From owner-software@net.bio.net Sat Oct 01 23:00:00 1994 Path: biosci!agate!spool.mu.edu!uwm.edu!rutgers!netnews.upenn.edu!news.drexel.edu!dunx1.ocs.drexel.edu!dunx1.ocs.drexel.edu!not-for-mail From: st93mey7@dunx1.ocs.drexel.edu (Frederick Thum) Newsgroups: bionet.software Subject: Tierra on the Internet Date: 2 Oct 1994 15:25:33 -0400 Organization: Drexel University, Phila. Pa. Lines: 20 Message-ID: <36n1fd$qid@dunx1.ocs.drexel.edu> NNTP-Posting-Host: dunx1.ocs.drexel.edu X-Newsreader: TIN [version 1.2 PL2] I have obtained a copy of Tierra, a program that simulates an evolution and an ecosystem through computer code. I have got the regular version of Tierra working fine (with the exception that it would not compile on a DEC/4000), but I would like to run it so that it could share genebanks with other computers running it over the Internet. I got the copy of NeTierra, but the instructions for setup are unclear. Has anyone done this? Any help would be appreciated - Fred Thum -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Frederick L. Thum III (st93mey7@post.drexel.edu) "Diatoms are as diatoms do." - Forrest Gump -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-software@net.bio.net Sat Oct 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!wupost!news.miami.edu!miasun.med.miami.edu!FirstLight.chroma.med.miami.edu From: rb@chroma.med.miami.edu (Richard J. Bookman) Newsgroups: bionet.software Subject: Re: Scientific Graphing Date: Sun, 2 Oct 1994 15:04:14 -0500 Organization: University of Miami School of Medicine Lines: 34 Distribution: world Message-ID: <9410021504.AA14195@FirstLight.chroma.med.miami.edu> References: <199409241557.IAA24705@net.bio.net> Reply-To: rb@chroma.med.miami.edu (Richard J. Bookman) NNTP-Posting-Host: mac2.med.miami.edu X-Newsreader: InterCon TCP/Connect II 1.2.1 In article <199409241557.IAA24705@net.bio.net>, MJOHNSO3@UA1VM.UA.EDU (Mark J) writes: > Anybody have email or snailmail addresses for: > MicroCal Software - makers of "Origin" > whoever sells or makes "Kaleidagraph" > the creators/sellers of "Igor Pro" > I am looking for something as easy to use and as complete as the > Sigmaplot pack age is on the Windows platform - but made for use on a > Mac Power PC. > > Thanks in advance. = Mark J > It is my understanding that the native version of IGOR Pro is nearly ready to go out for beta testing. The original timetable was to have it out by the end of the year. An October release for beta-testing is consistent with the original goal. You can contact the creators (good word choice!) as: wavemetrics@applelink.apple.com R. Bookman University of Miami School of Medicine From owner-software@net.bio.net Sat Oct 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!wupost!news.miami.edu!miasun.med.miami.edu!FirstLight.chroma.med.miami.edu From: rb@chroma.med.miami.edu (Richard J. Bookman) Newsgroups: bionet.software,bionet.virology Subject: Re: Virology Teaching Resources on the Internet Date: Sun, 2 Oct 1994 15:14:22 -0500 Organization: University of Miami School of Medicine Lines: 37 Distribution: world Message-ID: <9410021514.AA22789@FirstLight.chroma.med.miami.edu> References: Reply-To: rb@chroma.med.miami.edu (Richard J. Bookman) NNTP-Posting-Host: mac2.med.miami.edu X-Newsreader: InterCon TCP/Connect II 1.2.1 Xref: biosci bionet.software:9499 bionet.virology:904 > SHAMELESS PLUG: > I am currently looking for a job in New Zealand or Australia, > particularly one related to bioinformatics. If you have any leads for me, > please email me. > Thank you! > ------ > > Stephan Spencer > Developer and Administrator of WWW Server for Virology > Institute for Molecular Virology > University of Wisconsin-Madison > sspencer@rhino.bocklabs.wisc.edu > You may want to contact my colleague David Adams who is, unfortunately, leaving Miami to take a chair in Brisbane. dadams@mednet.med.miami.edu He is an electrophysiologist, but he might know of some opportunities to do things right that are opening up in Brisbane. Also, contact Axon Research (Dr. Alan Finkel, Pres.) in Melbourne...they do a lot of software development for physiology and biophysics. good luck, R. Bookman From owner-software@net.bio.net Sat Oct 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!raffles.technet.sg!merlion.singnet.com.sg!merlion.singnet.com.sg!arman From: arman@merlion.singnet.com.sg (Arman Esmaili) Newsgroups: bionet.software Subject: Help Desk Software Wanted Date: 1 Oct 1994 05:17:24 GMT Organization: Singapore Telecom Internet Service Lines: 11 Message-ID: <36ird4$dol@merlion.singnet.com.sg> NNTP-Posting-Host: merlion.singnet.com.sg X-Newsreader: TIN [version 1.2 PL2] My company is looking for a Help Desk logging/inquiry software to run on a LAN. Could anyone recommend any to us? Thanks Arman. -- ----------------------------------------------------------------------------- arman@singnet.com.sg Arman & Janice Esmaili From owner-software@net.bio.net Sat Oct 01 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!scripps.edu!misrael From: misrael@scripps.edu (Mark Israel) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Re: program to obtain 3d coordinates from stereo pictures Date: 2 Oct 1994 19:51:51 GMT Organization: The Scripps Research Institute, La Jolla, California, USA Lines: 29 Message-ID: <36n30n$nou@riscsm.scripps.edu> References: <9410011655.AA08195@nick.med.usf.edu> NNTP-Posting-Host: struct.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Xref: biosci bionet.molbio.proteins:2795 bionet.software:9500 In article <9410011655.AA08195@nick.med.usf.edu>, gquinn@NICK.MED.USF.EDU (Gregory Quinn) writes: > Does anyone know anything about the program that can produce 3d > coordinates from stereo pictures of proteins? Here's some info on it that was recently posted to bionet.xtallography: | Subject: Re:Extracting Coorodinates from Stereo Diagrams. | Newsgroups: bionet.xtallography | From: raman@BIOC01.UTHSCSA.EDU (C.S.RAMAN) | Organization: BIOSCI International Newsgroups for Molecular Biology | Date: 16 Aug 1994 06:41:55 -0700 | Message-ID: <9408161342.AA02724@bioc01.uthscsa.edu> | | [...] | | In addition to what I had told you about its existence in the PDB, here | is what I recently found. The program is still called STEREO and has | been substantially modified (original version 1974 Michael Rossmann) by | Jin-Bi Dai also at purdue. The latest version of the program is dated | 1994 and you can obtain a copy of the source and associated man page | from the latter author. | | Jin-Bi Dai can be reached via e-mail at: | | b4x@mace.cc.purdue.edu -- misrael@scripps.edu Mark Israel From owner-software@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!news.sprintlink.net!howland.reston.ans.net!agate!cat.cis.Brown.EDU!news2.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc-news.harvard.edu!news Newsgroups: bionet.software Subject: protein homology modelling program Message-ID: <1994Oct2.191304.35069@hulaw1.harvard.edu> From: sali@tamika.harvard.edu (Andrej Sali) Date: 2 Oct 94 19:13:02 EDT Keywords: program, homology modelling, comparative modelling, protein modelling Nntp-Posting-Host: tamika.harvard.edu Lines: 73 MODELLER PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 11, October 1, 1994 Copyright(c) 1989-1994 Andrej Sali All Rights Reserved Written by Andrej Sali Birkbeck College, University of London, London, UK Imperial Cancer Research Fund, London, UK Harvard University, Cambridge, USA Andrej Sali, Department of Chemistry, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA. Tel: (617) 495 1775. Fax: (617) 496 3204. E-mail: sali@tammy.harvard.edu. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. The program includes a 100-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to non-profit institutions. First, please use the anonymous ftp account on tammy.harvard.edu (IP 128.103.96.19) to copy the files from the pub/modeller directory to your computer. Print and sign the license form (academic-license.ps) and mail or fax it to Andrej Sali. You will then receive the encryption key (MODELLER_KEY) with which you will be able to unpack the encrypted distribution file (modeller11-exec.tar.Z.cr). See file INSTALLATION for installation instructions. MODELER is also available as part of QUANTA, a large program with many other functionalities including interactive graphics, CHARMm, and X-PLOR. If you are interested in this commercial version please contact Ms. Jo Ellen Collins at Molecular Simulations Inc, 16 New England Executive Park, Burlington, MA 01803-5297, tel: (617) 229 9800, fax: (617) 229 9899, email: jcollins@msi.com. ** CONTENTS: src\ sources or executables for MODELLER and associated programs modlib\ libraries and data files for the programs scripts\ script files used to compile and use MODELLER doc\ MODELLER documentation Makefile Makefile for compiling/installing MODELLER modules; used by the Install script modeller11.README this file INSTALLATION how to install MODELLER Install compilation and installation script tests\ tests and examples From owner-software@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!news.sprintlink.net!howland.reston.ans.net!agate!cat.cis.Brown.EDU!news2.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc-news.harvard.edu!news Newsgroups: bionet.software Subject: protein homology modelling program Message-ID: <1994Oct2.191159.35068@hulaw1.harvard.edu> From: sali@tamika.harvard.edu (Andrej Sali) Date: 2 Oct 94 19:11:58 EDT Keywords: program, homology modelling, comparative modelling, protein modelling Nntp-Posting-Host: tamika.harvard.edu Lines: 73 MODELLER PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 11, October 1, 1994 Copyright(c) 1989-1994 Andrej Sali All Rights Reserved Written by Andrej Sali Birkbeck College, University of London, London, UK Imperial Cancer Research Fund, London, UK Harvard University, Cambridge, USA Andrej Sali, Department of Chemistry, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA. Tel: (617) 495 1775. Fax: (617) 496 3204. E-mail: sali@tammy.harvard.edu. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. The program includes a 100-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to non-profit institutions. First, please use the anonymous ftp account on tammy.harvard.edu (IP 128.103.96.19) to copy the files from the pub/modeller directory to your computer. Print and sign the license form (academic-license.ps) and mail or fax it to Andrej Sali. You will then receive the encryption key (MODELLER_KEY) with which you will be able to unpack the encrypted distribution file (modeller11-exec.tar.Z.cr). See file INSTALLATION for installation instructions. MODELER is also available as part of QUANTA, a large program with many other functionalities including interactive graphics, CHARMm, and X-PLOR. If you are interested in this commercial version please contact Ms. Jo Ellen Collins at Molecular Simulations Inc, 16 New England Executive Park, Burlington, MA 01803-5297, tel: (617) 229 9800, fax: (617) 229 9899, email: jcollins@msi.com. ** CONTENTS: src\ sources or executables for MODELLER and associated programs modlib\ libraries and data files for the programs scripts\ script files used to compile and use MODELLER doc\ MODELLER documentation Makefile Makefile for compiling/installing MODELLER modules; used by the Install script modeller11.README this file INSTALLATION how to install MODELLER Install compilation and installation script tests\ tests and examples From owner-software@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!news.sprintlink.net!howland.reston.ans.net!agate!cat.cis.Brown.EDU!news2.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc-news.harvard.edu!news Newsgroups: bionet.software Subject: protein homology modelling program Message-ID: <1994Oct2.191334.35070@hulaw1.harvard.edu> From: sali@tamika.harvard.edu (Andrej Sali) Date: 2 Oct 94 19:13:33 EDT Keywords: program, homology modelling, comparative modelling, protein modelling Nntp-Posting-Host: tamika.harvard.edu Lines: 73 MODELLER PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 11, October 1, 1994 Copyright(c) 1989-1994 Andrej Sali All Rights Reserved Written by Andrej Sali Birkbeck College, University of London, London, UK Imperial Cancer Research Fund, London, UK Harvard University, Cambridge, USA Andrej Sali, Department of Chemistry, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA. Tel: (617) 495 1775. Fax: (617) 496 3204. E-mail: sali@tammy.harvard.edu. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. The program includes a 100-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to non-profit institutions. First, please use the anonymous ftp account on tammy.harvard.edu (IP 128.103.96.19) to copy the files from the pub/modeller directory to your computer. Print and sign the license form (academic-license.ps) and mail or fax it to Andrej Sali. You will then receive the encryption key (MODELLER_KEY) with which you will be able to unpack the encrypted distribution file (modeller11-exec.tar.Z.cr). See file INSTALLATION for installation instructions. MODELER is also available as part of QUANTA, a large program with many other functionalities including interactive graphics, CHARMm, and X-PLOR. If you are interested in this commercial version please contact Ms. Jo Ellen Collins at Molecular Simulations Inc, 16 New England Executive Park, Burlington, MA 01803-5297, tel: (617) 229 9800, fax: (617) 229 9899, email: jcollins@msi.com. ** CONTENTS: src\ sources or executables for MODELLER and associated programs modlib\ libraries and data files for the programs scripts\ script files used to compile and use MODELLER doc\ MODELLER documentation Makefile Makefile for compiling/installing MODELLER modules; used by the Install script modeller11.README this file INSTALLATION how to install MODELLER Install compilation and installation script tests\ tests and examples From owner-software@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!wupost!kuhub.cc.ukans.edu!mbcf!heath Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Promega on the Internet Message-ID: <1994Oct1.142817.8747@mbcf> From: heath@mbcf.stjude.org (Richard) Date: 1 Oct 94 14:28:17 -600 References: <1994Sep29.181744.29696@genes.icgeb.trieste.it> Organization: St. Jude Children's Research Hospital Lines: 34 Xref: biosci bionet.molbio.methds-reagnts:19151 bionet.software:9509 In article <1994Sep29.181744.29696@genes.icgeb.trieste.it>, raffa@biocell.irmkant.rm.cnr.it (MEG-CNR) writes: > In article > tan@aeolus.vmsmail.ethz.ch (Song Tan) writes: > ........ >> >> Technical support by email would be my highest priority. >> ......... >> Biolabs has very good email technical support and I think it's in the best > interest of other biotech companies to offer similar services. >> >> Technical notes online would be next in line. It would allow the >> researcher to get the information more efficiently and I believe it's also >> economically beneficial to Promega. >> >> -- >> Song Tan >> email: tan@aeolus.vmsmail.ethz.ch > > I definitively agree. > Meanwhile could you provide the Biolabs e-mail address? > > Raffaele Matteoni > Inst Cell Biology CNR > Roma I-OO137 Italy > > raffa@biocell.irmkant.rm.cnr.it I agree with all of the above! And here is NEB's email from the back of their catalog: info@neb.com Richard From owner-software@net.bio.net Sun Oct 02 23:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.software Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!pasteur.fr!univ-lyon1.fr!swidir.switch.ch!newsfeed.ACO.net!Austria.EU.net!EU.net!uunet!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!demon!pplros.demon.co.uk!tomlinson From: Anthony Tomlinson Subject: Re: Promega on the Internet Message-ID: X-Xxmessage-Id: X-Xxdate: Mon, 3 Oct 1994 15:51:09 GMT Sender: news@demon.co.uk (Usenet Administration) Nntp-Posting-Host: pplros.demon.co.uk Organization: PPL Therapeutics X-Newsreader: Nuntius Version 1.2 References: <1994Sep29.181744.29696@genes.icgeb.trieste.it> <1994Sep30.095101.11072@rzu-news.unizh.ch> Date: Mon, 3 Oct 1994 14:49:52 GMT Lines: 19 Xref: biosci bionet.molbio.methds-reagnts:19134 bionet.software:9508 In article Stephan Spencer, sspencer@rhino.bocklabs.wisc.edu writes: >I (and Promega) would like to know who out there would like to see Promega >on the World Wide Web, and what you would like to see (catalog, technical >notes, online ordering, tech support, etc...) > >Second question.. would you use their services online? Would you order >online? I agree with everyone else - New product info, technical bulletins and protocol updates would all be appreciated on www, and an email address for specific questions (a la NEB) will surely be a must for all molbiol suppliers in a few years. Unsolicited advertising via email would be intolerable though, and I couldn't order via the Internet because of the ordering system we operate. Maybe if more companies were online, ordering depts might come around.... From owner-software@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!CS.Arizona.EDU!uunet!europa.eng.gtefsd.com!uhog.mit.edu!news.mtholyoke.edu!news.umass.edu!news2.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc-news.harvard.edu!news Newsgroups: bionet.software Subject: homology modelling program Message-ID: <1994Oct2.191512.35071@hulaw1.harvard.edu> From: sali@tamika.harvard.edu (Andrej Sali) Date: 2 Oct 94 19:15:11 EDT Keywords: protein modelling, homology modelling, comparative modelling Nntp-Posting-Host: tamika.harvard.edu Lines: 73 MODELLER PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS MODELLER 11, October 1, 1994 Copyright(c) 1989-1994 Andrej Sali All Rights Reserved Written by Andrej Sali Birkbeck College, University of London, London, UK Imperial Cancer Research Fund, London, UK Harvard University, Cambridge, USA Andrej Sali, Department of Chemistry, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA. Tel: (617) 495 1775. Fax: (617) 496 3204. E-mail: sali@tammy.harvard.edu. ** DESCRIPTION: MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints (A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. The program includes a 100-page manual. MODELLER is written in Fortran and is meant to run on a UNIX system. ** DISTRIBUTION: MODELLER is available free of charge to non-profit institutions. First, please use the anonymous ftp account on tammy.harvard.edu (IP 128.103.96.19) to copy the files from the pub/modeller directory to your computer. Print and sign the license form (academic-license.ps) and mail or fax it to Andrej Sali. You will then receive the encryption key (MODELLER_KEY) with which you will be able to unpack the encrypted distribution file (modeller11-exec.tar.Z.cr). See file INSTALLATION for installation instructions. MODELER is also available as part of QUANTA, a large program with many other functionalities including interactive graphics, CHARMm, and X-PLOR. If you are interested in this commercial version please contact Ms. Jo Ellen Collins at Molecular Simulations Inc, 16 New England Executive Park, Burlington, MA 01803-5297, tel: (617) 229 9800, fax: (617) 229 9899, email: jcollins@msi.com. ** CONTENTS: src\ sources or executables for MODELLER and associated programs modlib\ libraries and data files for the programs scripts\ script files used to compile and use MODELLER doc\ MODELLER documentation Makefile Makefile for compiling/installing MODELLER modules; used by the Install script modeller11.README this file INSTALLATION how to install MODELLER Install compilation and installation script tests\ tests and examples From owner-software@net.bio.net Sun Oct 02 23:00:00 1994 Newsgroups: bionet.software Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!spool.mu.edu!howland.reston.ans.net!swiss.ans.net!solaris.cc.vt.edu!news.duke.edu!godot.cc.duq.edu!toads.pgh.pa.us!newsfeed.pitt.edu!dsinc!ub!galileo.cc.rochester.edu!news From: CAAL@BPHVAX.BIOPHYSICS.ROCHESTER.EDU (Charles Alexander) Subject: Seqapp problem Message-ID: <1994Oct3.144031.5758@galileo.cc.rochester.edu> Sender: news@galileo.cc.rochester.edu Nntp-Posting-Host: bphvax.biophysics.rochester.edu Organization: DEPT. OF BIOPHYSICS, UNIVERSITY OF ROCHESTER Date: Mon, 3 Oct 94 14:40:31 GMT X-News-Reader: VMS NEWS v1.25 Lines: 21 Hello all, I have been trying to use Don Gilbert's freeware sequence editing program for the Mac, Seqapp. However, I'm having a difficult time saving sequences in the single-sequence or multi-sequence editor window. When you specify the save option everything seems to work fine but when you try to re-open it later the sequence is missing, although the file name exists. I'm sure the solution is embarrasingly simple but for the life of me I cannot figure it out. The problem also seems intermittent. Any suggestions ? Thank you Charles Alexander Div. of Medical Informatics University of Rochester Rochester, New York e-mail: caal@bphvax.biophysics.rochester.edu From owner-software@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!nac.no!nntp.uio.no!NewsWatcher!user From: olam@radium.uio.no (Ola Myklebost) Newsgroups: bionet.software Subject: Re: sequence alignment software Date: Mon, 03 Oct 1994 12:45:46 +0100 Organization: Inst for Cancer Research, Oslo Lines: 15 Distribution: world Message-ID: References: <9409212316.AA01445@sprcore.bih.harvard.edu> <35spl4$auj@news.rz.uni-duesseldorf.de> NNTP-Posting-Host: pcdnr05.uio.no I recently tried a new co-processor card for PC/Windows which soon is to be marketed by the Norwegian company MedProbe. The card contains a custom made homology-searcing chip, and with its accompanying software you may load genbank etc in RAM and search homologies VERY fast (minutes). It was said to be much cheaper than competing products. Ola -- Ola Myklebost Email ola.myklebost@labmed.uio.no Dept of Tumor Biology Inst for Cancer Research Tel +47-2293-4299 The Norwegian Radium Hospital Fax +47-2252-2421 N-0310 OSLO, Norway From owner-software@net.bio.net Sun Oct 02 23:00:00 1994 Path: biosci!s.u-tokyo!news.tisn.ad.jp!news.u-tokyo.ac.jp!sinetnews!daffy!uwvax!uchinews!vixen.cso.uiuc.edu!howland.reston.ans.net!news.sprintlink.net!redstone.interpath.net!ddsw1!willis.cis.uab.edu!maze.dpo.uab.edu!ramermac.nrc.uab.edu!user From: ramer@nrc.uab.edu (Kevin W. Ramer) Newsgroups: bionet.software,bionet.software.acedb Subject: Re: Mac Printing (Was Visualisation of Postscript files in Macs?) Date: Mon, 03 Oct 1994 09:48:33 -0600 Organization: University of Alabama at Birmingham Lines: 27 Distribution: world Message-ID: References: <36cs42$jko@calvin.st-and.ac.uk> <36hd6l$ehm@lyra.csx.cam.ac.uk> NNTP-Posting-Host: ramermac.nrc.uab.edu Xref: biosci bionet.software:9507 bionet.software.acedb:447 In article , flip@bogie2.bio.purdue.edu (Phillip D. Russell) wrote: > > I guess you don't have the laserwriter 8 extention. You can print > multiple pages on one sheet from any program. > > The laserwriter 8 extention should be at all FTP site with > Mac shareware. > I believe that your best bet is an Apple site. e.g ftp.apple.com:/dts/mac/sys.soft or ftp.austin.apple.com, et. al. I don't think that this software is permitted on most sites. > Flip > > -- > __@ Phillip "Flip" Russell | Purdue University __@ > _ -_,_-\<,_flip@bogie2.bio.purdue.edu | West Lafayette, IN _ -\<,_ > (_)-----/-(_) The important things... (_)-/-(_) > My bikes and my Macintosh -- Kevin W. Ramer ramer@nrc.uab.edu Programmer Analyst Neurobiology Research Center University of Alabama at Birmingham From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!univ-lyon1.fr!jussieu.fr!u-psud.fr!trefle!oger From: oger@trefle Newsgroups: bionet.software Subject: Does anybody know anything about computer assisted RFLPs? Date: 4 Oct 94 15:34:27 WET Organization: Institut des Sciences Vegetales C.N.R.S. Lines: 1 Message-ID: <1994Oct4.153427.1@trefle> NNTP-Posting-Host: trefle.isv.cnrs-gif.fr From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!univ-lyon1.fr!jussieu.fr!u-psud.fr!trefle!oger From: oger@trefle Newsgroups: bionet.software Subject: Does anybody know anything about Computer Assisted RFLPs Date: 4 Oct 94 15:44:22 WET Organization: Institut des Sciences Vegetales C.N.R.S. Lines: 11 Message-ID: <1994Oct4.154422.1@trefle> NNTP-Posting-Host: trefle.isv.cnrs-gif.fr I am actually searching for a program that would simulate the migration of DNA fragments through an agarose or an acrylamide gel. The aim would be to generat e RFLPs of fragments of interest, sequenced by others to compare the profiles t o the one I got. If anyone knows anything about such a program just let me know at the following E-mail address "oger@trefle.isv.cnrs-gif.fr" (Phil OGER) or y ou can answer through the news network. Thanks to any one for help. Phil OGER From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news Newsgroups: bionet.software Subject: searching patterns including sek. structures Message-ID: <1994Oct4.130524.146@immunbio.mpg.de> From: HAESS@IMMUNBIO.MPG.DE (Gunther Häß) Date: 4 Oct 94 13:05:23 +0100 Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24Lines: 12 Lines: 12 Hi netters I'm searching for an amino-acid pattern searching program that includes the secondary structere in the pattern. It should be able to find, for example, a pattern of amino-acid on one side of an alpha helix or in an angle of 90 degrees in the horizontal cut around one special amino-acid. Does anybody know about a program which could perform such things? Please answer to haess@immunbio.mpg.de From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!howland.reston.ans.net!spool.mu.edu!mnemosyne.cs.du.edu!nyx10.cs.du.edu!not-for-mail From: rnusbick@nyx10.cs.du.edu (robert nusbickel) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Promega on the Internet Date: 4 Oct 1994 07:22:35 -0600 Organization: University of Denver, Dept. of Math & Comp. Sci. Lines: 13 Message-ID: <36rkur$nbj@nyx10.cs.du.edu> References: <1994Sep29.181744.29696@genes.icgeb.trieste.it> <1994Oct1.142817.8747@mbcf> NNTP-Posting-Host: nyx10.cs.du.edu Xref: biosci bionet.molbio.methds-reagnts:19175 bionet.software:9514 This discussion about PROMEGA placing there materials on the net has got me thinking. How's about a service which would be sort of like a directory of all the suppliers information, including ordering information, protocols, and descriptions of the materials, and make this available through the net? It certainly would be advantageous to the suppliers to put their information into one location and it would be great for researchers to have only one place to check on reagents, etc. What do you think? Just looking for some opinions. Andy Nusbickel From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!urmel.informatik.rwth-aachen.de!newsserver.rrzn.uni-hannover.de!news From: crmlbhvr@onramp.ca (Criminal Behaviour) Subject: Lotus 1-2-3 for Windows Message-ID: <1994Oct4.002402.6059@newsserver.rrzn.uni-hannover.de> Sender: news@newsserver.rrzn.uni-hannover.de (News Service) Organization: RRZN X-Newsreader: WinVN 0.92.6 Date: Tue, 4 Oct 1994 00:24:02 GMT Lines: 11 I have Lotus 1-2-3 for Windows Release 5, when I try to run it, it displays the logo screen then halts loading. Does anyone know why? I called the Lotus support line but they want money to answer even 1 question. I'm running a 486/33 with Windows 3.1 and 8 MB of RAM. Also I'm using Qemm 7.04 it that makes any difference and as well I'm running Stacker 4.0. This is really frustrating and I need the program for my program at school. Any help would be great. -CB From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!galaxy.ucr.edu!