From owner-software@net.bio.net Sat Jun 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news-e2a.gnn.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: rmeader726@aol.com (RMeader726) Newsgroups: bionet.software Subject: Dr Meader's mailing list Date: 1 Jun 1996 23:28:59 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 8 Sender: root@newsbf02.news.aol.com Message-ID: <4or1pr$i27@newsbf02.news.aol.com> Reply-To: rmeader726@aol.com (RMeader726) NNTP-Posting-Host: newsbf02.mail.aol.com Doctors/Nurses/Pas/Students, Remind4 medical diagnosis software has been renamed DiagnosisPro. Email me for details/info and reprint of review article on Remind4 that appeared in Medical Software Reviews Journal, July 1995. Charles Meader, MD at 'Cmeader@mv.mv.com' or 'Rmeader726@aol.com' We now have a home page as well: http://home.aol.com/Rmeader726 Get on our mailing list....no strings. From owner-software@net.bio.net Sat Jun 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!iol!usenet From: tynan@iol.ie Newsgroups: bionet.software Subject: Ms Word6 Date: Sun, 02 Jun 1996 16:31:04 GMT Organization: Ireland On-Line Lines: 4 Message-ID: <4osfqp$9gt@nuacht.iol.ie> NNTP-Posting-Host: dialup-021.portlaoise.iol.ie X-Newsreader: Forte Free Agent 1.0.82 Anyone out there know where I can find Tutorials Microsoft Word on the net, Please E-Mail me at tynan@iol.ie From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!howland.reston.ans.net!Germany.EU.net!Dortmund.Germany.EU.net!gsf.de!news From: Kornelie Frech Newsgroups: bionet.software Subject: Announcing CoreSearch Release 1.2 Date: Mon, 03 Jun 1996 10:33:47 +0200 Organization: GSF-Forschungszentrum Lines: 28 Message-ID: <31B2A36B.41C6@gsf.de> NNTP-Posting-Host: orion.gsf.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; OSF1 V3.0 alpha) We would like to announce the availability of CoreSearch Release 1.2 for UNIX. CoreSearch is available as source code for UNIX at ftp://ariane.gsf.de/pub/unix/ or http://www.gsf.de/biodv/ CoreSearch is used to identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences. CoreSearch creates the same consensus descriptions as the program ConsInd, so that the program ConsInspector (which is also available at this site) can be used to scan new sequences for matches to the detected binding site. CoreSearch supresses elements already identified in the sequences. Therefore multiple independent elements can be detected in successive program runs using the sequence file created in the previous run. The method is described in Wolfertstetter,F., Frech,K., Herrmann,G., Werner,T. Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm Comp. Appl. Biosci. 12, 71-80 (1996). From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!AUG.UKL.UNI-FREIBURG.DE!kulmburg From: kulmburg@AUG.UKL.UNI-FREIBURG.DE (Peter Kulmburg) Newsgroups: bionet.software Subject: Video from microscope to Mac Date: 3 Jun 1996 01:03:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear collegues, I am using videoshop 3.0.2.D on a power PC 7500 with sytem D1-7.5.2. to take shots of my cells when moving towards a cytokine source. Unfortunately, the cells migrate very slowly and I would like to take a photo only every minute or so. However, I am not able to do slow motion movies below 1 picture per second. If I try it, the program cancels with error #4. To run it proper again I have to discharge the preferences in the system folder. The apple dealer and the avid-hotline were unable to help me. Is there anybody who has a solution for this problem or knows a program suitable for my experiments? Thank you for your help Peter Peter KULMBURG at home Tel./Fax:+49 761 80 84 39 at work: Tel.: +49 761 270/7208 or 7207 Fax: /7217 From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: kulmburg@aug.ukl.uni-freiburg.de (Peter Kulmburg) Newsgroups: bionet.software Subject: Video from microscope to Mac Date: 3 Jun 1996 10:24:24 +0100 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4oub08$sc4@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk Dear collegues, I am using videoshop 3.0.2.D on a power PC 7500 with sytem D1-7.5.2. to take shots of my cells when moving towards a cytokine source. Unfortunately, the cells migrate very slowly and I would like to take a photo only every minute or so. However, I am not able to do slow motion movies below 1 picture per second. If I try it, the program cancels with error #4. To run it proper again I have to discharge the preferences in the system folder. The apple dealer and the avid-hotline were unable to help me. Is there anybody who has a solution for this problem or knows a program suitable for my experiments? Thank you for your help Peter Peter KULMBURG at home Tel./Fax:+49 761 80 84 39 at work: Tel.: +49 761 270/7208 or 7207 Fax: /7217 From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.vub.ac.be!usenet From: FAHMY Thierry Newsgroups: bionet.software Subject: xlSTAT, a data analysis toolbox for Excel Date: Mon, 03 Jun 1996 16:30:17 -0700 Organization: Brussels Free Universities VUB/ULB Lines: 17 Message-ID: <31B37589.17F@ulb.ac.be> NNTP-Posting-Host: gmma-pc6.ulb.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win95; I; 16bit) Dear bionet readers, xlSTAT version 2.0 is now available. xlSTAT is a powerful and easy to use data analysis toolbox for Excel (5.0/7.0 - PC/Mac). Many tools available; for the regression tool, an automatic interpretation is done. Any information on xlSTAT can be found at the following address : http://seine.inapg.inra.fr/~fahmy Current price is 95$. Best regards, Thierry FAHMY, xlSTAT author From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news.ox.ac.uk!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!news.cc.ic.ac.uk!cb-11.sm.ic.ac.uk!user From: b.robertson@ic.ac.uk (Brian Robertson) Newsgroups: bionet.software,bionet.software.gcg,bionet.software.staden Subject: Software to extract annotation fields from EMBL/GenBank entries. Date: Mon, 03 Jun 1996 14:09:53 +0100 Organization: Imperial College School of Medicine at St. Mary's, London, U.K. Lines: 39 Message-ID: NNTP-Posting-Host: cb-11.sm.ic.ac.uk Xref: biosci bionet.software:15675 bionet.software.gcg:1825 bionet.software.staden:195 The amount of bacterial genome data available as sequenced cosmids of 30-40 kb is increasing rapidly. Our problem is that we need to keep track of newly discovered genes as they appear, so they can be incorporated into our research program as appropriate. For this we need to create lists of probable genes identified in the annotations for each cosmid. This can then be circulated to laboratory workers. An example of this kind of annotation is shown below. We would like to extract the "/note" field, which contains the probable function of the gene, and create a list of these for each cosmid. FT CDS_pept complement(3043..4155) FT /note="MTCY190.03c, probable anthranilate FT phosphoribosyltransferase, trpD, len: 370, similar to eg FT SW:TRPD_LACCA P17170, (43.2% identity in 308 aa overlap), FT initiation codon uncertain, gtg at 4086 favoured by FT homology but this has no clear ribosome binding site" Does anyone know of a way of extracting this information from database entries and creating a list? Is there any software avaialable that has this as one of its options, or would a shell script be needed? If a shell script is required, can anyone help with writing one? I'm afraid it's beyond my capabilities..... Thanks for your help. Brian Robertson -- Dr. Brian D. Robertson Dept. Medical Microbiology Imperial College School of Medicine at St Mary's Norfolk Place London W2 1PG, U.K. b.robertson@ic.ac.uk From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!chi-news.cic.net!nntp.coast.net!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.rediris.es!news.cica.es!obelix.cica.es!not-for-mail From: claros@obelix.cica.es (Manuel G. CLAROS) Newsgroups: bionet.software Subject: Re: Protein secondary structure analysis Date: 3 Jun 1996 12:30:09 GMT Organization: Universidad de Malaga y el CICA por su apoyo Lines: 13 Message-ID: <4oulsh$7ol@erika.cica.es> References: <4oi0p7$i6d@ccshst05.uoguelph.ca> NNTP-Posting-Host: obelix.cica.es Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8895-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Desde un rincon del alma, Yeyan Zhang nos confiesa: > a/beta sheets or hydrophobic clusture analysis. Are there any programs ^^^^^^^^^^^ Try TopPred II. You can find it at ftp.ens.fr/pub/molbio or at ftp.ebi.ac.uk/pub/software/mac or at the stanford ftp site. -- Manuel G. CLAROS -. .