From owner-software@net.bio.net Sat Apr 01 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!cri.ens-lyon.fr!news.imag.fr!news.ujf-grenoble.fr!news-merci.ujf-grenoble.fr!dyogen1.ujf-grenoble.fr!mongelar From: mongelar@dyogen1.ujf-grenoble.fr (Mongelard Fabien) Newsgroups: bionet.software Subject: File Compression Software Date: 1 Apr 1995 15:09:50 GMT Organization: Universite Joseph Fourier - Grenoble 1, Grenoble, France Lines: 19 Distribution: world Message-ID: <3ljqbu$3gi@ujf-iab.ujf-grenoble.fr> NNTP-Posting-Host: dyogen1.ujf-grenoble.fr Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit I'm using the UNIX 'pack' command (Huffman coding) to minimize the size of my image files on a SGI workstation. Does anybody here know about a MS-DOS software able to handle packed files ? Thanks in advance. -- \ /// (. .) /---------------------------------------+------------o0O-(_)-O0o-----\ | Mongelard Fabien | Institut A. Bonniot | | Laboratoire 'DyOGen' |Universite Fourier, Grenoble| | Dynamique de l'Organisation du Genome | 38706 La Tronche FRANCE | +---------------------------------------+----------------------------+ | Phone me:(33) 76 54 94 62. fax me:(33) 76 54 94 14. | | E-mail me: Fabien.Mongelard@ujf-grenoble.fr | | Or leave me alone... | \--------------------------------------------------------------------/ From owner-software@net.bio.net Sat Apr 01 23:00:00 1995 Path: biosci!agate!violet.berkeley.edu!che1a-hg From: che1a-hg@violet.berkeley.edu (Matthew) Newsgroups: bionet.software Subject: Re: PDB -> DXF or 3DS (Rendering) Date: 2 Apr 1995 06:55:21 GMT Organization: University of California, Berkeley Lines: 16 Distribution: world Message-ID: <3llhop$nrs@agate.berkeley.edu> References: <3l60kg$bl7@hrz-ws11.hrz.uni-kassel.de> <3l62ep$r1d@rs18.hrz.th-darmstadt.de> NNTP-Posting-Host: violet.berkeley.edu X-Newsreader: TIN [version 1.2 PL2] Martin Kroeker (martin@tutor.oc.chemie.th-darmstadt.de) wrote: : pdb2pov, available at least from ftp.povray.org (and probably mirrored in : Oldenburg ?). I was just trying to write a conversion myself! I'd love to get my hands on a pdb2pov converter, and save myself hours of work :) But when I looked for the file on ftp.povray.org, I couldn't seem to find it. I hate to trouble you with such a silly request (I'm probably looking in the wrong directory), but could you please be more specific on the location of the file? Thanks in advance! ------------- Matthew Gianni From owner-software@net.bio.net Sat Apr 01 23:00:00 1995 Path: biosci!agate!library.ucla.edu!csulb.edu!paris.ics.uci.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: XDIR - Free Unix/Motif/X-based Cross-Platform File manager Date: Sun, 02 Apr 1995 09:05:34 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 30 Message-ID: References: <3lkfsc$dr1@nntp3.u.washington.edu> NNTP-Posting-Host: buggus.mmg.uci.edu In article <3lkfsc$dr1@nntp3.u.washington.edu>, learn@valis.microbiol.washington.edu (Jerry Learn) wrote: > Harry Mangalam (mangalam@uci.edu) wrote: <> > > : It's free to academics - Check out the URL: > > : http://www.llnl.gov/liv_comp/xdir.html > > It looks nifty and I downloaded it but it appears to need motif libraries to > compile. I don't happen to have these. Are they available for free? No, the motif libs are not free, but they are shipped with most development systems; they may be in a nonstandard place (what platform do you have?). If you really don't have them, you can still use MOTIF if the executable is statically linked to the executable (much larger file size but it works). But you still have to find someone who will do it for you. If you have an SGI, I might be able to do it for you, or you could ask the developers of the pkg to put a statically linked exe on their ftp site for you. Harry -- Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 --- knowledge is fractal --- http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Sat Apr 01 23:00:00 1995 Path: biosci!grizzly.com!markd From: markd@grizzly.com (Mark Diekhans) Newsgroups: bionet.software Subject: Re: File Compression Software Date: 2 Apr 1995 11:08:45 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <199504021705.KAA27468@Grizzly.COM> References: <3ljqbu$3gi@ujf-iab.ujf-grenoble.fr> NNTP-Posting-Host: net.bio.net >I'm using the UNIX 'pack' command (Huffman coding) to minimize the size >of my image files on a SGI workstation. >Does anybody here know about a MS-DOS software able to handle packed >files ? I suggest GNU gzip for both Unix and DOS. It products much better compression than pack. Its available from prep.ai.mit.edu:pub/gnu/gzip* From owner-software@net.bio.net Sat Apr 01 23:00:00 1995 Path: biosci!agate!library.ucla.edu!csulb.edu!paris.ics.uci.edu!news.service.uci.edu!buggus.mmg.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: File Compression Software Date: Sun, 02 Apr 1995 09:01:07 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 19 Distribution: world Message-ID: References: <3ljqbu$3gi@ujf-iab.ujf-grenoble.fr> NNTP-Posting-Host: buggus.mmg.uci.edu In article <3ljqbu$3gi@ujf-iab.ujf-grenoble.fr>, mongelar@dyogen1.ujf-grenoble.fr (Mongelard Fabien) wrote: > I'm using the UNIX 'pack' command (Huffman coding) to minimize the size > of my image files on a SGI workstation. > Does anybody here know about a MS-DOS software able to handle packed > files ? NO, but why not just use the copylefted zip/unzip, gzip, or even compress - these all have freeware relatives that run on DOS. Or just use a compressed image format (compressed TIFF, GIF, JPEG)? harry -- Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 --- knowledge is fractal --- http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Sat Apr 01 23:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!jobone!lynx.unm.edu!dns1.NMSU.Edu!dkim From: dkim@nmsu.edu (Daniel Kim) Newsgroups: bionet.software Subject: Re: Windows for 286 Date: 30 Mar 1995 18:30:17 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 57 Sender: dkim@verdi.nmsu.edu Message-ID: <3letbp$28a@dns1.NMSU.Edu> NNTP-Posting-Host: verdi.nmsu.edu Hello: Re: Windows 286. If you are looking for something to drive a Win/286-specific application, I can't help you, but if you want a multitasking GUI for an old '286, then this can help: Try GeoWorks Ensemble. It is a preemptively multitasking, multithreaded, object-oriented graphical operating system for the PC compatible. In order to run _well_, it only needs a '286 with 2 Mb RAM (I have a 286/12, 3 Mb RAM, 20 Mb HDD). It allows long (32 character) filenames with annotations, and has a convenient point and click interface. Moving files is just click-and-drag (rather like the Mac). The full applications suite includes a word processor (about 90% of the features of W4W, but in about 1/50 the disk space), spreadsheet (pretty basic), text editor, flat file database, comm program, scheduler/calendar, banner maker, screen saver, draw program (also imports graphics, but only works to 16-colors), rolodex/addressbook. There are two games (tetris and solitaire). This is a FAST system. It is especially good on limited hardware resources like mine. It needs a bit of tinkering so it doesn't crash out (setting files = and buffers = to appropriate levels is a big help). Individual apps can crash and burn, and you still can use the other apps. See newsgroup comp.os.geos for more info, esp the FAQ. A shareware demo, with all features,but only the word processor and text editor applications, can be had by anon FTP: from a .sig: Try Geopublish, the shareware version of Geoworks Ensemble! Positively SCREAMS, while providing a full GUI interface. Includes a desktop publisher. ftp://130.219.44.141/pub/geos/publish This is the same os that is used in the Tandy Z-PDA and Casio handheld pen-based computers. Geos has a patented generic user interface that can be mapped to a specific user interface, so an app that runs on the handheld can theoretically also run on the desktop. It is a handy feature. IBM actually has a Presentation Manager interface for GEOS called SchoolView. Geos will not run Windows applications. Geos will not run DOS sessions in a multitasked window Geos is made by a company smaller than the janitorial staff for Microsoft (i.e. they don't have the resources to properly market the desktop os, nor can they make a new driver every week) On the other hand, Geos will give you many of the buzzwords of Win95 in a small cheap package (purchase direct from GeoWorks for about $80 US). Try it out. These days, 10+ MB of hard drive space is nothing, so what do you have to lose? Daniel Kim From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!bcc.ac.uk!is.bbsrc.ac.uk!pc0519.ri.afrc.ac.uk!user From: Andy.Law@bbsrc.ac.uk (Andy Law (Big Nose)) Newsgroups: bionet.software Subject: Re: REQ: Help converting Netscape bookmark to test Date: Mon, 03 Apr 1995 12:14:35 +0000 Organization: Roslin Institute Lines: 24 Message-ID: References: NNTP-Posting-Host: pc0519.ri.afrc.ac.uk X-Newsreader: Value-Added NewsWatcher 2.0b24.0+ In article , aj519@FreeNet.Carleton.CA (Robert W Beggs) wrote: > Bio-Netters - > > As the subject line states, I'm looking for assistance in > converting the bookmark file of a NetScape browser into text, so that I > will have a readable list of sites and their associated URLs. Any > suggestions? > > Robb Beggs In the Mac version, you will find the Bookmarks in the Netscape Folder inside the Preferences folder of the system Folder. They are already in a text file, albeit somewhat obscure in their layout. The file is called MCOM-Bookmarks.html. Remember to make a duplicate copy before tinkering with the contents, as Netscape reads this file to generate the Bookmark menu. -- Andy Law ( Andy.Law @ bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Path: biosci!daresbury!news!ajb From: ajb@s-crim1.dl.ac.uk (Alan Bleasby) Newsgroups: bionet.software Subject: [ANNOUNCE] OWL/PRINTS/align/smite (new versions) Date: 03 Apr 1995 17:40:28 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 18 Distribution: bionet Message-ID: NNTP-Posting-Host: s-crim1.dl.ac.uk OWL25.2/PRINTS8.0/align/SMITE are now available via anon-ftp from: s-ind2.dl.ac.uk pub/database/prints pub/database/owl ncbi.nlm.nih.gov repository/PRINTS repository/OWL ... and EMBnet mirroring sites. PRINTS now contains 350 protein features, the corresponding sequence alignments are in the `align' directory. As PRINTS has changed format very slightly (to add more text info) I have also supplied the source code of the SMITE query language plus its necessary indexing software. Regard the s/w side as a `beta' release. It's UNIX-specific (in this distribution). Alan Bleasby SEQNET/EMBnet/Bionet Daresbury Laboratory From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!Germany.EU.net!nntp.gmd.de!dearn!blekul11!jan.eggermont Nntp-Posting-Host: 134.58.181.40 Date: Mon, 3 Apr 1995 11:41:42 +0200 From: Jan.Eggermont@med.kuleuven.ac.be (Jan Eggermont) Newsgroups: bionet.software Distribution: world Subject: Re: Plasmid Drawing Programs Message-ID: References: <1995Mar29.150901@pomona> <3lej3k$ibi@news.cc.utah.edu> Organization: KU Leuven Lines: 23 In article <3lej3k$ibi@news.cc.utah.edu>, David Stillman wrote: > I am using MacPlasmap 2.05, now available for $200 (I think) from CGC > Scientific > 314-652-6533, fax 314-652-6631 > Many new features: importing from GenBank, from DNA Strider Pict files, > from MacDraw, and now make linear maps. > I like it. > Do you whether they have an e-mial address? Also, is there a demo version available for this version? Thanks, Jan -- Jan Eggermont Jan.Eggermont@med.kuleuven.ac.be Laboratorium voor Fysiologie - KU Leuven Campus Gasthuisberg B-3000 Leuven tel 32-16-345938 Belgium fax 32-16-345991 From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!not-for-mail From: 9224076@ul.ie (Stephen Mulcahy) Newsgroups: bionet.software Subject: Test post -Please ignore!! Date: 3 Apr 1995 10:29:06 -0500 Organization: UTexas Mail-to-News Gateway Lines: 6 Sender: nobody@cs.utexas.edu Message-ID: <9504031527.AA23675@itdsrv1.ul.ie> NNTP-Posting-Host: news.cs.utexas.edu This is a test! -------------------------------------------------------------------------------------------- Stephen "Divil" Mulcahy 9224076@ul.ie 3rd Industrial Biochemistry, University of Limerick (Eire) WWW: http://skynet.ul.ie/~stephen From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!spool.mu.edu!torn!news.unb.ca!peinet.pe.ca!peinet.pe.ca!not-for-mail From: stewart@bud.peinet.pe.ca (Paul Stewart) Newsgroups: bionet.software Subject: labware Date: 3 Apr 1995 13:55:23 -0400 Organization: PEINet, Charlottetown, Prince Edward Island, Canada Lines: 11 Sender: stewart@bud.peinet.pe.ca Distribution: world Message-ID: <3lp99r$gmh@bud.peinet.pe.ca> NNTP-Posting-Host: bud.peinet.pe.ca Does anyone know a Web or FTP site where I could get non-windows software for a PC (80286, stop laughing!) which will automatically formulate vrious solutions and media from an inputted formula? I found many for the Mac, but nothing on the shareware circuit for DOS. Also, am looking for a database of formulations for microbiology and tissue culture. Thanx... ABIOGEN c/o Paul Stewart RR #2 Vernon Bridge Prince Edward Island CANADA C0A 2E0 From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!oleane!jussieu.fr!pasteur.fr!univ-lyon1.fr!swidir.switch.ch!news.unige.ch!ugsc2a!tuinen From: tuinen@sc2a.unige.ch Subject: GelReader and LC630 problems Message-ID: <1995Apr3.161821.1@ugsc2a> Lines: 7 Sender: usenet@news.unige.ch Organization: University of Geneva, Switzerland Date: Mon, 3 Apr 1995 14:18:21 GMT Could somebody help me. When I want to run the NCSA GelReader2.0.5LCsi on a LC630 Mac, the computer crashes when I want to select the lanes of a gel. The problem arises also on a Quadra both runing with the 68040 processors, whereas the program work whithout any problem on an "old" LC This is independant on the co-pro as both versions of the GelReader don't work. Diederik van Tuinen