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!cs.utexas.edu!geraldo.cc.utexas.edu!austin.lockheed.com!not-for-mail From: mcinroy@austin.lockheed.com (John W. McInroy) Newsgroups: bionet.software,bionet.population-bio,sci.bio Subject: Software to track wildlife migration? Date: 4 Oct 1994 16:43:46 -0500 Organization: Lockheed Austin Division Lines: 94 Message-ID: <36siai$1jq@antares.Austin.Lockheed.COM> NNTP-Posting-Host: antares.austin.lockheed.com Xref: biosci bionet.software:9521 bionet.population-bio:817 sci.bio:11159 Last month I posted the following item: : I am looking for software that can be used to : track phenomena such as the movement of banded : birds or other wildlife. I would appreciate : any information available. : I will summarize responses and post them. : John McInroy [McInroy@Austin.Lockheed.com] Thanks to all who responded. As promised, here is a summary of the responses that I have received so far: ------------------------------------------------------------------------------- From: "Dr Tristram Wyatt, Continuing Education" . . . wildtrak is one such programme you can get details by writing to Dr I Todd, Dept of Zoology, univ of oxford, south parks rd, oxford, OX1 3PS, UK regards t ------------------------------------------------------------------------------- From: bss119@thunder ( Mr. R.D.McKay) Organization: University of Wales, Bangor. I'm not sure how applicable it would be, but would one of the telemetry software packages be of any use? I believe the US Fish and Game people have put one out through the University of Idaho called simply Home Range. A better option would be Robert Kenward's program Ranges IV (or maybe even V by now). This allows associated variable with fixes, and I have seen it used to determine home range over time slices. Kenward works for the UK Institute of Terrestrial Ecology (ITE). -- Valerian. BSS119@bangor.ac.uk [from my response:] Do you happen to have an e-mail address for R. Kenward? From: "Mr. R.D.McKay" . . . Sorry, I don't have an e-mail address for the guy. I'll send you a postal as soon as I can get my hands on one. . . . ---------------------------------------------------------------------------- From huberr@bkfug.kfunigraz.ac.at Ukn Oct 4 07:38:32 1994 . . . I have written a program for the analysis of homeranges for the Apple Macintosh. The program is currently in a beta version and will be distributed as postcard ware. The documentation is still very sketchy, and the software may still contain a few bugs (actually I am sure it does). If you are interested then you are more than welcome to give the program a spin. It accepts ASCII TEXT files containing the X and Y coordinates of consecutive captures; the coordinates are separated by a tab, captures are separated by carriage returns - so nothing out of the ordinary. I am working on recompiling it for the Power PC but have not completed that yet. You can then use a variety of analyses to estimate homeranges, calculate activity centers, etc. It also does some contour plots and surface plots of utilisation distributions. It would help me greatly to hear of other people applying it to their data sets and what would come in handy for other users. I intend to publish the program and its availability later this fall - if all goes well. So let me know if you are interested. You can access the program and a folder containing sample documents via FTP from 143.50.28.74 using 'Home' and 'Range'. Note this is case sensitive. Hope this is of any help, Lobsterman Robert Huber /\ Snailmail: Karl-Franzens-University Graz / \ Dept. Zoology, Div. Neuroethology --/----\-- Universitaetsplatz 2 |_|____|_| A-8010 Graz | /\ | AUSTRIA | \/ |___ old EMail: Lobsterman@edvz.uni-graz.ada.at |______/ new Email: Robert.Huber@kfunigraz.ac.at __/ Grazer Tel: Austria (316) 380-5281 (office) / Uhrturm or 380-5604 (lab) or 380-5597 (secretary) Fax: Austria (316) 381-255 --------------------------------------------------------- | I can't see Texas from here! | | and Harvard Square neither | --------------------------------------------------------- From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!rutgers!netnews.upenn.edu!dsinc!ub!acsu.buffalo.edu!ubvms.cc.buffalo.edu!ORBASHU From: orbashu@ubvms.cc.buffalo.edu Subject: SSCP analysis/Help Message-ID: Sender: nntp@acsu.buffalo.edu Nntp-Posting-Host: ubvmsa.cc.buffalo.edu Reply-To: orbashu@ubvms.cc.buffalo.edu Organization: University at Buffalo Date: Tue, 4 Oct 1994 20:47:09 GMT Lines: 1 I don't know if its a FAQ, I am interested in using SSCP to detect single base pair differences. I have never done SSCP before therefore I am interested in knowing the procedure etc I can follow. Any suggestions are appreciated. Thanx From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!rutgers!netnews.upenn.edu!dsinc!ub!acsu.buffalo.edu!ubvms.cc.buffalo.edu!ORBASHU From: orbashu@ubvms.cc.buffalo.edu Subject: Nucleic acid data base using blast Message-ID: Sender: nntp@acsu.buffalo.edu Nntp-Posting-Host: ubvmsa.cc.buffalo.edu Reply-To: orbashu@ubvms.cc.buffalo.edu Organization: University at Buffalo Date: Tue, 4 Oct 1994 20:38:13 GMT Lines: 1 I have an accession no. of a gene I am interested in getting the sequence from Genebank using blast server at ncbi. Could somebody tell me how I can retreive the info? I will appreciate any help. I used to be able to retreive using retreive @genebank... I've lost the info now. Please help From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!sgiblab!sgigate.sgi.com!olivea!koriel!lll-winken.llnl.gov!overload.lbl.gov!ames!waikato!canterbury.ac.nz!chmeds.ac.nz!gordon From: gordon@chmeds.ac.nz Newsgroups: bionet.software,bionet.general Subject: Anatomy on a disk? Message-ID: <1994Oct4.183453.608@chmeds.ac.nz> Date: 4 Oct 94 18:34:53 +1200 Lines: 16 Xref: biosci bionet.software:9511 bionet.general:11395 I'm looking for an anatomy CDROM - lots of pictures of human anatomy, software not important as the pictures are going to be used (in a training setting) to accompany other material. Photorealism is required; good line drawings would be an added bonus. I've seen lots of these written about in the press but now that I need one I cannot locate any vendors! Any leads? Slainte Gordon -- Gordon Findlay, Computer Scientist, Christchurch School of Medicine Nuclear-free New Zealand !SYSTEM-F-SYSERR: System Email: Gordon@CHMEDS.AC.NZ !error. Hit any user to Paper: PO Box 4345, Christchurch, NEW ZEALAND !continue. Voice: +64-3-364 0540 ! From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!cs.utexas.edu!convex!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!mail1.sas.upenn.edu!smoore From: smoore@mail1.sas.upenn.edu (Sean David Moore) Newsgroups: bionet.software Subject: alignment for windows Date: 4 Oct 1994 16:58:40 GMT Organization: University of Pennsylvania Lines: 26 Message-ID: <36s1k0$647@netnews.upenn.edu> NNTP-Posting-Host: mail1.sas.upenn.edu X-Newsreader: TIN [version 1.2 PL2-upenn1.1] I am looking for an alignment program for DNA and Proteins for Windows. We recently revieved GeneRunner, it aligns only blocks...I want to allow for Gap-penalties etc. A nice cheap program will do, Gene Runner does the rest. I have no association with Gene Runner or Hastings software...merely stating a point. PLease supply me with a source as well. Thanks in Advance. -- Sean Moore VAMC Philadelphia, Medical College of Pennsylvania, and the University of Pennsylvania... . smoore@sas.upenn.edu From owner-software@net.bio.net Mon Oct 03 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!EU.net!sunic!umdac!Peter.Lundberg From: peterl@umdix.umdc.umu.se (Peter Lundberg) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Promega on the Internet Date: 4 Oct 1994 17:36:27 GMT Organization: Phys Chem, University of Umea, Sweden Lines: 8 Sender: -Not-Authenticated-[2976] Message-ID: <36s3qr$gse@kitten.umdc.umu.se> References: <1994Sep29.181744.29696@genes.icgeb.trieste.it> <1994Oct1.142817.8747@mbcf> <36rkur$nbj@nyx10.cs.du.edu> NNTP-Posting-Host: plgmac.chem.umu.se X-Posted-From: InterNews 1.0@kitten.umdc.umu.se. Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.molbio.methds-reagnts:19193 bionet.software:9518 I vote YES for this suggestion! 73, Peter ================================== Peter Lundberg Email: peterl@umdix.umdc.umu.se ============761.91141============= From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!swrinde!sgiblab!sgigate.sgi.com!enews.sgi.com!decwrl!netcomsv!ix.netcom.com!netcom.com!weix From: weix@netcom.com (Patrick Weix) Subject: Re: Promega on the Internet Message-ID: Organization: NETCOM On-line Communication Services (408 261-4700 guest) References: <1994Sep29.181744.29696@genes.icgeb.trieste.it> <1994Oct1.142817.8747@mbcf> <36rkur$nbj@nyx10.cs.du.edu> Date: Wed, 5 Oct 1994 03:15:54 GMT Lines: 28 Xref: biosci bionet.molbio.methds-reagnts:19271 bionet.software:9538 rnusbick@nyx10.cs.du.edu (robert nusbickel) writes: >This discussion about PROMEGA placing there materials on the net has got >me thinking. How's about a service which would be sort of like a directory >of all the suppliers information, including ordering information, >protocols, and descriptions of the materials, and make this available >through the net? It certainly would be advantageous to the suppliers to >put their information into one location and it would be great for >researchers to have only one place to check on reagents, etc. What do you >think? >Just looking for some opinions. I tell you, I would much rather grep a database than thumb through catalog after catalog trying to guess where all my items are listed. Another plus, will make comparison shopping a snap. I'm all for it. Patrick >Andy Nusbickel -- "The large print giveth, and the small print taketh away." Tom Waits /------------------------------------------------------------\ | Patrick Weix weix@netcom.com | | UT Southwestern Medical Center weix@utsw.swmed.edu | | 5323 Harry Hines Blvd tel: (214) 648-5050 | | Dallas, TX 75235 fax: (214) 648-5453 | \------------------------------------------------------------/ From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!convex!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!dsinc!ub!galileo.cc.rochester.edu!troi.cc.rochester.edu!mshelly From: mshelly@troi.cc.rochester.edu (Mark A. Shelly) Subject: EIA (ELISA) software Message-ID: <1994Oct5.134136.20645@galileo.cc.rochester.edu> Keywords: Elisa, EIA Sender: news@galileo.cc.rochester.edu Nntp-Posting-Host: troi.cc.rochester.edu Organization: University of Rochester - Rochester, New York Date: Wed, 5 Oct 94 13:41:36 GMT Lines: 17 Simple question: I'm looking for options for EIA or ELISA software to assist in analysis of these assays. Should include robust analysis options, along with import and export options. We're considering Macintosh, DOS, and Windows solutions. Is anything cross-platform compatible? Thanks in advance, Mark Shelly, M.D. University of Rochester mshelly@medicine.rochester.edu (716)461-6821 From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!cs.utexas.edu!convex!news.duke.edu!usenet From: Sheetz Lab Newsgroups: bionet.software Subject: Re: Promega on the Internet Date: 5 Oct 1994 21:31:12 GMT Organization: Duke University Medical Center Lines: 33 Distribution: world Message-ID: <36v5v0$ese@news.duke.edu> References: NNTP-Posting-Host: sizzle.cellbio.duke.edu In article sspencer@rhino.bocklabs.wisc.edu (Stephan Spencer) writes: >I (and Promega) would like to know who out there would like to see Promega >on the World Wide Web, and what you would like to see (catalog, technical >notes, online ordering, tech support, etc...) > >Second question.. would you use their services online? Would you order >online? > >If enough people respond positively, I think Promega execs will be >convinced to make themselves available on the Info Superhighway. Right now >they are sceptical that researchers will want to order online... It's a great idea to include on-line catalog as well as the tech info.. USB used to distribute their very informative catalogs on disk (before join with Amersham). Promega also distributed their beautiful protocols etc in meetings. Tech support like NEB's will certainly help everyone. As for ordering, most institutions are restricted by their ordering department. So far, we have been getting around it by 1) getting a standing PO and 2) getting a regular PO if your ordering department allow you to order over the phone by yourself. Once you have a PO issued (regular or standing), you can fax/phone/mail/e-mail, in most instances. I have been using Sigma's Sigma Direct for most orders from SIgma, and Genset for Oligos ordering for the last couple of years. It 's wonderful to order this way since we can send in orders anytime of the day/week and keep a copy of our orders. It would be better if Sigma Direct can be accessed via internet instead by Modem. Anyhow, as more of us push the ordering department by partially bypassing them like this, they begin to learn to change and enter the modern world. Recently, the Duke system gave up their archaic way of requiring a written requisition handed in person and we can now request a PO by sending in an e-mail to them and get it the second day. Good luck with the rest of you and let's push them! Hanry Yu. From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!jobone!heifetz.msen.com!zib-berlin.de!fauern!lrz-muenchen.de!news.informatik.uni-muenchen.de!wap18.zi.biologie.uni-muenchen.de!salger From: salger@wap18.zi.biologie.uni-muenchen.de (Klaus Salger) Newsgroups: bionet.software Subject: Re: alignment for windows Date: 5 Oct 1994 23:19:49 GMT Organization: Institut fuer Informatik der Universitaet Muenchen Lines: 40 Distribution: world Message-ID: <36vcal$8pl@arcadia.informatik.uni-muenchen.de> References: <36s1k0$647@netnews.upenn.edu> <36ukh8$5nj@news.doit.wisc.edu> NNTP-Posting-Host: wap18.zi.biologie.uni-muenchen.de X-Newsreader: TIN [version 1.2 PL2] lehn@facstaff.wisc.edu wrote: : In article <36s1k0$647@netnews.upenn.edu>, writes: : > Path: : news.doit.wisc.edu!saimiri.primate.wisc.edu!sdd.hp.com!spool.mu.edu!howland.reston. : ans.net!cs.utexas.edu!convex!