From owner-software@net.bio.net Fri Jan 01 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!diablo.theplanet.net!join.news.pipex.net!pipex!duke.telepac.pt!news.telepac.pt!not-for-mail From: "Henrique d'Aguiar" Newsgroups: bionet.software Subject: Can anybody give/sell me HIP HOP EJAY FULL VERSION? Date: Sat, 2 Jan 1999 15:54:07 -0100 Lines: 4 Message-ID: <76lite$fca$1@duke.telepac.pt> NNTP-Posting-Host: 194.65.220.249 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Can anybody give/sell me HIP HOP EJAY FULL VERSION? Please reply to flammabledance@yahoo.com From owner-software@net.bio.net Sat Jan 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!ptdnetP!newsgate.ptd.net!newsfeed00.btx.dtag.de!newsfeed01.btx.dtag.de!newsmm00.btx.dtag.de!news.btx.dtag.de!not-for-mail From: FJauch@t-online.de (Frank Jauch) Newsgroups: bionet.software Subject: queation... Date: Sun, 03 Jan 1999 14:04:08 +0100 Lines: 5 Message-ID: <368F6AC8.16D238CF@t-online.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news02.btx.dtag.de 915368617 22604 03641396944-0001 990103 13:03:37 X-Complaints-To: abuse@t-online.de X-Sender: 03641396944-0001@t-online.de X-Mailer: Mozilla 4.05 [de]C-DT (Win95; I) Hi.. does anybody know a ALIAS comparable cheap software for ordinary PC. A.ERK From owner-software@net.bio.net Sat Jan 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news-backup-west.sprintlink.net!news.sprintlink.net!itssrv1.ucsf.edu!macmac-2.ucsf.edu!user From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) Newsgroups: bionet.software Subject: Re: Can anybody give/sell me HIP HOP EJAY FULL VERSION? Date: Sat, 02 Jan 1999 18:13:30 -0700 Organization: University of California, San Francisco Lines: 26 Message-ID: References: <76lite$fca$1@duke.telepac.pt> NNTP-Posting-Host: macmac-2.ucsf.edu In article <76lite$fca$1@duke.telepac.pt>, "Henrique d'Aguiar" wrote: > Can anybody give/sell me HIP HOP EJAY FULL VERSION? > Please reply to flammabledance@yahoo.com Is HIP the HIP1 histidine permease from S.cerevisiae and HOP one of the meiosis genes? If so, you can grab it by PCR from the genome. Alternatively, if Hop is the hsp70/hsp90 binding protein and and Hip the hsc70 interacting protein you'll have to ask the people who cloned them if you want the full length version. Fascinating proteins... Amazingly, I don't think anyone's come up with a use for the abbreviation/acrony "EJAY" but I'm sure there's a gene lurking in the wings (probably the wings of drosophila). Bernard (and, yes, I know this is probably not what he was after) -- Bernard P. Murray, PhD Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA From owner-software@net.bio.net Sat Jan 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!ams.news.uu.net!uunet!in3.uu.net!news.ici.net!not-for-mail From: "Hilton Evans" Newsgroups: bionet.software Subject: Molecular Mechanics Date: Sat, 2 Jan 1999 20:24:40 -0500 Organization: ChemPen Software Lines: 7 Message-ID: <76mgm4$3p$1@bashir.ici.net> Reply-To: "Hilton Evans" NNTP-Posting-Host: d-gnaps-11.ici.net Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 http://home.ici.net/~hfevans/chempen3d.htm -- Hilton Evans ChemPen3D for Win95/NT From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!isdnet!pasteur.fr!ezili.sis.pasteur.fr!bortz From: bortzmeyer@pasteur.fr (Stephane Bortzmeyer) Newsgroups: bionet.software Subject: Re: BLAST 2.0 executables for Linux libc5 systems Date: 4 Jan 1999 11:19:03 GMT Organization: Institut Pasteur Lines: 27 Sender: bortz@ezili.sis.pasteur.fr (Stephane Bortzmeyer) Message-ID: <76q837$nfl$1@desdemone.pasteur.fr> References: NNTP-Posting-Host: ezili.sis.pasteur.fr X-Trace: desdemone.pasteur.fr 915448743 24053 157.99.60.56 (4 Jan 1999 11:19:03 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 4 Jan 1999 11:19:03 GMT To: aiyar@ebv.oncology.wisc.edu, letondal, bortzmeyer@debian.org X-Newsreader: xrn 9.01 In article , aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) writes: > For users Linux libc5 systems who need to perform BLAST searches of > locally indexed databases, I have made BLAST 2.0 libc5 executables > available for download from "http://ebv.oncology.wisc.edu/~aiyar" And for libc6 users (who are probably the vast majority), a Debian package of Blast is available: http://www.debian.org/Packages/unstable/misc/blast2.html It is dynamically linked so users of other NCBI-tools programs can share the huge code of the NCBI libraries. I prefer the package approach since it allows esay installation and removal, and consistency (all the documentation in /usr/doc, etc). For information about Debian, see: http://www.debian.org/ Users of other libc6 distribution (mostly RedHat) can use the "alien" program to install Debian packages: http://kitenet.net/programs/alien/ See more biology packages in: http://www.pasteur.fr/units/sis/debian/biology-en.html From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!194.125.133.14!news.indigo.ie!HEAnet!server5.netnews.ja.net!daresbury!not-for-mail From: Sangeeta Sawant Newsgroups: bionet.software Subject: looking for search utility using phi-psi data as query.... Date: 5 Jan 1999 10:15:01 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 30 Message-ID: <76son5$h1q$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk Original-To: bio-software@dl.ac.uk content-length: 1282 Return-Path: Hello everybody, I am looking for a free/shareware utility which: 1. accepts a query in the form of phi-psi dihedral angles of amino acid residues (sequence may or may not be specified), 2. can search a set of 3D structures of proteins for the given query, 3. can find the matches within a specified range of deviation of the dihedral angles and, 4. list the peptides of matching conformations from the structure data. If such a utility is available, I would be interested in using it. Any help would be welcome and appreciated. Thanks and best wishes for the new year! Sangeeta +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Mrs. Sangeeta Sawant + + Research Fellow email : sangeeta@bioinfo.ernet.in + + Bioinformatics Centre phone : +91-20-355039 + + University of Pune fax : +91-20-350087 + + Ganeshkhind + + Pune - 411007 + + India. + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 From: lisa_crawford@cmagroup.com Newsgroups: bionet.software Subject: JOB: Director of Engineering; Medical Instrumentation, R&D, Hardware, Software Date: 5 Jan 1999 14:55:06 GMT Organization: Career Marketing Associates Lines: 51 Message-ID: <76t94a$r0e$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.216 X-Trace: news1.rmi.net 915548106 27662 206.247.5.216 (5 Jan 1999 14:55:06 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 5 Jan 1999 14:55:06 GMT Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.gtei.net!news.ums.edu!haven.umd.edu!news.cs.jhu.edu!news4.his.com!news.lightlink.com!news-xfer.mccc.edu!news.maxwell.syr.edu!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail We would greatly appreciate your networking assistance on the following career opportunity. If you, or someone you know of meets the requirements please let us know. Southeast Michigan; Director of Engineering; Medical Instrumentation, R&D, Hardware, Software -Title: Director of Engineering -Location: SE Michigan -Full Time, Salaried, Excellent Benefits, Nice Bonus Plan (Solid Relocation Package) This professional will manage the R&D software and engineering groups. Responsible for the engineering design of new instrumentation systems which meet specification, quality, schedule and cost goals. Interface heavily with the instrument manufacturing and disposables development groups. Principal Duties and Responsibilities: Provide overall supervision of the R&D hardware and software engineering groups. Provide technical leadership as related to various internal and external issues. Responsible for the overall engineering design of new instrumentation systems. Assure that systems meet specifications and all quality, schedule and cost goals of development plans. Responsible for the manufacturability of all designs. Interface heavily with the instrument and disposables manufacturing groups. Manage the hiring and maintenance of engineering resources required to support product development program. Maintain an awareness of new technologies and identify those which might be applied to help achieve the short and long term goals. Minimum Skill and Knowledge Requirements or Equivalent Masters degree in engineering. Ten years of project management and R&D departmental management experience. Ability to analyze complex information relating to a broad spectrum of technical, market and general business situations. Must be knowledgeable of medical instrumentation, specifically clinical laboratory and patient monitoring applications. Please refer to JO# 7742RJS in your response. Thank You lisa_crawford@cmagroup.com Lisa Crawford Sr. Researcher & Associate Recruiter ljc@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!uunet!in3.uu.net!xmission!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!logbridge.uoregon.edu!news.fas.harvard.edu!not-for-mail From: "Toshinori Endo" Newsgroups: bionet.software Subject: Re: Algorithm for Restriction Enzyme Analysis Date: Mon, 4 Jan 1999 12:51:59 -0500 Organization: Harvard University, Cambridge, Massachusetts Lines: 10 Message-ID: <76quvg$jog$1@news.fas.harvard.edu> References: <76f0l4$jh$1@nnrp1.dejanews.com> NNTP-Posting-Host: xterm3.harvard.edu Mime-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 If you want to program with c or c++, you may want to use use regular expression library such as GNU rx or lex (lexical analyzer generator). Another choice is to use Perl. This would be much easier. If you don't know what regular expression is, please type 'man grep' on UNIX command line for explanation. Toshinori Endo From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!cnn.nas.nasa.gov!newsfeed.berkeley.edu!sunqbc.risq.qc.ca!newsflash.concordia.ca!canopus.cc.umanitoba.ca!not-for-mail From: Brian Fristensky Newsgroups: bionet.software Subject: Re: Algorithm for Restriction Enzyme Analysis Date: Mon, 04 Jan 1999 17:38:44 -0600 Organization: University of Manitoba Lines: 86 Message-ID: <36915104.143274EB@cc.umanitoba.ca> References: <76f0l4$jh$1@nnrp1.dejanews.com> NNTP-Posting-Host: brassica.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.06 [en] (X11; U; SunOS 5.5.1 sun4u) Gabor E. Tusnady wrote: > > Hello, > > >Hi All, > >I am in trouble. I am developing an algorithm for restriction enzyme analysis > >but it is taking too long. The reason is because there are so many degenerate > >bases in the DNA sequence and thus it takes very long to analyze for all of > >them considering the possible combiantions they make. All the more the > >recognition sequence also have degenerate bases. Is there anybody out there to > >help me optimize the algorithm? Yes, there is. So thanking in advance to all > >those who respond. > >Ravi Gupta. > >Research Scholar > > There is a little program, called restenzyme on the net: > http://www.enzim.hu/~tusi/restric/restenzyme.html > > It uses a very simple table: > > nwryhmksdacgt > ACGT n+++++++++++++ > AT w+++++++-++--+ > GA r+++-++++++-+- > CT y++-+++-++-+-+ > CAT h+++++++++++-+ > AC m++++++-++++-- > TG k+++++-+++--++ > CG s+-+++++++-++- > GAT d++++++++++-++ > A a+++-++--++--- > C c+--+++-+--+-- > G g+-+---+++--+- > T t++-++-+-+---+ > > so if you have a degenerated sequence and degenerated recognition site of > the restriction enzymes, this table shows whether they can be the same. > For example the sequence: ...acacnwk... > the rec. site: ...dynctyh... > characters from the table: ...