From owner-software@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ais.net!logbridge.uoregon.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.dknet.dk!not-for-mail From: Dan Pedersen Newsgroups: bionet.software Subject: Spreadsheet invention Date: Fri, 02 Jan 1998 01:13:21 +0100 Organization: ProFunda Lines: 20 Message-ID: <34AC30FA.10F6@pip.dknet.dk> Reply-To: profunda@pip.dknet.dk NNTP-Posting-Host: cph252.ppp.dknet.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Dear Scientist, My partner Henrik Kjaer and I have developed a new spreadsheet in which - from the top-level you can copy/paste/fill text/values/formulas from/into the layers. >From interviews with scientists in biology/chemical/economical/math areas we learned that the new flexibility is an advantage when working with layers of data in these branches. To further discuss and develop the invention we need input from the users working in your areas. Therefore we should be glad if those interested would go to http://isa.dknet.dk/~profunda to view our invention and give us your opinion. There is a demo of the first version too - that Mac-users can download for free (soon also Windows), and you can register to receive info in future too. Thanks in advance - and have a nice day, Dan Pedersen From owner-software@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!131.103.1.114!news1.chicago.iagnet.net!iagnet.net!129.79.6.160!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Netscape or IE most used? Date: 2 Jan 1998 18:57:18 GMT Organization: Biology, Indiana University - Bloomington Lines: 66 Message-ID: <68jdae$231$1@flotsam.uits.indiana.edu> References: <68j5nq$eca$1@nntp1.ba.best.com> NNTP-Posting-Host: chipmunk.bio.indiana.edu Summary on HTTP browser use by biologists using IUBio archive From http://iubio.bio.indiana.edu/ logs -- 66% Netscape -- 18% MS Internet Explorer -- 16% remainder of ~ 100 different kinds of browsers; many are software agents Notes: -- 10% of callers use a version of Netscape not supporting complex features. -- Overall, ~25% of callers user a browser that doesn't, or may not, support complex features. These features include frames, tables, various color and font controls, java and javascript. -- support for software agents needs to be kept in mind. These frequently return data more-or-less directly to users, but we have no way to know what user interface is like. Expect agents to increase in importance as users seek software solutions to seeking and digesting relevant data. 98246 raw references examined; 79420 references used in final statistics generation. -- all calls from identifiable robots (robots.txt) were removed Start Date of Report: Sat Aug 9 08:17:20 1997 End Date of Report: Mon Oct 6 17:49:24 1997 Browser kinds (only those w/ >100 count) Browser Percent Count Browser full name (one of many variants) ----------------- ------ ------ --------------------------------------- AOL 1.9 1519 Mozilla/2.0 (Compatible; AOL-IWENG 3.0; CERN-LineMode/2 2.8 2253 CERN-LineMode/2.15 libwww/2.17 (^^ these calls are software agents, esp. mag.com, using SRS databanks) Crescent 0.2 120 Crescent Internet ToolPak HTTP OLE Contro Cyberdog/2 0.1 91 Cyberdog/2.0 GET/0 0.3 200 GET/0.5 libwww-perl/0.40 Java1 0.4 303 Java1.1.3beta Lynx/2 0.4 407 Lynx/2.6 libwww-FM/2.14 MSI Explorer/2 0.9 745 Mozilla/1.22 (compatible; MSIE 2.0; Windows MSI Explorer/3 15.8 12562 Mozilla/2.0 (compatible; MSIE 3.01; Windows MSI Explorer/4 1.5 1295 Mozilla/4.0 (compatible; MSIE 4.0; Windows Netscape/0 0.2 148 Mozilla/0.96 beta Netscape/1 1.7 1367 Mozilla/1.1N Netscape/2 8.8 6978 Mozilla/2.02 Netscape/3 39.7 31502 Mozilla/3.03 Netscape/4 13.6 10778 Mozilla/4.03 Netscape total -- 65.8 Slurp/2 0.2 198 Slurp/2.0 (^^^ this must be a crawler robot that is misbehaving) Symantec 0.1 119 Symantec WebFind Page Validation WebCompass 0.4 336 WebCompass 2.0 WebCopy/0 0.7 585 WebCopy/0.98b7 http_get 5.1 4047 http_get (^^ these calls are mostly software agents using SRS databanks) testrank/0 0.1 104 testrank/0.3 libwww-perl/0.40 ----------------- ------ ------ ---------------------------------------- -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: yoroya@aol.com (Yoroya) Newsgroups: bionet.software Subject: $7,500.00 Mac-based "3-D BrainStation" Brain Imaging Analysis System Date: 2 Jan 1998 02:21:06 GMT Lines: 25 Message-ID: <19980102022100.VAA29504@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Dear biomedical researcher/clinical diagnostician: "3-D BrainStation" is a $7,500.00 Macintosh-based brain imaging analysis package that can analyze anatomical images from CT or MRI scans or metabolic images from PET or SPECT scans. It is capable of 3-D volume reconstruction and display, multi-volume registration, ROI creation and data analysis, cortical surface pattern mapping, and multi-modal image fusion of anatomical and metabolic images thereby acting as a powerful research or diagnostic tool for the neuroscientist or clinician. This image analysis system is among the most powerful and versatile ones on the market today and only intended for the serious biomedical researcher and clinical diagnostician willing to make an investment in the best that money can buy. Don't be fooled by cheap imitations. Nothing out there can match the quality and versatility of "3-D BrainStation". If you can find a Mac-based brain imaging analysis system that can do as much as "3-D BrainStation" for less money, please let me know. I would like to research and compare its capabilities to ours. Visit our website and ask for more information, or contact me directly. I look forward to helping you expand the depth and breadth of your current biomedical imaging analytical capabilities soon. Sincerely, Robert L. Hummel Tel: 410-876-8055 Sales & Marketing E-mail: loats@loats.com Loats Associates, Inc. URL: http://www.loats.com From owner-software@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: yoroya@aol.com (Yoroya) Newsgroups: bionet.software Subject: $7,500.00 Mac-based "3-D BrainStation" Brain Imaging Analysis System Date: 2 Jan 1998 02:27:33 GMT Lines: 25 Message-ID: <19980102022700.VAA00487@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Dear biomedical researcher/clinical diagnostician: "3-D BrainStation" is a $7,500.00 Macintosh-based brain imaging analysis package that can analyze anatomical images from CT or MRI scans or metabolic images from PET or SPECT scans. It is capable of 3-D volume reconstruction and display, multi-volume registration, ROI creation and data analysis, cortical surface pattern mapping, and multi-modal image fusion of anatomical and metabolic images thereby acting as a powerful research or diagnostic tool for the neuroscientist or clinician. This image analysis system is among the most powerful and versatile ones on the market today and only intended for the serious biomedical researcher and clinical diagnostician willing to make an investment in the best that money can buy. Don't be fooled by cheap imitations. Nothing out there can match the quality and versatility of "3-D BrainStation". If you can find a Mac-based brain imaging analysis system that can do as much as "3-D BrainStation" for less money, please let me know. I would like to research and compare its capabilities to ours. Visit our website and ask for more information, or contact me directly. I look forward to helping you expand the depth and breadth of your current biomedical imaging analytical capabilities soon. Sincerely, Robert L. Hummel Tel: 410-876-8055 Sales & Marketing E-mail: loats@loats.com Loats Associates, Inc. URL: http://www.loats.com From owner-software@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsxfer3.itd.umich.edu!news1.best.com!nntp1.ba.best.com!shell7.ba.best.com!jquinn From: Greg Newsgroups: bionet.software Subject: Netscape or IE most used? Date: 2 Jan 1998 16:47:54 GMT Organization: BEST Internet Communications, Inc. Lines: 16 Message-ID: <68j5nq$eca$1@nntp1.ba.best.com> NNTP-Posting-Host: shell7.ba.best.com X-Trace: 883759674 14730 jquinn 206.184.139.132 X-Newsreader: TIN [UNIX 1.3 unoff BETA 970731; i386 FreeBSD 2.2.5-STABLE] Hi, I am currently embarking on several web based projects at the non-profit research Institute that I work at, and given the increasing divergence of the dynamic HTML and client side scripting (ie Javascript) between Netscape and MS Internet Explorer browser types, I was wondering whether the relative usage of these browsers has been reported for University/non-profits. I know that the current figure is given as 40% share for Microsoft, but (at least here in the US) Macs seem to be dominant in the medical/biological research community, and my guess is that Netscape is still very dominant at these types of institutes. (Coding for some clever client-side stuff takes an enormous amount of work and it's not necessarily practical to 'dual code' for both Netscape and MSIE). Thanks Greg From owner-software@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: yoroya@aol.com (Yoroya) Newsgroups: bionet.software Subject: $4,995.00 PC-based "Inquiry" Biotech Image Analysis System Date: 2 Jan 1998 02:24:06 GMT Lines: 23 Message-ID: <19980102022400.VAA29936@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Dear biomedical researcher/clinical diagnostician: "Inquiry" is a $4,995.00 PC-based image analysis package that can analyze whole-body, receptor, and metabolic autoradiographic images, chromosome spreads for morphometric karyotyping, 1-D and 2-D electrophoretic gels for densitometric analysis, images for quantitative in situ hybridization studies, images for 3-D tumor and lesion volume studies, grain counting, and more. This image analysis system is among most powerful and versatile ones on the market today and only intended for the serious biomedical researcher and clinical diagnostician willing to make an investment in the best that money can buy. Don't be fooled by cheap imitations. Nothing out there can match the quality and versatility of "Inquiry". If you can find a PC-based biotech image analysis system that can do as much as "Inquiry" for less money, please let me know. I would like to research and compare its capabilities to ours. Visit our website and ask for more information, or contact me directly. I look forward to helping you expand the depth and breadth of your current biomedical imaging analytical capabilities soon. Sincerely, Robert L. Hummel Tel: 410-876-8055 Sales & Marketing E-mail: loats@loats.com Loats Associates, Inc. URL: http://www.loats.com From owner-software@net.bio.net Thu Jan 01 22:00:00 1998 Path: biosci!TUNA.NET!amiller From: amiller@TUNA.NET ("Andrew Miller") Newsgroups: bionet.software Subject: free medical image 3D visualization software for Windows95/NT Date: 1 Jan 1998 16:51:01 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <19980102004953199.AAA169@Meldar> NNTP-Posting-Host: net.bio.net Hello, Just to let you know there's free medical image 3D visualization software (called NeuroModeller) for the Wintel environment available at: http://www.freeyellow.com/members2/amiller/index.html (version 1.07) http://users.infohouse.com/amiller/home.htm (version 1.06) .... download file size is 640 KB. NeuroModeller is a research effort of Cornell Medical Center, Division of Neurosurgery. Sincerely, Andrew Miller, MD amiller@infohouse.com From owner-software@net.bio.net Fri Jan 02 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!newsfeed.ecrc.net!news.duesseldorf.ecrc.net!RRZ.Uni-Koeln.DE!news.rhrz.uni-bonn.de!usenet From: uzs108@ibm.rhrz.uni-bonn.de (Mark) Newsgroups: bionet.software Subject: REQ: Targa video-driver Date: Sat, 03 Jan 1998 00:03:59 GMT Organization: Regionales Hochschulrechenzentrum Lines: 16 Message-ID: <68jv9c$lqi@news.rhrz.uni-bonn.de> NNTP-Posting-Host: rhrz-ts2-p3.rhrz.uni-bonn.de X-Newsreader: Forte Free Agent 1.0.82 Hi I'm looking for a video-driver for a TARGA win32k-videocard The driver should be able to run under win3.x or win95 Somebody out there who can help me ? thanks in advance Mark =============================== =============================== From owner-software@net.bio.net Fri Jan 02 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!feed1.news.luth.se!luth.se!