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!dsinc : !netnews.upenn.edu!mail1.sas.upenn.edu!smoore : > I am looking for an alignment program for DNA and Proteins for Windows. : > We recently revieved GeneRunner, it aligns only blocks...I want to allow : > for Gap-penalties etc. A nice cheap program will do, Gene Runner does : > the rest. : > : > -- : > Sean Moore : Try MACAW, its a great program avaliable by anonymous FTP : from NCBI at: : ncbi.nlm.nih.gov : Its avaliable in both a Windows and Mac version. As far as I know MACAW does also align only blocks - no global alignments (with gap penalties etc.). The DOS-version of ClustalV would do the job (there is no Windows-version). Klaus Klaus Salger Zoologisches Institut AG MacWilliams Luisenstr. 14 80333 Muenchen Germany phone : ++49 (0)89 5902 -502 FAX : -450 e-mail: salger@zi.biologie.uni-muenchen.de From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!fconvx.ncifcrf.gov!fcsparc6!pnh From: pnh@fcsparc6.ncifcrf.gov (Paul N Hengen) Subject: Re: Promega on the Internet Message-ID: Summary: Technical support Sender: Paul N. Hengen Nntp-Posting-Host: fcsparc6.ncifcrf.gov Organization: Frederick Cancer Research and Development Center References: Date: Wed, 5 Oct 1994 18:07:01 GMT Lines: 21 Xref: biosci bionet.molbio.methds-reagnts:19250 bionet.software:9534 Stephan Spencer (sspencer@rhino.bocklabs.wisc.edu) wrote: : I (and Promega) would like to know who out there would like to see Promega : on the World Wide Web, and what you would like to see (catalog, technical : notes, online ordering, tech support, etc...) That Promega is interested in providing technical support on the WWW is quite a switch form their usual policies. When I asked Promega why they read methds-reagnts and do not respond to people having trouble with their products, the answer I got was "We don't think it's appropriate to help people on the net. They should call instead". I would definitely like to see technical support, but I doubt we'll get any more than advertisements on WWW. Thanks, but no thanks. ******************************************************************************* * Paul N. Hengen, Ph.D. /--------------------------/* * National Cancer Institute |Internet: pnh@ncifcrf.gov |* * Laboratory of Mathematical Biology | Phone: (301) 846-5581 |* * Frederick Cancer Research and Development Center| FAX: (301) 846-5598 |* * Frederick, Maryland 21702-1201 USA /--------------------------/* * - - Methods FAQ list -> http://fconvx.ncifcrf.gov:2001/~pnh/info.html - - * ******************************************************************************* From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!COMPBIO2.MED.WAYNE.EDU!steve From: steve@COMPBIO2.MED.WAYNE.EDU (Stephen Krawetz) Newsgroups: bionet.software Subject: Image composition software for SUN Solaris 2.3 Date: 5 Oct 1994 11:46:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410051847.AA00713@compbio3.med.wayne.edu> NNTP-Posting-Host: net.bio.net I am looking for some software that will run on a SUN under SOLARIS 2.3 for basic image processing to prepare images for publications. I would the program to set up an 8.5 x 11 page upon which I can place and change the multiple objects. What I need is cut + paste Label stretch background corrections box and line drawing and a few symbols as well as various character sets. Is there anything like that out their. Freeware or Shareware if possible. From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!rutgers!csn!carbon!saimiri.primate.wisc.edu!news.doit.wisc.edu!news From: lehn@facstaff.wisc.edu Newsgroups: bionet.software Subject: Re: alignment for windows Date: Wed, 05 Oct 94 11:25:28 EDT Organization: Division of Information Technology Lines: 23 Message-ID: <36ukh8$5nj@news.doit.wisc.edu> References: <36s1k0$647@netnews.upenn.edu> NNTP-Posting-Host: islet.medsch.wisc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage In article <36s1k0$647@netnews.upenn.edu>, writes: > Path: news.doit.wisc.edu!saimiri.primate.wisc.edu!sdd.hp.com!spool.mu.edu!howland.reston. ans.net!cs.utexas.edu!convex!news.duke.edu!godot.cc.duq.edu!newsfeed.pitt.edu!dsinc !netnews.upenn.edu!mail1.sas.upenn.edu!smoore > I am looking for an alignment program for DNA and Proteins for Windows. > We recently revieved GeneRunner, it aligns only blocks...I want to allow > for Gap-penalties etc. A nice cheap program will do, Gene Runner does > the rest. > > -- > Sean Moore Try MACAW, its a great program avaliable by anonymous FTP from NCBI at: ncbi.nlm.nih.gov Its avaliable in both a Windows and Mac version. From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!rutgers!netnews.upenn.edu!ccat.sas.upenn.edu!aaron From: aaron@ccat.sas.upenn.edu (Aaron Pawlyk) Newsgroups: bionet.software Subject: Test Date: 5 Oct 1994 18:06:45 GMT Organization: University of Pennsylvania Lines: 2 Message-ID: <36upvl$8ts@netnews.upenn.edu> NNTP-Posting-Host: ccat.sas.upenn.edu X-Newsreader: Tin 1.1 PL4 This is a test From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: 2020221%LAVALVX1.earn@earn-relay.ac.uk Newsgroups: bionet.software Subject: signoff Date: 5 Oct 1994 20:44:04 +0100 Lines: 1 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <36uvm4$2ti@mserv1.dl.ac.uk> Original-To: bio-software@DL.AC.UK signoff bionet-news Robert J. Bojanowski From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!jobone!heifetz.msen.com!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!news.informatik.uni-muenchen.de!wap18.zi.biologie.uni-muenchen.de!salger From: salger@wap18.zi.biologie.uni-muenchen.de (Klaus Salger) Newsgroups: bionet.software Subject: Re: Commercial Windows Sequence-Handling Software... Date: 5 Oct 1994 17:04:13 GMT Organization: Institut fuer Informatik der Universitaet Muenchen Lines: 29 Distribution: world Message-ID: <36umad$3ge@arcadia.informatik.uni-muenchen.de> References: NNTP-Posting-Host: wap18.zi.biologie.uni-muenchen.de X-Newsreader: TIN [version 1.2 PL2] Ed Rybicki (ed@molbiol.uct.ac.za) wrote: : Does anyone know of a commercial package running under Windows 3.1x, which can: : 1) handle nucleotide sequence data (eg: generate restriction maps, translate : in all ORFs, highlight); : 2) design PCR primers : 3) etc? : I downloaded a demo of one a while back, and it looked wondeful, and now I : can't find it again or remember what it was! Anyone have any idea? : Thanks, Ed, this wonderful program might have been VectorNT. It can handel sequences, Primers and a lot of other things. The demo version is available on ftp.bio.indiana.edu/molbio/ibmpc/vntd-demo.exe. (I have no affiliation with Informax...) Klaus Klaus Salger Zoologisches Institut AG MacWilliams Luisenstr. 14 80333 Muenchen Germany phone : ++49 (0)89 5902 -502 FAX : -450 e-mail: salger@zi.biologie.uni-muenchen.de From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!quagga.ru.ac.za!inet.up.ac.za!news From: root@biochem.up.ac.za (Fourie Joubert) Newsgroups: bionet.software Subject: Image processing for Solaris? Date: 5 Oct 1994 08:46:45 GMT Organization: University of Pretoria Lines: 15 Message-ID: <36tp5l$bek@inet.up.ac.za> Reply-To: fourie@ccnet.up.ac.za NNTP-Posting-Host: biochem.up.ac.za Hi Does anyone know of a public domain image analysis package that will compile under Solaris? I tried ALV and DNAGUI but couldn't get them compiled under Solaris 2.3. Any help would be sincerely appreciated! --- Fourie Joubert Department of Biochemistry University of Pretoria fourie@ccnet.up.ac.za +27-12-420-2011 From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: mosaic Message-ID: <1994Oct5.123704.13891@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <36u30i$bpr@mserv1.dl.ac.uk> Distribution: bionet Date: Wed, 5 Oct 1994 12:37:04 GMT Lines: 22 suter@VAX.MPIZ-KOELN.MPG.d400.de wrote: : where can i get get I fwhere can i : mosaic software ? How to get Mosaic, what to expect, and more? We are aware of the need to provide training... Watch bionet.software.www for the WWW introduction course, starting Monday Oct 10, 1994! The course will be done by F.Eggen- berger as part of EMBnet Switzerland Services. Regards Reinhard Doelz EMBnet Switzerland -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!newshost.lanl.gov!.lanl.gov!kvr From: kvr@.lanl.gov (Ken Van Riper) Newsgroups: bionet.software Subject: Looking for Human Models Date: 5 Oct 1994 12:56:17 GMT Organization: Los Alamos National Laboratory Lines: 12 Distribution: world Message-ID: <36u7ph$hs@newshost.lanl.gov> NNTP-Posting-Host: u2.lanl.gov Keywords: phantom I am looking for computer models of humans (of all ages, size, and sexes) for use in Monte Carlo simulations of radiation diagnostics and therapy. For efficient Monte Carlo simulations, we require models constructed of quadratic surfaces (planes, spheres, cylinders, ellipsiods, elliptical cylinders, ...) Any leads would be appreciated, as would direct reply by email. Ken Van Riper kvr@lanl.gov Radiation Transport Group, Los Alamos National Laboratory From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: suter@VAX.MPIZ-KOELN.MPG.d400.de Newsgroups: bionet.software Subject: mosaic Date: 5 Oct 1994 12:34:42 +0100 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <36u30i$bpr@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk hi, where can i get get I fwhere can i mosaic software ? clemens From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!quagga.ru.ac.za!ucthpx!uctvax.uct.ac.za!pc24.mic.uct.ac.za!ed Newsgroups: bionet.software Subject: Commercial Windows Sequence-Handling Software... Message-ID: From: ed@molbiol.uct.ac.za (Ed Rybicki) Date: Wed, 5 Oct 1994 11:39:52 UNDEFINED Distribution: world Organization: Microbiology Dept., Univ. Cape Town Keywords: Windows, sequence Nntp-Posting-Host: pc24.mic.uct.ac.za X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] Lines: 27 Does anyone know of a commercial package running under Windows 3.1x, which can: 1) handle nucleotide sequence data (eg: generate restriction maps, translate in all ORFs, highlight); 2) design PCR primers 3) etc? I downloaded a demo of one a while back, and it looked wondeful, and now I can't find it again or remember what it was! Anyone have any idea? Thanks, ___________________________________________________________________ | Ed Rybicki, PhD | "Lord, won't you buy me | | (ed@molbiol.uct.ac.za) | | | Dept Microbiology | A Mer-ce-des Benz..." | | University of Cape Town | | | Private Bag, Rondebosch | "My friends all drive Porsches | | 7700, South Africa | | | fax: 27-21-650 4023 | I must make amends..." | | phone: 650-3265 | (Janis Joplin, Pearl, 1971) | -------------------------------------------------------------------- From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!jobone!heifetz.msen.com!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!news.informatik.uni-muenchen.de!wap18.zi.biologie.uni-muenchen.de!salger From: salger@wap18.zi.biologie.uni-muenchen.de (Klaus Salger) Newsgroups: bionet.software Subject: Re: Nucleic acid data base using blast Date: 5 Oct 1994 17:23:08 GMT Organization: Institut fuer Informatik der Universitaet Muenchen Lines: 23 Distribution: world Message-ID: <36unds$3ge@arcadia.informatik.uni-muenchen.de> References: NNTP-Posting-Host: wap18.zi.biologie.uni-muenchen.de X-Newsreader: TIN [version 1.2 PL2] orbashu@ubvms.cc.buffalo.edu wrote: : I have an accession no. of a gene I am interested in getting the sequence : from Genebank using blast server at ncbi. Could somebody tell me how I : can retreive the info? I will appreciate any help. I used to be able to : retreive using retreive @genebank... I've lost the info now. Please help You could also get the genbank entry (fast) by gophering to "fly.bio.indiana.edu/77/.indices/genbank". This is a seachable gopher index which will find not only the accession number but also the gene's name. Klaus Klaus Salger Zoologisches Institut AG MacWilliams Luisenstr. 14 80333 Muenchen Germany phone : ++49 (0)89 5902 -502 FAX : -450 e-mail: salger@zi.biologie.uni-muenchen.de From owner-software@net.bio.net Tue Oct 04 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!news.mic.ucla.edu!steve3.mbi.ucla.edu!rkagan From: Ron Kagan Newsgroups: bionet.software Subject: Re: Nucleic acid data base using blast Date: 5 Oct 1994 00:21:16 GMT Organization: Dept. of Chemistry and Biochemistry, ULCA Lines: 29 Distribution: world Message-ID: <36srhs$oln@news.mic.ucla.edu> References: NNTP-Posting-Host: steve3.mbi.ucla.edu X-UserAgent: Nuntius v1.1.2 X-XXMessage-ID: X-XXDate: Tue, 4 Oct 94 17:24:26 GMT In article , orbashu@ubvms.cc.buffalo.edu writes: >I have an accession no. of a gene I am interested in getting the sequence from >Genebank using blast server at ncbi. Could somebody tell me how I can retreive >the info? I will appreciate any help. I used to be able to retreive using >retreive @genebank... I've lost the info now. Please help Send a message to: retrieve@ncbi.nlm.nih.edu Specify in the body of the message: DATALIB gb BEGIN Ron Kagan ********************************************************************** "My Kindness is not random, and nothing senseless was ever beautiful." - J. Zabriskie ********************************************************************** Ron Kagan rkagan@ewald.mbi.ucla.edu From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!galaxy.ucr.edu!