+++++++... > Most of the time this will work, but what if there is a degenerate base in the query sequence? For example, if you have y in the query sequence, it should still match a y in the restriction site. In the FSAP package http://home.cc.umanitoba.ca/~psgendb/FSAP.html BACHREST and INTREST use Pascal sets to simplify ambiguity comparisons: (* Array NUCSET holds sets of nucleotides *) (* using the conventions of IUPAC-IUB *) NUCSET[A]:= [A];NUCSET[C]:= [C];NUCSET[G]:= [G];NUCSET[T]:= [T]; NUCSET[R]:= [A,G,R];NUCSET[Y]:= [C,T,Y];NUCSET[S]:= [C,G,S]; NUCSET[M]:= [A,C,M];NUCSET[K]:= [G,T,K];NUCSET[W]:= [A,T,W]; NUCSET[B]:= [C,G,T,B,Y,K,S];NUCSET[D]:= [A,G,T,W,R,D,K]; NUCSET[H]:= [A,C,T,M,Y,W,H];NUCSET[V]:= [A,C,G,M,R,S,V]; NUCSET[N]:= [A..N]; AMBIGUOUS:= NUCSET[N] - [A,C,G,T]; Since set operations are built into the language, this makes dealing with ambiguities quick and easy. For example, if SEQ[Sk] in PATTERN[Pj] then (*CHARACTER MATCHED*) decides if the sequence element Sk matches the restriction pattern element Pj. If I was writing it today, I'd probably implement the ambiguity relationships as Java classes, and then check to see whether a sequence element was an element of the class. =============================================================================== Brian Fristensky | Department of Plant Science | University of Manitoba | All kings is mostly rapscallions. Winnipeg, MB R3T 2N2 CANADA | frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Mark Twain (1835-1910) FAX: 204-261-5732 | http://home.cc.umanitoba.ca/~frist/ =============================================================================== From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!isdnet!fu-berlin.de!eravci.dialup.fu-berlin.DE!not-for-mail From: "MURAT ERAVCI" Newsgroups: bionet.software Subject: ImageMaster 2D Software Date: Mon, 4 Jan 1999 15:43:51 +0100 Organization: Freie Universitaet Berlin Lines: 9 Message-ID: <76qjta$ij0$1@fu-berlin.de> NNTP-Posting-Host: eravci.dialup.fu-berlin.de (130.133.237.57) Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Access: 16 17 18 X-Trace: fu-berlin.de 915460842 19040 (none) 130.133.237.57 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Who has got the ImageMaster 2D Software, or is already using it ? I would be very happy if you could contact me for further corrospondence. Thank You Murat Eravci My Email is eravci@zedat.fu-berlin.de From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!newsgate.netvigator.com!news.netvigator.com!usenet From: cathy168@yahoo.com Newsgroups: bionet.plants.education,bionet.software,bionet.software.acedb,bionet.software.srs,bionet.software.x-plor Subject: Successful business!Earn more $$$$$ Date: Thu, 07 Jan 1999 21:53:31 +0800 Organization: Netvigator Lines: 41 Message-ID: <3694BC5B.485445A@yahoo.com> NNTP-Posting-Host: hhtck002175.netvigator.com Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------487F57E49C6C6B962207EE37" X-Mailer: Mozilla 4.06 [en] (Win95; I) Xref: biosci bionet.plants.education:4496 bionet.software:22584 bionet.software.acedb:2100 bionet.software.srs:1323 bionet.software.x-plor:2229 This is a multi-part message in MIME format. --------------487F57E49C6C6B962207EE37 Content-Type: multipart/alternative; boundary="------------8E11FD86060A6ACA7CB72013" --------------8E11FD86060A6ACA7CB72013 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --------------8E11FD86060A6ACA7CB72013 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit   --------------8E11FD86060A6ACA7CB72013-- --------------487F57E49C6C6B962207EE37 Content-Type: text/plain; charset=us-ascii; name="international business opportunity-1.txt" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="international business opportunity-1.txt" International Business Opportunity We have an exceptional independent, international business opportunity supported by a fast track training system. Almost anyone can do it with time and effort. Learn from those that have achieved and follow their success track! Call now for details: (852) 82010112 Partick Kwok or e-mail to: cathy168@yahoo.com --------------487F57E49C6C6B962207EE37-- From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed1.telenordia.se!newsfeed.sunet.se!news01.sunet.se!news99.sunet.se!news.net.uni-c.dk!not-for-mail From: "Søren W. Rasmussen" Newsgroups: bionet.software Subject: Dnatools, revision 230 Date: Wed, 06 Jan 1999 13:22:39 +0100 Organization: UNI-C Lines: 16 Message-ID: <3693558F.E6A24779@crc.dk> NNTP-Posting-Host: 130.226.182.97 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.net.uni-c.dk 915625832 33576 (None) 130.226.182.97 X-Complaints-To: usenet@news.net.uni-c.dk X-Mailer: Mozilla 4.03 [en] (Win95; I) Version 5.1.230 of the DNATools sequencing software package is available now. Read more about functions and improvements at: http://www.crc.dk/phys/A01B04_dnatools.htm Regards Søren -- Dr. scient. Søren W. Rasmussen Carlsberg Laboratory, Department of Physiology 10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark Phone 45 3327 5230 / 45 3616 2259, Fax 45 3327 4766 E-mail swr@crc.dk, Homepage http://www.crc.dk/phys/ From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!cs.utexas.edu!news.unt.edu!news From: Chris Fields Newsgroups: bionet.software Subject: LINUX and modems Date: Wed, 06 Jan 1999 03:15:33 -0600 Organization: University of North Texas Lines: 21 Message-ID: <369329B5.CFF67659@jove.acs.unt.edu> Reply-To: "cjfields @jove.acs.unt.edu" NNTP-Posting-Host: remote20.server1.local.premium.dialup.unt.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) I am currently in the middle of installing RedHat LINUX on a new hard drive (Intel Pentium box). I plan on buying a new modem that will be cross-compatible with Windows (as much as I hate Windows, I can't abandon Genedoc and Prophet). I would like a modem preferrably with a high baud rate (>30 kbs). Does anybody with some experience on this have any suggestions? C. J. Fields Graduate Student, Dept. of Biological Sciences The University of North Texas Denton, TX email : cjfields@jove.acs.unt.edu \\\\\\\\\\\\\\\\\\\\oooooooooooooooo//////////////////// "Giving money and power to government is like giving whiskey and car keys to teenage boys" -P. J. O'Rourke "Join the military. Travel to exotic places, meet exciting people, then kill them" -Anonymous ////////////////////oooooooooooooooo\\\\\\\\\\\\\\\\\\\\ From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.wli.net!howland.erols.net!newscore.univie.ac.at!news.iif.hu!botond.enzim.hu!tusi From: "Gabor E. Tusnady" Newsgroups: bionet.software Subject: Re: Algorithm for Restriction Enzyme Analysis Date: Mon, 4 Jan 1999 17:49:46 +0100 Organization: IIF Lines: 53 Message-ID: References: <76f0l4$jh$1@nnrp1.dejanews.com> NNTP-Posting-Host: botond.enzim.hu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To: bioinfo@my-dejanews.com In-Reply-To: <76f0l4$jh$1@nnrp1.dejanews.com> Hello, >Hi All, >I am in trouble. I am developing an algorithm for restriction enzyme analysis >but it is taking too long. The reason is because there are so many degenerate >bases in the DNA sequence and thus it takes very long to analyze for all of >them considering the possible combiantions they make. All the more the >recognition sequence also have degenerate bases. Is there anybody out there to >help me optimize the algorithm? Yes, there is. So thanking in advance to all >those who respond. >Ravi Gupta. >Research Scholar There is a little program, called restenzyme on the net: http://www.enzim.hu/~tusi/restric/restenzyme.html It uses a very simple table: nwryhmksdacgt ACGT n+++++++++++++ AT w+++++++-++--+ GA r+++-++++++-+- CT y++-+++-++-+-+ CAT h+++++++++++-+ AC m++++++-++++-- TG k+++++-+++--++ CG s+-+++++++-++- GAT d++++++++++-++ A a+++-++--++--- C c+--+++-+--+-- G g+-+---+++--+- T t++-++-+-+---+ so if you have a degenerated sequence and degenerated recognition site of the restriction enzymes, this table shows whether they can be the same. For example the sequence: ...acacnwk... the rec. site: ...dynctyh... characters from the table: ...+++++++... thus the enzyme restricts this sequence, and you dont have to compare all the combinations, only get the correspondeng matrix elements. Best regards, Gabor E. Tusnady Institute of Enzymology www.enzim.hu/~ _/_/_/_/_/_/ _/ _/_/_/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/_/_/ _/_/_/ _/ @enzim.hu From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!newsfeed.berkeley.edu!remarQ73!supernews.com!remarQ69!not-for-mail From: Shahira Newsgroups: sci.image.processing,bionet.software Subject: Image Analysis Training Date: Tue, 05 Jan 1999 18:28:53 -0500 Organization: Posted via RemarQ, http://www.remarQ.com - Discussions start here! Lines: 56 Message-ID: <3692A035.CB48C8D4@mediacy.com> NNTP-Posting-Host: 209.183.197.221 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: 915579363 YWQRDLINAC5DDD1B7C usenet87.supernews.com X-Complaints-To: newsabuse@remarQ.com X-Mailer: Mozilla 4.06 [en] (Win98; U) Media Cybernetics will be offering a series of hands-on training classes on Image-Pro Plus and Optimas software. 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The course is designed for anyone involved in image acquisition, processing, and analysis. Whether you use Image-Pro Plus or not, this workshop will give you the knowledge you need to learn and understand imaging concepts and theories. For a listing of course descriptions, dates, and locations, visit http://www.mediacy.com/training.htm Seating is limited, so we encourage you to make plans today to attend. Shahira Hoffman Media Cybernetics 8484 Georgia Avenue Silver Spring, MD 20910 301-495-3305 x260 fax: 301-495-5964 mailto:shahira@mediacy.com From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!torn!onlink3.onlink.net!not-for-mail From: DARIN BOUCHER Newsgroups: bionet.software Subject: Y2K Date: Thu, 07 Jan 1999 15:18:06 -0500 Organization: Ontario Northland--ONLink Lines: 1 Message-ID: <3695167E.344B@onlink.net> NNTP-Posting-Host: kpkg1-11.onlink.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) Is Windows 3.11 compliant? From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 From: glarocque@cfl.forestry.ca (Guy Larocque) Newsgroups: bionet.software Subject: 99 ISEM meeting announcement & call for papers Date: Wed, 06 Jan 1999 17:09:08 -0500 Organization: Canadian Forest Service Lines: 163 Message-ID: NNTP-Posting-Host: CFLMACGL.CFL.FORESTRY.CA Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.4 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!news1.bellglobal.com!torn!webster.srv.gc.ca!news.NRCan.gc.ca!glarocque -------------------------------------------------------------------------- ANNOUNCEMENT AND CALL FOR PAPERS 1999 MEETING INTERNATIONAL SOCIETY FOR ECOLOGICAL MODELLING NORTH AMERICAN CHAPTER Spokane, Washington, U.S. 8-12 AUGUST 1999 -------------------------------------------------------------------------- The 1999 meeting of the North American Chapter of the International Society for Ecological Modelling (ISEM) will be held in Spokane, Washington, USA, 8-12 August 1999, in conjunction with the annual meeting of the Ecological Society of America (ESA). The meetings will take place at the Spokane's Opera House and Convention Center. The ISEM meeting will include workshops, symposia, contributed paper and poster sessions, business meeting and social event. Abstracts are invited for contributed papers, symposiums, workshops and poster session. Oral presentations will be limited to 20 minutes including 5 minutes for questions and discussion. Posters will be presented in a special session. Abstracts may be on any topic in systems ecology and ecological modelling, broadly defined. Abstracts, inclusive of citation and text, are to be no more than 230 words, and should be submitted electronically in ASCII format to: glarocque@cfl.forestry.ca before January 30, 1999. If possible, those who cannot submit electronically should submit an abstract on diskette in ASCII format. If necessary three (3) hard copies can be sent by regular (snail) mail to the Program Chair. Please adhere strictly to the following format: Abstracts should include a statement of objectives, brief description of methods used, concise presentation of results, and a summary of conclusions/inferences drawn. Avoid this type of statements "results will be discussed". Abstract information included with abstract must include: Author to contact Institution Complete mailing address (Street address, City, State, Country, zip code) Phone number E-mail address Name of person presenting the paper Preference for oral or poster presentation Affiliation with society - are you a member of ESA and/or ISEM Abstract format (see example below): CAPITALIZE all authors' names, state abbreviation, country. For the FIRST author, list the last name first, then first name, middle initial. For any other authors, type first name, initial last name. Place an ASTERISK by the last name of the person presenting the paper. Name of institution (but not department affiliation or street address). Where two or more authors have different addresses, place a superscript number after each author's name and a corresponding superscript before each author's address if necessary for clarity. Without skipping a line or moving to a new line, type the title of the presentation. Skip a line before beginning the text of the abstract. DO NOT INDENT any part of the abstract itself. The abstract should be a single paragraph. Symbols and Special Fonts Where necessary, bracket underlines, superscripts, subscripts, or Greek letters with the following symbols. We will search and replace with the appropriate text. Text Symbol to use: Example Underline underline before and after _Quercus rubra_ (Quercus rubra) the text to be underlined Superscript use an "up carat" before and ^2^ (2) after the text to be superscripted Subscript use the "circa" sign before and @4@ (4) after the text to be subscripted Greek letters spell out letter in capitals SIGMA, ALPHA, DELTA Example format: Author to contact: Mike Nelson Institution: Western Oregon State University Mailing address: Department of Biology, Western Oregon State University, Monmouth, OR 97328-2345 Phone Number: 541-555-5555 ext 1111 E-mail: nelsonm@biol.wosu.edu Presentor: Mike Nelson Preference: Poster Member of: ESA Example: NELSON^1^, M. K., J.L. SMITH^2^ and P.W. BRANT^3^. Western Oregon State University, Monmouth, OR, 97328, USA^1^, Portland State University, Portland, OR 97220^2^, and Evergreen College, Washington, WA, 99345^3^. The role of microbial community dynamics in grassland species composition. Species composition of grasses in coastal native grassland communities dominated by _Agropyron smithii_, was significantly correlated with changes in numbers of organisms in each functional group in the soil foodweb, and diversity of those functional groups. Correlation of grass species with ALPHA diversity of the nematode community showed the greatest..... (maximum 230 words) For more information, visit the ESA web site (http://esa.sdsc.edu/esa/) or the NA-ISEM web site (http://ecomod.tamu.edu/~ecomod/isem.html). Guy R. Larocque Program chair ********************************************** Guy Larocque, Ph.D. Research Scientist Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055, du P.E.P.S. P.O. Box 3800 Ste-Foy (Quebec) G1V 4C7 Canada Tel: (418) 648-5791 Fax: (418)648-5849 E-mail: glarocque@cfl.forestry.ca -- Guy Larocque, ing.f., Ph.D. Research Scientist - Chercheur scientifique Canadian Forest Service - Service canadien des forêts Laurentian Forestry Centre - Centre de Foresterie des Laurentides 1055 rue du P.E.P.S. P.O. Box 3800 Ste-Foy (Quebec) G1V 4C7 Tel: (418) 648-5791 Fax: (418)648-5849 E-mail: glarocque@cfl.forestry.ca From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!howland.erols.net!