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!193.166.5.150.MISMATCH!news.funet.fi!news.kolumbus.fi!news.uninet.ee!not-for-mail From: "nikvikon" Newsgroups: bionet.software Subject: Re: Netscape or IE most used? Date: 3 Jan 1998 12:52:45 GMT Lines: 5 Message-ID: <01bd1845$8ecdbd60$0613ccc2@computer-1> References: <68j5nq$eca$1@nntp1.ba.best.com> <68jdae$231$1@flotsam.uits.indiana.edu> NNTP-Posting-Host: ch6.anet.ee X-Trace: saast.uninet.ee 883831965 26532 (None) 194.204.19.6 X-Complaints-To: news@news.uninet.ee X-Newsreader: Microsoft Internet News 4.70.1154 Where can I get Netscape? Help me please. -- Nikvikon. From owner-software@net.bio.net Sat Jan 03 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!206.230.20.253!news.fuse.net!not-for-mail From: Goober Newsgroups: alt.binaries.dominion.warez,alt.binaries.dominion.warez.decrypted,alt.japanese.neojapan.warez.ibmpc,alt.japanese.neojapan.warez.ibm-pc,alt.warez.godz,alt.warez.ibm-pc.games,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software Subject: Re: cool warez... NO WAREZ AT ALL Date: Sat, 03 Jan 1998 22:50:20 -0800 Organization: Goober Lines: 10 Message-ID: <34AF312B.23A@Goober.com> References: <01bd102a$77aded80$e179d484@eric> Reply-To: Goober@Goober.com NNTP-Posting-Host: intrepid-231.fuse.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Xref: biosci bionet.software:20250 bionet.software.acedb:1564 bionet.software.gcg:2933 this site contain a no warez... Druzil wrote: > > this site contain a lot of cool warez... > > http://www.chez.com/druzil2 > > ce site contient beaucoup de warez... > > http://www.chez.com/druzil2 From owner-software@net.bio.net Sat Jan 03 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!sunqbc.risq.qc.ca!news.uunet.ca!neon.Mlink.NET!d32.dynamic-ip.mlink.net!user From: d356644@er.uqam.ca (Yves Bilodeau) Newsgroups: bionet.software Subject: Artificial Life Survey Date: Sun, 04 Jan 1998 00:20:46 -0500 Organization: UQAM Lines: 22 Message-ID: Reply-To: d356644@er.uqam.ca NNTP-Posting-Host: d32.dynamic-ip.mlink.net Artificial Life as Media Questionnaires intended toward general public and expert users who have been interacting with Artificial Life cybernetic organisms (agents, bots, viruses, simulations, Tamagotchis, robots). It is part of a research project on Artificial Life and how it is perceived by users. Please, take a few minutes to answer one (or more, if it's relevant) of the related questionnaires. English version: http://www.comm.uqam.ca/~vorn/questionnaire/ALIFEsurvey.html French version: http://www.comm.uqam.ca/~vorn/questionnaire/rechercheVA.html Your comments are welcome. Thanks for your help. Yves Bilodeau Departement de Communication (Media Studies) Universite du Quebec a Montreal d356644@er.uqam.ca From owner-software@net.bio.net Sun Jan 04 22:00:00 1998 From: carib@suva.is.com.fj (jamie) Newsgroups: bionet.software Subject: hello Date: Mon, 05 Jan 1998 17:49:53 +1300 Organization: Internet Services, Fiji Lines: 1 Message-ID: NNTP-Posting-Host: dialup3.suva.is.com.fj Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.internetmci.com!202.84.255.3!news.hkt.net!news.is.com.fj!dialup3.suva.is.com.fj!user cxcxcxcxcxcx From owner-software@net.bio.net Sun Jan 04 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!zdc-e!super.zippo.com!lotsanews.com!news.ycc.yale.edu!morpheus.cis.yale.edu!skoufs From: Emmanuel Skoufos Newsgroups: bionet.software Subject: ISO Alignment and Phylogenetic Tree Software Date: Mon, 5 Jan 1998 10:49:57 -0500 Organization: Yale University Lines: 37 Message-ID: References: NNTP-Posting-Host: morpheus.cis.yale.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: skoufs@morpheus.cis.yale.edu In-Reply-To: Dear Bionetters: I am looking for a *single* software package (shareware or commercial product at a reasonable cost - < $ 500) that runs on Wintel platforms and does the following things: -Aligns multiple DNA and protein sequences *and* -Builds phylogenetic trees based on the alignments. Optimally, cutting and pasting of the sequences is allowed and the tree building is an easily executed option on the command menu/tool bar. I tried several packages that either did not allow tree construction (DNASIS, Prophet) or the user interface was inpractically complicated (PHYLIP). I know that there are a few programs for Macs (including the DNASIS version for the Mac) that can do this. If you have any products in mind for a PC, or if any of the products you are using does the trick, please let me know. Emmanouil Emmanouil Skoufos, PhD Section of Neurobiology and Center for Medical Informatics Yale University School of Medicine 333 Cedar Street New Haven, CT 06520 203-785-3730 emmanouil.skoufos@yale.edu From owner-software@net.bio.net Sun Jan 04 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!194.162.162.196!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!uni-muenster.de!asterix.uni-muenster.de!hohoff From: "Carsten Hohoff" Newsgroups: bionet.software Subject: prediction of protein-protein contact sites Date: Mon, 5 Jan 1998 14:45:39 +0100 Organization: Westfaelische Wilhelms-Universitaet Muenster, Germany Lines: 13 Sender: "Carsten Hohoff" Message-ID: NNTP-Posting-Host: asterix.uni-muenster.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I have evidence that two proteins interact with each other. I know the tertiary structure of one and can model the 3D structure of the other on the basis of related proteins - is there any program that allows for the prediction of the sites of protein-protein interaction? Thanx in advance Carsten Hohoff Dept. of Biochem. Univ. of Muenster From owner-software@net.bio.net Sun Jan 04 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!206.229.87.25!news-peer.sprintlink.net!news-peer-east.sprintlink.net!news.sprintlink.net!Sprint!news.idt.net!newspeer.monmouth.com!newsxfer.visi.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!gwilliam From: gwilliam@hgmp.mrc.ac.uk (Gary Williams) Newsgroups: bionet.software Subject: Re: Has anyone tried Genotator? Date: 5 Jan 1998 14:48:14 GMT Organization: UK HGMP Resource Centre Lines: 28 Message-ID: <68qrre$64c$1@niobium.hgmp.mrc.ac.uk> References: <349EA182.A9AD2D61@decode.is> NNTP-Posting-Host: gallium.hgmp.mrc.ac.uk In article <349EA182.A9AD2D61@decode.is>, Daníel Óskarsson wrote: >This is a multi-part message in MIME format. >--------------0779D29215C2D46E047D3873 >Content-Type: text/plain; charset=us-ascii >Content-Transfer-Encoding: 7bit > >How do people like genotator? >Is there some other software available that can merge the outputs of >different exons finders? We have an interactive WWW system called NIX that currently combines the results of tRNAscan, RepeatMasker, BLAST (against vector, ecoli, sts, htg, gss, embl, est, swissprot and trembl), GRAIL (cpg, ploIIIprom, exons, gap2, rpttv, smprpt) TSSW, Fex, Hexon, MZEF, Genemark, Genefinder, FGene .... and some others that we are thinking of including. You have to be registered as a user of the UK MRC's Human Genome Mapping Project Resource Centre - but registration is free for academic users. NIX is available at: http://menu.hgmp.mrc.ac.uk/menu-bin/Nix/Nix.pl There is a link to this from our home page: http://www.hgmp.mrc.ac.uk/ Gary Williams Tel: +44 1223 494522 mailto:G.Williams@hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From owner-software@net.bio.net Sun Jan 04 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!newsfeed.internetmci.com!205.216.200.9!news.fidnet.com!not-for-mail From: "Dennis W. Jay, Ph.D., DABCC" Newsgroups: sci.med.laboratory,alt.med.software,bionet.software,sci.med.telemedicine,sci.med.pathology Subject: Conversion software from JCS Date: Sun, 04 Jan 1998 17:15:06 -0600 Organization: Fidelity Communications, Inc. Lines: 358 Message-ID: <34B017FA.6A7A@fidnet.com> NNTP-Posting-Host: sullivan-mo-117.fidnet.com Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------6FFE70CB36AD" X-Mailer: Mozilla 3.0 (Win95; U) This is a multi-part message in MIME format. --------------6FFE70CB36AD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Are you looking for a program to convert medical lab tests from common to metric units and vice versa? Jay Clinical Services now has a program which converts to and from common and metric units for over 300 analytes. JCSConvert runs under Windows 95 or Windows NT and requires about 3 Mb of disk space. The database is in ASCII format which allows the user to add other analytes as needed by editing with Notepad or any other word processor. Since I'm on the computer a lot, I wrote this program to aid in interpreting analyte values from the literature. I find this program particularly useful when browsing through articles on the net. If you would like a copy, please send a check or money order made out to Jay Clinical Services in the amount of $49.95 to the address below. If you would like further information, I would be glad to talk to you either by phone or e-mail. -- Jay Clinical Services Clinical Laboratory Software & Consulting 303 Market Street 573-834-2112 (Office and voice mail) P.O. Box 111 573-834-2113 (FAX) Berger, MO 63014 http://www.jaycs.com e-mail: djay@jaycs.com --------------6FFE70CB36AD Content-Type: image/jpeg; name="JCSConvert.jpg" Content-Transfer-Encoding: base64 Content-Disposition: inline; filename="JCSConvert.jpg" /9j/4AAQSkZJRgABAQEBLAEsAAD/2wBDAAUDBAQEAwUEBAQFBQUGBwwIBwcHBw8LCwkMEQ8S EhEPERETFhwXExQaFRERGCEYGh0dHx8fExciJCIeJBweHx7/2wBDAQUFBQcGBw4ICA4eFBEU Hh4eHh4eHh4eHh4eHh4eHh4eHh4eHh4eHh4eHh4eHh4eHh4eHh4eHh4eHh4eHh4eHh7/wAAR CAFBAUIDASIAAhEBAxEB/8QAHwAAAQUBAQEBAQEAAAAAAAAAAAECAwQFBgcICQoL/8QAtRAA AgEDAwIEAwUFBAQAAAF9AQIDAAQRBRIhMUEGE1FhByJxFDKBkaEII0KxwRVS0fAkM2JyggkK FhcYGRolJicoKSo0NTY3ODk6Q0RFRkdISUpTVFVWV1hZWmNkZWZnaGlqc3R1dnd4eXqDhIWG h4iJipKTlJWWl5iZmqKjpKWmp6ipqrKztLW2t7i5usLDxMXGx8jJytLT1NXW19jZ2uHi4+Tl 5ufo6erx8vP09fb3+Pn6/8QAHwEAAwEBAQEBAQEBAQAAAAAAAAECAwQFBgcICQoL/8QAtREA AgECBAQDBAcFBAQAAQJ3AAECAxEEBSExBhJBUQdhcRMiMoEIFEKRobHBCSMzUvAVYnLRChYk NOEl8RcYGRomJygpKjU2Nzg5OkNERUZHSElKU1RVVldYWVpjZGVmZ2hpanN0dXZ3eHl6goOE 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biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!metro.atlanta.com!news1.hlc.net!news From: "alex" Newsgroups: bionet.software Subject: i need a program that will do a random pick for a few basketball teams. Date: 6 Jan 1998 00:29:50 GMT Organization: A customer of Epoch Networks Lines: 4 Message-ID: <01bd189c$baa3be60$4e27a8cf@decayative> NNTP-Posting-Host: everydayislikesunday.tea-house.com X-Newsreader: Microsoft Internet News 4.70.1162 i need a program that will do a random pick every day. i need it to randomly pick which teams will play together. Thank you if you can help me. From owner-software@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: Recomb98: Registration Date: 5 Jan 1998 16:05:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801060004.QAA16024@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net CALL FOR RECOMB 98 Registration Registration is now starting for RECOMB 98. Please visit our website for registration instructions: http://www.mssm.edu/biomath/recomb98.html If you do NOT want to be in our mailing list, please reply with Subject line "Recomb98: remove". From owner-software@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!sanbi.ac.za!andrey From: andrey@sanbi.ac.za (Andrey A Ptitsyn) Newsgroups: bionet.software Subject: Re: ISO Alignment and Phylogenetic Tree Software Date: 5 Jan 1998 23:58:15 -0800 Organization: SANBI Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <34B1D39D.6E61ECC5@sanbi.ac.za> References: NNTP-Posting-Host: net.bio.net Try VOSTORG, which is for MS DOS, but still functional and does what you want. You can download it from ftp://ftp.bionet.nsc.ru/pub/biology/ (then follow subdirectories) Good luck. Andrey Ptitsyn Emmanuel Skoufos wrote: > > Dear Bionetters: > > I am looking for a *single* software package (shareware or commercial > product at a reasonable cost - < $ 500) that runs on Wintel platforms and > does the following things: > > -Aligns multiple DNA and protein sequences > > *and* > > -Builds phylogenetic trees based on the alignments. > > Optimally, cutting and pasting of the sequences is allowed and the tree > building is an easily executed option on the command menu/tool bar. > > I tried several packages that either did not allow tree construction > (DNASIS, Prophet) or the user interface was inpractically complicated > (PHYLIP). I know that there are a few programs for Macs (including the > DNASIS version for the Mac) that can do this. > > If you have any products in mind for a PC, or if any of the products you > are using does the trick, please let me know. > > Emmanouil > > Emmanouil Skoufos, PhD > Section of Neurobiology and > Center for Medical Informatics > Yale University School of Medicine > 333 Cedar Street > New Haven, CT 06520 > 203-785-3730 > emmanouil.skoufos@yale.edu From owner-software@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!ggr.co.uk!gzz78923 From: gzz78923@ggr.co.uk Newsgroups: bionet.software Subject: New DBsolve version Date: 6 Jan 1998 12:42:37 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801062041.UAA00435@ukwsv7.ggr.co.uk> NNTP-Posting-Host: net.bio.net DBsolve: software for metabolic, enzymatic and receptor-ligand binding simulation. Version 4.05 contains receptor-ligand-binding example: simultaneous fitting to O DE equations, implicit and explicit algebraic functions. http://sirius.iteb.serpukhov.su/~igor/ From owner-software@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: Recomb98: Registration Date: 5 Jan 1998 16:05:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801060004.QAA16026@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net CALL FOR RECOMB 98 Registration Registration is now starting for RECOMB 98. Please visit our website for registration instructions: http://www.mssm.edu/biomath/recomb98.html If you do NOT want to be in our mailing list, please reply with Subject line "Recomb98: remove". From owner-software@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news-peer-east.sprintlink.net!news.sprintlink.net!Sprint!rill.news.pipex.net!pipex!news-lond.gip.net!news-stkh.gip.net!news.gsl.net!gip.net!news.kolumbus.fi!news.uninet.ee!kadri.ut.ee!tamm!tmargus From: tmargus@tamm.eenet.ee (Tonu Margus) Newsgroups: bionet.software Subject: Multiple PCR primer analysis? Date: 6 Jan 1998 14:45:47 GMT Organization: Estonian Biocentre Lines: 11 Message-ID: <68tg2r$isb$1@kadri.ut.ee> NNTP-Posting-Host: tamm.ebc.ee Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: kadri.ut.ee 884097947 19339 (None) 193.40.23.2 X-Complaints-To: usenet@kadri.ut.ee X-Newsreader: TIN [version 1.2 PL2] Hi, Do somebody knows, is there some program what can analyze (predict) how you PCR praimers are behaiving in mixture, if you are using more than two oligos at time. For example you have 10 different primers in mix. To avoid that one primer of one pair anneals with another praimer from another pair. Tõnu Margus From owner-software@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!newsfeed.nacamar.de!univ-lyon1.fr!news.ujf-grenoble.fr!ciril.fr!u-strasbg.fr!news From: pingouin@chouchen.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: ISO Alignment and Phylogenetic Tree Software Date: 6 Jan 1998 08:06:23 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 59 Message-ID: <68solv$osm@news.u-strasbg.fr> References: Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: chouchen.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 To: skoufs@pantheon.yale.edu [posted and mailed] In article , Emmanuel Skoufos writes: > Dear Bionetters: > > I am looking for a *single* software package (shareware or commercial > product at a reasonable cost - < $ 500) that runs on Wintel platforms and > does the following things: > > -Aligns multiple DNA and protein sequences > > *and* > > -Builds phylogenetic trees based on the alignments. > > Optimally, cutting and pasting of the sequences is allowed and the tree > building is an easily executed option on the command menu/tool bar. > > I tried several packages that either did not allow tree construction > (DNASIS, Prophet) or the user interface was inpractically complicated > (PHYLIP). I know that there are a few programs for Macs (including the > DNASIS version for the Mac) that can do this. > > If you have any products in mind for a PC, or if any of the products you > are using does the trick, please let me know. Well, for sure, you can try ClustalX, which is free (well, we accept your $500 grant anyway if you don't know what to do with it ;-). It performs multiple alignment of protein or DNA (using a transversion/transition matrix if needed or any matrix you would like to use). It also builds simple phylogenetic trees (but I recommand you try Phylip ALSO if you need important tree analysis). Everything is driven by pull down menus. You can cut and paste sequences to change the order or to make a hand-driven ordering alignment. This software should fit your needs, hopefully. You can get the last version and doc at : ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ Also, for an overview of the programme, just have a look at: Nucleic Acids Research Volume 25, Issue 24, Dec 15 1997 (hey! That was my birthday ;-). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Julie D. Thompson, Toby J. Gibson, Frédéric Plewniak, François Jeanmougin and Desmond G. Higgins pp. 4876-4882 And please let me know if everything works well at your site. François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-software@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!news.maxwell.syr.edu!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!207.44.3.66!news-out.microserve.net!news-in.microserve.net!not-for-mail From: "Robert P. Gendron" Newsgroups: bionet.software Subject: Free sotware for teaching ecology Date: Tue, 06 Jan 1998 12:03:58 -0500 Organization: Microserve Information Systems (800)-380-INET Lines: 24 Distribution: world Message-ID: <34B263FE.D1DD259E@grove.iup.edu> NNTP-Posting-Host: ppp1-40.pittgate1.microserve.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; U) If you teach college-level ecology you may be interested in two programs I wrote for my ecology class. You can download them from my web site and use them free of charge. POPSIZE is a simulation of the mark-recapture method for estimating population size. I use it to supplement an exercise carried out with real populations in the field. With this program students can run hundreds or thousands of simulated mark-recapture experiments and observe the result. Sample size, mortality and emigration can all be varied to see how this affects the estimate. There are also two models to choose from. In addition to what it teaches about the mark-recapture method this program also gives students a more intuitive grasp of statistical sampling in general. For example, students should have a better understanding of what a 95% confidence limit means after running the simulation 1000 times and observing that the confidence limits do not always encompass the true population size. COMPETE teaches about the Lotka-Volterra competition model. By varying parameters such as initial population size, reproductive rate and competition coefficients tudents can carry out "what if" experiments to study the theoretical dynamics of competing populations. To download these programs go to http://www.iup.edu/~rgendron From owner-software@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!205.139.102.6!news.fta.com!not-for-mail From: "Mike Clark" Newsgroups: alt.binaries.w-software,alt.comp.software.tools,aol.commerce.computers.forsale,aol.commerce.general,bionet.software,bionet.software.pc,bit.software,biz.comp.software,comp.infosystems.www.servers.misc,comp.infosystems.www.servers.ms-windows,comp. Subject: +++ Microsoft SiteServer 2.0 Enteprise $200 +++ Date: Mon, 5 Jan 1998 22:16:35 -0800 Organization: Internet Partners, Inc. Lines: 8 Message-ID: <68si36$dvm$1@news.fta.com> NNTP-Posting-Host: ip-port-cs0-37.ipinc.net X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 One copy of Microsoft SiteServer 2.0 for $200. No box or maulas, just the CDs factory sealed with the CD Key on the back. Email if interested. MC From owner-software@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!204.71.76.137!news.campus.mci.net!n-f-m From: "Michael W. Thompson" Newsgroups: bionet.software Subject: Re: Netscape or IE most used? Date: Tue, 06 Jan 1998 19:59:44 -0500 Organization: CampusMCI Lines: 22 Message-ID: <34B2D380.169888F5@nowhere.noway.nohow> References: <68j5nq$eca$1@nntp1.ba.best.com> <68jdae$231$1@flotsam.uits.indiana.edu> <01bd1845$8ecdbd60$0613ccc2@computer-1> Reply-To: nospam@nospam.noway.nohow NNTP-Posting-Host: s26-pm07.uky.campus.mci.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (Win95; I) nikvikon wrote: > Where can I get Netscape? Help me please. > > -- > Nikvikon. http://www.netscape.com -- Michael W. Thompson Univ. of Kentucky, Dept. of Biochemistry Western Kentucky Photo Gallery: http://sac.uky.edu/~mthom0/sitemap.htm Wildflowers of Western Kentucky: http://sac.uky.edu/~mthom0/flora.htm From owner-software@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!daresbury!uninett.no!news-feed.ifi.uio.no!recycled.news.erols.com!nntp.news.xara.net!xara.net!news.itg.net.uk!usenet From: "Mark Gillespie" Newsgroups: bionet.software Subject: Fax On Demand Date: Wed, 7 Jan 1998 19:45:19 -0000 Organization: Lines: 8 Message-ID: <690lv5$ms0$1@heliodor.xara.net> NNTP-Posting-Host: 194.126.95.166 X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Anybody know of some good Fax On Demand Server Software? NT4 or DOS based, for about 300 documents? From owner-software@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!newscore.univie.ac.at!newsfeed.Austria.EU.net!magnet.at!not-for-mail From: tom@freetech-mall.com (Freetech) Newsgroups: bionet.software Subject: !BULK MAIL SOFTWARE FOR THE BEST PRICE!! Date: Wed, 07 Jan 1998 23:46:02 GMT Organization: magnet Gesellschaft für digitale Kommunikation m.b.H Lines: 9 Message-ID: <34b40957.7821176@news.magnet.at> NNTP-Posting-Host: 195.3.66.37 X-Newsreader: Forte Free Agent 1.11/32.235 WHEN YOU ORDER ANY OF OUR BULK MAIL PROFRAMMS YOU GET 5 MILLION EMAIL ADDRESSES FOR FREE!!! FOR MORE INFO: http://www.freetech-mall.com From owner-software@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!wuff.mayn.de!news-nue1.dfn.de!news-mue1.dfn.de!rzg.mpg.de!not-for-mail From: Petra Maierl Newsgroups: bionet.microbiology,bionet.software Subject: PEDANT update Date: Wed, 07 Jan 1998 13:14:51 +0100 Organization: MIPS Lines: 77 Message-ID: <34B371BB.167E@mips.biochem.mpg.de> NNTP-Posting-Host: roe.mips.biochem.mpg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.04 (X11; I; OSF1 V3.2 alpha) Xref: biosci bionet.microbiology:12103 bionet.software:20271 The PEDANT genome analysis server has been updated. Three new genomic sequences have been added: - M.thermoautotrophicum - A.fulgidus - B.burgdorferi The Bacillus subtilis genome is now complete. The following genomes have been updated: - S.cerevisiae - M.genitalium - M.pneumoniae - M.jannaschii - Synechocystis sp. - H.influenzae - E.coli Your comments and criticisms are welcome. ---------------------------------------------------------------- PEDANT: Protein Extraction, Description, and ANalysis Tool http://pedant.mips.biochem.mpg.de/frishman/pedant.html Features: - Twelve complete and one partial genomes plus one plasmid analyzed so far: S.cerevisiae M.genitalium M.jannaschii Synechocystis sp. H.influenzae E.coli H.pylori B.subtilis M.thermoautotrophicum A.fulgidus B.burgdorferi S.solfataricus (fragment) Rhizobium sp. (plasmid) - Exhaustive functional and structural classification of the predicted open reading frames from fully sequenced genomes using a combination of sequence comparison and prediction techniques - Functional assignment of ORFs on the basis of FASTA2 and BLAST2 similarity searches