Makefile file. I think the problem is on how to fix the Makefile. I would like to get in touch with those who had the experience for installing Raster3D in rs6000 workstation. Any reply will be highly appreciated. Chih-Che (Gary) Lin ! chih-che@cae.wisc.edu Dept. of Bacteriology, University of Wisconsin - Madison From owner-software@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!news.cs.umb.edu!hsdndev!husc-news.harvard.edu!husc.harvard.edu!husc7.harvard.edu!mlevin Newsgroups: bionet.software Subject: Anyone know of molec. bio. software to run on Mainframes/workstations? Message-ID: <2o16bp$hr8@scunix2.harvard.edu> From: mlevin@husc7.harvard.edu (Michael Levin) Date: 7 Apr 1994 14:46:17 GMT Distribution: usa Organization: Harvard University, Cambridge, MA NNTP-Posting-Host: husc7.harvard.edu Lines: 11 I am looking for names (and phone numbers, if available) of companies which make molecular biology software that runs on mainframes or workstations (Vaxes, Unix workstations - Suns, Iris, etc.). I am not interested in companies which make software only for PCs or Macs. Please reply to mlevin@husc7.harvard.edu. Mike Levin From owner-software@net.bio.net Wed Apr 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!not-for-mail From: jones@bsm.biochemistry.ucl.ac.uk (David Jones) Newsgroups: bionet.software Subject: MEMSAT - Transmembrane Helix Prediction Date: 7 Apr 1994 17:53:33 -0500 Organization: University College London Lines: 50 Sender: daemon@cs.utexas.edu Message-ID: <1994Apr6.204317.55431@ucl.ac.uk> NNTP-Posting-Host: cs.utexas.edu MEMSAT - MEMbrane protein Structure And Topology Program ======================================================== I have been getting quite a few requests for source code to the above program for which we ask people to complete a license agreement form. I have therefore placed a copy of the academic license agreement on our FTP server. Those wishing for a copy of the source (which will compile on just about any Unix platform) should just print out the agreement form (it's an ASCII file), read it and if you agree with the terms, sign it and fax it or (air)mail to me at the address below. Don't forget to give me your e-mail address so that I can mail you back the source files. The file is /pub/MEMSAT/acad_lic.txt on ftp.biochem.ucl.ac.uk (128.40.46.11). Abbreviated version of original posting follows: ************************************************************************* I am making the PC implementation of the new membrane protein structure prediction method described in Jones, D.T., Taylor, W.R. & Thornton, J.M. (1994) A Model Recognition Approach to the Prediction of All-Helical Membrane Protein Structure and Topology. Biochemistry (USA) 33:3038-3049. available by anonymous FTP. The software is available free if you intend to use the program for purely academic research or teaching, those wishing to use the program commercially must contact me for further details. Operators of biosoftware FTP sites please feel free to make the files available at your own site, as long as the files are not altered. To obtain the file (a self-extracting archive) ftp to the address ftp.biochem.ucl.ac.uk (128.40.46.11), username "anonymous", password "your-email-address", and obtain the files /pub/MEMSAT/README and /pub/MEMSAT/memsatpc.exe. >---------------------------------------------------------------------------< This message was written, produced and executively directed by Dr David Jones Email: jones@bioc.bsm.ucl.ac.uk | JANET: jones@uk.ac.ucl.bioc.bsm Address: Dept. of Biochemistry | Tel: +44 71 387 7050 x3879 and Molecular Biology, University | Fax: +44 71 380 7193 College, London WC1E 6BT, U.K. | Disclaimer: STANDARD > KEYWORDS : OPINIONS MY OWN NOBODY ELSE'S WHATSOEVER From owner-software@net.bio.net Wed Apr 06 23:00:00 1994 Newsgroups: bionet.software,comp.lang.postscript Path: biosci!daresbury!trane.uninett.no!eunet.no!EU.net!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!wfischer From: wfischer@bio.indiana.edu (Will Fischer) Subject: Re: Postscript conversion. Message-ID: Followup-To: bionet.software,comp.lang.postscript Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu Organization: Biology, Indiana University - Bloomington X-Newsreader: TIN [version 1.1 PL8] References: <2nq61uINNdhc@jumbo.read.tasc.com> Date: Thu, 7 Apr 1994 20:45:49 GMT Lines: 36 Xref: biosci bionet.software:7823 comp.lang.postscript:8282 David Sprogis (dhsprogis@tasc.com) wrote: : In article , pmiguel@bilbo.bio.purdue.edu says: : > : > What programs exist that (somewhat) intelligently convert a Postscript : >or EPS file to TIFF or PICT (etc.) so that it can be modified with a : >typical graphics program (e.g. MacDraw, Canvas, etc.)