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: josephryan@yahoo.com Newsgroups: bionet.software Subject: Announce: netgrail.plx 0.03 Date: Wed, 06 Jan 1999 21:42:41 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 49 Message-ID: <770lch$8qc$1@nnrp1.dejanews.com> NNTP-Posting-Host: 168.143.5.76 X-Article-Creation-Date: Wed Jan 06 21:42:41 1999 GMT X-Http-User-Agent: Mozilla/4.05 [en] (X11; I; Linux 2.0.35 i586) X-Http-Proxy: 1.0 x13.dejanews.com:80 (Squid/1.1.22) for client 168.143.5.76 netgrail.plx 0.03 Alpha ===================== netgrail.plx is a simple client used to create valid requests to the GRAIL server. This utility does not support some of the more complex queries that Grail allows, most notably, netgrail.plx does not allow for parameters to be sent to options. It is great, however, for basic queries from the command line and automating sequence annotation. netgrail.plx was tested on a variety of unix flavors as well as windows. DOWNLOAD: netgrail.plx is available from ftp://ftp.nhgri.nih.gov/pub/software/netgrail/ DEPENDANCIES: Perl For a quick overview of Grail: http://www.hgmp.mrc.ac.uk/GenomeWeb/nuc-geneid.html#7 Public Domain Notice ===================== This software/database is "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties for the United States Government and thus cannot be copyrighted. This software/database is freely available to the public for use without a copyright notice. Restrictions cannot be placed on its present or future use. Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the National Human Genome Research Institute (NHGRI) and the U.S. Government does not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI and the U.S. Government disclaims all warranties as to performance, merchantability or fitness for any particular purpose. Enjoy! -- Joseph Ryan Programmer National Human Genome research Institute -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!newspeer.monmouth.com!news.he.net!news.pagesat.net!news.itis.com!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: LINUX and modems Date: 6 Jan 1999 13:31:11 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 22 Sender: reguser@ebv.oncology.wisc.edu Message-ID: References: <369329B5.CFF67659@jove.acs.unt.edu> Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu User-Agent: slrn/0.9.5.4 (UNIX) On Wed, 06 Jan 1999 03:15:33 -0600, Chris Fields (cjfields@jove.acs.unt.edu) wrote: >I am currently in the middle of installing RedHat LINUX on a new hard >drive (Intel Pentium box). I plan on buying a new modem that will be >cross-compatible with Windows (as much as I hate Windows, I can't >abandon Genedoc and Prophet). I would like a modem preferrably with a >high baud rate (>30 kbs). Does anybody with some experience on this >have any suggestions? I have a SupraExpress 56e external modem that supports both K56flex and V.90. It works well with Linux. I've been using it for over a year. Many PCI internal modems sold currently are "winmodems" -- that require Win 3.1/95/98/NT and will not work with Linux. Later, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research http://aiyar.cjb.net From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!newspeer.monmouth.com!oleane!jussieu.fr!univ-lyon1.fr!univ-aix.fr!not-for-mail From: Eric Blanc Newsgroups: bionet.software Subject: Re: Help Date: Wed, 06 Jan 1999 08:08:44 +0100 Organization: Universite de la Mediterranee Aix en Provence Lines: 26 Message-ID: <36930BFC.2781@afmb.cnrs-mrs.fr> References: <76ult5$pre$1@smtp2.nbnet.nb.ca> NNTP-Posting-Host: afmb83.cnrs-mrs.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.univ-aix.fr 915605040 5177 194.214.212.83 (6 Jan 1999 06:44:00 GMT) X-Complaints-To: usenet@news.univ-aix.fr NNTP-Posting-Date: 6 Jan 1999 06:44:00 GMT To: jake X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) jake wrote: > > Could someone tell me where I can download a copy of winzip at no cost > > Greatly appreciated > > Clint > > Please send a response to clintmac@nbnet.nb.ca > > -- Try: http://www.winsite.com http://www.filez.com http://tucows.belgium.eu.net/ -- _________________________________________________________________ Eric Blanc NMR Group Postdoc., Webmaster for AFMB WWW: http://afmb.cnrs-mrs.fr/~eric/ AFMB CNRS-UPR 9039 Email: eric@afmb.cnrs-mrs.fr 31 Ch J. Aiguier Fax: 33-4-91-16-45-36 13402 Marseille CEDEX 20 Phone: 33-4-91-16-45-29 FRANCE From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!news1.bellglobal.com!torn!smtp2.nbnet.nb.ca!not-for-mail From: "jake" Newsgroups: bionet.software Subject: Help Date: Tue, 5 Jan 1999 23:35:48 -0400 Organization: NBTel Internet Lines: 12 Message-ID: <76ult5$pre$1@smtp2.nbnet.nb.ca> NNTP-Posting-Host: mctnts04c61.nbnet.nb.ca X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Could someone tell me where I can download a copy of winzip at no cost Greatly appreciated Clint Please send a response to clintmac@nbnet.nb.ca -- From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!uninett.no!news.net.uni-c.dk!news.daimi.au.dk!not-for-mail From: Kasper Dreyer Newsgroups: bionet.software Subject: Please recommend a DNAanalysis software package? Date: Thu, 07 Jan 1999 15:50:07 +0100 Organization: Aarhus Universitet Lines: 20 Message-ID: <3694C941.43228F0@imsb.au.dk> NNTP-Posting-Host: imsb-94.imsb.au.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Trace: xinwen.daimi.au.dk 915720578 4546 255.255.255.255 (7 Jan 1999 14:49:38 GMT) X-Complaints-To: news@daimi.au.dk NNTP-Posting-Date: 7 Jan 1999 14:49:38 GMT X-Mailer: Mozilla 4.06 (Macintosh; I; PPC) Hi Our group is about to invest in a DNA/protein analysis software package and would like to hear you opinion on any programs you have worked with. We are considering the Lasergene99, mainly because we have used Lasergene so far. We primarily use it for keeping track of our constructs, for designing subclonings, for primer design and some simple protein features. Import of ABI sequencing files would be an advantage. Thank you very much - after all - it is a jungle out there. Yours sincerely Cand. scient Kasper Dreyer Institute of Molecular and Structural Biology Aarhus University Denmark From owner-software@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!cs.utexas.edu!news.unt.edu!news From: Chris Fields Newsgroups: bionet.software Subject: LINUX and Modems Date: Wed, 06 Jan 1999 03:30:37 -0600 Organization: University of North Texas Lines: 24 Message-ID: <36932D3D.B9DC9255@jove.acs.unt.edu> Reply-To: "cjfields @jove.acs.unt.edu" NNTP-Posting-Host: remote20.server1.local.premium.dialup.unt.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) Sorry if this double-posted: I am currently installing RedHat LINUX onto a Pentium (a separate hard drive from the Windows OS). I plan on buying a modem that would be cross compatible with both operating systems. I would give up Windows completely, but I am dependent on Genedoc and a few other Windows-only programs. Does anybody have any suggestions? I would like (if possible) to get something with a high baud rate (pref. >30 kbs). -- C. J. Fields Graduate Student, Dept. of Biological Sciences The University of North Texas Denton, TX email : cjfields@jove.acs.unt.edu \\\\\\\\\\\\\\\\\\\\oooooooooooooooo//////////////////// "Giving money and power to government is like giving whiskey and car keys to teenage boys" -P. J. O'Rourke "Join the military. Travel to exotic places, meet exciting people, then kill them" -Anonymous ////////////////////oooooooooooooooo\\\\\\\\\\\\\\\\\\\\ From owner-software@net.bio.net Fri Jan 08 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.32.206.55!newsfeed.berkeley.edu!netnews.com!isdnet!pasteur.fr!jussieu.fr!moka.ccr.jussieu.fr!not-for-mail From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN) Newsgroups: bionet.software Subject: 3D motif Date: 8 Jan 1999 11:41:29 +0100 Organization: CCR - Universites Paris VI/VII - Paris - France Lines: 12 Message-ID: <774ncp$34q8@moka.ccr.jussieu.fr> NNTP-Posting-Host: moka.ccr.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Subj.: 3D motif I have written a spatial alignment programme which reads the cartesian coordinates of two molecules and outputs the maximal common 3D-motif. (algorithm described in: Comput.Chem.1998,22[6],pp.463-465). The computing time is roughly proportional to the product n1*n2 of the number of atoms of the two molecules. Free copies are loadable by ftp on various computers, including DEC-alpha (VMS and unix), IBM RS6000 serie (and SP2), CRAY Y and J90, SGI O2 (and any mips1 to mips4 SGI). Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, ESA 7086) ptitjean@ccr.jussieu.fr From owner-software@net.bio.net Fri Jan 08 22:00:00 1999 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!EU.net!newsfeed.Austria.EU.net!Austria.EU.net!not-for-mail From: "Jack Dalton" Newsgroups: bionet.software Subject: kann mir jemand LEXIROM leihen (Innsbruck)? Date: Fri, 8 Jan 1999 20:10:42 +0100 Organization: Customer of EUnet Austria Lines: 13 Message-ID: <775lhv$lq8$2@fleetstreet.Austria.EU.net> NNTP-Posting-Host: dialup161.innsbruck.at.eu.net X-Trace: fleetstreet.Austria.EU.net 915822975 22344 193.80.64.161 (8 Jan 1999 19:16:15 GMT) X-Complaints-To: abuse@Austria.EU.net NNTP-Posting-Date: 8 Jan 1999 19:16:15 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Hallo! Kann mir jemand in INNSBRUCK die Software LEXI-ROM von Microsoft (Vollversion) bitte für 1 oder 2 Tage leihen? Ich würde mir nämlich gerne die Vollversion auf CDROM brennen. Als Gegenleistung kann ich andere Software herleihen (WIN98 ...)leihen. THANKYA Jack From owner-software@net.bio.net Fri Jan 08 22:00:00 1999 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.cwix.com!203.97.37.7!newsfeed.clear.net.nz!ihug.co.nz!not-for-mail From: "John" Newsgroups: bionet.software,hk.comp.software Subject: Software World Date: 8 Jan 1999 07:38:19 GMT Organization: The Internet Group Ltd Lines: 5 Message-ID: <01be3ad9$6addfd40$2edad5cf@sun-xia.ihug.co.nz> NNTP-Posting-Host: p46-max1.akl.ihug.co.nz X-Newsreader: Microsoft Internet News 4.70.1155 Hi, my friends. Please go to: http://members.tripod.com/~best_web/software.html You can find a lot of useful software. From owner-software@net.bio.net Fri Jan 08 22:00:00 1999 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: boracay@hotmail.com Newsgroups: bionet.software Subject: Resume biomedical engineer - FL Date: Fri, 08 Jan 1999 21:26:00 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 39 Message-ID: <775t55$qls$1@nnrp1.dejanews.com> NNTP-Posting-Host: 209.86.186.76 X-Article-Creation-Date: Fri Jan 08 21:26:00 1999 GMT X-Http-User-Agent: Mozilla/4.07 (Macintosh; I; PPC, Nav) X-Http-Proxy: 1.0 x4.dejanews.com:80 (Squid/1.1.22) for client 209.86.186.76 BIOMEDICAL ENGINEER Email: boracay@hotmail.com Location: Miami, FL EMPLOYMENT SOUGHT I am a biomedical engineer whose skills are ideal to assist those involved in research. I have ten years of experience doing this at the National Institutes of Health in Bethesda, MD. I am willing to work with you on a specific project, contract, short term or long term basis. Ideal work might allow working as a consultant, developer and research collaborator via your on site location or remote. ONSITE AVIALABILITY: S. Florida, worldwide via remote EMPLOYMENT KEYWORDS Biomedical engineering, research, electrical engineering, instrumentation, data acquisition, densitometry, video, imaging, quantitative measurements, Fortran, Pascal, LabView, C, assembly, microprocessors, NIH Image, Apple Macintosh, PC, ophthalmic, cardiovascular and neurological systems and instrumentation, computer automation, computer control, web, www, computer communications. EDUCATION Undergraduate: Catholic University of America, Washington, DC 20064. Degree: Bachelor of Electrical Engineering - 1989 with emphasis in Biomedical and Computer Engineering Graduate: Johns Hopkins University/ Whiting School of Engineering, Baltimore, MD, 21218. Degree: Master of Science in Electrical Engineering - 1992 -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Fri Jan 08 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: lisa_crawford@cmagroup.com Newsgroups: bionet.software Subject: Job: Upstate NY; Program Manager; Hardware, Software, OEM Date: 8 Jan 1999 21:21:05 GMT Organization: Career Marketing Associates Lines: 37 Message-ID: <775ss1$ma0$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.216 X-Trace: news1.rmi.net 915830465 22848 206.247.5.216 (8 Jan 1999 21:21:05 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 8 Jan 1999 21:21:05 GMT Upstate NY; Program Manager; Hardware, Software, OEM -Title: Program Manager -Location: Upstate NY -Salaried, Full-Time, Solid Benefits, Bonus Plan (Relocation Assistance Available) Retained Search. Initial selection deadline 1/15/99 This is a very key position and will involve leading and managing a ( revenue is $15M/yr; development budget $1.2M) hardware/software core technology product development and release cycle. Project management of a project with significant software content is essential. Will be a key member of the senior management team and report directly to the VP R&D/Development. Will have responsibility for approximately 10 software developers and 5 EE/ME's. Experience in an ISO 9000 environment important. Client is on its way to CMM levels 2&3. This is a process focused organization that will need a strong tactical leader that is aggressive and clear in setting goals and direction. Must be able to go toe to toe with strong marketing personalitie. Will play a role in establishing client's common architecture. Position will involve a great deal of of Marketing, OEM and Customer interface (30-35%) so ability to nail down requirements and specifications a must. About 50% of time will be spent in a refiner/maximizer/ actionizer role driving a well defined, mature engineering/software process. Approximately 15-20% time will be spent on performance appraisals and admin aspects of program. Please refer to JO# 7697RJS in your response. lisa_crawford@cmagroup.com Lisa Crawford Sr. Researcher & Associate Recruiter ljc@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Fri Jan 08 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!logbridge.uoregon.edu!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: Tree from pairwise comparisons? Date: 9 Jan 1999 07:56:49 GMT Organization: University of Washington Genetics Lines: 12 Message-ID: <777241$fda$1@nntp4.u.washington.edu> References: <36967DD1.41C6@zdna.micro.umass.edu> NNTP-Posting-Host: evolution.genetics.washington.edu X-Trace: nntp4.u.washington.edu 915868609 15786 (None) 140.142.17.40 X-Complaints-To: help@cac.washington.edu Summary: distance matrix methods In article <36967DD1.41C6@zdna.micro.umass.edu>, ciufo@zdna.micro.umass.edu wrote: > >Does anyone know of a software program which can construct >a tree from pairwise comparison data? Um, any phylogeny program that can use matrices of distances? There are perhaps 40 such. -- Joe Felsenstein joe@genetics.washington.edu Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA From owner-software@net.bio.net Fri Jan 08 22:00:00 1999 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!uunet!in1.uu.net!news.shore.net!newsfeed.xcom.net!woodstock.news.demon.net!demon!howland.erols.net!news.net.uni-c.dk!news.daimi.au.dk!not-for-mail From: Bent.Nagstrup@kba.sks.aau.dk (Bent Nagstrup) Newsgroups: bionet.software Subject: Re: LINUX and modems Date: 9 Jan 1999 12:27:18 GMT Organization: Research Unit for Molecular Medicine, Aarhus University Hospital, Denmark Message-ID: <777hv6$7m9$1@xinwen.daimi.au.dk> References: <369329B5.CFF67659@jove.acs.unt.edu> NNTP-Posting-Host: kba.sks.aau.dk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Trace: xinwen.daimi.au.dk 915884838 7881 255.255.255.255 (9 Jan 1999 12:27:18 GMT) X-Complaints-To: news@daimi.au.dk NNTP-Posting-Date: 9 Jan 1999 12:27:18 GMT X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) Lines: 17 In article , aiyar@ebv.oncology.wisc.edu says... >Many PCI internal modems sold currently are "winmodems" -- that >require Win 3.1/95/98/NT and will not work with Linux. Also, I'd always recommend an external modem, because if the darn thing hangs it's quicker to just switch off the modem and try again, instead of your whole computer... -- Bent Nagstrup M.Sc. Research Unit for Molecular Biology, Aarhus University ---- A bus station is where the bus stops, A train station is where the train stops, On my desk I have a workstation.... From owner-software@net.bio.net Fri Jan 08 22:00:00 1999 Message-ID: <36967DD1.41C6@zdna.micro.umass.edu> Date: Fri, 08 Jan 1999 16:51:13 -0500 From: "ciufo@zdna.micro.umass.edu" Organization: University of Massachusetts, Microbiology X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Tree from pairwise comparisons? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 128.119.49.24 X-Trace: 8 Jan 1999 16:56:23 -0500, 128.119.49.24 Lines: 10 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!128.119.166.60!umass.edu!oit.umass.edu!128.119.49.24 Hello all, Does anyone know of a software program which can construct a tree from pairwise comparison data? Any information will be appreciated. Thanks, Stacy Ciufo From owner-software@net.bio.net Fri Jan 08 22:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!news-nyc.telia.net!masternews.telia.net!news-stkh.gip.net!news.gsl.net!gip.net!newsfeed1.funet.fi!news.utu.fi!not-for-mail From: Amir Snapir Newsgroups: bionet.software Subject: Re: Please recommend a DNAanalysis software package? Date: Fri, 08 Jan 1999 10:02:43 +0200 Organization: University of Turku Lines: 39 Message-ID: <3695BBA3.6334E2E1@utu.fi> References: <3694C941.43228F0@imsb.au.dk> NNTP-Posting-Host: crst3.far.utu.fi Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.utu.fi 915782566 588 130.232.97.14 (8 Jan 1999 08:02:46 GMT) X-Complaints-To: usenet@news.utu.fi NNTP-Posting-Date: 8 Jan 1999 08:02:46 GMT X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en Have a look at Prophet ( http://www.utu.fi/med/farmakol/prophet/ ). It's not bug free and it has little tendency to crash (somehow even when it crashes you don't loose your work) but fairly powerful and... it's free! Kasper Dreyer wrote: > Hi > > Our group is about to invest in a DNA/protein analysis software package and > would like to hear you opinion on any programs you have worked with. > We are considering the Lasergene99, mainly because we have used Lasergene so > far. > We primarily use it for keeping track of our constructs, for designing > subclonings, for primer design and some simple protein features. Import of ABI > sequencing files would be an advantage. > > Thank you very much - after all - it is a jungle out there. > > Yours sincerely > > Cand. scient > Kasper Dreyer > Institute of Molecular and Structural Biology > Aarhus University > Denmark -- ___________________________________ Amir Snapir Department of Clinical Pharmacology University of Turku - Finland mailto:snapir@utu.fi Tel: +358-2-333 7220 ___________________________________ From owner-software@net.bio.net Sat Jan 09 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!news.tele2.nl!newsgate.cistron.nl!het.net!news.worldonline.nl!not-for-mail From: "J. Huges" Newsgroups: bionet.software Subject: Y2K Tools Date: Sun, 10 Jan 1999 21:42:22 +0100 Organization: WorldOnline News server Lines: 12 Message-ID: <77b3c5$o1k$1@news.worldonline.nl> NNTP-Posting-Host: vp236-128.worldonline.nl X-Trace: news.worldonline.nl 916000965 24628 195.241.236.128 (10 Jan 1999 20:42:45 GMT) X-Complaints-To: abuse@worldonline.nl NNTP-Posting-Date: 10 Jan 1999 20:42:45 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 L.S. Can anyone inform me which tools are most powerful to track Y2K problems on (Windows) PC's? I heard there are some pretty good packages around; how do they work? Please mail to jhuges@worldonline.nl Many thanks! From owner-software@net.bio.net Sat Jan 09 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news.sprintlink.net!cs.utexas.edu!news.unt.edu!news From: Chris Fields Newsgroups: bionet.software Subject: Re: LINUX and modems Date: Sun, 10 Jan 1999 15:57:40 -0600 Organization: University of North Texas Lines: 23 Message-ID: <36992254.6707ED7D@jove.acs.unt.edu> References: <369329B5.CFF67659@jove.acs.unt.edu> <777hv6$7m9$1@xinwen.daimi.au.dk> Reply-To: "cjfields @jove.acs.unt.edu" NNTP-Posting-Host: remote57.server1.local.premium.dialup.unt.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 Just wanted to respond back with good news. I took the advice of staying away from "Winmodems" and purchased a Zoom 56K. Works wonderfully on Win95, WinNT, and LINUX (had to disable the Plug-n-Play for NT, but I always thought that PnP was cheating anyway). Thanks for the responses. They helped wonderfully. Now, if they would only port Genedoc to LINUX (hint hint... ) -- C. J. Fields Graduate Student, Dept. of Biological Sciences The University of North Texas Denton, TX email : cjfields@jove.acs.unt.edu \\\\\\\\\\\\\\\\\\\\oooooooooooooooo//////////////////// "Giving money and power to government is like giving whiskey and car keys to teenage boys" -P. J. O'Rourke "Join the military. Travel to exotic places, meet exciting people, then kill them" -Anonymous ////////////////////oooooooooooooooo\\\\\\\\\\\\\\\\\\\\ From owner-software@net.bio.net Sun Jan 10 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: lisa_crawford@cmagroup.com Newsgroups: bionet.software Subject: JOB: Director of Engineering; Medical Instrumentation, R&D, Hardware, Software Date: 11 Jan 1999 17:56:34 GMT Organization: Career Marketing Associates Lines: 46 Message-ID: <77de0i$3fc$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.216 X-Trace: news1.rmi.net 916077394 3564 206.247.5.216 (11 Jan 1999 17:56:34 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 11 Jan 1999 17:56:34 GMT Southeast Michigan; Director of Engineering; Medical Instrumentation, R&D, Hardware, Software -Title: Director of Engineering -Location: SE Michigan -Full Time, Salaried, Excellent Benefits, Nice Bonus Plan (Solid Relocation Package) This professional will manage the R&D software and engineering groups. Responsible for the engineering design of new instrumentation systems which meet specification, quality, schedule and cost goals. Interface heavily with the instrument manufacturing and disposables development groups. Principal Duties and Responsibilities: Provide overall supervision of the R&D hardware and software engineering groups. Provide technical leadership as related to various internal and external issues. Responsible for the overall engineering design of new instrumentation systems. Assure that systems meet specifications and all quality, schedule and cost goals of development plans. Responsible for the manufacturability of all designs. Interface heavily with the instrument and disposables manufacturing groups. Manage the hiring and maintenance of engineering resources required to support product development program. Maintain an awareness of new technologies and identify those which might be applied to help achieve the short and long term goals. Minimum Skill and Knowledge Requirements or Equivalent Masters degree in engineering. Ten years of project management and R&D departmental management experience. Ability to analyze complex information relating to a broad spectrum of technical, market and general business situations. Must be knowledgeable of medical instrumentation, specifically clinical laboratory and patient monitoring applications. Please refer to JO# 7742RJS in your response. lisa_crawford@cmagroup.com Lisa Crawford Sr. Researcher & Associate Recruiter ljc@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Sun Jan 10 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: lisa_crawford@cmagroup.com Newsgroups: bionet.software Subject: JOB: Florida; Staff Scientist/Engineer; Electrophysiology, Algorithms, Signal Processing Date: 11 Jan 1999 17:59:55 GMT Organization: Career Marketing Associates Lines: 31 Message-ID: <77de6r$3gs$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.216 X-Trace: news1.rmi.net 916077595 3612 206.247.5.216 (11 Jan 1999 17:59:55 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 11 Jan 1999 17:59:55 GMT Florida; Staff Scientist/Engineer; Electrophysiology, Algorithms, Signal Processing -Title: Staff Scientist/Engineer -Location: Florida -Salaried, Full-Time, Excellent Benefits (Excellent Relocation Package Available) This professional will be actively involved in leading advanced cardiovascular EP product development. Ideal candidate will have PhD/MS in either Biomedical Engineering, CS, EE, Physics or Computer Science with a solid clinical appreciation of cardiovascular electrophysiology. Technical skills should include: Advanced algorithms, signal processing and software development. Experience with Windows NT, Win32 and C/C++ skills would be a plus. Must bring in EP expertise either through engineering, or through the science route; preferably both. Ideal candidate will have industrial, or have collaborated in an industrial product development effort. Technical leadership/mentoring experience would also be helpful. Please refer to JO# 7216RJS in your response. lisa_crawford@cmagroup.com Lisa Crawford Sr. Researcher & Associate Recruiter ljc@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Sun Jan 10 22:00:00 1999 Path: biosci!ms.bd.com!Bill_A_Nussbaumer From: Bill_A_Nussbaumer@ms.bd.com Newsgroups: bionet.software Subject: Less tedious procedure for aligning nt sequences Date: 11 Jan 1999 06:10:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <852566F6.004C4F76.00@7crmta_md.ms.bd.com> NNTP-Posting-Host: net.bio.net Bill A Nussbaumer@BDX 01/11/99 09:02 AM Hi all, I'm in the process of a 10 day evaluation of the Lasergene DNA analysis software package. I'm currently trying to use megalign to determine consensus between a gene among numerous organism strains. Performing an Entrez search yielded 27 different sequences of interest. I exported these sequences into a single text file and then cut and paste them into their own individual text files. Following this I used the EditSeq module of the software to convert the sequence files into *.seq files one at a time. At this point it was easy to enter the files into Meg-align but the first steps of this procedure are quite tedious. With only 27 sequences it's bearable (it took about 30 - 45 minutes), but in the future if I have hundreds of genes this method would be unacceptable. Does anyone have any suggestions on how to more quickly get sequences into alignment either using DNAStar or otherwise. I am fairly new to this aspect of DNA analysis and am not completely familiar with all of the Blast and Entrez tools as of yet. Thanks for any suggestions, Bill Nussbaumer From owner-software@net.bio.net Sun Jan 10 22:00:00 1999 Path: biosci!SENTURY.COM!Directmarketing From: Directmarketing@SENTURY.COM Newsgroups: bionet.software Subject: FREE! Download! URL Submission Software! Over 700+ Search Engines & Links (Growing Monthly!) Date: 11 Jan 1999 04:44:37 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 68 Sender: daemon@net.bio.net Distribution: world Message-ID: <199901111244.EAA02623@net.bio.net> Reply-To: Sentury@marketing.com NNTP-Posting-Host: net.bio.net Dear bio-soft * * * ADVERTISE! * * * YOUR BUSINESS OR RESUME ALL OVER THE WORLD! 700+ Search Engines & Links and Growing Monthly! This is a great opportunity for Students, Businesses and Employment Seekers!, Promote your Resume, Business or Personal Website for world wide exposure! Make it easier for yourself and get the advantage? Do you have a Website? Why not submit to as many search engines as possible? 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Thank you in advance for your time and consideration. __________________________________ From owner-software@net.bio.net Sun Jan 10 22:00:00 1999 Path: biosci!ms.bd.com!Bill_A_Nussbaumer From: Bill_A_Nussbaumer@ms.bd.com Newsgroups: bionet.software Subject: Re: Less tedious procedure for aligning nt sequences Date: 11 Jan 1999 10:40:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 62 Sender: daemon@net.bio.net Distribution: world Message-ID: <852566F6.00657CF2.00@7crmta_md.ms.bd.com> NNTP-Posting-Host: net.bio.net Bill A Nussbaumer@BDX 01/11/99 01:32 PM That's a good point, thanks. My primary computer is a PC so windows compatible software is my preference. However, I have access to several Macs in the lab so I wont rule out helpful suggestions not available on Wintel machines. If any Unix software is required the only way I could use it would be to download bash (or something similar). Bill Nussbaumer todd@andrew2.stanford.edu on 01/11/99 12:44:51 PM To: Bill A Nussbaumer/BALT/BDX cc: Subject: Re: Less tedious procedure for aligning nt sequences In article <852566F6.004C4F76.00@7crmta_md.ms.bd.com>, Bill_A_Nussbaumer@ms.bd.com wrote: >Does anyone have any >suggestions on how to more quickly get sequences into alignment either >using DNAStar or otherwise. I am fairly new to this aspect of DNA analysis >and am not completely familiar with all of the Blast and Entrez tools as of >yet. > You don't say what kind of computer you're using, and since DNAStar is available for both Windows and Macs, you may get a bunch of irrelevent responses. But probably the easiest way to do what you want is to get the freely available ClustalW or ClustalX, which is available for both Macs and PCs. This program does multiple alignments and provides consensus sequences and exports a number of different file formats that can be used by other programs. It reads FASTA format files, which I believe is an option that Entrez gives you. You can get ClustalX from: ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ There's a bit of a description at: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html Good luck, Todd -- Dr. Todd Richmond Carnegie Institution of Washington 260 Panama Street Email: todd@andrew.stanford.edu Stanford, CA 94305 Homepage: http://cellwall.stanford.edu From owner-software@net.bio.net Sun Jan 10 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!sunqbc.risq.qc.ca!carnaval.risq.qc.ca!not-for-mail From: no.junk.casgrain@ere.umontreal.ca (Philippe Casgrain) Newsgroups: bionet.software Subject: Re: Tree from pairwise comparisons? Message-ID: References: <36967DD1.41C6@zdna.micro.umass.edu> Organization: Université de Montréal X-Newsreader: MT-NewsWatcher 2.4.1 Lines: 14 Date: Mon, 11 Jan 1999 16:46:09 GMT NNTP-Posting-Host: 132.204.120.97 X-Trace: carnaval.risq.qc.ca 916073169 132.204.120.97 (Mon, 11 Jan 1999 11:46:09 EDT) NNTP-Posting-Date: Mon, 11 Jan 1999 11:46:09 EDT wrote: > Does anyone know of a software program which can construct > a tree from pairwise comparison data? There are several of them; you can check out T-Rex (Mac and Win 95/98/NT) at the following address: Philippe -- Remove no.junk to reply via email. Sorry about that. From owner-software@net.bio.net Sun Jan 10 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!ics1a.sanger.ac.uk!birney From: Ewan Birney Newsgroups: bionet.software Subject: Wise2.1.16 Beta release Date: Mon, 11 Jan 1999 19:51:36 +0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 44 Message-ID: NNTP-Posting-Host: ics1a.sanger.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 916084298 26368 193.60.84.184 (11 Jan 1999 19:51:38 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 11 Jan 1999 19:51:38 GMT Wise2 beta release The latest release of Wise2 (Wise2.1.16b) has been released. Wise2 is a package which specialises in the comparison of DNA sequence at the level of it conceptual translation. More information can be found at http://www.sanger.ac.uk/Software/Wise2/ The latest release has the following highlights: - Can be built with pthreads support for SMP boxes - Contains a script (halfwise) to sensibly compare large DNA sequences against Pfam - More output formats and better defaults in the programs Some of the functionality of the Wise2 package is available through Web forms. For example, to compare a DNA sequence against Pfam, the following form can be used to submit your DNA sequence http://www.sanger.ac.uk/Software/Wise2/pfamsearch.shtml The package contains a number of other resources which are more experimental including - an alpha release of the DNA block aligner (dba) program - The generalised gap penalities algorithm implemented. - A working C and Perl API to the functionality in the package. The package contains extensive documentation which is bundled in the distribution and available on the web site. For more information, use the above web sites, or email Ewan Birney at Ewan Birney http://www.sanger.ac.uk/Users/birney/ From owner-software@net.bio.net Mon Jan 11 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newsfeed1.swip.net!swipnet!news.tele2.nl!newsfeed.wirehub.nl!surfnet.nl!news.leidenuniv.nl!not-for-mail From: Marc van der Linde Newsgroups: bionet.software Subject: Re: Y2K Date: Tue, 12 Jan 1999 14:11:39 -0600 Organization: Leiden University Lines: 8 Message-ID: <369BAC7B.F191233A@rulsfb.leidenuniv.nl> References: <3695167E.344B@onlink.net> Reply-To: linde@rulsfb.leidenuniv.nl NNTP-Posting-Host: rul88f.leidenuniv.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: highway.leidenuniv.nl 916146688 6984 132.229.50.188 (12 Jan 1999 13:11:28 GMT) X-Complaints-To: usenet@highway.leidenuniv.nl NNTP-Posting-Date: 12 Jan 1999 13:11:28 GMT To: DARIN BOUCHER X-Mailer: Mozilla 4.05 [en] (Win95; I) NO! There is a bug in the filemanager and some other minor bugs, see further on www.mirosoft.com Marc DARIN BOUCHER wrote: > > Is Windows 3.11 compliant? From owner-software@net.bio.net Mon Jan 11 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newspeer.monmouth.com!rill.news.pipex.net!pipex!main.de.uu.net!news-reader.dortmund.de.uu.net!not-for-mail From: Kay Hofmann Newsgroups: bionet.software Subject: treetool under Linux? Date: Tue, 12 Jan 1999 09:09:20 +0000 Organization: MEMOREC Lines: 25 Message-ID: <369B1140.D0AB1E65@memorec.com> NNTP-Posting-Host: 194.175.75.210 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.32 i686) X-Accept-Language: en Has anybody managed to compile a working version of treetool under Linux? GDE works fine, there are executables out there and compilation under current Red Hat system also works without too much trouble. Treetool, however, is a different story. I did not find precompiled executables. The compilation was not so easy, after some hacking I got a running version that crashes whenever I try to save or print something. (A real try-out version, apparently) Any ideas? Many thanks in advance, Kay Hofmann =========================================================== Kay Hofmann, PhD Tel: +49 (221) 950 4814 Bioinformatics Group FAX: +49 (221) 950 4848 MEMOREC Stoffel GmbH Stoeckheimer Weg 1 D50829 Koeln/Germany E-mail: Kay.Hofmann@memorec.com From owner-software@net.bio.net Mon Jan 11 22:00:00 1999 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!news.maxwell.syr.edu!newspeer.monmouth.com!news.gate.net!not-for-mail From: "TDC" Newsgroups: bionet.software Subject: software for your websight, check it out Date: Tue, 12 Jan 1999 10:51:20 -0500 Organization: CyberGate, Inc. Lines: 4 Message-ID: <77freq$a5e$1@news.gate.net> NNTP-Posting-Host: ws4.datachan.com X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 www.objecttiger.com computer software for the office worker gamer for website development From owner-software@net.bio.net Mon Jan 11 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!ams.uu.net!ffx.uu.net!in5.uu.net!news.worldbank.org!not-for-mail From: Darren Dorkin Newsgroups: bionet.software Subject: Biology CD-Rom: College Level Intro Course Date: Mon, 11 Jan 1999 14:45:53 -0500 Organization: worldbank.org Lines: 10 Message-ID: <369A54F1.3E29@worldbank.org> NNTP-Posting-Host: pn750807.worldbank.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.02 (WinNT; I) I am interested in an excellent Biology CD-Rom that covers what would be considered a Freshman College level introductory biology course. Most CD-Roms I found focussed on specific areas of biology, as opposed to a thorough overview. Please email me directly with any suggestions. Thank you. ddorkin@worldbank.org From owner-software@net.bio.net Mon Jan 11 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.tli.de!unlisys!news.snafu.de!cs.tu-berlin.de!zrz.TU-Berlin.DE!