supplemented by detection of PROSITE patterns and motifs and comparisons with conserved sequence blocks - Automatic attribution of sequences with significantly related PIR entries to one of the PIR super-families - Functional classification of gene products through similarity searches against several curated master gene sets from bacteria and yeast with manually assigned functional classes - Extraction of available 3D information through Smith-Waterman similarity comparisons of every sequence with the STRIDE database of secondary structure assignments - Secondary structure and transmembrane region predictions - Detection of low-complexity and coiled coil regions ---------------------------------------------------------------- Dmitrij Frishman, Petra Maierl, and Hans-Werner Mewes Munich Information Centre for Protein sequences/GSF http://www.mips.biochem.mpg.de M.pneumoniae From owner-software@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!newscore.univie.ac.at!newsfeed.Austria.EU.net!magnet.at!not-for-mail From: tom@freetech-mall.com (Freetech) Newsgroups: bionet.software Subject: A FREE..!WHEN YOU ORDER ANY OF OUR BULK MAIL PROGRAMMS YOU GET 5MILLION EMAIL ADDRESSES FOR FREE!!! Date: Wed, 07 Jan 1998 23:46:09 GMT Organization: magnet Gesellschaft für digitale Kommunikation m.b.H Lines: 5 Message-ID: <34b40960.7830425@news.magnet.at> NNTP-Posting-Host: 195.3.66.37 X-Newsreader: Forte Free Agent 1.11/32.235 for more info: http://www.freetech-mall.com From owner-software@net.bio.net Tue Jan 06 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!128.122.253.92!newsfeed.nyu.edu!news.nyu.edu!mcrcr1.med.nyu.edu!user From: browns02@mcrcr.med.nyu.edu (Stuart M. Brown) Newsgroups: bionet.software Subject: Re: Multiple PCR primer analysis? Date: Wed, 07 Jan 1998 10:58:43 -0500 Organization: NYU-MC Research Computing Resource Lines: 38 Message-ID: References: <68tg2r$isb$1@kadri.ut.ee> NNTP-Posting-Host: mcrcr1.med.nyu.edu X-Trace: news.nyu.edu 884188199 9127 (None) 128.122.135.49 X-Complaints-To: usenet@news.nyu.edu In article <68tg2r$isb$1@kadri.ut.ee>, tmargus@tamm.eenet.ee (Tonu Margus) wrote: > Hi, > > > Do somebody knows, is there some program what can analyze (predict) how you > PCR praimers are behaiving in mixture, if you are using more than two oligos > at time. For example you have 10 different primers in mix. > > To avoid that one primer of one pair anneals with another praimer from > another pair. > > Tõnu Margus I have used a program called Right Primer that has multiple primer (multiplex) analysis. I can't say how theoretically valid this analysis might be. From a practical standpoint, most multiplex PCRs seem to work just fine unless you have some totally obvious complementarity between primers. Right Primer BioDisk Software P.O. Box 26447 San Francisco, CA 94126 U.S.A. Voice: (800) 664-DISK/(415) 951-9031 Fax: (415) 951-0102 Internet: sales@biodisk.com Price is $395.00. Non-profits and accredited Colleges and Universities are entitled to a special educational price of $245.00. OUTSIDE NORTH AMERICA: Price is $450.00 or $295.00 for non-profits. -- Stuart M. Brown, Molecular Biology Consultant NYU-MC Research Computing Resource, Dept. of Cell Biology 550 First Ave, New York, NY 10016 Phone: (212)263-7689 FAX: (212)263-8139 From owner-software@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!eerie.fr!jussieu.fr!saphir.jouy.inra.fr!not-for-mail From: Farid Chetouani Newsgroups: bionet.software Subject: ESSA : AN RNA SECONDARY STRUCTURE TOOL Date: Thu, 08 Jan 1998 08:05:38 +0100 Organization: CNRS IBCG LBME Lines: 54 Message-ID: <34B47AC2.5DCE@ibcg.biotoul.fr> NNTP-Posting-Host: ossau.toulouse.inra.fr Mime-Version: 1.0 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5 sun4d) Content-Disposition: inline Received: from hpsrv.biotoul.fr (hpsrv.biotoul.fr [192.93.46.1]) by ossau.toulouse.inra.fr (8.8.8/8.8.8) with SMTP id HAA18052 for ; Thu, 8 Jan 1998 07:54:56 +0100 (MET) Received: from oceane.cict.fr by hpsrv.biotoul.fr with SMTP id AA17099; Thu, 8 Jan 98 07:56:22 +0100 Posted-Date: Thu, 08 Jan 1998 07:54:43 +0100 Received-Date: Thu, 8 Jan 98 07:56:22 +0100 Received: from news.cict.fr (news.cict.fr [195.220.59.3]) by oceane.cict.fr (8.8.3/8.7.4) with SMTP id HAA16753; Thu, 8 Jan 1998 07:54:49 +0100 (MET) Received: by news.cict.fr (SMI-8.6/SMI-SVR4) id HAA21012; Thu, 8 Jan 1998 07:54:46 +0100 To: bionet-software-www@moderators.usenet.fr.net Path: not-for-mail From: Farid Chetouani Newsgroups: bionet.software.gcg,bionet.software.www Subject: ESSA : AN RNA SECONDARY STRUCTURE TOOL Date: Thu, 08 Jan 1998 07:54:43 +0100 Organization: CNRS IBCG LBME Message-Id: <34B47833.47B8@ibcg.biotoul.fr> Nntp-Posting-Host: ossau.toulouse.inra.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5 sun4d) Cc: farid@ibcg.biotoul.fr Hello ESSA software propose an approach of RNA secondary structure analysis based on extensive viewing within a friendly graphical interface. This computer program is organized around the display of folding models produced by two complementary methods suitable to draw long RNA molecules. Any feature of interest can be managed directly on the display and highlighted by a rich combination of colors and symbols with emphasis given to structural probe accessibilities. ESSA includes also a word searching procedure allowing an easy visual identification of structural features even complex and degenerated. Analysis functions make it possible to calculate the thermodynamic stability of any part of a folding using several models and compare homologous aligned RNA both in primary and secondary structure. for more information or download go to th url http://www-bia.inra.fr/T/essa/Doc/essa_home.html sincerely yours ESSA team From owner-software@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!howland.erols.net!ais.net!uunet!in1.uu.net!iafrica.com!uct.uni.net.za!csir.uni.net.za!news.up.ac.za!biomac.up.ac.za!user From: fourie@scientia.up.ac.za (Fourie Joubert) Newsgroups: bionet.molec-model,bionet.software Subject: sybdb script in DOCK? Date: Thu, 08 Jan 1998 13:06:12 +0200 Organization: University of Pretoria Lines: 9 Message-ID: NNTP-Posting-Host: biomac.up.ac.za Xref: biosci bionet.molec-model:1977 bionet.software:20277 Hi Does anyone know of an update for the sybdb script in DOCK4.0 that works with Sybyl 6.2 or 6.3's SPL? Thanks! Fourie Joubert fourie@scientia.up.ac.za From owner-software@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!newsfeed.eerie.fr!jussieu.fr!pasteur.fr!not-for-mail From: Annick Thébault Newsgroups: bionet.software Subject: Ftp server for molecular biology in Pasteur Institute Date: Fri, 09 Jan 1998 10:53:38 +0100 Organization: Institut Pasteur Lines: 8 Message-ID: <34B5F3A0.7363@pasteur.fr> NNTP-Posting-Host: eper.sis.pasteur.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: montespan.pasteur.fr 884339507 15317 (None) 157.99.60.45 X-Complaints-To: newsmaster@pasteur.fr X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC) CC: thebault@pasteur.fr Please visit our ftp server (ftp://ftp.pasteur.fr/pub/GenSoft) It contains distributions for molecular biology packages for Unix, MacIntosh and Windows, as well a a mirror of IUBio archive. --- Annick Thébault - SIS - Institut Pasteur - Paris thebault@pasteur.fr From owner-software@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!205.252.116.205!howland.erols.net!vixen.cso.uiuc.edu!Lightyear From: Lightyear@uiuc.edu (Matthew Vaughn) Newsgroups: bionet.software Subject: Re: Low emission computer monitor Date: Fri, 09 Jan 1998 13:23:23 -0600 Organization: US Robotics and Mechanical Men Lines: 28 Message-ID: References: <695jiq$7ms@snews2.zippo.com> NNTP-Posting-Host: bushlab1.life.uiuc.edu X-Newsreader: MT-NewsWatcher 2.3.5 X-Face: $VCBL>c'm[sO:~:%UH#A--p2Mjs163<#Yal[|)8@\?Yj"&7`l(h:-VDzvSu3! 2AU,zEj|^Fu`Igw%qgr'0e)V:pp@$OG&,gIYy>Z"$VO#CX0"&:4vH|sekTYL[r"tT} I'd consider an LCD screen as your solution... you will pay for a newer one but there may be used (grayscale) out there for less.. In article <695jiq$7ms@snews2.zippo.com>, "M. Muz Zviman" wrote: > Hi, > We are looking for a low em emission SVGA monitor for electrophysiology rig. > I would appreciate any recommendations. > > > Muz > > > > ******************************************************************** > M. Muz Zviman, Ph.D. > Monell Chemical Senses Center > Philadelphia, PA 19104 In theory, there is no difference between theory and practice; in practice, however, there is no similarity Matthew Vaughn University of Illinois Department of Biology 190 ERML 1201 W. Gregory Drive Urbana, IL 61801 mwvaugh@uiuc.edu From owner-software@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!vixen.cso.uiuc.edu!howland.erols.net!newsfeed.internetmci.com!205.185.79.5!zdc!szdc!super.zippo.com!newsp.zippo.com!snews2 From: "M. Muz Zviman" Newsgroups: bionet.software Subject: Low emission computer monitor Date: Fri, 9 Jan 1998 11:37:58 -0500 Organization: Monell Chemical Senses Center Lines: 16 Message-ID: <695jiq$7ms@snews2.zippo.com> NNTP-Posting-Host: p-779.newsdawg.com X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Hi, We are looking for a low em emission SVGA monitor for electrophysiology rig. I would appreciate any recommendations. Muz ******************************************************************** M. Muz Zviman, Ph.D. Monell Chemical Senses Center Philadelphia, PA 19104 From owner-software@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!128.223.220.30!logbridge.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!csn!nntp-xfer-1.csn.net!news-2.csn.net!not-for-mail From: resume@peakweb.com (Colorado Online Job Connection) Newsgroups: comp.protocols.dicom,alt.image.medical,bionet.software Subject: Job - US CO - Software Developer, DICOM C / C++ Date: Fri, 09 Jan 1998 20:50:08 GMT Organization: Peak Career Management, Inc. Lines: 43 Message-ID: <34b68d42.14297683@news-2.csn.net> Reply-To: resume@peakweb.com NNTP-Posting-Host: 204.133.28.11 X-Newsreader: Forte Free Agent 1.1/32.230 Rocky Mountain based Visualization Software Development Firm needs the following: Medical Imaging Developer - C / C++, DICOM Top compensation and benefits Also need: Windows Project Lead Windows C++ Developers Mac Developers Visualization (OpenGL/X- Windows) Developers Quality Software Engineers Technical Sales Engineers Medical Software Product Manager Experience in Visualization and commercial software development a BIG Plus. Development firm is in a major growth transition. Join an excellent team in the Rockies. If you are interested, please contact Steve Parker at (303)316-0800 or email your resume to stevep@peakweb.com and reference "Job Code - DICOMStevePNews" in the subject line of your email. Do not fax or snail mail your resume. Thanks Steve Parker Peak Career Management Inc. Posted by: ------------------------------------- Employers "WebWire" your jobs on the Colorado Online Job Connection http://www.jobsincolorado.com cojcinfo@peakweb.com Hosted by: Peak Career Management, Inc. Contact: Steve Parker, stevep@peakweb.com (303)316-0800, FAX (303)316-0700 From owner-software@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!biosci!not-for-mail From: Gil Kedem Newsgroups: bionet.software,bionet.software.gcg Subject: New company interested in learning your unmet bioinformatics software needs Date: 9 Jan 1998 01:35:54 -0800 Organization: Kedem Associates (http://www.yoga.com/kedem) Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <34AD1FA0.A8E083F2@yoga.com> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:20279 bionet.software.gcg:2938 Hello, Kedem Associates is a recently formed, tiny startup founded to provide AFFORDABLE bioinformatics software. We are located in the biotech hotbed of Cambridge, MA. As a new firm, we are interested in learning about your unmet bioinformatics software needs. For instance, what web-based tools would you need to provide interfaces to such public programs as BLAST, fasta, multi-alignment, etc. Do you already use such tools--if so which? Are there other affordable tools you would like to see in the marketplace? Also, would anyone be interested in software that provides web-based system integration of public databases? If so, what kind of tools do you envision? Finally, what kind of software needs do you see emerging for biochips or molecular diagnostics? Your thoughts would be appreciated--we will respond to each email. Thanks, Gil -- Gil Kedem Kedem Associates gil@yoga.com 617-497-6374 87 Fresh Pond Pkwy, Cambridge, MA 02138 From owner-software@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!newshost.lanl.gov!not-for-mail From: Carla Kuiken Newsgroups: bionet.software Subject: UNIX database software? Date: Fri, 09 Jan 1998 15:11:29 -0700 Organization: Los Alamos National Laboratory Lines: 17 Message-ID: <34B6A091.A52@t10.lanl.gov> NNTP-Posting-Host: intron.lanl.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4m) We're a small group maintaining a sequence database on a UNIX platform. We're currently using Sybase for our database work, but this is getting prohibilively expensive, so we're looking for an alternative. The database is not large, but it's fairly complicated. We're in the process providing web access to it (which is why Sybase suddenly wants a lot more money for the license). We store genetic sequences and background info, and are currently adding links to Medline, Genbank etc. What database programs (if any) do other people use for this type of work? There must be more to choose from than just Informix, Sybase and Oracle, but we haven't seen much yet. Any tips, advice or horror stories much appreciated! Thanks very much in advance. Carla Kuiken HIV Sequence Database Los Alamos National Laboratory From owner-software@net.bio.net Fri Jan 09 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!newsxfer3.itd.umich.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!europa.clark.net!194.159.255.21!dispose.news.demon.net!demon!bullseye.news.demon.net!demon!newsfeed.xs4all.nl!xs4all!nestorix2.xs4all.nl!user From: a_team@dds.nl (A-team) Newsgroups: bionet.software,sci.image.processing Subject: NIH-Image ftp address correction Date: Sat, 10 Jan 1998 16:57:52 +0100 Organization: XS4ALL, networking for the masses Sender: @asd12-29.dial.xs4all.nl Message-ID: NNTP-Posting-Host: asd12-29.dial.xs4all.nl X-XS4ALL-Date: Sat, 10 Jan 1998 16:55:28 CET X-XS4ALL-User: amtha@xs4all.nl on asd12-29.dial.xs4all.nl Lines: 13 Rather than ... ftp://zippy.nimh.nih.gov/pub/image ... as I abusively mentioned, the correct URL is or the free image processing program. Versions for PC are also available, but you might try to locate them at www.scioncorp.com Ard From owner-software@net.bio.net Fri Jan 09 22:00:00 1998 Newsgroups: bionet.software Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!newsfeed.acns.nwu.edu!uchinews!news From: "John S. Moses" Subject: Re: UNIX database software? X-Nntp-Posting-Host: ntcs-ip3.uchicago.edu Content-Type: text/plain; charset=us-ascii Message-ID: <34B70475.21F7B5C6@genetics.uchicago.edu> Sender: news@midway.uchicago.edu (News Administrator) Reply-To: jmoses@redsea.uchicago.edu Content-Transfer-Encoding: 7bit Organization: Department of Human Genetics References: <34B6A091.A52@t10.lanl.gov> Mime-Version: 1.0 Date: Sat, 10 Jan 1998 05:17:41 GMT X-Mailer: Mozilla 4.04 [en] (Win95; I) Lines: 53 Hi Carla, Check out the following sites. They may be robust enough for what you would like to do, but web-enabling them is well documented. SQL Databases: PostgreSQL: http://www.postgresql.org/ MiniSQL: http://www.hughes.com.au/ MySQL: http://www.tcx.se/ Server-side web-scripting: PHP/FI: http://php.iquest.net/ Hope that helps...John. Carla Kuiken wrote: > We're a small group maintaining a sequence database on a UNIX platform. > We're currently using Sybase for our database work, but this is getting > prohibilively expensive, so we're looking for an alternative. > > The database is not large, but it's fairly complicated. We're in the > process providing web access to it (which is why Sybase suddenly wants a > lot more money for the license). We store genetic sequences and > background info, and are currently adding links to Medline, Genbank etc. > > What database programs (if any) do other people use for this type of > work? There must be more to choose from than just Informix, Sybase and > Oracle, but we haven't seen much yet. Any tips, advice or horror stories > much appreciated! Thanks very much in advance. > > Carla Kuiken > HIV Sequence Database > Los Alamos National Laboratory -- ------------------------------------- Office of Information Systems Department of Human Genetics The University of Chicago 924 E. 57th St., R133 Chicago, IL 60637 U.S.A. Phone: (773) 834-1038 Fax: (773) 834-0505 e-mail: jmoses@genetics.uchicago.edu Web: http://www.genes.uchicago.edu From owner-software@net.bio.net Fri Jan 09 22:00:00 1998 From: thomas@evolution.bmc.uu.se (Thomas Sicheritz) Subject: Re: UNIX database software? Newsgroups: bionet.software References: <34B6A091.A52@t10.lanl.gov> Lines: 35 X-Newsreader: TIN [UNIX 1.3 unoff BETA release 960725] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit NNTP-Posting-Host: evolution.bmc.uu.se Message-ID: <34b75e9e.0@newsfeed.uu.se> Date: 10 Jan 98 11:42:22 GMT Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!209.95.128.196!news-nyc.telia.net!masternews.telia.net!fci-se!fci!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!130.238.7.13.MISMATCH!newsfeed.uu.se!evolution.bmc.uu.se!not-for-mail In bionet.software Carla Kuiken wrote: : We're a small group maintaining a sequence database on a UNIX platform. : We're currently using Sybase for our database work, but this is getting : prohibilively expensive, so we're looking for an alternative. : The database is not large, but it's fairly complicated. We're in the : process providing web access to it (which is why Sybase suddenly wants a : lot more money for the license). We store genetic sequences and : background info, and are currently adding links to Medline, Genbank etc. : What database programs (if any) do other people use for this type of : work? There must be more to choose from than just Informix, Sybase and : Oracle, but we haven't seen much yet. Any tips, advice or horror stories : much appreciated! Thanks very much in advance. : Carla Kuiken : HIV Sequence Database : Los Alamos National Laboratory We use postgresql(http://www.postgresql.org) together with Tcl/Tk and perl for our 'whole genome sequencing project' at Gnomics http://evolution.bmc.uu.se/~siv/gnomics/ The database is called CAPdb ... -thomas (P.S its free ...) -- Sicheritz Ponten Thomas E. UPPSALA UNIVERSITY Vaksalagatan 29C S-753 31 Uppsala Biomedical Center Home: +46 18 129021 Department of Molecular Biology BMC: +46 18 4714214 BOX 590 S-751 24 UPPSALA Sweden Fax +46 18 557723 http://evolution.bmc.uu.se/~thomas De Chelonian Mobile ... The Turtle Moves ... From owner-software@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.125.85.9!news.mv.net!newspump.wustl.edu!newsreader.wustl.edu!not-for-mail From: reece@whoville.wustl.edu Newsgroups: bionet.software Subject: RASMOL: linux patch for 2.6beta Date: 11 Jan 1998 16:50:46 -0600 Organization: Biophysics & Biochemistry, Washington University, St. Louis, USA Lines: 32 Message-ID: <82n2h2fwvt.fsf@whoville.wustl.edu> Reply-To: Reece Kimball Hart NNTP-Posting-Host: whoville.wustl.edu X-Attribution: Reece X-URL: X-Newsreader: Gnus v5.5/Emacs 20.2 -----BEGIN PGP SIGNED MESSAGE----- This patch is for RasMol 2.6beta on linux systems. It has no effect in other environments. It corrects the following compilation errors: rasmol.c: In function `FetchCharacter': rasmol.c:491: `WaitSet' has an incomplete type rasmol.c:497: warning: passing arg 2 of `select' ... rasmol.c:497: warning: passing arg 3 of `select' ... rasmol.c:497: warning: passing arg 4 of `select' ... rasmol.c: At top level: rasmol.c:112: storage size of `OrigWaitSet' isn't known rasmol.c:113: storage size of `WaitSet' isn't known The patch is available at http://dasher.wustl.edu/~reece/src/RasMol2.6b-linux-01.patch.gz ftp://dasher.wustl.edu/pub/reece/src/RasMol2.6b-linux-01.patch.gz - -- Reece Hart, http://dasher.wustl.edu/~reece/ Do not send unsolicited bulk email. Boycott companies which do so. -----BEGIN PGP SIGNATURE----- Version: 2.6.3ia Charset: noconv Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface iQCVAwUBNLlMskxUVHHReKr5AQGydgP9HK/GGm9A28jYbN5fDk6Ox/WWuF5UO/Ce rUrZYPgcYcmWjkl9zQMUfErYOSlCN+Vnj1M+qtyBKCU1ji88Qs9Hy1bh339E9+HF s2837ySCToPw+la/3Yp8btwcVUI48BtPdIXPgrXnqqH5yh9t1EvmOWji/XbmVI1y 6OGEwtLB23Y= =n8kW -----END PGP SIGNATURE----- From owner-software@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!news.scripps.edu!not-for-mail From: Duncan McRee Newsgroups: bionet.xtallography,bionet.software,sci.techniques.xtallography Subject: XtalView 3.2 available Date: Sat, 10 Jan 1998 16:49:13 -0800 Organization: The Scripps Research Institute Lines: 38 Message-ID: <34B81709.AD43277F@scripps.edu> Reply-To: dem@scripps.edu NNTP-Posting-Host: pppuser240.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) Xref: biosci bionet.xtallography:3979 bionet.software:20289 XtalView 3.2 is available for downloading at: http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html XtalView is free to academics and non-profits. XtalView is a crystallographic software package for fitting electron density maps and solving structures by MIR and MAD that works on most UNIX platforms. Molecular modelers will find XtalView/xfit very useful. Details on new features can be found at: http://www.scripps.edu/pub/dem-web/toc.html A short synopsis of some new features in the fitting program: SigmaA coefficient maps FFT's in both directions built in change- map resolution/terms on-the-fly Refine-while-fit of a residue range - drag side-chains into density Raster3D interface New dictionaries, noH, polarH, allH, more conformers Real-time contour levels Ribozyme code added to residue insert Anisotropic B (U's) including "ORTEP-like" eggs SHELX-97 support including LIST 6 CIF format Split-residue support IRIX 6 added and LINUX "unwanted geatures" removed Duncan McRee Molecular Biology - MB8 The Scripps Research Institute 10550 N. Torrey Pines Rd La Jolla, CA 92037 (619)784-9235 dem@scripps.edu From owner-software@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cam-news-feed3.bbnplanet.com!news.bbnplanet.com!das-news2.harvard.edu!oitnews.harvard.edu!news From: Jong Park Newsgroups: bionet.software Subject: Re: Low emission computer monitor Date: Sat, 10 Jan 1998 20:47:48 -0500 Organization: Church Lab. Genetics/Harvard Med. School Lines: 26 Message-ID: <34B824C4.63DE@rascal.med.harvard.edu> References: <695jiq$7ms@snews2.zippo.com> NNTP-Posting-Host: arep.med.harvard.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V4.0 alpha) To: "M. Muz Zviman" M. Muz Zviman wrote: > > Hi, > We are looking for a low em emission SVGA monitor for electrophysiology rig. > I would appreciate any recommendations. > > Muz > > ******************************************************************** > M. Muz Zviman, Ph.D. > Monell Chemical Senses Center > Philadelphia, PA 19104 Use LCD monitor. I have a long experience of monitors and in my personal opinion, we should stop using CRTs as soon as possble and replace them with LCD. Regards, http://www.cat.nyu.edu/fox/lcd-monitors.html Jong From owner-software@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!Supernews60!supernews.com!Supernews69!not-for-mail From: "joedapro" Newsgroups: bionet.software Subject: NEW ! PC BASED BUSINESS WILL MAKE YOU SUCCEED IN MLM ! Date: Sat, 10 Jan 1998 21:35:09 -0800 Organization: All USENET -- http://www.Supernews.com Lines: 37 Message-ID: <699ks3$d93$1@usenet76.supernews.com> NNTP-Posting-Host: 13603@207.211.62.211 X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 These will be your activities: * POST A FEW ARTICLES TO USENET NEWSGROUPS (Like this one). * WHEN PEOPLE REPLY, SEND THEM OUR FREE SOFTWARE VIA E-MAIL AS ATTACHMENT. OR GIVE THEM YOUR WEB PAGE ADDRESS WHERE THEY CAN DOWNLOAD IT. * THE SOFTWARE PROVIDES THE COMPLETE INFORMATION AND TOOLS NEEDED TO RUN THIS AMAZING BUSINESS. * WAIT FOR THE ORDERS (AND CHECKS) TO COME IN THE MAIL. * WHEN THE ORDERS COME IN, SEND THEM OUR PRODUCTS VIA E-MAIL. YOU DON'T PAY POSTAGE. * KEEP POSTING ARTICLES UNTIL YOU RECEIVE AT LEAST 10 ORDERS. * THIS SIMPLE STEPS WILL PRODUCE YOU THOUSANDS OF DOLLARS !. IT'S THAT EASY !. BUSINESS DOESN'T HAVE TO BE COMPLICATED. STICK WITH OUR BUSINESS AND IN A FEW MONTHS YOU WILL NOT BE THE SAME !. HOW IS THIS POSSIBLE ? THANKS TO COMPUTERS, ELECTRONIC PRODUCTS, E-MAIL AND THOUSANDS OF PEOPLE FROM ALL OVER THE WORLD WILLING TO WORK AS A TEAM, HELPING EACH OTHER. REPLY TO THIS ARTICLE AND I WILL SEND YOU A FREE COPY OF OUR EXCLUSIVE SOFTWARE, PC-SUPER-MLM. Contact Joe at: joedapro@hotmail.com Subject: PSM From owner-software@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!news.syd.connect.com.au!