From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Newsgroups: bionet.software Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!loglady.ninds.nih.gov!johnk From: johnk@spasm.niddk.nih.gov (John Kuszewski) Subject: Biosym, Tripos, and Sarin Message-ID: <1995Apr3.200348.17054@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: spasm.niddk.nih.gov Reply-To: johnk@spasm.niddk.nih.gov (John Kuszewski) Organization: National Insts. of Health Date: Mon, 3 Apr 1995 20:03:48 GMT Lines: 27 I was surprised to hear this morning on the CBS radio news that the doomsday cult in Japan that gassed the Tokyo subway had purchased copies of "sophisticated molecular design software" from Biosym and Tripos. I haven't the foggiest idea what they intended to do with it. Does anyone know which programs they bought? Does anyone know why they didn't buy anything from Molecular Simulations? We xplor types feel snubbed around here that our code didn't appeal to these weirdos. :-/ -- _____________ | ___/_ | |/ / -- /\ // /-- || || / /|| || || / / || || ||/ / || John Kuszewski || |/ /| || johnk@spasm.niddk.nih.gov || / /|| || \/ / / || \/ that's MISTER protein G to you! |/__/| | /_________| From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!hermes.acs.ryerson.ca!gemini!jnaughto From: jnaughto@ee.ryerson.ca (JASON NAUGHTON) Newsgroups: bionet.software Subject: ESDI DRIVE SOFTWARE?? Date: 3 Apr 1995 20:45:55 GMT Organization: Ryerson Polytechnic University Lines: 12 Message-ID: <3lpmq3$19sr@hermes.acs.ryerson.ca> NNTP-Posting-Host: gemini.ee.ryerson.ca X-Newsreader: TIN [version 1.2 PL2] Hey, I've just come across some old ESDI drives and I wanted to see if I could get them up and running. The only problem is that I require to do a low level format on the ESDI drive. It's not like the old MFM's that the low-level formatting soft is in the bois, supposally there's software I need. Sooo if anyone has the maintiance software that is required to format the drive it would be most appriciated.... Cheers Jason From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!uunet!in1.uu.net!nntp.cac.washington.edu!homer13.u.washington.edu!jkoz From: Jeff Kozlowski Newsgroups: bionet.software Subject: DNA Sequencing on Macintosh? Date: Mon, 3 Apr 1995 15:16:00 -0700 Organization: University of Washington Lines: 9 Message-ID: NNTP-Posting-Host: nntp2.u.washington.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Anyone out there know of a good application that will automatically read DNA sequences from autoradiography film? I would appreciate any help. Jeff email jkoz@saul.u.washington.edu (not jkoz@u.wash....) From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!paladin.american.edu!newsfeed.ACO.net!edvz.sbg.ac.at!wst!floeckn From: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Subject: Protein Fold Identification Tool Message-ID: Lines: 35 Sender: floeckn@wst (Floeckner Hannes) Reply-To: floeckn@wst.edvz.sbg.ac.at (Floeckner Hannes) Organization: University of Salzburg / Austria Date: Mon, 3 Apr 1995 16:07:54 GMT ______________________________________________ | | | ProFIT - Protein Fold Identification Tool | |______________________________________________| Version 0.9 Beta for SGI and DEC ALPHA Workstations ProFIT (Protein Fold Identification Tool) combines an aminoacid sequence with a database of 3D structures, and has the potential to detect a fold related to the native structure of the input sequence. This is a beta-release. It is still experimental and will change during the following months. For a description of the program, the approaches used, the expected success rate and the quality of information retrieved, please consult the accompanying manuscript. ProFIT V0.9 Beta is freely available for academic users. You can down-load ProFIT V0.9 Beta by anonymous ftp from Gundi.came.sbg.ac.at (141.201.27.11) Licenses are distributed on a one machine one license basis. A license is valid for one year. Licenses are free of charge for academic users. For commercial licenses please contact: Manfred.J.Sippl Center Of Applied Molecular Engineering Jakob-Haringer Str. 1 A-5020 Salzburg / AUSTRIA E-Mail: sippl@olga.came.sbg.ac.at From owner-software@net.bio.net Sun Apr 02 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!univ-lyon1.fr!news.imag.fr!ciril.fr!usenet From: claverie@lien.u-nancy.fr (CLAVERIE Remy) Newsgroups: bionet.software Subject: ANNOUNCEMENT OF THE 3rd EBEA CONGRESS Date: 3 Apr 1995 16:28:57 GMT Organization: Laboratoire d'Instrumentation en Electronique de Nancy Lines: 62 Message-ID: <3lp7o9$j07@arcturus.ciril.fr> Reply-To: ebea.nancy96@lien.u-nancy.fr NNTP-Posting-Host: gbm0.lien.u-nancy.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: WinVN 0.92.6+ Some of you told me that the file mail.doc was unreadable so, I post it again. For more informations, send a mail to: ebea.nancy96@lien.u-nancy.fr Thank you ANNOUCEMENT AND FIRST CALL FOR PAPERS 3 th INTERNATIONAL CONGRESS OF the European BioElectromagnetics Association 29 FEB-2 MARCH 1996 linked with COST 244 CONGRESS : 2-3 march 1996 at "Le Palais des Congrès" NANCY, France The purpose of the third international EBEA congress is to provide an international meeting for scientific exchange on the fields of research involving electromagnetic interactions with biological tissues. Physical, mathematical and biological scientists, engineers and physicians and other people interested in the Interaction of Electromagnetic fields with biological systems are expected at the Congress The Congress of the European COST Project 244 (Biomedical effects of Electromagnetic Fields) will be held also at "Le Palais des Congrès", Nancy , 2 and 3 march 1996, linked with the EBEA Congress The technical and scientific program consists on 3 days of plenary and technical sessions with general and specific interests (see topics below). The poster sessions will include platform presentation and prizes will be awarded to authors of the best poster. The student paper competition will provide opportunities for yopung researchers worldwide to present their work to panels of experts and achieve special recognition and awards from the scientific Community Deadlines : Abstracts Will not be accepted after december first 1995 Additionnal registration fees are requested after january 15 , 1996 Topics of the E.B.E.A. CONGRESS Physical aspects : Theoretical considerations for bioeffects of EMF's ; Mathematical modeling ; EMF simulation inside biological bodies ; Numerical methods ; Physical and biochemical bases of cellular interaction mechanisms. Physical modeling : EM properties of biological tissues, phantoms ; Methodology of measured EMF quantities ; Measurement techniques and existing instrumentation ; Experimental guidelines for laboratory experiments .Hazardous EMF and biological effects : Biological response to EMF ; low frequency bioeffects ; High frequency bioeffects ; EMF interaction mechanisms and exposure evaluation ; Electrical injury ; Biological effects of High and low power EMF ; Electric field effects on nerve regeneration. Therapeutic applications and evaluation of EMI Evaluation of treatment methods and devices based on EMI ; Hyperthermia, ablathermia, stimulation, etc. ; Wound healing ; EM- field enhanced soft tissue repair We invite you to come and share your scientific work with colleagues from both Europe and other parts of the world. We are sure you will enjoy becoming acquainted with the latest developpments in the EMI and visiting Nancy and the famous beautiful "Place Stanislas". Plan to participate and return the attached application form Registration, hotel reservation and abstract forms will be sent after reception of this application form. Congress Chairmen : Gérard PRIEUR and Mustapha NADI Correspondance : EBEA-Nancy 96 L.I.E.N. University Henri POINCARÉ - Nancy 1 Tél. : (33) 83 91 20 71 BP 239 - 54506 Vandoeuvre les Nancy Fax : (33) 83 91 23 91 France e-mail : ebea.nancy96@lien.u-nancy.fr From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msunews!harbinger.cc.monash.edu.au!yoyo.aarnet.edu.au!news.adelaide.edu.au!usenet From: rmorona@microb.adelaide.edu.au Newsgroups: bionet.software Subject: Epitope prediction Date: 4 Apr 1995 03:09:21 GMT Organization: University of Adelaide Lines: 9 Distribution: world Message-ID: <3lqd91$4qq@quandong.itd.adelaide.edu.au> NNTP-Posting-Host: micro25.microbiology.adelaide.edu.au Keywords: prediction epitope X-Newsreader: Can anyone help me out with user friendly programs to predict epitopes (B and T cell) ? I have many of the "classics", but they are just that! I am looking for something from the 90's which is capable of predicting with some accuracy. Dr Renato Morona Email: rmorona@microb.adelaide.edu.au From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!not-for-mail From: ole@mango.mef.ki.se (Ole Matzura) Newsgroups: bionet.software Subject: RNAdraw update! - V0.99-08 Date: 4 Apr 1995 07:14:52 -0500 Organization: UTexas Mail-to-News Gateway Lines: 38 Sender: nobody@cs.utexas.edu Message-ID: NNTP-Posting-Host: news.cs.utexas.edu Hello there! Version 0.99-08 of Rnadraw is now available! New features are: 1) 'Import GCG PlotFold -H' option lets you import ouput from the PlotFold -H prgram in the GCG package, parseing multiple structures in the .CON file to seperate structure entries. This enables you to do suboptimal structure calculation with GCG MFOLD, proccess the results with GCG PlotFold using the -H command line parameter, and import and view all structures in Rnadraw. 2) Some minor quirk fixes in the sequence editor, updated help files and some minor bug fixes. The next and final pre-V1.0 version available will allow you to edit and modify all Energy Parameters used by the calculation algorithms interactively. You will be able to save your own 'setups' of energies, making it easy to apply new parameters as well as monitoring structure changes in response to energy changes. Available in mid April. If you want to get direct update and program info, add your name to the RNAdraw mailing list by sendin your E-mail address to me at the below address. Good Luck! Ole Matzura ------------------------------------------------------------ Ole Matzura ole@mango.mef.ki.se Dept. of Medical Physics Karolinska Inst. Stockholm, Sweden FAX:+46-8-326505 ------------------------------------------------------------ From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!GN.APC.ORG!infomed!ICT.SLD.CU!FRANZ From: infomed!ICT.SLD.CU!FRANZ@GN.APC.ORG (Franz Torres Barbosa) Newsgroups: bionet.software Subject: DNA programs?? Date: 3 Apr 1995 21:36:09 -0700 Organization: Centro de Inmunologia Molecular Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504040025.AA04874@infomed> NNTP-Posting-Host: net.bio.net Hello netters : I'm a computer programmer and I just began in a new job(related with biotechnology proceses) . I have to automate, like first task, a laboratory which test the DNA of the monoclonal antibodies released. It use differents techniques such as : Hybridisation, PCR, DotBlot, InmunoBlot. It also tests virusses of mice. I would like to know if anybody have an idea or references to existing computer programs related with this subject. Or any mathematical approach or algorithm. If you can send me a file with help I'll be very glad. Please contact me by e-mail at franz@ict.sld.cu, I'm not subscribe to bio-software list. THANKS IN ADVANCE, franz. From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!sunews!swsscsc1!abrchamp From: "G. T. Champion" Newsgroups: bionet.general,bionet.software Subject: Field experimentation conference Date: Tue, 4 Apr 1995 12:11:21 +0100 Organization: University of Reading, U.K. Lines: 5 Message-ID: NNTP-Posting-Host: swsscsc1.reading.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Xref: biosci bionet.general:14477 bionet.software:11691 An AAB meeting in December 1995 will cover all aspects of field experimentation. If you are interested in further details regarding this conference please contact g.t.champion@reading.ac.uk. Please state your interest; i.e. as a delegate, to present a paper or poster, or to exhibit field experimentation equipment. From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!not-for-mail From: ole@mango.mef.ki.se (Ole Matzura) Newsgroups: bionet.software Subject: RNAdraw update! - V0.99-08 Date: 4 Apr 1995 06:27:22 -0500 Organization: UTexas Mail-to-News Gateway Lines: 36 Sender: nobody@cs.utexas.edu Message-ID: NNTP-Posting-Host: news.cs.utexas.edu Hello there! Version 0.99-08 of Rnadraw is now available! New features are: 1) 'Import GCG PlotFold -H' option lets you import ouput from the PlotFold -H prgram in the GCG package, parseing multiple structures in the .CON file to seperate structure entries. This enables you to do suboptimal structure calculation with GCG MFOLD, proccess the results with GCG PlotFold using the -H command line parameter, and import and view all structures in Rnadraw. 