-. .-. .-. . -> claros@cica.es <- Biologia Molecular ||X|||\ /|||X|||\ /| No quiero cambiar, no puedo, Facultad Ciencias |/ \|||X|||/ \|||X|| no quiero ser una frase mas. E-29071 Malaga ' `-' `-' `-' `- (Esclarecidos) From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!newsxfer2.itd.umich.edu!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!news.imag.fr!ciril.fr!usenet From: Frederic Plewniak Newsgroups: bionet.software Subject: DBWatcher (was 'MINORE: Anyone gotten this to work?') Date: Mon, 03 Jun 1996 14:56:26 +0200 Organization: IGBMC Lines: 164 Message-ID: <31B2E0FA.6B64@igbmc.u-strasbg.fr> References: <4opt23$ke7@nntp1.best.com> NNTP-Posting-Host: didon.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.5 sun4m) Greg wrote: > > Question: has anyone modified this program to run on Solaris (or even Irix > for that matter). It seems like a really useful idea which I could > find immediate use for. Alternatively, is there a similar publicly > available service running on the 'net somewhere? > It is not exactly what MINORE does but I have just written a C program running on Solaris (DBWatcher 1.00) which does something similar with local databases. I am still documenting it but you can already dowload the current pre-release version : ftp://ftp-igbmc.u-strasbg.fr/pub/DBWatcher/dbwatcher.tar.Z Current features include : 1) Performs BLAST searches and keeps track of previous searches to report **only novel similarities** 2) Checks for database updates, sequence modification, settings changes and performs searches **only when necessary** 3) Searches are arranged in jobs and results for each job are sent to **one or several** e-mail addresses. DBWatcher comes with a companion program, SetDBWatcher, which provides an X Graphical User Interface for managing the jobs. (SetDBWatcher requires the NCBI ToolKit for compilation.) FYI, here is a first draft of the README.DBWatcher file : ################################################################################ DBWatcher version 1.0 for Sun/Solaris (May 1996) ################################################################################ Frederic PLEWNIAK Plewniak@igbmc.u-strasbg.fr CNRS - LGME 6520 IGBMC - Strasbourg, France -------------------------------------------------------------------------------- DBwatcher is a program handling periodic BLAST searches to find similarities to your own sequences. It keeps track of the previous searches and only performs new ones when necessary (i.e. when the database has been updated, the sequence has been modified, or when settings have been changed). Only novel similarities are reported, thus saving the time of browsing through bulky result files. When executed daily (as a cron job) it ensures that you are informed as soon as new sequences similar to yours are incorporated into a given database. This is most valuable in association with an automatic database update procedure. Results are sent by electronic mail to one or several addresses making DBWatcher particularly suitable for collaborative database survey as well as for users who do not have access to locally maintained databases. -------------------------------------------------------------------------------- REQUIREMENTS ================================================================================ DBWAtcher requires a working version of the BLAST programs which can be obtained from ncbi.nlm.nih.gov anonymous ftp site in the /blast directory. Alternatively, DBWatcher can use the GCG versions of the BLAST programs. The following environment variables should be set to their appropriate value for both regular and GCG versions : $BLASTDB : Directory containing the BLAST databases $BLASTMAT : Directory containing the BLAST comparison matrices $BLASTFILTER : Directory containing the seg and xnu filter programs For more information concerning BLAST programs, please consult the BLAST help at http://www.ncbi.nlm.nih.gov/BLAST/blast_help.html or the BLAST documentation in the GCG Program Manual. This version has only been tested with GCG BLAST programs on Sun/Solaris 2.5 but it should be portable to other Unix boxes. Binaries are provided for Sun/Solaris 2.5. Of course, these requirements are only for the site actually running the BLAST programs and DBWatcher. Remote sites only need an e-mail box to receive results. -------------------------------------------------------------------------------- SETTING UP JOBS ================================================================================ DBWatcher jobs can be created manually or with the SetDBWatcher GUI if you have access to X/Motif libraries. SetDBWatcher takes care of everything including available programs and databases so you don't have to worry too much about creating and managing your jobs. Here are some instructions though, just in case you might want to do things by hand or develop your own way of setting up jobs. Jobs are stored in the DBWatcher Home Directory as follows : DBWatcher Home Directory | ---------------------------------- ... | | user1 user2 | | --------------------------- | | | | Job1 anotherjob Myjob | | | ----------------- ---------------- ---------------- | | | | | | | | | | | | config seqs log tmp config seqs log tmp config seqs log tmp | | | | | | | | | ---- ---- ---- | | | ---- ---- ---- | | | | | | | | | | | | | | | s1 s2 s1 s2 s1 s2 myseq myseq myseq sX sY sX sY sX sY Directories user1, user2, etc should be named after the username of the user who will be responsible for running DBWatcher. There might be any number of job directories in users' directories, having any valid UNIX directory name. In each job directory there should be the following : config : config file seqs/ : sequences directory log/ : log directory used to keep track of previous searches files in this directory are created automatically. tmp/ : directory used to store the last results files in this directory are created automatically. Sequences in the seqs/ directory should be in FastA (Pearson) format. The config file should have the following format : - 1st line : Job name (any character accepted) - 2nd line : Blast program name - 3rd line : Database name - 4th line : Extra parameters - 5th line : P(N) threshold above which results are not reported - 6th line : e-mail addresses to send the results -----------------Example of config file---------------------------------------- Job Name gcg_blastn gbnew V=250 B=250 -filter seg 1e-3 John.Smith@institute.dom.xx Anyone@anywhere.xx -----------------End of example------------------------------------------------ Best regards, Fred Frederic PLEWNIAK Plewniak@igbmc.u-strasbg.fr CNRS - LGME 6520 IGBMC - Strasbourg, France From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Newsgroups: bionet.software Path: biosci!rutgers!uwm.edu!chi-news.cic.net!nntp.coast.net!swidir.switch.ch!scsing.switch.ch!news.rccn.net!ciup2.ncc.up.pt!news.uminho.pt!news.ci.uminho.pt!not-for-mail From: Antonio Jose Subject: Amiga Emulator For P.C. Message-ID: <31B2CFD2.487E@ci.uminho.pt> Date: Mon, 03 Jun 1996 13:43:14 +0200 X-Mailer: Mozilla 2.0 (WinNT; I) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 4 Hi ! I'm looking for an Amiga emulator for P.C.. If you know a U.R.L. or F.T.P. site where I can find it, please e-mail me. Thanks . Toze. Si21001@ci.uminho.pt From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: "Michael D. Baron" Newsgroups: bionet.software Subject: Re: 'Pretty box' or alike software? Date: Mon, 03 Jun 1996 10:38:15 -0700 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 22 Message-ID: <31B32307.69DC@bbsrc.ac.uk> References: <4okbn7$rec@mserv1.dl.ac.uk> NNTP-Posting-Host: pc0258.avri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Gilles VACHON