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!vixen.cso.uiuc.edu!ruger-5.slip.uiuc.edu!user From: r-larkin@uiuc.edu (Ron Larkin) Newsgroups: bionet.software,bionet.population-bio,sci.bio Subject: Re: Software to track wildlife migration? Date: Wed, 05 Oct 1994 20:58:25 -0600 Organization: Illinois Natural History Survey Lines: 23 Message-ID: References: <36siai$1jq@antares.Austin.Lockheed.COM> NNTP-Posting-Host: ruger-5.slip.uiuc.edu Xref: biosci bionet.software:9539 bionet.population-bio:827 sci.bio:11185 In article <36siai$1jq@antares.Austin.Lockheed.COM>, mcinroy@austin.lockheed.com (John W. McInroy) wrote: > Last month I posted the following item: > : I am looking for software that can be used to > : track phenomena such as the movement of banded > : birds or other wildlife. I would appreciate > : any information available. John, Having missed the original post, I don't see much direct connection between "wildlife migration", banding data, and the home range analysis programs listed in your summary posting. Nevertheless, you may be interested in a review article on home range software that appears in the summer '94 Wildlife Society Bulletin. It reviews about a dozen packages that run on PC's. I can send you a reprint if you like. Regards, Ron Larkin Illinois Natural History Survey r-larkin@uiuc.edu PS Is Lockheed applying its technology and muscle to wildlife matters??? From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!scsing.switch.ch!yogi!bioftp.unibas.ch!doelz Newsgroups: bionet.software Subject: Remember the data... Re: Can XXXXXX replace YYY package? Or almost?? Message-ID: <1994Oct6.105608.13879@comp.bioz.unibas.ch> From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Date: Thu, 6 Oct 1994 10:56:08 GMT References: <36vkk9$gtq@mace.cc.purdue.edu> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Lines: 32 Xiaomu Niu (xniu@mace.cc.purdue.edu) wrote: : But here is the question: (sorry for the long introduction) : Can XXXXXX replace YYY completely or nearly? What about speed? It : seems we have people here running XXXXXX on a Mac SE with a CD-ROM : happily. If we understand right, ZZZ covers most of YYY's functions, : and it's available for free. Without getting involved in judging user interface and affodability, keep in mind that a central installation ought to provide up-to-date data in its literal meaning (weekly, for example). You will possibly have a hard time to get this into PC/Mac based products. Sure you can paint your restriction maps as nice as you want with any software, but as soon as external data sets (databases) are involved a centralized, up-to-date facility is unaviodable. And, Training is usually cheaper as better resources (including the net) will cope. Last, complexity and continuity are items which have a high rating in customer's view, so be careful in moving to another technology unless you made sure that people can move their data, results, and procedures easily. Regards Reinhard Doelz -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!agate!spool.mu.edu!news.nd.edu!glambertimac.bio.nd.edu!user From: William.L.Perry.13@nd.edu (William.L.Perry) Newsgroups: bionet.software Subject: PAUP...Where to get Date: 6 Oct 1994 12:52:36 GMT Organization: University of Notre Dame Lines: 3 Message-ID: NNTP-Posting-Host: glambertimac.bio.nd.edu Hi, I am looking for the program by Swofford called PAUP. I need to install it for an upcoming class project. Any pointers on addresses to swofford or FTP sites would be greatly appreciated From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!convex!convex!constellation!news.uoknor.edu!aardvark.ucs.uoknor.edu!jwickham From: jwickham@aardvark.ucs.uoknor.edu (WICKHAM,JOHN) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Promega on the Internet Date: 5 Oct 1994 23:08 CDT Organization: University of Oklahoma - University Computing Services Lines: 24 Distribution: world Message-ID: <5OCT199423082068@aardvark.ucs.uoknor.edu> References: <36rkur$nbj@nyx10.cs.du.edu> NNTP-Posting-Host: 129.15.10.11 News-Software: VAX/VMS VNEWS 1.41 Xref: biosci bionet.molbio.methds-reagnts:19282 bionet.software:9541 In article <36rkur$nbj@nyx10.cs.du.edu>, rnusbick@nyx10.cs.du.edu (robert nusbickel) writes... >This discussion about PROMEGA placing there materials on the net has got >me thinking. How's about a service which would be sort of like a directory >of all the suppliers information, including ordering information, >protocols, and descriptions of the materials, and make this available >through the net? It certainly would be advantageous to the suppliers to >put their information into one location and it would be great for >researchers to have only one place to check on reagents, etc. What do you >think? > >Just looking for some opinions. > > >Andy Nusbickel Invitrogen now offers plasmid sequences via internet. I've also e-mailed to Stratagene to obtain similair information. Product databases could be very useful, especially when technical help via AT&Tnet can be slow and/or difficult to obtain. Although, I certainly don't want Biotech reps responding to questions with the sole intention of selling a product... Quyen Wickham From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!mozo.cc.purdue.edu!not-for-mail From: xniu@mace.cc.purdue.edu (Xiaomu Niu) Newsgroups: bionet.software Subject: Can DNAsis replace GCG package? Or almost?? Date: 5 Oct 1994 20:41:29 -0500 Organization: Purdue University Lines: 37 Message-ID: <36vkk9$gtq@mace.cc.purdue.edu> NNTP-Posting-Host: mace.cc.purdue.edu Please pardon my lack of knowledge in this subject, but we are trying to decide what kind of sequence analysis package (hardware and software) to purchase. We've been spending about $1000 per year using the GCG package provided by a computing center here on Purdue campus, and since we project more usage in the future, we decided that it's time to have our own. After a brief search of faq's and archived postings, as well as talking with collegues here, it seems to us that GCG is beyond our reach: we don't wish to buy highend workstations. We want a program or a set of programs with most if not all of the functions provided by GCG, but with a nicer interface (we've been using line mode for our GCG here by telnet). We narrowed our choices down to two: (1) a 486/586 pc running linux and X-windows (2) a Machintosh or a Power Mac With the first one, we can run MS-Windows with Hitachi's DNAsis for window, or we install Linux and run GDE plus other freely availabe sequence analysis programs for unix, something like BIRCH (but running on a pc). With the second choice, we probably have to purchase the MacDNAsis from Hitachi. Or we can try GeneWorks (?) also. But here is the question: (sorry for the long introduction) Can DNAsis replace GCG completely or nearly? What about speed? It seems we have people here running DNAsis on a Mac SE with a CD-ROM happily. If we understand right, GDE covers most of GCG's functions, and it's available for free. Please respond to this account or post here. If there is enough interest, I'll glad to post a summary. Thank you in advance. Xiaomu From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!convex!news.duke.edu!news-feed-1.peachnet.edu!umn.edu!lenti.med.umn.edu!nrd From: nrd@lenti.med.umn.edu (Neal Dalton) Subject: Re: mosaic Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: lenti.med.umn.edu Organization: University of Minnesota, Twin Cities X-Newsreader: TIN [version 1.2 PL2] References: <36u30i$bpr@mserv1.dl.ac.uk> Distribution: bionet Date: Thu, 6 Oct 1994 15:17:53 GMT Lines: 17 suter@VAX.MPIZ-KOELN.MPG.d400.de wrote: : where can i get get I fwhere can i : mosaic software ? ftp.ncsa.uiuc.edu in /Mosaic/... For windows try: WinWeb (ftp://ftp.einet.net/einet/pc/winweb.zip) or Cello (ftp://fatty.law.cornell.edu/pub/LII/Cello/cello.zip) People seem to perfer WinWeb. There is also a macweb or something, but Mosaic seem to work OK on a MAC. Unlike windows, which is a problem in itself. Neal From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!uunet!zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Promega on the Internet Followup-To: bionet.molbio.methds-reagnts,bionet.software Date: 6 Oct 1994 15:31:50 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 12 Distribution: world Message-ID: <371596INNhbt@sat.ipp-garching.mpg.de> References: <5OCT199423082068@aardvark.ucs.uoknor.edu> NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] Xref: biosci bionet.molbio.methds-reagnts:19297 bionet.software:9549 WICKHAM,JOHN (jwickham@aardvark.ucs.uoknor.edu) wrote: : Invitrogen now offers plasmid sequences via internet. Could you go into some detail? (Which kind of service (WWW, gopher, ftp), which address?) --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "People are DNA's way of making more DNA." (Edward O. Wilson, 1975) */ From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!news.itd.umich.edu!um.cc.umich.edu!schlyer From: schlyer@um.cc.umich.edu (B. Schlyer) Newsgroups: bionet.software Subject: XY->digital Date: Thu, 6 Oct 1994 11:08:07 Organization: University of Michigan Lines: 9 Message-ID: NNTP-Posting-Host: 141.211.127.155 X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Help. I'm looking for a program to digitize XY data from a strip chart recorder following scanning it into something like a bitmap image. I know of a commercial product, UN-PLOT-IT, I believe, from a Utah company however I would like to know if there is shareware or public domain software available. Thanks in advance. schlyer@um.cc.umich.edu From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Newsgroups: bionet.software From: Duncan@genesys.demon.co.uk (Duncan Clark) Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!demon!genesys.demon.co.uk!Duncan Subject: Which Mac for NIH Image? Distribution: world Organization: GeneSys Ltd. Reply-To: Duncan@genesys.demon.co.uk X-Newsreader: Newswin Alpha 0.6 Lines: 20 Date: Thu, 6 Oct 1994 14:36:01 +0000 Message-ID: <106303186wnr@genesys.demon.co.uk> Sender: usenet@demon.co.uk Hi Folks, I'd like to use NIH image but have only 486 PC's. I therefore need a Mac. I already capture images to the PC and can output an image in a format readable by NIH Image. The Mac would be used solely for NIH Image and will be used relatively infrequently and processing speed isn't high on priorities. Use would be by one or two people only. So which Mac? What is the minimum configuration that Image requires without taking O/N to do the simplest of tasks? many thanks Duncan ----------------------------------------------------------------------------- Duncan Clark | Internet: duncan@genesys.demon.co.uk G4ELJ | Compuserve: 100015.1406@compuserve.com ----------------------------------------------------------------------------- From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: worm@dsa.mpi-muelheim.mpg.de (Karl-Heinz Worm) Newsgroups: bionet.software Subject: Re: mosaic Date: 6 Oct 1994 15:33:43 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3711s7$qt9@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk doelz@comp.bioz.unibas.ch (Reinhard Doelz) wrote: >How to get Mosaic, what to expect, and more? We are aware of the need to >provide training... Watch bionet.software.www for the WWW introduction >course, starting Monday Oct 10, 1994! The course will be done by F.Eggen- >berger as part of EMBnet Switzerland Services. > Sorry about the following question but how/where can I watch bionet.software.www? Hope its not too stupid. Karl From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uchinews!quads!ecec From: ecec@quads.uchicago.edu (Eric Cabot) Subject: Re: SSCP analysis/Help Message-ID: <1994Oct6.132707.8853@midway.uchicago.edu> Followup-To: bionet.methods-reagents Sender: news@uchinews.uchicago.edu (News System) Reply-To: ecec@midway.uchicago.edu Organization: University of Chicago References: Date: Thu, 6 Oct 1994 13:27:07 GMT Lines: 46 You ask about SSCP analysis. I wonder why you ask it here rather than in the methods newgroup-to which I am redirecting follow-ups. The basic SSCP procedure is pretty simple. The way I do it (See Genetics 137:175-188) is as follows: -Perform your PCR with a little bit of 32P labelled nucleotide included. You can cut your PCR reaction volume down to 5 or 10 ul since you probably won't need much product. -Heat 1-3 ul of your PCR product together with 9 ul of denaturing buffer at 94 C for 2-3 min. (denat. buffer is 95% formamide, 10mM NaOH, 0.5% bromphenol blue, 0.5% xylene cyanol; this is equivalent to the left over stop solution from an otherwise exhausted sequencing kit). -Chill on ice immediately for at least 5 minutes prior to electrophoresis of the entire preparation on a polyacrylamide gel under non-denaturing condditions. Don't let your gel get to hot! If you want to run it quickly, then run it in a cold-room. You sometimes have to play around a bit with the concentration of acrylamide and the degree of cross-linking but straight out of the bottle gels for proteins should work fine for a first approximation. -Dry the gel onto a piece of 3mm chromatography paper and autoradiograph it. Alternates: -Instead of using 32P you can simply silver stain the gel. I originally used silver staining myself, but found that others in our lab tended to overexpose their gels (irreversibly), apparently out of "greed". -If your PCR product is rather long, you might want to cut 5-8 ul with an appropriate restriction enzyme in a 10 ul reaction volume, and then use 1-3 ul of that in the denaturation step. Needless to say, but I'll say it anyway, make sure to include both positive and negative controls. If you have some alleles that you know differ by a single base pair, then try them out first. It is also instructive to run undenatured vs. denatured samples on the gel until you get used to the technique-which shouldn't take long. -Eric Cabot - From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sun4nl!news.nic.surfnet.nl!mira.sara.nl!VM1.SARA.NL!A428ENDE From: A428ENDE@VM1.SARA.NL Newsgroups: bionet.software Subject: Re: Can DNAsis replace GCG package? Or almost?? Date: Thu, 06 Oct 94 09:28:04 CET Organization: S.A.R.A. Academic Computing