? : > : > By "intelligently" I mean in such a way that text remains text, not : >an arbitrary assembly of graphics. : I guess I don't know what exactly you want, but it sounds like : you want to convert from PostScript to TIFF in such a way as to be able : to edit the resulting TIFF - the edit mode you want being one where you : can select and edit the text (embodied in the TIFF) in the same way you : might edit text in a word processor. [munch] : In summary, I think you are looking for something which may : not exist. I doubt this is relevant, but there is a product called "Tailor" available for NeXTSTEP machines which is alleged to allow editing of almost any PS files. Haven't used it myself, but there are demos on the archive sites. NeXTSTEP now runs on PCs, and will soon be available for HP and other machines (check comp.sys.next.advocacy). -- ________________________________________________________________________ \\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/\\/ Will Fischer wfischer@indiana.edu Gradual Student Department of Biology Indiana University Bloomington, Indiana 47401 USA From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!JAGUAR.CSC.WSU.EDU!THOMPSON From: THOMPSON@JAGUAR.CSC.WSU.EDU ("Steve Thompson: VADMS genetics") Newsgroups: bionet.software Subject: further postscript enquiries Date: 8 Apr 1994 16:07:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <940408160829.21e098a8@JAGUAR.CSC.WSU.EDU> NNTP-Posting-Host: net.bio.net Hi Bio-Soft'ers - To throw another question into the ongoing PostScript file format conversion utility discussion .... My boss was curious, has anybody ever heard of a way to display PostScript to a Tek 4107 tube (or emulation) off of a VAX/VMS system. We are aware that Ghostscript will run on the VAX but, as far as I understand, requires an X/Motif window for display. GhostScript additionally can produce a PICT imagefile; does anybody know of a utility to display that PICT image within a non-X VAX world? We routinely move images of many different formats to the appropriate platform for display and realize that is the "right way" to do it, but were playing with ideas for teaching demos within the VAX/Tek emulation constraint of our present teaching lab. Previously we have produced demos with GCG Figure and VAX DCL scripts as well as MacroModel log files, but have recently been experimenting with more complex images. Many of these have been produced with Raster3D/MolScript/etc. and result in PostScript output. Just wonderin'... Thanks - Steve Steven M. Thompson Consultant in Molecular Genetics and Sequence Analysis VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory Washington State University, Pullman, WA 99164-1224, USA AT&Tnet: (509) 335-0533 or 335-3179 FAX: (509) 335-0540 INTERnet: THOMPSON@jaguar.csc.wsu.edu From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!math.ohio-state.edu!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.belwue.de!orion.mgen.uni-heidelberg.de!andreas From: andreas@orion.mgen.uni-heidelberg.de (Andreas Helke) Newsgroups: bionet.software,comp.lang.postscript Subject: Re: Postscript conversion. Followup-To: bionet.software,comp.lang.postscript Date: 8 Apr 1994 08:06:04 GMT Organization: InterNetNews at News.BelWue.DE (Stuttgart, Germany) Lines: 47 Message-ID: <2o339c$n24@news.belwue.de> References: <2nq61uINNdhc@jumbo.read.tasc.com> NNTP-Posting-Host: orion.mgen.uni-heidelberg.de X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:7827 comp.lang.postscript:8289 David Sprogis (dhsprogis@tasc.com) wrote: : In article , pmiguel@bilbo.bio.purdue.edu says: : > : > What programs exist that (somewhat) intelligently convert a Postscript : >or EPS file to TIFF or PICT (etc.) so that it can be modified with a : >typical graphics program (e.g. MacDraw, Canvas, etc.)? : > : > By "intelligently" I mean in such a way that text remains text, not : >an arbitrary assembly of graphics. : > Tscript (Teletypesetting Company, Brookline, MA) can do the EPS to TIFF : >or PICT conversion but the resulting file contains one big graphics image : >-- no text. Microsoft Word can convert an EPS file to a lesser extent : >in that it can print it okay but displays it only as a large grey : >box. Canvas does essentially the same thing. : > : > The postscript file comes from the GCG program PRETTYPLOT. If GCG could : >create TIFF or PICT graphics files there wouldn't be a problem -- but GCG : >seems to be made to allow output to a printer or printer-formated file : >only. : > : >Phillip : Hey Phillip, : In summary, I think you are looking for something which may : not exist. Perhaps you should consider using a paint-box which reads : PostScript files - I think Corel Draw does and more than likely Adobe : products do - they are respondsible for PostScript. Good luck in your search. : I know and like: I do not think that any PC or MAC program exists which can convert back an arbitrary postscript file into an editable vector graphic. Some programs use a subset of postscript as their native storage format. But they can only read their special format and not a normal postscript file. The job of recreating a editable vector grafic out of a postscript file is probably just too complicated. It would shurely bee a useful feature for any graphics program. Andreas -- Andreas Helke Institut fuer