2) Some minor quirk fixes in the sequence editor, updated help files and some minor bug fixes. The next and final pre-V1.0 version available will allow you to edit and modify all Energy Parameters used by the calculation algorithms interactively. You will be able to save your own 'setups' of energies, making it easy to apply new parameters as well as monitoring structure changes in response to energy changes. Available in mid April. If you want to get direct update and program info, add your name to the RNAdraw mailing list by sendin your E-mail address to me at the below address. Good Luck! Ole Matzura ------------------------------------------------------------ Ole Matzura ole@mango.mef.ki.se Dept. of Medical Physics Karolinska Inst. Stockholm, Sweden FAX:+46-8-326505 ------------------------------------------------------------ From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!convex!news.duke.edu!news-feed-1.peachnet.edu!usenet.eel.ufl.edu!gmi!msunews!harbinger.cc.monash.edu.au!lugb!news From: Paul Robert Fisher Subject: Re: Postscript files into Windows Sender: news@lugb.latrobe.edu.au (News System) Message-ID: <1995Apr4.072202.4970@lugb.latrobe.edu.au> Date: Tue, 4 Apr 1995 07:22:02 GMT References: Organization: La Trobe University Lines: 11 Jeffrey A. Millstein wrote: > > Perhaps I'm being naive, but is there a way to incorporate a postscript > file into a Windows program. I'm not talking about EPS, but a output to > a postscript printer that is captured into a file. Yes there is. You need 2 programmes - ghostscript and ghostview along with a library of fonts for ghostscript. They are available for Windows on the internet. I think, but can't remember for sure, that they come with the GNU public licence agreement. One site that has them is ftp.cica.indiana.edu. Good luck. Paul Fisher. From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!psgrain!ee.und.ac.za!ucthpx!ovisun.ovi.ac.za!ovisun.ovi.ac.za!not-for-mail From: basil@ovi.ac.za (Basil Allsopp) Newsgroups: bionet.software Subject: Re: Fragment assembly question Date: 4 Apr 1995 08:33:58 -0000 Organization: Onderstepoort Veterinary Institute Lines: 22 Sender: basil@ovisun.ovi.ac.za Distribution: world Message-ID: <3lr09m$2vh@ovisun.ovi.ac.za> References: <3lf1jp$5bo@fermat.mayo.edu> Reply-To: basil@ovi.ac.za NNTP-Posting-Host: ovisun.ovi.ac.za In article 5bo@fermat.mayo.edu, Black.John@mayo.edu (J. Logan Black) writes: > Are there any fragment assembly programs available for PC other than > netting into GCG somewhere? Maybe I am dense but GCG is awkward > and I would like to find a better way. When assembling a big project GCG is > too difficult to use. Also what is the best protein software available for PC. > I need to convert DNA/RNA to protein and analyze the protein for MW and > other characteristics. The best fragment assembly software is STADEN, see the newsgroup bionet.software.staden. It also does the other things you mention. The latest version of the program is for Unix, but there used to be a PC version, marketed by Amersham International. It may not have been updated for several years, but it was fully functional as stood about 5 years ago. -- --- Basil Allsopp | E-mail basil@ovisun.ovi.ac.za Onderstepoort Veterinary Institute | Phone +27 12 5299385 Onderstepoort 0110, South Africa | Fax +27 12 5299431 From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!utnut!utzoo!mes From: mes@zoo.toronto.edu (Mark Siddall) Subject: Re: PAUP Message-ID: Date: Tue, 4 Apr 1995 03:17:32 GMT References: Organization: U of Toronto Zoology Lines: 33 In article frey@umnw.ethz.ch (Daniel Frey) writes: >Hello > I'm looking out for a leagalized copy of paup for the macintosh. Does >anybody know how to get it? I'd really appreciate to get some >informations or a piece of advice. > >Thanks a lot I am afraid that there is no way to get PAUP legally at the moment. The Illinois Natural History Survey has been distributing it for years. Dave does not distribute it himself. At the moment, I believe that INHS has suspended distribution. (My understanding is that they do this now and then to the frustration of many). PAUP 4.?.? is likely to be released this summer (?) but there are NO guarantees on this!! Mind you I have seen it in action and it is worth waiting for. (Though perhaps it should be renamed to "PULP" as it has likelihood built in to it I am led to believe. Wether or not it will still be handled by INHS is not known. There are rumours of a Sinauer interest as with MacClade. Although this may be informative, I am afraid it mey not help you. I would try INHS, and no I do not have an address or phone#. Mark -- Mark E. Siddall "I don't mind a parasite... mes@vims.edu I object to a cut-rate one" Virginia Inst. Marine Sci. - Rick Gloucester Point, VA, 23062 From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!library.ucla.edu!csulb.edu!csus.edu!news.ucdavis.edu!okra.ece.ucdavis.edu!varma From: varma@okra.ece.ucdavis.edu (Hemant Varma) Newsgroups: bionet.molbio.proteins,bionet.software Subject: E-mail address needed Date: 4 Apr 1995 17:09:21 GMT Organization: University of California, Davis Lines: 25 Message-ID: <3lrug1$r6s@mark.ucdavis.edu> NNTP-Posting-Host: okra.ece.ucdavis.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.proteins:4179 bionet.software:11697 i Hello, I was wondering if anybody knows an e-mail address of the following authors in Brazil: A.C. Gaudio and Y. Takahata of the following paper: Calculation of molecular surface area with numerical factors Computers & Chemistry Vol. 16, No.4, 277-284 I am basically looking for the program that they wrote to compute the accessible surface areas. Any help would be appreciated. Critiques on their method are welcome as well! Thanks, Hemant From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!ns1.faseb.org!darwin.sura.net!martha.utk.edu!MENDEL.PRG.UTK.EDU!agoslen From: agoslen@utkvx.utk.edu (alan goslen) Newsgroups: bionet.software Subject: searching for most probable number software Date: Tue, 4 Apr 1995 12:10:18 Organization: University of Tennessee Lines: 7 Message-ID: NNTP-Posting-Host: mendel.prg.utk.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hi, I am looking for software that would help in determining most probable number (MPN) of bacteria. It should be useful for all kinds of dilutions and assay formats. Appreciate for the time and help Udayakumar Matrubutham e-mail: Udai@utkvx.utk.edu From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!library.ucla.edu!csulb.edu!csus.edu!news.ucdavis.edu!okra.ece.ucdavis.edu!varma From: varma@okra.ece.ucdavis.edu (Hemant Varma) Newsgroups: bionet.molbio.proteins,bionet.software Subject: GEPOL Date: 4 Apr 1995 16:06:40 GMT Organization: University of California, Davis Lines: 18 Message-ID: <3lrqqg$i2t@mark.ucdavis.edu> NNTP-Posting-Host: okra.ece.ucdavis.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.proteins:4177 bionet.software:11695 hello everyone, Here is one more request. I am looking for a program called GEPOL. It has been developed by E. Silla et al. (J. of Mol. Garphics, 1990, Vol 8 (168-172). They give a e-mail address, but that does not work from here.. Any information will be greatly appreciated. I will soon post a summary of all the available programs that compute accessible surface areas..Thanks to all those who responded and were kind enough to share the information.. Hemant varma@cs.ucdavis.edu From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!news.lth.se!news.lu.se!bosse-q840.wblab.lu.se!bo.servenius From: Bo Servenius Subject: Program for calculation of MW and pI Content-Type: text/plain; charset=ISO-8859-1 Message-ID: <1995Apr4.144402.22926@nomina.lu.se> X-Xxmessage-Id: X-Xxdate: Tue, 4 Apr 1995 16:44:56 GMT Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: bosse-q840.wblab.lu.se Content-Transfer-Encoding: 8bit Organization: lund university X-Newsreader: Nuntius 2.0_68K Mime-Version: 1.0 Date: Tue, 4 Apr 1995 14:44:02 GMT Lines: 20 Dear Netters: Is there any easy to use program for mac to calculate MW and pI of a peptide sequences? yours BOSSE _________________________________________________________________________ Bo Servenius, Ph.D | bo.servenius@wblab.lu.se The Wallenberg lab | http://www.wblab.lu.se Lund University | phone: +46-46-2224325 office P.O.Box 7031 | +46-46-2224640 lab S-220 07 Lund | +46-46-159194 home Sweden | fax +46-46-2224324 Europe | pager: +46-0740-153870 ___________________________________|_____________________________________ From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: roxanne@odin.mda.uth.tmc.edu (Roxanne Hall) Newsgroups: bionet.software Subject: A Protein Database Date: 4 Apr 1995 22:06:54 +0100 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3lscde$3er@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk, genbankb@dl.ac.uk, embl-db@dl.ac.uk Can anyone refer me to a protein database or a database search utility which can select a protein based on the Molecular Weight and one other physical characteristic (i.e. the Isoelectric Point). Thank you in advance for your assistance. _____________________________________________________________________________ Roxanne Hall, Computer Programmer II ** In a world where there is so Biomathematics, University of Texas, ** much to be done, M.D. Anderson Cancer Center ** I feel strongly that there must 1515 Holcombe Blvd., MS 237, ** be something for me to do. Houston, Texas 77030 ** ** - Dorthea Dix E-Mail: roxanne@odin.mda.uth.tmc.edu ** Phone: 713/792-2604 From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!aaRS!art From: art@aaRS (Arturo J. Morales) Newsgroups: bionet.software Subject: DNA Strider Date: 4 Apr 1995 20:50:22 GMT Organization: Massachvsetts Institvte of Technology Lines: 15 Message-ID: <3lsbee$ks6@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: aars.mit.edu X-Newsreader: TIN [version 1.2 PL1] I just started using DNA strider, but the version i have is 1.00 Q. is there a newer version around? or at least an updated RE library? Thanks Art -- Arturo J. Morales (RPI '94) | art@aars.mit.edu Department of Biology | Massachvsetts Institvte of Technology http://www.mit.edu:8001/afs/athena.mit.edu/user/a/j/ajm1/www/top.html ---------------------------------------------------------------------------- "That Person you see in the Mirror is made up of D-Amino Acids" --C.P. From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!biosci!not-for-mail From: recipon@ncbi.nlm.nih.gov (Herve Recipon) Newsgroups: bionet.software,bionet.protista,bionet.plants Subject: Improvements to BLAST databases Date: 4 Apr 1995 15:14:10 -0700 Organization: National Center for Biotechnology Information Lines: 86 Sender: biohelp@net.bio.net Distribution: world Message-ID: <1995Apr4.155840.2864@nlm.nih.gov> Reply-To: recipon@ncbi.nlm.nih.gov NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:11700 bionet.protista:290 bionet.plants:6308 As part of NCBI's ongoing efforts to provide BLAST users with access to the most up-to-date, comprehensive and useful databases, the following changes are planned for BLAST databases: 1) Closer synchronization between BLAST and other NCBI databases. 2) Separation of EST data from other non-redundant nucleotide sequences. 3) A new non-redundant protein sequence database. 4) Discontinued support for seldom-used or unmaintained databases. We expect to implement these changes in July 1995. More details about each proposed change are provided below. If you have any questions or concerns, please direct them to blast-help@ncbi.nlm.nih.gov Closer synchronization between BLAST and other databases: BLAST databases will be built from the same source data that are now used for Entrez, the Retrieve e-mail server and the daily updates. This means that sequences identified in a BLAST search will always be accessible from NCBI search services. As part of the project to improve synchrony among BLAST and other forms of the sequence databases, every sequence will have a unique identifier called the "gi" number. The gi number of an entry changes with each update to the sequence data, something not necessarily true for the accession number or locus name. This will allow Entrez or Retrieve users to be certain that they are retrieving exactly the sequence identified by BLAST. Additionally a gi number allows easy automated retrieval of sequences from database interfaces. Retrieval by accession number or locus name will, of course, continue to be supported. The non-redundant BLAST nucleotide databases contain all of the data submitted to the international sequence database collaborators: GenBank, EMBL and DDBJ. Since data are quickly exchanged among the three, there is no need to search them individually. Therefore the option of specifying a specific database will be removed. Users may be assured of searching all publically available sequences, regardless of the database of origin. Separation of EST data: In order to give users more control over their BLAST searches, the EST division will be split off from the other GenBank divisions. This separation is necessitated by the phenomenal growth in the EST division, which will increase by about 4000 to 6000 sequences/week until the summer of 1996. Partitioning the non-redundant database will assure that non-EST matches are not masked by the tremendous number of EST sequences. Conversely it will be straightforward to search the EST division and be assured of only EST hits. While this change will require that some users modify their search strategy, we believe that the ability to better specify the contents of the database will make BLAST searches much more productive for most users. The reconfigured databases will retain the names "nr" and "dbest" so as not to break existing scripts. The "new" nr will also differ from the current non-redundant nucleotide database in having a common origin with Entrez and other NCBI source databases. New non-redundant protein sequence database: The protein sequences now available in Entrez will be searchable in a non-redundant database called "nr". This database will be comprised of pdb; swiss-prot; pir sequences not found in pdb or swiss-prot; prf not covered in pdb, swiss-prot or pir; and all conceptual translations from GenBank sequences not in any of the other databases. As with the non-redundant nucleotide database, the nr protein database will be derived from the same source as Entrez and other NCBI databases. A second new protein sequence database containing only sequences from swiss-prot and pdb will also be available. This database, called "spdb", will allow users to restrict searches to these two highly annotated sources. Discontinued support for databases: The Kabat, EPD, and TFD databases are either infrequently used or not regularly updated. Therefore BLAST access to these databases will be discontinued. --blast-help@ncbi.nlm.nih.gov From owner-software@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!not-for-mail From: 9224076@ul.ie (Stephen Mulcahy) Newsgroups: bionet.software Subject: Visualising Biomolecules... Date: 4 Apr 1995 04:48:35 -0500 Organization: UTexas Mail-to-News Gateway Lines: 14 Sender: nobody@cs.utexas.edu Message-ID: <9504040947.AA05593@itdsrv1.ul.ie> NNTP-Posting-Host: news.cs.utexas.edu Hi, We are currently studying how Lysozyme works as a model of how Enzymes work in general and I'm wondering if there is anything around in terms of images / animations that would help in this? I can place anything I find on our anonymous ftp archive for other's use aswell. Thanks for your help. -stephen BTW Can anyone recommend a good source of [free] bio/chem related clip-art -------------------------------------------------------------------------------------------- Stephen "Divil" Mulcahy 9224076@ul.ie 3rd Industrial Biochemistry UG, University of Limerick (Eire) WWW: http://skynet.ul.ie/~stephen From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!sol.ctr.columbia.