Services Amsterdam Lines: 45 Message-ID: <17047852A.A428ENDE@VM1.SARA.NL> References: <36vkk9$gtq@mace.cc.purdue.edu> NNTP-Posting-Host: vm1.sara.nl X-Newsreader: NNR/VM S_1.3.2 In article <36vkk9$gtq@mace.cc.purdue.edu> xniu@mace.cc.purdue.edu (Xiaomu Niu) writes: > We narrowed our choices down to two: > (1) a 486/586 pc running linux and X-windows > (2) a Machintosh or a Power Mac > > With the first one, we can run MS-Windows with Hitachi's >DNAsis for window, or we install Linux and run GDE plus other freely >availabe sequence analysis programs for unix, something like BIRCH >(but running on a pc). Although we bought DNAsis on a Mac, I still believe that we made the wrong dess ision. With a 586 (which is much cheaper than a PowerMac 8100) you can indeed r un linux and take advantage of all the software available in the Unix environme nt and you have a very fast PC with all the advantages and programs in this env ironment (there are also a lot of Public domain and Shareware available). > With the second choice, we probably have to purchase the >MacDNAsis from Hitachi. Or we can try GeneWorks (?) also. > > But here is the question: (sorry for the long introduction) >Can DNAsis replace GCG completely or nearly? What about speed? It >seems we have people here running DNAsis on a Mac SE with a CD-ROM >happily. If we understand right, GDE covers most of GCG's functions, >and it's available for free. Don't buy the Hitachi MacDNAsis! It is full of bugs and strange things. For exa mple sometimes you can use small letters in your sequence (handy if you are alm ost sure that this is the base you read) but it converts them randomly to upper case. In the contig manager it has a very strange way of aligning the sequences and sometimes ruin your files by introducing hyphens (it can do it in the mult iple but it does it also in your sequences!). Complement, reverse and reverse + complement are not what you expect and so on. It has no ways to format the outp ut of all the operations so everything must be done in a drawing program or tex t editor. And I feel that I don't have all the possibilities which were impleme nted in GCG (for example blast). Does someone have the email number of Hitachi, because they are very hard to reach from Europe. > Please respond to this account or post here. If there is >enough interest, I'll glad to post a summary. Thank you in advance. Please do. May be we can also invest in something better. Henk van de Kamer CHLAMY@SARA.NL From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!uunet!news.pipeline.com!malgudi.oar.net!sun!oucsace!gwelch From: gwelch@oucsace.cs.ohiou.edu (Grattan Welch) Subject: WWW Browser for Windows Message-ID: Organization: Ohio University CS Dept,. Athens Date: Thu, 6 Oct 1994 21:26:35 GMT Lines: 5 I am looking for a WWW browser (not Mosaic) that can be used with Windows running in standard mode. The program should be able to handle graphics like Mosaic can. Is such a program available? From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: WWW setup, again [Re: mosaic] Message-ID: <1994Oct6.160741.22681@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <3711s7$qt9@mserv1.dl.ac.uk> Distribution: bionet Date: Thu, 6 Oct 1994 16:07:41 GMT Lines: 217 Karl-Heinz Worm (worm@dsa.mpi-muelheim.mpg.de) wrote: : Sorry about the following question but how/where can I watch : bionet.software.www? Hope its not too stupid. bionet.software.www is like any other newsgroup in the bionet system. As WWW is slightly advanced in terms of being a different communication technology, the newsgroup, additionally, keys contributions in 'html' documents so that links are resolved in the 'hypertext' system, and may point to the contribution of the originators, or the subject of the message, respectively. This server runs at the Biocomputing Facility of Basel University. The URL for this server is http://www.ch.embnet.org/bio-www/info.html and has the following structure: Contributions to the Group [this is a chronological, marked-up page] Servers [for services affecting retrieval or search engines, both announcements and updates] Archives [for archives of data and any kind of massive information] Descriptions [for site descriptions who update or announce a site running a server] Training/Services [specific services offered via WWW] Discussion [any discussion on topics above, as well as implementation or systematic issues. ] Keith Robison's WWW Server Index page [Link to the site where all bio-www servers are registered]. User-contributed Link Page [you may add your own links in WWW here, or have a message sent to the newsgroup from Mosaic (forms required)] To access the information provided by this and remote WWW sites you need a program (called WWW client or browser) that allows to communicate with the remote WWW server. The browser may either be locally installed or on a remote computer. If you are directly connected to the Internet it is recommended to install the client software locally. The disadvantage of accessing the Web by a remotely running client is a lack of full functionality and poorer performance. If your computer is directly connected to the Internet and you want to use WWW, you should install a browser. The advantages of a locally running browser are full functionality and better performance. WWW browsers are available for most environments including: * AIX * HP-UX * IRIX * MacOS 7.x * MS Windows 3.x * NeXTStep * OSF/1 * Ultrix * VMS * X11/Motif WWW browser software is copyrighted but usually free for academic use. Specifically, WWW browser software is available from FTP.NCSA.UIUC.EDU in the /Mosaic directory, or VMS versions possibly on info.cern.ch. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= All this, and more, will be presented in the information teaching series as announced by Florian Eggenberger and the information will start flowing at October 10, 1994. We are well aware of a 'catch22' situation which implies that the information on WWW is not suitable to be viewed by WWW itself. Therefore, the Newsgroup bionet.software.www is used. The following information is true for all bionet groups as far as the principle goes, and has been adapted to be valid for bionet.software.www specifically. Subject: BIOSCI:EMAIL/USENET INSTRUCTIONS ========================================== The BIO-WWW/bionet.software.www newsgroup is ready for operation. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Subscribing to this group: ************************** IF YOU USE USENET NEWS: you need do nothing other than participate in bionet.software.www when it appears in your newsreader. Depending upon your news software, this may entail you having to answer a prompt indicating that you want to subscribe. You might also try the command "g bionet.software.www" in rn-like newsreaders. IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: please send the word help in the body of your message to MXT@dl.ac.uk to retrieve general server usage instructions. To subscribe to the BIO-WWW list, first be sure that you are sending mail from the address at which you wish to receive news postings, and then send the command SUB bionet-news.bionet.software.www to MXT@dl.ac.uk. This message will be automatically read by the computer and your e-mail address will be extracted from the mail header and added to the list. IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: log in to the computer account in which you would like to receive mail (not an account that you use infrequently) and send a mail message to the Internet address biosci-server@net.bio.net Leave the Subject: line of the message blank and enter the following line into the body of the mail message: subscribe bio-www This message will be automatically read by our computer and your e-mail address will be extracted from the mail header and added to the list. Canceling your subscription: **************************** IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: first be sure that you are sending mail from the address at which you signed up to receive news postings, and then send the command (in the body of your mail message) UNSUB bionet-news.bionet.software.www to MXT@dl.ac.uk. This message will be automatically read by the computer and your e-mail address will be extracted from the mail header and removed from the list. IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: send a message to biosci-server@net.bio.net exactly as described above for subscribing except include the text unsubscribe bio-www in the body of the message. Please be sure to send the message from the account whose address matches the one on the list. If your address differs, we will be notified automatically and will remove you manually from the list if we can determine what was your old address. Please contact biosci-help@net.bio.net if you have problems. IF YOU HAVE A PROBLEM: ********************** Please send a message to one of the following addresses depending upon your location Address Location ------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim and someone on the staff will help you. PLEASE DO NOT send mail to our personal e-mail addresses as this will delay a response to your request for help. How to post a message to the group: *********************************** If you use news, simply post a message into bionet.software.www. Be sure to set your "distribution" to either bionet or world or else the message might not leave your site!! NOTE - this group is moderated and posts will not appear automatically until the moderator receives and approves them. To post by e-mail, mail your message to one of the following addresses depending upon your location: Posting Address Location --------------- -------- bio-www@daresbury.ac.uk Europe, Africa, and Central Asia bio-www@net.bio.net Americas and the Pacific Rim PLEASE DO NOT SEND SUBSCRIPTION REQUESTS TO THE POSTING +++++++++++++++++++++++++++++++++++++++++++++++++++++++ ADDRESSES as you will bother everyone on the newsgroup!!! +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ How to reply to a message on the group: *************************************** If you are using a newsreader, simply use the reply or follow-up command on your newsreader (these vary from program to program) to send either private or public replies. If you are using e-mail, replies to messages that you receive will *NOT* be automatically returned to the group. This is the standard for Internet mailing lists as opposed to BITNET LISTSERVs which often send all replies back to everyone. You must be certain that your reply contains either of the two newsgroup posting addresses above in your message header if you want to share it with everyone on the group. Otherwise in most cases your reply may go back to only the original poster of the message to which you are replying. ALWAYS be certain that you examine the address on your messages before you send them!!! Once a message is sent there is no way to cancel it or bring it back!!! Some non-Internet compliant mail systems may attempt to send replies to our error-trapping address called BIOSCI-REQUEST. If yours does this, please be sure to readdress your message to bio-www@net.bio.net or bio-www@daresbury.ac.uk if you want to send it to the newsgroup. Regards Reinhard Doelz -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!rutgers!gatech!swrinde!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!news.mic.ucla.edu!news.bc.net!vanbc.wimsey.com!unixg.ubc.ca!quartz.ucs.ualberta.ca!news.ucalgary.ca!pc22.mid.ucalgary.ca!user From: macklon@acs.ucalgary.ca (PMacklon) Subject: Re: EIA (ELISA) software Message-ID: Date: Thu, 6 Oct 1994 18:35:08 GMT References: <1994Oct5.134136.20645@galileo.cc.rochester.edu> Organization: U. of C. Lines: 35 In article <1994Oct5.134136.20645@galileo.cc.rochester.edu>, mshelly@troi.cc.rochester.edu (Mark A. Shelly) wrote: > Simple question: > > I'm looking for options for EIA or ELISA software to assist in analysis of > these assays. Should include robust analysis options, along with import and > export options. > > We're considering Macintosh, DOS, and Windows solutions. Is anything > cross-platform compatible? > > Thanks in advance, > > Mark Shelly, M.D. > University of Rochester We use (and have not had a plague of troubles with) Delta Soft III. Contact the manufacturer for more information: BioMetallics, Inc. P.O. Box 2251, Princeton, NJ 08543 609-275-0133 800-999-1961 fax 609-275-9485 I do not if it has cross platform capabilities, but does have export-ability. We are running it on an old Mac SE, connected to a Bio-Tek EL340 Elisa reader. Good luck. Peter > mshelly@medicine.rochester.edu > (716)461-6821 From owner-software@net.bio.net Wed Oct 05 23:00:00 1994 Path: biosci!daresbury!hgmp.mrc.ac.uk!nimp003.nimr.mrc.ac.uk!bionir From: bionir@nimr.mrc.ac.uk (Frank Norman) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Promega on the Internet: Biotechnet Date: 6 Oct 1994 17:30:05 GMT Organization: National Institute for Medical Research Lines: 27 Message-ID: References: <1994Sep29.181744.29696@genes.icgeb.trieste.it> <1994Oct1.142817.8747@mbcf> <36rkur$nbj@nyx10.cs.du.edu> NNTP-Posting-Host: nimp003.nimr.mrc.ac.uk Xref: biosci bionet.molbio.methds-reagnts:19307 bionet.software:9553 In article <36rkur$nbj@nyx10.cs.du.edu> rnusbick@nyx10.cs.du.edu (robert nusbickel) writes: >From: rnusbick@nyx10.cs.du.edu (robert nusbickel) >Subject: Re: Promega on the Internet >Date: 4 Oct 1994 07:22:35 -0600 >How's about a service which would be sort of like a directory >of all the suppliers information, including ordering information, >protocols, and descriptions of the materials, and make this available >through the net? It certainly would be advantageous to the suppliers to >put their information into one location and it would be great for >researchers to have only one place to check on reagents, etc. What do you >think? I was just about to ask whether such a thing exists - I guess it doesn't! But there is something called Biotechnet, which has some basic info. telnet biotechnet.com login BIOTECH password bguide ----- Frank Norman | National Institute for Medical Research Deputy Librarian | The Ridgeway, Mill Hill, London NW7 1AA | f-norman@uk.ac.mrc.nimr | tel 081 959 3666 ext 2380 fax 081 913 8534 f-norman@nimr.mrc.ac.uk From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!server2.rz.uni-leipzig.de!news.urz.tu-dresden.de!TUDURZ!petzoldt From: petzoldt@TUDURZ.urz.tu-dresden.de (Thomas Petzoldt Hydrobiologie) Newsgroups: bionet.software Subject: Re: Software for organizing reprints Date: 4 Oct 94 08:37:38 GMT Organization: TU Dresden (URZ) Lines: 22 Message-ID: References: <9409270002.AA21919@phage.cshl.org> NNTP-Posting-Host: tudurz.urz.tu-dresden.de lodhi@CSHL.ORG (Muhammad A. Lodhi) writes: >Hello Netters: >Does anyone know about any shareware for organizing reprints? For >organizing my collection of the references and reprints. Any lead will be >appreciated. >Thanks in advance >Muhammad Lodhi BIBDB (bibdb14e.zip) from Eyal Doron, which is distributed as a literature database manager for TeX databases may also be used for general references management. I am very satisfied with it. The best: It's FREE. Thomas -- ------------------------------------------------------------------------------ Thomas Petzoldt, Institut for Hydrobiology, Dresden University of Technology petzoldt@tudurz.urz.tu-dresden.de Phone: +49-351-463 4954 / Fax: +49-351-463 7108 From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.funet.fi!news.csc.fi!news.helsinki.fi!kruuna!stenberg From: stenberg@cc.Helsinki.FI (Dag Stenberg) Newsgroups: bionet.software Subject: Re: Which Mac for NIH Image? Date: 7 Oct 1994 08:56:15 GMT Organization: University of Helsinki Lines: 24 Distribution: world Message-ID: <3732ff$nvj@hybrid27.Helsinki.FI> References: <106303186wnr@genesys.demon.co.uk> NNTP-Posting-Host: kruuna.helsinki.