molekulare Genetik, Universitaet Heidelberg Im Neuenheimer Feld 230 69122 Heidelberg From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!ucbvax!dog.ee.lbl.gov!ihnp4.ucsd.edu!library.ucla.edu!news.ucdavis.edu!josquin.ucdavis.edu!john From: john@josquin.ucdavis.edu (John Gillespie) Newsgroups: bionet.software Subject: entrez under linux? Message-ID: Date: 8 Apr 94 17:54:55 GMT Sender: usenet@ucdavis.edu (News Guru) Organization: University of California, Davis Lines: 5 X-Newsreader: TIN [version 1.2 PL2] The title sez it: Has anyone ported entrez to linux? john jhgillespie@ucdavis.edu From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!math.ohio-state.edu!magnus.acs.ohio-state.edu!csn!boulder!gauthere From: gauthere@beagle (Daniel Gautheret) Newsgroups: bionet.software,comp.lang.postscript Subject: Re: Postscript conversion. Date: 8 Apr 1994 17:33:28 GMT Organization: University of Colorado at Boulder Lines: 35 Message-ID: <2o44h8$64g@lace.Colorado.EDU> References: <2nq61uINNdhc@jumbo.read.tasc.com> <2o339c$n24@news.belwue.de> NNTP-Posting-Host: beagle.colorado.edu Xref: biosci bionet.software:7832 comp.lang.postscript:8296 andreas@orion.mgen.uni-heidelberg.de (Andreas Helke) writes: >I do not think that any PC or MAC program exists which can convert back >an arbitrary postscript file into an editable vector graphic. Some programs >use a subset of postscript as their native storage format. But they can >only read their special format and not a normal postscript file. The job >of recreating a editable vector grafic out of a postscript file is probably >just too complicated. It would shurely bee a useful feature for any graphics >program. May be you have missed the message posted by George White (gwhite@trevnx.bio.dfo.ca) a few days ago. The next release of Ghostscript will contain a utility that converts PS files into Adobe Illustrator files. All texts, lines, curves, etc. in the original file become _editable_ by illustrator. If you don't want to wait for the next Ghostscript release, you can retrieve the individual utility from: % Jason Olszewski (olszewsk@splash.princeton.edu) % % anonymous ftp: toby.princeton.edu /pub/olszewsk/ps2ai.ps % URL ftp://toby.princeton.edu/pub/olszewsk You'll need Ghostscript (Mac or Unix) to use it though. I tried it and it works. Daniel -- ------------------------------------------------------------------------------ Daniel Gautheret - MCD Biology - University of Colorado - Campus Box 347 Boulder CO 80309-0347 Tel: (303) 492-8595 - Fax: (303) 492-7744 ------------------------------------------------------------------------------ From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!nigel.msen.com!zib-berlin.de!netmbx.de!Germany.EU.net!news.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news Newsgroups: bionet.software Subject: Re: Postscript conversion. Message-ID: <1994Apr8.120349.116@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 8 Apr 94 12:03:48 +0100 References: <2nq61uINNdhc@jumbo.read.tasc.com> <2o339c$n24@news.belwue.de> Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24In-Reply-To: andreas@orion.mgen.uni-heidelberg.de's message of 8 Apr 1994 08:06:04 GMTLines: 31 Lines: 31 In <2o339c$n24@news.belwue.de> andreas@orion.mgen.uni-heidelberg.de writes: > I do not think that any PC or MAC program exists which can convert back > an arbitrary postscript file into an editable vector graphic. Some programs > use a subset of postscript as their native storage format. But they can > only read their special format and not a normal postscript file. The job > of recreating a editable vector grafic out of a postscript file is probably > just too complicated. It would shurely bee a useful feature for any graphics > program. Once again: CorelDraw does a pretty good job doing exactly this thing. Of course, it's not a 100% but around 95% or even more. I tried several packages and found CorelDraw to be the best. I am not quite sure whether this feature is part of the basic program or some addition. Regards Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!CALSHP.CALS.WISC.EDU!triplett From: triplett@CALSHP.CALS.WISC.EDU Newsgroups: bionet.software Subject: Re: Need advice Date: 8 Apr 1994 09:14:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9404081614.AA00270@calshp.cals.wisc.edu> NNTP-Posting-Host: net.bio.net Hi Jennifer, Your last emnaail message to eme was a bit garbled. Can you send it to me again. Eric Triplett From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!MCZ.HARVARD.EDU!dmw From: dmw@MCZ.HARVARD.EDU (Dan Weinreich) Newsgroups: bionet.software Subject: Re: New ABI Analysis Upgrade? Date: 8 Apr 1994 05:38:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: bionet Message-ID: References: <2o3dhr$pt2@mserv1.dl.ac.uk> Reply-To: Dan Weinreich NNTP-Posting-Host: net.bio.net Phil: Would it be an immense time-sink for you to develop and post a public domain New-ABI-format-to-Old-ABI-format converter? From what you say, ABI would give you the technical details for free, so long as you