wrote: > > Hi all, > > I am trying to make nice alignments of two protein sequences for the first t= > ime. > I realize we don't have a software to make boxes etc... > Someone told me Pretty box is useful to do the job. > Is it available ot is there a similar program to nicely align seuences? Gilles, do you want to *align* the two sequences,or display an existing alignment? If the former, PRETTYBOX, PRETTYPLOT, BOXSHADE, ALSCRIPT etc. will not help, as they all display preexisting multiple alignments. You need a program to compute the optimum alignment of the two sequences. I use the GCG programs GAP or BESTFIT for this, I haven't used any non-GCG programs. If you just want to display, PRETTYPLOT and PRETTYBOX are part of the EGCG package, I think. The others are available from various FTP sites, look at recent messages in this group. best of luck, Michael D. Baron michael.baron@bbsrc.ac.uk From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!wizard.pn.com!news1.channel1.com!news.channel1.com!channel1!harold.drabkin Distribution: world Newsgroups: bionet.software Subject: SOFTWARE IN SPANISG LANGU From: harold.drabkin@channel1.com (Harold Drabkin) Message-ID: <40.5726.3162@channel1.com> References: <4oekin$5if@newsbf02.news.aol.com> Date: Mon, 03 Jun 1996 19:18:00 -0640 Organization: Channel 1(R) 617-864-0100 Info Lines: 18 Subject: SOFTWARE IN SPANISG LANGUAGE E> E E>I'm looking for software in spanish language to export to E>southAmerica.Educational Technical, financial,games and more. E>Please send info to EDI95@aol.com I just saw something in MicroCenter (they're a chain of computer stores; the one I saw it is is in Cambridge) that you might be interested in. Can't remember the name, but what it does is translates all Windows menu items, etc. into any one of several languages on the fly. --- * OLXWin 1.00 * Cross river *THEN* insult alligator. From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Bernhard Pflesser Newsgroups: bionet.software,bionet.biology.cardiovascular,bionet.diagnostics,bionet.general,bionet.neuroscience Subject: VBC96--CALL FOR PARTICIPATION Date: 3 Jun 1996 11:12:15 -0700 Organization: University Hospital Eppendorf / Hamburg Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:15680 bionet.biology.cardiovascular:1012 bionet.diagnostics:848 bionet.general:21973 bionet.neuroscience:14413 -------------------------------------------------------------------- Fourth International Conference on VISUALIZATION IN BIOMEDICAL COMPUTING Sept. 22 - Sept. 25, 1996 Hamburg, Germany -------------------------------------------------------------------- CALL FOR PARTICIPATION The "Call for Participation" of VBC'96 is now available! Please visit our WWW-Page to find detailed information about the preliminary program, registration, social events and more: =================================== http://www.uke.uni-hamburg.de/vbc96 =================================== or contact us via: Institute of Mathematics and Computer Science in Medicine (IMDM) Department of Computer Science in Medicine Pav. 70 University Hospital Eppendorf Martinistrasse 52 D-20246 Hamburg Germany Phone : +49-40-4717 3652 Fax : +49-40-4717 4882 E-mail: vbc96@uke.uni-hamburg.de -------------------------------------------------------------------- Scope Following Georgia Tech, the University of North Carolina, and the Mayo Institutions, the University of Hamburg will host the 4th conference on Visualization in Biomedical Computing (VBC'96). Its goal is to enhance and promote the science of computer based visualization of biomedical information, especially about the various aspects of the human body. An interdisciplinary, international group of scientists, engineers, and clinicians will present and discuss the state of the art concerning algorithms, the rapidly increasing number of applications, and the practical problems of system design. ------------------------------------------------------------------------ Topics Theory and Algorithms Applications Systems * Models of * Diagnostics with * Hardware/Software Visualization MRI, CT, PET/SPECT, Tools * Rendering Algorithms MEG Ultrasound etc. * Interactive * Image Analysis * Microscopy Imaging Workstations and * Multi-Modality Image * Surgical and Networks Registration and Stereotactic * Virtual Reality User Fusion Planning Interfaces * Shape Description * Surgery Simulation * Novel Image and Characterization * Image Guided Acquisition Equipment * Spatial Knowledge Surgery * Special Processors Modeling * Endoscopy * Artificial Simulation Intelligence in * Radiation Visualization Treatment Planning * Visual Perception * Biomechanics and and Communication Orthopedics * Virtual / Augmented * Dentistry and Reality Paradigms Orthodontics * Prothetics Development * Modeling the human body (with emphasis on the brain) * Anatomy Atlases (with emphasis on VISIBLE HUMAN) * Medical and Biological Education ------------------------------------------------------------------------ Format According to the interdisciplinary nature of the conference, it has a single track of sessions with 25 minute papers. Posters and demonstrations will be located next to the auditorium. Tutorials will be held the day before the official opening (Sept. 22) as in the previous meetings. ------------------------------------------------------------------------ Proceedings Proceedings will be published in Lecture Notes in Computer Science, Springer Verlag Heidelberg-New York. They will be available at the time of the conference. ------------------------------------------------------------------------ Visits Visits to laboratories in Hamburg will be arranged for the day after the conference (IMDM, Philips Research, Dept. of Computer Science) ------------------------------------------------------------------------ Location University of Hamburg, main building, in walking distance to the city which surrounds the beautiful Alster lake. ------------------------------------------------------------------------ Previous Conferences 1990 Georgia Institute of Technology, Atlanta, GA Proceedings: First Conference on Visualization in Biomedical Computing, IEEE Computer Society Press, 1990 1992 University of North Carolina, Chapel Hill, NC Proceedings: Visualization in Biomedical Computing II, Proc. SPIE 1808, 1992 1994 Mayo Foundation, Rochester, MN Proceedings: Visualization in Biomedical Computing 1994, Proc. SPIE 2359, 1994 ------------------------------------------------------------------------ Conference Committee Chairman Karl Heinz Hoehne, University of Hamburg Program Committee Ron Kikinis (Chair), Harvard Medical School Nicholas Ayache, INRIA, Sophia-Antipolis Jean Louis Coatrieux, University of Rennes Takeyoshi Dohi, University of Tokyo James Duncan, Yale University Alan C. Evans, Montreal Neurological Inst. Norberto Ezquerra, Georgia Tech, Atlanta Henry Fuchs, UNC, Chapel Hill Guido Gerig, ETH Zuerich Eric Grimson, MIT, Cambridge David Hawkes, Guy's Hospital London Arie Kaufman, State University of New York Andres Kriete, University of Giessen Hal Kundel, University of Pennsylvania Heinz Lemke, Free University of Berlin David Levin, University of Chicago Heinrich Mueller, University of Dortmund Chuck Pelizzari, University of Chicago Stephen Pizer, UNC, Chapel Hill Richard Robb, Mayo Foundation / Clinic Siegfried Stiehl, University of Hamburg Paul Suetens, University of Leuven Andrew Todd-Pokropek, University College London Jun-Ichiro Toriwaki, Nagoya University Michael Vannier, Washington University, St Louis Max Viergever, Utrecht University Coordinators Bernhard Pflesser, Thomas Schiemann, Rainer Schubert, IMDM ------------------------------------------------------------------------ Supporting Organisations University of Hamburg The Institute of Electrical and Electronics Engineers (IEEE) German Society of Computer Science (GI) German Society of Medical Informatics, Biometrics, and Epidemiology (GMDS) e.V. ------------------------------------------------------------------------ From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software,bionet.software.gcg,bionet.software.staden,bionet.software.srs Subject: Re: Software to extract annotation fields from EMBL/GenBank entries. Date: 03 Jun 1996 15:49:48 GMT Organization: The Sanger Centre Lines: 68 Message-ID: References: NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: b.robertson@ic.ac.uk's message of Mon, 03 Jun 1996 14:09:53 +0100 Xref: biosci bionet.software:15679 bionet.software.gcg:1826 bionet.software.staden:196 bionet.software.srs:260 In article b.robertson@ic.ac.uk (Brian Robertson) writes: > The amount of bacterial genome data available as sequenced cosmids of > 30-40 kb is increasing rapidly. Our problem is that we need to keep track > of newly discovered genes as they appear, so they can be incorporated into > our research program as appropriate. For this we need to create lists of > probable genes identified in the annotations for each cosmid. This can > then be circulated to laboratory workers. > > An example of this kind of annotation is shown below. We would like to > extract the "/note" field, which contains the probable function of the > gene, and create a list of these for each cosmid. >FT CDS_pept complement(3043..4155) >FT /note="MTCY190.03c, probable anthranilate >FT phosphoribosyltransferase, trpD, len: 370, similar to eg >FT SW:TRPD_LACCA P17170, (43.2% identity in 308 aa overlap), >FT initiation codon uncertain, gtg at 4086 favoured by >FT homology but this has no clear ribosome binding site" Clearly a job for SRS and ICARUS. Try the bionet.software.srs newsgroup (this message is crossposted there) ... But beware - these fields are often describing homologies rather than confirmed functional assignments (how firm the assignments are depends from project to project). Also, different projects will use different methods for formatting the initial annotation. There is as yet no consensus on how the data should be presented. Then again, you also need to keep up with changes to the entries in case the annotation includes a new homology, or the predicted gene changes (splice sites in eukaryotes, or the gtg alternative start codon in the example you used) >If a shell script is required, can anyone help with writing one? I'm >afraid it's beyond my capabilities..... Sadly, it's a little more complicated than that :-) What SRS can do is extract the features of interest for new/changed entries, for a given organism, since the last run. Something like: % getz "([emnew-org:Mycobacterium tuberculosis] & \ [emnew-dat#19960500:])" \ -f 'id acc dat def fts' >! mtcds.may96 ... which takes only a second or two to run. You can also do the same query through any of the SRSWWW servers (it will work on EMNEW or on GBNEW, updates for EMBL or GenBank). ICARUS in turn can be used to parse out the feature table fields of interest, assuming that all entries have some common format (in this case, all orf names start MTC but you could also look for "/gene=" to pick other entries). ICARUS is due sometime soon (in SRS 5). Meanwhile, other languages like Perl can do the job, although they are a little more complicated to write. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!newsfeed.internetmci.com!in1.uu.net!interaccess!d202.tp.interaccess.com!pesto From: pesto@interaccess.com (fuzzy logic) Newsgroups: bionet.software Subject: re: softram-yuk! thanx all ;D Date: Mon, 3 Jun 1996 09:32:09 -0600 Organization: InterAccess,Chicagoland's Full Service Internet Provider Lines: 6 Message-ID: NNTP-Posting-Host: d202.tp.interaccess.com X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] To all that have offerred suggestions and excellent helping hands: Softram is off my system! I followed several ideas from you wonderful folks and my 'puter is happy again and working better than ever! Thanx again 'netizens! Fuzzy logic From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!nntp.coast.net!oleane!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.vub.ac.be!usenet From: FAHMY Thierry Newsgroups: bionet.software Subject: xlSTAT, a data analysis toolbox for Excel Date: Mon, 03 Jun 1996 16:40:19 -0700 Organization: Brussels Free Universities VUB/ULB Lines: 19 Message-ID: <31B377E3.3C53@ulb.ac.be> NNTP-Posting-Host: gmma-pc6.ulb.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win95; I; 16bit) Dear bionet.software readers, xlSTAT version 2.0 is now available. xlSTAT is a powerful and easy to use data analysis toolbox for Excel (5.0/7.0 - PC/Mac). Many tools are available (regression, PCA, classification, Discriminant analysis, ...); for the regression tool, an automatic interpretation is done. Any information on xlSTAT can be found at the following address : http://seine.inapg.inra.fr/~fahmy Current price is 95$. Best regards, Thierry FAHMY, xlSTAT author From owner-software@net.bio.net Sun Jun 02 23:00:00 1996 Path: biosci!AUG.UKL.UNI-FREIBURG.DE!kulmburg From: kulmburg@AUG.UKL.UNI-FREIBURG.DE (Peter Kulmburg) Newsgroups: bionet.software Subject: Video from microscope to Mac Date: 3 Jun 1996 01:33:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear collegues, I am using videoshop 3.0.2.D on a power PC 7500 with sytem D1-7.5.2. to take shots of my cells when moving towards a cytokine source. Unfortunately, the cells migrate very slowly and I would like to take a photo only every minute or so. However, I am not able to do slow motion movies below 1 picture per second. If I try it, the program cancels with error #4. To run it proper again I have to discharge the preferences in the system folder. The apple dealer and the avid-hotline were unable to help me. Is there anybody who has a solution for this problem or knows a program suitable for my experiments? Thank you for your help Peter Peter KULMBURG at home Tel./Fax:+49 761 80 84 39 at work: Tel.: +49 761 270/7208 or 7207 Fax: /7217 From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Newsgroups: bionet.software Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!Norway.EU.net!EU.net!newsfeed.internetmci.com!in2.uu.net!fox.almaden.ibm.com!garlic.com!news.scruz.net!cruzio.com!news From: rmiller@cruzio.com (Robert Miller) Subject: databases? Organization: Cruzio Community Networking System, Santa Cruz, CA Date: Tue, 4 Jun 1996 01:42:03 GMT Message-ID: X-Newsreader: Forte Free Agent 1.0.82 X-Nntp-Posting-Host: mbay89.cruzio.com Sender: news@cruzio.com (The News User) Lines: 7 I'm looking for some kind of database to use which crossreferences plants with enviroment,... soil, shade, sunny, bushes, trees, etc. ... If there is nothing out there to be had I will make a data base to do the job but , being lazy, and not wanting to look up all the different requirements for all the different plants to input into a database, ..... Any help in the right direction would be helpful. From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.math.psu.edu!news.cac.psu.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!swrinde!cssun.mathcs.emory.edu!hobbes.cc.uga.edu!news From: russell@dogwood.botany.uga.edu (Russell L. Malmberg) Newsgroups: bionet.software Subject: Compiled: Molphy / Protml.exe Win95/NT command line Date: 4 Jun 1996 12:57:24 GMT Organization: Botany Department, University of Georgia Lines: 22 Distribution: world Message-ID: <4p1brk$o5q@hobbes.cc.uga.edu> Reply-To: russell@dogwood.botany.uga.edu NNTP-Posting-Host: twopaths.botany.uga.edu X-Newsreader: News for Windows NT X1.0-90 for Intel CPU running Win95 or NT: ============= http://dogwood.botany.uga.edu/malmberg/software.html Molph22.intel.zip ============= I recently compiled the molecular phylogenetics (Molphy 2.2) programs of Adachi and Hasegawa. This includes the program Protml.exe, which computes phylogenetic trees from amino acid sequences based on maximum likelihood. On a pentium the program runs quite nicely. All credit is due to the authors. I just ran my compiler, and posted the results here. Russell ******************************** Russell L. Malmberg russell@dogwood.botany.uga.edu ******************************** From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!rebecca!rpi!bushnt From: bushnt@rebecca.its.rpi.edu (Timothy Paul Bushnell) Newsgroups: bionet.software Subject: PAUP 4.0 Release date? Date: 4 Jun 1996 02:47:04 GMT Organization: Rensselaer Polytechnic Institute Lines: 14 Message-ID: <4p0838$83m@usenet.rpi.edu> NNTP-Posting-Host: rebecca.its.rpi.edu Hello All. I am wondering if anyone has any information on PAUP 4.0 The last rumor I heard (a couple of months ago) was a June release, but I can't find the post or the address of teh distributor. If anyone has any information, I would appreciate it. Thanks in advance. Tim Bushnell Rensselaer Biology Department From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!01-newsfeed.univie.ac.at!newsfeed.ACO.net!embdec.bcc.univie.ac.at!usenet From: walter@gem.univie.ac.at (Glaser Walter) Newsgroups: bionet.software Subject: Help with MAPMAKER/EXP 3.0b needed Date: 4 Jun 1996 08:45:58 GMT Organization: Vienna University Computing Center Lines: 12 Message-ID: <4p0t46$5cc@embdec.bcc.univie.ac.at> NNTP-Posting-Host: 6105b.bcc.univie.ac.at Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 I am using the PC-Version MAPMAKER/EXP 3.0b (FTP from genome.wi.mit.edu mapm3pc1.exe mapm3pc2.exe ) When the Program starts the default linkage criteria are both set to zero and not to LOD 3.0 and 50cM as stated in the manual. When I try to change the zero values with 'default linakge criteria 3.0 80' the program reports: 'error illegal value' and refuses to change the values. Thanks for the help in advance Walter Glaser Inst. of Microbiol. and Genetics Vienna Biocenter E-mail: walter@gem.univie.ac.at From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!newsjunkie.ans.net!newsfeeds.ans.net!lantana.singnet.com.sg!nuscc.nus.sg!bemlab11 From: bemlab11@leonis.nus.sg (Ang Ah Sah Pearlyn) Newsgroups: bionet.software Subject: Money changer software Date: 4 Jun 1996 03:15:43 GMT Organization: National University of Singapore Lines: 2 Message-ID: <4p09ov$9d4@nuscc.nus.sg> NNTP-Posting-Host: bemlab11@leonis.nus.sg X-Newsreader: TIN [version 1.2 PL2] I am looking for a package of Money changer software, any advice would be appricated. From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!sgigate.sgi.com!nntp.coast.net!trellis.wwnet.com!news.inc.net!news.us.world.net!usenet From: andrewb@mail.paclink.com (Andrew Beames) Newsgroups: bionet.software Subject: Help with the opening of .DLL files Date: 4 Jun 1996 03:04:40 GMT Organization: None Lines: 6 Message-ID: <4p0948$44q@news.us.world.net> NNTP-Posting-Host: port9.paclink.com Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 I need some help opening .DLL files. I need them to open Doom95. If anyone could tell me how please do, it would make me very happy. Just tell me the program I need to open these files. Send your suggestions to Andrew Beames From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!swrinde!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!news.rhrz.uni-bonn.de!news.rwth-aachen.de!newsserver.rrzn.uni-hannover.de!tubsibr!rzlimes.gbf-braunschweig.de!news From: uka@gbf-braunschweig.de (Uwe Kaerst) Newsgroups: bionet.software Subject: RE: SOFTRAM! OUCH! Date: 4 Jun 1996 06:50:00 GMT Organization: GBF Lines: 35 Message-ID: <4p0mao$ar6@rzlimes.gbf-braunschweig.de> References: NNTP-Posting-Host: etnuka.gbf-braunschweig.de Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (beta 2) In article , pesto@interaccess.com says... > >Had Softram on my system took it off and now I get an error message >stating windows is looking for a device file to start up and then I get > c:\softram1.386 >I cannot get rid of this! I cannot go back into my windows setup because >of this freaking message! Anybody got any ideas besides formatting my >"c" drive? > If this is on the wrong ng, sorry! > Hi, I suggest you look in your system.ini file in the windows directory; there should be a line device=softram1.386, probalbly in the 386enhanced section. Just delete this line, save the file (use notepad or edit - it must be a plain text file) and try again. Hope this helps - I never tried softram Uwe -- Uwe Kaerst Dept. Enzymology GBF - Gesellschaft fuer Biotechnologische Forschung Mascheroder Weg 1 D-38124 Braunscheig, Germany Tel: +(49) 531 6181 318 Fax: +(49) 531 2612313 EMAIL: kaerst@gbf-braunschweig.de -- Disclaimer -- Standard > Keyword : Opinions, my own, nobody else's, no affiliation, whatsoever ... From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!nntp.uio.no!news.cais.net!newsfeed.internetmci.com!news.exodus.net!news1.best.com!nntp1.best.com!dawagner From: dawagner@nntp.best.com (David Wagner) Newsgroups: bionet.software Subject: Software Research Database (free) Date: 4 Jun 1996 21:35:01 GMT Organization: Best Internet Communications Lines: 19 Message-ID: <4p2a65$joi@nntp1.best.com> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Subject: Software Research Database (free) Please try the largest WWW site devoted to software developers and information technologists, inquiry.com. inquiry.com features Ask the Pro pages for Java, Web, Javascript, Visual Basic, C++, Delphi, VRML, Oracle Power Objects and more. Search our database of over 100,000+ published technical articles for free. Be sure to register for unlimited free access. From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!usenet.eel.ufl.edu!bofh.dot!tank.news.pipex.net!pipex!blackbush.xlink.net!news.fhg.de!marilyn.ita.fhg.de!user From: zakaria@ita.fhg.de (Hayssam Zakaria) Newsgroups: bionet.software Subject: Re: Video from microscope to Mac Date: Tue, 04 Jun 1996 09:30:57 +0100 Organization: Fraunhofer Institut Lines: 9 Distribution: world Message-ID: References: NNTP-Posting-Host: marilyn.ita.fhg.de error #4 is a division by zero, no idea what might cause that. But you could try NIH image. It has plug ins to use as a frame grabber as far as i know. Have a look at their page at http://rsb.info.nih.gov/nih-image. It's a great software package and it's for free ! Hayssam Zakaria FhG_IGB From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!gvls1!udel!cnn.Princeton.EDU!usenet From: Patrick McNutt Newsgroups: bionet.software Subject: Automation of Video and Force Tracings Date: Tue, 04 Jun 1996 11:49:17 -0400 Organization: Princeton University Lines: 11 Message-ID: <31B45AFD.56F7@phoenix.princeton.edu> NNTP-Posting-Host: solomon.princeton.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) Dear Colleagues, We are presently using a VCR with input from a b/w CCD and NIH image frame grabbing to measure physical deformation of a compressed aggregate of cells. Additionally we are using a Cahn Ventron balance attached to a chart recorder taking force measurements from parallel plates as compression is occuring. Does anyone know of software which could allow us to automate this- ie, a system that will take and chart input from a Cahn balance and also frame-grab at specific time points? Any thoughts on how to hook up an old Cahn balance without a computer link is also welcome. Thanks From owner-software@net.bio.net Mon Jun 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!caen!kuhub.cc.ukans.edu!kuhub.cc.ukans.edu!nntp Newsgroups: bionet.software Subject: Re: WWW sites for contig assembly or restriction enzyme mapping? Message-ID: <1996Jun4.153219.120785@kuhub.cc.ukans.edu> From: RNAworld@ (Dr. Peter Gegenheimer) Date: 4 Jun 96 15:32:19 CDT Reply-To: pgegen@kuhub.cc.ukans.edu (Dr. Peter Gegenheimer) References: Organization: UNiversity of Kansas, Dept. of Biochemistry Nntp-Posting-Host: rnaworld.bio.ukans.edu X-Newsreader: IBM NewsReader/2 v1.2.5 Lines: 11 In , mangalam@uci.edu (Harry Mangalam) writes: >In article , >"Rab A. Harper" wrote: > >Also, there are 2 other restriction enzyme analysis programs that might be >of interest. >1) Bruce Fristensky's 'intrest' and 'bachrest' programs @ > http://home.cc.umanitoba.ca/~psgendb/programs.html His name is Brian Fristensky. P. Gegenheimer/U Kansas, Biochem/pgegen@kuhub.cc.ukans.edu From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!in1.uu.net!newsfeed.pitt.edu!godot.cc.duq.edu!newsgate.duke.edu!raphael.acpub.duke.edu!nc1 From: Namjin Chung Newsgroups: bionet.software Subject: Re: Software on Mac Date: Wed, 5 Jun 1996 11:17:58 -0400 Organization: Duke University, Durham, NC, USA Lines: 27 Message-ID: References: NNTP-Posting-Host: raphael.acpub.duke.