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL0] Duncan Clark (Duncan@genesys.demon.co.uk) wrote: > What is the minimum configuration that Image requires > without taking O/N to do the simplest of tasks? You can fetch the newest manual from zippy.nimh.nih.gov with anonymous ftp. My manual is not absolutely recent, but it says that at least 4 Mb of memory is required. A monitor capable of displaying 256 gray shades or color is also needed. "It normally needs an FPU". Our ver 1.53 is actually given 4.5 Mb, although the manual says it will work with 2.5 Mb. Our System 7 takes up 2.5 Mb, so it would seem to me that 4 Mb is not perhaps enough. I have never tried running Image on any SE30, the slowest machines we have here. ------------------------------------------------------------------ Dag Stenberg MD PhD stenberg@cc.helsinki.fi Institute of Biomedicine tel: int.+358-0-1918532 Department of Physiology fax: int.+358-0-1918681 P.O.Box 9 (Siltavuorenpenger 20 J) tlx: 1002125 finuh sf FIN-00014 University of Helsinki,Finland X.400: /C=FI/A=FUMAIL/P=INET/O=HELSINKI/OU=CC/S=STENBERG/ ------------------------------------------------------------------ From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: WWW Browser for Windows Message-ID: <1994Oct7.083627.15741@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: Date: Fri, 7 Oct 1994 08:36:27 GMT Lines: 17 Grattan Welch (gwelch@oucsace.cs.ohiou.edu) wrote: : I am looking for a WWW browser (not Mosaic) that can be used with Windows : running in standard mode. The program should be able to handle graphics : like Mosaic can. Is such a program available? Watch bionet.software.www, starting next monday, the WWW teleteaching project will tell you about Cello and WinWeb. Regards Reinhard -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: Dietmar Tietz Newsgroups: bionet.software Subject: Re: XY->digital Date: 7 Oct 1994 09:27:23 +0100 Lines: 29 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3730pb$p3f@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: bio-soft@dl.ac.uk > Help. > I'm looking for a program to digitize XY data from a strip chart recorder > following scanning it into something like a bitmap image. I know of a > commercial product, UN-PLOT-IT, I believe, from a Utah company however I would > like to know if there is shareware or public domain software available. > Thanks in advance. > > schlyer@um.cc.umich.edu > There is a nice little program around called DataThief. It is freeware and it is available from the Mac-Info archives at Stanford University and its mirror sites. I believe it was in the graphics directory. If you cannot find it, please contact me. Cheers, Dietmar Tietz ****************************************************************** * Dietmar Tietz, Ph.D., Research Scientist * * Biostatistics, Justus-Liebig-University * * Ludwigstr. 27, D-35390 Giessen, Germany * * Phone: +49-(641)-702-6015 * * Fax: +49-(641)-702-5995 * * Email: Dietmar.Tietz@Uni-Giessen.de * ****************************************************************** From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!bjd12 From: bjd12@cus.cam.ac.uk (Ben Davis) Newsgroups: bionet.software Subject: HB plus ? Date: 7 Oct 1994 08:53:42 GMT Organization: University of Cambridge, England Lines: 19 Message-ID: <3732am$nkt@lyra.csx.cam.ac.uk> NNTP-Posting-Host: grus.cus.cam.ac.uk X-Newsreader: TIN [version 1.2 PL2] Hi, I seem to remember a program called (smthg like) HB plus, for locating hydrogen bonds in a protein structure. But, I've lost any details I might once have had - anyone got an ftp site or contact address for me ? Thanks, Ben -- ______________________________________________________________________________ Ben Davis, MRC Protein Function and Design, Cambridge, UK ______________________________________________________________________________ "They can make me do it, but they can't make me do it with dignity." From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Newsgroups: bionet.molbio.methds-reagnts,bionet.software Path: biosci!agate!msuinfo!harbinger.cc.monash.edu.au!bunyip.cc.uq.oz.au!marlin.jcu.edu.au!news From: robert@chironex.jcu.edu.au Subject: Re: Promega on the Internet Message-ID: <1994Oct7.052903.12602@marlin.jcu.edu.au> Sender: news@marlin.jcu.edu.au (USENET News System) Organization: James Cook University X-Newsreader: Date: Fri, 7 Oct 94 05:29:03 GMT Lines: 25 Xref: biosci bionet.molbio.methds-reagnts:19340 bionet.software:9556 In article weix@netcom.com (Patrick Weix) writes: >I tell you, I would much rather grep a database than thumb through >catalog after catalog trying to guess where all my items are listed. >Another plus, will make comparison shopping a snap. Another bonus is that we can see from country to country what the prices are like, thereby stopping unnecessary loading of prices ! Cheers, Robert ------------------------------------------------------------------------- Dr Robert J. Coelen fax: 61-77-791 526 Dept of Biomedical and Tropical Veterinary Sciences phone: 61-77-815 024 James Cook University of North Queensland Townsville-just-about-on-THE-reef, Q, 4811 -----------------------from the land d r--------------------------- o e w d n n u From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.lth.se!news.lu.se!bosse-q840.wblab.lu.se!Bo.Servenius From: Bo Servenius Subject: RAID for DNA databases??? Message-ID: <1994Oct7.160326.7465@nomina.lu.se> X-Xxmessage-Id: X-Xxdate: Fri, 7 Oct 94 17:04:01 GMT Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: bosse-q840.wblab.lu.se Organization: Lund university, Sweden X-Useragent: Version 1.1.3 Date: Fri, 7 Oct 1994 16:03:26 GMT Lines: 21 Dear Netters! I am considering to buy a SPARCstorage Array 100 for my Sun Sparcstation10-54 system. I am running gcg backage and the standard databases as EMBL and Swissprot. However I foresee that these databases and other db I would like to install will fill up my disks within some few month and think that a disk array would be the final solution to the ratrace inbetween my disks and the db. I have no experience of the technic nor the RAID concepts. For example how will the different RAID levels influence the performance of db I/O for our applications. Any comments or tips would be very much appreciated. yours BOSSE From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!bcc.ac.uk!arco2.afrc.ac.uk!pc0519.ri.afrc.ac.uk!user From: lawa@bbsrc.ac.uk (Andy Law (Big Nose)) Newsgroups: bionet.software Subject: Re: Can DNAsis replace GCG package? Or almost?? Date: 7 Oct 1994 12:16:13 GMT Organization: Roslin Institute Lines: 46 Message-ID: References: <36vkk9$gtq@mace.cc.purdue.edu> <17047852A.A428ENDE@VM1.SARA.NL> NNTP-Posting-Host: pc0519.ri.afrc.ac.uk In article <17047852A.A428ENDE@VM1.SARA.NL>, A428ENDE@VM1.SARA.NL wrote: > In article <36vkk9$gtq@mace.cc.purdue.edu> > Although we bought DNAsis on a Mac, I still believe that we made the wrong > dessision. With a 586 (which is much cheaper than a PowerMac 8100) you can > indeed run linux and take advantage of all the software available in the Unix > environment and you have a very fast PC with all the advantages and programs > in this environment (there are also a lot of Public domain and Shareware > available). You can also access UNIX environments from a Mac. Just as easily (if not easier). There is also a lot of Public/Shareware software available for the Mac as well. Hell, you can even run PC software on the PowerMacs with Softwindows, although not at any speed :) The PowerMac 8100 is too pricy compared to the 7100. The increase in performance that you get with the faster model is not worth the extra money. If you decide to go down the Mac route, then I reckon the 7100 is the best bet at the moment. Prices do tend to fluctuate rapidly though and there are all sorts of rumours about new models kicking around. As to MacDNAsis being buggy, well I can't comment on that because I haven't seen it, but I get the general impression that most of the micro-based DNA analysis software is crappy, difficult to use and full of bugs. I also get the feeling that so many scientists are so used to having to fight with monolithic mainframe programs that they just accept whatever lands in front of them on their PC and assume that it is just the way things are. THAT MAKES ME MAD!!!! The only way that the software companies are ever going to produce decent software that does the job and is easy to use is if we the users make their lives miserable until they do so. If you find a program that is not intuitive or which makes your job more difficult to do than it might be, then tell them about it. And keep telling them about it until they change it. I'm sorry, I have digressed from the subject of the original posting. To get back a bit more to the thread of things, DNASTAR is full of bugs and dreadful to use and the ABI software is little better. So, it seems, is MacDNAsis. Let's have a crusade against this stuff. Let the publishers know what you think. Andy Law ( Lawa @ bbsrc.ac.uk Big Nose in Edinburgh ) --- Campaigning for usable software --- From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!cisun2000.unil.ch!pcanat402.unil.ch5‚ßÌ@!gilles.bronchti From: gilles.bronchti@ia.unil.ch (Gilles Bronchti) Newsgroups: bionet.software Subject: Re: Which Mac for NIH Image? Date: Fri, 7 Oct 1994 12:11:19 UNDEFINED Organization: Institut d'Anatomie UNILausanne Lines: 32 Distribution: world Message-ID: References: <106303186wnr@genesys.demon.co.uk> <3732ff$nvj@hybrid27.Helsinki.FI> NNTP-Posting-Host: pcanat402.unil.ch X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] In article <3732ff$nvj@hybrid27.Helsinki.FI> stenberg@cc.Helsinki.FI (Dag Stenberg) writes: >From: stenberg@cc.Helsinki.FI (Dag Stenberg) >Subject: Re: Which Mac for NIH Image? >Date: 7 Oct 1994 08:56:15 GMT >Duncan Clark (Duncan@genesys.demon.co.uk) wrote: >> What is the minimum configuration that Image requires >> without taking O/N to do the simplest of tasks? >You can fetch the newest manual from zippy.nimh.nih.gov with anonymous >ftp. My manual is not absolutely recent, but it says that at least 4 Mb >of memory is required. A monitor capable of displaying 256 gray shades >or color is also needed. "It normally needs an FPU". > Our ver 1.53 is actually given 4.5 Mb, although the manual says it >will work with 2.5 Mb. Our System 7 takes up 2.5 Mb, so it would seem to >me that 4 Mb is not perhaps enough. > I have never tried running Image on any SE30, the slowest machines we >have here. We are currently running NIH-Image on a quadra 950 with 32MB ram. You can run Image with much less memory (although I would not recommend less than 8 Mb, if you have enough disk space for swap. But, if you need to open a reasonable number of images you will rapidly run out of memory. Moreover, memory swaps are very slow. Gilles Gilles Bronchti Institute of Anatomy University of Lausanne rue du Bugnon, 9 1004 Lausanne - Switzerland gilles.bronchti@ia.unil.ch From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: joshi@bioinfo.ernet.in (R.R.Joshi) Newsgroups: bionet.software Subject: Query about promoter seq Date: 7 Oct 1994 08:12:22 +0100 Lines: 18 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <372scm$lor@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk Hi everybody, This may be a simple thing to do, but do not know how to do it. I have a set of eight DNA sequences, out of which four are part of promoter sequences and the other four are non-promoters. I which to find which four are promoters and the nonpromoters. Is there any server or software which can do this fast.? Can I use any search program to find the promoter sequence? Thanks in advance R.R.Joshi #################################################################### # Dr.R.R.Joshi * Tel: 