don't also incorporate them into your (very fine) for-profit product. I agree that it's shortsighted of ABI not to support development of products which add value to theirs without cutting into their market. ------------------------------------------------------------------- Dan Weinreich email: dmw@mcz.harvard.edu Harvard University usmail: 26 Oxford Street Museum of Comparative Zoology Cambridge, MA 02138 voice: (617) 495-1954 fax: (617) 495-5667 ------------------------------------------------------------------- From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: ptaylor@crc.ac.uk (Dr. P.L. Taylor) Newsgroups: bionet.software Subject: New ABI Analysis Upgrade? Date: 8 Apr 1994 12:01:15 +0100 Lines: 38 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2o3dhr$pt2@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk C.J. Hussussian, MD (cjh@helix.nih.gov) wrote : >Our lab is currently running several sequence-dependent projects and we >make heavy use of our ABI sequencer. We have found that for our work >Sequencher (GeneCodes, Ann Arbor, MI) is far and away the best assembly >program available. Much of is functionality comes from the ability to >directly download the analysis files from the ABI and compare the >chromatograms from the aligned sequences in an efficient and intuitive >way. Recently we have become aware of a possible upgrade in the ABI >analysis software that would compress the analysis files in such a way >as to render them unreadable to third party sequence assembly software >such as Sequencher. Yes, I've been discussing this today with my local ABI representative. ABI do produce a software development kit which allows software to read the new file format. It's free to non-commercial developers, but if your software is distributed for money you have to pay. As the author of GeneJockeyII, which reads and extracts information from ABI sample files, I'm going to have to modify my program to deal with this. My distributor, Biosoft, is currently negotiating with ABI to obtain a copy of the development kit, however, knowing ABI, I rather expect that the fee will be excessive. If this should happen it will be necessary to crack the new file format and write my own routines to decompress the data. (It's a lot of work, but after all, all the existing non-ABI programs which read this data were made by people who cracked the original file format, since ABI has always considered this information as proprietary, and refused to release it.) Perhaps the authors of Sequencher, DNAStar, MacVector and myself should get together to discuss a joint approach here. It would make far more sense, however, for ABI to encourage third-party software development by publishing the file format. ABI would lose nothing by this, and would avoid causing considerable anguish to their users. Phil Taylor mbplt@seqnet.dl.ac.uk ptaylor@hgmp.mrc.ac.uk From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!noc.near.net!news.delphi.com!usenet From: Jennifer Ulishney Newsgroups: bionet.software Subject: Need advice Date: Thu, 7 Apr 94 22:01:47 -0500 Organization: Delphi (info@delphi.com email, 800-695-4005 voice) Lines: 3 Message-ID: NNTP-Posting-Host: bos1c.delphi.com ething that will help me to understand Biology better. Leave me E-mail if you have any suggestions From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!news.unige.ch!ugcmu!dlowry From: dlowry@cmu.unige.ch Subject: FASTA location Message-ID: <1994Apr8.073809.1@ugcmu> Lines: 9 Sender: usenet@news.unige.ch Organization: University of Geneva, Switzerland Date: Fri, 8 Apr 1994 05:38:09 GMT Can somebody please tell me where I can get the PC version of FASTA? I looked at NCBI but didn't know WHERE exactly...so I gave up. Thanks in advance! Dorothy Lowry University of Geneva, Switzerland From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!swrinde!sdd.hp.com!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Subject: Re: entrez under linux? Message-ID: Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu Organization: Biology, Indiana University - Bloomington References: Date: Fri, 8 Apr 1994 19:04:01 GMT Lines: 14 My only comment is that compiling entrez/unix requires Motif x-window libraries, and there is no free Motif for linux. There is a $200 Motif library for linux (from who it escapes me at the moment...). It may or may not be possible to distribute binaries for entrex/linux w/o a fee. However, whoever has a linux box mostly likely already has an MSWindows box, so they could use the MSWindows binary of entrez. I haven't tried entrez/ncbitools on linux. If I do, I'll let people know. -- don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!swrinde!emory!europa.eng.gtefsd.com!library.ucla.edu!news.ucdavis.edu!josquin.ucdavis.edu!john From: john@josquin.ucdavis.edu (John Gillespie) Subject: Re: entrez under linux? Message-ID: Sender: usenet@ucdavis.edu (News Guru) Organization: University of California, Davis X-Newsreader: TIN [version 1.2 PL2] References: Date: Fri, 8 Apr 1994 20:41:25 GMT Lines: 20 Don Gilbert (gilbertd@sunflower.bio.indiana.edu) wrote : My only comment is that compiling entrez/unix requires : Motif x-window libraries, and there is no free Motif for : linux. There is a $200 Motif library for linux (from who : it escapes me at the moment...). It may or may not be : possible to distribute binaries for entrex/linux w/o a fee. : However, whoever has a linux box mostly likely already has : an MSWindows box, so they could use the MSWindows binary : of entrez. : I haven't tried entrez/ncbitools on linux. If I do, I'll : let people know. : -- don : -- : -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu Other programs (e.g. Mosaic) are distributed with the Motif binaries statically bound at no charge. As for the MSWindows suggestion... well, let's not start yet another MS bash! From owner-software@net.bio.net Thu Apr 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!trane.uninett.no!daresbury!not-for-mail From: ptaylor@crc.ac.uk (Dr. P.L. Taylor) Newsgroups: bionet.software Subject: New ABI Analysis Upgrade? Date: 8 Apr 1994 17:23:52 +0100 Lines: 25 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2o40eo$ddp@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk Dan Weinreich (dmw@mcz.harvard.edu) wrote : >Phil: > >Would it be an immense time-sink for you to develop and post a public >domain New-ABI-format-to-Old-ABI-format converter? From what you say, ABI >would give you the technical details for free, so long as you don't also >incorporate them into your (very fine) for-profit product. > >I agree that it's shortsighted of ABI not to support development of >products which add value to theirs without cutting into their market. The problem here is that ABI don't give out details of their file formats; what they supply is a c library to which you can link your code. This is free, but you have to sign an agreement not to distribute any software which uses it beyond your immediate site. Thus I can solve my own immediate problem but not supply the solution to others. I suspect it will just have to be done the hard way as usual :-) Phil Taylor | MRC Reproductive Biology Unit | Centre for Reproductive Biology | 37 Chalmers Street mbplt@uk.ac.dl.seqnet | Edinburgh EH3 9EW ptaylor@hgmp.mrc.ac.uk | Scotland. From owner-software@net.bio.net Fri Apr 08 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!ihnp4.ucsd.edu!library.ucla.edu!news.ucdavis.edu!othello.ucdavis.edu!ez027854 From: ez027854@othello.ucdavis.edu (Mike Oda) Subject: An Application Wishlist Query Message-ID: Sender: usenet@ucdavis.edu (News Guru) Organization: University of California, Davis X-Newsreader: TIN [version 1.2 PL2] Date: Sat, 9 Apr 1994 00:08:37 GMT Lines: 22 Howdy, A friend of mine (a retired C-coder) and I (a soon to be PhD in biochemistry) are considering starting a collaboration/company, which utilizes our collective expertise. We have been mulling over a number of ideas but have not yet committed ourselves to a particular project so we are open to suggestions. So if you have ever had the experience where you said to yourself, "Gee I bet I could have published this data months ago if I had a program that did..." we would like to hear from you. If your idea is good and its implementation demands a significant input from you, we are open to having a third partner. ;) The machines we are considering coding for are the PC and Mac most likely in C++. Thanks in advance, Michael Oda ez027854@hamlet.ucdavis.edu PS. Please don't write me if your idea is "I need a program to help me lower my methane production" or "I would like to see a program that creates a pattern of lights on my screen that place my cat in a hypnotic trance." While amusing, I'd prefer these joke ideas be posted and not mailed to me directly. This way I wont feel obligated to respond. ;) From owner-software@net.bio.net Fri Apr 08 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Pancreatic Islet Conference by MBONE packet Video Followup-To: bionet.software Date: 9 Apr 1994 00:16:53 GMT Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 198 Message-ID: NNTP-Posting-Host: buggus.mmg.uci.edu *** Announcement *** Pancreatic Islet Microcirculation Symposium by Internet Multicast Packet Video Friday, April 15th: 8:00am - 12:30pm Pacific Time from the Long Beach Regional Medical Education Center at The Long Beach VA Medical Center, Long Beach, California Or (with apologies to Tom Robbins) Another Roadside Attraction on the Information Superhighway Multicast videoconferencing is still in its infancy but will become progressively more widespread as more sites are Internetworked. Even now there are times when you can have your choice of several conferences to 'attend' merely by clicking on one of several icons. These conferences are typically broadcast-only because of organizational issues, but the technology is inherently interactive - all people can talk and be heard by all others 'attending'. I assume that quite soon you will have the ability to attend your favorite meetings without actually being there. There is a useful FAQ available by FTP ( venera.isi.edu:mbone/faq.txt ) which describes multicasting and how to obtain the software required to view these conferences. There have been many such conferences multicast, but mostly on the topic of the Internet itself or related technology issues. This is one of the first such conferences to be presented on a non-computer topic. As such, it will appeal to some readers who are not familiar with the underlying technology. If, after reading the FAQ, and consulting your own technoweenies, you are still have unresolved questions, let me know and I'll try to help. This conference will also be substantially broadcast-only, with one presenter (Susan Bonner Weir of Harvard) giving her presentation remotely from the Laboratory of Computer Science at MIT (you can watch her directly or watch the mixed re-broadcast from Long Beach). If you have questions for any of the speakers up to broadcast time, you can fax them to the center (310 494 5785) up to and including the time of the conference and they will be asked for you during the Q+A after the speaker finishes. You may also email questions to me (mangalam@uci.edu) until the 13th and I will forward them to the conference. On the day of the conference you may email questions to the conference itself (questions@vambone.long-beach.va.gov), but they will be held til the Q+A if they are not received during the talk. ------------------------------------------------------------------------------ Here's the Program Schedule: PANCREATIC ISLET MICROCIRCULATION SYMPOSIUM Long Beach Regional Medical Education Center Building 11 Auditorium Long Beach VA Medical Center April 15, 1994 The aim of this Pancreatic Microcirculation Symposium is to establish and summarize the current state of knowledge of islet microcirculation, and its influences on the surrounding tissue, such as acinar and ductular cells. This is critical to gain an understanding of islet physiology and its overall relationship to glucose homeostasis. Since the islet contains four major cell types, there exists a current debate on the intra islet communication between these cell types, which is dependent on the islet microcirculation. Furthermore, a second debate is ongoing about the revascularization of islets following islet transplantation. The conference will help determine the current state of knowledge on this issue. The symposium is also designed to exchange information concerning the current techniques to evaluate and manipulate the islet microcirculation. The leading authorities in these fields have been invited to exchange their knowledge concerning microcirculation of the pancreatic islets. Early Morning Session Moderator: F. Charles Brunicardi, M.D. Introductory Remarks 8:00 - 8:15 am Edward Passaro Jr., M.D. Chief of Surgery, VAMC West Los Angeles Jule D. Moravec, Ph.D. Director, VAMC Long Beach Stuart C. Gilman, M.D. Director, Long Beach RMEC Glen Kauffman Health Sciences, UC Irvine Homeokinesis Among the Islands 8:15 - 8:45 am Harold Wayland, Ph.D. - Keynote Speaker The Microvascularization of the Islets of 8:45 - 9:00 am Langerhans: Anatomy and Functional Implications Susan Bonner-Weir, Ph.D (*) Physiological Assessment and Evaluation of the 9:00 - 9:15 am Path of the Microvasculature of the Pancreatic Islet. John Stagner, M.D. Pulsatility of Islet Hormone Secretion 9:15 - 9:30 am Eli Ipp, M.D. Dynamic In Vivo Observation of Rat Islet 9:30 - 9:45 am Microcirculation . Paul Guth, M.D. High Resolution Microscopy of the 9:45 - 10:00 am Living Pancreas "In Situ". Robert McCuskey, Ph.D. Question and Answer Session 10:00 - 10:15 am BREAK: 15 minutes 10:15 - 10:30 am Late Morning Session Moderator: Edward H. Livingston, M.D. Autoregulation of the Pancreatic Islet 10:30 - 10:45 am Microcirculation. Tom Howard, M.D. Methodology for the In-Vivo, Chronic Study of 10:45 - 11:00 am Microvascular Hemodynamics. Applications to Ischemia Reperfusion. Marcos Intaglietta, Ph.D. Techniques for Measurement of Pancreatic Blood 11:00 - 11:15 am Flow and Assessment of Pancreatic Ischemia. Stanley Ashley, M.D. Computer Assisted Image Analysis of 11:15 - 11:30 am Microcirculation. Anthony Cheung, Ph.D. Structure and Function During Islet 11:30 - 11:45 am Inflammation. Arthur Charles, M.D., Ph.D. Angiogenesis and Revascularization of 11:45 - 12:00 pm Freely Transplanted Pancreatic Islet Grafts. Michael Menger, M.D. Controversies of Islet Physiology and 12:00 - 12:15 pm Future Directions. Charles Brunicardi, M.D. Questions and Answers 12:15 - 12:30 pm * Nb: This lecture will be broadcast from Boston via Internet Multicast Backbone, integrated into the proceedings at Long Beach, and rebroadcast as part of the conference. Thanks to: - Dr. John McClosky and the Laboratory for Computer Science at MIT for the use of their facilities for Dr. Bonner-Weir's presentation. - Van Jacobson, Ron Frederick, and the other mboneheads who wrote the tools that made this possible. This broadcast is made possible in part by equipment