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: Carsten Jacobi Newsgroups: bionet.software Subject: phrapview installation? Date: Tue, 12 Jan 1999 18:26:43 +0100 Organization: GWDG, Goettingen Lines: 21 Message-ID: <369B85D3.38CED840@gwdg.de> NNTP-Posting-Host: 134.76.70.111 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 Hi, I'm trying to install phrapview on our machine (a SUN under solaris 2.6). As far as I can see all other programms (phred/phrap/consed) are running only phrapview refuses to work :( What version of perl, Tk, Tcl and which modules do I have to install? And where can I get it? Thanks Carsten -------------------------------------------------------------------------------------------------------------------------- Dr. Carsten Jacobi Goettingen Genomics Laboratory Institute of Microbiology and Genetics Grisebachstrasse 8 D-37077 Goettingen From owner-software@net.bio.net Mon Jan 11 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newspeer1.nac.net!netnews.com!newsfeed.gamma.ru!Gamma.RU!news1.spb.su!news.RUNNet.ru!news.rnd.runnet.ru!not-for-mail From: "Vladimir V.Vasilchenko" Newsgroups: bionet.software Subject: Online Tutorial for Windows 95 applications programming with FORTRAN Date: 12 Jan 1999 17:51:26 GMT Organization: *** Lines: 5 Message-ID: <01be3e5d$ca2733c0$e8f8d0c3@vvv.gis.rnd.runnet.ru> NNTP-Posting-Host: vvv.gis.rnd.runnet.ru X-Trace: oberon.rnd.runnet.ru 916163486 13806 195.208.248.232 (12 Jan 1999 17:51:26 GMT) X-Complaints-To: usenet@oberon.rnd.runnet.ru NNTP-Posting-Date: 12 Jan 1999 17:51:26 GMT X-Newsreader: Microsoft Internet News 4.70.1155 Online Tutorial for Windows 95 applications programming with FORTRAN (http://www.gis.rnd.runnet.ru/team/clubs/FClub.html ) was updated... Vladimir V.Vasilchenko From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!SUNM.SHCNC.AC.CN!xietao From: xietao@SUNM.SHCNC.AC.CN (xietao) Newsgroups: bionet.software Subject: Help! Software to extract motif from alignment produced by CLUSTAL W. Date: 13 Jan 1999 00:36:45 -0800 Organization: SIBC Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <199901130832.QAA27602@sunm.shcnc.ac.cn> Reply-To: xietao@sunm.shcnc.ac.cn NNTP-Posting-Host: net.bio.net Daer All: Could somebody tell me a free software(PC or UNIX) which is good at extracting motifs from sequence alignment produced by CLUSTAL W? Thanks! Tao Xie (Sam) 99/1/13 ----------------------------------------------------- Xie Tao Bioinformatics & Protein Engineering Lab. Shanghai Institute of Biochemistry, Academia, Sinica P. O. BOX 33# 320# Yue Yang Road, Shanghai, P. R. China, 200031 Telephone: (86)-(21)-64374430-255 Fax:(86)-(21)-64338357 E-mail: xietao@sunm.shcnc.ac.cn Web-Page: http://202.127.24.111/xietao/ ----------------------------------------------------- From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!isdnet!pasteur.fr!ezili.sis.pasteur.fr!bortz From: bortzmeyer@pasteur.fr (Stephane Bortzmeyer) Newsgroups: bionet.software Subject: Re: Please recommend a DNAanalysis software package? Date: 13 Jan 1999 09:58:36 GMT Organization: Institut Pasteur Lines: 9 Sender: bortz@ezili.sis.pasteur.fr (Stephane Bortzmeyer) Message-ID: <77hqoc$2hv$1@desdemone.pasteur.fr> References: <3694C941.43228F0@imsb.au.dk> <3695BBA3.6334E2E1@utu.fi> NNTP-Posting-Host: ezili.sis.pasteur.fr X-Trace: desdemone.pasteur.fr 916221516 2623 157.99.60.56 (13 Jan 1999 09:58:36 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 13 Jan 1999 09:58:36 GMT To: Amir Snapir X-Newsreader: xrn 9.01 In article <3695BBA3.6334E2E1@utu.fi>, Amir Snapir writes: > Have a look at Prophet ( http://www.utu.fi/med/farmakol/prophet/ ). It's not bug > free and it has little tendency to crash (somehow even when it crashes you don't > loose your work) but fairly powerful and... it's free! "Free" as in "free beer" (you pay nothing) but not as in "free speech". I don't find the sources? Apparently, it runs only on MS-Windows? From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Message-ID: <369CE166.6FAB12E8@doelz.com> Date: Wed, 13 Jan 1999 19:09:42 +0100 From: Reinhard Doelz Organization: Verlag Ute Doelz X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 Subject: Re: Help! Software to extract motif from alignment produced by CLUSTAL W. References: <199901130832.QAA27602@sunm.shcnc.ac.cn> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Newsgroups: bionet.software Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-peer.gip.net!news.gsl.net!gip.net!portc01.blue.aol.com!arl-news-svc-4.compuserve.com!news-master.compuserve.com!nntp-nih2naab.compuserve.com Lines: 20 Hi, clustalw can write GCG's MSF format, which is in turn recognized by many software packages (including GCG's if you have access to a licensed copy :-) ) You might try to use SEALS, which is free software, released into the public domain. (http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html) I haven't tried it myself, though. regards Reinhard xietao wrote: > > Daer All: > > Could somebody tell me a free software(PC or UNIX) which is good > > at extracting motifs from sequence alignment produced by CLUSTAL W? > From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: craffi@my-dejanews.com Newsgroups: bionet.software Subject: wu-blast executables on 4-way PentiumII Linux systems? Date: Wed, 13 Jan 1999 18:33:06 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 24 Message-ID: <77iot1$537$1@nnrp1.dejanews.com> NNTP-Posting-Host: 199.93.107.66 X-Article-Creation-Date: Wed Jan 13 18:33:06 1999 GMT X-Http-User-Agent: Mozilla/4.5 [en] (WinNT; U) X-Http-Proxy: 1.0 x4.dejanews.com:80 (Squid/1.1.22) for client 199.93.107.66 I followed the earlier thread regarding blast performance on Linux systems with interest, I'd also be greatly interested in any pointers, URL's or comments concerning experiences with the Wash-U blast distribution and how it runs and performs on Linux systems. Primarily I use wu-blast on AlphaServer 4100 and 8400 systems, I'm interested in seeing how the benchmarks from these systems stack up against say one of the 450MHZ 4-way PII Xenon Linux compute servers that VA Research is offering. It would be interesting to see how a Linux box with 2GB memory does on a cost vs. performance ratio when compared to the Alpha's. I'll summarize any responses and if I get my hands on a VA Research system I'll report my experiences. Regards, Chris Dagdigian cdagdigian@genetics.com -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!remarQ73!supernews.com!news.he.net!news.pagesat.net!news.itis.com!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: Please recommend a DNAanalysis software package? Date: 13 Jan 1999 15:49:06 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 43 Sender: reguser@ebv.oncology.wisc.edu Message-ID: References: <3694C941.43228F0@imsb.au.dk> <3695BBA3.6334E2E1@utu.fi> <77hqoc$2hv$1@desdemone.pasteur.fr> Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu User-Agent: slrn/0.9.5.4 (UNIX) On 13 Jan 1999 09:58:36 GMT, Stephane Bortzmeyer (bortzmeyer@pasteur.fr) wrote: >In article <3695BBA3.6334E2E1@utu.fi>, > Amir Snapir writes: >> Have a look at Prophet ( http://www.utu.fi/med/farmakol/prophet/ ). It's not bug >> free and it has little tendency to crash (somehow even when it crashes you don't >> loose your work) but fairly powerful and... it's free! > >"Free" as in "free beer" (you pay nothing) but not as in "free speech". >I don't find the sources? Apparently, it runs only on MS-Windows? Hello Stephane, You are correct; Prophet is free as in "free beer". My recollection is that the home site "www-prophet.bbn.com" had versions for some unices available -- notably Solaris/SPARC, but not Linux on any platform. One of their programmers / website caretaker had stated on this newsgroup that: a) a Linux version was not available because the widget-set they used on Solaris and Windows were not available for Linux (it wasn't Motif, or Qt -- I cannot remember the name). b) that sources were not available because they were too large to download I responded to him on point "b", offering to send him a blank tape, or the archival space and bandwidth that others might download it, and was then informed that their contract with NIH prevented them from distributing the source. That's unfortunate because most programs developed at NCBI itself appear to be distributed as source (the NCBI toolkit is a prominent example), which facilitates porting applications to many many more platforms than can be done by a single group of programmers. Not to mention the intellectual advantages of open-source software. Sorry for the proselytizing -- I firmly believe, as I am sure you do, that scientific software would greatly benefit from being open-source. Cheers, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research http://aiyar.cjb.net From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news.sprintlink.net!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: josephryan@yahoo.com Newsgroups: bionet.software Subject: Re: treetool under Linux? Date: Wed, 13 Jan 1999 14:29:25 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 38 Message-ID: <77iajp$ng3$1@nnrp1.dejanews.com> References: <369B1140.D0AB1E65@memorec.com> NNTP-Posting-Host: 165.112.61.34 X-Article-Creation-Date: Wed Jan 13 14:29:25 1999 GMT X-Http-User-Agent: Mozilla/4.08 [en] (X11; U; Linux 2.0.36 i586; Nav) X-Http-Proxy: 1.0 x6.dejanews.com:80 (Squid/1.1.22) for client 165.112.61.34 You might wanna check... SAL (Scientific Applications on Linux) http://www.llp.fu-berlin.de/lsoft/index.shtml Molecular Linux http://evolution.bmc.uu.se/~thomas/mol_linux/ In article <369B1140.D0AB1E65@memorec.com>, Kay Hofmann wrote: > Has anybody managed to compile a working version of treetool > under Linux? > > GDE works fine, there are executables out there and compilation > under current Red Hat system also works without too much trouble. > > Treetool, however, is a different story. I did not find precompiled > executables. The compilation was not so easy, after some hacking > I got a running version that crashes whenever I try to save > or print something. (A real try-out version, apparently) > > Any ideas? > > Many thanks in advance, > > Kay Hofmann > > =========================================================== > Kay Hofmann, PhD Tel: +49 (221) 950 4814 > Bioinformatics Group FAX: +49 (221) 950 4848 > MEMOREC Stoffel GmbH > Stoeckheimer Weg 1 > D50829 Koeln/Germany E-mail: Kay.Hofmann@memorec.com > -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 From: "Download" Newsgroups: alt.collecting.stamps.software,alt.comp.software.easter-eggs,alt.comp.software.financial.peachtree,alt.comp.software.tools,alt.fan.dean-stark.software.tester,alt.med.software,alt.video.dvd.software,bionet.software,bionet.software.acedb,bionet.sof Subject: DOWNLOAD PIX FROM THE NEWS WITH AN ONLY CLICK Date: Thu, 14 Jan 1999 12:09:33 +0100 Organization: - Lines: 8 Message-ID: <77hv4k$3gi$1@lola.ctv.es> NNTP-Posting-Host: infon624.jet.es X-Trace: lola.ctv.es 916226004 3602 195.55.158.112 (13 Jan 1999 11:13:24 GMT) X-Complaints-To: usenet@lola.ctv.es NNTP-Posting-Date: 13 Jan 1999 11:13:24 GMT X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Path: biosci!news.ic.sunysb.edu!news-nysernet-16.sprintlink.net!news-east1.sprintlink.net!news-peer-europe.sprintlink.net!news.sprintlink.net!Sprint!newsfeed1.swip.net!swipnet!masternews.telia.net!News.Amsterdam.UnisourceCS!newsfeed.mad.ttd.net!newsfeed.bcn.ttd.net!lola!lola.ctv.es!not-for-mail Xref: biosci bionet.software:22622 bionet.software.acedb:2102 Download thousands of pix from thew news with an only click. FREE SOFTWARE http://www.lanzadera.com/pix4u/ .. . From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!rill.news.pipex.net!pipex!ams.uu.net!ffx.uu.net!in2.uu.net!news1-gui.server.ntli.net!news-feed.ntli.net!news5-gui.server.ntli.net!news-feed.ntli.net!server4.netnews.ja.net!is.bbsrc.ac.uk!Andy.Law From: Andy.Law@bbsrc.ac.uk (Andy Law) Newsgroups: bionet.software Subject: Pedigree Drawing Source Code? Date: Wed, 13 Jan 1999 11:31:39 +0000 Organization: Roslin Institute Lines: 17 Message-ID: NNTP-Posting-Host: pc1076.ri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.4 I need to draw some complex pedigrees along with some associated information (genotypings) through a cgi-based interface. I particularly like the IGD/X-Ped diagrams which separate out multiple instances of the same sire or dam for separate families but labels them in a consistent way to show that there are other entries. Is there anything freely available that I can use a starting point to achieve this, or am I on my own with it? I'm not bothered about source code language - any old thing will do. Much thanks in advance of any help you all may be able to provide. Later Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!YAHOO.COM!pin4733 From: pin4733@YAHOO.COM Newsgroups: bionet.software Subject: ..your web site Date: 13 Jan 1999 15:48:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 76 Sender: daemon@net.bio.net Distribution: world Message-ID: <199901132347.PAA17043@net.bio.net> NNTP-Posting-Host: net.bio.net We'll Submit Your Site To Over 900 Search Engines, Directories, & Indices For A "One Time Cost" Of Only $ 39.95 *** 100% Money Back Guarantee *** *** Immediately Increase Your Sites Exposure *** For Less Than 4 Cents Each We Will Submit Your Web Site To Over 900 Of The Net's Hottest Search Engines, Directories & Indices. If your site isn't listed in the Search Engines, how can people find you to buy your products or services? 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From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!HORUSGHN.COM!hzhang From: hzhang@HORUSGHN.COM (Hong Zhang) Newsgroups: bionet.software Subject: iHo(TM) Announcement Date: 13 Jan 1999 13:10:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: <369D09EA.943403A9@horusghn.com> Reply-To: hzhang@horusghn.com NNTP-Posting-Host: net.bio.net --------------543CE9F0B04B64BD293439A9 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Re: Free Membership in iHoTM: A Neural Network Experimentation Engine Dear Doctor, iHoNet.com is Horus Global HealthNet's new neural network research experimentation site (visit: www.iHoNet.com). iHoTM is a free, web-based neural network training tool designed to help researchers explore the concept and use of neural networks. iHoTM is designed to facilitate data analysis work using multiple inputs/biomarkers. If you have any questions or would like more information about custom-designed neural networks, email me at info@horusghn.com. Sincerely, Dr. H. Zhang Vice President, Chief Information Officer Horus Global HealthNet --------------543CE9F0B04B64BD293439A9 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Re: Free Membership in iHoTM:  A Neural Network Experimentation Engine

Dear Doctor,

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iHoTM is a free, web-based neural network training tool designed to help researchers explore the concept and use of neural networks.  iHoTM is designed to facilitate data analysis work using multiple inputs/biomarkers.