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: On 1 Jun 1996, S. Wang wrote: > > Suggestions wanted. We are looking for a comprehensive, user-friendly > DNA/Protein sequence analysis software, any suggestion would be highly > appreciated. Our major concerns are: performance on Macintosh; price; > and license to multi-user (four research groups, about 10 users). Thanks > in advance. > > Shaojiu Wang/Dept. of Entomology(Geneva)/Cornell Univ. > sw59@cornell.edu > Try MacVector. That's the best and easy-to-use sequence analysis software on Mac OS, as far as I know. Price is quite expensive; more than $2000. It's from Eastman Kodak, and you could try demo program from Sigma (~$5). Hope this helps. ************************************************************************* * | * * Namjin Chung | E-mail: nc1@acpub.duke.edu * * Duke University Medical Center | chung006@mc.duke.edu * * Box 3345 | Voice: +1 (919) 684-2363 * * Durham, NC 27710 | Fax: +1 (919) 681-8253 * * | * ************************************************************************* From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!nntp.earthlink.net!usenet From: finn@nasw.org (Robert Finn) Newsgroups: bionet.software,bionet.general Subject: Bibliographic software Date: Wed, 05 Jun 1996 15:55:47 GMT Organization: Earthlink Network, Inc. Lines: 15 Message-ID: <4p4ag2$keh@ecuador.it.earthlink.net> Reply-To: finn@nasw.org NNTP-Posting-Host: tsa-oc-20.earthlink.net X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.software:15700 bionet.general:22007 I'm writing an article for The Scientist on bibliographic software. I'm interested in interviewing several scientists who have experience with some of the most prominent commercial titles in this area . These include ProCite, Papyrus, EndNote, Reference Manager, Library Master, and Bookends. I wish to conduct telephone interviews over the next few days. Please respond by email to finn@nasw.org, with a sentence or two about yourself, your phone number, and the best times to reach you. Thank you. Robert Finn finn@nasw.org From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!nntp.coast.net!fu-berlin.de!zrz.TU-Berlin.DE!news.dfn.de!ikarus.rz.tu-clausthal.de!news From: coms@sun.rz.tu-clausthal.de (Martin Stoermer) Newsgroups: bionet.software Subject: Re: HTML Editor Date: Wed, 5 Jun 1996 13:17:17 -400 Organization: Institut für Organische Chemie Lines: 42 Distribution: world Message-ID: <4p3q8d$k7l@ikarus.rz.tu-clausthal.de> NNTP-Posting-Host: uhura.ioc.tu-clausthal.de Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-NewsReader: QNews v0.9b4 Beta 15 Apr 1994 Evaluation copy. In article <4omrj0$6k7@cwis-20.wayne.edu> dwomble@cmb.biosci.wayne.edu wrote: > This is an interesting question. What do other people who actually > maitain web sites use? Well I have built three and am currently maintaining one and a bit. I have to agree with you in that text editors are the way to go if you want to follow the Unix philosophy (i.e care about what the codes do and say). Hoopy WYSIWYG editors are good for those that don't want to learn HTML from scratch and would rather concentrate on the content (dare I say it, the Mac philosophy?). Internet Assistant for Word exports reasonably good HTML, but I always trim out the Word headers in a text editor afterwards. Plain old Editor if I happen to be unfortunate enough to be in front of a Dos box, BBEdit (In my opinion the absolute best text editor ever) if I'm on my Mac, and vi if I'm in a telnet session. Have only had a short play with Pagemill but it looks really good. Still pays to look at the codes 'though. Who knows when you'll have to dial in one day when you're on the road and fix a dead link, and only telnet is allowed. My optimum environment would be a Mac, with two clients, Netscape for all the fancy stuff, and MacWeb or Mosaic to make sure the HTML is pure. Bbedit with all its HTML extensions for the actual writing and a good graphics program like GraphicConverter or GifConverter, or Photoshop for scanning in photos. There are also good HTML table ditors, shareware and comm. but I haven't used them yet. I try to adhere to HTML 2.0 Cheers, -- Martin ************************************************************** Dr. Martin Stoermer Institut für Organische Chemie der Technischen Universität Clausthal D-38678 Clausthal-Zellerfeld email: coms@asterix.rz.tu-clausthal.de http://www.tu-clausthal.de/ioc/ ************************************************************** From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!cs.tu-berlin.de!uni-erlangen.de!news.tu-chemnitz.de!News.HTWM.De!news.HRZ.HAB-Weimar.DE!news.uni-jena.de!news.uni-leipzig.de!mlucom4.urz.uni-halle.de!newsmaster From: Ulf Reimer Newsgroups: bionet.software Subject: How to compare 3d Protein structures? Date: Wed, 05 Jun 1996 13:52:58 +0000 Organization: MPG AG"Enzymol. der Pept. Bindg." Lines: 14 Message-ID: <31B5913A.41C6@biochemtech.uni-halle.de> NNTP-Posting-Host: trans.biochemtech.uni-halle.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; IRIX 5.3 IP12) Dear Netters! Is there any program known which allows to compare 3D structure of different PDB Files? Thank you! Ulf -- | ulf@cis.biochemtech.uni-halle.de Ulf Reimer | Phone: +49 0345 5522819 | Fax: +49 0345 5511972 Kurt Mothes Str. 3 | Max Planck-Gesellschaft e.V. D-06120 Halle (Saale) | AG "Enzymologie der Peptidbindung" Germany From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!netnews.upenn.edu!dsinc!newsfeed.pitt.edu!scramble.lm.com!news.math.psu.edu!news.cac.psu.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!cdc2.cdc.net!news.texas.net!nntp.primenet.com!news.cais.net!news.abs.net!explorer.csc.com!uunet!in2.uu.net!news.u.washington.edu!tench.microbiol.washington.edu!user From: learn@u.washington.edu (Jerry Learn) Newsgroups: bionet.software Subject: Re: PAUP 4.0 Release date? Date: Tue, 04 Jun 1996 20:39:14 -0700 Organization: University of Washington Lines: 35 Message-ID: References: <4p0838$83m@usenet.rpi.edu> NNTP-Posting-Host: tench.microbiol.washington.edu X-Newsreader: Yet Another NewsWatcher 2.1.8 In article <4p0838$83m@usenet.rpi.edu>, bushnt@rebecca.its.rpi.edu (Timothy Paul Bushnell) wrote: > Hello All. > > I am wondering if anyone has any information on PAUP 4.0 > The last rumor I heard (a couple of months ago) was a June > release, but I can't find the post or the address of > teh distributor. > > If anyone has any information, I would appreciate it. > Timothy, I've never heard anything so solid as a June release date for PAUP 4.0 (aka PAUP*), only that it was expected sometime this summer. I have it on good authority that the software is still in pre-beta testing, so even this might be optimistic. The program will be distributed by Sinauer Associates; check out their WWW site at or send e-mail to . Like you, I'm eagerly looking forward to its release. _____ Jerry Learn Research Associate Dept. of Microbiology | Learn@u.washington.edu University of Washington | Phone: (206) 616-4286 Box 357740 | Seattle, WA 98195-7740 USA | FAX: (206) 616-1575 From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!netnews.upenn.edu!news.cc.swarthmore.edu!news.cse.psu.