330195 # # c/o Prof.A.S.Kolaskar * Fax: 330087 # # Bioinformatics Centre * email: joshi@bioinfo.ernet.in # # University of Poona * # # PUNE-411007 * # # INDIA * # #################################################################### From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!uunet!newsflash.concordia.ca!canopus.cc.umanitoba.ca!orwell!frist From: frist@ccu.umanitoba.ca (Brian Fristensky) Newsgroups: bionet.software Subject: Re: Can DNAsis replace GCG package? Or almost?? Date: 6 Oct 1994 21:17:44 GMT Organization: The Univeristy of Manitoba. Lines: 51 Distribution: world Message-ID: <371pho$9nd@canopus.cc.umanitoba.ca> References: <36vkk9$gtq@mace.cc.purdue.edu> Reply-To: frist@ccu.umanitoba.ca NNTP-Posting-Host: orwell.cc.umanitoba.ca In article gtq@mace.cc.purdue.edu, xniu@mace.cc.purdue.edu (Xiaomu Niu) writes: > We narrowed our choices down to two: > (1) a 486/586 pc running linux and X-windows > (2) a Machintosh or a Power Mac > > With the first one, we can run MS-Windows with Hitachi's > DNAsis for window, or we install Linux and run GDE plus other freely > availabe sequence analysis programs for unix, something like BIRCH > (but running on a pc). > > With the second choice, we probably have to purchase the > MacDNAsis from Hitachi. Or we can try GeneWorks (?) also. > > But here is the question: (sorry for the long introduction) > Can DNAsis replace GCG completely or nearly? What about speed? It > seems we have people here running DNAsis on a Mac SE with a CD-ROM > happily. If we understand right, GDE covers most of GCG's functions, > and it's available for free. > One of the main reasons for creating BIRCH in the first place (aside from the fact that I had free access to Unix workstations and NO FUNDS to buy commercial software) was that there is no such thing as a package that does everything. GCG does some things better than most other packages, some things less well, and many things not at all. The same will be true of DNAsis, GeneWorks, the Staden programs, or any single package. No one package does everything, and certainly none do everything well. BIRCH is nothing more than a hierarchical directory structure of databases, programs, and documentation. The beauty of GDE is that it is trivial to add new programs to the menus. If you tie yourself to a single commercial package, you have only the capabilities that the authors build into it, and have to interconvert file formats when you want to use programs from elsewhere. On a system such as BIRCH, we can mix and match programs from many sources, letting GDE take care of converting file formats for us. At the same time, all of the programs from the various packages (eg. FASTA, XYLEM, FSAP, PHYLIP, MBCRR, Oxford, etc.) are still useable as standalone programs, if desired. =============================================================================== Brian Fristensky | Department of Plant Science | A question is like a knife that slices University of Manitoba | through the stage backdrop and gives us Winnipeg, MB R3T 2N2 CANADA | a look at what lies hidden behind. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Milan Kundera, THE UNBEARABLE LIGHTNESS FAX: 204-261-5732 | OF BEING =============================================================================== From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!Germany.EU.net!news.dfn.de!zeus.rbi.informatik.uni-frankfurt.de!jurpool0.rz.uni-frankfurt.de!brion.rz.uni-frankfurt.de!jui From: jui@brion.rz.uni-frankfurt.de (Uwe Harmening) Newsgroups: bionet.software Subject: Plant sociology Date: 7 Oct 1994 16:05:35 GMT Organization: University Frankfurt/M Lines: 25 Message-ID: <373rkf$iga@jurpool0.rz.uni-frankfurt.de> NNTP-Posting-Host: brion.rz.uni-frankfurt.de X-Newsreader: Tin 1.1 PL4 Hello, i am looking for software to prepare tables in plant sociology. There are some products around which are not shareware. The ones i know do not have any database functionality. Do you know about some software that has this functionality and is able to produce at least raw tables out of the data? Or do you have any other experiences? Thanx in advance. -- cu Jui harmening@cellbiology.uni-frankfurt.d400.de AK Molekulare Zellbiologie Uwe Harmening Marie-Curie-Str.9 D-60438 Frankfurt Germany From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uunet!newsflash.concordia.ca!canopus.cc.umanitoba.ca!asimov!frist From: frist@ccu.umanitoba.ca (Brian Fristensky) Newsgroups: bionet.software Subject: Re: Can DNAsis replace GCG package? Or almo Date: 7 Oct 1994 14:19:36 GMT Organization: The Univeristy of Manitoba. Lines: 39 Distribution: world Message-ID: <373ldo$kjl@canopus.cc.umanitoba.ca> References: Reply-To: frist@ccu.umanitoba.ca NNTP-Posting-Host: asimov.cc.umanitoba.ca In article 0710941317180001@pc0519.ri.afrc.ac.uk, lawa@bbsrc.ac.uk (Andy Law (Big Nose)) writes: > In article <17047852A.A428ENDE@VM1.SARA.NL>, A428ENDE@VM1.SARA.NL wrote: > As to MacDNAsis being buggy, well I can't comment on that because I > haven't seen it, but I get the general impression that most of the > micro-based DNA analysis software is crappy, difficult to use and full of > bugs. I also get the feeling that so many scientists are so used to having > to fight with monolithic mainframe programs that they just accept whatever > lands in front of them on their PC and assume that it is just the way > things are. THAT MAKES ME MAD!!!! > ( Lawa @ bbsrc.ac.uk Big Nose in Edinburgh ) > --- Campaigning for usable software --- I think the pendulum has begun to swing the other way. I now use a Sun Unix system for virtually everything I do: word processing, mail, graphics, news, budget juggling, and oh yes , sequence analysis -- because these tasks are EASIER to do in the OpenWindows environment than on any personal computer system I've seen. With the increasingly central role of networks in many aspects of everyday work, Unix is beginning to look more and more attractive. When you look at the cost of buying, maintaining, upgrading, and (gasp) configuring a bunch of PC's for a large lab or department, you don't have to get to a very large number of units before it becomes cost- effective to buy a Unix server and X-terminals. Sun Microsystems has a slogan "The network IS the computer". I think this nicely sums up many of the reasons that centralized computing is an idea whose time has come - again. =============================================================================== Brian Fristensky | Department of Plant Science | A question is like a knife that slices University of Manitoba | through the stage backdrop and gives us Winnipeg, MB R3T 2N2 CANADA | a look at what lies hidden behind. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Milan Kundera, THE UNBEARABLE LIGHTNESS FAX: 204-261-5732 | OF BEING =============================================================================== From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!rutgers!uwm.edu!news.alpha.net!MathWorks.Com!news.duke.edu!news-feed-1.peachnet.edu!darwin.sura.net!guvax.acc.georgetown.edu!guvax.acc.georgetown.edu!nntp Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: MEDLINE on-line for a fee? Message-ID: <1994Oct7.183227.13098@guvax> From: dan@biochem1.basic-sci.georgetown.edu Date: 7 Oct 94 18:32:27 -0500 References: Distribution: World,world Organization: Georgetown University Nntp-Posting-Host: dan.basic-sci.georgetown.edu Lines: 15 Xref: biosci bionet.software:9572 comp.sys.mac.scitech:2460 In article m3047@halcyon.com (Fred Morris) writes: >I would really love to hear from a company that is providing MEDLINE access >over the internet; for a fee is fine. If it's searchable with WAIS, >great; if it's searchable with AppleSearch, even better. > >-- > >Fred Morris VAX/VMS, Macintosh, distributed/remote computing guru >m3047@halcyon.com > Why not use grateful med from medlars/nlm? From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!nwnexus!news.halcyon.com!blv-pm0-ip14.halcyon.com!user From: m3047@halcyon.com (Fred Morris) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: MEDLINE on-line for a fee? Followup-To: bionet.software,comp.sys.mac.scitech Date: 7 Oct 1994 19:59:55 GMT Organization: VAX/VMS and Macintosh guru Lines: 8 Distribution: usa Message-ID: NNTP-Posting-Host: blv-pm0-ip14.halcyon.com Xref: biosci bionet.software:9571 comp.sys.mac.scitech:2459 I would really love to hear from a company that is providing MEDLINE access over the internet; for a fee is fine. If it's searchable with WAIS, great; if it's searchable with AppleSearch, even better. -- Fred Morris VAX/VMS, Macintosh, distributed/remote computing guru m3047@halcyon.com From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!guvax.acc.georgetown.edu!guvax.acc.georgetown.edu!nntp Newsgroups: bionet.software Subject: NIH R01 grant forms Message-ID: <1994Oct7.114704.13051@guvax> From: dan@biochem1.basic-sci.georgetown.edu Date: 7 Oct 94 11:47:04 -0500 Reply-To: dan@biochem1.basic-sci.georgetown.edu Distribution: World,world Organization: Georgetown University Keywords: NIH R01 Grant forms Nntp-Posting-Host: dan.basic-sci.georgetown.edu Lines: 1 From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!festival!news From: ajharmar@castle.ed.ac.uk (Tony Harmar) Subject: gene construction kit Message-ID: X-Posted-From: InterNews 1.0.4@bmu13.bmu.mrc.ac.uk Sender: -Not-Authenticated-[4674] Organization: MRC Brain Metabolism Unit Xdisclaimer: No attempt was made to authenticate the sender's name. Date: Fri, 7 Oct 1994 10:08:33 GMT Lines: 5 I am trying to find an e-mail address for Textco, the publishers of gene Contruction Kit and DNA Inspector, or for Bob Gross, the author Help much appreciated From owner-software@net.bio.net Thu Oct 06 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.lth.se!news.lu.se!bosse-q840.wblab.lu.se!Bo.Servenius From: Bo Servenius Subject: RAID for DNA databases??? Message-ID: <1994Oct7.160611.7610@nomina.lu.se> X-Xxmessage-Id: X-Xxdate: Fri, 7 Oct 94 17:06:45 GMT Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: bosse-q840.wblab.lu.se Organization: Lund university, Sweden X-Useragent: Version 1.1.3 Date: Fri, 7 Oct 1994 16:06:11 GMT Lines: 21 Dear Netters! I am considering to buy a SPARCstorage Array 100 for my Sun Sparcstation10-54 system. I am running gcg backage and the standard databases as EMBL and Swissprot. However I foresee that these databases and other db I would like to install will fill up my disks within some few month and think that a disk array would be the final solution to the ratrace inbetween my disks and the db. I have no experience of the technic nor the RAID concepts. For example how will the different RAID levels influence the performance of db I/O for our applications. Any comments or tips would be very much appreciated. yours BOSSE From owner-software@net.bio.net Fri Oct 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!pipex!uunet!powergrid.electriciti.com!usenet From: cdhoover@powergrid.electriciti.com (Christopher Hoover) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Promega on the Internet Date: 7 Oct 1994 23:57:17 GMT Organization: ElectriCiti Lines: 31 Sender: -Not-Authenticated-[5183] Distribution: world Message-ID: <374n8t$mc@powergrid.electriciti.com> References: <5OCT199423082068@aardvark.ucs.uoknor.edu> <371596INNhbt@sat.ipp-garching.mpg.de> NNTP-Posting-Host: slip30.electriciti.com X-Posted-From: InterNews 1.0.1@slip30.electriciti.com Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.molbio.methds-reagnts:19386 bionet.software:9575 To make it easier for researchers to access technical information regarding Invitrogen products, we have recently set up Internet Anonymous FTP and Gopher sites. Invitrogen Gopher/FTP sites contain: * Invitrogen vector sequences and resrtriction analyses * Product Manuals for use with common word processing programs * Citations for Invitrogen expression systems, vectors and isolation kits * Information on new products * E-mail addresses for Invitrogen personnel To access our Gopher site, connect to Ògopher.electriciti.comÓ and click on the Invitrogen folder. For anonymous FTP, connect with the following parameters: Host: ftp.electriciti.com User ID: anonymous Password: enter your e-mail address here Directory: /invitrogen We look forward to your comments and suggestions. For questions, please contact: Christopher Hoover Technical Service Invitrogen Corp 800-955-6288 ext. 217 619-597-6217 Fax cdhoover@electriciti.com From owner-software@net.bio.net Fri Oct 07 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!ihnp4.ucsd.edu!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!olivea!sgigate.sgi.com!enews.sgi.com!decwrl!netcomsv!ix.netcom.com!netcom.com!weix From: weix@netcom.com (Patrick Weix) Subject: Re: Can DNAsis replace GCG package? Or almost?? Message-ID: Organization: NETCOM On-line Communication Services (408 261-4700 guest) References: <36vkk9$gtq@mace.cc.purdue.edu> <17047852A.A428ENDE@VM1.SARA.NL> Date: Sat, 8 Oct 1994 00:29:38 GMT Lines: 14 This may sound stupid, but it all depends on the type of work that you do. If you are doing multiple sequence alignments, you probably need some sort of mainframe. If you just need to edit sequences for publication, then try some of the academic freeware on fly.bio.indiana.edu or others. Just my 1/50 of a dollar, Patrick -- "The large print giveth, and the small print taketh away." Tom Waits /------------------------------------------------------------\ | Patrick Weix weix@netcom.com | | UT Southwestern Medical Center weix@utsw.swmed.edu | | 5323 Harry Hines Blvd tel: (214) 648-5050 | | Dallas, TX 75235 fax: (214) 648-5453 | \------------------------------------------------------------/ From owner-software@net.bio.net Fri Oct 07 23:00:00 1994 Path: biosci!agate!msuinfo!netnews.upenn.edu!gopher.cs.uofs.edu!jaguar.uofs.edu!cannon From: