From owner-software@net.bio.net Tue Jun 01 00:08:00 1999 Path: biosci!worldnet.att.net!cosmo26 From: cosmo26@worldnet.att.net ("Raman Hansi") Newsgroups: bionet.software Subject: pBK-CMV Date: 31 May 1999 18:08:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: <000301beabca$67b65a60$ad59480c@compaq> NNTP-Posting-Host: net.bio.net This is a multi-part message in MIME format. ------=_NextPart_000_0004_01BEAB8F.AEBC4680 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, You can obtain this vector from New England Biolab. I unfortunately do = not have their web address at this time. Good Luck ------=_NextPart_000_0004_01BEAB8F.AEBC4680 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
    Hello,
 
You can obtain this vector from New England = Biolab.  I=20 unfortunately do not
have their web address at this time.
 
Good Luck
------=_NextPart_000_0004_01BEAB8F.AEBC4680-- From owner-software@net.bio.net Tue Jun 01 04:45:00 1999 Path: biosci!DMSNA.DMS.UNINA.IT!duy82 From: duy82@DMSNA.DMS.UNINA.IT Newsgroups: bionet.software Subject: ADV: Photo Mousepads......These are cool! Date: 31 May 1999 22:45:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 120 Sender: daemon@net.bio.net Distribution: world Message-ID: <199905311914UAA53812@heyemailsavestrees.csse.muroran-it.ac.jp> NNTP-Posting-Host: net.bio.net To be removed from our mailing list please call 800-242-0363 ext. 2759 This is a one time mailing and you will not receive another offer. Please click delete. GREAT GRADUATION GIFT IDEA! MOUSEPADS WITH YOUR FAVORITE PHOTOS! Need a new look for your desk? Need a new mousepad to go with your new computer? Now you can have your favorite photos printed onto mousepads! Photo mousepads are our most popular gift year after year! 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BOX #782 ROSS, CA 94957 * Please allow 3 weeks for delivery. * Remember to include the proper shipping and handling fees ORDER TODAY ! c 7 From owner-software@net.bio.net Tue Jun 01 07:30:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.algonet.se!algonet!newsfeed1.uni2.dk!news.get2net.dk!not-for-mail From: "Thomas Hoeg-Jensen" Newsgroups: bionet.software References: <3752FCF9.A02AC5D3@univie.ac.at> Subject: Re: MacOS emulation for PC's? Lines: 13 X-Newsreader: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Message-ID: Date: Tue, 1 Jun 1999 10:24:44 +0200 NNTP-Posting-Host: 152.73.112.242 X-Complaints-To: abuse@uni2.dk X-Trace: news.get2net.dk 928225484 152.73.112.242 (Tue, 01 Jun 1999 10:24:44 MET DST) NNTP-Posting-Date: Tue, 01 Jun 1999 10:24:44 MET DST Organization: UNI2 Internet Kunde Hmm, yes it exists, but I forgot the name. They had a demo on the web. Try Altavista. Thomas Hoeg-Jensen, Denmark Andi wrote in message <3752FCF9.A02AC5D3@univie.ac.at>... >Does somebody know if there is a MacOs emulation programm available for >IBM compatible PCs? >Please let me know if there is one and where I can get it! Thank you! >weinhausl@ccri.univie.ac.at > From owner-software@net.bio.net Tue Jun 01 07:47:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!diablo.theplanet.net!news-lond.gip.net!news.gsl.net!gip.net!tank.news.pipex.net!pipex!newsfeed.nacamar.de!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail From: timc@chiark.greenend.org.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: MacOS emulation for PC's? Date: 01 Jun 1999 09:39:46 +0100 (BST) Organization: Linux Unlimited Message-ID: <6As*uCo1n@news.chiark.greenend.org.uk> References: <3752FCF9.A02AC5D3@univie.ac.at> NNTP-Posting-Host: rrw1000.sel.cam.ac.uk Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) Lines: 16 >Does somebody know if there is a MacOs emulation programm available for >IBM compatible PCs? >Please let me know if there is one and where I can get it! Thank you! >weinhausl@ccri.univie.ac.at Yes. Executor, by ARDI. It's quite good, as long as your program does not require System 7 (it's some time since I've used it, so their System 7 support may be better now than it used to be). See www.ardi.com It's quite inexpensive, too. Tim. From owner-software@net.bio.net Tue Jun 01 09:52:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!WCG!news.airnews.net!cabal12.airnews.net!cabal1.airnews.net!news-f.iadfw.net!usenet From: chiavarini@casaccia.enea.it (Salvatore Chiavarini) Newsgroups: bionet.software Subject: Re: MacOS emulation for PC's? Date: Tue, 01 Jun 1999 10:45:06 GMT Organization: ENEA CR Casaccia Lines: 19 Message-ID: <1A7A7B77BFD727E7.D8C2BFE71705636B.8EE2C69D3F246534@library-proxy.airnews.net> X-Orig-Message-ID: <3753b75e.80617576@library.airnews.net> References: <3752FCF9.A02AC5D3@univie.ac.at> Reply-To: chiavarini@casaccia.enea.it Abuse-Reports-To: abuse at airmail.net to report improper postings NNTP-Proxy-Relay: library3 NNTP-Posting-Time: Tue Jun 1 05:45:25 1999 NNTP-Posting-Host: !alB]1k-X(6Qoe^&7g*-&T2\; (Encoded at Airnews!) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent 1.5/32.452 On Mon, 31 May 1999 23:20:02 +0200, Andi wrote: >Does somebody know if there is a MacOs emulation programm available for >IBM compatible PCs? >Please let me know if there is one and where I can get it! Thank you! >weinhausl@ccri.univie.ac.at The best (and maybe the only) available emulators are Executor (www.ardi.com) and Fusion (www.microcode-solutions.com). They use completely different approaches: Executor creates a pseudo-Mac shell for running Mac programs and relies upon a built-from-scratch emulation (that is no Mac ROMs are needed), at the expense of a quite low compatibility; on the other hand, Fusion emulates 68040 code and uses true Mac ROMs images for the system emulation (therefore you must have a Mac to build ROM images and use Fusion). Personally, I do prefer Fusion, as it gives you an almost complete compatibility and peripherals support. Good luck! From owner-software@net.bio.net Tue Jun 01 12:12:00 1999 Date: Tue, 01 Jun 1999 15:07:08 +0200 From: zjons@vetbio.unizh.ch (Zophonias O. Jonsson) Newsgroups: bionet.software Subject: Re: MacOS emulation for PC's? Message-ID: References: <3752FCF9.A02AC5D3@univie.ac.at> <1A7A7B77BFD727E7.D8C2BFE71705636B.8EE2C69D3F246534@library-proxy.airnews.net> X-Newsreader: MT-NewsWatcher 2.4.4 X-Face: 8{u^Us:5ci;-2R"U]II#$oBc NNTP-Posting-Host: 130.60.120.44 X-NNTP-Posting-Host: 130.60.120.44 X-Trace: 1 Jun 1999 15:07:15 +0100, 130.60.120.44 Organization: University of Zurich Lines: 50 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!feed2.news.luth.se!luth.se!news-ge.switch.ch!news-zh.switch.ch!rzunews1.unizh.ch!zjons In article <1A7A7B77BFD727E7.D8C2BFE71705636B.8EE2C69D3F246534@library-proxy.airnews.net>, chiavarini@casaccia.enea.it wrote: > On Mon, 31 May 1999 23:20:02 +0200, Andi > wrote: > > >Does somebody know if there is a MacOs emulation programm available for > >IBM compatible PCs? > >Please let me know if there is one and where I can get it! Thank you! > >weinhausl@ccri.univie.ac.at > > The best (and maybe the only) available emulators are Executor (www.ardi.com) > and Fusion (www.microcode-solutions.com). There is a third one, which I can't remember the name of, but it is the worst of them so don't bother. > They use completely different > approaches: Executor creates a pseudo-Mac shell for running Mac programs and > relies upon a built-from-scratch emulation (that is no Mac ROMs are needed), at > the expense of a quite low compatibility; on the other hand, Fusion emulates > 68040 code and uses true Mac ROMs images for the system emulation (therefore you > must have a Mac to build ROM images and use Fusion). > Personally, I do prefer Fusion, as it gives you an almost complete compatibility > and peripherals support. > > Good luck! The bottom line is that these emulators emulate 680x0 processors and are therefore quite useless at emulating a lot of current mac software which is power PC only. I tried out executor and must say that the only "useful" thing that I could do with it was to play Jewelbox. Sincerely Zophonias -- _____________________________________________________________________ Zophonias O. Jonsson Institut fur Veterinarbiochemie Tel: (41-1)-635-54-76 Universitat Zurich-Irchel Fax: (41-1)-635-68-40 Winterthurerstrasse 190 CH-8057 Zurich Switzerland _____________________________________________________________________ From owner-software@net.bio.net Tue Jun 01 13:26:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.amsterdam.nl.net!sun4nl!surfnet.nl!news.leidenuniv.nl!not-for-mail From: "Martijn van Duijn" Newsgroups: bionet.software Subject: Re: MacOS emulation for PC's? Date: Wed, 2 Jun 1999 04:13:40 +0200 Organization: University of Leiden The Netherlands Lines: 14 Message-ID: <7j0psq$i83$1@highway.leidenuniv.nl> References: <3752FCF9.A02AC5D3@univie.ac.at> NNTP-Posting-Host: ruly2s.medfac.leidenuniv.nl X-Trace: highway.leidenuniv.nl 928246490 18691 132.229.11.59 (1 Jun 1999 14:14:50 GMT) X-Complaints-To: usenet@highway.leidenuniv.nl NNTP-Posting-Date: 1 Jun 1999 14:14:50 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 There is also something called Basilisk. It is quite new, and still in a beta stage, but look around for in altavista or something. Martijn Andi wrote in message news:3752FCF9.A02AC5D3@univie.ac.at... > Does somebody know if there is a MacOs emulation programm available for > IBM compatible PCs? > Please let me know if there is one and where I can get it! Thank you! > weinhausl@ccri.univie.ac.at > From owner-software@net.bio.net Tue Jun 01 14:25:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.amsterdam.nl.net!sun4nl!surfnet.nl!rug.nl!not-for-mail From: Hans-Christian Hege Newsgroups: sci.engr.biomed,sci.image.processing,sci.physics.research,bionet.biophysics,bionet.software Subject: JOB: Ph.D. scholarship at ZIB (Berlin, Germany) Date: 1 Jun 1999 15:10:33 GMT Organization: Konrad-Zuse-Zentrum (ZIB) Lines: 56 Approved: p.helbig@jb.man.ac.uk (sci.physics.research) Message-ID: <3752B2DD.975230C9@zib.de> NNTP-Posting-Host: gladia.astro.rug.nl Xref: biosci bionet.biophysics:5030 bionet.software:23537 Image Processing / Computational Geometry Graduate Fellowship Konrad-Zuse-Zentrum fuer Informationstechnik Berlin (ZIB) Konrad-Zuse-Zentrum fuer Informationstechnik Berlin (ZIB) invites students who are interested in pursuing a Ph.D. to apply for a fellowship in the Graduate Fellowship Program "Temperature Dependent Effects for Therapy and Diagnostics". This program is in close connection to the collaborate research centre 273 "Hyperthermia in Oncology: Methods and Clinic" at Humboldt University Berlin (speaker: Prof. Dr. R. Felix). The fellowship is available for two years with possibility of extension. The taxfree scholarship is DM 2.690,- per month for qualified students according to the regulations of the German Research Foundation (DFG). Research Areas: - algorithms for deforming anatomical grid models - algorithms for mapping grid models to medical image data - image analysis, registration and fusion Requirements: - above average masters degree (or diploma) in computer science, mathematics or physics - profound knowledge in image processing and/or computational geometry - good acquaintance with object oriented programming in C++ - interest in medical problems. We expect a high degree of commitment. In return we offer an interesting field of work, an opportunity for creativity, a highly motivated research team, excellent machinery equipment and favourable working conditions. Application: We particularly encourage female applicants, since women are underrepresented in science and ZIB is engaged in enlarging the quota. Handicapped applicants will be preferred on terms of equal qualification. Applications with photo, curriculum vitae in tabular form and customary documents quoting the title "Graduiertenkolleg -- Scientific Visualization" should be submitted to Prof. Dr. Peter Deuflhard Konrad-Zuse-Zentrum fuer Informationstechnik Berlin (ZIB) Takustr. 7 14195 Berlin-Dahlem Germany For further information contact Dr. Martin Seebass (seebass@zib.de, phone: +49-30-84185-328) and see http://www.zib.de/Visual. From owner-software@net.bio.net Tue Jun 01 16:29:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!130.185.14.36!torn!nott!uottawa!s866370 From: s866370@aix2.uottawa.ca (Greg Singer) Newsgroups: bionet.software Subject: Re: MacOS emulation for PC's? Date: 1 Jun 1999 17:16:32 GMT Organization: University of Ottawa Lines: 11 Message-ID: <7j14hg$sb4$1@mercury.cc.uottawa.ca> References: <7j0psq$i83$1@highway.leidenuniv.nl> NNTP-Posting-Host: aix2.uottawa.ca Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.1 PL8] > Does somebody know if there is a MacOs emulation programm available for > IBM compatible PCs? > Please let me know if there is one and where I can get it! Thank you! > weinhausl@ccri.univie.ac.at Check out VMac (www.vmac.org). It's not that good, but it's free and it runs on many different platforms. You'll need a ROM image from a real Mac, though (if you don't have any moral objections to it, you can probably find an illegal ROM image on the WWW). - Greg Singer From owner-software@net.bio.net Tue Jun 01 23:05:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!nntp.cs.ubc.ca!news.UVic.CA!hera.bioc.uvic.ca!user From: cupton@uvic.ca (Chris Upton) Newsgroups: bionet.software Subject: Database searches - updating Date: Tue, 01 Jun 1999 17:02:56 -0800 Organization: UVIC Lines: 17 Message-ID: NNTP-Posting-Host: hera.bioc.uvic.ca X-Trace: uvaix7e1.comp.UVic.CA 928281577 333354 142.104.33.102 (1 Jun 1999 23:59:37 GMT) X-Complaints-To: abuse@UVic.CA NNTP-Posting-Date: 1 Jun 1999 23:59:37 GMT Hi, I'm interested in searching the protein database with 200 proteins on a routine basis. I have a system to do the searches (FASTA) in batch locally (via a perl script), but I'd like to be notified when there's a new hit with good score. Somehow an old and new reuslt file has to be compared. Does anyone have a program to do this sort of thing? I've used swiss-shop, but I eventually want to incorporate this notification into another program for displaying the results graphically. Any ideas appreciated! Chris Upton From owner-software@net.bio.net Tue Jun 01 23:52:00 1999 Path: biosci!263.NET!tongyg From: tongyg@263.NET (Yigang Tong) Newsgroups: bionet.software Subject: Shareware/freeware for inclusion body prediction, please? Date: 1 Jun 1999 17:52:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <37547DB4.9FA9245A@263.net> Reply-To: tongyg@263.net NNTP-Posting-Host: net.bio.net Does anybody know a place where the software can be download? Thanks. Yigang Tong From owner-software@net.bio.net Wed Jun 02 01:03:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.wli.net!portc04.blue.aol.com!audrey01.news.aol.com!not-for-mail From: dtopscribe@aol.com (DTopScribe) Newsgroups: bionet.software Subject: Sales Invoice/Stock control MS Access97 application Lines: 14 NNTP-Posting-Host: ladder07.news.aol.com X-Admin: news@aol.com Date: 2 Jun 1999 01:57:32 GMT Organization: AOL, http://www.aol.co.uk Message-ID: <19990601215732.19064.00003577@ng-fr1.aol.com> If you might be interested in a high quality Access97 application to handle your Invoicing, Purchase Orders and Stock Control check out the simulation of DTS Sales Order Processing on my site. Sales, Purchase Orders and Customer Statements all print on plain paper with pre-printed quality. The application on the site is a UK version but there is one available for North America. http://members.aol.com/dtopscribe/page1.htm This posting is not Spam - to the best of my knowledge I've restricted it to those Newsgroups where it's likely to be of relevance. So if I've offended anyone - Sorry. From owner-software@net.bio.net Wed Jun 02 05:56:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!oleane!jussieu.fr!univ-angers.fr!ciril.fr!news.u-strasbg.fr!not-for-mail From: plewniak@igbmc.u-strasbg.fr (Frederic PLEWNIAK) Newsgroups: bionet.software Subject: Re: Database searches - updating Date: Wed, 02 Jun 1999 06:47:14 GMT Organization: IGBMC Lines: 15 Message-ID: <3754d1ff.1727914@news.u-strasbg.fr> References: Reply-To: plewniak@igbmc.u-strasbg.fr NNTP-Posting-Host: chouchen.u-strasbg.fr X-Trace: news.u-strasbg.fr 928309941 2485 130.79.78.242 (2 Jun 1999 07:52:21 GMT) X-Complaints-To: usenet@u-strasbg.fr NNTP-Posting-Date: 2 Jun 1999 07:52:21 GMT X-Newsreader: Forte Free Agent 1.11/32.235 Hi Chris, > I'm interested in searching the protein database with 200 proteins on a >routine basis. > >I have a system to do the searches (FASTA) in batch locally (via a perl >script), but I'd like to be notified when there's a new hit with good >score. > You may want to check : http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/ Cheers, Fred From owner-software@net.bio.net Wed Jun 02 07:04:00 1999 Path: biosci!PN3.VSNL.NET.IN!abt From: abt@PN3.VSNL.NET.IN ("Dr.Abhay Shendye") Newsgroups: bionet.software Subject: Need free educational software in Mol Bio Date: 2 Jun 1999 01:04:50 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: <3754E4D4.E484460B@pn3.vsnl.net.in> References: <374D1B66.3E7CFA46@crc.dk> NNTP-Posting-Host: net.bio.net Dear Netters, I have recently joined this discussion group, so please forgive me if I am posting a too basic question repeated several times earlier. I have done some genetic engineering during my Ph.D.. Now it has come to teaching the same to undergraduates who can't lay their hands much ta the same in practicals. I find it extremely difficult to make them imagine the steps at molecular level. Could you please help me obtain some software that will allow the students perform RE digestion, ligation, PCR, mutation, recombination etc. on PC. I already have DNASIS which can be used to teach restriction mapping. Thanks in advance. Yours sincerely, Dr. Abhay Shendye. From owner-software@net.bio.net Wed Jun 02 09:08:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.nacamar.de!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!server2.netnews.ja.net!news.nott.ac.uk!news.nottingham.ac.uk!granby!paxamr From: adam moore Newsgroups: bionet.software Subject: Re: Database searches - updating Date: Wed, 2 Jun 1999 10:43:41 +0100 Organization: ACS, The University of Nottingham Lines: 15 Message-ID: References: NNTP-Posting-Host: granby.ccc.nottingham.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 928316622 20293 128.243.40.43 (2 Jun 1999 09:43:42 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 2 Jun 1999 09:43:42 GMT To: Chris Upton X-Sender: paxamr@granby In-Reply-To: On Tue, 1 Jun 1999, Chris Upton wrote: > Hi, > I'm interested in searching the protein database with 200 proteins on a > routine basis. > Some of what you want is probably in bioperl - http://bio.perl.org Adam Moore Virtual School of Molecular Sciences School of Pharmaceutical Science, University of Nottingham http://www.vsms.nottingham.ac.uk/vsms/ Personal Page:http://www.ccc.nottingham.ac.uk/~paxamr/ From owner-software@net.bio.net Wed Jun 02 09:09:00 1999 Path: biosci!sb-roscoff.fr!est From: est@sb-roscoff.fr (laminaria.EST) Newsgroups: bionet.software Subject: retrieving sequences after a BLAST? Date: 2 Jun 1999 03:09:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <9906021004.AA27511@olrik.sb-roscoff> NNTP-Posting-Host: net.bio.net Hello, I would like to know if someone is aware of a software that would automaticaly retrieve the target sequences, identified by a BLAST search, from a server ( eg : retrieve@genbank.bio.net) and save them localy. Thank you for reading my message. Florent Crepineau From owner-software@net.bio.net Wed Jun 02 13:40:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!oleane!pasteur.fr!ezili.sis.pasteur.fr!bortz From: bortzmeyer@pasteur.fr (Stephane Bortzmeyer) Newsgroups: bionet.software Subject: News about the Debian packages: installation with apt is now possible Date: 2 Jun 1999 14:35:16 GMT Organization: Institut Pasteur Lines: 23 Sender: bortz@ezili.sis.pasteur.fr (Stephane Bortzmeyer) Message-ID: <7j3ff4$80k$1@desdemone.pasteur.fr> NNTP-Posting-Host: ezili.sis.pasteur.fr X-Trace: desdemone.pasteur.fr 928334116 8212 157.99.60.56 (2 Jun 1999 14:35:16 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 2 Jun 1999 14:35:16 GMT X-Newsreader: xrn 9.01 Some news about the binary packages I maintain for the Debian GNU/Linux operating system. You can now install them with the package manager apt, which automatically retrieves packages over the network and install them. Just one command to install a package and all the libraries it depends on (for instance, 'apt-get install njplot'). Apt users should add this line to their sources.list: deb ftp://ftp.pasteur.fr/pub/computing/debian-biology stable biology (PC with i386 processors only, others should use the regular Debian repositories.) See details and instructions here: http://www.pasteur.fr/units/sis/debian/biology-en.html -- "Best viewed with any browser" http://www.anybrowser.org/ From owner-software@net.bio.net Wed Jun 02 15:38:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.direct.ca!news.UVic.CA!hera.bioc.uvic.ca!user From: cupton@uvic.ca (Chris Upton) Newsgroups: bionet.software Subject: Re: Database searches - updating Date: Wed, 02 Jun 1999 09:35:55 -0800 Organization: UVIC Lines: 22 Message-ID: References: <3754d1ff.1727914@news.u-strasbg.fr> NNTP-Posting-Host: hera.bioc.uvic.ca X-Trace: uvaix7e1.comp.UVic.CA 928341155 119316 142.104.33.102 (2 Jun 1999 16:32:35 GMT) X-Complaints-To: abuse@UVic.CA NNTP-Posting-Date: 2 Jun 1999 16:32:35 GMT In article <3754d1ff.1727914@news.u-strasbg.fr>, plewniak@igbmc.u-strasbg.fr wrote: > Hi Chris, > > > I'm interested in searching the protein database with 200 proteins on a > >routine basis. > > > >I have a system to do the searches (FASTA) in batch locally (via a perl > >script), but I'd like to be notified when there's a new hit with good > >score. > > > You may want to check : > http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/ > > Cheers, > Fred Thanks for the info. I'll check out your site. Cheers, Chris From owner-software@net.bio.net Wed Jun 02 17:40:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.berkeley.edu!su-news-hub1.bbnplanet.com!news.gtei.net!news.good.net!news.goodnet.com!not-for-mail From: "Hilton Evans" Newsgroups: bionet.software Subject: Many Organic Reactions Lines: 5 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: <_Qe53.5636$S4.29802@news.goodnet.com> Date: Wed, 2 Jun 1999 14:34:30 -0400 NNTP-Posting-Host: 207.180.42.23 X-Trace: news.goodnet.com 928348602 207.180.42.23 (Wed, 02 Jun 1999 11:36:42 MDT) NNTP-Posting-Date: Wed, 02 Jun 1999 11:36:42 MDT Organic Reactions -- http://home.ici.net/~hfevans/reactions.htm ChemPen3D -- Molecular Mechanics for Win95/NT -- http://home.ici.net/~hfevans/chempen3d.htm ChemPen -- Chemical Structure Drawing -- http://home.ici.net/~hfevans/chempen.htm Coming Summer 1999 -- ChemPen+NMR From owner-software@net.bio.net Wed Jun 02 17:42:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!su-news-hub1.bbnplanet.com!news.gtei.net!news.good.net!news.goodnet.com!not-for-mail From: "Hilton Evans" Newsgroups: bionet.software Subject: Molecular Mechanics Lines: 9 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: Date: Wed, 2 Jun 1999 14:36:33 -0400 NNTP-Posting-Host: 207.180.42.23 X-Trace: news.goodnet.com 928348726 207.180.42.23 (Wed, 02 Jun 1999 11:38:46 MDT) NNTP-Posting-Date: Wed, 02 Jun 1999 11:38:46 MDT -- Hilton Evans Organic Reactions -- http://home.ici.net/~hfevans/reactions.htm ChemPen3D Molecular Mechanics for Win95/NT -- http://home.ici.net/~hfevans/chempen3d.htm Chempen Chemical Structure Drawing -- http://home.ici.net/~hfevans/chempen.htm Coming Summer 1999 -- NMR Shifts Prediction From owner-software@net.bio.net Wed Jun 02 21:06:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!diablo.theplanet.net!news-lond.gip.net!news.gsl.net!gip.net!colt.net!Pollux.Teleglobe.net!server-b.cs.interbusiness.it!not-for-mail From: "DRASTIGO" Newsgroups: bionet.software Subject: per tutti Date: Tue, 1 Jun 1999 20:43:04 +0200 Organization: Centro Servizi Interbusiness Lines: 6 Message-ID: <7j3ruv$qa6$19@fe2.cs.interbusiness.it> NNTP-Posting-Host: 195.31.160.18 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 http://www.euroweb2000.net/automan quando vale la pena perdere un minuto, o anche due, per vedere un sito web di sicuro successo. From owner-software@net.bio.net Wed Jun 02 21:23:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.berkeley.edu!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail From: greg@franklin.burnham-inst.org (Dr. Greg Quinn) Newsgroups: bionet.software Subject: Re: retrieving sequences after a BLAST? Date: 2 Jun 1999 22:19:04 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 31 Distribution: world Message-ID: <7j4ako$3ip$1@franklin.ljcrf.edu> References: <9906021004.AA27511@olrik.sb-roscoff> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] If you are doing a netBlast with GCG, I believe that NetFetch can parse the blast output file and fetch the cited sequences from the NIH site. Also, Nigel Brown's program, MVIEW will 'extract' alignments from a BLAST search to create a multiple alignment (with some caveats); this sometimes obviates the need to pull sequences depending on what you have in mind for the database matches. laminaria.EST (est@sb-roscoff.fr) wrote: : Hello, : : I would like to know if someone is aware of a software that would automaticaly retrieve the target sequences, identified by a BLAST search, from a server ( eg : retrieve@genbank.bio.net) and save them localy. : : Thank you for reading my message. : : Florent Crepineau -- ***************************************** Computational Biology Group The Burnham Institute (formerly La Jolla Cancer Research Inst.) 10901 North Torrey Pines road La Jolla CA92037 Phone:(619) 646 3103 Email: greg@franklin.ljcrf.edu http://franklin.ljcrf.edu/greg ***************************************** From owner-software@net.bio.net Wed Jun 02 21:54:00 1999 Path: biosci!COMPUTER.ORG!fvega From: fvega@COMPUTER.ORG ("Francisco M. De La Vega") Newsgroups: bionet.software Subject: Job: Bioinformatics Data Analyst Date: 2 Jun 1999 15:54:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 68 Sender: daemon@net.bio.net Distribution: world Message-ID: <3755B3FE.D9DF9B4E@computer.org> NNTP-Posting-Host: net.bio.net Subject: US-CA: Bioinformatics Data Analyst Date: Mon, 24 May 1999 11:20:29 -0700 From: "Francisco M. De La Vega" To: employment@net.bio.net Bioinformatics Data Analyst Scientist I/II Job Number: XHX9873 Department: GAN Synthesis and Arrays Job Description: Working closely with experimental researchers and other members of the Bioinformatics team, the candidate will be responsible for processing and analyzing data derived from high-throughput DNA chip experiments. You will identify and automate repetitive tasks to enhance data retrieval, manipulation, and analysis. Additional responsibilities include: scientific data transformation; integration of off- the-shelf bioinformatics and chemioinformatics software products; database integration; application of clustering, multivariate statistics, visualization and data mining tools; development of analytical methods and custom scripts to integrate diverse computational tools. Job Requirements: This position requires the knowledge and skills normally acquired through completion of a MS/PhD in Molecular Biology, Genetics, Statistics, Chemioinformatics, Computer Science or related field, and 1-3 years of relevant experience. To qualify, the candidate must have experience in generating useful information from massive output of data, an appreciation of the use of statistical methods and mathematics in the interpretation of biological data, knowledge of bioinformatics tools (e.g. GCG), and demonstrated computer skills including experience with UNIX, Windows NT, and scripting languages (e.g. perl, Tcl/Tk, Phyton). An excellent understanding of the biology behind sequencing, genetic mapping and fingerprinting, and transcriptional profiling is necessary. Hands-on experience with multivariate statistics, cluster analysis, database technologies, SQL, data mining, UNIX shell, Web/CGI, additional programming skills (Java, C++, C), and a record of publishing is a plus. Application Information: In exchange for your talents, we offer a competitive salary and benefits package with advancement potential for your career. For consideration, please fax your resume to 650 638-5874, e-mail to biocareer@perkin-elmer.com, or send your resume, referencing job number, to PE Applied Biosystems, Human Resources Department, 850 Lincoln Centre Drive, Foster City, CA 94404. PE Applied Biosystems is an equal opportunity employer. From owner-software@net.bio.net Thu Jun 03 12:06:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!hub1.ispnews.com!cyc12.deja.bcandid.com!nntp1.deja.com!nnrp2.deja.com!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: gmei@my-deja.com Newsgroups: bionet.software Subject: Question: How to use Repbase with RepeatMasker? Date: Wed, 02 Jun 1999 17:34:07 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 39 Message-ID: <7j3pue$ovi$1@nnrp1.deja.com> NNTP-Posting-Host: 209.51.243.142 X-Article-Creation-Date: Wed Jun 02 17:34:07 1999 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.01; Windows NT) X-Http-Proxy: 1.1 x41.deja.com:80 (Squid/1.1.22) for client 209.51.243.142 Hi: I have a question of using Repbase with RepeatMasker. We have received a licensed version of hrap/cross_match/swat package and I installed it on our Digital alpha unix machine. I run "make" file and got the executable of the "cross_match". I have test run the "RepeatMasker" on the same machine and it worked fine (I compared the output from our "RepeatMasker" and from http://www.mgu.har.mrc.ac.uk/repeat/RepeatMasker and they yeilded the same result). It seems that "RepeatMasker" use the files in "Libraries" subdirectory to do its comparision. Now we have also licensed the "Repbase" and got the following files: README.html humrep.ref invrep.ref plnapp.ref pseudo.ref simple.ref README.txt humsub.ref mamapp.ref plnrep.ref rodapp.ref vrtrep.ref humapp.ref invapp.ref mamrep.ref pseapp.ref rodrep.ref So my question is: In order to use Repbase with RepeatMasker, is it just simply to move the "ref" files into the "Libraries" subdirectory of the RepeatMasker? Or I need to do something else such as to modify RepeatMasker's perl code? If you reply, please send a copy to zlmei@hotmail.com Thanks in advance. Guang Mei Sent via Deja.com http://www.deja.com/ Share what you know. Learn what you don't. From owner-software@net.bio.net Thu Jun 03 14:05:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!newspeer.clara.net!news.clara.net!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!warwick!globin.bio.warwick.ac.uk warwick.ac.uk!webadmin From: Newsgroups: bionet.general,sci.bio.misc,bionet.software Subject: UK PhD Studentships in Protein Structure Date: 3 Jun 1999 14:46:49 GMT Organization: University of Warwick, UK Message-ID: <7j64gp$i0i$1@holly.csv.warwick.ac.uk> NNTP-Posting-Host: globin.warwick.ac.uk X-Trace: holly.csv.warwick.ac.uk 928421209 18450 137.205.152.108 (3 Jun 1999 14:46:49 GMT) X-Complaints-To: abuse@csv.warwick.ac.uk NNTP-Posting-Date: 3 Jun 1999 14:46:49 GMT User-Agent: tin/pre-1.4-980818 ("Laura") (UNIX) (IRIX64/6.2 (IP26)) Lines: 39 Xref: biosci bionet.general:33207 bionet.software:23554 The following PhD Studentship projects are available in the Protein Structure Group at the University of Warwick. Full funding for these projects is available for UK nationals only. A "fees only" award can be made to EU nationals, however. -------------------------------------------------------------- "Study of protein and peptide structure by mass spectrometry" (BBSRC Industrial CASE Studentship with ICI) Supervisors: Professor H Dalton and Professor K Jennings -------------------------------------------------------------- "Prediction of Protein-Protein Interactions in Proteomes" (BBSRC Special Studentship) Supervisor: Dr David Jones -------------------------------------------------------------- "The development of data resources and methods for automated annotation and structure prediction of transmembrane genome sequences" (MRC Bioinformatics Studentship) Supervisor: Dr David Jones -------------------------------------------------------------- "Analysis of the folding pathways of kinase domains" (BBSRC Industrial CASE Studentship with Zeneca) Supervisor: Dr Teresa Pinheiro -------------------------------------------------------------- For more details, please see the departmental Web pages: http://www.bio.warwick.ac.uk From owner-software@net.bio.net Thu Jun 03 14:26:00 1999 Reply-To: "warez" From: "warez" Newsgroups: bionet.software Subject: Norman: Who is the biggest deceiver? Date: Thu, 3 Jun 1999 17:09:00 +0400 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 NNTP-Posting-Host: dialup40.sia.telecom.lt Message-ID: <37569c6e@news.takas.lt> X-Trace: 3 Jun 1999 17:17:02 +0100, dialup40.sia.telecom.lt Path: biosci!rutgers!nntp.upenn.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!newsfeed.tli.de!news.algonet.se!algonet!masternews.telia.net!news.takas.lt!dialup40.sia.telecom.lt Lines: 24 About "some bad words from some guys in the newsgroups": I should say that it is the normal thing in our world. When people are doing the same thing (selling), there is some kind of competition between them. Also you can not be liked by everyone. Those people who write there about unrecieved orders, lost payments are simply lying, because I do not know them at all. They are not my clients. Instead of informing me about lost orders and money, they write to the newsgroups shouting to the whole world about "Norman - deceiver". Who is the biggest deceiver? If my clients have some problems, first of all they inform me about - so they recieve Help. Anyway everyone have his right of choice! Norman From owner-software@net.bio.net Thu Jun 03 15:15:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!logbridge.uoregon.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Need free educational software in Mol Bio Date: 3 Jun 1999 16:09:25 GMT Organization: Biology, Indiana University - Bloomington Lines: 20 Message-ID: <7j69bl$94e$1@jetsam.uits.indiana.edu> References: <374D1B66.3E7CFA46@crc.dk> <3754E4D4.E484460B@pn3.vsnl.net.in> NNTP-Posting-Host: chipmunk.bio.indiana.edu Molecular biology public software archives are found at: ebi - ftp://ftp.ebi.ac.uk/pub/software/ or http://www.ebi.ac.uk/software/software.html iubio - ftp://iubio.bio.indiana.edu/molbio/ or http://iubio.bio.indiana.edu/soft/molbio/ Alternate sites for the IUBio molecular biology collection: ftp://ftp.funet.fi/pub/sci/molbio/iubiomolbio ftp://ftp.sunet.se/pub/molbio ftp://ftp.nig.ac.jp/pub/mirror/IUBIO/molbio ftp://ftp.uam.es/pub/mirror/molbio, ftp://ftp.pasteur.fr/pub/GenSoft/mirrors/IUBio/molbio http, ftp://mic3.hensa.ac.uk/hosts/iubio.bio.indiana.edu/molbio/ ftp://bioinformatics.weizmann.ac.il/pub/software/mac and software/ibmpc -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Fri Jun 04 01:20:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news-in-central.sprintlink.net!news.sprintlink.net!news.aecom.yu.edu!not-for-mail From: Jil Tardiff Newsgroups: bionet.software,bionet.molbio.methods-reagents Subject: Anyone using standalone Primer3? Date: Thu, 03 Jun 1999 21:39:25 -0400 Organization: Albert Einstein College of Medicine Lines: 29 Message-ID: <37572E4D.BEF0F039@westnet.com> NNTP-Posting-Host: tnt.aecom.yu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en What a week! I will not devulge the ugly details, but suffice it to say, I have to get a standalone Linux workstation up and running with some basic molbio packages. Almost everything is going OK at present (big thanks to Alan Williams), but I am very stumped with Primer3. This machine is *not* hooked up to the Internet, so we need to use a standalone primer prediction package. The machine is running RH 6.0 (I'm not sure what version of gcc to be honest) and kernel 2.2.9 . First of all, I cannot get the source packages to pass the primer_test.pl file, it bombs almost immediately. (the executable *seems* to compile OK). So, I tried a statically linked ELF binary, but (and this is the embarrassing part), I cannot figure out *what* the exact command line should be! I have an example file in Boulder IO format and the program kicks out "Format should be ./primer3 [-format_output] " and that it takes standard input. I've tried multiple permutations to no avail. This is frustrating in the extreme (to say the least), and data is piling up on me....(and my poor student) Any and all help would be greatly appreciated, Jil From owner-software@net.bio.net Fri Jun 04 02:09:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!206.24.6.7!news.westnet.com!not-for-mail From: Jil Newsgroups: bionet.software,bionet.molbio.methods-reagents Subject: Re: Anyone using standalone Primer3? Date: Thu, 03 Jun 1999 22:56:39 -0400 Organization: WestNet Internet Services Lines: 27 Message-ID: <37574067.19E4A015@westnet.com> References: <37572E4D.BEF0F039@westnet.com> NNTP-Posting-Host: p16.pm3-4.westnet.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.6 [en] (X11; I; Linux 2.2.5-15 i686) X-Accept-Language: en Oh well, nothing quite like answering one's own post....but I had one last go at it this evening, and got it. Thank goodness! It may have been painful, but I've learned a ton. Thanks for lending an ear. Jil > What a week! I will not devulge the ugly details, but suffice it to > say, I have to get a standalone Linux workstation up and running with > some basic molbio packages. > From owner-software@net.bio.net Fri Jun 04 06:52:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!newsfeed.nacamar.de!rz.uni-karlsruhe.de!news.uni-stuttgart.de!news.urz.uni-heidelberg.de!genius.embnet.dkfz-heidelberg.de!un691cs From: CSC Newsgroups: bionet.software Subject: Re: Norman: Who is the biggest deceiver? Date: Fri, 4 Jun 1999 09:41:23 +0200 Organization: University of Heidelberg, Germany Message-ID: References: <37569c6e@news.takas.lt> NNTP-Posting-Host: genius.embnet.dkfz-heidelberg.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To: warez In-Reply-To: <37569c6e@news.takas.lt> Lines: 33 On Thu, 3 Jun 1999, warez wrote: > About "some bad words from some guys in the newsgroups": > I should say that it is the normal thing in our world. > When people are doing the same thing (selling), there is > some kind of competition between them. > Also you can not be liked by everyone. > Those people who write there about unrecieved orders, > lost payments are simply lying, because I do not know > them at all. > They are not my clients. > Instead of informing me about lost orders and money, > they write to the newsgroups shouting to the whole > world about "Norman - deceiver". > Who is the biggest deceiver? > If my clients have some problems, first of all they > inform me about - so they recieve Help. > > Anyway everyone have his right of choice! > > Norman I see your point, Norman, well spoken ! However, this newsgroup is not intended for any commercial activity, so please turn to alt. moneygrabbing.quick.getrich or some such group. ------------------ Clemens Suter-Crazzolara, PhD -------------------- German Cancer Research Center DKFZ Dept. Molecular Biophysics (H0200) INF 280, 69120 Heidelberg, Germany ---------------------------------------------------------------------- From owner-software@net.bio.net Fri Jun 04 07:06:00 1999 Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!hammer.uoregon.edu!newsfeed.direct.ca!cyclone.bc.net!unixg.ubc.ca!dcwong From: dcwong@unixg.ubc.ca (Donald Chun Kit Wong) Newsgroups: bionet.software Subject: Looking for curve fitting software for ELISA Date: 4 Jun 1999 08:00:47 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 8 Message-ID: <7j813f$ip4$1@nntp.ucs.ubc.ca> NNTP-Posting-Host: interchange.ubc.ca X-Newsreader: TIN [version 1.2 PL2] We need a curve fitting program for the standard curve for a number of ELISA we're running. I would appreciate any suggestions as to a good program to use for Win98. Thanks! Donald Wong Dept. of Pathology The University of British Columbia From owner-software@net.bio.net Fri Jun 04 08:35:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.icl.net!bignews.mediaways.net!newsfeed.nacamar.de!chico.franken.de!news-nue1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: Steffen Schmidt Newsgroups: bionet.software Subject: Measureing an area Date: Fri, 04 Jun 1999 10:30:30 +0200 Organization: GWDG, Goettingen Lines: 39 Message-ID: <37578EA5.B739E5B2@Uni-MolGen.gwdg.de> NNTP-Posting-Host: 134.76.70.64 Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------DA7D87DD1E3C7A281C178D58" X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en This is a multi-part message in MIME format. --------------DA7D87DD1E3C7A281C178D58 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I want to measure the size of a cell on a crickets'wing. Therefore I use an EM and save the picture as a bitmap. Has anyone an idea how to measure an area in a bitmap-picture? It would be appreciable when there would be a tool which can automatically select the wanted area - like the magic wand mask tool of Corel Photo-Paint. Thanks Steffen --------------DA7D87DD1E3C7A281C178D58 Content-Type: text/x-vcard; charset=us-ascii; name="sschmid2.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Steffen Schmidt Content-Disposition: attachment; filename="sschmid2.vcf" begin:vcard n:Schmidt;Steffen tel;work:Arbeitsgruppe PD Dr. R. Sterner x-mozilla-html:FALSE url:http://www.gwdg.de/~sschmid3 org:Institut für Mikrobiologie und Genetik;Abteilung für molekulare Genetik und präparative Molekularbiologie adr:;;Grisebachstr. 8;37077 Göttingen;;; version:2.1 email;internet:sschmid2@Uni-MolGen.gwdg.de title:Georg-August Universität Göttingen fn:Steffen Schmidt end:vcard --------------DA7D87DD1E3C7A281C178D58-- From owner-software@net.bio.net Fri Jun 04 14:35:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!wn4feed!wn3feed!worldnet.att.net!208.134.241.18!newsfeed.cwix.com!128.174.5.49!vixen.cso.uiuc.edu!NewsNG.Chicago.Qual.Net!128.255.56.80!news.uiowa.edu!not-for-mail From: Todd Scheetz Newsgroups: bionet.software Subject: Re: Anyone using standalone Primer3? Date: Fri, 04 Jun 1999 10:29:41 -0500 Organization: The University of Iowa Lines: 47 Message-ID: <3757F0E5.A66E6DED@uiowa.edu> References: <37572E4D.BEF0F039@westnet.com> NNTP-Posting-Host: huge.eng.uiowa.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.6 [en] (X11; I; Linux 2.2.5 i686) X-Accept-Language: en Jil, You have tried re-directing STDIN, right? We use Primer3 here as a stand-alone package, and I've included an example of what a command looks like when we run it. (with the executable named primer.) % primer < selected.1998-03 > candidates.1998-03 So selected.1998-03 is the input file in Boulder IO format, and the candidates.1998-03 file is the outputfile. Hope this helps, -Todd Jil Tardiff wrote: > > What a week! I will not devulge the ugly details, but suffice it to > say, I have to get a standalone Linux workstation up and running with > some basic molbio packages. > > Almost everything is going OK at present (big thanks to Alan Williams), > but I am very stumped with Primer3. > > This machine is *not* hooked up to the Internet, so we need to use a > standalone primer prediction package. > > The machine is running RH 6.0 (I'm not sure what version of gcc to be > honest) and kernel 2.2.9 . > > First of all, I cannot get the source packages to pass the > primer_test.pl file, it bombs almost immediately. (the executable > *seems* to compile OK). So, I tried a statically linked ELF binary, but > (and this is the embarrassing part), I cannot figure out *what* the > exact command line should be! I have an example file in Boulder IO > format and the program kicks out "Format should be ./primer3 > [-format_output] " and that it takes standard input. I've tried > multiple permutations to no avail. > > This is frustrating in the extreme (to say the least), and data is > piling up on me....(and my poor student) > > Any and all help would be greatly appreciated, > > Jil From owner-software@net.bio.net Fri Jun 04 17:27:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!nntp.cs.ubc.ca!news.UVic.CA!hera.bioc.uvic.ca!user From: cupton@uvic.ca (Chris Upton) Newsgroups: bionet.software Subject: Perl scripts Date: Fri, 04 Jun 1999 11:24:47 -0800 Organization: UVIC Lines: 10 Message-ID: NNTP-Posting-Host: hera.bioc.uvic.ca X-Trace: uvaix7e1.comp.UVic.CA 928520487 132006 142.104.33.102 (4 Jun 1999 18:21:27 GMT) X-Complaints-To: abuse@UVic.CA NNTP-Posting-Date: 4 Jun 1999 18:21:27 GMT Hi, Does anyone have public domain perl scripts (or anything) for taking a DNA sequence and generating: %AT nucleotide frequency dinucleotide frequency (actual and expected) codon use Cheers, Chris From owner-software@net.bio.net Sat Jun 05 11:34:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsmangler.inet.tele.dQ!not-for-mail From: "Bo Bergmann" Newsgroups: bionet.software Subject: HPLC-WIZARD beta version 1.02 Date: 5 Jun 1999 12:28:51 GMT Organization: Tele Danmark Internet Lines: 6 Message-ID: <01beaf4e$5aeb9110$25a4f9c3@bergmann> NNTP-Posting-Host: ip37.boanxr7.ras.tele.dk X-Trace: news.inet.tele.dk 928585731 22842 195.249.164.37 (5 Jun 1999 12:28:51 GMT) X-Complaints-To: Department of Abuse NNTP-Posting-Date: 5 Jun 1999 12:28:51 GMT X-Newsreader: Microsoft Internet News 4.70.1157 HPLC-WIZARD beta version 1.02 is now ready for downloading and evaluation at http://home5.inet.tele.dk/daller/index.htm From owner-software@net.bio.net Sat Jun 05 13:06:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news-in-west1.sprintlink.net!news.sprintlink.net!news.aecom.yu.edu!not-for-mail From: Jil Tardiff Newsgroups: bionet.software Subject: Re: Anyone using standalone Primer3? Date: Sat, 05 Jun 1999 09:55:55 -0400 Organization: Albert Einstein College of Medicine Lines: 66 Message-ID: <37592C6B.B79BA475@westnet.com> References: <37572E4D.BEF0F039@westnet.com> <3757F0E5.A66E6DED@uiowa.edu> NNTP-Posting-Host: tnt.aecom.yu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en To: Todd Scheetz Todd, You hit the nail on the head. I've been learning UNIX/Linux from the ground up and for the life of me I couldn't figure out how to redirect STDIN! Really basic. And strangely enough, none of the several books I checked explained explicitly how to do it. Oh well, live and learn. The standalone Primer3 seems quite nice. My student is *thrilled*. She designed her last set of human-based primers by hand. She did a great job, but it was painful, so I think this will help her out. Thanks again, Jil Todd Scheetz wrote: > Jil, > > You have tried re-directing STDIN, right? We use Primer3 here as a > stand-alone package, and I've included an example of what a command > looks like when we run it. (with the executable named primer.) > > % primer < selected.1998-03 > candidates.1998-03 > > So selected.1998-03 is the input file in Boulder IO format, and the > candidates.1998-03 file is the outputfile. > > Hope this helps, > -Todd > > Jil Tardiff wrote: > > > > What a week! I will not devulge the ugly details, but suffice it to > > say, I have to get a standalone Linux workstation up and running with > > some basic molbio packages. > > > > Almost everything is going OK at present (big thanks to Alan Williams), > > but I am very stumped with Primer3. > > > > This machine is *not* hooked up to the Internet, so we need to use a > > standalone primer prediction package. > > > > The machine is running RH 6.0 (I'm not sure what version of gcc to be > > honest) and kernel 2.2.9 . > > > > First of all, I cannot get the source packages to pass the > > primer_test.pl file, it bombs almost immediately. (the executable > > *seems* to compile OK). So, I tried a statically linked ELF binary, but > > (and this is the embarrassing part), I cannot figure out *what* the > > exact command line should be! I have an example file in Boulder IO > > format and the program kicks out "Format should be ./primer3 > > [-format_output] " and that it takes standard input. I've tried > > multiple permutations to no avail. > > > > This is frustrating in the extreme (to say the least), and data is > > piling up on me....(and my poor student) > > > > Any and all help would be greatly appreciated, > > > > Jil From owner-software@net.bio.net Sat Jun 05 22:33:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!howland.erols.net!spring.edu.tw!feeder.seed.net.tw!news.seed.net.tw!not-for-mail From: "chung" Newsgroups: alt.tv.cartoon-network,alt.tv.networks.cbc,alt.tv.twilight.zone,alt.tv.twin-peaks,alt.twosixhundred.uk,at.network.eunet,at.network.ping,bionet.software,bionet.software.acedb Subject: Re: §Ú¬Ý¹L³Ì§ÖªºÁÈ¿ú¤è®×¤F Date: 5 Jun 1999 23:27:23 GMT Organization: SEEDNet News Service Lines: 43 Message-ID: <7jcbor$qo9$1@news.seed.net.tw> NNTP-Posting-Host: 210.68.34.24 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Xref: biosci bionet.software:23567 bionet.software.acedb:2383 pasd wrote in message news:... > > §A¥i¥H¶i¨Ó³o¸Ì¬Ý¬Ý¹CÀ¸³W«h¡I > http://www.casinotreasure.com:8080/original/chinese/?10ch > ================================================== > ¿Ë·RªºªB¤Í¡A³o¬O¨Ó¦ÛCasino Treasure ªº°Ý­Ô¡A¥@¤W³Ì°ª¯Åªººô¸ô½ä«°¡C > ±z¥i¥Hª±½ä«°¹CÀ¸´N¹³¦b©Ô´µºû¥[´µ¤@¼Ë¡A¥ß§YĹ¯u¿ú¡A¨Ã¥B´N¦b±zªº¹q¸£«e¡I > űoªº¿ú±N·|¶×¤J±zªº«H¥Î¥d©Î¥HÀYµ¥¶l¥ó±N¬üª÷¤ä²¼±Hµ¹±z¡C > ©Ò¦³ªº·sª±®a·|¦¬¨ì US$5 ªºÃا·í¥L²Ä¤@¦¸ÁʶRÄw½X¡AÁÂÁÂ¥L¥[¤J Casino > Treasure¡C > ±z¤]¥i¥H§K¶Oª±¹CÀ¸¡C > ¦b¤@­Óµ´¨ÎªºµêÀÀ¯u¹êªºÀô¹Ò¤¤±z¥i¥H»P¨ä¥¦ª±®a²á¤Ñ¡AÁܽбzªºªB¤Í©Î¥æ·sªB¤Í¡C > ================================================== > ª± Game ÁÙ¥i¥HÁÈ¿ú? > §Ú­Ì¦w¸Ë¦n³nÅ餧«á¡A¥ý¥Î§K¶OÄw½Xª±¤F¤@¤U¡A > µM«á¥Î«H¥Î¥d¨ê¤F¬üª÷ $10 ¤¸ª±15¤ÀÄÁ¡A > ¤pŤF¤@¨Ç¨£¦n´N¦¬¡A³s¦P¥L­Ì­PÃتº $30 ¤@°_§â¥¦§I²{¡A > ¤@¦@´«¦^¤F$55 ¬üª÷¡A®t¤£¦hÁȤF$1500 ¥x¹ô¡A¯uªº«Ü¤£¿ù¡I > http://www.casinotreasure.com:8080/original/chinese/?10ch > ================================================== > ¦n¯¸³ø³ø http://top.banner.com.tw > ~ TOP Banner ¼öªùºô¯¸±Æ¦æº] ~ > ¦b³o¸Ì§A±N¦³¾÷·|±o¨ì 30MB §K¶OªÅ¶¡ > ¡]¤ä´© Front Page 98 , FTP , CGI......¡^ > ¥u­n§A¥[¤J·|­û¡A¬O§K¶Oªº³á¡I > ¸Ô²Ó»¡©ú : http://top.banner.com.tw > > > > > > > > > > > > > > From owner-software@net.bio.net Mon Jun 07 10:55:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news.net.uni-c.dk!news.daimi.au.dk!not-for-mail From: "Ditlev Brodersen" Newsgroups: bionet.software Subject: XAct: A program for construction of crystallisation trials Date: Mon, 7 Jun 1999 13:46:59 +0200 Organization: IMSB, Aarhus University, Denmark Lines: 60 Message-ID: <7jgbgr$43gsn$1@xinwen.daimi.au.dk> Reply-To: "Ditlev Brodersen" NNTP-Posting-Host: dings.imsb.au.dk X-Trace: xinwen.daimi.au.dk 928756059 4309911 255.255.255.255 (7 Jun 1999 11:47:39 GMT) X-Complaints-To: news@daimi.au.dk NNTP-Posting-Date: 7 Jun 1999 11:47:39 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 SOFTWARE ANNOUNCEMENT: ***************************************************************** XAct 1.0 for Windows 95/98 A Program for Contruction, Automated Setup, and Bookkeeping of Crystallisation Experiments Macromolecular Crystallography Institute of Molecular and Structural Biology Aarhus University Denmark ***************************************************************** XAct is a stand-alone application for Microsoft Windows 95/98 that can be used to construct, maintain, and record the results of many crystallisation experiments. Through an extensive object-oriented data structure, the program supports multiple users each with many crystallisation experiments organised in a hierarchical fashion. The program has been developed in the Laboratory for Macromolecular Crystallography, Institute of Molecular and Structural Biology, Aar- hus University, Denmark headed by Asc. Prof. Jens Nyborg. XAct is being used on a daily basis in our laboratory by technicians, students, grad. students, and post.doc.'s to set up crystalisation trials in an organised way. At the moment, the program can be down- loaded in a late beta-version. The software is available free of change to all academic users after the registration form has been completed. Registration and download is done through the XAct homepage at http://zombie.imsb.au.dk/xact This page also contains additional information about the software, screen shots, manual, references, etc. The program supports automatic dispensing of the designed solutions using a Gilson model 222 autosampler attached to the PC. We are espe- cially interested in response from people who have this equipment in the lab and who might wish to use it for setting up crystallisation trials. Ditlev Brodersen -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- __ /_/\ Ditlev E. Brodersen Phone: +45 8942 5021 / /\ \ M.Sc., Ph.D. student Fax : +45 8620 1222 / / /\ \ IMSB, Aarhus University Email: ding@imsb.au.dk / / /\ \ \ Gustav Wieds Vej 10c WWW : http://imsb.au.dk/~ding/ / /_/__\ \ \ DK-8000 Aarhus C /_/______\_\/\ Denmark \_\_________\/ From owner-software@net.bio.net Mon Jun 07 17:21:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!newsswitch.lcs.mit.edu!newsfeed.ecrc.net!newsfeed.nacamar.de!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!newsfeed.ed.ac.uk!not-for-mail From: Daniel Barker Newsgroups: bionet.software Subject: Announce: LVB phylogeny program for OS/2 Date: Mon, 07 Jun 1999 19:11:16 +0100 Organization: Edinburgh University Lines: 13 Message-ID: <375C0B44.473AAFEE@holyrood.ed.ac.uk> NNTP-Posting-Host: dialup-111.publab.ed.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: scotsman.ed.ac.uk 928779147 29455 129.215.38.111 (7 Jun 1999 18:12:27 GMT) X-Complaints-To: usenet@scotsman.ed.ac.uk NNTP-Posting-Date: 7 Jun 1999 18:12:27 GMT X-Mailer: Mozilla 4.51 [en] (Win98; I) X-Accept-Language: en LVB is a free phylogeny program that uses the simulated annealing heuristic to seek parsimonious trees. See http://www.icmb.ed.ac.uk/sokal.html A ready to run version for OS/2 is now available, but not yet on the Web. If interested, please e-mail me and I will send an attachment. The OS/2 distribution is a ZIP file, 106KB in size. Acknowledgement: LVB for OS/2 was compiled by Martin "Herbert" Dietze. -- Daniel Barker. From owner-software@net.bio.net Tue Jun 08 01:59:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed1.earthlink.net!uunet!lax.uu.net!ffx.uu.net!newsfeed.attap.net!mango.singnet.com.sg!dahlia.singnet.com.sg!columbine.singnet.com.sg!not-for-mail From: "Chan Bok" Newsgroups: bionet.software Subject: ANNOUNCING AXON2000 (Idea Processor) Date: 8 Jun 1999 02:53:15 GMT Organization: Singapore Telecommunications Ltd Lines: 13 Message-ID: <01beb157$24c34280$LocalHost@default> NNTP-Posting-Host: qtns02926.singnet.com.sg X-Newsreader: Microsoft Internet News 4.70.1155 Axon Research has released the millennium version of Axon2000, a state-of-the-art idea visualization tool. See Axon Research's website for more details. A FREE Lite version is downloadable from Axon Research's website at: http://web.singnet.com.sg/~axon2000 ===================================================== Chan Bok E-mail: axon2000@mbox2.singnet.com.sg Axon Research Web: http://web.singnet.com.sg/~axon2000 5, Lengkok Merak Tel: (065)-7360422 Singapore 248860 Fax: (065)-7379016 ===================================================== From owner-software@net.bio.net Tue Jun 08 06:55:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!wn4feed!worldnet.att.net!205.252.116.205!howland.erols.net!newsfeed1.telenordia.se!news.algonet.se!algonet!uninett.no!news.net.uni-c.dk!not-for-mail From: "S.W. Rasmussen" Newsgroups: bionet.software Subject: Re: Need free educational software in Mol Bio Date: Tue, 08 Jun 1999 09:48:21 +0100 Organization: UNI-C Lines: 43 Message-ID: <375CD8D5.C0A2CB3C@crc.dk> References: <374D1B66.3E7CFA46@crc.dk> <3754E4D4.E484460B@pn3.vsnl.net.in> NNTP-Posting-Host: ppp1.crc.dk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.net.uni-c.dk 928827809 18430 130.226.184.128 (8 Jun 1999 07:43:29 GMT) X-Complaints-To: usenet@news.net.uni-c.dk NNTP-Posting-Date: 8 Jun 1999 07:43:29 GMT X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en Dear Dr. Shendye, DNATools is a collection of functions for basic analysis of DNA and protein sequences. In case you wish to get more information on the program please visit the homepage: http://www.crc.dk/phys/A01B04_dnatools.htm The program package can be used free of charge for a testing period of 3 months. This testing period can be extended - still free of charge - for non-commercial users. Regards Søren "Dr.Abhay Shendye" wrote: > > Dear Netters, > > I have recently joined this discussion group, so please forgive me if I am posting a too basic > question repeated several times earlier. > > I have done some genetic engineering during my Ph.D.. Now it has come to teaching the same to > undergraduates who can't lay their hands much ta the same in practicals. I find it extremely difficult > to make them imagine the steps at molecular level. > > Could you please help me obtain some software that will allow the students perform RE digestion, > ligation, PCR, mutation, recombination etc. on PC. I already have DNASIS which can be used to teach > restriction mapping. > > Thanks in advance. > > Yours sincerely, > > Dr. Abhay Shendye. -- Soeren W. Rasmussen, Dr. scient. Department of Physiology Carlsberg Laboratory Copenhagen, Denmark swr@crc.dk, http://www.crc.dk/phys From owner-software@net.bio.net Tue Jun 08 13:24:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newspeer.clara.net!news.clara.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!not-for-mail From: Arne Mueller Newsgroups: bionet.software Subject: Re: retrieving sequences after a BLAST? Date: Tue, 08 Jun 1999 15:15:06 +0100 Organization: Imperial Cancer Research Fund Message-ID: <375D256A.D78C6733@icrf.icnet.uk> References: <9906021004.AA27511@olrik.sb-roscoff> <7j4ako$3ip$1@franklin.ljcrf.edu> NNTP-Posting-Host: jumbo.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5C-SGI [en] (X11; I; IRIX64 6.5 IP25) X-Accept-Language: en Lines: 29 "Dr. Greg Quinn" wrote: > > If you are doing a netBlast with GCG, I believe that NetFetch can parse > the blast output file and fetch the cited sequences from the NIH site. > > Also, Nigel Brown's program, MVIEW will 'extract' alignments from a > BLAST search to create a multiple alignment (with some caveats); this > sometimes obviates the need to pull sequences depending on what you > have in mind for the database matches. Hi, Mview aligns the sequences reported in the blastfile which is very often only a fragment of the sequence (the highest scoring part) but mview is able to produce output in html and link the sequences to SRS so you can click on the sequence names and get the full database entry from SRS. Have a look at http://mathbio.nimr.mrc.ac.uk/nbrown/mview/ greetings, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ From owner-software@net.bio.net Tue Jun 08 20:02:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.atl!newsfeed.mia!news.cdc.gov NNTP-Posting-Host: 158.111.57.70 Newsgroups: bionet.software Date: Tue, 8 Jun 1999 16:53:59 -0400 Message-ID: <375D82FA.7170065A@nic.smsu.edu> From: Scott Handley X-Mailer: Mozilla 4.6 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 Subject: Re: Looking for curve fitting software for ELISA References: <7j813f$ip4$1@nntp.ucs.ubc.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 17 I've had years of happiness with the following program. http://www.ebicom.net/~dhyams/cvxpt.htm Donald Chun Kit Wong wrote: > We need a curve fitting program for the standard curve for a number of > ELISA we're running. I would appreciate any suggestions as to a good > program to use for Win98. Thanks! > > Donald Wong > Dept. of Pathology > The University of British Columbia From owner-software@net.bio.net Tue Jun 08 20:18:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newspeer.monmouth.com!newsfeed.atl!newsfeed.mia!news.cdc.gov NNTP-Posting-Host: 158.111.57.70 Newsgroups: bionet.software Date: Tue, 8 Jun 1999 16:56:50 -0400 Message-ID: <375D83A5.805DDB99@cdc.gov> From: Scott Handley Organization: Center for Disease Control and Prevention X-Mailer: Mozilla 4.6 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 Subject: Re: Looking for curve fitting software for ELISA References: <7j813f$ip4$1@nntp.ucs.ubc.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 17 I've had years of happiness with the following program. http://www.ebicom.net/~dhyams/cvxpt.htm Donald Chun Kit Wong wrote: > We need a curve fitting program for the standard curve for a number of > ELISA we're running. I would appreciate any suggestions as to a good > program to use for Win98. Thanks! > > Donald Wong > Dept. of Pathology > The University of British Columbia From owner-software@net.bio.net Wed Jun 09 09:57:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!oleane!jussieu.fr!univ-angers.fr!ciril.fr!news.u-strasbg.fr!frenzy.u-strasbg.fr!francis.durst From: francis.durst@bota-ulp.u-strasbg.fr (Francis Durst) Newsgroups: bionet.software Subject: Re: retrieving sequences after a BLAST? Date: Wed, 9 Jun 1999 12:51:57 LOCAL Organization: CNRS Lines: 43 Message-ID: References: <9906021004.AA27511@olrik.sb-roscoff> <7j4ako$3ip$1@franklin.ljcrf.edu> <375D256A.D78C6733@icrf.icnet.uk> NNTP-Posting-Host: frenzy.u-strasbg.fr X-Trace: news.u-strasbg.fr 928929186 18316 130.79.129.1 (9 Jun 1999 11:53:06 GMT) X-Complaints-To: usenet@u-strasbg.fr NNTP-Posting-Date: 9 Jun 1999 11:53:06 GMT X-Newsreader: Trumpet for Windows [Version 1.0 Rev B.7] In article <375D256A.D78C6733@icrf.icnet.uk> Arne Mueller writes: >From: Arne Mueller >Subject: Re: retrieving sequences after a BLAST? >Date: Tue, 08 Jun 1999 15:15:06 +0100 >"Dr. Greg Quinn" wrote: >> >> If you are doing a netBlast with GCG, I believe that NetFetch can parse >> the blast output file and fetch the cited sequences from the NIH site. >> >> Also, Nigel Brown's program, MVIEW will 'extract' alignments from a >> BLAST search to create a multiple alignment (with some caveats); this >> sometimes obviates the need to pull sequences depending on what you >> have in mind for the database matches. >Hi, >Mview aligns the sequences reported in the blastfile which is very often >only a fragment of the sequence (the highest scoring part) but mview is >able to produce output in html and link the sequences to SRS so you can >click on the sequence names and get the full database entry from SRS. >Have a look at http://mathbio.nimr.mrc.ac.uk/nbrown/mview/ > greetings, > Arne >-- >Arne Mueller >Biomolecular Modelling Laboratory You may also use Octopus by Patrick Durand, which displays Blast (and Fasta) output, shows sequence info etc, lets you select some or all sequences and displays them aligned in an editor window. You can save them as an .MSF file. http://www.lmcp.jussieu.fr/~durand/HtmlDoc/software/octopus/octo_main.html Francis =============================================================== Francis Durst CNRS / Institut de Biologie Moleculaire des Plantes 28, rue Goethe 67083 Strasbourg, France From owner-software@net.bio.net Wed Jun 09 14:24:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!newsswitch.lcs.mit.edu!newspump.monmouth.com!newspeer.monmouth.com!isdnet!ciril.fr!univ-angers.fr!not-for-mail From: Armel Le Bail Newsgroups: sci.techniques.xtallography,bionet.xtallography,bionet.software,sci.med.pharmacy Subject: ESPOIR 2.00 release Date: Wed, 09 Jun 1999 17:25:54 +0200 Organization: Universite du Maine - France Lines: 23 Message-ID: <375E8782.637070E1@aviion.univ-lemans.fr> Reply-To: lebail@aviion.univ-lemans.fr NNTP-Posting-Host: pcb4122.univ-lemans.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.univ-angers.fr 928941538 45984 193.52.30.155 (9 Jun 1999 15:18:58 GMT) X-Complaints-To: newsmaster@univ-angers.fr NNTP-Posting-Date: 9 Jun 1999 15:18:58 GMT X-Mailer: Mozilla 4.51 [en] (Win95; I) X-Accept-Language: en Xref: biosci bionet.xtallography:4767 bionet.software:23582 The new ESPOIR 2.0 release has passed successfully the SDPD Round Robin sample II test (tetracycline hydrochloride) by the molecular replacement method. It can now be considered as a serious competitor in this field as well as in the Monte Carlo from "scratch" field. It is still proposed under the GNU license (source available, business and modifications possible if the source remains open) at : http://www.cristal.org/sdpd/espoir/ In fact, available competitors are few (PowderSolve, Endeavour, Promet...), though many others have produced results (OCTOPUS, GAP, DRUID, ROTSEARCH....) and ESPOIR is the only open code on the market (FORTRAN). Best, and have fun with it, -- Armel Le Bail - Universite du Maine, Laboratoire des Fluorures, CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France http://www.cristal.org/ From owner-software@net.bio.net Wed Jun 09 15:30:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!lzcpc1.dl.ac.uk!l.cranswick From: l.cranswick@dl.ac.uk (Lachlan Cranswick) Newsgroups: sci.techniques.xtallography,bionet.xtallography,bionet.software,sci.med.pharmacy Subject: Re: ESPOIR 2.00 release Date: Wed, 9 Jun 1999 17:14:55 LOCAL Organization: Daresbury Laboratory, UK Message-ID: References: <375E8782.637070E1@aviion.univ-lemans.fr> NNTP-Posting-Host: lzcpc1.dl.ac.uk X-Trace: mserv2.dl.ac.uk 928944856 9259 148.79.160.252 (9 Jun 1999 16:14:16 GMT) X-Complaints-To: newsmaster@dl.ac.uk NNTP-Posting-Date: 9 Jun 1999 16:14:16 GMT X-Newsreader: Trumpet for Windows [Version 1.0 Rev B.7] Lines: 53 Xref: biosci bionet.xtallography:4768 bionet.software:23583 In article <375E8782.637070E1@aviion.univ-lemans.fr> Armel Le Bail writes:>The new ESPOIR 2.0 release has passed successfully the SDPD>Round Robin sample II test (tetracycline hydrochloride) by the>molecular replacement method. It can now be considered as a >serious competitor in this field as well as in the Monte Carlo >from "scratch" field. >It is still proposed under the GNU license (source available, >business and modifications possible if the source remains open) >at : http://www.cristal.org/sdpd/espoir/ >In fact, available competitors are few (PowderSolve, Endeavour, >Promet...), though many others have produced results (OCTOPUS, >GAP, DRUID, ROTSEARCH....) and ESPOIR is the only open >code on the market (FORTRAN). >Best, and have fun with it, >-- >Armel Le Bail - Universite du Maine, Laboratoire des Fluorures, >CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France >http://www.cristal.org/ Given ESPOIR uses extracted intensities - has it been tested/how good is it on single crystal HKL data (0% overlap) in suggesting a starting model? Am mainly thinking in terms of datasets with poor intensity, ambigious spacegroup, etc - but it should work by default on good quality data(?). Surely if ESPOIR/Monte Carlo methods can do a good job with intensities extracted from powder data, it should be able to do at least as well on single crystal data(?) Lachlan. =========== Lachlan M. D. Cranswick Collaborative Computational Project No 14 (CCP14) for Single Crystal and Powder Diffraction Daresbury Laboratory, Warrington, WA4 4AD U.K Tel: +44-1925-603703 Fax: +44-1925-603124 E-mail: l.cranswick@dl.ac.uk Ext: 3703 Room C14 NEW CCP14 Web Domain (Under heavy construction): http://www.ccp14.ac.uk From owner-software@net.bio.net Wed Jun 09 16:03:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.tli.de!isdnet!oceanite.cybercable.fr!not-for-mail From: Cristal Newsgroups: sci.techniques.xtallography,bionet.xtallography,bionet.software,sci.med.pharmacy Subject: Re: ESPOIR 2.00 release Date: Wed, 09 Jun 1999 19:00:16 +0200 Organization: Private Lines: 44 Message-ID: <375E9DA0.2B3043F3@cybercable.tm.fr> References: <375E8782.637070E1@aviion.univ-lemans.fr> Reply-To: cristal@cybercable.tm.fr NNTP-Posting-Host: r1m103.cybercable.tm.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: oceanite.cybercable.fr 928947471 13023 195.132.1.103 (9 Jun 1999 16:57:51 GMT) X-Complaints-To: usenet@oceanite.cybercable.fr NNTP-Posting-Date: 9 Jun 1999 16:57:51 GMT X-Mailer: Mozilla 4.51 [fr] (Win95; I) X-Accept-Language: fr Xref: biosci bionet.xtallography:4769 bionet.software:23585 Lachlan Cranswick wrote : > Given ESPOIR uses extracted intensities - has it been > tested/how good is it on single crystal HKL data > (0% overlap) in suggesting a starting model? > Am mainly thinking in terms of datasets with poor intensity, > ambigious spacegroup, etc - but it should work by default > on good quality data(?). > > Surely if ESPOIR/Monte Carlo methods can do a good job with > intensities extracted from powder data, it should be able to do > at least as well on single crystal data(?) In general, who can do the hard work, can do the simple. Single crystal data-like were tested. Yes, ESPOIR is able to determine structures from single crystal data. But the upper complexity limit is ridiculously low if compared with direct methods. In the "from scratch" option (i.e. starting from completely random models), the maximum number of independent atoms is 15-30 : really small ! The maximum complexity for using ESPOIR in the MR (Molecular Replacement) mode (locating a known fragment) is not well known, but degrees of freedom (DoF) may be of the order 50-100 (however, the ESPOIR 2.00 version can locate only one fragment, corresponding to 6 DoF). Further developments will concern the consideration of torsion angles and rotating/translating several fragments together. Reasons for not being able to determine a structure from single crystal data may be quite numerous. If the crystal is twinned by merohedry, ESPOIR will be very helpful, for instance, since an option for working from a powder pattern regenerated from the |Fs| is included. This option will restitute a non-twinned set of powder data, though loosing some information in strict orverlapping peaks. Best Armel Le Bail - Université du Maine, Laboratoire des Fluorures, CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France http://www.cristal.org/ From owner-software@net.bio.net Wed Jun 09 20:25:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!colt.net!Pollux.Teleglobe.net!server-b.cs.interbusiness.it!news.tin.it!not-for-mail From: "Gianluca Del Maschio" Newsgroups: bionet.software Subject: Information needed Date: Wed, 9 Jun 1999 23:14:28 +0200 Organization: TIN Message-ID: <7jmlbq$lac$1@nslave1.tin.it> NNTP-Posting-Host: a-pn4-16.tin.it X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Lines: 10 Looking for some tips or on-line manuals for building an intresting web site. You can e-mail your messages to gdmmail@tin.it I thank anyone who will help me. From owner-software@net.bio.net Thu Jun 10 01:56:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!hammer.uoregon.edu!newsfeed.wli.net!portc04.blue.aol.com!audrey01.news.aol.com!not-for-mail From: rjgrimaila@aol.com (RjGrimaila) Newsgroups: bionet.software Subject: Need help with perl to encode/decode ASN.1 Lines: 6 NNTP-Posting-Host: ladder05.news.aol.com X-Admin: news@aol.com Date: 10 Jun 1999 02:50:14 GMT Organization: AOL http://www.aol.com Message-ID: <19990609225014.15306.00002967@ng-cq1.aol.com> Does anyone have experience with perl to encode/decode ASN.1 formatted records? ASN.1 looks ideal for complex sequence records. I'd like to extend existing perl code to save ASN.1 objects to an Oracle database. I'm aware of Convert::BER.pm, but haven't had a chance to RTFM. RAy From owner-software@net.bio.net Thu Jun 10 09:49:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!colt.net!news0.de.colt.net!newscore.gigabell.net!newscore.ipf.de!fu-berlin.de!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!biosci From: TaxFree@020.co.uk Newsgroups: bionet.software Subject: IRS, BUSINESS TAX CREDITS -- FREE INFORMATION Date: 10 Jun 1999 11:43:18 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: <199906101042.FAA05584@mail-gw4adm.rcsntx.swbell.net> NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 929011398 21642 193.62.192.80 (10 Jun 1999 10:43:18 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 10 Jun 1999 10:43:18 GMT X-Received: from mserv1.dl.ac.uk (root@mserv1.dl.ac.uk [148.79.160.65]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA04493; Thu, 10 Jun 1999 11:43:14 +0100 (BST) X-Received: from mail-gw4adm.rcsntx.swbell.net (mail-gw4.rcsntx.swbell.net [151.164.30.54]) by mserv1.dl.ac.uk with ESMTP id LAA04190 (8.8.8/5.4[ref postmaster@dl.ac.uk] for dl.ac.uk from TaxFree@020.co.uk); Thu, 10 Jun 1999 11:43:14 +0100 (BST) X-Precedence: first-class X-Received: from oemcomputer (ppp-209-79-196-25.scrm01.pacbell.net [209.79.196.25]) by mail-gw4adm.rcsntx.swbell.net (8.8.5/8.8.5) with SMTP id FAA05584; Thu, 10 Jun 1999 05:42:57 -0500 (CDT) X-To: allmyfriends@msn.com Lines: 29 Help Your Company Leverage With the IRS! Free Up Space While Helping Charity Learn How Donating Unwanted Inventory & Merchandise Will Benefit You Learn Ways to Take Major BusinessTax Deductions While Helping the World For FREE Information mailto: world123@mailroom.com Call 800-952-9066 ==================================================== This message is sent in compliance of the new e-mail bill:SECTION 301. "Per Section 301, Paragraph (a)(2)(C) of S. 1618, furthertransmissions to you by the sender of this email may be stopped at no cost to you." For Removal mailto:TaxFree@020.co.uk Prevent bulk emailers from mailing you in the future. ==================================================== --- From owner-software@net.bio.net Thu Jun 10 09:51:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!news.demon.co.uk!demon!kovcomp.demon.co.uk!not-for-mail From: Warren Kovach Newsgroups: bionet.software,sci.bio.ecology,sci.geo.geology,sci.stat.consult Subject: ANNOUNCE: MVSP 3.1 now available Date: Thu, 10 Jun 1999 11:45:25 +0100 Organization: Kovach Computing Services Message-ID: Reply-To: WarrenK@kovcomp.co.uk NNTP-Posting-Host: kovcomp.demon.co.uk X-NNTP-Posting-Host: kovcomp.demon.co.uk:158.152.48.110 X-Trace: news.demon.co.uk 929011526 nnrp-02:9840 NO-IDENT kovcomp.demon.co.uk:158.152.48.110 X-Complaints-To: abuse@demon.net Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Virtual Access by Atlantic Coast PLC, http://www.soft-shop.com Lines: 42 Dear colleague, The latest update to MVSP, our multivariate stats package, is now available. The major new features in version 3.1 include: 1) The ability to assign individual cases to groups. The group names are then printed on output and dendrograms, and the groups are depicted on scatterplots as different symbols. 2) Three new coefficients - Bray Curtis, Modified Morisita and Baroni-Urbani Buser. 3) Excel 97 files can now be imported. 4) Several minor bugs have been fixed. This is a FREE upgrade for all owners of MVSP 3.0. To get this upgrade simply download the evaluation version from our web site (at the address below) and install it over your existing copy of MVSP. It will automatically pick up your registration information and be converted into the fully working version. For more information about MVSP and to download the trial version please visit our web site: http://www.kovcomp.co.uk/mvsp/ Note: If you have previously only used the trial version but wish to try out this new version you may contact us for an extension to the trial period. -- Dr. Warren L. Kovach Kovach Computing Services 85 Nant-y-Felin, Pentraeth, Isle of Anglesey Wales LL75 8UY U.K. Internet: WarrenK@kovcomp.co.uk WWW: http://www.kovcomp.co.uk/ Tel.(UK): 01248-450414, (Intl.): +44-1248-450414 Fax (UK): 0870-054-3180, (Intl.): +44-870-054-3180 From owner-software@net.bio.net Thu Jun 10 12:20:00 1999 Path: biosci!NHGRI.NIH.GOV!jfryan From: jfryan@NHGRI.NIH.GOV (Joe Ryan) Newsgroups: bionet.software Subject: Re: Need help with perl to encode/decode ASN.1 Date: 10 Jun 1999 06:20:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <19990610091426.B14876@nhgri.nih.gov> References: <19990609225014.15306.00002967@ng-cq1.aol.com> NNTP-Posting-Host: net.bio.net Ray, I have written a program which runs GENSCAN, FGENES, MZEF, GRAIL2, RepeatMasker, Sputnik and BLAST and prints the output as ASN.1. Which can then be viewed graphically using NCBI's Sequin Program. You are welcome to have a look at my code which is freely available at http://genome.nhgri.nih.gov/genemachine/ I also found readseq to be very helpful in the process of learning ASN.1. After converting a FASTA formatted sequence to ASN.1 using readseq, I was able to get an idea of the basic format. You may also want to have a look at SEALS (or contact the author) http://www.ncbi.nlm.nih.gov/Walker/SEALS/ I know that an ASN.1 perl module was in the works but am not sure on the status of this. Oh and the on-line docs for "The DDBJ/EMBL/GenBank Feature Table Definition" http://www.ncbi.nlm.nih.gov/collab/FT/index.html You may also consider XML for sequence records. There has been considerable work done in this area and there are many freely available parsers already available in several languages. See these URLs for more info... http://www.proteometrics.com/BIOML/ http://ala.vsms.nottingham.ac.uk/biodom/ http://bio.perl.org/Projects/XML/ Good Luck, Joe -- Joseph Ryan programmer National Human Genome Research Institute On Thu, Jun 10, 1999 at 02:50:14AM +0000, RjGrimaila wrote: > Does anyone have experience with perl to encode/decode ASN.1 formatted records? > ASN.1 looks ideal for complex sequence records. I'd like to extend existing > perl code to save ASN.1 objects to an Oracle database. I'm aware of > Convert::BER.pm, but haven't had a chance to RTFM. > > RAy > From owner-software@net.bio.net Thu Jun 10 14:10:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newspeer.monmouth.com!solomon.io.com!news.tamu.edu!not-for-mail From: Ing-Nang Wang Newsgroups: bionet.software Subject: pc WPerfect v9.0 to mac MS Office98 conversion? Date: Thu, 10 Jun 1999 09:42:48 -0500 Organization: Texas A&M University, College Station, Texas Lines: 15 Message-ID: <375FCEE8.BBC53609@unix.tamu.edu> Reply-To: inw0137@unix.tamu.edu NNTP-Posting-Host: cowboy.tamu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Date: 10 Jun 1999 14:40:39 GMT X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.3 IP32) Dear people: I am pulling my hairs out on this one. My boss has a pc Word Perfect v9.0 and I have a mac MS Office98. We are now working on a manuscript with a lot of symbols and Greek letters in it. We can't seem to be able to preserve the symbols and Greek letters during the conversion. First, is it even possible to convert between these two extremes? Second, if yes, where can I find it? We are just two innocent by-standers caught between these companies. Help us please!!! -- Ing-Nang Wang Dept. of Biochemistry and Biophysics Texas A&M University College Station, TX From owner-software@net.bio.net Thu Jun 10 18:20:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!news.maxwell.syr.edu!dispose.news.demon.net!demon!news.demon.co.uk!demon!fssc.demon.co.uk!not-for-mail From: "Herbert M Sauro" Newsgroups: bionet.software Subject: Announcement: WinSCAMP upgrade Date: Thu, 10 Jun 1999 20:09:12 +0100 Message-ID: <929042086.27222.0.nnrp-07.c2de3927@news.demon.co.uk> NNTP-Posting-Host: fssc.demon.co.uk X-NNTP-Posting-Host: fssc.demon.co.uk:194.222.57.39 X-Trace: news.demon.co.uk 929042086 nnrp-07:27222 NO-IDENT fssc.demon.co.uk:194.222.57.39 X-Complaints-To: abuse@demon.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Lines: 80 ANNOUNCEMENT June 1999 Metabolic Simulation and Control Analysis Software For those registered to use WinSCAMP there is an update to version 1.0 at: http://www.fssc.demon.co.uk/Biotech/biotech.htm or via my main page at: http://www.fssc.demon.co.uk The update is in the form of a patch zip file. To use this patch, unzip the file to get at the executable. Run the executable patch file. Once running you will need to give the path and name to the old version of WinSCAMP. Tip: if you copy the patch file to the same location as the old WinSCAMP you do not need to supply WinSCAMP's location. Finally you need to give the name of the new version, currently, new.exe. If you wish you can leave this name as it is and once the 'new.exe' is generated by the patch file, rename it to winscamp.exe. This patch upgrades WinSCAMP 1.0 to 1.1 IMPORTANT There are two other downloads available at the above site which registered users should also download. There is an update to the core SCAMP files, version 2.71 which are required for the new version of WinSCAMP. There is also an extra.zip file which contains amongst other files, a new and updated help file. This help file is in the new HtmlHelp format. Copy the files in extra.zip to the WinSCAMP directory and copy the files in SCAMP.zip to your SCAMP directory. What's new in version 1.1? There have been a number of significant changes: 1. Configurable syntax highlighting to the SCAMP script files. 2. Many more graphing options including export, preview and full graph style editing. 3. WinSCAMP can now find the enzyme database! 4. Changed size of editing area, moved options buttons to the preferences dialog box. 5. Many more options in the preferences dialog box. 6. Added a previous files reopen history menu. 7. New Help file, now in HtmlHelp format, you will need Internet Explorer 4 or Win98 installed on your system for this to work. There is a microsoft update at my web for thsoe who don't have the most recent help engine. 8. General bug fixes and tidying up. The next upgrade will concentrate on the core SCAMP files and the WinSCAMP scripting wizard. What is WinSCAMP? WinSCAMP is the windows 95/98 front-end to the metabolic simulation and control analysis package called SCAMP. SCAMP is based on a simple scripting language which is used to describe metabolic and chemical reaction schemes. WinSCAMP allows one to easily write and develop SCAMP script files, run the models and display the results as tables, 2D and 3D graphs. Although SCAMP is freeware, WinSCAMP is not. This is because it's development incurred real monetary expenditure. WinSCAMP can be registered for 30 US dollars. If there are any problems, questions etc. please get in touch! Enjoy Herbert Sauro -- Herbert M Sauro email: HSauro@fssc.demon.co.uk Telephone: Home: 0131 226 1342 Work: 0131 347 4445 ---------------------------------------------------------------------------- ------------- "He who cannot draw on 3000 years is living from hand to mouth" Goethe "Ah, but a man's reach should exceed his grasp, or what's a heaven for?" R Browning. From owner-software@net.bio.net Thu Jun 10 20:41:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!hammer.uoregon.edu!vixen.cso.uiuc.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: pc WPerfect v9.0 to mac MS Office98 conversion? Date: 10 Jun 1999 21:35:23 GMT Organization: Biology, Indiana University - Bloomington Lines: 14 Message-ID: <7jpb2r$5l7$1@flotsam.uits.indiana.edu> References: <375FCEE8.BBC53609@unix.tamu.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu Have you looked at current MacLink translators? - DataViz has made a business out of being a rosetta stone for the software industry -- they always keep up to date w/ word perfect and msword, other wordprocessors, graphics formats, spreadsheets, for mac and mswindows and some unix software. find at http://www.dataviz.com - Don -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Fri Jun 11 01:19:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.cwix.com!208.155.48.9!news.binc.net!nntp.chorus.net!news.itis.com!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Help with searching an oligonucleotide database Date: 11 Jun 1999 02:15:10 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 24 Sender: reguser@ebv.oncology.wisc.edu Message-ID: Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu User-Agent: slrn/0.9.5.6 (UNIX) Hello: I have a large number of oligonucleotide sequences available as as fasta format database. These oligos range in length from 15 nucleotides to about 100 nucleotides. I would like to search a larger sequence (3 - 5 kb) against this database -- so that I can identify all the oligos that lie in the large sequence, and use them as PCR primers or whatever. What publically available programs are suitable for this search? I have tried using Bill Pearson's fasta or ssearch programs, but they appear unsuitable (or I don't know what command line parameters to pass). Fasta/ssearch find both perfect and imperfect matches, while I would like to find perfect matches over the entire length of the oligonucleotide. Thanks, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research aiyar@ebv.oncology.wisc.edu From owner-software@net.bio.net Fri Jun 11 06:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news.idt.net!peerfeed.news.psi.net!uunet!ffx.uu.net!in5.uu.net!icx.net!not-for-mail From: "David B. Hedrick" Newsgroups: bionet.software Subject: Re: Measureing an area Date: Fri, 11 Jun 1999 02:51:41 -0400 Organization: Hedrick Services Lines: 61 Message-ID: <3760B1FC.175A@icx.net> References: <37578EA5.B739E5B2@Uni-MolGen.gwdg.de> Reply-To: davidbhedrick@icx.net NNTP-Posting-Host: pm14v.icx.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news3.icx.net 929084075 30491 207.51.10.86 (11 Jun 1999 06:54:35 GMT) X-Complaints-To: abuse@icx.net NNTP-Posting-Date: 11 Jun 1999 06:54:35 GMT X-Mailer: Mozilla 3.01C-KIT (Win95; U) Steffen: Wow. What software do you use? You could blow up the image, print it out, cut out the cricket wing cell, and weigh the piece of paper. Now, stop laughing, I'm serious. Do the same for something you took an EM of and that you know the area of to determine the scale. Cut out and weight 5 copies of the same image to determine the variation in your method. Maybe try different types of paper to find one that is constant. Regular lazer jet paper works fine and is cheap. If this cricket wing business is something you're going to do once and quit, this quick and dirty method might get you done quicker than something more computerized. Or, Visual basic (and almost all other programming languages) will let you determine the color of a pixel of a bitmap. You could use Corel Photo-Paint or Paint Shop Pro to simplify the image - 2 color only, and use the magic wand to copy the cell to a blank bitmap. Then a very simple program could count the colored pixels. You could even have it color each pixel as it is counted so you can see that it is working correctly. Or, when you increase the magnification of an image in Paint Shop Pro to the maximum, you can clearly see the individual pixels. You could count them yourself. Use a drawing tool with a color not used in your image to mark out each one as you count. Or, you could hire someone like, well, like me to do it for you. Have fun! > Hi, > > I want to measure the size of a cell on a crickets'wing. Therefore I use > an EM and save the picture as a bitmap. Has anyone an idea how to > measure an area in a bitmap-picture? It would be appreciable when there > would be a tool which can automatically select the wanted area - like > the magic wand mask tool of Corel Photo-Paint. > > Thanks > Steffen > > --------------------------------------------------------------- > > Name: sschmid2.vcf > Part 1.2 Type: text/x-vcard > Encoding: 7bit > Description: Card for Steffen Schmidt -- ~DBH Technical writing, literature search, and data analysis at the interface of chemistry and biology. davidbhedrick@icx.net David B. Hedrick P.O. Box 16082 Knoxville, TN 37996 From owner-software@net.bio.net Fri Jun 11 07:49:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software Subject: Re: Help with searching an oligonucleotide database Date: 11 Jun 1999 09:05:44 +0100 Organization: The Sanger Centre Message-ID: References: NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 929088298 15567 193.60.84.160 (11 Jun 1999 08:04:58 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 11 Jun 1999 08:04:58 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Lines: 26 aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) writes: > I have a large number of oligonucleotide sequences available as > as fasta format database. These oligos range in length from 15 > nucleotides to about 100 nucleotides. > > I would like to search a larger sequence (3 - 5 kb) against this > database -- so that I can identify all the oligos that lie in the > large sequence, and use them as PCR primers or whatever. > > What publically available programs are suitable for this search? There will are applications in EMBOSS that we can easily modify to do this. Sounds like a good idea - we will add it soon. EMBOSS is the European Molecular Biology Open Software Suite of sequence analysis programs. It is GPL (and LGPL) licensed and is currently available as a pre-beta release. The EMBOSS home page is http://www.sanger.ac.uk/Software/EMBOSS/ -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-software@net.bio.net Fri Jun 11 09:39:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!newsfeed.nacamar.de!serra.unipi.it!bigarea.area.ba.cnr.it!not-for-mail From: friard@molinette.unito.it (Olivier) Newsgroups: bionet.software Subject: Last version of FASTA Scan (3.2.4 for win95/98/NT4) Date: Fri, 11 Jun 1999 08:15:06 GMT Organization: CNR - Area di Ricerca - Bari,Italy Message-ID: <3760c2bf.346402881@news.ba.cnr.it> NNTP-Posting-Host: pcgen018.molinette.unito.it X-Newsreader: Forte Free Agent 1.11/32.235 Lines: 29 Hi, The last version of FASTA Scan (3.2.4 for win95/98/NT4) is freely downloadable at: http://pcgen018.molinette.unito.it/programs.html Some bugs were fixed and some options added: - FASTA Scan works with FASTA version 3.2t05 (May 12, 1999) of Pearson package - You can now select peptidic sequences from FASTA output with the cut-off option - You can now select all sequences that have an homology percent greater than an arbitrary value Comments, critics and suggestions are welcome at friard@molinette.unito.it Thank you for the attention Olivier Friard P.S. This page contains other small software (for Win95/98/NT4) for sequences analysis From owner-software@net.bio.net Fri Jun 11 16:23:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: guffanti@tigem.it (Alessandro Guffanti) Newsgroups: bionet.software Subject: Re: Re : EST clustering Date: Fri, 11 Jun 1999 17:17:26 GMT Organization: TIGEM Sender: aguffant@193.43.101.186 Message-ID: <376143a0.13182558@news.hgmp.mrc.ac.uk> References: <199905201257.OAA04130@joe.sb-roscoff> NNTP-Posting-Host: 193.43.101.186 X-Trace: niobium.hgmp.mrc.ac.uk 929121461 22387 193.43.101.186 (11 Jun 1999 17:17:41 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 11 Jun 1999 17:17:41 GMT X-Newsreader: Forte Free Agent 1.11/32.235 Lines: 25 Hi. I suggest using cap2 / cap3 software for EST assembly. The algorithm seems to be particularly fit for these tasks. The programs are available from X.Huang: huang@mtu.edu. An on-line version is available for testing at http://hercules.tigem.it/ASSEMBLY/assemble.html http://hercules.tigem.it/cgi-bin/uniestass.pl http://hercules.tigem.it/BLASTEXTRACT/estextract.html You will need a (quite powerful) UNIX workstation anyway. Best wishes, Alessandro Guffanti, TIGEM. >Tvenkatesh@synapticcorp.com wrote: >> >> Dear All >> I am looking for EST clustering software. I would appreciate any >> suggestions. >___________________________ From owner-software@net.bio.net Fri Jun 11 16:30:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: guffanti@tigem.it (Alessandro Guffanti) Newsgroups: bionet.software Subject: DNA Assembly for Windows Date: Fri, 11 Jun 1999 17:24:47 GMT Organization: TIGEM Lines: 11 Sender: aguffant@193.43.101.186 Message-ID: <376145fc.13786673@news.hgmp.mrc.ac.uk> Reply-To: guffanti@tigem.it NNTP-Posting-Host: 193.43.101.186 X-Trace: niobium.hgmp.mrc.ac.uk 929121893 22615 193.43.101.186 (11 Jun 1999 17:24:53 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 11 Jun 1999 17:24:53 GMT X-Newsreader: Forte Free Agent 1.11/32.235 Dear All: are you aware of some shareware / cheap program for doing Sequence Assembly on Windows PCs ? Thanks for any help, Alessandro G. - TIGEM From owner-software@net.bio.net Fri Jun 11 16:59:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!colt.net!newspeer.clara.net!news.clara.net!remarQ-uK!rQdQ!supernews.com!remarQ.com!remarQ69!news.remarQ.com!not-for-mail From: "John Choi" Newsgroups: bionet.software Subject: Crashed Hard Drives? Date: Fri, 11 Jun 1999 10:48:44 -0700 Organization: Encore Software, Inc. Message-ID: <929123533.139.33@news.remarQ.com> Reply-To: "John Choi" NNTP-Posting-Host: 207.171.0.59 NNTP-Posting-Date: Fri, 11 Jun 1999 17:52:13 GMT X-Trace: 929123533.139.33 L1LSDA6WP003BCFABC qube-02.us-ca.remarq.com X-Complaints-To: newsabuse@remarQ.com MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002B_01BEB3F7.F9FDB3C0" X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Lines: 278 This is a multi-part message in MIME format. ------=_NextPart_000_002B_01BEB3F7.F9FDB3C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hard Drive Mechanic Deluxe https://www.encoresoftware.com/hard_drive_mechanic_deluxe.asp?promo_id=3D= usenet&PRODUCT_ID=3D28 The Only Utility That Recovers From Crashes & Warns of Disasters! - New Advanced Rescue Algorithms: Recovers automatically from over 98% = of software crashes on drives of any size - S.M.A.R.T. 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------=_NextPart_000_002B_01BEB3F7.F9FDB3C0-- From owner-software@net.bio.net Fri Jun 11 21:32:00 1999 Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!dog.ee.lbl.gov!newsfeed.berkeley.edu!news.algonet.se!algonet!newsfeed.tli.de!newsfeed.nacamar.de!serra.unipi.it!newsfeed.cineca.it!newsfeed.nettuno.it!server-b.cs.interbusiness.it!news.tin.it!not-for-mail From: "tin" Newsgroups: ab.software.developers,alt.collecting.stamps.software,alt.comp.software.easter-eggs,alt.comp.software.financial.peachtree,alt.comp.software.njdm,alt.comp.software.tools,alt.med.software,alt.video.dvd.software,bionet.software,bionet.software.acedb Subject: office 2000 preview cercasi Followup-To: ab.software.developers, alt.collecting.stamps.software, alt.comp.software.easter-eggs, alt.comp.software.financial.peachtree, alt.comp.software.njdm, alt.comp.software.tools, alt.med.software, alt.video.dvd.software, bionet.software, bionet.software.acedb Date: Fri, 11 Jun 1999 23:45:21 +0100 Organization: TIN Lines: 53 Message-ID: <7js05p$m2j$7@nslave1.tin.it> NNTP-Posting-Host: a-pa6-21.tin.it Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_005A_01BEB464.78131B80" X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Xref: biosci bionet.software:23607 bionet.software.acedb:2400 This is a multi-part message in MIME format. ------=_NextPart_000_005A_01BEB464.78131B80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =E8 uscita una versione di office 2000 preview,in italiano, prima della = versione ufficiale, intorno al mese di marzo. ho urgente bisogno di reperire questo cd in originale prima del 18/6/99. Premetto che questo cd non ha nessun valore commerciale ma sono disposto = a pagarlo. Chiunque ne fosse in possesso o mi possa aiutare a reperilo, scriva a = gianfire@lexsystem.it grazie anticipatamente ------=_NextPart_000_005A_01BEB464.78131B80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
=E8 uscita una versione di office 2000 preview,in italiano, prima = della=20 versione ufficiale, intorno  al mese di marzo.
 
ho urgente bisogno di reperire questo cd in originale prima del=20 18/6/99.
 
Premetto che questo cd non ha nessun valore commerciale ma sono = disposto a=20 pagarlo.
 
Chiunque ne fosse in possesso o mi possa aiutare a reperilo, scriva = a gianfire@lexsystem.it
 
grazie anticipatamente
------=_NextPart_000_005A_01BEB464.78131B80-- From owner-software@net.bio.net Fri Jun 11 23:07:00 1999 Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!hammer.uoregon.edu!newshub.northeast.verio.net!hermes.visi.com!news-out.visi.com!news-kc-17.sprintlink.net!news-central.sprintlink.net!news-peer1.sprintlink.net!news-in-central.sprintlink.net!news.sprintlink.net!itssrv1.ucsf.edu!mac-daddy.ucsf.edu!user From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) Newsgroups: bionet.software Subject: Re: pc WPerfect v9.0 to mac MS Office98 conversion? Date: Fri, 11 Jun 1999 16:39:51 -0700 Organization: UCSF Lines: 23 Message-ID: References: <375FCEE8.BBC53609@unix.tamu.edu> NNTP-Posting-Host: mac-daddy.ucsf.edu In article <375FCEE8.BBC53609@unix.tamu.edu>, inw0137@unix.tamu.edu wrote: > I am pulling my hairs out on this one. My boss has a pc Word Perfect > v9.0 and I have a mac MS Office98. We are now working on a manuscript > with a lot of symbols and Greek letters in it. We can't seem to be able > to preserve the symbols and Greek letters during the conversion. First, > is it even possible to convert between these two extremes? Second, if > yes, where can I find it? We are just two innocent by-standers caught > between these companies. Help us please!!! When I've been doing a similar procedure the limitation appeared to be in Microsoft's import filter (they've never been particularly good). I gave up and used a series of macros to convert all problematic characters before transfer eg. I changed all mu characters to **mu**. After importing the document I reversed the substitutions using more macros. Where possible I've preferred using a commonly readable and stable format such as RFT. Bernard -- Bernard P. Murray, PhD Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA From owner-software@net.bio.net Sat Jun 12 05:31:00 1999 Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!news.sgi.com!nntp.primenet.com!newsfeed.berkeley.edu!news2.best.com!news3.best.com!nntp1.ba.best.com!not-for-mail From: "www.genomejobs.com" Newsgroups: bionet.software Subject: Bioinformatics Jobs at www.genomejobs.com Date: Fri, 11 Jun 1999 23:18:33 -0700 X-Newsreader: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Lines: 25 Message-ID: <3761fce9$0$207@nntp1.ba.best.com> NNTP-Posting-Host: dynamic28.pm08.sf3d.best.com X-Trace: nntp1.ba.best.com 929168617 207 209.24.235.220 Bioinformatics Jobs at www.genomejobs.com Genome Jobs is the central resource for employment in Genomics, Bioinformatics, Biotechnology and Biocomputing. 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From owner-software@net.bio.net Sat Jun 12 11:41:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!news.maxwell.syr.edu!news-peer.gip.net!news.gsl.net!gip.net!spring.edu.tw!feeder.seed.net.tw!news.seed.net.tw!not-for-mail From: "win98" Newsgroups: bionet.software Subject: Macromedia Flash 4.0 Full version download Date: 12 Jun 1999 12:35:26 GMT Organization: SEEDNet News Service Message-ID: <7jtk6e$rn$1@news.seed.net.tw> NNTP-Posting-Host: hw242-87.dialup.seed.net.tw X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Lines: 6 Macromedia Flash 4.0 9145KB Macromedia Director 7 ShockWave Internet Studio http://come.to/sogood From owner-software@net.bio.net Mon Jun 14 10:40:00 1999 Path: biosci!HYPERMART.NET!HYIP.Invest From: HYIP.Invest@HYPERMART.NET Newsgroups: bionet.software Subject: 50% Returns per MONTH! Date: 14 Jun 1999 04:39:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <199906141139.EAA10400@net.bio.net> NNTP-Posting-Host: net.bio.net ================================ Average Returns 50% Returns Per MONTH! ================================ And You're Insured Against ANY Financial Loss so There's NOTHING To Lose! Dear Investor, We've discovered a legitimate High Yield Investment Program that pays average returns of 50% per MONTH, and has never missed a payment in the 3 years it's existed! . . . Although the returns are CONSISTENTLY high, they are not "guaranteed" - however you ARE insured against ANY financial loss, so you've got absolutely nothing to lose! This program is where we put OUR money, however we are NOT the program organizers. For information regarding participation, sign and fax the below form to (530) 937 7885 OR (530) 937 7933. 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I agree that any information I receive is strictly confidential and for my own private viewing, and will not be passed onto any other party for any reason. _________________________________________ Signature _________________________________________ Printed Name From owner-software@net.bio.net Mon Jun 14 11:51:00 1999 Path: biosci!CECALC.ULA.VE!golfredo From: golfredo@CECALC.ULA.VE (Golfredo Catalani) Newsgroups: bionet.software Subject: dnamnl (phylip) Date: 14 Jun 1999 05:51:20 -0700 Organization: CeCalCULA Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: <3764FBC8.14F423F7@cecalc.ula.ve> NNTP-Posting-Host: net.bio.net --------------D523C2E185621D51D644B167 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi...!! I have a big trouble.... I compile phylip in linux & aix, but command line dnaml dont work succesfull, say ....can't read infile. -- Golfredo Catalani http://www.cecalc.ula.ve --------------D523C2E185621D51D644B167 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi...!!
I have a big trouble....
I compile phylip in linux & aix,
but command line dnaml
dont work succesfull,
say  ....can't read infile.
 
  
-- 
Golfredo Catalani
http://www.cecalc.ula.ve
  --------------D523C2E185621D51D644B167-- From owner-software@net.bio.net Mon Jun 14 12:35:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!logbridge.uoregon.edu!newspeer1.nac.net!news.maxwell.syr.edu!news-was.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: Steffen Schmidt Newsgroups: bionet.software Subject: Re: Measureing an area Date: Mon, 14 Jun 1999 12:39:15 +0200 Organization: GWDG, Goettingen Lines: 104 Message-ID: <3764DBD3.D310BE77@Uni-MolGen.gwdg.de> References: <37578EA5.B739E5B2@Uni-MolGen.gwdg.de> <3760B1FC.175A@icx.net> NNTP-Posting-Host: 134.76.70.66 Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------EDADB98CD30BF578F46BFEA4" X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en To: a.mueller@icrf.icnet.uk This is a multi-part message in MIME format. --------------EDADB98CD30BF578F46BFEA4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "David B. Hedrick" wrote: > Steffen: > > Wow. What software do you use? > > You could blow up the image, print it out, cut out the cricket wing > cell, and weigh the piece of paper. Now, stop laughing, I'm serious. > Do the same for something you took an EM of and that you know the area > of to determine the scale. Cut out and weight 5 copies of the same > image to determine the variation in your method. Maybe try different > types of paper to find one that is constant. Regular lazer jet paper > works fine and is cheap. If this cricket wing business is something > you're going to do once and quit, this quick and dirty method might get > you done quicker than something more computerized. > Thanks for that straight forward solution :-). At the moment I am simplifying the image in black and white. Then I measure with the pick-tool of Corel Photo-Paint the whole picture. The grey-value gives me a value of 0-255 which I then normalize to 100 %. With the help of the EM-scale I can determine the size of the wing. A friend of mine suggested to convert the picture into an ASCII-file with 'xv' (black-and-white) and then counting the black pixel by the command grep '255' datei | wc. > Or, Visual basic (and almost all other programming languages) will let > you determine the color of a pixel of a bitmap. You could use Corel > Photo-Paint or Paint Shop Pro to simplify the image - 2 color only, and > use the magic wand to copy the cell to a blank bitmap. Then a very > simple program could count the colored pixels. You could even have it > color each pixel as it is counted so you can see that it is working > correctly. > > Or, when you increase the magnification of an image in Paint Shop Pro > to the maximum, you can clearly see the individual pixels. You could > count them yourself. Use a drawing tool with a color not used in your > image to mark out each one as you count. > > Or, you could hire someone like, well, like me to do it for you. > > Have fun! > > > Hi, > > > > I want to measure the size of a cell on a crickets'wing. Therefore I use > > a