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!news From: pvharju@students.wisc.edu (peter harju) Newsgroups: bionet.software Subject: Help me, I need software Date: 5 Jun 1996 03:06:52 GMT Organization: UW-Madison Lines: 12 Message-ID: <4p2tkc$1u5e@news.doit.wisc.edu> NNTP-Posting-Host: f183-155.net.wisc.edu X-Newsreader: WinVN 0.99.5 Can you help me? I need to find out how I can get software at a reasonable price? However, I want to be certain that it is virus-free. Can anyone please help me? Also, I need to have the telephone numbers of the manufacturers of Excel, Lotus, MS Word, etc. Thank you, Bianca From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Newsgroups: bionet.software Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!nih-csl!postman From: bernard@elsie.nci.nih.gov (Bernard Murray) Subject: Re: How to compare 3d Protein structures? Message-ID: <1996Jun5.193615.2254@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: ermintrude.nci.nih.gov Organization: National Institutes of Health, Bethesda, MD X-Newsreader: WinVN 0.99.7 References: <31B5913A.41C6@biochemtech.uni-halle.de> Date: Wed, 5 Jun 1996 19:36:15 GMT Lines: 25 In article <31B5913A.41C6@biochemtech.uni-halle.de>, reimer@biochemtech.uni-halle.de says... > >Dear Netters! > >Is there any program known which allows to compare 3D structure of >different PDB Files? > >Thank you! If you are running unix then you can contact Andrew Martin at University College, London for a copy of ProFit. This will fit two PDB files and give RMS differences. I've used gcc to compile it for Linux, our Sun, an SG and a Convex and they all run it just nicely. Andrew prefers you to contact him directly as he wants to know who is actually using the program and keeps you informed of updates. Martin is martin@bsm.biochemistry.ucl.ac.uk Bernard Bernard Murray, Ph.D. bernard@elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA) "Accept the pain, Frank." - Dr. Forrester, MST3k (The Unearthly) From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!CSMC.EDU!NECHIPORUK From: NECHIPORUK@CSMC.EDU (ALEX NECHIPORUK/CSMC/TEL 310 855 7612) Newsgroups: bionet.software Subject: sequence assembly Date: 5 Jun 1996 11:08:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <01I5JM5JX4MA9AOJ02@CSMC.EDU> NNTP-Posting-Host: net.bio.net Dear Netters, I am sequencing a novel gene. We pulled multiple cDNAs from the libraries. After they fully sequenced I'll have to align all sequences together. Can anyone recommend a user friendly software (I prefer PC-DOS or Windows based) for multiple sequence fragment assembly. Thanks, Alex. From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!sgigate.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!warwick!leicester!usenet From: "Dr E. Buxbaum" Newsgroups: bionet.software Subject: Re: databases? Date: 5 Jun 1996 08:39:13 GMT Organization: University of Leicester, UK (PCFS User) Lines: 7 Message-ID: <4p3h3h$h3o@falcon.le.ac.uk> References: NNTP-Posting-Host: pc47.msb.le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) In Germany, Belgium and the Netherlands there is a school project running, were pupils list the plants growing on a place near their school and put the information into a data base on the Internet. This data base then calculates pointer values acording to ELLENBERG. There was a paper on this in the June issue of c't magazine. I can check the bibliographic details and the net sites if you are interested. From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!cdc2.cdc.net!newsfeed.concentric.net!news2.acs.oakland.edu!nntp.coast.net!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet From: "Luca Ida Giovanni TOLDO (Ph.D.)" Newsgroups: bionet.software Subject: Re: The Java Lattice Date: Wed, 05 Jun 1996 19:06:39 +0200 Organization: European Molecular Biology Laboratory Lines: 27 Distribution: world Message-ID: <31B5BE9E.CB1@embl-heidelberg.de> References: <31A5EE82.15FB@laue.biochem.ubc.ca> <4oel9j$di@merkurius.lu.se> Reply-To: toldo@embl-heidelberg.de NNTP-Posting-Host: toldo1.lt.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b3 (Macintosh; I; PPC) To: Bo Servenius Bo Servenius wrote: > > >"Java-based Molecular > >Biologists Workbench" which I am keeping up at > >http://www.embl-heideberg.de/~toldo/JaMBW.html > > sorry - this link does not work > > yours I am sorry, but I always miss the L in Heidelberg ... the address to the JaMBW page is http://www.embl-heidelberg.de/~toldo/JaMBW.html watch out, many mol bio applets are on it and more will appear soon.. news from a couple of days about a BIG bio-software Java project will be available from there ... contributions are open from everybody ! regards Dr. Luca Ida Giovanni TOLDO (Ph.D.) European Molecular Biology Laboratory Computer Group Heidelberg Germany From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!netnews.upenn.edu!dsinc!ub!newserve!news.cc.geneseo.edu!news From: john haynie Newsgroups: bionet.software Subject: Re: Video from microscope to Mac Date: Wed, 05 Jun 1996 12:16:35 -0400 Organization: SUNY Geneseo Lines: 131 Message-ID: <31B5B2E3.6676@uno.cc.geneseo.edu> References: <4oub08$sc4@mserv1.dl.ac.uk> NNTP-Posting-Host: mendel.bio.geneseo.edu Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) Peter, I tried out an application called QuickSnap which does exactly what = you require. I include the README from that application. Although = it refers to a QuickCam, I found that it would work with any camera = attached to the video port of an AV board. = I wasn't able to get into the utoronto server to check if the = application is still there. You might try archie. Here is the README. Hope this helps. QuickSnap 0.9.5 A cool application for your connectix quickcam ! ____________________________________________________________________ QuickSnap is a time-lapse and still image photography application = for use with a Connectix QuickCam. It can save images directly as JPEG's files and also features automatic exposure = with spot metering. This means you can make time-lapse movies of = flowers opening under real world lighting conditions !!! New Features 0.9: =80 New windowing structure allows multiple photo's. =80 The viewfinder window does not need to be foremost. =80 You can copy picture to the desk scrap from the viewfinder. =80 Can grab pictures while in the background ! =80 Time Stamping option New Features 0.9.5: =80 Much Better Movie Recording Options =80 If you Quit while recording the Movie will be saved. =80 Single Frame Recording. QuickSnap is shareware. If you use this program, the fee is = US$25.00. You will receive a registration code which will turn on = various cool features like "JPEG comments" and Pausing & Single = Frame Recording of Time Lapse Movies. Oh yeah, it will also = customise the application. Send the registration fee to Tim Molteno, P.O. Box 1220, = Princeton, = NJ 08542-1220 U.S.A. Hey, if you really can't afford it, just send me a postcard, or = email me a JPEG as an attachment to a "thank you for writing this software" note = (tim@jurgen.physics.utoronto.ca). The latest version and updates, information e.t.c. are available = from the world wide web site = "http://jurgen.physics.utoronto.ca:8080/~tim/Perspicuity.htmd/TXT.ht ml" System Requirements. Connectix QuickCam (installed) System 7.1 or later. 68020 or higher processor. QuickTime 2.0 & Multimedia Tuner The multimedia tuner is available from ftp.support.apple.com and = makes things work heaps better. ____________________________________________________________________ __ I used Metrowerks Codewarrior 5 to write this application on a = Powerbook Duo 4/200 with RamDoubler and I used Infinity Windoid 2.6 for the Info window WDEF routines. QuickSnap is copyright =A9 Tim Molteno 1994-95. All rights reserved. Peter Kulmburg wrote: > = > Dear collegues, > = > I am using videoshop 3.0.2.D on a power PC 7500 with sytem D1-7.5.2. to > take shots of my cells when moving towards a cytokine source. > Unfortunately, the cells migrate very slowly and I would like to take a > photo only every minute or so. > However, I am not able to do slow motion movies below 1 picture pe= r > second. If I try it, the program cancels with error #4. To run it proper > again I have to discharge the preferences in the system folder. The apple= > dealer and the avid-hotline were unable to help me. Is there anybody who > has a solution for this problem or knows a program suitable for my > experiments? > = > Thank you for your help Peter > = > Peter KULMBURG at home Tel./Fax:+49 761 80 84 39 > at work: Tel.: +49 761 270/7208 or 7207 Fax: /7217 -- = -=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D= -=3D-=3D-=3D-=3D-=3D-=3D-=3D- John Haynie | haynie@uno.cc.geneseo.edu Biology Dept/SUNY | http://darwin.bio.geneseo.edu/ Geneseo, NY 14454-1401 | From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!EU.net!chsun!news.eunet.ch!usenet From: username@webster.ch Newsgroups: bionet.software Subject: I need update Date: 5 Jun 1996 15:31:35 GMT Organization: Webster University Lines: 5 Message-ID: <4p498n$g3l@news.eunet.ch> NNTP-Posting-Host: 193.72.179.114 X-Newsreader: News Xpress Version 1.0 Beta #4 Dear friends: I very unforturnatelly bought a PCMCIA CD-ROM without driver for win'95. The model is ARGOSY PCMCIA CD-ROM, that's all. Or, if you can tell me how can config a real mode driver working well under win'95? Thaks a lot. From owner-software@net.bio.net Tue Jun 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!sdd.hp.com!col.hp.com!usenet.eel.ufl.edu!bofh.dot!warwick!jones From: jones@bsm.bioc.ucl.ac.uk (David Jones) Newsgroups: bionet.software Subject: Re: How to compare 3d Protein structures? Date: 5 Jun 1996 17:56:30 GMT Organization: University of Warwick, Coventry, UK Lines: 32 Message-ID: <4p4hof$l7a@violet.csv.warwick.ac.uk> References: <31B5913A.41C6@biochemtech.uni-halle.de> NNTP-Posting-Host: globin.bio.warwick.