From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!NIGHTSHADE.CIT.CORNELL.EDU!epaul From: epaul@NIGHTSHADE.CIT.CORNELL.EDU ("Edie Paul") Newsgroups: bionet.software Subject: NCBI Vibrant Toolkit Date: 1 Dec 1994 11:05:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <9412011859.AA09572@nightshade.cit.cornell.edu> I will soon be undertaking the development of a graphical user interface that I would like to run on multiple platforms, particularly UNIX and MS Windows. I am considering the Vibrant toolkit for this, but I'd be interested in hearing any pros/cons/comments anyone has, as well as suggestions for other public domain (or fairly inexpensive) software to do the same kind of thing. Linux for the PCs is not an option. Thanks, Edie Paul epaul@nightshade.cit.cornell.edu From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!library.ucla.edu!news.mic.ucla.edu!steve3.mbi.ucla.edu!visick From: Jon Visick Newsgroups: bionet.software Subject: Re: Bibliography package Date: 2 Dec 1994 00:56:52 GMT Organization: UCLA Lines: 5 Distribution: world Message-ID: <3blrck$idt@news.mic.ucla.edu> References: NNTP-Posting-Host: steve3.mbi.ucla.edu X-UserAgent: Nuntius v1.1.2 X-XXMessage-ID: X-XXDate: Fri, 2 Dec 94 04:57:50 GMT Darrell Pogue, dpogue@obsnsrv1.bio.uoknor.edu writes: >I am looking for a bibliography package for windows. Any suggestions? EndNote is the best, hands down. It's not "for" Windoze, but it will run under Windoze, if you must. From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!HEMEROTECA.ICFES.GOV.CO!internet From: internet@HEMEROTECA.ICFES.GOV.CO (Usuarios de Internet) Newsgroups: bionet.software Subject: Oferring a new Institute of Eco-Genetics in Amazonian Biodiversity Date: 2 Dec 1994 08:41:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Sir or Lady: This is a NEWS-Letter to inform you of the existance of a brand new INSTITUTE OF ECOLOGICAL-GENETICS TO STUDY THE AMAZONIAN=20 BIODIVERSITY . For further information write=20 to: Dr. Hugo Hoenigsberg =09 Instituto de Genetica-Ecologica y Biodiversidad Amazonica Cra.4 No.71-69 Bogota D.C.COLOMBIA. FAX: 612 7369 You can sent your C.V.to our personal address above. We are considering=20 applications to fill posts as research scientific staff members.=20 Evolutionary-Biologists, geneticists,ecologists, systematist,=20 botanists,zoologists, mathematicians and other Ph.D. individuals=20 interested in neo-tropical biological research with at least 10 years of=20 research experience preferably, but not exclusively, in the trop=A1cs, and= =20 about 10 published scientific papers will be considered. This new=20 Institute will study Amazonian biodiversity. Although its main purpose is= =20 research it will by inclination help, not only to preserve the Amazonian=20 biodiversity , but also to diseminate the gospel of international=20 management of the most wonderful world natural reserve for which it is=20 worth to dedicate ones life. There will also be graduate degrees to be=20 dealt with. For academic life within the Institute, please contact=20 the Rector of the Amazonian University as follows: =20 Dr. Ernesto Fajardo Universidad de la Amazonia Florencia, Caqueta Colombia. FAX: (988 35) 8231 Florencia is the capital of the State of Caqueta, and Caqueta is one of=20 the three Amazonian States of Colombia. We will be working closely with=20 Peruvian and Brazilian scientist interested in Amazonian biodiversity.=20 Our Central offices and research labs will be in Florencia's souroundings. = =20 Hoping to see you soon=20 Yours truly, =20 =20 Hugo Hoenigsberg From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!Germany.EU.net!EU.net!julienas!genethon!manu From: manu@genethon.fr (Emmanuel Barillot) Subject: clone ordering software Message-ID: <1994Dec2.182655@genethon.fr> Originator: manu@genethon.genethon.fr Sender: news@genethon.fr Nntp-Posting-Host: genethon.genethon.fr Organization: Genethon -- Human Genome Research Centre Date: Fri, 2 Dec 1994 17:26:55 GMT Lines: 5 I am looking for a software ordering cosmids from their Restriction Fragment fingerprints. I would like to try several programs, interactive or fully automatic. If you know about such programs or if you have experience in this area, please let me know. From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!bnr.co.uk!bmdhh222.bnr.ca!bcarh8ac.bnr.ca!bcarh189.bnr.ca!nott!nrcnet0.nrc.ca!ratilal From: "reithm@imb.lan.nrc.ca" Newsgroups: bionet.software Subject: Re: BLAST or BLAST-like software for Windows Date: 2 Dec 1994 13:34:45 GMT Organization: National Research Council, Canada Lines: 45 Message-ID: <3bn7pl$55m@nrcnet0.nrc.ca> References: <3blef9$p1j@news.CCIT.Arizona.EDU> NNTP-Posting-Host: reith.imb.nrc.ca valeryt@ag.arizona.edu (Valery Thompson) wrote: > > I am looking for some software to perform BLAST searches that I can run > directly from my PC. I have tried the network version available from NCBI and > find it very cumbersome to use particularly since it is a DOS only program > and I have to not only exit Windows, but also unload my Windows network > driver in order to use it. I have a demo copy of WinGenie which has > several nice programs for sequence searching and sequence alignment, > but requires me to send the requests by email. > > Is there anything available that combines the abilities of these two programs? > Any input would be appreciated. > > Valery Thompson > Muscle Biology Group > University of Arizona The WWW/Mosaic search by way of NCBI is a good one, although I find it cumbersome to save the results of these searches. Another alternative is to multiplex your packet driver so as to be able to run Windows and DOS software simultaneously. Pktmux (at boombox.micro.umn.edu in /pub/pc/packet-drivers/drivers) does this nicely. The relevant lines of my autoexec.bat are: ODIPKT 1 99 pktmux pktdrv 60 pktdrv 61 WINPKT 0X61 ODIPKT loads the packet driver at interrupt 0x63, pktmux multiplexes it twice (the default) at 0x60 and 0x61 - pktdrv statements. Winpkt is then loaded at 0x61 so that BLAST can use the packet driver at 0x60, which it requires. In Windows, make sure to set TCPMAN (assuming you're using Trumpet winsock) to use the packet driver at 0x61. You can then open a DOS window within Windows and run the BLAST software in it. I've set up a batch file to run multiple searches one after the other, using the same set of parameters. I find this the most convenient way to do lots of searches at one time. Mike Reith Marine Biology NRC Institute for Marine Biosciences reithm@imb.lan.nrc.ca From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: nce@rri.sari.ac.uk (Nigel Eastmond) Newsgroups: bionet.software Subject: GeneRunner Question Date: 2 Dec 1994 15:46:55 -0000 Organization: Rowett Research Institute Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3bnfhf$h3i@mserv1.dl.ac.uk> Apparently-To: I recently came across a GeneRunner for Windows output for a probe I am interested in. The printout shows the possible dimers, bulge loops etc. linked to the oligo by | signs and + signs. What difference does the use of the two bonding signs signify? o------------------------------oOo------------------------------o | Nigel C. Eastmond | Email nce@rri.sari.ac.uk | | Rowett Research Institute | Tel +44 244 712751 | | Aberdeen | Fax +44 244 715349 | | Scotland | | o------------------------------oOo------------------------------o From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: Bibliography package Date: 2 Dec 1994 08:57:25 GMT Organization: University of Cambridge, England Lines: 14 Message-ID: <3bmnhl$alb@lyra.csx.cam.ac.uk> References: <3blrck$idt@news.mic.ucla.edu> NNTP-Posting-Host: mole.bio.cam.ac.uk Jon Visick writes: > Darrell Pogue, dpogue@obsnsrv1.bio.uoknor.edu writes: >>I am looking for a bibliography package for windows. Any suggestions? >EndNote is the best, hands down. It's not "for" Windoze, but >it will run under Windoze, if you must. A combination of Refs and WinRefer will do everything EndNote for the Macintosh can do (including DDE to your word-processor), and will only cost you 30 pounds, and no upgrade charges either. Plus they're both Windows programs. Tim. From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!spool.mu.edu!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!newsflash.concordia.ca!nstn.ns.ca!ac.dal.ca!ac.dal.ca!nntp Newsgroups: bionet.software Subject: Re: Grateful Med under OS/2 Message-ID: <1994Dec1.232317.30843@ac.dal.ca> From: JWChish@AC.DAL.CA (Jeffrey Chisholm) Date: 1 Dec 94 23:23:17 -0400 References: <94332.153831RROXBY@MAINE.MAINE.EDU> Organization: Dalhousie University Nntp-Posting-Host: jchisholm.med.dal.ca X-Newsreader: WinVN 0.92.6+ Lines: 30 In article <94332.153831RROXBY@MAINE.MAINE.EDU>, Robert Roxby says: > >Is anybody running Grateful Med under OS/2? I just received the package >and have not received a logon id yet, but the installation seems >rather definate about having NCSA somethin-or-other telnet. >I have the telnet that comes with IBM TCP/IP for OS/2 v 2.0. >If experience is any guide, this will be a problem. Like >to have any experiences or advice, though. Thanks, >Bob Any telnet should do, although many don't support color ansi. I'm not all that familiar with OS/2, but if it will run winsock compliant aplications, the telnet client from Dart Communications is the best I've seen. I think it is either shareware or freeware and available on many ftp sites. Alternatively you can email me for access to it on my ftp site. The file is called vt220.exe. The program, has very nice easy on the eyes text and supports color ansi, keymapping and a range of other useful features. Also, the program seems much more stable than other telnet clients I have run under windows. BTW, I have a very fast link!! Jeffrey Chisholm Lipoprotein Research Group Dept. of Biochemistry Dalhousie Universiy Halifax, N.S., Can. JWCHISH@AC.DAL.CA From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!SIUMED.EDU!clawyer From: clawyer@SIUMED.EDU (Carl Lawyer) Newsgroups: bionet.software Subject: Re: Visible Human Date: 2 Dec 1994 15:25:56 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <9412022314.AA28368@siumed.edu> NNTP-Posting-Host: net.bio.net At 7:08 PM 12/2/94 +0000, Janna Ore Nugent wrote: >This week the National Library of Medicine unveiled >Visible Man, the male componant of their Visible Human >project. Stories in the paper said that parts of Visible >Man were already available on the Internet, but a source >was not given. > >Does anybody know where to get Visible Man files on >the Internet? How about getting the whole 15 BG on >tape? > >Thanks for any information, > >Janna Ore Nugent >Visualization Lab Manager >Biological Sciences Division >The University of Chicago > >janna@bio-3.bsd.uchicago.edu reply from C. Lawyer: there are a few sample images available from hyperdoc@nlm.nih.gov From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!rutgers!mbcl!hey From: hey@mbcl.rutgers.edu Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Dictating DNA sequences to a computer Message-ID: <3930.2ed1da15@mbcl.rutgers.edu> Date: 22 Nov 94 11:46:29 EDT Lines: 84 Xref: biosci bionet.molbio.methds-reagnts:21653 bionet.software:10238 Dictating DNA sequences. I thought others might be interested in the way I have recently been entering DNA sequence data, from autoradiograms, to a computer. The system is easier than using a digitizer, and comprably priced if you already own a quick PC clone (probably cheaper, I have not recently priced audio digitizers). The components: Quick PC clone microcomputer (I use a 486 66Mhz Dell) with at least 16 meg RAM. IBM OS/2 2.1 or 3.0 operating system. IBM Personal Dication System for OS/2: This includes a hardware component, (a plug in card), a microphone, and a software component. The hardware and software sell separately and both are about $500. I bought mine thru Indelible Blue (800-776-8284). Contact IBM, not me, for more info. Rimstar programmer's editor - OS/2 version. Rimstar Technology Inc. (603) 778-2500. This is also available thru Indelible Blue or directly from the company. How it works: The dicatation system works in two modes, dicatation and application control. The dictation mode is nifty and very impressive, with a 30,000 word vocabulary that can be augmented. However in my experience it is not ideal for entering DNA sequence data. Instead I use the application control feature of the dictation system. This is basically a system whereby navigation through applications and windows that are open within the graphical interface of OS/2 is done by dicatation of commands. Under application control, the dictation software only recognizes a relatively small set of words, i.e. those that currently make sense for the windows that are open. It is also quite easy to dictate macros to add additional functions to application control. It turns out that the Rimstar editor can be directed quite well under application control dictation. Furthermore this editor is highly configurable, and has a full featured macro language (very much like C) with a built in compiler. What I have done is to create a set of dictation macros so that I can speak a small set of commands that cause the editor to write the different bases of a DNA sequence. Each dictation macro triggers a macro function written in the Rimstar macro language. The different commands I use are associated with the following functions: - write 'A' and beep at 800 hz for 150 millisecs. - write 'C' and beep at 1200 hz for 150 millisecs. - write 'G' and beep at 1500 hz for 150 millisecs. - write 'T' and beep at 1800 hz for 150 millisecs. - write 'N' and beep at 400 hz for 150 millisecs. - delete the previous character and beep twice. The beeping provides an audio cue that the editor has received the intended command. All other Rimstar menu commands are also accessible by dictation. In particular "save" is frequently used to save the file. Any choice of words can be used for these functions, including the simple words "A", "C" etc. However the dictation system does require clear speech with at least very short pauses between spoken commands. In practice I have found a different set of words to be more forgiving of vagaries in speech and less likely to be mistaken as other Rimstar menu commands. I use - "ALL" for the A function. - "CHEESE" for the C function. - "GRAIN" for the G function. - "TICK" for the T function. - "N" for the N function. - "BACKSPACE" for the delete function. Probably the biggest downside to all this is that you sound a little goofy. By the way, Rimstar also makes a great sequence editor, especially for multiple sequences. It has essentially unlimited line lengths, very easy column blocking and movement, and is highly configureable. Brian Smith, the author has even written a macro that causes the four letters A, C, G and T to appear in different colors. Very handy for allignements. Jody Hey Department Biological Sciences Rutgers University hey@mbcl.rutgers.edu From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: NCBI Vibrant Toolkit Date: 2 Dec 1994 13:22:10 GMT Organization: Biology, Indiana University - Bloomington Lines: 10 Distribution: world Message-ID: <3bn722$ib0@usenet.ucs.indiana.edu> References: <9412011859.AA09572@nightshade.cit.cornell.