and expertise contributed by Silicon Graphics, Inc. Test Drive an Indy Today! --- Harry J Mangalam, Dean's Office, College of Medicine and Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 856-4824, fax (714) 856 8598, mangalam@uci.edu From owner-software@net.bio.net Fri Apr 08 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!xlink.net!wega.fibronics.de!neutron!jui From: jui@neutron.nacamar.de (Uwe Harmening) Subject: Multiple alignment software seeked Organization: NACAMAR Development Center Date: Thu, 7 Apr 1994 12:55:51 GMT X-Newsreader: TIN [version 1.2 PL2] Message-ID: <1994Apr7.125551.5305@neutron.nacamar.de> Lines: 22 Hallo world, I am looking for a software on PC that basically does the same as GCG or Genius Husar (in Heidelberg). We want to do multiple alignment of DNA-sequences at university. Is this possible with PC-Gene or DNAsis? We have got Windows-PCs (486-33). I heard abaout Macawwin (or so), has anybody experiences with that? Thanx Uwe Harmening -- Tschoe Jui ----Emptiness is Form; Form is Emptiness---- Fidonet: 2:244/1370.11 Internet: jui@neutron.nacamar.de Snailnet: no way! From owner-software@net.bio.net Fri Apr 08 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!xlink.net!wega.fibronics.de!neutron!jui From: jui@neutron.nacamar.de (Uwe Harmening) Subject: Multiple alignment software seeked Organization: NACAMAR Development Center Date: Thu, 7 Apr 1994 12:57:28 GMT X-Newsreader: TIN [version 1.2 PL2] Message-ID: <1994Apr7.125728.5395@neutron.nacamar.de> Lines: 21 Hallo world, I am looking for a software that basically does the same as GCG or Genius Husar (in Heidelberg). We want to do multiple alignment of DNA-sequences at university. Is this possible with PC-Gene or DNAsis? We have got Windows-PCs (486-33). I heard abaout Macawwin (or so), has anybody experiences with that? Thanx Uwe Harmening -- Tschoe Jui ----Emptiness is Form; Form is Emptiness---- Fidonet: 2:244/1370.11 Internet: jui@neutron.nacamar.de Snailnet: no way! From owner-software@net.bio.net Fri Apr 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!Eli.Meir From: meir@zoology.washington.edu (Eli Meir) Newsgroups: bionet.software Subject: New Statistics Program (shareware) Date: 9 Apr 1994 00:43:48 GMT Organization: Dept. of Zoology, Univ. of Washington Lines: 27 Sender: -Not-Authenticated-[2137] Message-ID: <2o4to4$c1k@news.u.washington.edu> NNTP-Posting-Host: quaternary.zoology.washington.edu X-Posted-From: InterNews 1.0@news.u.washington.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. I have just released a Macintosh statistics program to anonymous ftp sites. Called I Ching Squared, it is geared towards neurophysiologists (it was written to accompany my free data acquisition and analysis program Spike Studio, available at the same ftp sites). However, the program might be useful to others as well. It does a few relatively simple stats such as means, medians, standard deviations, chi squares, and 6 or 7 more, and makes histograms. It also will find event lengths, periods, and phases (using one of several algorithms). Aside from the neurophys. stuff, the nice thing about this stats package is that it will perform the same operations on multiple files with a single command, so that if you want a set of stats on 50 different files, you can do it all with one command. I Ching Squared is shareware, should work on any Macintosh computer, and can be found at the umich site (mac.archive.umich.edu I think its 128.95.68.64 Look in the directory /mac/misc/math for I Ching Squared, in /mac/util/science for Spike Studio). It can also be found at info_mac at stanford, or the info_mac mirror at washington univ. (wuarchive.wustl.edu Look in the directory /systems/mac/info_mac/sci). I can probably be persuaded to customize it for you. Hope this is useful to someone, and feel free to write me with questions. Eli Meir Dept of Zoology, Univ of Washington meir@zoology.washington.edu From owner-software@net.bio.net Fri Apr 08 23:00:00 1994 Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!emory!nigel.msen.com!zib-berlin.de!news.th-darmstadt.de!fauern!btr0x1.hrz.uni-bayreuth.de!news From: btb305@btr0x1.hrz.uni-bayreuth.de Newsgroups: bionet.software Subject: taxonomy-soft Date: 9 Apr 1994 08:20:01 GMT Organization: University of Bayreuth (FRG) Lines: 12 Message-ID: <2o5ofh$ko8@btr0x1.hrz.uni-bayreuth.de> NNTP-Posting-Host: btb3d1.bio.uni-bayreuth.de X-Newsreader: Dear Netters, I am looking for zoologic-taxonomy software for use in biology-teaching. If you know of any ftp-server or gopher-server or commercial system which are related to this please tell me (Mail!). Ruediger Beer University of Bayreuth, Germany Department for Animal Physiology 95440 Bayreuth From owner-software@net.bio.net Sat Apr 09 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!pipex!sunic!EU.net!dkuug!uts!news.daimi.aau.dk!biobase!NewsWatcher!user From: agp@biobase.aau.dk (Anders Gorm Pedersen) Subject: Request:Molecular biology clipart? Message-ID: Followup-To: bionet.software Sender: news@biobase.aau.dk (USENET News System) Organization: University of Copenhagen Date: Sun, 10 Apr 1994 15:17:54 GMT Lines: 11 I think this question has been asked before, but I missed the answer: Is there some FTP server with scientific clipart (more specifically mol.biol. clipart) that you could use for slides and such? Any pointer will be greatly appreciated. You can mail me at agp@biobase.aau.dk. ======== Anders Gorm Pedersen, internet: agp@biobase.aau.dk University of Copenhagen, institute of molecular biology. From owner-software@net.bio.net Sat Apr 09 23:00:00 1994 Path: biosci!niftyserve.or.jp!HGF02633 From: HGF02633@niftyserve.or.jp (=?ISO-2022-JP?B?GyRAQFBETT1TPCMbKEo=?