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!199.125.85.9!news.mv.net!newspump.wustl.edu!newsreader.wustl.edu!not-for-mail From: reece@whoville.wustl.edu Newsgroups: bionet.software Subject: RASMOL: spaceorb patch for 2.6beta Date: 11 Jan 1998 17:16:53 -0600 Organization: Biophysics & Biochemistry, Washington University, St. Louis, USA Lines: 29 Message-ID: <82k9c6fvoa.fsf@whoville.wustl.edu> Reply-To: Reece Kimball Hart NNTP-Posting-Host: whoville.wustl.edu X-Attribution: Reece X-URL: X-Newsreader: Gnus v5.5/Emacs 20.2 -----BEGIN PGP SIGNED MESSAGE----- This patch adds SpaceOrb360 support to RasMol 2.6beta. This patch has only been tested with Linux; compatibility reports and patches for other systems are appreciated. The SpaceOrb is a 6 degree of freedom joystick. It looks like a baseball mounted on a short shaft; the baseball rotates ±20° or so and translates about ±5mm from rest. See http://www.spaceorb.com. Thanks to John Stone for orb.[ch]. The patch is available at http://dasher.wustl.edu/~reece/src/RasMol2.6b-spaceorb-01.patch.gz ftp://dasher.wustl.edu/pub/reece/src/RasMol2.6b-spaceorb-01.patch.gz - -- Reece Hart, http://dasher.wustl.edu/~reece/ -----BEGIN PGP SIGNATURE----- Version: 2.6.3ia Charset: noconv Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface iQCVAwUBNLlS1UxUVHHReKr5AQGfIgP/dr+SRTsRWAakjP1so8BmxoeWK3gTBVGQ gWU9fRiCYz1lE/lLVExULQOfRN34vSQt3nGp2OkrAbAr645xAP89qJiD82QeY5SH dCs3EwcSmJtYffxz1yGVXxdKSLizcEA9fM7QuMweRta8c1WnnrtPReub82PnZ2tM 22HTQqbelKw= =Al3k -----END PGP SIGNATURE----- From owner-software@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!vixen.cso.uiuc.edu!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!portc02.blue.aol.com!audrey02.news.aol.com!not-for-mail From: jlulchen@aol.com (Jlulchen) Newsgroups: bionet.software Subject: a multiple alignment program wanted? Date: 12 Jan 1998 00:12:04 GMT Lines: 8 Message-ID: <19980112001200.TAA10490@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Hi, I need a UNIX or other machine based program to do multiple alignments analysis of DNA sequences. Currently I am using clustalw to do the analysis download from NCBI site. Is there anyone who knows other software to do multiple DNA sequence alignments other than clustalw? Many thanks if you can give me info how to get the software! I can be reached at jlulchen@aol.com From owner-software@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!164.67.42.145!awabi.library.ucla.edu!132.239.254.208!ihnp4.ucsd.edu!news1.ucsd.edu!jstrout From: jstrout@ucsd.edu (Joseph J. Strout) Newsgroups: bionet.software Subject: Re: GelReader on PowerPC Mac Date: Mon, 12 Jan 1998 12:46:37 -0800 Organization: UCSD Lines: 25 Message-ID: References: <69dah2$doh@newsops.execpc.com> NNTP-Posting-Host: gandalf.ucsd.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 In article <69dah2$doh@newsops.execpc.com>, Alan Friedman wrote: >For years, I ran NCSA GelReader on my old Mac II and had no problems. >However, the software would sometimes fail to run on my Performa 6116CD; >but not always... However >the problem was solved when I ran a game that requires that the monitor >control panel be set to 256 colors. When a friend came over to see the >problem with gel reader, it ran perfectly! When we switched back to >thousands of colors, it failed again. This is fairly common among poorly written Mac software; the Instrutech "Pulse + PulseFit" electrophysiology software has similar limitations, not mentioned anywhere in the documentation. (Good Mac software would either tell you it can't run at the higher screen depth, or just change it for you.) You're absolutely right, this is a gotcha to watch for, and thanks for pointing it out! Cheers, -- Joe ,------------------------------------------------------------------. | Joseph J. Strout Department of Neuroscience, UCSD | | jstrout@ucsd.edu http://www-acs.ucsd.edu/~jstrout/ | `------------------------------------------------------------------' From owner-software@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!205.173.251.8!news.iamerica.net!not-for-mail From: "nice" Newsgroups: bionet.software Subject: Looking for Telephone program. Date: 12 Jan 1998 22:13:45 GMT Organization: LDS iAmerica, ISP Lines: 7 Message-ID: <01bd1fb7$e2777e00$1b4a65cf@default> NNTP-Posting-Host: 207.101.74.27 X-Newsreader: Microsoft Internet News 4.70.1161 My mom has a Packard Bell computer. It came with a program called "Call Center" It allows you to make calls from the computer and it is also acts as an answering machine. I have an Acer computer and am looking for a program like hers. I don't neccesarly want the software for talking over the Internet.I know that there are a lot of them "Internet" ones out there. I want just a telephone program. From owner-software@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!howland.erols.net!recycled.news.erols.com!nntp.news.xara.net!xara.net!server5.netnews.ja.net!news.york.ac.uk!not-for-mail From: Alex Knight Newsgroups: bionet.software Subject: MacStripe - Coiled Coil Prediction for Macintosh Date: Mon, 12 Jan 1998 14:38:14 +0000 Organization: University of York Lines: 52 Sender: aek4@york.ac.uk Message-ID: <34BA2AD6.699F9F74@york.ac.uk> Reply-To: aek4@york.ac.uk NNTP-Posting-Host: biolpc229.york.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) MacStripe is a program for the prediction and analysis of potential coiled-coil regions in protein sequences. A new and much improved version (2.0a1) is available to download now from: http://www.york.ac.uk/depts/biol/units/coils/coilcoil.html MacStripe is the ideal tool for anyone who wants to explore potential alpha-helical coiled coils in the sequence of their protein. With a full Macintosh interface, the results of analyses (raw data or publication quality plots) can easily be exported to other software. The "Inspector" window acts like a magnifying glass so you can study your protein on a residue-by-residue basis. MacStripe uses the algorithm of Andrei Lupas's COILS2 for detailed and reliable coiled-coil predictions. System Requirements: Macintosh with 68030, '040 or PowerPC processor; Colour Quickdraw; System 7.0 or better. Features: * Full Macintosh Interface * Uses established Lupas algorithm for coiled coil prediction * Full control of prediction parameters (matrix, window length, weighting) * Interactive exploration of coiled coil with "Inspector" window * Imports sequences from DNA Strider or DNASTAR formats * Reads sequences from text files in plain, FASTA or Staden formats * Uses FPU (where present) for maximum calculation speed * Plots optionally show 'skips' or 'stutters' in coiled coil which may be structurally important * Plots can be copied and pasted into other applications, saved as PICT files, or printed * Detailed statistics can be imported into spreadsheet or graphing programs * It's FREE! Please don't hesitate to contact me with suggestions, bug reports or complaints. Don't forget to check out the coiled-coil prediction web page for more information about MacStripe or other coiled-coil prediction resources. Alex -- Alex Knight (aek4@york.ac.uk) Biology Department University of York Heslington, York Y01 5DD +44 1904 434381 +44 1904 432860 (FAX) Coiled coil prediction web page: http://www.york.ac.uk/depts/biol/units/coils/coilcoil.html http://www.wi.mit.edu/matsudaira/coilcoil.html From owner-software@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!newsfeed.eerie.fr!jussieu.fr!saphir.jouy.inra.fr!not-for-mail From: Arnaud Chatonnet Newsgroups: bionet.software Subject: Re: UNIX database software? Date: Mon, 12 Jan 1998 15:03:29 +0100 Organization: INRA Lines: 10 Message-ID: <34BA22B1.3096@ensam.inra.fr> NNTP-Posting-Host: cypres.jouy.inra.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; HP-UX B.10.20 9000/819) Yes Use ACeDB it is great!!! -- ----------sans accents pour etre lu par tout le monde------------------- Arnaud Chatonnet Departement de physiologie animale Tel (33) 04 99 61 26 77 Institut National de la Recherche Agronomique Fax (33) 04 67 54 56 94 place Viala 34060 Montpellier cedex1 FRANCE E mail chatonne@ensam.inra.fr http://www.ensam.inra.fr/cholinesterase ------------------------------------------------------------------------ From owner-software@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!howland.erols.net!rill.news.pipex.net!pipex!news.algonet.se!funny.bahnhof.se!seunet!news2.swip.net!inet-1.pnu.com!not-for-mail From: Staffan Bergh Newsgroups: bionet.software Subject: Re: UNIX database software? Date: 12 Jan 1998 08:41:56 +0100 Organization: Pharmacia & Upjohn Lines: 11 Message-ID: References: <34B6A091.A52@t10.lanl.gov> NNTP-Posting-Host: sgibest.sto.se.pnu.com X-Newsreader: Gnus v5.3/Emacs 19.34 Carla, you should also check out ACEDB - http://probe.nalusda.gov:8000/acedocs/ /staffan Staffan Bergh Pharmacia & Upjohn, P14:5, SE-112 87 Stockholm, Sweden email: Staffan.Bergh@eu.pnu.com + Don't let that horse eat that violin phone: (int+46) 08 695 9884 + cried Chagall's mother fax: (int+46) 08 695 4084 + but he kept right on painting mobile: (int+46) 070 898 8829 + -- Lawrence Ferlinghetti From owner-software@net.bio.net Sun Jan 11 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeeds.sol.net!newsops.execpc.com!posts.execpc.com!daily-bugle.newsops.execpc.com!usenet From: Alan Friedman Newsgroups: bionet.software Subject: GelReader on PowerPC Mac Date: Mon, 12 Jan 1998 08:51:28 +0000 Organization: Exec-PC BBS Internet - Milwaukee, WI Lines: 16 Message-ID: <69dah2$doh@newsops.execpc.com> NNTP-Posting-Host: lafra-9.mdm.mke.execpc.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: daily-bugle.newsops.execpc.com 884616546 14097 (None) 169.207.78.11 X-Complaints-To: abuse@execpc.com X-Mailer: Mozilla 3.01 (Macintosh; U; PPC) For years, I ran NCSA GelReader on my old Mac II and had no problems. However, the software would sometimes fail to run on my Performa 6116CD; but not always. When I gave the "find band" command, I would get an insufficient memory message; I have 24 MB ram! I was desperate enough that I was about to purchase an old Mac just to run GelReader. However the problem was solved when I ran a game that requires that the monitor control panel be set to 256 colors. When a friend came over to see the problem with gel reader, it ran perfectly! When we switched back to thousands of colors, it failed again. I hope this suggestion will help those of you having problems with this software package. Alan Friedman Helix Biotech, Inc. helix@execpc.com From owner-software@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: ptribble@hgmp.mrc.ac.uk (Peter C. Tribble) Newsgroups: bionet.software Subject: Re: Ref PC' or Macs Date: 13 Jan 1998 17:30:03 GMT Organization: MRC Human Genome Mapping Project Resource Centre Lines: 15 Message-ID: <69g8ar$kmd$2@niobium.hgmp.mrc.ac.uk> References: <677a3v$qb5$1@cronkite.lanminds.com> <34986D0C.29@cc.umanitoba.ca> NNTP-Posting-Host: titanium.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article <34986D0C.29@cc.umanitoba.ca>, Brian Fristensky writes: > Funny, that's exactly the argument that made me decide to > dispense with PCs and Macs and run our lab entirely on > a Unix platform via X-terminals. Absolutely. Lab equipment often comes with special hardware to drive it, but we find general purpose computing is much cheaper to arrange on Unix boxes (not to mention more reliable, secure. etc). What I find interesting is that our lab people prefer it too... -- -Peter Tribble HGMP Computing Services http://www.hgmp.mrc.ac.uk/~ptribble/ From owner-software@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: ptribble@hgmp.mrc.ac.uk (Peter C. Tribble) Newsgroups: bionet.software Subject: Re: Netscape or IE most used? Date: 13 Jan 1998 17:25:03 GMT Organization: MRC Human Genome Mapping Project Resource Centre Lines: 32 Message-ID: <69g81f$kmd$1@niobium.hgmp.mrc.ac.uk> References: <68j5nq$eca$1@nntp1.ba.best.com> NNTP-Posting-Host: titanium.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article <68j5nq$eca$1@nntp1.ba.best.com>, Greg writes: > Hi, > I am currently embarking on several web based projects at the non-profit > research Institute that I work at, and given the increasing divergence of > the dynamic HTML and client side scripting (ie Javascript) between > Netscape and MS Internet Explorer browser types, I was wondering whether > the relative usage of these browsers has been reported for > University/non-profits. I know that the current figure is given as 40% > share for Microsoft, but (at least here in the US) Macs seem to be > dominant in the medical/biological research community, and my guess is > that Netscape is still very dominant at these types of institutes. > (Coding for some clever client-side stuff takes an enormous amount of work > and it's not necessarily practical to 'dual code' for both Netscape and > MSIE). From what we see, use of MSIE is much less than 40%. On the other hand, we still see lots of Netscape 2 and some netscape 1 and even the occasional netscape 0.93 coming in. Given that scientists generally won't have the latest hardware, they probably also don't want to or can't have a bloated heap of junk (aka the latest feature-ridden browser) making their machine slow to a crawl. Just avoid using the latest features. The whole point of the web is that it should be browser/hardware/whatever independent. Personally, I use HotJava and Chimera a lot, neither of which (thankfully) have too many of the latest "features". -- -Peter Tribble HGMP Computing Services http://www.hgmp.mrc.ac.uk/~ptribble/ From owner-software@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news-peer-east.sprintlink.net!news.sprintlink.net!Sprint!uunet!in1.uu.net!munnari.OZ.AU!bunyip.cc.uq.edu.au!not-for-mail From: "shodan" Newsgroups: bionet.software Subject: VCD software Date: Wed, 14 Jan 1998 15:25:04 +1100 Organization: University of Queensland Lines: 11 Message-ID: <69hid7$vec$1@nargun.cc.uq.edu.au> NNTP-Posting-Host: zzjchen.slip.cc.uq.edu.au X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 I have a MPEG card but I accidentally deleted the software that comes with that card (it is called Pcinema). Does anyone have that software, or any software which can take advantage of a MPEG card, please send it too me or tell me where to get it. I will be very grateful. (software such as Xing doesn't count, because it doesn't use the MPEG card at all) From owner-software@net.bio.net Tue Jan 13 22:00:00 1998 Message-ID: <34BA7AD8.787136ED@ultinet.net> Date: Mon, 12 Jan 1998 15:19:36 -0500 From: Louisa & Titus X-Mailer: Mozilla 4.04 [en] (Win95; U) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Where is anybody? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 207.99.47.136 Lines: 7 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!nac!207.99.16.200.MISMATCH!houdini.tds-tds.com!nntp1.nac.net!207.99.47.136 Hi: I want to learn more about the software about inverse dynamic in biomechanics. I couldn't see any message from this discussion group. May be something wrong? Titus From owner-software@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!sdu.edu.cn!lilab From: lilab@sdu.edu.cn (lab of MYXO) Newsgroups: bionet.software Subject: Bioactive Natural Products Database(BNPD) URL Needed! Date: 14 Jan 1998 05:30:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <34BCBDD7.3807@sdu.edu.cn> Reply-To: lilab@sdu.edu.cn NNTP-Posting-Host: net.bio.net I need the URL of Bioactive Natural Products Database(BNPD), developed by Berdy, with the collaboration of the NCI staff in Bethesda and Frederick, Maryland. Can anyone tell me it? Thanks in advance! _______________________________________________ Li Jian State Key Laboratory of Microbial Technology Department of Microbiology, Life Science College Shandong University Jinan 250100, P.R.China Tel:(86)(531)8564431(ext.411) Fax:(86)(531)8565234 Email: lilab@sdu.edu.cn _______________________________________________ From owner-software@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!arclight.uoregon.edu!wnfeed!204.127.130.5!worldnet.att.net!news.u.washington.edu!not-for-mail From: "Stephen R. Lasky, Ph.D." Newsgroups: bionet.software Subject: Re: Mol. Biol. Software Date: Wed, 14 Jan 1998 15:05:43 -0800 Organization: University of Washington Lines: 80 Message-ID: <69jgdo$lfc$2@nntp3.u.washington.edu> References: <349977D2.5B83@is2.nyu.edu> NNTP-Posting-Host: niflheim.mbt.washington.edu X-Trace: nntp3.u.washington.edu 884819192 21996 (None) 140.142.64.4 X-Complaints-To: help@cac.washington.edu X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Dave: I'm pretty sure that phred, phrap and consed are still available to non-profit, grant funded labs. I'll include the blurb at the beginning of the doc for phred that can be found at http://www.mbt.washington.edu/. This should give people the info about how to find out about copies of these programs: *|************************************************************************** *|* *| |* *| Program: phred |* *| Version: 0.960108 |* *| |* *| Copyright (c) 1992-1996 by Phil Green and Brent Ewing. |* *| All rights reserved. |* *| |* *| Redistribution of source code or executables, or use for any purpose |* *| other than calling DNA bases in an academic laboratory as part of |* *| strictly academic grant-funded or university-funded research requires |* *| explicit written permission from |* *| |* *| Phil Green |* *| Department of Molecular Biotechnology |* *| University of Washington |* *| Box 357730 |* *| Seattle, WA 98195-7730 |* *| |* *| phg@u.washington.edu |* *| |* *| Portions of the code or ideas are due to Dave Ficenec, LaDeana |* *| Hillier, Mike Wendl, and Tim Gleeson. These are indicated |* *| specifically in the relevant source files. |* *| >From what I have been able to determine, PHRAP and PHRED (and several >related utilities that work with them) are not freely distributed, although >they may have been at sometime in the past. While trying to track down a >source of these apps I found a press release dated several months ago from >Oxford Molecular (who sell GeneWorks, PC-Gene, AssemblyLign, MacVector, >etc.) announcing that the author(s) of PHRAP and PHRED (and the University >where he works) had sold the rights to these programs to OxMol. > >I would certainly welcome input from anyone who can correct me on this. > >Dave > >-------------------------------------------- >David F. Spencer, PhD >Dept. Of Biochemistry >Dalhousie University >Halifax, Nova Scotia >Canada > >dspencer@is.dal.ca >dspencer@rsu.biochem.dal.ca From owner-software@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news1.chicago.iagnet.net!iagnet.net!129.79.6.160!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: SeqPup, a free biosequence editor is updated [Java version] Date: 14 Jan 1998 23:34:12 GMT Organization: Biology, Indiana University - Bloomington Lines: 44 Message-ID: <69ji1k$op5$1@flotsam.uits.indiana.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu SeqPup, version 0.8, January 1998 SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs. It is usable on common computer systems that support the Java 1.1 runtime environment, including Macintosh, MS-Windows and X-Windows. Features include multiple sequence alignment and single sequence editing read and write several sequence file formats sequence feature editing, manipulation and marking in prints translate dna/protein, consensus, reverse/complement, and distance methods pretty print of alignments and sequences with boxed and shaded regions Internet Sequence Retrieval System (SRS), and NCBI-BLAST searches * User-definable links to external analysis programs, including ClustalW multiple alignment, CAP contig assembly, tacg restriction map * Remote program client-server interface, using CORBA protocol ( * - new this version) The major addition to this second Java release are methods for calling external applications. This application is a work in progress; it has bugs. It may be useful to you as is, but it is still prone to problems. Find this software at ftp://iubio.bio.indiana.edu/molbio/seqpup/java/ http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/ SeqPup is written using a free and portable class application framework called DCLAP, now converted to the new Java language. Developers will find the source code for this application and others in the iubio:/molbio/java/source folder. If you are an administrator of GCG software for your institution and would like to test an experimental version of the client-server interface to SeqPup with GCG at your site, please let me know. Comments, bug reports and suggestions are welcome and can be e-mailed to SeqPup@Bio.Indiana.Edu. -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Jaap Heringa Newsgroups: bionet.software Subject: PhD Studentship Available at NIMR, London Date: Wed, 14 Jan 1998 15:40:31 +0000 Organization: MRC Lines: 102 Message-ID: <34BCDC6F.CB633232@nimr.mrc.ac.uk> NNTP-Posting-Host: serine.nimr.mrc.ac.uk Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------8F6CFF47A22D4D844DC7376B" X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 6.2 IP22) --------------8F6CFF47A22D4D844DC7376B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit A three-year Predoctoral MRC-funded Fellowship is available to UK-Citizens in the Division of Mathematical Biology, National Institute for Medical Research (NIMR), Mill Hill, London. Head of the Division is Dr Willie Taylor. The following is a short outline of the project: PROTEIN STRUCTURAL DOMAINS AND REPEATS; ANALYSIS AND PREDICTION FROM SEQUENCE INFORMATION ALONE The recognition of domains in protein structures is an important prerequisite for areas in protein science such as NMR-based structural elucidation and fold recognition. A number of empirical observations render domain prediction from only sequence information feasible, e.g., (i) domain interfaces show a.a. compositions intermediate to those of core and surface regions, (ii) domain linker regions display distinct compositions and (iii) domains in many proteins are (distant) repeats of a same basic sequence stretch. The project will embark on analysing existing databanks of protein domains and use the information to devise sequence profiles against which query sequences can be matched: A newly developed sensitive protein segment detection method SEGS by Willie Taylor will be of great use at this stage. Of help also will be the sensitive repeat detection method REPRO (see Heringa & Taylor, Curr. Opin. Struct. Biol. 7:416-421, 1997). All above information will be implemented in a computer method aimed at delineating domain boundaries in protein sequences. For more information, contact Dr Jaap Heringa Division of Mathematical Biology National Institute for Medical Research (NIMR) The Ridgeway, Mill Hill, London NW7 1AA, U.K. Tel.: +44 181 959 3666 ext. 2293 Fax : +44 181 913 8545 Email: jaap.heringa@nimr.mrc.ac.uk WWW : http://mathbio.nimr.mrc.ac.uk --------------8F6CFF47A22D4D844DC7376B Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit A three-year Predoctoral MRC-funded Fellowship is available to UK-Citizens in
the Division of Mathematical Biology, National Institute for
Medical Research (NIMR), Mill Hill, London. Head of the Division
is Dr Willie Taylor.