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Dr. H. Zhang
Vice President, Chief Information Officer
Horus Global HealthNet
  --------------543CE9F0B04B64BD293439A9-- From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!easynet-fr!not-for-mail From: philimar@easynet.fr (Philippe Marquis) Newsgroups: bionet.software Subject: New free software Date: Wed, 13 Jan 1999 21:01:21 GMT Organization: [Posted via] Easynet France Lines: 35 Message-ID: <369d0930.4771612@news.easynet.fr> NNTP-Posting-Host: pop-metz-8.pops.easynet.fr X-Trace: buggy.easynet.fr 916261352 7677 195.114.93.8 (13 Jan 1999 21:02:32 GMT) X-Complaints-To: abuse@easynet.fr NNTP-Posting-Date: 13 Jan 1999 21:02:32 GMT X-Newsreader: Forte Free Agent 1.11/32.235 --------------------------------------------------------- Release of GRAPHPAP version 3.00 Unlimited and entirely free program for Windows 95/98/NT4 Download : http://perso.easynet.fr/~philimar/ --------------------------------------------------------- "Graph Paper Printer" is an application designed to print custom graph paper in any size and colours. Numerous options are available through dropdown lists : - Cartesian, polar, triangular diagrams. - Linear scales (metric, imperial, customizable). - Non-linear scales (logarithmic, quadratic, gaussian). - Music paper. - Mercator grids. GRAPHPAP is a must-have. The former version, already rewarded five stars by Ziff-Davis Net, has been acclaimed by a large range of users: - Scientists, engineers, researchers. - Teachers, students, schoolboys. - Navigators, geographers. - Musicians, composers. - Quilt, patchwork. - Architects, draftsmen, circuit-boards designers. - Modelists, hobbyists, radio-amateurs ... Dr Philippe Marquis Biologiste des hopitaux METZ-FRANCE philimar@easynet.fr From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.nero.net!not-for-mail From: Marmitako Newsgroups: bionet.software Subject: Re: Please recommend a DNAanalysis software package? Date: Wed, 13 Jan 1999 12:39:49 -0800 Organization: Kokotxas, SA Lines: 13 Message-ID: <369D0495.50FDC60C@bcc.orst.edu> References: <3694C941.43228F0@imsb.au.dk> <3695BBA3.6334E2E1@utu.fi> <77hqoc$2hv$1@desdemone.pasteur.fr> Reply-To: palenzuo@bcc.orst.edu NNTP-Posting-Host: bartholomew2-526.orst.edu Mime-Version: 1.0 Content-Type: text/plain; charset=x-user-defined Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en Ashok Aiyar wrote: > > You are correct; Prophet is free as in "free beer". The free downloadable version only works for a limited period of time: after that it not longer runs withour registering. I have not tried to call them for the key, but I asumed that this registration is not free. Am I wrong? Marmitako From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!cyclone.swbell.net!typhoon-sf.pbi.net.POSTED!not-for-mail Message-ID: <369CF2EA.B098AF74@pacbell.net> From: Ron Kagan Organization: Quest Diagnostics X-Mailer: Mozilla 4.5 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software Subject: Re: clustalw References: <77h090$f3p@bgtnsc02.worldnet.att.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 29 Date: Wed, 13 Jan 1999 11:24:26 -0800 NNTP-Posting-Host: 207.105.194.203 X-Complaints-To: abuse@pacbell.net X-Trace: typhoon-sf.pbi.net 916255443 207.105.194.203 (Wed, 13 Jan 1999 11:24:03 PDT) NNTP-Posting-Date: Wed, 13 Jan 1999 11:24:03 PDT Peter: I use CLUSTALW 1.74 running on Solaris 2.5.1. I run CLUSTALW from a shell script: first I create the alignment (in my case, a profile alignment): $CLUSTAL/clustalw -sequences -PROFILE1=$LOGS/final.aln -PROFILE2=$FSA/$fsaname -PWDNAMATRIX=CLUSTALW -DNAMATRIX=CLUSTALW -outfile=$ALIGN/$alignfile Then I create the tree from the alignment file: $CLUSTAL/clustalw -infile=$ALIGN/$alignfile -tree -kimura -outputtree=nj -outputtree=phylip -outputtree=dist I hope this helps! Ron Kagan Peter Rogan wrote: > I would like to generate a Neighbor-Joining tree from the command line using > the Sun Solaris version of clustalw. The documentation says it's possible > but the software ignores the command (other commands are not ignored, > ie. -align). Does anyone have a suggestion? > > Pete Rogan From owner-software@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!wn3feed!worldnet.att.net!135.173.83.225!attworldnet!newsadm From: "Peter Rogan" Newsgroups: bionet.software Subject: clustalw Date: 13 Jan 1999 02:26:40 GMT Organization: AT&T WorldNet Services Lines: 8 Message-ID: <77h090$f3p@bgtnsc02.worldnet.att.net> NNTP-Posting-Host: 12.79.44.114 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 I would like to generate a Neighbor-Joining tree from the command line using the Sun Solaris version of clustalw. The documentation says it's possible but the software ignores the command (other commands are not ignored, ie. -align). Does anyone have a suggestion? Pete Rogan From owner-software@net.bio.net Wed Jan 13 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.wli.net!sunqbc.risq.qc.ca!news.uow.edu.au!news.usyd.edu.au!sunb.ocs.mq.edu.au!keli From: phains@NOSPAMproteome.org.au (Peter Hains) Newsgroups: bionet.software Subject: Re: Help! Software to extract motif from alignment produced by CLUSTAL W. Date: Thu, 14 Jan 1999 21:48:13 GMT Organization: APAF Lines: 44 Distribution: world Message-ID: <77ll6b$cr1$1@sunb.ocs.mq.edu.au> References: <199901130832.QAA27602@sunm.shcnc.ac.cn> NNTP-Posting-Host: apaf29.proteome.org.au X-Newsreader: News Xpress 2.01 I have used and would recommend MEME, available via a Web interface at: http://www.sdsc.edu/meme/meme/website/ If you're really keen, the maker of Genedoc has ported the MEME code to run under Windoze DOS mode available at: ftp://ftp.netcom.com/pub/ka/karl/ Regards, Peter. In article <199901130832.QAA27602@sunm.shcnc.ac.cn>, xietao@sunm.shcnc.ac.cn wrote: >Daer All: > >Could somebody tell me a free software(PC or UNIX) which is good > >at extracting motifs from sequence alignment produced by CLUSTAL W? > >Thanks! > >Tao Xie (Sam) 99/1/13 >----------------------------------------------------- >Xie Tao >Bioinformatics & Protein Engineering Lab. >Shanghai Institute of Biochemistry, Academia, Sinica >P. O. BOX 33# >320# Yue Yang Road, Shanghai, P. R. China, 200031 >Telephone: (86)-(21)-64374430-255 >Fax:(86)-(21)-64338357 >E-mail: xietao@sunm.shcnc.ac.cn >Web-Page: http://202.127.24.111/xietao/ >----------------------------------------------------- > I'm afraid I don't have a clever saying to put here. Remove NOSPAM to e-mail me. Peter Hains Ph. +61 2 9850 6216 Australian Proteome Analysis Facility Fax. +61 2 9850 6200 Level 4 Building F7B Macquarie University, Sydney 2109 From owner-software@net.bio.net Wed Jan 13 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!nntp.flash.net!news.maxwell.syr.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!not-for-mail From: Joshua Udall Newsgroups: bionet.software Subject: RFLP automation Date: Thu, 14 Jan 1999 14:31:23 -0600 Organization: University of Wisconsin, Madison Lines: 51 Sender: reguser@144.92.244.182 Message-ID: <369E541A.2101F604@students.wisc.edu> NNTP-Posting-Host: 144.92.244.182 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: zh-CN To: jaudall@students.wisc.edu I'm looking for some software which would do analysis of RFLP image files in a batch mode. Most image software I've been able to find requires one to actually look, and perhaps modify, the bands etc. recognized by the camera. For the most part, these packages don't export the allele scores to a text file either - how tedious! Of course, I think that every autorad should be examined by the researcher, however, for mapping experiments, I only care if the genotype has allele A or allele B. Consquently, I'd like the software to process n number of images, read the data, then put it all in one file for me. First, I'd like the software assume an autorad is perfect (standardized) - see my thoughts on methodology below. Second, read the tiff file, analyze it, then append output of genotypic data to a growing data matrix. The key to automating this process is giving the program near perfect data ie. no blotches, distinct lanes, clear crisp bands. I think it could be done easily. See below. (Anyone done this yet?) Hand scoring RFLPs: Create an acetate sheet with grey lines representing lanes. There should be two lanes more than actually on the gel. Place the acetate sheet on top of the autorad and color in the alleles. In the first two extra lanes, artifically color in the parental genotypes. These will act as approximate genotype standards for each tier. Then color the bands for each genotype on the acetate sheet. If there is more than one allele/probe use two colors. Data aquisition: I place the acetate sheets in a particular order (probe name), and I write the name in order in a file. I use a scanner w/ doc feeder to create a separate tiff for every n acetate sheets (enough for the population size). Every n scans, the program writes a new tiff with the probe as the file name. Genotypes (lane id's) will also be read from a simple text file. Data analysis: The program then reads and analyses (tiff by tiff) the colected data. After each analysis, a matrix is assembled as a simple text file of mapping data. Anyone have any ideas about working software or peices of software that would do this? My best lead is Image from Sanger. From owner-software@net.bio.net Wed Jan 13 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: lisa_crawford@cmagroup.com Newsgroups: bionet.software Subject: JOB: West Palm, Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging Date: 14 Jan 1999 15:50:19 GMT Organization: Career Marketing Associates Lines: 27 Message-ID: <77l3nr$ngu$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.216 X-Trace: news1.rmi.net 916329019 24094 206.247.5.216 (14 Jan 1999 15:50:19 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 14 Jan 1999 15:50:19 GMT West Palm, Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging **We are also working similar medical imaging software positions for clients in NE USA, Midwest, PNW, CA and BC Canada. -Senior Software Engineer -Southeast Florida Coastal -Salaried, Full-Time, Excellent Benefits (Relocation Assistance Available) Medical DICOM knowledge would be a major plus. Experience with C/C++ and NT required. Image manipulation, compression, edge detection, analysis, all good things to have. Please refer to JO# 5253RJS in your response. lisa_crawford@cmagroup.com Lisa Crawford Sr. Researcher & Associate Recruiter ljc@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Wed Jan 13 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!newsxfer.itd.umich.edu!news.itd.umich.edu!not-for-mail Message-ID: <369E510B.D16724BF@umich.edu> From: MDB Reply-To: mdblmq@umich.edu Organization: Univ. of Michigan X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Plasmid drawing software Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Lines: 8 Date: Thu, 14 Jan 1999 15:18:22 -0500 NNTP-Posting-Host: 141.211.156.94 X-Trace: news.itd.umich.edu 916345169 141.211.156.94 (Thu, 14 Jan 1999 15:19:29 EDT) NNTP-Posting-Date: Thu, 14 Jan 1999 15:19:29 EDT Hello out there, Is anyone aware of Mac software that would allow me to easily draw circular plasmid maps? Douglas Benson Univ. of Michigan From owner-software@net.bio.net Wed Jan 13 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newsfeed.ecrc.net!newsfeed.nacamar.de!dispose.news.demon.net!demon!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!news.nottingham.ac.uk!not-for-mail From: plxsrt@pln1.nott.ac.uk Newsgroups: bionet.software Subject: Re: Please recommend a DNAanalysis software package? Date: Thu, 14 Jan 1999 14:35:43 GMT Organization: ACS, The University of Nottingham Message-ID: <77kvb1$o3b$1@oyez.ccc.nottingham.ac.uk> References: <3694C941.43228F0@imsb.au.dk> <3695BBA3.6334E2E1@utu.fi> <77hqoc$2hv$1@desdemone.pasteur.fr> NNTP-Posting-Host: dmg.life.nottingham.ac.uk X-Trace: oyez.ccc.nottingham.ac.uk 916324513 24683 128.243.116.22 (14 Jan 1999 14:35:13 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 14 Jan 1999 14:35:13 GMT X-Newsreader: Forte Free Agent 1.0.82 Lines: 11 Someone has to pay for all the time it takes to develop software applications. Scientific software released "free with source" has often already been paid for by research funding. Has Prophet been paid for in this way? Simon T From owner-software@net.bio.net Wed Jan 13 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.atl!falcon.america.net!news.pagesat.net!news.itis.com!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: LINUX and modems Date: 14 Jan 1999 13:57:07 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 19 Sender: reguser@ebv.oncology.wisc.edu Message-ID: References: <369329B5.CFF67659@jove.acs.unt.edu> <777hv6$7m9$1@xinwen.daimi.au.dk> <36992254.6707ED7D@jove.acs.unt.edu> Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu User-Agent: slrn/0.9.5.4 (UNIX) On Sun, 10 Jan 1999 15:57:40 -0600, Chris Fields (cjfields@jove.acs.unt.edu) wrote: >Thanks for the responses. They helped wonderfully. Now, if they would >only port Genedoc to LINUX (hint hint... ) There are lots of other alignment editors available for Linux, some of which are available from Thomas Sicheritz' Molecular Linux page: http://evolution.bmc.uu.se/~thomas/mol_linux/ Having said this, let me add that the 16-bit versions of GeneDoc work very well when used under WABI/Linux. Cheers, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research http://aiyar.cjb.net From owner-software@net.bio.net Wed Jan 13 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.concentric.net!news.he.net!news.pagesat.net!news.itis.com!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: Please recommend a DNAanalysis software package? Date: 14 Jan 1999 15:23:56 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 15 Sender: reguser@ebv.oncology.wisc.edu Message-ID: References: <3694C941.43228F0@imsb.au.dk> <3695BBA3.6334E2E1@utu.fi> <77hqoc$2hv$1@desdemone.pasteur.fr> <77kvb1$o3b$1@oyez.ccc.nottingham.ac.uk> Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu User-Agent: slrn/0.9.5.4 (UNIX) On Thu, 14 Jan 1999 14:35:43 GMT, plxsrt@pln1.nott.ac.uk (plxsrt@pln1.nott.ac.uk) wrote: >Someone has to pay for all the time it takes to develop software >applications. Scientific software released "free with source" has >often already been paid for by research funding. Has Prophet been >paid for in this way? As stated by a Prophet developer on this newsgroup, Prophet development was contracted by the NIH. If that is true, then yes it was paid for. Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research http://aiyar.cjb.net From owner-software@net.bio.net Wed Jan 13 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Plasmid drawing software Date: 14 Jan 1999 23:37:44 GMT Organization: Biology, Indiana University - Bloomington Lines: 8 Message-ID: <77lv48$utq$1@flotsam.uits.indiana.edu> References: <369E510B.D16724BF@umich.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu You will find one or two free plasmid draw software programs for macos listed in http://iubio.bio.indiana.edu/soft/molbio/Listings.html - don -- -- d.gilbert--biocomputing--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Jan 14 22:00:00 1999 Path: biosci!SUNM.SHCNC.AC.CN!xietao From: xietao@SUNM.SHCNC.AC.CN (xietao) Newsgroups: bionet.software Subject: Re: Re: Help! Software to extract motif from alignment produced by CLUSTAL W. Date: 14 Jan 1999 21:19:07 -0800 Organization: SIBC Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <199901150514.NAA09150@sunm.shcnc.ac.cn> Reply-To: xietao@sunm.shcnc.ac.cn NNTP-Posting-Host: net.bio.net >I have used and would recommend MEME, available via a Web interface at: >http://www.sdsc.edu/meme/meme/website/ >If you're really keen, the maker of Genedoc has ported the MEME code to >run under Windoze DOS mode available at: ftp://ftp.netcom.com/pub/ka/karl/ >Regards, Peter. Dear Peter: Thank you for your reply! Actually, I have used MEME before. But it need your give it several parameters: Short or Wide motif, how many you want to get etc. And, it did not use Alignment methods. So, what I prefer is I send an alignment in to it, and it give out motif(highly conserve) region. I think PROSITE and BLOCKS are make in this way. But I can not find a suitble software that can run under my PC and be merged into a batch work. Could you give me more comments? Thank you! Sam ----------------------------------------------------- Xie Tao Bioinformatics & Protein Engineering Lab. Shanghai Institute of Biochemistry, Academia, Sinica P. O. BOX 33# 320# Yue Yang Road, Shanghai, P. R. China, 200031 Telephone: (86)-(21)-64374430-255 Fax:(86)-(21)-64338357 E-mail: xietao@sunm.shcnc.ac.cn Web-Page: http://202.127.24.111/xietao/ ----------------------------------------------------- From owner-software@net.bio.net Thu Jan 14 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news.sprintlink.net!cs.utexas.edu!news.unt.edu!news From: Chris Fields Newsgroups: bionet.software Subject: Re: Please recommend a DNAanalysis software package? Date: Thu, 14 Jan 1999 22:28:57 -0600 Organization: University of North Texas Lines: 31 Message-ID: <369EC409.567AAD73@jove.acs.unt.edu> References: <3694C941.43228F0@imsb.au.dk> <3695BBA3.6334E2E1@utu.fi> <77hqoc$2hv$1@desdemone.pasteur.fr> <369D0495.50FDC60C@bcc.orst.edu> Reply-To: "cjfields @jove.acs.unt.edu" NNTP-Posting-Host: remote5.server1.local.premium.dialup.unt.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 The registration is free. Your best bet is to use the e-mail; I couldn't get them to respond via the toll-free number. Marmitako wrote: > > Ashok Aiyar wrote: > > > > You are correct; Prophet is free as in "free beer". > > The free downloadable version only works for a limited period of time: > after that it not longer runs withour registering. I have not tried to > call them for the key, but I asumed that this registration is not free. > Am I wrong? > > Marmitako -- C. J. Fields Graduate Student, Dept. of Biological Sciences The University of North Texas Denton, TX email : cjfields@jove.acs.unt.edu \\\\\\\\\\\\\\\\\\\\oooooooooooooooo//////////////////// "Giving money and power to government is like giving whiskey and car keys to teenage boys" -P. J. O'Rourke "Join the military. Travel to exotic places, meet exciting people, then kill them" -Anonymous ////////////////////oooooooooooooooo\\\\\\\\\\\\\\\\\\\\ From owner-software@net.bio.net Thu Jan 14 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.wli.net!howland.erols.net!fu-berlin.de!news.uni-stuttgart.de!news.belwue.de!stremob.pci.chemie.uni-tuebingen.de!user From: kaifr@uni-tuebingen.de (Dr. Kai-Uwe Froehlich) Newsgroups: bionet.software Subject: Re: Plasmid drawing software Date: Fri, 15 Jan 1999 08:39:02 +0100 Organization: Phys.-chem. Institut, Universitaet Tuebingen Lines: 54 Message-ID: References: <369E510B.D16724BF@umich.edu> NNTP-Posting-Host: stremob.pci.chemie.uni-tuebingen.de In article <369E510B.D16724BF@umich.edu>, mdblmq@umich.edu wrote: > Hello out there, > > Is anyone aware of Mac software that would allow me to easily draw > circular plasmid maps? > > Douglas Benson > Univ. of Michigan Hi Douglas, I have written a plasmid drawing program for the Macintosh which I have released as Freeware. It allows to draw circular or linear maps. It was originally intended for our lab use, so it is anything but polished. It converts lists of restriction sites and fragment/gene positions into Postscript files. Its weak points in short - It is a Hypercard stack, so you need Hypercard to run it (luckily, speed is no problem, there are no processor intensive steps involved) - The output are Postscript files in Illustrator format. To view and to further edit the picture (which you will have to, see below), you need either Adobe Illustrator, or the Shareware EPStoPICT, which produces a fully editable, object oriented PICT version of the graphics. - The program does not care for overlapping labels, so in most cases you must do some fine-tuning On the other hand, the program - allows "electronic cloning", so you can quickly construct new plasmids from those already entered in the program - can draw all plasmids at the same size, but also using the same (or any you want) scale (that was the primary reason for me to write the program, most commercial programs had (still have?) no way to specify the drawing scale (except by different magnification in the page setup) - draws linear and circular maps, allows borders of various widths and fills of grays, arrows... - Output quality is great, thanks to Postscript - The price is right For a more detailed description, including screen shots of the output graphics, see and that is also the place to download the stack: (BTW, there is also a stack for the organization of plasmid/strain collections available) Kai ----------------------------------------------------------------------- Dr. Kai-Uwe Fröhlich, Physiologisch-chemisches Institut, Hoppe-Seyler-Str. 4, 76072 Tübingen, Germany From owner-software@net.bio.net Thu Jan 14 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!diablo.theplanet.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: "Leonid A. Sadofiev" Newsgroups: bionet.software Subject: Announce: Antiviral plug-in for Netscape Navigator Date: 15 Jan 1999 06:41:02 -0000 Organization: h s gistology c bio f Lines: 20 Message-ID: <77mntu$3uc$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk Mime-Version: 1.0 Original-To: bio-soft@dl.ac.uk content-length: 450 Return-Path: Dear Colleagues, I'm glad to inform you that DrNet32 - the free antiviral plug-in for Netscape Navigator could be downloaded from www.spbnet.spb.ru/drnet Main features are: Detection of known and unknown viruses Removing viruses from infected files Software works "on the fly" and absolutelly transparent for user. Please visit our web-site www.spbnet.spb.ru/drnet for more information and download a free version of DrNet32. Leonid A. Sadofiev From owner-software@net.bio.net Thu Jan 14 22:00:00 1999 Path: biosci!ms.bd.com!Bill_A_Nussbaumer From: Bill_A_Nussbaumer@ms.bd.com Newsgroups: bionet.software Subject: Re: Gene Runner Date: 15 Jan 1999 13:09:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 57 Sender: daemon@net.bio.net Distribution: world Message-ID: <852566FA.0072F282.00@7crmta_md.ms.bd.com> NNTP-Posting-Host: net.bio.net Bill A Nussbaumer@BDX 01/15/99 04:02 PM Hi, You may want to look into the program mkcompat.exe. It comes with Win95 and you should find it in your Windows/System folder or just type "mkcompat" in the run command. The idea is that it will make Windows 3.1 programs compatable with Windows95. I used it on Oligo per the developers instructions and had no problems. Unfortunately I am unable to provide you with specifics on what each setting in the program will do but you may want to check Microsoft's site for more info. Bill Nussbaumer palenzuo@ava.bcc.orst.edu on 01/15/99 02:11:36 PM Please respond to palenzuo@ava.bcc.orst.edu To: bio-soft@net.bio.net cc: (bcc: Bill A Nussbaumer/BALT/BDX) Subject: Gebe Runner Hi, I have been using Gene Runner v 3.02 for a few years and I have got used to it, finding it very useful for my needs. However, it is a 16 bit application, at it uses an awkward file manager which cannot recognize long file names. Everything else works fine under win95, but this limitation on filenames length makes if a tittle of a pain when handling big sequence libraries. The question is, anybody knows of an upgrade for win 95? (don't think so because the company doesn't seem to exist any more), or is there an easy way to make this application use a long name-compatible file manager?. I have tried other packages, but most of them are too complicated, too simple or too expensive for what I need. I haven't found a good equivalent of Generunner's oligo analysis menu. From owner-software@net.bio.net Thu Jan 14 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.nero.net!not-for-mail From: Oswaldo Newsgroups: bionet.software Subject: Gebe Runner Date: Fri, 15 Jan 1999 11:11:36 -0800 Organization: Kokotxas, SA Lines: 20 Message-ID: <369F92E8.A2D41BAC@bcc.orst.edu> Reply-To: palenzuo@bcc.orst.edu NNTP-Posting-Host: bartholomew2-526.orst.edu Mime-Version: 1.0 Content-Type: text/plain; charset=x-user-defined Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en Hi, I have been using Gene Runner v 3.02 for a few years and I have got used to it, finding it very useful for my needs. However, it is a 16 bit application, at it uses an awkward file manager which cannot recognize long file names. Everything else works fine under win95, but this limitation on filenames length makes if a tittle of a pain when handling big sequence libraries. The question is, anybody knows of an upgrade for win 95? (don't think so because the company doesn't seem to exist any more), or is there an easy way to make this application use a long name-compatible file manager?. I have tried other packages, but most of them are too complicated, too simple or too expensive for what I need. I haven't found a good equivalent of Generunner's oligo analysis menu. Thank you guys for any input, Oswaldo From owner-software@net.bio.net Thu Jan 14 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!nntp.flash.net!news.maxwell.syr.edu!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: lisa_crawford@cmagroup.com Newsgroups: bionet.software Subject: JOB: Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging Date: 15 Jan 1999 16:14:38 GMT Organization: Career Marketing Associates Lines: 27 Message-ID: <77nphe$j8s$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.216 X-Trace: news1.rmi.net 916416878 19740 206.247.5.216 (15 Jan 1999 16:14:38 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 15 Jan 1999 16:14:38 GMT West Palm, Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging **We are also working similar medical imaging software positions for clients in NE USA, Midwest, PNW, CA and BC Canada. -Senior Software Engineer -Southeast Florida Coastal -Salaried, Full-Time, Excellent Benefits (Relocation Assistance Available) Medical DICOM knowledge would be a major plus. Experience with C/C++ and NT required. Image manipulation, compression, edge detection, analysis, all good things to have. Please refer to JO# 5253RJS in your response. lisa_crawford@cmagroup.com Lisa Crawford Sr. Researcher & Associate Recruiter ljc@cmagroup.com IT & Software Solutions Team Career Marketing Associates http://www.cmagroup.com/IT.html From owner-software@net.bio.net Thu Jan 14 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news-in-east1.sprintlink.net!news.sprintlink.net!itssrv1.ucsf.edu!macmac-2.ucsf.edu!user From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) Newsgroups: bionet.software Subject: Re: Plasmid drawing software Date: Thu, 14 Jan 1999 19:35:27 -0700 Organization: University of California, San Francisco Lines: 16 Message-ID: References: <369E510B.D16724BF@umich.edu> NNTP-Posting-Host: macmac-2.ucsf.edu In article <369E510B.D16724BF@umich.edu>, mdblmq@umich.edu wrote: > Hello out there, > Is anyone aware of Mac software that would allow me to easily draw > circular plasmid maps? > Douglas Benson > Univ. of Michigan Fire up you favourite web browser and look for "MacPlasMap". I believe that v1.82 is fully functional shareware whereas the later (2.x) versions are partially crippled demonstration programs. Bernard -- Bernard P. Murray, PhD Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA From owner-software@net.bio.net Sat Jan 16 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!205.147.0.99!news.digilink.net!not-for-mail From: "Van Mittal-Henkle" Newsgroups: bionet.software Subject: Announcing HMMpro 2.2 Hidden Markov Model software Date: Thu, 14 Jan 1999 17:23:27 -0800 Organization: DigiLink Network Services Lines: 32 Message-ID: <77ralo$68c$1@la-mail4.digilink.net> NNTP-Posting-Host: mail.netid.com X-Newsreader: Microsoft Outlook Express 4.72.2110.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 HMMpro 2.2, the latest release of Net-ID's Hidden Markov Model (HMM) simulator for biological sequence analysis, is now available for downloading. HMMpro's Graphical User Interface allows users to interactively build, fine tune, and analyze models of protein families or DNA functional elements. These models can then be used for multiple alignments, pattern discovery, and sensitive data mining. A command line interface is also available for batch processing. HMMpro 2.2 is available from Net-ID's web site: http://www.netid.com You can check out the complete list of technical features of this release at: http://www.netid.com/html/hmmpro_technical_features.html The highlights of HMMpro version 2.2 include: * support for editing individual emission & transition weights * the ability to fix emission or transition weights on a node by node basis during training * support for importing and exporting HMMER 2.x models 30 day evaluation copies of HMMpro 2.2 are now available to all users. Licenses for academic users are free. Net-ID, Inc. From owner-software@net.bio.net Sat Jan 16 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsxfer3.itd.umich.edu!jobone!dailyplanet.srl.ford.com!eccws1.dearborn.ford.com!news From: Manfred Friedrich Newsgroups: bionet.software Subject: Re: Less tedious procedure for aligning nt sequences Date: Sun, 17 Jan 1999 13:08:58 +0100 Organization: Ford Motor Company Lines: 46 Message-ID: <36A1D2DA.3478@gw.ford.com> References: <852566F6.00657CF2.00@7crmta_md.ms.bd.com> Reply-To: mfriedr2@gw.ford.com NNTP-Posting-Host: 19.187.6.199 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01C (Win95; I) To: Bill_A_Nussbaumer@ms.bd.com Bill_A_Nussbaumer@ms.bd.com wrote: > > Bill A Nussbaumer@BDX > 01/11/99 01:32 PM > > That's a good point, thanks. My primary computer is a PC so windows > compatible software is my preference. However, I have access to several > Macs in the lab so I wont rule out helpful suggestions not available on > Wintel machines. If any Unix software is required the only way I could use > it would be to download bash (or something similar). > > Bill Nussbaumer > > todd@andrew2.stanford.edu on 01/11/99 12:44:51 PM > > To: Bill A Nussbaumer/BALT/BDX > cc: > Subject: Re: Less tedious procedure for aligning nt sequences > > In article <852566F6.004C4F76.00@7crmta_md.ms.bd.com>, > Bill_A_Nussbaumer@ms.bd.com wrote: > >Does anyone have any > >suggestions on how to more quickly get sequences into alignment either > >using DNAStar or otherwise. I am fairly new to this aspect of DNA > analysis > >and am not completely familiar with all of the Blast and Entrez tools as > of > >yet. > > > You don't say what kind of computer you're using, and since DNAStar is > available for both Windows and Macs, you may get a bunch of irrelevent > responses. But probably the easiest way to do what you want is to get the > freely available ClustalW or ClustalX, which is available for both Macs > and PCs. This program does multiple alignments and provides consensus > sequences and exports a