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu I use NCBI toolkit, esp. Vibrant, for cross-platform app development, and it works well. I prefer C++ and have a C++ application framework based in part on MacApp and built on top of the NCBI toolkit. See ftp://ftp.bio.indiana.edu/util/dclap/... for this software source and demo applications. -- don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Newsgroups: bionet.software Path: biosci!rutgers!gatech!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: NCBI Vibrant Toolkit Message-ID: <1994Dec2.182029.15148@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <9412011859.AA09572@nightshade.cit.cornell.edu> Date: Fri, 2 Dec 1994 18:20:29 GMT Lines: 66 Edie Paul (epaul@NIGHTSHADE.CIT.CORNELL.EDU) wrote: : I will soon be undertaking the development of a graphical user interface : that I would like to run on multiple platforms, particularly UNIX and MS : Windows. I am considering the Vibrant toolkit for this, but I'd be : interested in hearing any pros/cons/comments anyone has, [..] We use VIBRANT as platform on OSF/1, IRIX, Mac, Windows, and AXP/VMS. It is a quite convenient toolkit and certainly worth looking at as an alternative to commercial products. Depending on the sophisticatedness you might need to invest some time as the callbacks require a lot of programming but this is an effect of a GUI and inherent to the method. Before you start on Windows, make sure you select a proper compiler - we got it running on both Visual C++ from Microsoft (16 bit) and Borland C++ on the Win32s, but did not look in detail into other products. The 'make' utility should be supported as we had problems with Turbo C from Borland. On the Macintosh we use Think C and successfully solved the small problems with the MacTCP package which you must have purchased separately. We have investigated SUIT as an alternative (University of Virginia), but the SUIT routines are much lower-level and require even more programming work. Tk/tcl is also an alternative but not necessarily a brilliant option if you want to distribute your code as the client or remote user must have this installed if he/she wants to run your code. Check out the Portable GUI Development Kit FAQ from news.answers (Author Wade Guthrie) for a comprehensive overview including commercial packages. (SUIT does not currently on Macintosh, which renders it useless for us). A remark on developing with UNIX/Windows source code compatible systems; 32 bit programming makes things a lot easier as memory models play a significantly smaller role, so if you can afford to force your users to go for the extensions then it might be worth to do so. There are quite a few demo examples coming with the NCBI distribution. VIBRANT non-NCBI examples are available from Don Gilbert's kit in C++. Our code is in ftp://bioftp.unibas.ch/archive_data/survival/csource, to see how the binaries look on different platforms check out Entrez or use our code example we developed as part of the Survival Guide, on ftp://bioftp.unibas.ch/archive_data/survival/binaries. We published another piece of code which is a very simple application of VIBRANT, see ftp://bioftp.unibas.ch/programs/bioftp-sw/Dbcomp/bin for the various platforms and ftp://bioftp.unibas.ch/programs/bioftp-sw/Dbcomp/src for source. Dbcomp was developed by F.Eggenberger in our lab. The sources are in C as we are programming on today's zoo of all operating systems - let us know if the code does not run on any of the VIBRANT-supported platforms. Without heating the C++ vs Smalltalk vs C war, yes we tried all of them but C seems to be the only (affordable) language currently. (In terms of ease of use, API's to other software, licensing fees, availability of CASE tools in public domain etc.) Closing, we appreciate that NCBI makes VIBRANT available and thank the developers there, in particular Jonathan Kahns, for their support. Regards Reinhard Doelz EMBnet Switzerland -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Thu Dec 01 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!uchinews!bio-7.bsd.uchicago.edu!janna From: janna@bio-7.bsd.uchicago.edu (Janna Ore Nugent) Subject: Visible Human Message-ID: <1994Dec2.190834.4409@midway.uchicago.edu> Keywords: Visible Human, Visible Man Sender: news@uchinews.uchicago.edu (News System) Organization: Biological Sciences Division, The University of Chicago Date: Fri, 2 Dec 1994 19:08:34 GMT Lines: 18 This week the National Library of Medicine unveiled Visible Man, the male componant of their Visible Human project. Stories in the paper said that parts of Visible Man were already available on the Internet, but a source was not given. Does anybody know where to get Visible Man files on the Internet? How about getting the whole 15 BG on tape? Thanks for any information, Janna Ore Nugent Visualization Lab Manager Biological Sciences Division The University of Chicago janna@bio-3.bsd.uchicago.edu From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!news.ecn.bgu.edu!newspump.wustl.edu!cerberus-138.wustl.edu!usenet From: HAVILAND@KIDS.WUSTL.EDU (David L. Haviland, Ph.D.) Newsgroups: bionet.software Subject: Re: Bibliography package Date: 2 Dec 1994 22:59:42 GMT Organization: Washington University School of Med. Lines: 22 Distribution: world Message-ID: <3bo8su$l5n@cerberus-138.wustl.edu> References: <3blrck$idt@news.mic.ucla.edu> NNTP-Posting-Host: kids2.wustl.edu X-News-Reader: VMS NEWS v1.25 In-Reply-To: visick@ewald.mbi.ucla.edu's message of 2 Dec 1994 00:56:52 GMT In <3blrck$idt@news.mic.ucla.edu> visick@ewald.mbi.ucla.edu writes: > Darrell Pogue, dpogue@obsnsrv1.bio.uoknor.edu writes: > >I am looking for a bibliography package for windows. Any suggestions? > > EndNote is the best, hands down. It's not "for" Windoze, but > it will run under Windoze, if you must. Having tried BOTH Endnote and Papyrus, I beg to differ. Though neither one is designed for Windows, in MY hands Papyrus was easier to use, easier to customize, and interacted with WordPerfect better than Endnote did. I returned Endnote and never looked back. Papyrus is also quite a bit cheaper than its competition. No extra "modules" needed. A Windows version is forthcoming after the Mac version is released - or so I've been told. David *Other than a satisfied customer, not affilied with RSD in any way...* From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!ix.netcom.com!netnews From: QZAR@ix.netcom.com (charles foulk) Newsgroups: bionet.software Subject: PCB CAD PROGRAM NEEDED Date: 3 Dec 1994 16:03:04 GMT Organization: Netcom Lines: 8 Distribution: world Message-ID: <3bq4ro$gqu@ixnews1.ix.netcom.com> NNTP-Posting-Host: ix-orl2-22.ix.netcom.com I am looking for a shareware or simalar pcb design program for turning schematics into track layouts Anyone got any ideads? Thanks Zac :) From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!boulder!tali.hsc.colorado.edu!news From: ikled@njc.org (David Ikle) Newsgroups: bionet.software Subject: Re: Visible Human Date: 3 Dec 1994 14:18:01 GMT Organization: National Jewish Hospital Lines: 7 Sender: -Not-Authenticated-[7598] Distribution: world Message-ID: <3bpump$iij@tali.hsc.colorado.edu> References: <9412022314.AA28368@siumed.edu> NNTP-Posting-Host: 198.243.65.21 X-Posted-From: InterNews 1.0.4@198.243.65.21 Xdisclaimer: No attempt was made to authenticate the sender's name. Try http://www.nlm.nih.gov and select the Visible Human Project. David N. Ikle, Ph.D. Biostatistics and Academic Computing National Jewish Hospital Denver, CO 80206 ikled@njc.org From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!agate!boulder!tali.hsc.colorado.edu!news From: ikled@njc.org (David Ikle) Newsgroups: bionet.software Subject: eXodus experience Date: 3 Dec 1994 14:30:27 GMT Organization: National Jewish Hospital Lines: 11 Sender: -Not-Authenticated-[7598] Message-ID: <3bpve3$ioa@tali.hsc.colorado.edu> NNTP-Posting-Host: 198.243.65.21 X-Posted-From: InterNews 1.0.4@198.243.65.21 Xdisclaimer: No attempt was made to authenticate the sender's name. Does anyone have an opinion on White Pine eXodus XWindows emulator? Is it netive PowerPC yet? How does it compare to MacX? David N. Ikle, Ph.D. Biostatistics and Academic Computing National Jewish Hospital Denver, CO 80206 ikled@njc.org From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!portal.gmu.edu!mason1.gmu.edu!dsklarew From: dsklarew@mason1.gmu.edu (Daniel M Sklarew) Newsgroups: bionet.software Subject: Re: FREE INTERNET PROVIDERS Date: 3 Dec 1994 08:34:04 GMT Organization: George Mason University, Fairfax, Virginia, USA Lines: 14 Message-ID: <3bpahs$mrr@portal.gmu.edu> References: <3biuaq$ejj@speedy.interbahn.com> NNTP-Posting-Host: mason1.gmu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: TIN [version 1.2 PL2] info (info@interbahn.com) wrote: : : FREE INTERNET ACCESS : : Full service Internet gateway : : Includes shell and slip accounts : : local dial up in most areas of U.S.A. : : for full info dial via modem: 914-365-0179 : : reply by E-mail to info@interbahn.com : or telnet: Interbahn.com This is a crock -- they'll give you so many free days of service if you sign up for their pay-service. Basically, false and deceptive advertising. Where's the Internet Better Business Bureau??? From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!ihnp4.ucsd.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: Mac or PC: the results of the poll Date: Fri, 02 Dec 1994 18:39:14 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 18 Message-ID: References: <3bfkl1$ro0@lirmm.lirmm.fr> <3bhr5h$6dc@sat.ipp-garching.mpg.de> <3bk6od$9lp@lyra.csx.cam.ac.uk> NNTP-Posting-Host: buggus.mmg.uci.edu > I do believe that at the conference held by Apple-IBM-Motorola a few weeks > ago to announce their Hardware Reference Platform they said it would run > the following OS's: Mac OS (obviously), Windows NT (this I've already > seen running), AIX, and Solaris. > > -jason and os/2, PowerOpen (PPC/more open version of AIX?), taligent, and of course, LINUX!! (probably before some of the others). -- Harry J Mangalam, Microbiology and Molecular Genetics, College of Medicine, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598, --- That which does not kill me, makes me grouchier --- http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!msunews!netnews.upenn.edu!news.drexel.edu!dunx1.ocs.drexel.edu!dunx1.ocs.drexel.edu!not-for-mail From: st93mey7@dunx1.ocs.drexel.edu (Frederick Thum) Newsgroups: bionet.software Subject: Re: Visible Human Date: 3 Dec 1994 18:38:12 -0500 Organization: Drexel University, Phila. Pa. Lines: 21 Message-ID: <3bqvh4$t59@dunx1.ocs.drexel.edu> References: <1994Dec2.190834.4409@midway.uchicago.edu> NNTP-Posting-Host: dunx1.ocs.drexel.edu X-Newsreader: TIN [version 1.2 PL2] Janna Ore Nugent (janna@bio-7.bsd.uchicago.edu) wrote: : This week the National Library of Medicine unveiled : Visible Man, the male componant of their Visible Human : project. Stories in the paper said that parts of Visible : Man were already available on the Internet, but a source : was not given. Michael J. Ackerman is the Project Director. I do not have his email address available, although it should not be difficult to find. : Does anybody know where to get Visible Man files on : the Internet? How about getting the whole 15 BG on : tape? From the correspondence I have received thus far, the files are available to individuals after they sign a licensing agreement (still free, though). The complete set is available on DAT for a $1,000 processing fee. Contact Ackerman for details. - Fred Thum From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!ns1.faseb.org!darwin.sura.net!tulane!Dean.Bottino From: bottino@math.tulane.edu (Dean Bottino) Newsgroups: bionet.software Subject: amoeboid locomotion visualization Date: 3 Dec 1994 23:01:58 GMT Organization: Computer Science Dept., Tulane Univ., New Orleans, LA Lines: 12 Sender: -Not-Authenticated-[3898] Message-ID: <3bqtd6$3ii@news.cs.tulane.edu> NNTP-Posting-Host: ppp9.tcs.tulane.edu X-Posted-From: InterNews 1.0@news.cs.tulane.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. I was wondering where I could access some movies (quicktime, etc) of amoeboid locomotion. Many articles I am reading mention movies presented at conferences, etc... I would like to see them. I am working on a computer model of such locomotion and I wanted to get a better idea of what the things look like when they're moving. If there aren't any computer movies out there, is there a way to get information about movies on videotape? Mathematicians don't watch many movies, so I'm kind of clueless on this. Thanks. bottino@math.tulane.edu From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!panix!cmcl2!yale.edu!yale!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Newsgroups: bionet.software Subject: Re: OB-GYN and Astronomy Software for PCs Date: 30 Nov 1994 21:06:45 GMT Organization: National Insts. of Health Lines: 30 Distribution: world Message-ID: <3biph5$m0a@babyblue.cs.yale.edu> References: <3bhse7$5kd@newsbf01.news.aol.com> Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) NNTP-Posting-Host: spasm.niddk.nih.gov In article <3bhse7$5kd@newsbf01.news.aol.com>, alexkara@aol.com (AlexKara) writes: |> Hi all, |> |> I'd like to know if there is any type of OB-GYN software or Astrology (Not |> Astronomy) software out there in the market. |> |> I can't seem to find anything in the stores, since they are concentrating |> on the games and non-serious software. Please forgive me if this isn't |> the right news group for this kind of posting, but I really don't know |> where else to look. |> |> Please advise, thank you in advance... |> |> Alex K. Another fine posting brought to you by AOL. -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uunet!news.uiowa.edu!panda From: J. Monahan Newsgroups: bionet.software Subject: Re: Digital Imaging Software and Hardware Date: 3 Dec 1994 19:29:32 GMT Organization: U of Iowa Panda System Lines: 31 Distribution: world Message-ID: <786483286-1-51539@blue.weeg.uiowa.edu> References: Reply-To: jmonahn@blue.weeg.uiowa.edu NNTP-Posting-Host: blue.weeg.uiowa.edu The free software called "Image" is available for the Mac from the anon. ftp site: zippy.nimh.nih.gov I believe it can do the analysis you need. Also, you can use a digitizing board with a mac, Video Spigot, for example, to capture single frames of video to be opened in the image analysis software. Joe Monahan In note , umdoble@mail.cc.umanitoba.ca (Brad Doble) writes: >Our lab currently has a microscope equipped with a CCD colour video camera >and colour monitor. We would like to store images (videocassette >recorder?) and then analyze them using a computer (we currently have a >computer with a 66 MHz 486 processor, 8 Megabytes RAM, 250 MB hard drive, >and a standard svga graphics card). What additional hardware (RAM, >graphics cards, hard disk space, etc.) is required, and what good software >programs are currently in use to analyze image data? The types of >analyses we would like to do include: i) counting labelled or stained >cells vs. control cells ; ii) measuring the intensity of fluorescent >markers; iii) determing morphometric values; etc. The purchase of >another computer may be possible with our budget so please don't hesitate >to describe setups with Macintoshes if you feel they are best for the task >at hand. Also, I would like to have an idea of the cost of the hardware >and software required. > >Any feedback will be greatly appreciated. > > Thanks in advance, > > Brad Doble From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uunet!news.uiowa.edu!panda From: J. Monahan Newsgroups: bionet.software Subject: Re: Font w/ male&female symbols wanted Date: 3 Dec 1994 19:24:16 GMT Organization: U of Iowa Panda System Lines: 27 Distribution: world Message-ID: <786482969-0-51539@blue.weeg.uiowa.edu> References: <3ah0ur$iua@ixnews1.ix.netcom.com> Reply-To: jmonahn@blue.weeg.uiowa.edu NNTP-Posting-Host: blue.weeg.uiowa.edu The new system font available for the Mac has the font called "Zeal" that includes the male-female symbols. You have to load Zeal, open the Key Caps application that comes with the system software then depress the option key to see the symbols. Joe Monahan In note , carmean@sfu.ca (Dave Carmean) writes: >I am looking for a (free?) font for Macintosh that includes >male and female symbols. If you know of any (preferably with a >FTP/gopher/WWW address) I would greatly appreciate the information. > >I am also curious why these seem to be missing from symbols- I would at >least think the medical world would have some influence in their >inclusion. Or more cynically, the astrological world. > >Thanks in advance, >Dave Carmean >Biological Sciences >Simon Fraser University >Burnaby, BC CANADA V5A 1S6 > >carmean@sfu.ca From owner-software@net.bio.net Fri Dec 02 22:00:00 1994 Path: biosci!ns1.faseb.org!darwin.sura.net!tulane!Dean.Bottino From: bottino@math.tulane.edu (Dean Bottino) Newsgroups: bionet.software Subject: amoeboid locomotion visualization Date: 3 Dec 1994 22:54:53 GMT Organization: Computer Science Dept., Tulane Univ., New Orleans, LA Lines: 9 Sender: -Not-Authenticated-[3898] Message-ID: <3bqsvt$3bp@news.cs.tulane.edu> NNTP-Posting-Host: ppp9.tcs.tulane.edu X-Posted-From: InterNews 1.0@news.cs.tulane.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. I was wondering where I could access some movies (quicktime, etc) of amoeboid locomotion. Many articles I am reading mention movies presented at conferences, etc... I would like to see them. I am working on a computer model of such locomotion and I wanted to get a better idea of what the things look like when they're moving. If there aren't any computer movies out there, is there a way to get information about movies on videotape? Mathematicians don't watch many movies, so I'm kind of clueless on this. From owner-software@net.bio.net Sat Dec 03 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!EU.net!ub4b!idefix.CS.kuleuven.ac.be!blekul11!jan.eggermont Nntp-Posting-Host: 134.58.181.40 Date: Sat, 3 Dec 1994 13:59:33 +0100 From: Jan.Eggermont@med.kuleuven.ac.be (Jan Eggermont) Newsgroups: bionet.software Subject: Re: DNA Strider Message-ID: References: <3b0g10$4no@news.doit.wisc.edu> Organization: KU Leuven Lines: 24 In article <3b0g10$4no@news.doit.wisc.edu>, chih-che@cae.wisc.edu (Chih-Che Lin) wrote: > Hi there, > I am looking for a software named "DNA strider". If someone > out there happen to know this software, I will really > appreciate if you can tell me the company's phonenumber or > any information about this software. > > You can contact the author on this address: Christian Marck Service de Biochimie et de Génétique Moléculaire Bat 142 Centre d'Etudes de Saclay 91191 Gif-Sur-Yvette France -- Jan Eggermont Jan.Eggermont@med.kuleuven.ac.be Laboratorium voor Fysiologie - KU Leuven Campus Gasthuisberg B-3000 Leuven tel 32-16-345938 Belgium fax 32-16-345991 From owner-software@net.bio.net Sat Dec 03 22:00:00 1994 Path: biosci!newshost.lanl.gov!news.ttu.edu!news From: P.Doris@ttu.edu (Peter Doris) Newsgroups: bionet.software Subject: Re: Visible Human Date: 4 Dec 1994 16:35:24 GMT Organization: Texas Tech University Health Sciences Center Lines: 9 Sender: -Not-Authenticated-[4153] Message-ID: <3bsr4c$q33@hydra.acs.ttu.edu> References: <1994Dec2.190834.4409@midway.uchicago.edu> <3bqvh4$t59@dunx1.ocs.drexel.edu> NNTP-Posting-Host: cbb056.lubb.ttuhsc.edu X-Posted-From: InterNews 1.0.2b3@cbb056.lubb.ttuhsc.edu Xdisclaimer: No attempt was made to authenticate the sender's name. sample files can be obtained by gopher to gopher.nlm.nih.gov (port 70) they are gif format and about 250K each there is one sample file for each body region Peter A. Doris P.Doris@ttu.edu (806) 743 3046 From owner-software@net.bio.net Sat Dec 03 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!holzwarth3.life.uiuc.edu!user From: jbuberel@uiuc.edu (Jason L. Buberel) Newsgroups: bionet.software Subject: Re: Digital Imaging Software and Hardware Date: Sun, 04 Dec 1994 12:12:12 -0600 Organization: Universtiy of Illinois Lines: 68 Distribution: world Message-ID: References: <786483286-1-51539@blue.weeg.uiowa.edu> NNTP-Posting-Host: holzwarth3.life.uiuc.edu In article <786483286-1-51539@blue.weeg.uiowa.edu>, jmonahn@blue.weeg.uiowa.edu wrote: > The free software called "Image" is available for the Mac from the anon. ftp > site: zippy.nimh.nih.gov > I believe it can do the analysis you need. Also, you can use a digitizing > board with a mac, Video Spigot, for example, to capture single frames of video > to be opened in the image analysis software. > Joe Monahan > > > In note , > umdoble@mail.cc.umanitoba.ca (Brad Doble) writes: > >Our lab currently has a microscope equipped with a CCD colour video camera > >and colour monitor. We would like to store images (videocassette > >recorder?) and then analyze them using a computer (we currently have a > >computer with a 66 MHz 486 processor, 8 Megabytes RAM, 250 MB hard drive, > >and a standard svga graphics card). What additional hardware (RAM, > >graphics cards, hard disk space, etc.) is required, and what good software > >programs are currently in use to analyze image data? The types of > >analyses we would like to do include: i) counting labelled or stained > >cells vs. control cells ; ii) measuring the intensity of fluorescent > >markers; iii) determing morphometric values; etc. The purchase of > >another computer may be possible with our budget so please don't hesitate > >to describe setups with Macintoshes if you feel they are best for the task > >at hand. Also, I would like to have an idea of the cost of the hardware > >and software required. > > > >Any feedback will be greatly appreciated. > > > > Thanks in advance, > > > > Brad Doble I would second the reccomendation of using NIH Image for the macintosh. We have just recently gone into the digital imaging business, and have been quite pleased. We already had a camera and scope. To compliment this, we purchased a frame grabber board for $800. We threw the board into a PowerMac 7100, and it works wonderfully. Here are my reasons for thinking this is a good idea: 1. NIH Image is FREE. It will do all the analyses that you mention. There are many freely available user programmed macros for doing even more (like in situ grain counts), in addition to what you require. It even lets you do time lapse video microscopy. On top of all this, there is a native Power Mac version available (which means it is fully accelerated for the Power Mac...you should see it do 3-D texture maps). 2. No other image analysis software is free. At the recent neuroscience conference in Miami, I looked into all the other vendors offering digital image analysis software for mac and windows. These programs were all a bit fancier than NIH Image, but they started at about $1000. Some of them had some really high end features, but none of them offered the superior price/performance that NIH Image can. 3. The author of NIH Image, Wayne, is a great guy. He answers your questions via e-mail. There is also a mailing list devoted to the use of NIH Image, subscribed to by tons of more experienced NIH Image users, as well as Wayne himself. I don't think many other companies offer this kind of free technical support. 4. NIH Image creates standard TIFF image files. So, if you really wanted to, you could pass these images along to colleagues (sp?) using a DOS Computer. 5. There are many other programs on the PowerMac that you can use to: ready images for publication, archive, and enhance these TIFF files. From owner-software@net.bio.net Sat Dec 03 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!ericjj From: ericjj@unixg.ubc.ca (Eric Jay Jervis) Newsgroups: bionet.software Subject: Re: Bibliography package Date: 4 Dec 1994 07:56:38 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 2 Message-ID: <3brsnm$7cp@nnrp.ucs.ubc.ca> References: NNTP-Posting-Host: interchg.ubc.ca X-Newsreader: TIN [version 1.2 PL2] Darrell Pogue (dpogue@obsnsrv1.bio.uoknor.edu) wrote: : I am looking for a bibliography package for windows. Any suggestions? From owner-software@net.bio.net Sat Dec 03 22:00:00 1994 Path: biosci!cc.UManitoba.CA!gordonr From: gordonr@cc.UManitoba.CA (Richard Gordon) Newsgroups: bionet.software Subject: theoretical biology Date: 4 Dec 1994 03:47:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3bqtd6$3ii@news.cs.tulane.edu> NNTP-Posting-Host: net.bio.net International organization of theoretical biologists? Dear Colleague: We have been running a small Canadian Society Theoretical Biology (CSTB) for the past decade which has been attracting 1/3 international memberships. We charge only Can$25/yr for membership. We are at a critical juncture, needing new people to take active participation. With the cost of international travel and the lure of specialty conferences, it is difficult for us to get together physically. Yet there is a need for developing an intellectual community of like-minded scientists. Theoretical biologists are in a difficult position right now, perhaps analogous to theoretical physicists before quantum mechanics. There is great potential; we know the experimentalists need us; but in general they don't know that, and we have no niche. We think it is time to rethink whether the CSTB should continue to identify itself as a Canadian organisation, or whether we should become more explicitly international. It seems that our common bond is not Canadian residency, but rather a common international interest in theoretical biology and a desire to communicate. The services we have been able to offer to our members include a Newsletter, reduced rate subscriptions to the Journal of Biological Systems, and an Email network. We need to redefine our role, keeping in mind that there already exist several other organisations with overlapping interests, such as the SMB (Society for Mathematical Biology). The distinction between theoretical biology and mathematical biology is discussed in: Gordon, R. (1993). Careers in theoretical biology. Carolina Tips 56(3), 9-11. which might be a good point for beginning our deliberations. If you would like a copy of this just send a request to Dick Gordon at GordonR@cc.UManitoba.ca You are all encouraged to contribute to our discussion, whether or not you are a member of CSTB at the present time. Please send your comments to CSTB@biome.bio.ns.ca so that we can continue this discussion. To join, send the message subscribe cstb to Majordomo@biome.bio.ns.ca Dick Gordon, CSTB President Department of Radiology, University of Manitoba Room ON104, Health Sciences Centre, 820 Sherbrook Street Winnipeg, MB R3A 1R9 Canada Phone: (204) 787-1076, Fax: (204) 783-8565, E-mail: GordonR@cc.UManitoba.ca Bill Silvert, CSTB Secretary/Treasurer Habitat Ecology Division (HED), Bedford Inst. of Oceanography P. O. Box 1006, Dartmouth, Nova Scotia, CANADA B2Y 4A2. Tel. (902)426-1577 InterNet Address: silvert@biome.bio.ns.ca Fax (902)426-2256 HED runs a WWW server at URL=http://biome.bio.dfo.ca From owner-software@net.bio.net Sun Dec 04 22:00:00 1994 Newsgroups: bionet.software,comp.os.ms-windows.announce Path: biosci!galaxy.ucr.edu!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!uunet!nih-csl!shiloh.nimh.nih.gov!sgraham From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Subject: Refs 7.52: Bibliography software X-Original-Submission-Date: 3 Dec 1994 14: 27:07 GMT Message-ID: <1994Dec5.045400.21118@alw.nih.gov> Followup-To: comp.os.ms-windows.misc Originator: sgraham@shiloh.nimh.nih.gov X-Submissions-To: win-announce@shiloh.nimh.nih.gov Keywords: shareware, Windows 3.1, MedLine, bibliography Lines: 77 Sender: tjrc1@mole.bio.cam.ac.uk Organization: University of Cambridge, England Date: Mon, 5 Dec 1994 04:54:00 GMT Approved: sgraham@shiloh.nimh.nih.gov (Moderator) X-Administrivia-To: coma-request@shiloh.nimh.nih.gov Xref: biosci bionet.software:10257 comp.os.ms-windows.announce:856 I have uploaded the new version of my Refs bibliography package to the following sites: cyclin.zoo.cam.ac.uk:/pub/refs/refs752.zip and it should also appear, once it gets moved from the uploads directory, at: ftp.cica.indiana.ed:/pub/pc/win3/util/refs752.zip There is a World Wide Web page for Refs, from which you can obtain screenshots, and of course the program itself: http://cyclin.zoo.cam.ac.uk/pub/refs/ Here follows the readme for the program: Refs 7.52 ======== 03 December 1994 Introduction ------------ Refs is a program for creating browsing and maintaining academic reference databases. The program uses the common ASCII Unix refer file format and so is compatible with Unix refer, and also bibliography programs such as WinRefer. Refs can also import data files in other formats, in an easily expandable way. Modules are supplied to read ISI, Chemical Abstracts, Current Contents and Medline files, and the help file includes details for writing your own modules. Refs is shareware, and the distribution should contain the following files: REFS.EXE The program itself REFS.HLP The help file REFS.INI INI file REFEN.DLL English language DLL BIDS.FLT BIDS (ISI) Import filter MEDLINE.FLT Medline Import filter CHEM.FLT Chemical Abstracts filter CCRM.FLT Current Contents Reference Manager filter CTL3D.DLL Microsoft 3D library INSTALL.EXE Installation program INSTALL.INI Installation INI file. TEST.REF Example Unix refer data file README.TXT This file The program will work with Windows 3.1 or higher. Installation ------------ You will need PKUNZIP 2.04 or later to extract the ZIP file. 1. Extract this file into a spare directory. 2. Run INSTALL.EXE, which will install the program automatically. NB. INSTALL will notice an existing REFS.INI file and will back it up if required. Helpful suggestions, registrations and/or bug reports should be sent to: tjrc1@cus.cam.ac.uk T J R Cutts 194, Vinery Rd Cambridge CB1 3DS UK The registration fee is 30 pounds sterling, with discounts for multiple registrations. More details can be found in the help file. From owner-software@net.bio.net Sun Dec 04 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Looking for DNA sequence analysis programs that are freeware Date: 5 Dec 1994 22:14:25 GMT Organization: Biology, Indiana University - Bloomington Lines: 21 Message-ID: <3c03c1$ntp@usenet.ucs.indiana.edu> References: NNTP-Posting-Host: sunflower.bio.indiana.edu There are various macintosh, msdos/mswin, unix and some other computer system programs for DNA sequence analysis available at the archive sites including ftp.bio.indiana.edu (by anonymous ftp or gopher). Several of these are free, some are shareware, and there are a few demos of commercial programs here. One of the free ones, called SeqApp, for Macintoshes, was written by Don Gilbert (me). See the molbio/seqapp/ folder at the above archive. Another mac sequence analysis program you might try is 'dnastacks' I beleive that Will Gilbert, currently at U.New Hampshire, also wrote a sequence editor for VMS computers a while back, and it may have been called something like seqed. There are probably several sequence editors with a name something like that (programmers frequently name their software functionally, and not always very originally). -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Sun Dec 04 22:00:00 1994 Path: biosci!rutgers!gatech!swrinde!news.uh.edu!uhdvx3.dt.uh.edu!islam_y From: islam_y@uhdvx3.dt.uh.edu (Yasir, 640388286) Newsgroups: bionet.software Subject: Re: DNASTAR vs. GENECODES Date: 5 Dec 1994 16:17 CST Organization: University of Houston-Downtown Lines: 23 Distribution: world Message-ID: <5DEC199416175751@uhdvx3.dt.uh.edu> References: <199411182350.PAA21026@netcomsv.netcom.com> <1994Nov28.132237.17697@liberty.uc.wlu.edu> NNTP-Posting-Host: uhdvx3.dt.uh.edu X-Lunar-Date: 0 days, 1 hour, 0 minutes since the new moon News-Software: VAX/VMS VNEWS 1.42 In article <1994Nov28.132237.17697@liberty.uc.wlu.edu>, cjh@helix.nih.gov (C.J. Hussussian, MD) writes... >We have experience in our lab using both DNAStar and Sequencher from >Gene Codes. For the purposes of assembly and editing of sequences >generated on the ABI, Sequencher has by far the best interface. This >comes from the ability to view multiple stacked and aligned >chromatograms for instant checking of discordant bases. While DNAStar >allows viewing of chromatograms, they are not aligned and one wastes >time searching for the base in question. In addition, Sequencher has an >automatic vector removal feature which is very flexible, allowing one >to define any sequence as "vector". We find this useful in removing our >primer sequences prior to analysis. DNAStar comes with other modules >which offer functionality beyond sequence assembly (and beyond what >Sequencher provides), including good multiple alignment and primer >picking tools. We generally do our sequence assembly and editing in >Sequencher, then export text files to DNAStar for further analysis. > >Chris Hussussian, MD >NIH/NCHGR >Bldg. 49, Rm. 4A83 >Bethesda, MD 20892 >ph: (301)402-2029 >fax: (301)402-5602 >e-mail: cjh@helix.nih.gov From owner-software@net.bio.net Sun Dec 04 22:00:00 1994 Path: biosci!agate!spool.mu.edu!caen!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: jv27@cornell.edu (Joyce Van Eck) Newsgroups: bionet.software Subject: Looking for DNA sequence analysis programs that are freeware Followup-To: bionet.software Date: 5 Dec 1994 14:27:16 GMT Organization: Cornell University Lines: 6 Sender: jv27@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: 132.236.8.122 We have been informed that DNA sequence anaysis programs which are in the public domain (freeware) are available on the Internet. We would be interested in the names of any of these programs and where we can find them. Might one of these programs be entitled SEQ.ED (by Gilbert?)? Thank you! From owner-software@net.bio.net Sun Dec 04 22:00:00 1994 Path: biosci!agate!spool.mu.edu!bloom-beacon.mit.edu!usc!cs.utexas.edu!howland.reston.ans.net!ix.netcom.com!netnews From: shayashi@ix.netcom.com (Shigenari Hayashi) Newsgroups: bionet.software Subject: Re: Sequence comparison Date: 5 Dec 1994 08:06:45 GMT Organization: Netcom Lines: 50 Distribution: world Message-ID: <3buhml$287@ixnews1.ix.netcom.com> References: NNTP-Posting-Host: ix-sf5-21.ix.netcom.com In tchoi@binah.cc.brandeis.edu (Giltsu Choi) writes: > >I would like know there is any software >that I can use my study. here's my situation. > >I have 2kb upstream of A gene from two related species >and 2kb upstream of B gene from a species. B gene is >coordinately regulated with A gene in terms of >expression pattern. Now I want to do some sequence >comparisons to extract information such as >possible sequence elements for the regulation of these genes. >Is it possible to extract such things? >If it is, is there any program or any methods I can use? >If there isn't, is there any scientists whom I can talk? > >I'll appreciate your help. > >Sincerely, >Giltsu Choi > There are several ways in which you can perform such an analysis. While there are several different email servers which will search for possible regulatory regions in a queried sequence, you may find it easier (and more applicable to the situation that you detailed), to first analyze your sequences for regions of similarity. There are several software programs that will search for similarities in different sequences, depending upon the type of platform you're utilizing (i.e. Unix / DOS / etc.). Upon determining these regions(s) in your sequences, you can utilize a "consensus" sequence as a query for the previously mentioned email server search. Feel free to contact me if you have any further questions: E-mail: shayashi@mercury.sfsu.edu shayashi@ix.netcom.com ------------------------------------------------------------------------ ----------------------- Information is power --------------------- ---------------------- only when utilized ------------------ ----------------------- appropriately! --------------- ------------------------------------------------ -- Shigenari Hayashi E-mail: shayashi@ix.netcom.com shayashi@mercury.sfsu.edu From owner-software@net.bio.net Sun Dec 04 22:00:00 1994 Path: biosci!rutgers!gatech!swrinde!news.uh.edu!uhdvx3.dt.uh.edu!islam_y From: islam_y@uhdvx3.dt.uh.edu (Yasir, 640388286) Newsgroups: bionet.software Subject: Re: DNASTAR vs. GENECODES Date: 5 Dec 1994 16:21 CST Organization: University of Houston-Downtown Lines: 26 Distribution: world Message-ID: <5DEC199416210131@uhdvx3.dt.uh.edu> References: <199411182350.PAA21026@netcomsv.netcom.com> <1994Nov28.132237.17697@liberty.uc.wlu.edu> NNTP-Posting-Host: uhdvx3.dt.uh.edu X-Lunar-Date: 0 days, 1 hour, 1 minute since the new moon News-Software: VAX/VMS VNEWS 1.42 In article <1994Nov28.132237.17697@liberty.uc.wlu.edu>, cjh@helix.nih.gov (C.J. Hussussian, MD) writes... >We have experience in our lab using both DNAStar and Sequencher from >Gene Codes. For the purposes of assembly and editing of sequences >generated on the ABI, Sequencher has by far the best interface. This >comes from the ability to view multiple stacked and aligned >chromatograms for instant checking of discordant bases. While DNAStar >allows viewing of chromatograms, they are not aligned and one wastes >time searching for the base in question. In addition, Sequencher has an >automatic vector removal feature which is very flexible, allowing one >to define any sequence as "vector". We find this useful in removing our >primer sequences prior to analysis. DNAStar comes with other modules >which offer functionality beyond sequence assembly (and beyond what >Sequencher provides), including good multiple alignment and primer >picking tools. We generally do our sequence assembly and editing in >Sequencher, then export text files to DNAStar for further analysis. >send >Chris Hussussian, MD >NIH/NCHGR >Bldg. 49, Rm. 4A83 >Bethesda, MD 20892 >ph: (301)402-2029 >fax: (301)402-5602 >e-mail: cjh@helix.nih.gov From owner-software@net.bio.net Sun Dec 04 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!news.iastate.edu!pv3209.vincent.iastate.edu!srinum From: srinum@iastate.edu (SRINIVAS MUMMIDI) Newsgroups: bionet.software Subject: PHYLIP and PAUP programs Date: 5 Dec 94 19:55:31 GMT Organization: Iowa State University, Ames, Iowa Lines: 15 Message-ID: NNTP-Posting-Host: pv3209.vincent.iastate.edu Dear Netters: Can somebody help me in obtaining the following software packages: 1) Phylogeny Inference Package (PHYLIP) version 3.4 and 2) Phylogenetic analysis using parsimony (PAUP) version 3.0. Any information including telephone numbers, addresses etc., will be helpful. Thank you. Srinivas Mummidi -- SRINIVAS MUMMIDI srinum@iastate.edu Voice:(515)-294-6932(W);(515)-233-8071(H) 301, So.5th APT#304 Fax:(515)-294-1401 Ames IA 50011 From owner-software@net.bio.net Sun Dec 04 22:00:00 1994 Newsgroups: bionet.software Path: biosci!lhc!nih-csl!stimpy!owhite From: owhite@stimpy.tigr.org (smouldering dog) Subject: hydrophbicity programs Message-ID: <1994Dec5.225137.7724@alw.nih.gov> Sender: owhite@stimpy (smouldering dog) Organization: National Institutes of Health Date: Mon, 5 Dec 1994 22:51:37 GMT Lines: 7 I am looking for C-code for hydrophobicity calculation in peptides. If anyone could direct me to a site containing same that would be greatly appreciated. Thank you, Owen White The Institute for Genomic Research From owner-software@net.bio.net Mon Dec 05 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uknet!strath-cs!nntphost.dur.ac.uk!vega.dur.ac.uk!dbl3isd From: I S Downie Newsgroups: bionet.software Subject: Re: Pentium Jokes... Date: 6 Dec 1994 12:25:46 GMT Organization: University of Durham, Durham, UK. Lines: 12 Message-ID: <3c1l8a$g9l@mercury.dur.ac.uk> References: NNTP-Posting-Host: vega.dur.ac.uk X-Newsreader: TIN [version 1.2 PL2] : Q: What do you call a series of FDIV instructions on a Pentium? : A: Successive approximations. : Q: What algorithm did Intel use in the Pentium's floating point divider? : A: "Life is like a box of chocolates." (Source: F. Gump of Intel) Good ones! Praise from another anti-Pentium bod! Iain From owner-software@net.bio.net Mon Dec 05 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: hydrophbicity programs Date: 6 Dec 1994 10:18:51 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 15 Message-ID: <3c1dqb$1498@sat.ipp-garching.mpg.de> References: <1994Dec5.225137.7724@alw.nih.gov> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] smouldering dog (owhite@stimpy.tigr.org) wrote: > I am looking for C-code for hydrophobicity calculation in peptides. > If anyone could direct me to a site containing same that would be > greatly appreciated. A very simple C program is appended to the original article by Kyte and Doolittle (JMB 157, 105-132, 1982). --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "Science is the game you play with God to find out what His rules are." */ From owner-software@net.bio.net Mon Dec 05 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!pipex!uunet!heifetz.msen.com!zib-berlin.de!informatik.tu-muenchen.de!bensch From: bensch@Informatik.TU-Muenchen.DE (Ewald Bensch) Newsgroups: bionet.software,bit.general,biz.sco.general Subject: FORTRAN to programming flowchart Date: 6 Dec 1994 08:44:53 GMT Organization: Technische Universitaet Muenchen, Germany Lines: 27 Distribution: world Message-ID: <3c18a5$3om@hpsystem1.informatik.tu-muenchen.de> NNTP-Posting-Host: hphalle1a.informatik.tu-muenchen.de X-newsreader: xrn 7.00 Xref: biosci bionet.software:10265 biz.sco.general:11625 Hey. I'm surching for a tool with the subsequent spezification: A FORTRAN-source-program (or C-program) should be visualised as a programming flowchart. The output should be possible into an ASCII-file, as a postscript-file or as a screendump. FORTRAN77 (or FORTRAN66) should be handled (if it can handle Fortran90, it is perfectly qualified). I'm mostly interested to visualise GOTO-branches and jumps, to detect the programmflow. If you know the name of such a tool, who sales it, how much must I pay (public domain or licensed), then please give me answer via email to: bensch@sdm.de Bye. Bensch From owner-software@net.bio.net Mon Dec 05 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news2.near.net!das-news2.harvard.edu!fas-news.harvard.edu!nucleus!robison From: robison@nucleus.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: .GDEmenus code for ClustalW Date: 6 Dec 1994 23:04:40 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 18 Message-ID: <3c2qm8$dq4@decaxp.harvard.edu> NNTP-Posting-Host: nucleus.harvard.edu X-Newsreader: TIN [version 1.2 PL2] Has anyone out there interfaced ClustalW to GDE? Did you write specific menus? Could I steal them? (hint to UNIX software developers: since GDE is pretty popular, it wouldn't be a bad idea to include in your distribution the relevant GDE menu code for your programs). Thanks for any help. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@mito.harvard.edu From owner-software@net.bio.net Mon Dec 05 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunic!news.lth.se!news.lu.se!news!bolde From: bolde@biogen.wblab.lu.se (Bjšrn Olde) Subject: PCR-program for degenerate primers Message-ID: Followup-To: bionet.software Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: bjorno.wblab.lu.se Organization: Molecular Neurobiology, Wallenberg Lab., Lund, Sweden X-Newsreader: VersaTerm Link v1.1 Date: Tue, 6 Dec 1994 16:07:37 GMT Lines: 7 Where do I find a program that can be used in the design of degenerate PCR-primers? I would prefer a macintosh program. Bjorn Olde Molecular Neurobiology Wallenberg Laboratory Sweden From owner-software@net.bio.net Mon Dec 05 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!europa.eng.gtefsd.com!library.ucla.edu!ucsbuxb.ucsb.edu!poole From: poole@lifesci.ucsb.edu (poole) Newsgroups: bionet.software Subject: HyperChem on Irix5.2 Date: 6 Dec 1994 21:24:49 GMT Organization: University of California, Santa Barbara Lines: 6 Sender: -Not-Authenticated-[3870] Message-ID: <3c2kr1$lru@ucsbuxb.ucsb.edu> NNTP-Posting-Host: poole.lscf.ucsb.edu X-Posted-From: InterNews 1.0@ucsbuxb.ucsb.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. Our version of HyperChem for SGI (which unfortunately is no longer supported by the publishers) died when we went from IRIX 4.X to IRIX 5.2. If anyone has successfully installed HyperChem running under IRIX 5, I would appreciate knowing that it is possible. Stephen Poole poole@lifesci.ucsb.edu From owner-software@net.bio.net Mon Dec 05 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!gumby!wmichgw!458atkins From: BrianC.Atkins@wmich.edu Newsgroups: bionet.software Subject: ------>ATTENTION ALL PREMEDS!!!!! Message-ID: <1994Dec6.180050.24968@wmichgw> Date: 6 Dec 94 18:00:50 EDT Organization: Western Michigan University Lines: 14 Fellow Premeds: I trust that I share with you the goal of scoring well on the April '95 MCAT. I posted earlier asking for recommendations regarding a software package that could help prepare me for the coming quiz, and met such an overwhelming response that I was struck with an idea--- If you use the Macintosh platform, and are interested in a communal profit with your competition, email me for information. I AM NOT TRYING TO MAKE MONEY! I am merely trying to save money while preparing myself to present the best possible application to my target schools! I hope you will join me, so that you might do the same! Brian C. Atkins, Junior premed, Western Michigan University BrianC.Atkins@wmich.edu From owner-software@net.bio.net Mon Dec 05 22:00:00 1994 Path: biosci!MAILGATE.GLAXO.COM!agostino~mj%a1.usa.umc From: agostino~mj%a1.usa.umc@MAILGATE.GLAXO.COM ("Mike Agostino") Newsgroups: bionet.software Subject: how many receptors are there? Date: 6 Dec 1994 12:27:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <43329160214991.324212@USA> NNTP-Posting-Host: net.bio.net [This message is converted from WPS-PLUS to ASCII] There have been a lot of numbers kicked around, based on various techniques for estimating gene frequencies, that put the total number of G-protein coupled receptors encoded by the human genome at anywhere from a couple of hundred to several thousand. Does anyone out there in Netland have what they are comfortable with as a number for GPCR's? Or, do you have any idea where some of these estimates came from? If so, could you post or email me with it and please include where the estimate came from and how it was derived (no astrology, please). I realize that all of these estimates have an element of fantasy to them, so I promise not to publish or otherwise attribute an estimate to you unless you beg appropriately. It would probably be most useful to break it down into total and non-odorant/sensory receptors. I will post back to the net a summary of replies (with names omitted unless otherwise requested). Thanks, Rich Buckholz RGB12955@glaxo.com From owner-software@net.bio.net Mon Dec 05 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software,bionet.drosophila Subject: IUBio archive & FlyBase service outage Date: 6 Dec 1994 21:36:43 GMT Organization: Biology, Indiana University - Bloomington Lines: 13 Message-ID: <3c2lhb$psd@usenet.ucs.indiana.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu Xref: biosci bionet.software:10271 bionet.drosophila:721 IUBio Archive & the FlyBase services, at ftp.bio.indiana.edu, are not available this afternoon. I hope to have them back on-line in a few hours. The outage is due to a hardware upgrade and unexpected problems from the upgrade. Details: a long SCSI disk chain developed termination or signal problems, and corrupted the system disk. Note that tomorrow morning (5am EST ...) the IP address changes from 129.79.224.25 to 129.79.225.25. At this time also there may be a service interruption, as I have to change the computer hostname. -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!rutgers!uwm.edu!psuvax1!news.cc.swarthmore.edu!mac04.parrishd.swarthmore.edu!user From: ehom1@cc.swarthmore.edu (Erik Forbes Y. Hom '95) Newsgroups: bionet.software Subject: Question about Mulfold (M. Zuker et al.'s) Followup-To: bionet.software Date: Wed, 07 Dec 1994 14:35:33 +0000 Organization: Laboratory of Neurobiology, Swarthmore College Lines: 17 Message-ID: NNTP-Posting-Host: mac04.parrishd.swarthmore.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi netters! I have a copy of mulfold for the Mac. A limitation of this version: one can only fold a 300 base sequence. I, however, have a sequence of ~4000 that I want to fold to see if the start codon or SD domain could potentially interact with bases more distant than the neighboring ~150 bases (and the effect of mutations in these more distant domains on this interaction). Is there anyway I could do this without constructing some chimeric sequence between the initiation region and the distant region of interest (I don't think the results I would get from this would be very realistic)? Do you thing it is reasonable (thermodynamically) for a such a distant region (say ~500 bases away) to base pair with the initiation region? (I can't, for certain, justify one or the other because I can't do the folding!). What are the limitations for the UNIX version?? Help! Thanks for your time! Yours truly, erik From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Newsgroups: bionet.software Path: biosci!rutgers!gatech!swrinde!pipex!uunet!zib-berlin.de!gs.dfn.de!news.uni-bielefeld.de!techfak.uni-bielefeld.de!fuellen From: fuellen@techfak.uni-bielefeld.de (Georg Fuellen) Subject: Re: [wanted] computer dictionaries, biology, ecogoly, zoology... Sender: news@hermes.hrz.uni-bielefeld.de (News Administrator) Message-ID: Date: Wed, 7 Dec 1994 12:28:02 GMT References: Nntp-Posting-Host: moos.techfak.uni-bielefeld.de Organization: Universitaet Bielefeld, Technische Fakultaet. Lines: 40 Re: [wanted] computer dictionaries, biology, ecogoly, zoology... A small Molecular Genetics glossary is at http://www.gdb.org/Dan/DOE/prim6.html It is part of the document http://www.gdb.org/Dan/DOE/intro.html >>>> Primer on Molecular Genetics (Department of Energy) This primer was prepared by Denise Casey (Human Genome Management Information System - Oak Ridge National Laboratory) for the 1991-92 DOE Human Genome Program Report and modified for Web access by Dan Jacobson. The primer is now being extensively revised and updated by HGMIS. <<<< I'd be interested in any other pointers people may have. kindest regards, georg fuellen@dali.Mathematik.Uni-Bielefeld.DE fuellen@Techfak.Uni-Bielefeld.DE fuellen@MIT.EDU Dr Stephen R Covey, The 7 Habits of Highly Effective People, Habit #3: Put First Things First ! More information on the GNA-VSNS Biocomputing Course ca be found at http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/BCChome.html In article , ginster@magna.com.au writes: |> I'm very interested in finding some good dictionaries in a form accessable |> from on a computer, which give definitions of the words we would not |> usually find in your normal dictionary. These definitions, pertaining |> to biological sciences, and even geological sciences would be extreamly |> useful to me and my research. |> |> I am even offering to have this kind of thing available on the WWW, but |> I need the text. Obviously this is a big request, but instead of starting |> from scratch, I wondered if anyone here can help. |> |> any suggestions would be great. thanks in advance, |> |> Ginny |> ginster@magna.com.au From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Newsgroups: bionet.software Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!caen!hearst.acc.Virginia.EDU!murdoch!dayhoff.med.Virginia.EDU!wrp From: wrp@dayhoff.med.Virginia.EDU (William R. Pearson) Subject: PowerPC performance Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Date: Wed, 7 Dec 1994 16:01:38 GMT Lines: 39 I am in the process of converting the programs in the FASTA package over to the PowerPC and would like to share some observations. When I first converted FASTA to the PowerPC version, the speed-up over the 68K version was very modest, only about 33%. I then compared FASTA on the PPC to FASTA on an IBM RS/6000 with AIX (same architecture, different speeds and operating systems). I was dismayed that a FASTA search that took about 7 sec on the Unix RS/6K took more than 2 minutes on the PPC. Since the Unix system has a sophisticated preemptive scheduling mechanism and the MacPPC requires frequent poling to simulate multiprocessing, I checked to see whether my event checking routine was responsible for some of the difference. It was; removing the ChkEvent() routine decreased the time required from > 2 minutes to about 22 sec (on a PowerMac 8100/80). Still not as good as Unix, but in the ballpark. I have since modified the ChkEvent() routine to poll the system only once per second, and the performance loss is modest (28 vs 22 sec). Here, the MacPPC was so fast that it spent 80% of its time doing system polling and only 20% on my application. FASTA may also be slower on the Mac because of inefficiencies in the file system (and remember, the Unix time is a CPU time, not elapsed, so i/o time is not included, however that adds only about 1 sec). To focus on the relative CPU performance, I searched the PIR1 database with SSEARCH, which implements the Smith-Waterman algorithm. Here the results were much more impressive; the MacPPC took about 8 min while the Unix RS/6K took 6. Thus, for very CPU-intensive tasks, the 80 Mhz PowerMac performs about 75% as well as an IBM RS/6000 model 370. I suspect that performance scales well with clock speed on the MacPPC, so that the ~$2500 model 7100 (66 Mhz) would be equivalent to about 60% of a 370 (a 62 MHz chip set) at about 10% the price. Bill Pearson -- wrp@virginia.EDU Dept. of Biochemistry #440 U. of Virginia Charlottesville, VA 22908 From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!moose.bioc.cam.ac.uk!user From: nef@mole.bio.cam.ac.uk (Nick Fisher) Newsgroups: bionet.software Subject: "Good Times" e-mail virus is a HOAX Date: Wed, 07 Dec 1994 17:50:46 +0000 Organization: Cambridge University (Biochemistry Department) Lines: 11 Message-ID: NNTP-Posting-Host: moose.bioc.cam.ac.uk The so-called "Good Times" e-mail virus is a HOAX. It is IMPOSSIBLE for a text file to infect your computer. Only executable files can carry "active" virus code. The single purpose of this "virus" is to flood the Net with warnings posted by well-meaning people worried about computer security. Nick Fisher Dept of Biochemistry Cambridge University UK From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Dietmar Tietz Newsgroups: bionet.software Subject: Re: !!!!Warning: a virus is emailed (fwd) Date: 7 Dec 1994 14:04:32 -0000 Lines: 147 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3c4fdg$3li@mserv1.dl.ac.uk> X-Sender: gh43@hamster.hrz.uni-giessen.de MIME-Version: 1.0 Original-To: bioforum@dl.ac.uk, bio-soft@dl.ac.uk, bio-info@dl.ac.uk After mailing the first message, I received the following note stating that there is no "good times" email virus. I am sorry for any inconvenience this false alarm might have caused. I posted the virus alert, since it arrived from a usually reliable source. Dietmar Tietz ---------- Forwarded message ---------- ============================================================================= U.S. DOE's Computer Incident Advisory Capability ___ __ __ _ ___ __ __ __ __ __ / | /_\ / |\ | / \ | |_ /_ \___ __|__ / \ \___ | \| \__/ | |__ __/ Number 94-04 December 6, 1994 ------------------- A - T - T - E - N - T - I - O - N ------------------- | CIAC is available 24-hours a day via its two skypage numbers. To use | | this service, dial 1-800-759-7243. The PIN numbers are: 8550070 (for | | the CIAC duty person) and 8550074 (for the CIAC manager). Please keep | | these numbers handy. | ------------------------------------------------------------------------- Welcome to the fourth issue of CIAC Notes! This is a special edition to clear up recent reports of a "good times" virus-hoax. Let us know if you have topics you would like addressed or have feedback on what is useful and what is not. Please contact the editor, Allan L. Van Lehn, CIAC, 510-422-8193 or send E-mail to ciac@llnl.gov. $-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$ $ Reference to any specific commercial product does not necessarily $ $ constitute or imply its endorsement, recommendation or favoring by $ $ CIAC, the University of California, or the United States Government.$ $-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$ THE "Good Times" VIRUS IS AN URBAN LEGEND In the early part of December, CIAC started to receive information requests about a supposed "virus" which could be contracted via America OnLine, simply by reading a message. The following is the message that CIAC received: --------------------------------------------------------------------------- | Here is some important information. Beware of a file called Goodtimes. | | | | Happy Chanukah everyone, and be careful out there. There is a virus on | | America Online being sent by E-Mail. If you get anything called "Good | | Times", DON'T read it or download it. It is a virus that will erase your | | hard drive. Forward this to all your friends. It may help them a lot. | --------------------------------------------------------------------------- THIS IS A HOAX. Upon investigation, CIAC has determined that this message originated from both a user of America Online and a student at a university at approximately the same time, and it was meant to be a hoax. CIAC has also seen other variations of this hoax, the main one is that any electronic mail message with the subject line of "xxx-1" will infect your computer. This rumor has been spreading very widely. This spread is due mainly to the fact that many people have seen a message with "Good Times" in the header. They delete the message without reading it, thus believing that they have saved themselves from being attacked. These first-hand reports give a false sense of credibility to the alert message. There has been one confirmation of a person who received a message with "xxx-1" in the header, but an empty message body. Then, (in a panic, because he had heard the alert), he checked his PC for viruses (the first time he checked his machine in months) and found a pre-existing virus on his machine. He incorrectly came to the conclusion that the E-mail message gave him the virus (this particular virus could NOT POSSIBLY have spread via an E-mail message). This person then spread his alert. As of this date, there are no known viruses which can infect merely through reading a mail message. For a virus to spread some program must be executed. Reading a mail message does not execute the mail message. Yes, Trojans have been found as executable attachments to mail messages, the most notorious being the IBM VM Christmas Card Trojan of 1987, also the TERM MODULE Worm (reference CIAC Bulletin B-7) and the GAME2 MODULE Worm (CIAC Bulletin B-12). But this is not the case for this particular "virus" alert. If you encounter this message being distributed on any mailing lists, simply ignore it or send a follow-up message stating that this is a false rumor. Karyn Pichnarczyk CIAC Team ciac@llnl.gov - ------------------------------ Contacting CIAC If you require additional assistance or wish to report a vulnerability, call CIAC at 510-422-8193, fax messages to 510-423-8002 or send E-mail to ciac@llnl.gov. For emergencies and off-hour assistance, call 1-800-SKY-PAGE (759-7243) and enter PIN number 8550070 (primary) or 8550074 (secondary). The CIAC Duty Officer, a rotating responsibility, carries the primary skypager. The Project Leader carries the secondary skypager. If you are unable to contact CIAC via phone, please use the skypage system. - ------------------------------ This document was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the University of California nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation or favoring by the United States Government or the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or the University of California, and shall not be used for advertising or product endorsement purposes. - ------------------------------ End of CIAC Notes Number 94-04 94_12_06 **************************************** -----BEGIN PGP SIGNATURE----- Version: 2.6.i iQCVAgUBLuWRZAQmfXmOCknRAQEqaAQAk0P404YimdO59UDmL5CaAfqB4mzXh2vr iXpmjNRJroHSM0wlb9ClMGd4w7ubX4NH3m/8jopoAMBCehm1hMJAwZoiX0/E3gk0 91+lJAjT9NtPtKw0DbTxsw4vqqbGOOf3S6KZeQfIbM5JCv+TwWZjAbVSnhExYcNa mm05Ld7eVWk= =1RT1 -----END PGP SIGNATURE----- +-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-+ | Juergen Obermann Hochschulrechenzentrum der | | Tel: +49-641-702-2169 Justus-Liebig-Universitaet Giessen | | E-Mail: Juergen.Obermann Heinrich-Buff-Ring 44 | | @hrz.uni-giessen.de D-35392 Giessen | +-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-+ ****************************************************************** * Dietmar Tietz, Ph.D., Research Scientist * * Biostatistics, Justus-Liebig-University * * Ludwigstr. 27, D-35390 Giessen, Germany * * Phone: +49-(641)-702-9733 * * Fax: +49-(641)-702-9724 * * Email: Dietmar.Tietz@Uni-Giessen.de * ****************************************************************** From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!warwick!bham!bcm39.bham.ac.uk!j.d.brinck From: j.d.brinck@bham.ac.uk (Jason Brinck) Newsgroups: bionet.software Subject: Re: !!!!Warning: a virus is emailed (fwd) Date: Wed, 7 Dec 1994 14:40:15 Organization: The University of Birmingham Lines: 40 Distribution: bionet Message-ID: References: <3c414j$l80@mserv1.dl.ac.uk> <3c4alu$iru@lyra.csx.cam.ac.uk> NNTP-Posting-Host: bcm39.bham.ac.uk X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article <3c4alu$iru@lyra.csx.cam.ac.uk> tjrc1@mole.bio.cam.ac.uk (Tim Cutts) writes: >From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) >Subject: Re: !!!!Warning: a virus is emailed (fwd) >Date: 7 Dec 1994 12:43:42 GMT >Dietmar Tietz writes: >>> >>> A virus is circulating on the Internet. If you receive a message with >>> the header "xxx-1" DO NOT READ IT. Delete immediately or your disk will >>> require treatment by a virus-scanner. I have had two copies of this >>> message this morning (Sunday) already, but was warned by an early >>> morning phone call from a friend who got hit. >>> >>>************************************************************************ >>>>This crossed my virtual desk this afternoon. Does anyone have more info? >>>> >>>>>>> Somebody is sending e-mail under the title "good times". If you get >>>>>>anything >>>>>>> like this, DON'T DOWNLOAD THE FILE! ! ! ! ! ! ! ! ! ! It has a >>>virus that >>>>>>> rewrites your hard drive, and you lose anything on your hard >>>drive. Pleas >>>e >>>>>>> be careful and forward this mail to anyone you care about! >Please could we not have such scare stories? Such a virus is indeed a >worry, but there's no point in panicking everyone. Who dies the virus >affact? PC users? Mac users? Unix users? I find it very hard to >believe that there is any sort of virus that will affect any system >regardless of operating system/mail handler used. Please be more >specific. >Tim. No need to panic! This is a hoax From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!daresbury!hgmp.mrc.ac.uk!abrown From: abrown@crc.ac.uk (Mr. A. Brown) Newsgroups: bionet.software Subject: FAQ Date: 7 Dec 1994 13:38:03 GMT Organization: MRC Human Genome Resource Centre Lines: 10 Message-ID: <3c4drr$ctl@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Can any body e-mail me a copy of the FAQ for this news-group, or at least tell me where I can get hold of one?? == Alex Brown, e-mail: abrown@hgmp.mrc.ac.uk MRC Collaborative Centre, : a-brown@nimr.mrc.ac.uk 1-3 Burtonhole Lane, Tel. : 081-906 3811 Mill Hill, London NW7 1AD. U.K. Fax. : 081-906 1395 From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!daresbury!s-ind1!lhb From: lhb@s-ind1.dl.ac.uk (L. H. Bell) Newsgroups: bionet.software Subject: Re: .GDEmenus code for ClustalW Date: 7 Dec 1994 13:23:19 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 182 Sender: lhb@s-ind1 (L. H. Bell) Distribution: world Message-ID: <3c4d07$h9@mserv1.dl.ac.uk> References: <3c2qm8$dq4@decaxp.harvard.edu> Reply-To: lhb@seqnet.dl.ac.uk NNTP-Posting-Host: s-ind1.dl.ac.uk In article <3c2qm8$dq4@decaxp.harvard.edu>, robison@nucleus.harvard.edu (Keith Robison) writes: |> Has anyone out there interfaced ClustalW to GDE? Did you write specific |> menus? Could I steal them? |> Heres one - it writes the clustalw command line into a shell script so it can be run in batch. It was written for the SGI version of gde output into. Hope this helps, Lachlan Bell SEQNET http://www.dl.ac.uk/SEQNET/home.html (PS, if you spot any 'features' please e-mail them to me.) #********** item: clustalw #********** # # Run clustalw. Open output file with editor. Run another gde with # clustalw output as input. Remove all created files! # # Did funny naming of arguments because gde was getting confused with # variables that with similar names or the same names as in previous items: # # Supposedly takes gde format but I get 'Sequence format is unknown' when I try # itemmethod:(readseq in1 -a -p -f=nbrf>in1.cl;header.sh>in1.com; echo clustalw /output=GDE /outfile=$NAM /outorder=$ORDER /CASE=$BZA /infile=in1.cl /PWMATRIX=$XX /PWGAPOPEN=$YY /PWGAPEXT=$ZZ /align /MATRIX=$WW /GAPOPEN=$STZZ /GAPEXT=$TS /ENDGAPS=$CGH /GAPDIST=$KIK $PAS $HYDRO /MAXDIV=$EYQ /SCORE=$MNE /TYPE=$ASDA $TRANS \> in1.rpt>>in1.com; $BATCH)& itemhelp:clustalw_help in:in1 informat:genbank arg:BATCH argtype:choice_menu arglabel:Submit to batch? argchoice:Big:echo $RM in1* >> in1.com ;qsub -q big in1.com argchoice:Small:echo $RM in1* >> in1.com ;qsub -q fast in1.com argchoice:Interactive: echo '$REPORT' >> in1.com ; chmod 0700 in1.com ; in1.com ;$RM in1.cl in1.com ;$GDE $NAM argvalue:0 arg:NAM argtype:text arglabel:Put output in which file? argtext:clustalw_out arg:ASDA argtype:chooser arglabel:Sequence type? argchoice:Protein:PROTEIN argchoice:DNA/RNA:DNA arg:REPORT argtype:chooser arglabel:View assembly report? argchoice:No: argchoice:Yes:/exe1/bin/emacs in1.rpt& arg:BZA argtype:chooser arglabel:Should the residues be in - argchoice:Upper Case:upper argchoice:Lower Case:lower arg:ORDER argtype:choice_menu arglabel:Should the output order be - argvalue:0 argchoice:Same as input order:input argchoice:In alignment order:aligned arg:XX argtype:choice_menu arglabel:Use what matrix for pairwise aligning argvalue:2 argchoice:PAM:PAM argchoice:MD:MD argchoice:BLOSUM:BLOSUM arg:WW argtype:choice_menu arglabel:Use what matrix for multiple aligning argvalue:2 argchoice:PAM:PAM argchoice:MD:MD argchoice:BLOSUM:BLOSUM arg:YY argtype:slider arglabel:gap open penalty (pairwise) argmin:1 argmax:100 argvalue:10 arg:ZZ argtype:text arglabel:gap extending penalty (pairwise) [0.0-1.0] argtext:0.10 arg:STZZ argtype:slider arglabel:gap open penalty (multiple) argmin:1 argmax:100 argvalue:10 arg:TS argtype:text arglabel:gap extending penalty (multiple) [0.0-1.0] argtext:0.5 arg:TRANS argtype:chooser arglabel:DNA transitions weighted? argvalue:0 argchoice:No: argchoice:Yes:/TRANSITIONS arg:CGH argtype:chooser arglabel:Penalise end gaps? argvalue:0 argchoice:No:NO argchoice:Yes:YES arg:HYDRO argtype:chooser arglabel:Hydrophilic gaps? argvalue:0 argchoice:On: argchoice:Off:/NOHGAP arg:PAS argtype:chooser arglabel:Pascarella gaps? argvalue: argchoice:On: argchoice:Off:/NOPGAP arg:MNE arg:argtype:choice_menu arglabel:Scoring Method argchoice:Absolute:absolute argchoice:Percentage:percentage arg:KIK argtype:slider arglabel:gap separation penalty range? argmin:1 argmax:100 argvalue:8 arg:EYQ argtype:slider arglabel:% ident. for delay? argmin:1 argmax:100 argvalue:40 # # This takes a list as the argument therefore can't do # #arg:HRES #argtype:chooser #arglabel:List hydrophilic residues? #argvalue:0 #argchoice:No: #argchoice:Yes:/HGAPRESIDUES -----------start of header.sh #!/bin/csh -f # this first line needed echo "#\!/bin/csh -f" # set up movement to the current directory. This will be the one with # the input file in it. echo cd $cwd # the program & parameters are echoed from control line in gde ------------end of header.sh From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: "Bill Kupiec" Newsgroups: bionet.software Subject: Re: !!!!Warning- a virus is Date: 7 Dec 1994 14:10:15 -0000 Lines: 135 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3c4fo7$41h@mserv1.dl.ac.uk> Original-To: "Bio Software" >> A virus is circulating on the Internet. If you receive a message with >> the header "xxx-1" DO NOT READ IT. Delete immediately or your disk will >> require treatment by a virus-scanner. I have had two copies of this >> message this morning (Sunday) already, but was warned by an early >> morning phone call from a friend who got hit. >>************************************************************************ >>>This crossed my virtual desk this afternoon. Does anyone have more info? >>> >>>>>> Somebody is sending e-mail under the title "good times". If you get >>>>>anything >>>>>> like this, DON'T DOWNLOAD THE FILE! ! ! ! ! ! ! ! ! ! It has a >>virus that >>>>>> rewrites your hard drive, and you lose anything on your hard >>drive. Pleas >>e >>>>>> be careful and forward this mail to anyone you care about! >Date: Tue, 6 Dec 1994 15:23:09 -0800 >Message-Id: <199412062302.PAA23885@cheetah.llnl.gov> >Reply-To: karyn@cheetah.llnl.gov >Originator: ciac-notes@cheetah.llnl.gov >Sender: ciac-notes@cheetah.llnl.gov >From: Karyn Pichnarczyk >Subject: CIAC Notes 94-04 > > > U.S. DOE's Computer Incident Advisory Capability > ___ __ __ _ ___ __ __ __ __ __ > / | /_\ / |\ | / \ | |_ /_ > \___ __|__ / \ \___ | \| \__/ | |__ __/ > >Number 94-04 December 6, 1994 > > ------------------- A - T - T - E - N - T - I - O - N ------------------- >| CIAC is available 24-hours a day via its two skypage numbers. To use | >| this service, dial 1-800-759-7243. The PIN numbers are: 8550070 (for | >| the CIAC duty person) and 8550074 (for the CIAC manager). Please keep | >| these numbers handy. | > ------------------------------------------------------------------------- > >Welcome to the fourth issue of CIAC Notes! This is a special edition to >clear up recent reports of a "good times" virus-hoax. Let us know if you >have topics you would like addressed or have feedback on what is useful and >what is not. Please contact the editor, Allan L. Van Lehn, CIAC, >510-422-8193 or send E-mail to ciac@llnl.gov. > > $-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$ > $ Reference to any specific commercial product does not necessarily $ > $ constitute or imply its endorsement, recommendation or favoring by $ > $ CIAC, the University of California, or the United States Government.$ > $-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$-$ > >THE "Good Times" VIRUS IS AN URBAN LEGEND > >In the early part of December, CIAC started to receive information requests >about a supposed "virus" which could be contracted via America OnLine, simply >by reading a message. The following is the message that CIAC received: > > --------------------------------------------------------------------------- >| Here is some important information. Beware of a file called Goodtimes. | >| | >| Happy Chanukah everyone, and be careful out there. There is a virus on | >| America Online being sent by E-Mail. If you get anything called "Good | >| Times", DON'T read it or download it. It is a virus that will erase your | >| hard drive. Forward this to all your friends. It may help them a lot. | > --------------------------------------------------------------------------- > >THIS IS A HOAX. Upon investigation, CIAC has determined that this message >originated from both a user of America Online and a student at a university >at approximately the same time, and it was meant to be a hoax. > >CIAC has also seen other variations of this hoax, the main one is that any >electronic mail message with the subject line of "xxx-1" will infect your >computer. > >This rumor has been spreading very widely. This spread is due mainly to the >fact that many people have seen a message with "Good Times" in the header. >They delete the message without reading it, thus believing that they have >saved themselves from being attacked. These first-hand reports give a false >sense of credibility to the alert message. > >There has been one confirmation of a person who received a message with >"xxx-1" in the header, but an empty message body. Then, (in a panic, because >he had heard the alert), he checked his PC for viruses (the first time he >checked his machine in months) and found a pre-existing virus on his machine. > He incorrectly came to the conclusion that the E-mail message gave him the >virus (this particular virus could NOT POSSIBLY have spread via an E-mail >message). This person then spread his alert. > >As of this date, there are no known viruses which can infect merely through >reading a mail message. For a virus to spread some program must be executed. >Reading a mail message does not execute the mail message. Yes, Trojans have >been found as executable attachments to mail messages, the most notorious >being the IBM VM Christmas Card Trojan of 1987, also the TERM MODULE Worm >(reference CIAC Bulletin B-7) and the GAME2 MODULE Worm (CIAC Bulletin B-12). > But this is not the case for this particular "virus" alert. > >If you encounter this message being distributed on any mailing lists, simply >ignore it or send a follow-up message stating that this is a false rumor. > >Karyn Pichnarczyk >CIAC Team >ciac@llnl.gov > > >------------------------------ >Contacting CIAC > >If you require additional assistance or wish to report a vulnerability, call >CIAC at 510-422-8193, fax messages to 510-423-8002 or send E-mail to >ciac@llnl.gov. For emergencies and off-hour assistance, call 1-800-SKY-PAGE >(759-7243) and enter PIN number 8550070 (primary) or 8550074 (secondary). >The CIAC Duty Officer, a rotating responsibility, carries the primary >skypager. The Project Leader carries the secondary skypager. If you are >unable to contact CIAC via phone, please use the skypage system. > >------------------------------ >This document was prepared as an account of work sponsored by an agency of >the United States Government. Neither the United States Government nor the >University of California nor any of their employees, makes any warranty, >express or implied, or assumes any legal liability or responsibility for the >accuracy, completeness, or usefulness of any information, apparatus, product, >or process disclosed, or represents that its use would not infringe privately >owned rights. Reference herein to any specific commercial products, process, >or service by trade name, trademark, manufacturer, or otherwise, does not >necessarily constitute or imply its endorsement, recommendation or favoring >by the United States Government or the University of California. The views >and opinions of authors expressed herein do not necessarily state or reflect >those of the United States Government or the University of California, and >shall not be used for advertising or product endorsement purposes. > >------------------------------ >End of CIAC Notes Number 94-04 94_12_06 >**************************************** From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Newsgroups: bionet.molec-model,bionet.software Path: biosci!ns1.faseb.org!darwin.sura.net!fconvx.ncifcrf.gov!reming From: reming@ncifcrf.gov (Mary Remington) Subject: Palindrome search software Message-ID: Organization: Frederick Cancer Research and Development Center References: <3bn8vj$g3u@mercury.interpath.net> Date: Wed, 7 Dec 1994 12:42:33 GMT Lines: 4 Xref: biosci bionet.molec-model:182 bionet.software:10282 Does anyone know of a software program that will search DNA sequences for palindromes? Thanks, Mary From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: !!!!Warning: a virus is emailed (fwd) Date: 7 Dec 1994 12:43:42 GMT Organization: University of Cambridge, England Lines: 31 Distribution: bionet Message-ID: <3c4alu$iru@lyra.csx.cam.ac.uk> References: <3c414j$l80@mserv1.dl.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk Dietmar Tietz writes: >> >> A virus is circulating on the Internet. If you receive a message with >> the header "xxx-1" DO NOT READ IT. Delete immediately or your disk will >> require treatment by a virus-scanner. I have had two copies of this >> message this morning (Sunday) already, but was warned by an early >> morning phone call from a friend who got hit. >> >>************************************************************************ >>>This crossed my virtual desk this afternoon. Does anyone have more info? >>> >>>>>> Somebody is sending e-mail under the title "good times". If you get >>>>>anything >>>>>> like this, DON'T DOWNLOAD THE FILE! ! ! ! ! ! ! ! ! ! It has a >>virus that >>>>>> rewrites your hard drive, and you lose anything on your hard >>drive. Pleas >>e >>>>>> be careful and forward this mail to anyone you care about! Please could we not have such scare stories? Such a virus is indeed a worry, but there's no point in panicking everyone. Who dies the virus affact? PC users? Mac users? Unix users? I find it very hard to believe that there is any sort of virus that will affect any system regardless of operating system/mail handler used. Please be more specific. Tim. From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Dietmar Tietz Newsgroups: bionet.software Subject: !!!!Warning: a virus is emailed (fwd) Date: 7 Dec 1994 10:00:51 -0000 Lines: 48 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3c414j$l80@mserv1.dl.ac.uk> X-Sender: gh43@hamster.hrz.uni-giessen.de MIME-Version: 1.0 Original-To: bio-soft@dl.ac.uk > > A virus is circulating on the Internet. If you receive a message with > the header "xxx-1" DO NOT READ IT. Delete immediately or your disk will > require treatment by a virus-scanner. I have had two copies of this > message this morning (Sunday) already, but was warned by an early > morning phone call from a friend who got hit. > >************************************************************************ >>This crossed my virtual desk this afternoon. Does anyone have more info? >> >>>>> Somebody is sending e-mail under the title "good times". If you get >>>>anything >>>>> like this, DON'T DOWNLOAD THE FILE! ! ! ! ! ! ! ! ! ! It has a >virus that >>>>> rewrites your hard drive, and you lose anything on your hard >drive. Pleas >e >>>>> be careful and forward this mail to anyone you care about! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott F. Shaffer Eccles Institute of Human Genetics Bld 533 Rm 6140 University of Utah SLC, Utah 84112 Internet: sshaffer@corona.med.utah.edu (801) 585-5730 (801) 585-3599 ============================================================================ ****************************************************************** * Dietmar Tietz, Ph.D., Research Scientist * * Biostatistics, Justus-Liebig-University * * Ludwigstr. 27, D-35390 Giessen, Germany * * Phone: +49-(641)-702-9733 * * Fax: +49-(641)-702-9724 * * Email: Dietmar.Tietz@Uni-Giessen.de * ****************************************************************** From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!newsxfer.itd.umich.edu!caen!msunews!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!news From: ginster@magna.com.au Subject: [wanted] computer dictionaries, biology, ecogoly, zoology... Message-ID: Sender: news@ucc.su.OZ.AU Nntp-Posting-Host: magna.com.au Organization: Information Services, Sydney University, Sydney, NSW, Australia Date: Wed, 7 Dec 1994 04:35:23 GMT Lines: 17 I'm very interested in finding some good dictionaries in a form accessable from on a computer, which give definitions of the words we would not usually find in your normal dictionary. These definitions, pertaining to biological sciences, and even geological sciences would be extreamly useful to me and my research. I am even offering to have this kind of thing available on the WWW, but I need the text. Obviously this is a big request, but instead of starting from scratch, I wondered if anyone here can help. any suggestions would be great. thanks in advance, Ginny ginster@magna.com.au From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!nntp.crl.com!crl8.crl.com!not-for-mail From: sunger@crl.com (Stefan Unger) Newsgroups: bionet.molec-model,bionet.software Subject: Re: modelling on Power Mac? Followup-To: bionet.molec-model,bionet.software Date: 6 Dec 1994 21:16:21 -0800 Organization: CRL Dialup Internet Access (415) 705-6060 [Login: guest] Lines: 61 Message-ID: <3c3gf5$4u1@crl8.crl.com> References: <3bn8vj$g3u@mercury.interpath.net> NNTP-Posting-Host: crl8.crl.com X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molec-model:181 bionet.software:10278 There is a new MAC visualization and analysis package called Protein Expert that is currently being ported to Power MAC. e-mail me for more information. I am the distributor. Biosoftware Marketing 4151 Middlefield Rd, Ste 109 Palo Alto, CA 94303 415-858-0522 fax: 415-858-0521 sunger@crl.com current version 680xx with math-coprocessor. Justin Diachun (diachun@arris.com) wrote: : In article <3bn8vj$g3u@mercury.interpath.net> morgan@mercury.interpath.net (Morgan Ryan) writes: : > : >I just traded up my Mac to a 6100 PowerPC. Nice! But suddenly I have only : >one working molecular graphics program, RasMol, which has a native PPC : >version. MolView and MacMolecule are amazingly slow in emulation on the : >PPC (The PPC has its own math coprocessor, but it doesn't coprocess when : >emulating 68k...even speedy little MacMolecule takes minutes to come up). : > Do I have any other options? Has anyone ported MolScript to PPC? : >Are there any other programs available that I don't know about? (I've : >read the faq's and gone to NIH etc. I'm wondering if there is something : >newer around that hasn't been inserted in the usual online guides.) : > Also, is there a freeware modeller in existence that works like : >Ball-and-Stick? I'm just a hobbyist--can't afford lots of money for : >molecular software. What do people put on the well-equipped freeware Mac : >molecular graphics machine besides RasMol, MolView, MacMolecule and : >MacBabel? Anything? Thanks. Morgan Ryan / morgan@mercury.interpath.net : I have almost the exact same question, and a flyer on a new product. : Has anyone gotten anything from the Molecular Applications Group? : They list packages called Look (proteins), SegMod (homology), and : MacImdad. The MacImdad product looks interesting. It claims to have : a compressed PDB database that can be searched to pull up structures. : It is also available on PowerPC and other Mac systems. They offer a : free demo disk that I have asked for. The ad reads "Display - Analyze : - Print" so I guess it is in the RasMol field of applications. I : would like to hear how this product compares to anything else on the : market. : I have the following contact information on the flyer: : Molecular Applications Group : 445 Sherman Avenue, Suite T : Palo Alto, Ca 94306 : toll free: 1-800-229-7382 (USA only) : phone: 415-473-3030 : fax: 415-473-1795 : email: info@mag.com : disclaimer: I have no affiliation with MAG or knowledge of the product. : I am simply looking for unbiased 3rd party opinions. : -- : Justin Diachun : diachun@arris.com : System Administrator : Arris Pharmaceutical From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!lll-winken.llnl.gov!overload.lbl.gov!xpat.postech.ac.kr!news.kreonet.re.kr!sorak.kaist.ac.kr!cojoe From: cojoe@sorak.kaist.ac.kr (Doo Yeon Kim) Newsgroups: bionet.software Subject: Isoelectric point determination program? Date: 7 Dec 1994 03:30:30 GMT Organization: Korea Research Environment Open Network (KREONet) Lines: 12 Message-ID: <3c3a8m$lr4@news.kreonet.re.kr> NNTP-Posting-Host: sorak.kaist.ac.kr X-Newsreader: TIN [version 1.2 PL2] I need software or mail server which predict the isoelectric point from amino acid sequence. Please help me. -- ////////Doo Yeon Kim//////// From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!holzwarth3.life.uiuc.edu!user From: jbuberel@uiuc.edu (Jason L. Buberel) Newsgroups: bionet.software Subject: Re: PCR-program for degenerate primers Date: Tue, 06 Dec 1994 21:17:38 -0600 Organization: Universtiy of Illinois Lines: 24 Message-ID: References: NNTP-Posting-Host: holzwarth3.life.uiuc.edu In article , bolde@biogen.wblab.lu.se (Bjšrn Olde) wrote: > Where do I find a program that can be used in the design of degenerate > PCR-primers? I would prefer a macintosh program. > > Bjorn Olde > Molecular Neurobiology > Wallenberg Laboratory > Sweden Bjorn, I have been on the lookout also. If you find something good (for the Mac), please let me know. I will do likewise. -jason ================ Jason L. Buberel Graduate Student Nueroscience Pgm U of Illinois-UC ================ From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Newsgroups: bionet.molec-model,bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!arris!diachun From: diachun@arris.com (Justin Diachun) Subject: Re: modelling on Power Mac? Message-ID: Sender: usenet@arris.com Nntp-Posting-Host: oyster.arris.com Organization: Arris Pharmaceutical Corp. References: <3bn8vj$g3u@mercury.interpath.net> Date: Wed, 7 Dec 1994 02:34:21 GMT Lines: 45 Xref: biosci bionet.molec-model:180 bionet.software:10275 In article <3bn8vj$g3u@mercury.interpath.net> morgan@mercury.interpath.net (Morgan Ryan) writes: > >I just traded up my Mac to a 6100 PowerPC. Nice! But suddenly I have only >one working molecular graphics program, RasMol, which has a native PPC >version. MolView and MacMolecule are amazingly slow in emulation on the >PPC (The PPC has its own math coprocessor, but it doesn't coprocess when >emulating 68k...even speedy little MacMolecule takes minutes to come up). > Do I have any other options? Has anyone ported MolScript to PPC? >Are there any other programs available that I don't know about? (I've >read the faq's and gone to NIH etc. I'm wondering if there is something >newer around that hasn't been inserted in the usual online guides.) > Also, is there a freeware modeller in existence that works like >Ball-and-Stick? I'm just a hobbyist--can't afford lots of money for >molecular software. What do people put on the well-equipped freeware Mac >molecular graphics machine besides RasMol, MolView, MacMolecule and >MacBabel? Anything? Thanks. Morgan Ryan / morgan@mercury.interpath.net I have almost the exact same question, and a flyer on a new product. Has anyone gotten anything from the Molecular Applications Group? They list packages called Look (proteins), SegMod (homology), and MacImdad. The MacImdad product looks interesting. It claims to have a compressed PDB database that can be searched to pull up structures. It is also available on PowerPC and other Mac systems. They offer a free demo disk that I have asked for. The ad reads "Display - Analyze - Print" so I guess it is in the RasMol field of applications. I would like to hear how this product compares to anything else on the market. I have the following contact information on the flyer: Molecular Applications Group 445 Sherman Avenue, Suite T Palo Alto, Ca 94306 toll free: 1-800-229-7382 (USA only) phone: 415-473-3030 fax: 415-473-1795 email: info@mag.com disclaimer: I have no affiliation with MAG or knowledge of the product. I am simply looking for unbiased 3rd party opinions. -- Justin Diachun diachun@arris.com System Administrator Arris Pharmaceutical From owner-software@net.bio.net Tue Dec 06 22:00:00 1994 Path: biosci!MAILGATE.GLAXO.COM!agostino~mj%a1.usa.umc From: agostino~mj%a1.usa.umc@MAILGATE.GLAXO.COM ("Mike Agostino") Newsgroups: bionet.software Subject: how many receptors are there? Date: 7 Dec 1994 05:22:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <54122170214991.326948@USA> NNTP-Posting-Host: net.bio.net [This message is converted from WPS-PLUS to ASCII] There have been a lot of numbers kicked around, based on various techniques for estimating gene frequencies, that put the total number of G-protein coupled receptors encoded by the human genome at anywhere from a couple of hundred to several thousand. Does anyone out there in Netland have what they are comfortable with as a number for GPCR's? Or, do you have any idea where some of these estimates came from? If so, could you post or email me with it and please include where the estimate came from and how it was derived (no astrology, please). I realize that all of these estimates have an element of fantasy to them, so I promise not to publish or otherwise attribute an estimate to you unless you beg appropriately. It would probably be most useful to break it down into total and non-odorant/sensory receptors. I will post back to the net a summary of replies (with names omitted unless otherwise requested). Thanks, Rich Buckholz RGB12955@glaxo.com From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!news.bc.net!vanbc.wimsey.com!unixg.ubc.ca!not-for-mail From: mcclean@flair.law.ubc.ca (John McClean) Newsgroups: bionet.software Subject: Re: "Good Times" e-mail virus is a HOAX Date: 8 Dec 1994 00:08:30 GMT Organization: UBC FLAIR Project Lines: 17 Message-ID: <3c5ipu$j1i@nntp.ucs.ubc.ca> References: NNTP-Posting-Host: malik.law.ubc.ca X-Newsreader: WinVN 0.92.1 In article , nef@mole.bio.cam.ac.uk (Nick Fisher) says: > > >The so-called "Good Times" e-mail virus is a HOAX. It is IMPOSSIBLE for a >text file to infect your computer. Only executable files can carry >"active" virus code. Yes and No. There was I recall some years ago a 'text' file which if sent to the 'stdout' device of a PC using the DOS command TYPE, would cause some sort of havoc. This was because the file really had escape sequences which were sent to the display driver (i.e., if you looked at the file using a text editor it would look like rubbish). Granted, this is not really what you are referring to, and in any event is not really a virus as it cannot self-replicate. John McClean From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!GN.APC.ORG!infomed!ICT.SLD.CU!FRANZ From: infomed!ICT.SLD.CU!FRANZ@GN.APC.ORG Newsgroups: bionet.software Subject: (none) Date: 7 Dec 1994 21:29:43 -0800 Organization: Centro de Inmunologia Molecular Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9412071815.AA14426@infomed> NNTP-Posting-Host: net.bio.net subscribe From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!gpu!slyseng From: slyseng@gpu.srv.ualberta.ca (Susan Lyseng) Newsgroups: bionet.software Subject: Sequence Analysis Program for PC Date: 8 Dec 1994 00:59:17 GMT Organization: University of Alberta Lines: 15 Message-ID: <3c5lp5$6f0@quartz.ucs.ualberta.ca> NNTP-Posting-Host: gpu3.srv.ualberta.ca X-Newsreader: TIN [version 1.2 PL2] Hello! I'm looking for a PC compatable program that can do simple sequence analysis (restriction enzymes, ORF's, translation etc.). I've used Strider on the Mac and it was adequate for what I want to use it for--but I would really like a program for my PC (preferably Windows compatable!). Does anyone know of a ftp site that might have something like this? (I tried ftp.bio.indiana.edu but really had no clue what many of the programs were about, the readme files weren't that detailed.....) Many thanks, Susan Lyseng University of Alberta Canada From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!rutgers!csn!yuma!purdue!mozo.cc.purdue.edu!darwin2.bio.purdue.edu!user From: flip@bogie2.bio.purdue.edu (Phillip D. Russell) Newsgroups: bionet.molec-model,bionet.software Subject: Re: modelling on Power Mac? Date: Wed, 07 Dec 1994 18:59:24 -0600 Organization: Purdue University Lines: 39 Message-ID: References: <3bn8vj$g3u@mercury.interpath.net> NNTP-Posting-Host: darwin2.bio.purdue.edu Xref: biosci bionet.molec-model:184 bionet.software:10293 In article , diachun@arris.com (Justin Diachun) wrote: > In article <3bn8vj$g3u@mercury.interpath.net> morgan@mercury.interpath.net (Morgan Ryan) writes: > > > >I just traded up my Mac to a 6100 PowerPC. Nice! But suddenly I have only > >one working molecular graphics program, RasMol, which has a native PPC > >version. MolView and MacMolecule are amazingly slow in emulation on the > >PPC (The PPC has its own math coprocessor, but it doesn't coprocess when > >emulating 68k...even speedy little MacMolecule takes minutes to come up). > > Do I have any other options? Has anyone ported MolScript to PPC? > >Are there any other programs available that I don't know about? (I've > >read the faq's and gone to NIH etc. I'm wondering if there is something > >newer around that hasn't been inserted in the usual online guides.) > I have almost the exact same question, and a flyer on a new product. > Has anyone gotten anything from the Molecular Applications Group? > They list packages called Look (proteins), SegMod (homology), and > MacImdad. The MacImdad product looks interesting. It claims to have > a compressed PDB database that can be searched to pull up structures. > It is also available on PowerPC and other Mac systems. They offer a > free demo disk that I have asked for. The ad reads "Display - Analyze > - Print" so I guess it is in the RasMol field of applications. I > would like to hear how this product compares to anything else on the > market. We have a FREE program that runs native on the PowerMac and blows the commercial programs away. It's called MolView and you can get it from: http://www.bio.purdue.edu/MolView/MolView.html Flip -- __@ Phillip "Flip" Russell | Purdue University __@ _ -_,_-\<,_flip@bogie2.bio.purdue.edu | West Lafayette, IN _ -\<,_ (_)-----/-(_) The important things... (_)-/-(_) My bikes and my Macintosh From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!pipex!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Subject: Free/shareware NMR processing s/w Message-ID: Sender: news@demon.co.uk (Usenet Administration) Nntp-Posting-Host: visigoth.demon.co.uk Organization: Huh? Date: Thu, 8 Dec 1994 04:25:59 GMT Lines: 6 Does anybody know of free or shareware NMR processing s/w (for any m/c)? -- === James Petts === In the world of CD-ROM, a horse will always be an herbivorous quadruped, and there'll be endless examples to prove just that. But that world will never tell you how it feels to ride a horse. Or fall off it. From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!gatech!bloom-beacon.mit.edu!news.bu.edu!usenet From: cohen@med-card01.bu.edu (Jeffrey Cohen) Newsgroups: bionet.software Subject: NIH Image Macros for Cardiac Function Measurements Date: 8 Dec 1994 16:19:48 GMT Organization: Boston University Lines: 8 Sender: -Not-Authenticated-[7387] Message-ID: <3c7bn4$9ar@news.bu.edu> NNTP-Posting-Host: med-derm25.bu.edu X-Posted-From: InterNews 1.0.1@med-derm25.bu.edu Xdisclaimer: No attempt was made to authenticate the sender's name. I am looking for Macros to run on the Macintosh-based NIH Image software. I'd like to make measurements of left ventricular wall motion using Sheehan's centerline method. In addition, I want to measure LV volumes using Simpson's formula. If anyone has information about these Macros or any Macintosh-based programs to perform these measurements, please contact me at cohen@med-card01.bu.edu If this is the wrong place to post this message, please let me know. Thanks. Jeffrey Cohen From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Newsgroups: bionet.general,bionet.software Path: biosci!daresbury!sunsite.doc.ic.ac.uk!pipex!uknet!festival!castle.ed.ac.uk!proberts From: proberts@castle.ed.ac.uk (P Roberts) Subject: Plasmid drawing programs Message-ID: Sender: news@festival.ed.ac.uk (remote news read deamon) Organization: Edinburgh University Date: Thu, 8 Dec 1994 10:14:43 GMT Lines: 7 Xref: biosci bionet.general:12364 bionet.software:10301 Greetings, Please could someone recommend some plasmid drawing packages for the PC. They need to run on a 486 platform. Thanks, in advance, Paul From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!oleane!pipex!swrinde!howland.reston.ans.net!quagga.ru.ac.za!ucthpx!itu1.sun.ac.za!k4027.mikro.sun.ac.za!9050175 From: 9050175@MATIES.SUN.AC.ZA (M GAGIANO ) Newsgroups: bionet.software Subject: Help wanted on www and mosaic Date: Thu, 8 Dec 1994 05:51:45 GMT Organization: University of Stellenbosch, South Africa Lines: 10 Message-ID: <9050175.5.786865905@MATIES.SUN.AC.ZA> NNTP-Posting-Host: 146.232.84.17 Summary: Help wanted on www and mosaic Keywords: www and mosaic Could somebody please help. I want to aquire the software to access the Internet via Windows as well as e-mail and FTP through Windows. Where would I find this software and how would I go on about installing it. Please refer me to a FTP site where I could download this programmes from or get the necessary information from or send it to the following e-mail adresses: 9050175@maties.sun.ac.za 9050175@sunvax.ac.za Any help will be greatly appreciated. From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!spool.mu.edu!uwm.edu!psuvax1!news.cc.swarthmore.edu!mac04.parrishd.swarthmore.edu!user From: ehom1@cc.swarthmore.edu (Erik Forbes Y. Hom '95) Newsgroups: bionet.software Subject: Q: searching for phosphorylation sites Followup-To: bionet.software Date: Thu, 08 Dec 1994 00:17:14 +0000 Organization: Laboratory of Neurobiology, Swarthmore College Lines: 7 Message-ID: NNTP-Posting-Host: mac04.parrishd.swarthmore.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi netters, Could anyone here tell the best way to search for potential phosphorylation sites or sequence homologies to phosphorylated regions. Are there programs that do this for you? What would be the best way to proceed? Thanks in advanced for your help! erik From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uxa.cso.uiuc.edu!dalke From: dalke@uxa.cso.uiuc.edu (Andrew Dalke) Newsgroups: bionet.software Subject: Re: "Good Times" e-mail virus is a HOAX Date: 8 Dec 1994 05:37:02 GMT Organization: University of Illinois at Urbana Lines: 30 Message-ID: <3c661u$qi@vixen.cso.uiuc.edu> References: <3c5ipu$j1i@nntp.ucs.ubc.ca> NNTP-Posting-Host: uxa.cso.uiuc.edu In <3c5ipu$j1i@nntp.ucs.ubc.ca> John McClean said: > .... This was because the file really had escape sequences which >were sent to the display driver... Granted, this is not really what >you are referring to, and in any event is not really a virus as it cannot >self-replicate. You are bringing back the good old days back when I did those kinda tricks. :) On a DOS machine, if you set DEVICE=ANSI.SYS then the ansi device driver would be loaded. This interprets both keypresses and display output. You could use it to change the color, location, etc. of the text, with the appropriate escape sequence - something like ESC [ ; Alas, I've forgotten them :( Anyway, one of the things you could use this for is to reprogram the keys so that a keypress would return another character, or even a string. For instance, you could reprogram F1 to send the sequence "HELP", or whatever. In principle you could make it do something like map the enter key to "del *.*". That would be nasty. BTW, I can't think of anyway to make a reproducing an email message in ANSI escape code, so you don't have to worry about viruses from me. (Actually, I'm doing computer simulations of the poliovirus; so you do have to worry about viruses from me :) Andrew dalke@uiuc.ede From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!news.dfn.de!scsing.switch.ch!elna.ethz.ch!smac.ethz.ch!user From: tan@mol.biol.ethz.ch (Song Tan) Newsgroups: bionet.molec-model,bionet.software Subject: Re: Palindrome search software Date: Wed, 07 Dec 1994 19:27:53 +0100 Organization: ETH-Honggerberg (Swiss Federal Institute of Technology) Lines: 14 Message-ID: References: <3bn8vj$g3u@mercury.interpath.net> NNTP-Posting-Host: smac.ethz.ch Xref: biosci bionet.molec-model:185 bionet.software:10295 > Does anyone know of a software program that will search DNA sequences for > palindromes? Thanks, Mary Programs that analyze sequences for possible RNA stemloop structures should do the trick. STEMLOOP in the GCG package is one example. Hope this helps. -- Song Tan Institute for Molecular Biology and Biophysics ETH-Honggerberg (Swiss Federal Institute of Technology) 8093 Zurich, Switzerland email: tan@mol.biol.ethz.ch From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!olivea!sgigate.sgi.com!nocusuhs!info.usuhs.mil!NewsWatcher!user From: MSALMINEN_at_WRAIR__GUDE__1@mail.hjf.org (Mika Salminen) Newsgroups: bionet.software,bionet.virology Subject: FastDNAML for the DEC Alpha running VMS? Date: 8 Dec 1994 19:14:14 GMT Organization: Henry M. Jackson Foundation Lines: 10 Message-ID: NNTP-Posting-Host: 131.158.31.163 Xref: biosci bionet.software:10307 bionet.virology:1242 Hi Netters, I can't get FastDNAML compiled on our DEC Alpha running VMS. Has anyone out there been succesful, and if so could they point me to a place for ftp-ing the binaries? While I'm at it, has anyone added the program to GDE running on a Sun, and is that extension+ executables available? Thanks in advance, Mika Salminen From owner-software@net.bio.net Wed Dec 07 22:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!howland.reston.ans.net!nctuccca.edu.tw!aladdin.iii.org.tw!usenet From: kjhsiao@tpts1.seed.net.