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!holzwarth3.life.uiuc.edu!user From: jbuberel@uiuc.edu (Jason L. Buberel) Newsgroups: bionet.software Subject: Re: DNA Sequencing on Macintosh? Date: Tue, 04 Apr 1995 19:28:53 -0500 Organization: Universtiy of Illinois Lines: 29 Message-ID: References: NNTP-Posting-Host: holzwarth3.life.uiuc.edu In article , Jeff Kozlowski wrote: > Anyone out there know of a good application that will automatically read > DNA sequences from autoradiography film? I would appreciate any help. > > > Jeff > email jkoz@saul.u.washington.edu (not jkoz@u.wash....) Jeff, check out the NCSA's ftp server: ftp://ftp.ncsa.uiuc.edu/ They have a program, GelReader, that is supposed to do what you ask. I have not used it before, I just know it exists, and that it is FREE! Check it out. -jason ================ Jason L. Buberel Graduate Student Nueroscience Pgm U of Illinois-UC ================ From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!sunic!sunic.sunet.se!news.funet.fi!luotsi.uku.fi!usenet From: Matthias Niemitz Newsgroups: bionet.software Subject: PERCH NMR software, new release Date: 5 Apr 1995 10:00:48 GMT Organization: University of Kuopio, Finland Lines: 19 Message-ID: <3ltpog$hks@luotsi.uku.fi> NNTP-Posting-Host: s3038.uku.fi Dear NMR Spectroscopist: We proudly announce the latest release of the PERCH NMR software package including new, unique features covering every-day routine tools to sophisticated procedures for deconvolution and simulation/iteration. A free tutorial is available via World Wide Web and anonymous FTP. For more information please check: World Wide Web: http://www.uku.fi/~niemitz/perch.htm Anonymous FTP: FTP.FUNET.FI in directory: /pub/sci/chem/nmr or contact: PERCH Project phone: + 358 71 163242 University of Kuopio, P.O.B. 1627 telefax: + 358 71 163259 FIN-70211 Kuopio, FINLAND e-mail: perch@kummeli.uku.fi From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!bshomer From: bshomer@ebi.ac.uk (Benny Shomer) Subject: Re: DNA programs?? Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Tue, 4 Apr 1995 22:25:33 GMT References: <9504040025.AA04874@infomed> Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 74 Franz Torres Barbosa (infomed!ICT.SLD.CU!FRANZ@GN.APC.ORG) wrote: : Hello netters : : : I'm a computer programmer and I just began in a new job(related : with biotechnology proceses) . I have to automate, like first task, : a laboratory which test the DNA of the monoclonal antibodies : released. It use differents techniques such as : Hybridisation, : PCR, DotBlot, InmunoBlot. It also tests virusses of mice. : : I would like to know if anybody have an idea or references to : existing computer programs related with this subject. Or any : mathematical approach or algorithm. If you can send me a file with : help I'll be very glad. : Here is a clip from a search through the BioCatalogue for MolBio software, maintained at the EMBL outstation - EBI. The BioCatalogue is accessible through WWW at: http://www.ebi.ac.uk under "Documentation and software" or through gopher: gopher.ebi.ac.uk Hope it helps, Benny Shomer. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Benny Shomer External Biological Liasion Officer, EMBL outstation - The EBI, Hinxton Hall, Hinxton,Cambridge CB10 1RQ, UK Tel: +44-223-494437 Fax: +44-223-494468 Email: bshomer@EBI.ac.uk http://www.ebi.ac.uk/ebi_docs/staff/benny.html ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAME MOLBIO++ DOMAIN Sequence analysis DESCRIPTION molbio++ is a C++ library for molecular biosequence analysis. DESCRIPTION Major features include: DESCRIPTION classes and services for reading and writing sequence data in DESCRIPTION the following formats: Genbank Flatfile , EMBL / SwissProt DESCRIPTION GCG / Wisconsin , Fasta / Pearson , PIR , NCBI Retrieve Server DESCRIPTION (read-only) DESCRIPTION limited parsing of fields and features in biosequence files DESCRIPTION storing amino acid or nucleic acid sequences iterating over DESCRIPTION a biosequence DESCRIPTION calculating and storing counts or frequencies of amino acids DESCRIPTION or nucleotides DESCRIPTION device-independent graphics, via GCG's FIGURE program DESCRIPTION translating nucleotide sequences into proteins using DESCRIPTION the universal genetic code or modifications thereof. DESCRIPTION parsing BLAST output DESCRIPTION calculating pI and molecular weight of proteins amino acid DESCRIPTION hydropathy values of Kyte & Doolittle AUTHOR Keith Robison RT - ADDRESS Harvard University Department of Cellular and Developmental ADDRESS Biology Department of Genetics (Harvard Medical School) / HHMI CONTACT Keith Robison: robison@biosun.harvard.edu SITE ftp anonymous golgi.harvard.edu SITE Directory /pub/robison SITE-CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk OS Sparcstation LANGUAGE C ++ From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!cs.utexas.edu!swrinde!emory!news-feed-1.peachnet.edu!usenet.eel.ufl.edu!cobia.gulf.net!usenet From: Gayle Christopher Newsgroups: bionet.software Subject: gel electrophoresis analysis Date: 5 Apr 1995 14:36:11 GMT Organization: The Gulf Coast Internet Company Lines: 6 Message-ID: <3lu9sr$gnb@cobia.gulf.net> NNTP-Posting-Host: slip2.gulf.net hello, Could someone suggest software for 1D and/or 2D eletrophoretic gel analysis? Thank you. Gayle Christopher From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!news.funet.fi!news.csc.fi!siru.csc.fi!Heikki.Lehvaslaiho From: Heikki Lehvaslaiho Newsgroups: bionet.software Subject: Re: Program for calculation of MW and pI Date: 5 Apr 1995 12:47:27 GMT Organization: CSC Lines: 29 Distribution: world Message-ID: <3lu3gv$eh@pobox.csc.fi> References: <1995Apr4.144402.22926@nomina.lu.se> NNTP-Posting-Host: siru.csc.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.1_68K X-XXMessage-ID: X-XXDate: Wed, 5 Apr 1995 13:42:48 GMT In article <1995Apr4.144402.22926@nomina.lu.se> Bo Servenius, bo.servenius@wblab.lu.se writes: >Is there any easy to use program for mac to calculate MW and pI >of a peptide sequences? There is at least one which is not only accessible from Macs but from any Internet-connected computer: Compute pI/Mw http://expasy.hcuge.ch/ch2d/pi_tool.html Is it only one of the tools from the ExPASy World Wide Web (WWW) molecular biology server of the Geneva University Hospital and the University of Geneva . RGDS, -Heikki ______ _/ _/____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho _/_/_/_/_/ X.400: /G=Heikki/S=Lehvaslaiho/O=CSC/A=fumail/C=fi/ _/ _/ _/ Center for Scientific Computing _/ _/ _/ Tietotie 6, P.O. Box 405, FIN-02101 Espoo FINLAND _/ _/ _/ Phone: +358 0 457 2076 FAX: +358 0 457 2302 _/ URL: http://www.csc.fi/molbio/ __ _/_/_/_/_/________________________________________________________ From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!agate!usenet.hana.nm.kr!usenet.kornet.nm.kr!soback!hansol1 From: hansol1@soback.kornet.nm.kr (HANSOL (kornet)) Newsgroups: bionet.software Subject: (Q) Training Course on BioInformatics Date: 5 Apr 1995 12:42:38 GMT Organization: KORNET (Korea Telecom) Lines: 23 Message-ID: <3lu37u$8mp@usenet.kornet.nm.kr> NNTP-Posting-Host: soback.kornet.nm.kr X-Newsreader: TIN [version 1.2 PL2] Dear Netters ... There were several lists of the grad/training course on bioinformatics/computational biology ago . But there has been great changes after those lists were compiled ( 1992 or 1993 or so ) . So I believe we should have another new "The list of the graduate programs or training courses on the BioInformatics and Computational Biology around the World " Although the contributions from the Course Directors are expected Any comments would be certainly appreciated . If there are no volunteers to compile the list I could certainly take the job and post the result . p.s. Any version already compiled ? Then please let me be located ! Thanks for reading me and in advance . Sincerely Rhee Hwan-Seok email : hansol1@soback.kornet.nm.kr From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!uknet!daresbury!not-for-mail From: JAB5@VAX.YORK.AC.UK Newsgroups: bionet.software Subject: nih image Date: 5 Apr 1995 12:29:58 +0100 Lines: 7 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3ltuvm$7o6@mserv1.dl.ac.uk> Original-To: BIO-SOFT@dl.AC.UK Dear colleagues, Where might I find NIH image which DOES NOT require a floating-point co-processor? Thank you, Jim Brannigan Chemistry dept University of York, UK From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!news2.near.net!das-news2.harvard.edu!oitnews.harvard.edu!news.dfci.harvard.edu!usenet From: David_Levy.macmailgw.DFCI.harvard.edu (David N. Levy) Newsgroups: bionet.software Subject: Re: DNA Strider Date: 5 Apr 1995 19:07:08 GMT Organization: Dana-Farber Cancer Institute Lines: 19 Sender: -Not-Authenticated-[7889] Message-ID: <3lupos$flc@cisunix1.dfci.harvard.edu> References: <3lsbee$ks6@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: 155.52.20.30 X-Posted-From: InterNews 1.0.6@155.52.20.30 Xdisclaimer: No attempt was made to authenticate the sender's name. In article <3lsbee$ks6@senator-bedfellow.MIT.EDU> art@aaRS (Arturo J. Morales) writes: > Q. is there a newer version around? or at least an updated RE library? DNA Strider 1.2 came out in December 1991. I don't know of any updates since then, and if there are later versions I would appreciate hearing about that. Strider can be obtained with its instruction manual (which I recommend you get because there are some non-intuitive aspects of the program) from its author Christian Marck at Service de Biochimie - Department de Biologie -Bat 142, Centre d'Etudes Nucleaires de Saclay, 91191 GIF-SUR-YVETTE, CEDEX, FRANCE. C. Marck asks for $200.00 for the program, which I think is a fair price, though he is rather slow in responding sometimes. Version 1.2 has some nice facilites on it like protein and nucleaic acid comparison matrices and stem-loop predictions. I have a more or less updated restriction library, where I have added about 100 commercially availible enzymes to the library provided with the program. I can e-mail it to you. David Levy From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!newsserver.jvnc.net!synapse.bms.com!riversend.bms.com!user From: Roberts_Daniel_g.PRILVMS3@msmail.bms.com (Dan Roberts) Newsgroups: bionet.software Subject: Graphing Software your choice please??? Date: Wed, 05 Apr 1995 14:51:33 -0500 Organization: BMS Lines: 23 Message-ID: NNTP-Posting-Host: riversend.bms.com -- Netters. I need some help in selecting the best MAC based graphing program from the following list: Delta graph, Cricket graph, Sigma Plot, Kaleidagraph, GraphPad or some other choice. Up until now we have been doing curve fitting using Kaleidagraph. Well now that we all have MAC Excel 5.0 we would like to take advantage of the fact that Excel 5.0 may link to other apps. Our current version of Kaleidagraph doesn't support this and I am wondering if one of the above programs may in fact both link with Excel 5.0 and meet our needs with greater satisfaction. We use Kaleidagraph for two site curve fits and etc. Also, it might come in handy if such a graphing program would also interface as well with FoxPro. -- Dan Roberts BRISTOL-MYERS SQUIBB PHARM. RES. CENTER "Nature is last at Bats" PRINCETON, NEW JERSEY U.S.A. PLANET EARTH, MILKY-WAY GALAXY <<<>>>Roberts_Daniel_G.PriLVMS3@MSMAIL.BMS.COM From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Newsgroups: bionet.software Path: biosci!ns1.faseb.org!darwin.sura.net!nih-csl!sathya From: sathya@helix.nih.gov (Dr. B. K. Sathyanarayana) Subject: Looking for software for distance plot Message-ID: <1995Apr5.203919.10875@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: helix.nih.gov Reply-To: sathya@ncifcrf.gov Organization: National Institutes of Health, Bethesda, MD, 20892 Date: Wed, 5 Apr 1995 20:39:19 GMT Lines: 17 I am looking for a software that gives contoured distance plot for C-alpha atoms. As it is known this is symmetrical about the diagonal with x and y axis being the residue numbers. This is also used for identifying domains in proteins. (Ref: Principles of Protein Structures by Schulz and Schirmer, page 147) thanks sathya -- B.K. Sathya National Cancer Institute Frederick, Maryland sathya@ncifcrf.gov From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!aaRS!art From: art@aaRS (Arturo J. Morales) Newsgroups: bionet.software Subject: Plasmid software for IBM (Windows) Date: 5 Apr 1995 20:28:36 GMT Organization: Massachvsetts Institvte of Technology Lines: 25 Message-ID: <3luuhk$ltl@senator-bedfellow.MIT.EDU> NNTP-Posting-Host: aars.mit.edu X-Newsreader: TIN [version 1.2 PL1] I posted yesterday asking about a new version of DNA strider, but I guess that i have changed my mind and I have decided to (Hopefully) switch platforms to Windows NT (Already in Lab, and much faster than the macs...) Does anyone know of any Plasmid software for windows? I've seen the demo for GeneRuner, but the actual prg costs in the order of 1000 dollars, a little too much for my taste... I'm looking for something that