=) Newsgroups: bionet.software Subject: how to use tfd2prosite.c ? Date: 9 Apr 1994 17:21:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199404100021.JAA19835@inetnif.niftyserve.or.jp> NNTP-Posting-Host: net.bio.net Recently, I got tfd2prosite.c from ftp.embl-heidelberg.de by anonymous ftp. This program is intended to convert Gosh's TFD format to prosite format. However, the downloaded tfd2prosite.c (text file ?) contains only think C source code. How can I use this tfd2prosite.c as a program in my Macintosh. Please teach me. Sincerely yours, ========================================================================= Dr.Toshiharu Ishizuka Department of Biochemistry, Chiba University, School of Medicine 1-8-1, Inohana, Chuo-ku, Chiba, 260 JAPAN FAX +81-43-226-2041 E-mail QFH03407@niftyserve.or.jp tishizuk@twics.com ========================================================================= From owner-software@net.bio.net Sat Apr 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!Eli.Meir From: meir@zoology.washington.edu (Eli Meir) Newsgroups: bionet.software Subject: Re: Contour mapping program? Date: 10 Apr 1994 20:52:03 GMT Organization: Dept. of Zoology, Univ. of Washington Lines: 13 Sender: -Not-Authenticated-[7936] Message-ID: <2o9otj$ieh@news.u.washington.edu> References: NNTP-Posting-Host: quaternary.zoology.washington.edu X-Posted-From: InterNews 1.0@news.u.washington.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. I'm not sure exactly what type of contour mapping you want, but for the contour mapping I do there's a program called Transform (part of the SpyGlass series) that does a nice job on the mac. The group that wrote it is originally out of one of the supercomputer centers, though now they are a commercial outfit. The address is Spyglass Inc., 701 Devonshire Dr., C-17, Champaign, IL 61820. There are also several IBM programs that do contour plots. I believe you can also do them in some of the more general purpose math packages such as Matlab and Mathematica. Eli Meir Dept of Zoology, Univ of Washington meir@zoology.washington.edu From owner-software@net.bio.net Sat Apr 09 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!nih-csl!bernard From: bernard@elsie.nci.nih.gov (Bernard Murray) Subject: Re: Prograph Message-ID: <1994Apr10.204553.16932@alw.nih.gov> Summary: Source and answer Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: National Institutes of Health References: <2o9brp$4i0@charm.magnus.acs.ohio-state.edu> Date: Sun, 10 Apr 1994 20:45:53 GMT Lines: 34 In article <2o9brp$4i0@charm.magnus.acs.ohio-state.edu>, gchacko@magnus.acs.ohio-state.edu (George W Chacko) writes: > > Where do I get it and does it come with a driver for the HP-Laserjet > III? > > Thanks > > GC > > Hi, I grabbed my copy from the EMBL fileserver (you can collect it by email or ftp). I can't remember offhand if HP LJIII is supported directly. As I remember, the program uses the Borland Graphics Interface language as its own graphics language and provides a utility for converting this to HPGL format. Again, I don't have a LJIII so I don't know if this can print HPGL files directly but our old LJII had a utility that would allow this and I'm sure the same must be true for the III. Oh yes, for collection by email; NetServ@EMBL-Heidelberg.DE and send GET DOS_SOFTWARE:PROGRAPH.UAA and ftp is (I think) ftp.EMBL-Heidelberg.DE I am sure most of the local mirrors also have copies. Enjoy this (great) program!, Bernard Bernard Murray, Ph.D. bernard@elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA) From owner-software@net.bio.net Sat Apr 09 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!gchacko From: gchacko@magnus.acs.ohio-state.edu (George W Chacko) Newsgroups: bionet.software Subject: Prograph Date: 10 Apr 1994 17:09:13 GMT Organization: The Ohio State University Lines: 9 Message-ID: <2o9brp$4i0@charm.magnus.acs.ohio-state.edu> NNTP-Posting-Host: top.magnus.acs.ohio-state.edu Where do I get it and does it come with a driver for the HP-Laserjet III? Thanks GC From owner-software@net.bio.net Sat Apr 09 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!library.ucla.edu!csulb.edu!csus.edu!netcom.com!barbose.slip.netcom.com!barbose From: Jeffrey J Barbose Subject: Re: An Application Wishlist Query Message-ID: X-Xxmessage-Id: X-Xxdate: Sun, 10 Apr 1994 18:44:00 GMT S