The following is a short outline of the project:
 

               PROTEIN STRUCTURAL DOMAINS AND REPEATS;
     ANALYSIS AND PREDICTION FROM SEQUENCE INFORMATION ALONE

The recognition of domains in protein structures is an important
prerequisite for areas in protein science such as NMR-based
structural elucidation and fold recognition. A number of empirical
observations render domain prediction from only sequence information
feasible, e.g., (i) domain interfaces show a.a. compositions
intermediate to those of core and surface regions, (ii) domain
linker regions display distinct compositions and (iii) domains in
many proteins are (distant) repeats of a same basic sequence stretch.
The project will embark on analysing existing databanks of protein
domains and use the information to devise sequence profiles against
which query sequences can be matched: A newly developed sensitive
protein segment detection method SEGS by Willie Taylor will be of great
use at this stage. Of help also will be the sensitive repeat detection
method REPRO (see Heringa & Taylor, Curr. Opin. Struct. Biol. 7:416-421,
1997).  All above information will be implemented in a computer method
aimed at delineating domain boundaries in protein sequences.

For more information, contact
Dr Jaap Heringa
Division of Mathematical Biology
National Institute for Medical Research (NIMR)
The Ridgeway, Mill Hill,
London NW7 1AA, U.K.

Tel.: +44 181 959 3666 ext. 2293
Fax : +44 181 913 8545
Email: jaap.heringa@nimr.mrc.ac.uk
WWW :  http://mathbio.nimr.mrc.ac.uk 


 

--------------8F6CFF47A22D4D844DC7376B--


From owner-software@net.bio.net Tue Jan 13 22:00:00 1998
Path: biosci!newshost.lanl.gov!not-for-mail
From: Carla Kuiken 
Newsgroups: bionet.software
Subject: Thanks! was: Re: UNIX database software?
Date: Wed, 14 Jan 1998 10:32:54 -0700
Organization: Los Alamos National Laboratory
Lines: 28
Message-ID: <34BCF6C6.18F@t10.lanl.gov>
References: <34B6A091.A52@t10.lanl.gov>
NNTP-Posting-Host: intron.lanl.gov
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4m)

Thanks everyone for replying to this message. We're looking at the
options. It's good to know that there are some alternatives out there,
and who knows, it may even help Sybase come to their senses about their
licensing policy...

Carla Kuiken



Carla Kuiken wrote:
> 
> We're a small group maintaining a sequence database on a UNIX platform.
> We're currently using Sybase for our database work, but this is getting
> prohibilively expensive, so we're looking for an alternative.
> 
> The database is not large, but it's fairly complicated. We're in the
> process providing web access to it (which is why Sybase suddenly wants a
> lot more money for the license). We store genetic sequences and
> background info, and are currently adding links to Medline, Genbank etc.
> 
> What database programs (if any) do other people use for this type of
> work? There must be more to choose from than just Informix, Sybase and
> Oracle, but we haven't seen much yet. Any tips, advice or horror stories
> much appreciated! Thanks very much in advance.
> 
> Carla Kuiken
> HIV Sequence Database
> Los Alamos National Laboratory

From owner-software@net.bio.net Tue Jan 13 22:00:00 1998
Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail
From: "Jeremy D. Parsons" 
Newsgroups: bionet.software
Subject: Java trace viewer and Eugen Buehler
Date: Wed, 14 Jan 1998 12:35:26 +0000
Organization: European Bioinformatics Institute
Lines: 10
Message-ID: <34BCB10D.3C31E555@EBI.ac.uk>
NNTP-Posting-Host: o2-2.ebi.ac.uk
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 6.3 IP32)

I have extended Eugen Buehler's static Java trace viewer to become interactive
via a CORBA interface to the EST chromatograms held at the Genome Sequencing
Center in Washington University, Saint Louis USA. I would like to
publish this work in the journal Bioinformatics some time soon
but I first need to contact Eugen Buehler himself to agree co-authorship.
He did not reply to a message I sent to snafu@telerama.lm.com

Thanks,
    Jeremy Parsons


From owner-software@net.bio.net Wed Jan 14 22:00:00 1998
Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!uunet!in1.uu.net!hearst.acc.Virginia.EDU!murdoch.acc.Virginia.EDU!avery.med.Virginia.EDU!jw4n
From: jw4n@avery.med.Virginia.EDU (JW)
Newsgroups: bionet.software
Subject: postdoc for phosphatase research
Date: 15 Jan 1998 15:55:53 GMT
Organization: uva
Lines: 12
Message-ID: <69lbi9$pfc$1@murdoch.acc.Virginia.EDU>
NNTP-Posting-Host: avery.med.virginia.edu

A postdoc needed for protein phosphatase research in Dr. David
L. Brautigan's lab (Center for Cell Signaling, University of
Virginia Medical Center). Will start as soon as possible for
NIH granted project (see JBC 272:32308, 1997). If interested,
please send e-mail to Dr. Brautigan at db8g@virginia.edu. 

Please don't reply to this message.
-- 
Jun Wu
Markey Center for Cell Signaling
University of Virginia Medical Center
Box 577 HSC

From owner-software@net.bio.net Wed Jan 14 22:00:00 1998
Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!EU.net!Portugal.EU.net!news.rccn.net!news.ip.pt!not-for-mail
From: "Gustavo Salgado" 
Newsgroups: bionet.software
Subject: Voice Mail
Date: 15 Jan 1998 14:54:23 GMT
Organization: (Utilizador da IP)
Lines: 6
Message-ID: <01bd21c5$379aaec0$0901a8c0@gustavo.disconto>
NNTP-Posting-Host: 194.117.44.69
X-Newsreader: Microsoft Internet News 4.70.1155

I 'm looking for a software ( Voice Mail ) that i can work on it, like
connect to a database that I alredy have and then answer to the questions
of the client by quering the DB. So if you could tell me where can I
connect to have some answers or how can I get that kind of software contact
me. I would be grateful.


From owner-software@net.bio.net Wed Jan 14 22:00:00 1998
Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!feed1.news.luth.se!luth.se!Cabal.CESspool!bofh.vszbr.cz!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!207.20.0.50!peerfeed.ncal.verio.net!Supernews60!supernews.com!uunet!in4.uu.net!news.anet-chi.com!not-for-mail
From: toddc-NoSpAm@NoSpAm-anet-dfw.com (Todd C.)
Newsgroups: bionet.software
Subject: PEDANT protein info server
Date: Thu, 15 Jan 1998 22:23:24 GMT
Organization: ANET Internet Services
Lines: 6
Message-ID: <34be8c39.106774904@news.anet-dfw.com>
Reply-To: toddc-NoSpAm@NoSpAm-anet-dfw.com
NNTP-Posting-Host: 206.103.93.55
X-Newsreader: Forte Free Agent 1.1/32.230

Does anyome know what happened to PEDANT. Is it no longer publicly
accessable? 

http://pedant.mips.biochem.mpg.de/frishman/pedant.html



From owner-software@net.bio.net Wed Jan 14 22:00:00 1998
Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!204.59.152.222!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!global-one.pt!news.ip.pt!not-for-mail
From: "Gustavo Salgado" 
Newsgroups: bionet.software
Subject: Voice Mail Software
Date: 15 Jan 1998 17:20:34 GMT
Organization: (Utilizador da IP)
Lines: 6
Message-ID: <01bd21d9$ca8d0020$0901a8c0@gustavo.disconto>
NNTP-Posting-Host: 194.117.44.74
X-Newsreader: Microsoft Internet News 4.70.1155

I am looking for a voice mail software. It as to be a special software
because I need that software to connect to a Database and then give the
answer that my client needs. So what I realy need is to Know where can I
connect to have that kind of software or how can I get it. If you could
help me I would be grateful. 


From owner-software@net.bio.net Wed Jan 14 22:00:00 1998
Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!206.251.127.50!newsfeed.gte.net!news.he.net!Supernews60!supernews.com!Supernews69!not-for-mail
From: Ray Smith 
Newsgroups: sci.image.processing,bionet.software,sci.techniques.microscopy
Subject: Image-Pro Plus email Users Group
Date: Thu, 15 Jan 1998 11:34:38 -0500
Organization: Media Cybernetics, L.P.
Lines: 17
Message-ID: <34BE3A9E.7313@mediacy.com>
Reply-To: ray@mediacy.com
NNTP-Posting-Host: 5396@208.209.115.196
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Mailer: Mozilla 3.01Gold (Win95; I)

FYI: Image-Pro Plus users out there can subscribe to the Image-Pro Plus
email Users Group at .

The group has become an excellant help support resource for Image-Pro
users.

Regards,

-Ray
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Raymond Smith, Sales Information Systems Mgr.
"Image-Pro Plus - The Proven Solution"
Media Cybernetics, L.P.	
8484 Georgia Avenue                       
Silver Spring, MD 20910 U.S.A.
ray@mediacy.com
http://www.mediacy.com

From owner-software@net.bio.net Wed Jan 14 22:00:00 1998
Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!128.230.129.106!news.maxwell.syr.edu!dispose.news.demon.net!demon!bullseye.news.demon.net!demon!newsfeed.xs4all.nl!xs4all!nestorix2.xs4all.nl!not-for-mail
From: hen@freemail.nl
Newsgroups: bionet.software
Subject: SHAREWARE TOP TEN -=- VOTE AND WIN !!!!
Date: Thu, 15 Jan 1998 23:47:56 GMT
Organization: Don't like spam!
Message-ID: <69m3ga$f3v$13@news2.xs4all.nl>
NNTP-Posting-Host: spy03-14.dial.xs4all.nl
X-XS4ALL-Date: Thu, 15 Jan 1998 23:44:26 CET
X-Newsreader: Forte Free Agent 1.0.82
Lines: 7

Win a FREE! program...
Come and visit the SHAREWARE TOP TEN

Vote & Win!!!!!

http://come.to/shareware


From owner-software@net.bio.net Thu Jan 15 22:00:00 1998
Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!134.222.90.2!EU.net!Portugal.EU.net!news.rccn.net!news.ip.pt!not-for-mail
From: "Gustavo Salgado" 
Newsgroups: bionet.software
Subject: Voice mail
Date: 16 Jan 1998 09:41:58 GMT
Organization: (Utilizador da IP)
Lines: 7
Message-ID: <01bd2262$e8959b20$0901a8c0@gustavo.disconto>
NNTP-Posting-Host: 194.117.44.66
X-Newsreader: Microsoft Internet News 4.70.1155

I am looking for a voice mail software. It as to be a special software
because I need that software to connect to a Database and then give the
answer that my client needs. So what I realy need is to Know where can I
connect to have that kind of software or how can I get it. If you could
help me I would be grateful. 

e-mail: Disconto@ip.pt

From owner-software@net.bio.net Thu Jan 15 22:00:00 1998
Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news-peer.gip.net!news.gsl.net!gip.net!news.idt.net!nntp2.cerf.net!nntp3.cerf.net!ihnp4.ucsd.edu!munnari.OZ.AU!bunyip.cc.uq.edu.au!not-for-mail
From: A.Cavallaro@botany.uq.edu.au (Tony Cavallaro)
Newsgroups: bionet.software
Subject: KODAK 1D Software for sale (Austalia only)
Date: 16 Jan 1998 07:06:58 GMT
Organization: Dept of Botany, Uni of Queensland
Lines: 8
Message-ID: <69n0ui$d16$1@nargun.cc.uq.edu.au>
Reply-To: A.Cavallaro@botany.uq.edu.au
NNTP-Posting-Host: botella2.botany.uq.edu.au
Mime-Version: 1.0
Content-Type: Text/Plain; charset=US-ASCII
X-Newsreader: WinVN 0.99.8 (16bit)

I have version 1 of Kodak's 1D image analysis software. The software is 
complete with manuals registration card. The software is still unregistered.

If you are inter