besides having DNA strider features, looks into secondary structure of oligos (hairpins, etc...) and hopefully is easy to use, although that is not really a requirement :) Thanks in advance... Art -- Arturo J. Morales (RPI '94) | art@aars.mit.edu Department of Biology | Massachvsetts Institvte of Technology http://www.mit.edu:8001/afs/athena.mit.edu/user/a/j/ajm1/www/top.html ---------------------------------------------------------------------------- "That Person you see in the Mirror is made up of D-Amino Acids" --C.P. From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!ux1.cso.uiuc.edu!elarson From: elarson@ux1.cso.uiuc.edu (larson eric) Newsgroups: bionet.software Subject: Deltagraph Pro 3.5 a no go under Warp Date: 5 Apr 1995 19:04:44 GMT Organization: University of Illinois at Urbana Lines: 23 Message-ID: <3lupkc$btf@vixen.cso.uiuc.edu> NNTP-Posting-Host: ux1.cso.uiuc.edu Just a quick comment. The Deltagraph Pro 3.5 upgrade (or new) graphing program uses Win32s 1.23 which doesn't work (yet) under OS/2. I recommend holding off on purchasing (or upgrading) if your primary operating system is, or will be, OS/2 (their version 3.0 software works fine under OS/2 -- great program, it's a shame to lose it). Maybe it will get sorted out, but Deltapoint didn't seem very interested as to whether their software ran under OS/2, so don't say I didn't warn you. They do note that DeltaGraph 3.5 won't run under RISC NT machines either (why they tested this small subset and ignored an OS/2 market 100 times as is a puzzler for me). Anyway, save those upgrade dollars and spend them elsewhere. Good luck!. -- Eric Larson | University of Illinois at Urbana-Champaign USDA/Agronomy | 190 PABL; 1201 W. Gregory; Urbana, IL 61801 elarson@ux1.cso.uiuc.edu | Voice 217.244.3079 Fax 217.244.4419 Fidonet: 1:233/4.1 | My opinions are my own, but correct :-) From owner-software@net.bio.net Tue Apr 04 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!uunet!li.net!liuser32 From: mazz@li.net Newsgroups: bionet.software Subject: plankton images Date: Tue, 04 Apr 95 22:02:25 GMT Organization: LI Net (Long Island Network) Lines: 3 Message-ID: <3lsflh$b10_001@liuser32.li.net> NNTP-Posting-Host: liuser32.li.net X-Newsreader: News Xpress Version 1.0 Beta #3 does anyone know of any on-line access to images of diatoms and/or zooplankton...drawings are ok. species native to the north east US coast prefer. From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!news.sprintlink.net!news.primenet.com!ip144.flg.primenet.com!lockard From: lockard@primenet.com (Ben Lockard) Newsgroups: bionet.software Subject: Chemical flowcharts Date: Wed, 5 Apr 1995 16:58:23 LOCAL Organization: Primenet Lines: 11 Message-ID: NNTP-Posting-Host: ip144.flg.primenet.com X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] I'm a highschool student looking for a program or font that will allow me to draw flow charts of things like the Krebs cycle and EPS. I would perfer to draw the stuff myself so I can learn these charts in the process. Once it is on the computer I would like to output it to a poster. I know the cycles and how they relate and I know how to print using Postscript, but I can't find anything that will allow me to draw these cycles. I've taken a look at Chemical Pi from Linotype but I don't have a Macintosh. Ben Lockard Lockard@primenet.com From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!bcm!!jh691448 From: jh691448@.bcm.tmc.edu (Jing He) Newsgroups: bionet.software Subject: genetic algorithm? Date: 6 Apr 1995 22:49:08 GMT Organization: Baylor College of Medicine, Houston, Tx Lines: 8 Sender: jh691448@ (Jing He) Distribution: world Message-ID: <3m1r54$qj1@gazette.bcm.tmc.edu> NNTP-Posting-Host: condor.mbcr.bcm.tmc.edu Keywords: GA Hi, Could anyone tell me any information on where to get the genetic algorithm? Thank you. Jing From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!ra.nrl.navy.mil!usenet From: rwadkins@cbmse.nrl.navy.mil (rmw) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: ADAPT II on Mac? Date: 6 Apr 1995 19:05:32 GMT Organization: Naval Research Laboratory Lines: 6 Sender: -Not-Authenticated-[6745] Message-ID: <3m1e1s$phs@ra.nrl.navy.mil> NNTP-Posting-Host: rmw-6900.nrl.navy.mil X-Posted-From: InterNews 1.0.1@rmw-6900.nrl.navy.mil Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.software:11722 comp.sys.mac.scitech:4280 Is anyone running the pharmacokinetics program ADAPT II (Biomedical Simulations Resource) on a Macintosh? If so, how did you port it? Thanks for the help. Randy From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!newsxfer.itd.umich.edu!news.itd.umich.edu!sdering.uis.itd.umich.edu!shawn_Dering From: shawn_Dering@umich.edu Newsgroups: bionet.software Subject: pkzip/unzip Date: Thu, 6 Apr 1995 14:03:06 Organization: University of Michigan Lines: 12 Message-ID: NNTP-Posting-Host: sdering.uis.itd.umich.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev Final Beta #7] Anyone, Do you know where I can get a copy of pkzip/unzip compression package. I'm using a MS-Dos machine. Also, anything to unzip *.arc files would be helpful, too. Thanks. Send to: Shawn_Dering@dsc.umich.edu From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!sol.ctr.columbia.edu!news.oberlin.edu!ocvaxa.cc.oberlin.edu!SUL0904 From: sul0904@ocvaxa.cc.oberlin.edu (the svelte squirrel) Newsgroups: bionet.software Subject: Modeling software wanted Date: 6 Apr 1995 03:59:55 GMT Organization: Oberlin College, Oberlin, Ohio Lines: 10 Message-ID: <3lvovr$s5b@news.cc.oberlin.edu> Reply-To: sul0904@ocvaxa.cc.oberlin.edu NNTP-Posting-Host: ocvaxa.cc.oberlin.edu I am interested in modeling the acid/base physiology and transport > information of a grasshopper's (or any insect) gut. Any and all information > on applicable software would be greatly appreciated, especially pertaining > to a program called Stella (by High Performance Systems). > > Thanks, > Please email to : sul0904@ocvaxa.cc.oberlin.edu > > Sara Liao > From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!holzwarth3.life.uiuc.edu!user From: jbuberel@uiuc.edu (Jason L. Buberel) Newsgroups: bionet.software Subject: Re: Graphing Software your choice please??? Date: Thu, 06 Apr 1995 09:36:13 -0500 Organization: Universtiy of Illinois Lines: 58 Message-ID: References: NNTP-Posting-Host: holzwarth3.life.uiuc.edu In article , Roberts_Daniel_g.PRILVMS3@msmail.bms.com (Dan Roberts) wrote: > -- > Netters. I need some help in selecting the best MAC based graphing program from the > following list: > Delta graph, Cricket graph, Sigma Plot, Kaleidagraph, GraphPad or some other choice. > > Up until now we have been doing curve fitting using Kaleidagraph. Well now that > we all have MAC Excel 5.0 we would like to take advantage of the fact that Excel 5.0 > may link to other apps. Our current version of Kaleidagraph doesn't support this > and I am wondering if one of the above programs may in fact both link with Excel 5.0 > and meet our needs with greater satisfaction. We use Kaleidagraph for two site > curve fits and etc. > > Also, it might come in handy if such a graphing program would also interface as > well with FoxPro. > > > -- > Dan Roberts > BRISTOL-MYERS SQUIBB PHARM. RES. CENTER "Nature is last at Bats" > PRINCETON, NEW JERSEY U.S.A. PLANET EARTH, MILKY-WAY GALAXY > <<<>>>Roberts_Daniel_G.PriLVMS3@MSMAIL.BMS.COM Dan, I know that you can conrol DeltaGraph pro with AppleScript, so you could potentially link it with any other program that handles AppleScripting. As for direct links with Excel 5.0, I suppose you mean using OLE 2.0. I know of no Mac graphing program that supports OLE. For all of our graphing needs, DeltaGraph Pro is suffecient. It does handle custom curve fitting and has detailed control over the apearance of graphs. Plus, it is native for PowerPC. As far as FoxPro goes...the linking would be done with AppleScript, so this should work quite handily with DeltaGraph Pro. One program that I have not used, but is highly flexible and very programmable is Igor Pro. It has its own built in scripting language, and probably has support for AppleScripting. Hope this helps, jason ================ Jason L. Buberel Graduate Student Nueroscience Pgm U of Illinois-UC ================ From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: Deltagraph Pro 3.5 a no go under Warp Date: 6 Apr 1995 08:39:40 GMT Organization: University of Cambridge, England Lines: 24 Message-ID: <3m09cc$lbd@lyra.csx.cam.ac.uk> References: <3lupkc$btf@vixen.cso.uiuc.edu> NNTP-Posting-Host: mole.bio.cam.ac.uk elarson@ux1.cso.uiuc.edu (larson eric) writes: >Just a quick comment. The Deltagraph Pro 3.5 upgrade (or new) graphing >program uses Win32s 1.23 which doesn't work (yet) under OS/2. > >I recommend holding off on purchasing (or upgrading) if your primary >operating system is, or will be, OS/2 (their version 3.0 software works >fine under OS/2 -- great program, it's a shame to lose it). > >Maybe it will get sorted out, but Deltapoint didn't seem very interested as >to whether their software ran under OS/2, so don't say I didn't warn you. >They do note that DeltaGraph 3.5 won't run under RISC NT machines either >(why they tested this small subset and ignored an OS/2 market 100 times as >is a puzzler for me). > >Anyway, save those upgrade dollars and spend them elsewhere. As usual, the industry is kow-towing to Micro$oft, even though NT isn't selling very well at all. I hope the industry will wake up soon to the fact that OS/2 *is* selling, and that people are not goint to wait for Windows 95 forever. Tim. From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!sunic.sunet.se!umdac!news From: peterl@umdix.umdc.umu.se (Peter Lundberg) Newsgroups: bionet.software Subject: Re: Program for calculation of MW and pI Date: 6 Apr 1995 07:33:48 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 56 Sender: -Not-Authenticated-[8620] Message-ID: <3m05gs$8qb@kitten.umu.se> References: <1995Apr4.144402.22926@nomina.lu.se> NNTP-Posting-Host: plgmac.chem.umu.se X-Posted-From: InterNews 1.0.6@plgmac.chem.umu.se Xdisclaimer: No attempt was made to authenticate the sender's name. In article <1995Apr4.144402.22926@nomina.lu.se> Bo Servenius writes: > Is there any easy to use program for mac to calculate MW and pI > of a peptide sequences? Hej Bosse! There is an Excel spreadsheet for doing this (yes, it is for mac). Below is the readme info. I forgot where I ftp-ed it from. If you are interested - give me a 'call' 73, Peter =============== pI_protein 1.0v1 by Lars Henrik Oestergaard©1994. Introduction: This worksheet calculates the isoelectric point of a protein. I think that it will be possible to make the worksheet do the calculations faster. Fell free to make it better, it is not protected by any password. I would like to be able to simply type in an amino acid sequence and then let the worksheet do the rest (so you may see another version soon). Please give copies of the worksheet to everybody you think may use it, but don't charge money for it!!! You may also modify your personal copy, customising it to your needs. BUT please give the original copy to other interested Mac users. Input: Simple fill in the number of the specified charged amino acids in the boxed cells. Also fill in the pK value of the amino group in the N-terminus and the pK value of the carboxyl group in the C-terminus. You may find the values in the table on page one in the worksheet. Output: You are able to copy and print the results. The result consist of the total number of negative and positive charges at pH values ranging from 1-13 (with 0.5 pH units between each). These as well as their sum are also plotted in a chart as a function of the pH value. NB. The worksheet is made with excel version 3.0a. Lars Henrik Oestergaard Department of Chemistry Aarhus University DK-8000 Aarhus C Denmark (Internet: lho@biobase.aau.dk) ============================= O==O ================================== O==O O==O Peter Lundberg O==O O==O Email: peterl@umdix.umdc.umu.se O==O O==O ============761.91141============= O==O From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!newsxfer.itd.umich.edu!jobone!lynx.unm.edu!dns1.NMSU.Edu!dkim From: dkim@nmsu.edu (Daniel Kim) Newsgroups: bionet.software Subject: Whitehead Inst. PRIMER program for MSDOS Date: 3 Apr 1995 22:37:24 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 17 Message-ID: <3lptb4$jhd@dns1.NMSU.Edu> NNTP-Posting-Host: verdi.nmsu.edu Hello: I was reading the readme file for Whitehead Institute's PRIMER software (for design and analysis of PCR primers). I would like a compiled version that will work on an IBM PC compatible computer ('286 with monochrome). They wrote that one way to get primer is to ask someone who already has it, sooooo: Does anyone have a compiled executable version for the PC? Could I get a copy? Thanks.\ Daniel Kim dkim@verdi.nmsu.edu From owner-software@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!cs.utexas.edu!not-for-mail From: 9224076@ul.ie (Stephen Mulcahy) Newsgroups: bionet.software Subject: FTP archive Date: 6 Apr 1995 12:55:35 -0500 Organization: UTexas Mail-to-News Gateway Lines: 19 Sender: nobody@cs.utexas.edu Message-ID: <9504061754.AA15347@itdsrv1.ul.ie> NNTP-Posting-Host: news.cs.utexas.edu Firstly, I'd like to announce the existence of a science software archive at skynet.ul.ie We have a reasonable selection of scientific software in /pub/science which can be accessed anonymously. The site is currently under construction so any additions, advice or comments would be welcome. On a similar note regarding spreadsheets. I am interested in building up a repository of common spreadsheets for doing scientific work, be it chemical, biological or biochemical for either MS Excel or Lotus 1-2-3. Anybody that has any material to donate this repository can either upload it in /pub/uploads on skynet.ul.ie or email it to me. Any material I receive will be made available for public access. thanks -stephen -------------------------------------------------------------------------------------------- Stephen "Divil" Mulcahy 9224076@ul.ie 3rd Industrial Biochemistry UG, University of Limerick (Eire) WWW: http://skynet.ul.ie/~stephen From owner-software@net.bio.net Thu Apr 06 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!uunet!world!harmonic From: harmonic@world.std.com Subject: Announce> Student pricing for O-Matrix for Windows Message-ID: Keywords: data analysis, plotting, numerical analysis Organization: The World Public Access UNIX, Brookline, MA Date: Fri, 7 Apr 1995 04:04:42 GMT Lines: 20 Harmonic Software has announced student pricing of $50 for O-Matrix(R) for Windows. The student package includes all of the analysis and visualation capabilities of the $395 professional version but is being offered to students for a reduced price. O-Matrix for Windows is a high-performance interactive analysis and visualization tool that enables rapid development and execution of scientific and engineering applications. O-Matrix for Windows has a concise matrix-oriented language with a built-in editor, extensive graphics, a debugger, a help system, extensive mathematics and statistics functions, and features and performance exceeding other 'matrix-based' languages. If you have questions or wish to place an order please contact us at: Harmonic Software 12223 Dayton Avenue North, Seattle, WA 98133-8141 1-800-895-4546 (206) 367-8742 fax (206) 367-1067 harmonic@world.std.com (All orders are unconditionally guaranteed) From owner-software@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news From: Michael Woeroesch Newsgroups: bionet.software Subject: finite elements analysis of a human hip Date: 6 Apr 1995 18:45:42 GMT Organization: InterNetNews at News.BelWue.DE (Stuttgart, Germany) Lines: 12 Message-ID: <3m1csm$2g0@news.belwue.de> NNTP-Posting-Host: rghx50.gp.fht-esslingen.de Student in mechanical engineering needs informations about 3d-analysis (Finite elements; Ansys 5.0 & 5.1) of a human hip. I need also informations about the structure of the bone itself, the forces on the bone and different kinds of endoprothesises (shape and material). Some help would be nice. please answer to my email address: s637678@rghx50.gp.fht-esslingen.de From owner-software@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!brenner From: brenner@mole.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.software Subject: Re: Program for calculation of MW and pI Date: 7 Apr 1995 16:51:29 GMT Organization: University of Cambridge, England Lines: 14 Message-ID: <3m3qih$rqh@lyra.csx.cam.ac.uk> References: <1995Apr4.144402.22926@nomina.lu.se> NNTP-Posting-Host: mole.bio.cam.ac.uk Bo Servenius writes: >Dear Netters: >Is there any easy to use program for mac to calculate MW and pI >of a peptide sequences? Almost certainly the easiest thing to do is use the pI/MW computation page at http://expasy.hcuge.ch/ch2d/pi_tool.html Any machine with a forms-capable WWW viewer can use this system -- Steven E. Brenner | S.E.Brenner@bioc.cam.ac.uk MRC Laboratory of Molecular Biology | Hills Road | Office: +44 1223 402221 Cambridge CB2 2QH, UK | Fax: +44 1223 213556 From owner-software@net.bio.net Thu Apr 06 23:00:00 1995 Newsgroups: bionet.software,bionet.molbio.evolution Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!EU.net!Belgium.EU.net!idefix.CS.kuleuven.ac.be!infoserv.rug.ac.be!news.belnet.be!news.vub.ac.be!bioftp.unibas.ch!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!higgins From: higgins@ebi.ac.uk Subject: NJplot: graphical display of trees on MACDIR Sender: news@ebi.ac.uk (Mr news) Message-ID: <1995Apr7.155604@ebi.ac.uk> Date: Fri, 7 Apr 1995 14:56:04 GMT Lines: 35 Organization: European BioInformatics Institute Xref: biosci bionet.software:11728 bionet.molbio.evolution:2634 NJplot by Manolo Gouy Graphical Display of New Hampshire format trees on Macs. NJplot is a simple to use and extremely useful program for displaying New Hampshire format trees (nested parentheses; e.g. TREEFILE files from PHYLIP or the *.dnd, *.ph and *.phb files from Clustal W). It displays branch lengths and bootstrap information (if present) and allows the user to swap branches and change the position of the root. Trees can then be saved in PICT format which are readable by most Macintosh graphics packages. I included an earlier version of NJplot with Clustal W 1.5; this had a minor bug which sometimes clipped the left hand side of the trees. This, revised version is now included and is also available on its own. NJplot can be retrieved by anonmyous ftp from: ftp.ebi.ac.uk Get the file: /pub/software/mac/njplot.sea.hqx This is a BinHex encoded self extracting archive. Many thanks to Manolo Gouy, University of Lyon, France for making the program available!! Des Higgins, EMBL/EBI, Hinxton, UK. From owner-software@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!howland.reston.ans.net!news.starnet.net!wupost!uwm.edu!news.alpha.net!solaris.cc.vt.edu!news.duke.edu!news-feed-1.peachnet.edu!usenet.eel.ufl.edu!news.uoregon.edu!ntuix.ntu.ac.sg!raffles.technet.sg!nuscc.nus.sg!engcbh From: engcbh@leonis.nus.sg (Andre Choo) Newsgroups: bionet.software Subject: TFDsearch Date: 6 Apr 1995 06:26:30 GMT Organization: National University of Singapore Lines: 10 Message-ID: <3m01im$hhq@nuscc.nus.sg> NNTP-Posting-Host: engcbh@leonis.nus.sg X-Newsreader: TIN [version 1.2 PL2] I was wondering whether anyone has used TFDsearch by Lee Frank Kolakowski? I am having alot of difficulty with it. According to the instructions, no particular format is required because it automatically uses ReadSeq to convert to the appropriate format. When I execute the software, the results I get seem rather strange...I am able to get transcription factor sites beyond the length of the nucleotide sequence I submit for analysis (eg the sequence is only 688 but I get transcription sites at position 700). The sites listed within the actual sequence also do not correspond with the actual sequence. Not sure why this happens? Does anyone know the E-mail of the author so that I could contact him as well? Thanks! From owner-software@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!doc.news.pipex.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: pkzip/unzip Date: 7 Apr 1995 07:52:41 GMT Organization: University of Cambridge, England Lines: 28 Message-ID: <3m2r09$7oh@lyra.csx.cam.ac.uk> References: NNTP-Posting-Host: mole.bio.cam.ac.uk shawn_Dering@umich.edu writes: >Anyone, > > Do you know where I can get a copy of pkzip/unzip compression package. >I'm using a MS-Dos machine. Also, anything to unzip *.arc files would be >helpful, too. You will find PKZIP and PKUNZIP on almost any MSDOS ftp site. Remember that they are shareware, and you are obligated to pay for them. There is also a free PKZIP clone called zip, and a corresponding PKUNZIP clone called unzip. It creates files compatible with PKZIP 2.x. In my experience it actually manages better compression than PKZIP, although it is slower. It also manages directories rather better, and is available for lots of platforms (DOS, OS/2, Unix). If you use OS/2, it also correctly includes your files' extended attributes in the ZIP file. It is available both as source code and already compiled. Sources and MSDOS binaries are available from: ftp://romulus.ucs.uoknor.edu/src/pc/archivers/unzip Under that archivers/ directory you will also find ARC uncompressors, the latest version of PKZip (2.04g) and oodles of others. Tim. From owner-software@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!CS.Arizona.EDU!arizona!slarson From: slarson@cs.arizona.edu (Susan J. Larson) Newsgroups: bionet.software Subject: Re: DNA Strider Date: 7 Apr 1995 21:39:07 GMT Organization: U of Arizona, CS Dept, Tucson Lines: 12 Distribution: world Message-ID: <3m4bdr$oa3@optima.cs.arizona.edu> References: <3lsbee$ks6@senator-bedfellow.MIT.EDU> <3lupos$flc@cisunix1.dfci.harvard.edu> NNTP-Posting-Host: cougar.cs.arizona.edu In article <3lupos$flc@cisunix1.dfci.harvard.edu>, David_Levy.macmailgw.DFCI.harvard.edu (David N. Levy) writes: |> ...I have a more or less updated restriction library, where |> I have added about 100 commercially availible enzymes to the library |> provided with the program. I can e-mail it to you. David Levy Could you email it to me please? (Sorry for the post, I tried email to David but I don't think the address worked). Thanks, Susan Larson slarson@cs.arizona.edu From owner-software@net.bio.net Fri Apr 07 23:00:00 1995 Path: biosci!UMIN.U-TOKYO.AC.JP!masafumi-tky From: masafumi-tky@UMIN.U-TOKYO.AC.JP (Masafumi Watanabe) Newsgroups: bionet.software Subject: (none) Date: 8 Apr 1995 03:31:03 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504081034.AA16417@cc.umin.u-tokyo.ac.jp> NNTP-Posting-Host: net.bio.net help $B!!!!EOJU>;J8!wElBgIB1!Bh;0Fb2J!J(Bmasafumi-tky@umin.u-tokyo.ac.jp$B!K(B From owner-software@net.bio.net Sat Apr 08 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Where to find searchable index of old bionet postnings Date: 8 Apr 1995 23:57:21 GMT Organization: Biology, Indiana University - Bloomington Lines: 7 Message-ID: <3m77t1$pfd@usenet.ucs.indiana.edu> References: <1995Apr8.134726.742@nomina.lu.se> NNTP-Posting-Host: sunflower.bio.indiana.edu You can find a searchable bionet news archive at IUBio archive: gopher or http to iubio.bio.indiana.edu. look in the Network-News folder. There is a bionet news archive at net.bio.net (gopher or http there also). -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Sat Apr 08 23:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!sunic.sunet.se!news.lth.se!news.lu.se!bosse-q840.wblab.lu.se!bo.servenius From: Bo Servenius Subject: Re: Program for calculation of MW and pI Content-Type: text/plain; charset=ISO-8859-1 Message-ID: <1995Apr8.114314.2420@nomina.lu.se> X-Xxmessage-Id: X-Xxdate: Sat, 8 Apr 1995 13:44:04 GMT Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: bosse-q840.wblab.lu.se Content-Transfer-Encoding: 8bit Organization: lund university X-Newsreader: Nuntius 2.0_68K References: <1995Apr4.144402.22926@nomina.lu.se> <3m3qih$rqh@lyra.csx.cam.ac.uk> Mime-Version: 1.0 Date: Sat, 8 Apr 1995 11:43:14 GMT Lines: 30 In article <3m3qih$rqh@lyra.csx.cam.ac.uk> Steven Brenner, brenner@mole.bio.cam.ac.uk writes: >Almost certainly the easiest thing to do is use the pI/MW >computation page at http://expasy.hcuge.ch/ch2d/pi_tool.html >Any machine with a forms-capable WWW viewer can use this system Thanks for the link. Only problem is that this form can not do correct calculations for amidations or SS-bridges or any other type of modifications. Any advice wher to find a program that also can handle that? yours BOSSE >_________________________________________________________________________ Bo Servenius, Ph.D | bo.servenius@wblab.lu.se The Wallenberg lab | http://www.wblab.lu.se Lund University | phone: +46-46-2224325 office P.O.Box 7031 | +46-46-2224640 lab S-220 07 Lund | +46-46-159194 home Sweden | fax +46-46-2224324 Europe | pager: +46-0740-153870 ___________________________________|_____________________________________ From owner-software@net.bio.net Sat Apr 08 23:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!sunic.sunet.se!news.lth.se!news.lu.se!bosse-q840.wblab.lu.se!bo.servenius From: Bo Servenius Subject: Where to find searchable index of old bionet postnings Content-Type: text/plain; charset=ISO-8859-1 Message-ID: <1995Apr8.134726.742@nomina.lu.se> X-Xxmessage-Id: X-Xxdate: Sat, 8 Apr 1995 15:48:19 GMT Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: bosse-q840.wblab.lu.se Content-Transfer-Encoding: 8bit Organization: lund university X-Newsreader: Nuntius 2.0_68K Mime-Version: 1.0 Date: Sat, 8 Apr 1995 13:47:26 GMT Lines: 19 I have lost my old ref to where the biosci/bionet psotings are archived in a way that can be serached by gopher or www. Could you please help me out. yours bosse _________________________________________________________________________ Bo Servenius, Ph.D | bo.servenius@wblab.lu.se The Wallenberg lab | http://www.wblab.lu.se Lund University | phone: +46-46-2224325 office P.O.Box 7031 | +46-46-2224640 lab S-220 07 Lund | +46-46-159194 home Sweden | fax +46-46-2224324 Europe | pager: +46-0740-153870 ___________________________________|_____________________________________ From owner-software@net.bio.net Sat Apr 08 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!news.sprintlink.net!pipex!sunic!sunic.sunet.se!news.lth.se!news.lu.se!bosse-q840.wblab.lu.se!bo.servenius From: Bo Servenius Subject: Sequence database growth??? Content-Type: text/plain; charset=ISO-8859-1 Message-ID: <1995Apr9.155936.8313@nomina.lu.se> X-Xxmessage-Id: X-Xxdate: Sun, 9 Apr 1995 18:00:29 GMT Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: bosse-q840.wblab.lu.se Content-Transfer-Encoding: 8bit Organization: lund university X-Newsreader: Nuntius 2.0_68K Mime-Version: 1.0 Date: Sun, 9 Apr 1995 15:59:36 GMT Lines: 26 Dear Netters: Is there a site where I can find up to date statistics about EMBL, Genbank, SwissProt etc databases and their growth over the years. Nicest would be a prepared graph but tabled statistics could do. yours BOSSE PS Similar statistics about Internet, and internet tools, growth would also be very appreciated _________________________________________________________________________ Bo Servenius, Ph.D | bo.servenius@wblab.lu.se The Wallenberg lab | http://www.wblab.lu.se Lund University | phone: +46-46-2224325 office P.O.Box 7031 | +46-46-2224640 lab S-220 07 Lund | +46-46-159194 home Sweden | fax +46-46-2224324 Europe | pager: +46-0740-153870 ___________________________________|_____________________________________ From owner-software@net.bio.net Sat Apr 08 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news2.near.net!das-news2.harvard.edu!oitnews.harvard.edu!cmcl2!mcrcr6!mcsv29-p2.med.nyu.edu!waldep01 Newsgroups: bionet.software Subject: Re: Where to find searchable index of old bionet postnings Message-ID: From: waldep01@mcmcr6.med.nyu.edu (Paul D. Walden) Date: Sun, 9 Apr 1995 08:22:19 References: <1995Apr8.134726.742@nomina.lu.se> Organization: NYU Medical Center Nntp-Posting-Host: mcsv29-p2.med.nyu.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 28 In article <1995Apr8.134726.742@nomina.lu.se> Bo Servenius writes: >Subject: Where to find searchable index of old bionet postnings >From: Bo Servenius >Date: Sat, 8 Apr 1995 13:47:26 GMT >I have lost my old ref to where the biosci/bionet psotings are archived >in a way that can be serached by gopher or www. Could you please help me >out. >yours >bosse >_________________________________________________________________________ >Bo Servenius, Ph.D | bo.servenius@wblab.lu.se >The Wallenberg lab | http://www.wblab.lu.se >Lund University | phone: +46-46-2224325 office >P.O.Box 7031 | +46-46-2224640 lab >S-220 07 Lund | +46-46-159194 home >Sweden | fax +46-46-2224324 >Europe | pager: +46-0740-153870 >___________________________________|_____________________________________ Yes. Try - http://www.bionet.com or gopher://net.bio.net. Paul From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!agate!news.Stanford.EDU!cherry From: cherry@fafner.Stanford.EDU (Mike Cherry) Newsgroups: bionet.software Subject: Re: Where to find searchable index of old bionet postnings Date: 10 Apr 1995 02:24:35 GMT Organization: Stanford University Genetics Department Lines: 27 Message-ID: <3ma4t3$9g5@nntp.Stanford.EDU> References: <1995Apr8.134726.742@nomina.lu.se> NNTP-Posting-Host: fafner.stanford.edu In article , Paul D. Walden wrote: >In article <1995Apr8.134726.742@nomina.lu.se> Bo Servenius writes: >>Subject: Where to find searchable index of old bionet postnings >>From: Bo Servenius >>Date: Sat, 8 Apr 1995 13:47:26 GMT > >>I have lost my old ref to where the biosci/bionet psotings are archived >>in a way that can be serached by gopher or www. Could you please help me >>out. > >Yes. Try - http://www.bionet.com or gopher://net.bio.net. Actually bionet.com is a company called United Biogenics, NOT the BioNet we are talking about. There is a URL for the BioSci archives: http://www.bio.net/ but it currently links to the gopher server, gopher://net.bio.net:70/ You can also search via WAIS Inc.'s WWW interface. Start with the URL: http://wais.wais.com:80/newhomepages/directory-of-servers.html then search for biosci. I'd post the actually link to the biosci.src but its really long and will probably cause more trouble for people than the three steps involved by going straight to WAIS, Inc. Mike http://genome-www.stanford.edu/~cherry/ From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!harper From: harper@ebi.ac.uk (Rob Harper) Subject: Re: Sequence database growth??? Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Mon, 10 Apr 1995 14:52:40 GMT Lines: 80 Reply-To: harper@ebi.ac.uk References: <1995Apr9.155936.8313@nomina.lu.se> Organization: EMBL Outstation (Hinxton) The EBI - UK X-Newsreader: mxrn 6.18-16 In article <1995Apr9.155936.8313@nomina.lu.se>, Bo Servenius writes: >Dear Netters: > >Is there a site where I can find up to date statistics about EMBL, >Genbank, >SwissProt etc databases and their growth over the years. Nicest would >be a prepared graph but tabled statistics could do. Here is the appendix taken from the release 41 of EMBL, which shows the development of the database over the years. APPENDIX A: DATABASE GROWTH TABLE The following table shows the growth of the EMBL Nucleotide Sequence Database at each release. Release Month Entries Nucleotides ------- ------- ------- ----------- 1 06/1982 568 585433 2 04/1983 811 1114447 3 12/1983 1481 1654863 4 08/1984 1698 2147205 5 04/1985 2378 2874493 6 08/1985 4835 4567592 7 12/1985 5789 5622638 8 04/1986 6395 6353040 9 09/1986 7630 7813214 10 12/1986 8817 9766948 11 04/1987 11621 12189783 12 07/1987 12706 13638061 13 10/1987 14397 16023478 14 01/1988 15344 17272160 15 05/1988 17961 20318442 16 08/1988 19592 22625941 17 11/1988 20695 24211054 18 02/1989 22938 27249830 19 05/1989 24365 29066676 20 08/1989 26223 31240948 21 11/1989 28679 34748087 22 02/1990 31508 38165786 23 05/1990 34902 42923803 24 08/1990 37784 47354438 25 11/1990 41580 52900354 26 02/1991 43745 55859549 27 05/1991 46871 59915244 28 09/1991 54558 70448052 29 12/1991 57765 75400487 30 03/1992 63378 83574342 31 06/1992 72481 94390065 32 09/1992 79377 101292310 33 12/1992 89100 111413979 34 03/1993 99591 121420828 35 06/1993 108973 131880111 36 09/1993 127933 145401156 37 12/1993 146576 158171400 38 03/1994 167777 177550115 39 06/1994 182615 192195819 40 09/1994 209352 211017104 41 12/1994 230950 226259607 Happy graphing. R. Andrew Harper E-mail: harper@ebi.ac.uk EMBL Outstation - The EBI URL: http://www.ebi.ac.uk Hinxton Hall, Hinxton, Telephone: +44 (0)223 494 429 Cambridge CB10 1RQ U.K. Fax: +44 (0)223 494 468 From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!newsserver.pixel.kodak.com!clpd-newsserver!news.sprintlink.net!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!venus.sun.com!nntp-hub2.barrnet.net!news3.near.net!yale!usenet From: abonvin@volta.csb.yale.edu ("Alexandre Bonvin") Newsgroups: bionet.software Subject: X-PLOR www pages Date: 10 Apr 1995 17:47:41 GMT Organization: Yale University, Department of Computer Science, New Haven, CT Lines: 17 Message-ID: <3mbqvt$iih@babyblue.cs.yale.edu> NNTP-Posting-Host: volta.csb.yale.edu Dear netters, Xplor has now a www home page featuring the X-PLOR manual and tutorial files on-line. The address is: http://pauli.csb.yale.edu Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 | | Yale University, PO Box 208114 | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06511, USA | | ========================================================================== From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!venus.sun.com!nntp-hub2.barrnet.net!news3.near.net!yale!usenet From: abonvin@volta.csb.yale.edu ("Alexandre Bonvin") Newsgroups: bionet.software Subject: X-PLOR www pages (correction) Date: 10 Apr 1995 17:54:03 GMT Organization: Yale University, Department of Computer Science, New Haven, CT Lines: 17 Message-ID: <3mbrbr$ik0@babyblue.cs.yale.edu> NNTP-Posting-Host: volta.csb.yale.edu Dear netters, Xplor has now a www home page featuring the X-PLOR manual and tutorial files on-line. The official address is: http://xplor.csb.yale.edu (pauli in the previous posting should work as well) Alexandre ========================================================================== | Alexandre Bonvin PhD | Phone: (203) 432-5066 | | Mol. Biophys. & Biochemistry | Fax: (203) 432-6946 | | Yale University, PO Box 208114 | Email: abonvin@laplace.csb.yale.edu | | New Haven CT 06511, USA | | ========================================================================== From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!news.ucdavis.edu!csus.edu!netcom.com!NewsWatcher!user From: brom@netcom.com (Bill Romanow) Subject: Re: Visualising Biomolecules... Message-ID: Sender: brom@netcom14.netcom.com Organization: NETCOM On-line Communication Services (408 261-4700 guest) References: <9504040947.AA05593@itdsrv1.ul.ie> Date: Mon, 10 Apr 1995 15:05:19 GMT Lines: 28 Steve: Try RasMac. It's shareware, I don't recall where I d/l'ed it from but it's easy to use and works with images from Brookhaven Protein Dtata Base just fine! I'm sure you could find lysozyme there. In article <9504040947.AA05593@itdsrv1.ul.ie>, 9224076@ul.ie (Stephen Mulcahy) wrote: > Hi, > > We are currently studying how Lysozyme works as a model of how Enzymes work in general and I'm > wondering if there is anything around in terms of images / animations that would help in this? I can place > anything I find on our anonymous ftp archive for other's use aswell. Thanks for your help. > > -stephen > > BTW Can anyone recommend a good source of [free] bio/chem related clip-art > > -------------------------------------------------------------------------------------------- > Stephen "Divil" Mulcahy 9224076@ul.ie > 3rd Industrial Biochemistry UG, University of Limerick (Eire) > WWW: http://skynet.ul.ie/~stephen From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: IUbio and plasmid drawing help! Date: 10 Apr 1995 12:40:58 GMT Organization: Biology, Indiana University - Bloomington Lines: 5 Message-ID: <3mb90q$18s@usenet.ucs.indiana.edu> References: <1995Apr10.161755@cantva> NNTP-Posting-Host: sunflower.bio.indiana.edu There is a very old ibmpc program here called "plasmid paint". See the files "plasmid.uue" (uuencoded executable) and "plasmid.readme" in folder /molbio/ibmpc at iubio.bio.indiana.edu. -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!torn!ccshst05.cs.uoguelph.ca!ccshst01.cs.uoguelph.ca!hsidhu From: hsidhu@uoguelph.ca (Harmandeep Sidhu) Newsgroups: bionet.software Subject: RESTRICTION MAPPING SOFTWARE Date: 10 Apr 1995 23:39:06 GMT Organization: University of Guelph Lines: 7 Message-ID: <3mcfiq$75h@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] I have been trying to find some kind of software that can make linear or circular maps from individual cosmid maps. I am using the partial digestion method ( single enzyme ) to map the cosmid. Please help me or my Boss will chain me to the wall and feed me bread and water for the rest of the year. Thanking you in anticipation, Reg . From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!biosci!not-for-mail From: claros@biologie.ens.fr (Manuel G. CLAROS) Newsgroups: bionet.software,bionet.announce,bionet.molbio.methds-reagnts Subject: TopPred II 1.1.1 a new update Date: 10 Apr 1995 16:24:12 -0700 Organization: Dpt Biologie, Ecole Normale Superieure Lines: 48 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:11750 bionet.announce:1986 bionet.molbio.methds-reagnts:27004 A new release of the TopPred freeware is now available from the SUMEX server (sumex-aim.stanford.edu), soon at the EMBL server (ftp.ebi.ac.uk), and all the corresponding mirrors. And also by request to the author, in other words, me. Thanks to all the people that have recommend this software. application TopPred II version 1.1.1 description Prediction of transmembrane segments in integral membrane proteins, and the putative topologies authors Claros M.G and von Heijne G. literature CABIOS 10(6), 685-686 (1994) versions TopPred II is available as a "compatible" application, or as a "rapid" one. The rapid one needs 68020 processor, or later, and FPU. notes A postcript file containing the orignal paper about this software can be found with the programs. It could be printed out with the LaserWriter Utility accompanying the apple printers, or the old Print PS application. TopPred II has been designed in THINK Pascal 4.0.2 for Macintosh computers. If someone is interested in making a version compatible with other platforms, he may contact me. What is new? TopPred II 1.1.1 (April 1995) ============================= - "Integer overflow" error when more than 32 Kb of text is written on the Results window has been fixed. - Interrupts with command-colon and ESC have been implemented - The text results were not always printable. They should be now. - Moving a TEXT file on the TopPred icon will open it correctly. // \\ // \\ // \\ Un amigo es uno Manuel G. CLAROS \': | \\ // | :,\\': | \\ que lo sabe todo Ecole Normale Superieure \\ | | \\ // | | // \\ | | \\ sobre ti y a Genetique Moleculaire \\ | :,\\': | // \\ | :,\\ pesar de ello 46 rue d'Ulm \\ // \\ // \\ // te quiere. 75230 Paris Cedex 05 claros@biologie.ens.fr E. Hubbard From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!news.starnet.net!wupost!waikato!comp.vuw.ac.nz!canterbury.ac.nz!cantva!botn078 From: botn078@csc.canterbury.ac.nz Newsgroups: bionet.software Subject: IUbio and plasmid drawing help! Date: 10 Apr 95 16:17:55 +1200 Organization: University of Canterbury, Christchurch, New Zealand Lines: 22 Message-ID: <1995Apr10.161755@cantva> NNTP-Posting-Host: cantva.canterbury.ac.nz Hi there. A while ago I posted a request for a good plasmid drawing program for PCs. Someone answered my post by email, and suggested that I look at a demo of a program on the IUbio server. My problem is that I've only just located this server, but now I can't remember the name of what I'm looking for! And I can't find anything that might be what I'm looking for. And I've deleted the original email message telling me. So could that kind person who replied to my original post (or someone else equally kind) please post or mail me the name of this demo, and exactly how to find it on the IUbio server? Thanks heaps. Mark Silby Department of Plant and Microbial Sciences University of Canterbury Christchurch, New Zealand. email: M.Silby@botn.canterbury.ac.nz or botn078@csc.canterbury.ac.nz From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!TERRE.IRCM.UMONTREAL.CA!duhaimj%terre From: duhaimj%terre@TERRE.IRCM.UMONTREAL.CA (SI-Johanne Duhaime) Newsgroups: bionet.software Subject: pblastm Date: 10 Apr 1995 13:21:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Good afternoon, Does someone have heard about the program PBLASTm related to the company MERCK and looking in CDNA databank? Thank you Johanne Duhaime IRCM From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!reuter.cse.ogi.edu!engr.orst.edu!odo.PEAK.ORG!gaia.ucs.orst.edu!ava.bcc.orst.edu!masrelia From: masrelia@ava.bcc.orst.edu (Malin Masreliez) Newsgroups: bionet.software Subject: Pcprint on SGI? Date: 10 Apr 1995 19:13:53 GMT Organization: Oregon State University, Corvallis, Oregon Lines: 10 Message-ID: <3mc01h$kbt@gaia.ucs.orst.edu> NNTP-Posting-Host: ava.bcc.orst.edu Hello - I was wondering if anyone out there has compiled pcprint on an SGI machine running IRIX 4.0.5? If you have, and you have some pointers, please send me email at masrelia@bcc.orst.edu. Thanks in advance- Malin Young From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!news.hgmp.mrc.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software Subject: Re: Sequence database growth??? Date: 10 Apr 1995 19:25:41 GMT Organization: MRC Human Genome Resource Centre Lines: 22 Message-ID: References: <1995Apr9.155936.8313@nomina.lu.se> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: harper@ebi.ac.uk's message of Mon, 10 Apr 1995 14:52:40 GMT In article harper@ebi.ac.uk (Rob Harper) writes: > In article <1995Apr9.155936.8313@nomina.lu.se>, Bo Servenius writes: > >Is there a site where I can find up to date statistics about EMBL, > >Genbank, > >SwissProt etc databases and their growth over the years. Nicest would > >be a prepared graph but tabled statistics could do. > > Here is the appendix taken from the release 41 of EMBL, which shows the > development of the database over the years. > > APPENDIX A: DATABASE GROWTH TABLE Err, does this mean there is something wrong with Release 42 (March 95)? (grin :-) -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software Subject: Densitometric analysis of graphic files Date: 10 Apr 1995 11:41:22 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3mb20i$dlc@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk Hi all, using a videocamera connected to a PC I have obtained good images (in TIFF format) of electrophoresys gels. What kind of softare can I use to analyse (integration, 2D, 3D representation) these files? Any hint will be very appreciated. Franco *************************************************************************** Franco Dosio phone (39).11.6707697 Research Scientist fax (39).11.6707695 University of Turin dosio@ch.unito.it Istituto di Chimica Farmaceutica Applicata u196cfa@csivms.csi.it c.so Raffaello 31, 10125 Torino, Italy dosio@mvx36.csata.it *************************************************************************** From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!Germany.EU.net!EU.net!news2.EUnet.fr!pasteur.fr!usenet From: Nicolas Escriou Newsgroups: bionet.software Subject: Re: nih image Date: 10 Apr 1995 07:49:39 GMT Organization: Institut Pasteur Lines: 18 Distribution: world Message-ID: <3manuj$6td@montespan.pasteur.fr> References: <3ltuvm$7o6@mserv1.dl.ac.uk> NNTP-Posting-Host: 157.99.24.84 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.3_PPC X-XXDate: Mon, 10 Apr 1995 07:49:57 GMT In article <3ltuvm$7o6@mserv1.dl.ac.uk> , JAB5@VAX.YORK.AC.UK writes: >Subject: nih image >From: JAB5 >Date: 5 Apr 1995 12:29:58 +0100 >>Dear colleagues, >Where might I find NIH image which DOES NOT require a floating-point >co-processor? >Thank you, >Jim Brannigan Have a look in this archive site : ftp://zippy.nimh.nih.gov/pub/nih-image Current version of nih image is 1.57 : there is one for 68k Mac and a fat one with PPC code. But I don¹t remember if the 1.57 68k version requires a co-processor ... I think it does not. Otherwise, you can use softwarefpu, available from all good archive sites, which emulates a co-processor on your 68k Mac. --- Nico From owner-software@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!fp1-biology-4.uoregon.edu!user From: deans@oregon.uoregon.edu (Nancy L. Deans) Newsgroups: bionet.software Subject: Re: Densitometric analysis of graphic files Date: Mon, 10 Apr 1995 14:51:58 -0800 Organization: University of Oregon Lines: 22 Distribution: bionet Message-ID: References: <3mb20i$dlc@mserv1.dl.ac.uk> NNTP-Posting-Host: fp1-biology-4.uoregon.edu In article <3mb20i$dlc@mserv1.dl.ac.uk>, wrote: > Hi all, > using a videocamera connected to a PC I have obtained good images (in > TIFF format) of electrophoresys gels. What kind of softare can I use > to analyse (integration, 2D, 3D representation) these files? > Any hint will be very appreciated. > > Franco > > *************************************************************************** > Franco Dosio phone (39).11.6707697 > Research Scientist fax (39).11.6707695 > University of Turin dosio@ch.unito.it > Istituto di Chimica Farmaceutica Applicata u196cfa@csivms.csi.it > c.so Raffaello 31, 10125 Torino, Italy dosio@mvx36.csata.it > *************************************************************************** Franco I know of a program which allows the simple quatitation of graphic PICT images on Mac computers. There is probably a version for PC. Its called NIH IMAGE 1.5.1 and is available through the NIH server. Good luck Ted Michelini From owner-software@net.bio.net Mon Apr 10 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!rutgers!gatech!newsfeed.pitt.edu!uunet!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: PAUP Date: 11 Apr 1995 05:00:25 GMT Organization: University of Washington Genetics Lines: 34 Message-ID: <3md2d9$m4n@nntp3.u.washington.edu> References: NNTP-Posting-Host: nntp3.u.washington.edu Summary: Nothing to do with Illinois Natural History Survey Keywords: PAUP, phylogeny, software In response to a question about where to get PAUP, In article , Mark Siddall wrote: ... >I am afraid that there is no way to get PAUP legally at the moment. >The Illinois Natural History Survey has been distributing it for >years. Dave does not distribute it himself. At the moment, I believe that >INHS has suspended distribution. (My understanding is that they do this >now and then to the frustration of many). My understanding is that INHS has handed PAUP legally over to Dave and is not distributing it. Its unavailability is not due to whims on their part. Dave is trying to finish the new version and work out how it will be distributed. >PAUP 4.?.? is likely to be released this summer (?) but there are NO >guarantees on this!! It has gotten to beta-testing. >Wether or not it will still be handled by INHS is not known. There >are rumours of a Sinauer interest as with MacClade. Whether or not Sinauer will publish it, INHS will certainly not. >Although this may be informative, I am afraid it mey not help you. >I would try INHS, and no I do not have an address or phone#. I suspect you will not find contacting INHS useful as they are not going to publish it. ----- Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195 Internet: joe@genetics.washington.edu (IP No. 128.95.12.41) From owner-software@net.bio.net Mon Apr 10 23:00:00 1995 Path: biosci!news.cs.umb.edu!oitnews.harvard.edu!rutgers!gatech!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!fp1-biology-4.uoregon.edu!user From: deans@oregon.uoregon.edu (Nancy L. Deans) Newsgroups: bionet.software Subject: Re: Visualising Biomolecules... Date: Mon, 10 Apr 1995 14:56:27 -0800 Organization: University of Oregon Lines: 40 Message-ID: References: <9504040947.AA05593@itdsrv1.ul.ie> NNTP-Posting-Host: fp1-biology-4.uoregon.edu In article , brom@netcom.com (Bill Romanow) wrote: > Steve: > > Try RasMac. It's shareware, I don't recall where I d/l'ed it from but it's > easy to use and works with images from Brookhaven Protein Dtata Base just > fine! I'm sure you could find lysozyme there. > > In article <9504040947.AA05593@itdsrv1.ul.ie>, 9224076@ul.ie (Stephen > Mulcahy) wrote: > > > Hi, > > > > We are currently studying how Lysozyme works as a model of how Enzymes > work in general and I'm > > wondering if there is anything around in terms of images / animations > that would help in this? I can place > > anything I find on our anonymous ftp archive for other's use aswell. > Thanks for your help. > > > > -stephen > > H> > BTW Can anyone recommend a good source of [free] bio/chem related clip-art > > > > > -------------------------------------------------------------------------------------------- > > Stephen "Divil" Mulcahy 9224076@ul.ie > > 3rd Industrial Biochemistry UG, University of Limerick (Eire) > > WWW: http://skynet.ul.ie/~stephen Stephen, If you still need help, we have thousands of files on T4 Lysozyme here at the Institute of Molecular Biology, University of Oregon, Eugene, OR USA My Email is Tedm@uoxray.uoregon.edu Ted Michelini From owner-software@net.bio.net Mon Apr 10 23:00:00 1995 Newsgroups: bionet.software Path: biosci!lhc!borduas!francis From: francis@borduas.nlm.nih.gov (Francis Ouellette) Subject: Re: Sequence database growth??? Message-ID: <1995Apr11.022903.17829@nlm.nih.gov> Sender: news@nlm.nih.gov Organization: National Library of Medicine X-Newsreader: TIN [version 1.2 PL2] References: <1995Apr9.155936.8313@nomina.lu.se> Date: Tue, 11 Apr 95 02:29:03 GMT Lines: 95 Peter Rice (pmr@sanger.ac.uk) wrote: > In article harper@ebi.ac.uk (Rob Harper) writes: >> APPENDIX A: DATABASE GROWTH TABLE > Err, does this mean there is something wrong with Release 42 (March 95)? > (grin :-) > -- > -------------------------------------------------------------------- > Peter Rice | Informatics Division > E-mail: pmr@sanger.ac.uk | The Sanger Centre > Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, > Fax: (44) 1223 494919 | Cambs, CB10 1RQ > URL: http://www.sanger.ac.uk/~pmr/ | England just so you may have the latest numbers (as per Peter's note ... thanks Peter, I would have missed that!) ... I present the latest numbers from GenBank ... They are from gbrel.txt, which you can find in the /genbank directory at the NCBI anonymous FTP site (ncbi.nlm.nih.gov) regards to Peter, Rob and all others, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov 2.2.8 Growth of GenBank The following table lists the number of bases and the number of sequence records in each release of GenBank, beginning with Release 3 in 1982. Over the period 1982 to the present, the number of bases in GenBank has doubled approximately every 21 months. Release Date Base Pairs Entries 3 Dec 82 680338 606 14 Nov 83 2274029 2427 20 May 84 3002088 3665 24 Sep 84 3323270 4135 25 Oct 84 3368765 4175 26 Nov 84 3689752 4393 32 May 85 4211931 4954 36 Sep 85 5204420 5700 40 Feb 86 5925429 6642 42 May 86 6765476 7416 44 Aug 86 8442357 8823 46 Nov 86 9615371 9978 48 Feb 87 10961380 10913 50 May 87 13048473 12534 52 Aug 87 14855145 14020 53 Sep 87 15514776 14584 54 Dec 87 16752872 15465 55 Mar 88 19156002 17047 56 Jun 88 20795279 18226 57 Sep 88 22019698 19044 57.1 Oct 88 23800000 20579 58 Dec 88 24690876 21248 59 Mar 89 26382491 22479 60 Jun 89 31808784 26317 61 Sep 89 34762585 28791 62 Dec 89 37183950 31229 63 Mar 90 40127752 33377 64 Jun 90 42495893 35100 65 Sep 90 49179285 39533 66 Dec 90 51306092 41057 67 Mar 91 55169276 43903 68 Jun 91 65868799 51418 69 Sep 91 71947426 55627 70 Dec 91 77337678 58952 71 Mar 92 83894652 65100 72 Jun 92 92160761 71280 73 Sep 92 101008486 78608 74 Dec 92 120242234 97084 75 Feb 93 126212259 106684 76 Apr 93 129968355 111911 77 Jun 93 138904393 120134 78 Aug 93 147215633 131328 79 Oct 93 157152442 143492 80 Dec 93 163802597 150744 81 Feb 94 173261500 162946 82 Apr 94 180589455 169896 83 Jun 94 191393939 182753 84 Aug 94 201815802 196703 85 Oct 94 217102462 215273 86 Dec 94 230485928 237775 87 Feb 95 248499214 269478 88 Apr 95 286094556 352414 From owner-software@net.bio.net Mon Apr 10 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!tezcat.com!ewalker From: ewalker@tezcat.com (Edwin Walker) Newsgroups: bionet.software Subject: Human Body Date: 11 Apr 1995 05:58:08 GMT Organization: Walker Technologies Lines: 7 Message-ID: <3md5pg$ar9@quilla.tezcat.com> NNTP-Posting-Host: xochi.tezcat.com X-Newsreader: News Xpress Version 1.0 Beta #3 I was wondering if someone could help me locate some simple human body diagrams in some kinda of bmp or gif form. Does not have to be the greatest. ewalker@tezcat.com From owner-software@net.bio.net Mon Apr 10 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!gatech!bloom-beacon.mit.edu!ai-lab!cocoa-puffs!shade From: shade@cocoa-puffs.ai.mit.edu (Craig Zilles) Newsgroups: bionet.software Subject: wanted: Introductory level genetics tutorial software Date: 11 Apr 1995 15:06:32 GMT Organization: MIT Artificial Intelligence Lab Lines: 9 Sender: shade@cocoa-puffs (Craig Zilles) Distribution: world Message-ID: <3me5to$6rs@life.ai.mit.edu> NNTP-Posting-Host: cocoa-puffs.ai.mit.edu I'm looking for a nice graphical program to be used to teach a genetics class at a community college to non-majors. I picture something that will let you observe the traits of offspring given the traits of their parents (we're not talking rocket science here, just something that will keep the students busy for a little while). Prefered platforms are Apple II or Macintosh, but IBM is also doable. Replies by email (shade@ai.mit.edu) are prefered, but I'll be checking this group as well. -Craig From owner-software@net.bio.net Mon Apr 10 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!howland.reston.ans.net!news2.near.net!news3.near.net!yale!news.ycc.yale.edu!cadmium.csb.yale.edu!gardner From: gardner@cadmium.csb.yale.edu (Kevin Gardner) Newsgroups: bionet.software Subject: Re: Visualising Biomolecules... Date: 11 Apr 1995 13:42:24 GMT Organization: Yale University Lines: 18 Message-ID: <3me100$54g@news.ycc.yale.edu> References: <9504040947.AA05593@itdsrv1.ul.ie> NNTP-Posting-Host: cadmium.csb.yale.edu X-Newsreader: TIN [version 1.2 PL2] Bill Romanow (brom@netcom.com) wrote: : Try RasMac. It's shareware, I don't recall where I d/l'ed it from but it's : easy to use and works with images from Brookhaven Protein Dtata Base just : fine! I'm sure you could find lysozyme there. I wholeheartedly second this recommendation; there are additional versions (RasMol) that work on Unix/VAX/IBM platforms as well. The site is ftp://colonsay.dcs.ed.ac.uk/ftp/pub/rasmol/rasmac.sit.hqx. More info in README at same site. Kevin -- ************************************************************************* Kevin Gardner Glu-Leu-Val-Ile-Ser Yale University Dept. of Molecular Biophysics and Biochemistry Internet: gardner@zinc.csb.yale.edu Bitnet: gardner@yalemed From owner-software@net.bio.net Mon Apr 10 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!lamarck.sura.net!news.uky.edu!chuck From: Frank van de Loo Newsgroups: bionet.software Subject: Macaw format to msf? Date: 11 Apr 1995 12:44:25 GMT Organization: University of Kentucky Computing Services Lines: 5 Message-ID: <3mdtj9$4c5@service1.uky.edu> NNTP-Posting-Host: 128.163.192.190 Anyone know how to convert a Macaw alignment