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: TIN [version 1.2 PL2] Ulf Reimer (reimer@biochemtech.uni-halle.de) wrote: : Dear Netters! : Is there any program known which allows to compare 3D structure of : different PDB Files? : Thank you! Hundreds... well, at least a hundred. SSAP by C. Orengo at UCL and Dali by L. Holm at EMBL (EBI), are probably the best known. There is also STAMP from G. Barton at Oxford, and many others. If you just have some coordinates you want to scan and don't want to install any software, then you can just e-mail the coordinates (in PDB format) to dali@embl-heidelberg.de and wait for the search results in your mailbox. It can also be accessed via WWW - www.embl-heidelberg.de. Otherwise you can contact some of the above people to enquire about getting hold of the programs concerned. If you just want some references, then have a look at a fairly recent review by Holm and Sander - PROTEINS (1994) Vol 19:165-173. The actual mechanics of comparing protein structures is pretty much a solved problem now. What really isn't a solved problem is how to measure structural similarity after the comparison has been completed. >---------------------------------------------------------------------------< This message was written, produced and executively directed by Dr David Jones New Address: Dept. of Biological | Email: jones@globin.bio.warwick.ac.uk Sciences, University of Warwick, | Tel: +44 1203 523729 Coventry CV4 7AL, U.K. | Fax: +44 1203 523568 Disclaimer: STANDARD > KEYWORDS : OPINIONS MY OWN NOBODY ELSE'S WHATSOEVER From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!cri.ens-lyon.fr!bentley!deleage From: deleage@bentley (deleage@ibcp.fr) Newsgroups: bionet.software Subject: How to measure the volume of a PDB molecule? Date: 6 Jun 1996 14:16:52 GMT Organization: Institut de Biologie et Chimie des Proteines. CNRS-Lyon Lines: 15 Message-ID: <4p6p8k$9kh@cri.ens-lyon.fr> NNTP-Posting-Host: ibcp.fr X-Newsreader: TIN [version 1.2 PL1] Hi bionet developers, Is anybody knowing a program which is able to measure the volume of a protein knowing its coordinates? TKS to all -- ===================================================================== # Institut de Biologie et Chimie des Proteines. UPR 412-CNRS # # ***** ***** **** ***** Dr Gilbert Deleage # # # # # # # # # 7, passage du Vercors # # # ***** # # # 69367 Lyon Cedex 07,FRANCE # # # # # # #**** Tel: (33) 72-72-26-47 # # # # # # # # Fax: (33) 72-72-26-01 # # ***** ****** **** # deleage@ibcp.fr # ===================================================================== From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Geoff Barton Newsgroups: bionet.software Subject: Re: How to compare 3d Protein structures? Date: Thu, 06 Jun 1996 15:07:29 +0100 Organization: Laboratory of Molecular Biophysics Lines: 20 Message-ID: <31B6E621.7DE1@bioch.ox.ac.uk> References: <31B5913A.41C6@biochemtech.uni-halle.de> <4p4hof$l7a@violet.csv.warwick.ac.uk> NNTP-Posting-Host: weevil.biop.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) David Jones wrote: > > Ulf Reimer (reimer@biochemtech.uni-halle.de) wrote: > : Dear Netters! > > : Is there any program known which allows to compare 3D structure of > : different PDB Files? > > : Thank you! > > Hundreds... well, at least a hundred. SSAP by C. Orengo at UCL and > Dali by L. Holm at EMBL (EBI), are probably the best known. There is > also STAMP from G. Barton at Oxford, and many others. If you just have Maybe thousands??!! STAMP is available - see ftp://geoff.biop.ox.ac.uk/README for instructions Geoff. From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Geoff Barton Newsgroups: bionet.software Subject: Re: HTML Editor Date: Thu, 06 Jun 1996 14:50:15 +0100 Organization: Laboratory of Molecular Biophysics Lines: 4 Message-ID: <31B6E217.2F1C@bioch.ox.ac.uk> References: <4p3q8d$k7l@ikarus.rz.tu-clausthal.de> NNTP-Posting-Host: weevil.biop.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) I use the editor xemacs. It has a nice html mode with colour syntax highlighting. Geoff. From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!news2.cais.net!news.cais.net!van-bc!unixg.ubc.ca!news.bc.net!rover.ucs.ualberta.ca!news.ucalgary.ca!pc10.mid.ucalgary.ca!user From: sims@acs.ucalgary.ca (Kurt Sims) Newsgroups: bionet.software Subject: Re: SOFTRAM! OUCH! Date: Thu, 06 Jun 1996 08:51:35 -0700 Organization: University of Calgary (MID) Lines: 18 Message-ID: References: <4p0mao$ar6@rzlimes.gbf-braunschweig.de> NNTP-Posting-Host: @pc10.mid.ucalgary.ca In article <4p0mao$ar6@rzlimes.gbf-braunschweig.de>, uka@gbf-braunschweig.de (Uwe Kaerst) wrote: > In article , pesto@interaccess.com says... > > > >Had Softram on my system took it off and now I get an error message > >stating windows is looking for a device file to start up and then I get > > c:\softram1.386 > >I cannot get rid of this! I cannot go back into my windows setup because > >of this freaking message! Anybody got any ideas besides formatting my > >"c" drive? > > If this is on the wrong ng, sorry! > > > You should also look into your autoexec.bat and config.sys files and rem out any reference to it. I don't know if there will be anything in there relating to it though. Check your WIN.INI file to get rid of it as well. From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!oleane!jussieu.fr!moka.ccr.jussieu.fr!not-for-mail From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN) Newsgroups: bionet.software Subject: Re: How to compare 3d Protein structures? Date: 6 Jun 1996 15:29:31 +0200 Organization: CCR - Universites Paris VI/VII - Paris - France Lines: 19 Message-ID: <4p6mfr$17mj@moka.ccr.jussieu.fr> NNTP-Posting-Host: moka.ccr.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit References: <31B5913A.41C6@biochemtech.uni-halle.de> Ulf Reimer (reimer@biochemtech.uni-halle.de) wrote: > Dear Netters! > Is there any program known which allows to compare 3D structure of > different PDB Files? I have such a program. It computes a distance between two 3D molecules or fragments and minimizes it for all rotations and translations. I am looking for collaborations in this field. If you are interested, please send me the input files, and I shall return the coordinates of the superimposed molecules, the optimal rotation and translation, the similarity index, and optionnally the maximal common 3D substructure together with the pairwise atomic correspondence between the similar regions. I can also Email the graphical display stored in a postsript file. Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, URA34) ptitjean@ccr.jussieu.fr From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!newsfeed.internetmci.com!news.wwa.com!news.ucdavis.edu!quad!knight From: knight@quad.cs.ucdavis.edu (James Knight) Newsgroups: bionet.software,bionet.software.gcg,bionet.software.staden,bionet.software.srs Subject: Re: Software to extract annotation fields from EMBL/GenBank entries. Followup-To: bionet.software,bionet.software.gcg,bionet.software.staden,bionet.software.srs Date: 6 Jun 1996 00:06:07 GMT Organization: University of California, Davis Lines: 138 Message-ID: <4p57df$35l@mark.ucdavis.edu> References: NNTP-Posting-Host: quad.cs.ucdavis.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:15715 bionet.software.gcg:1827 bionet.software.staden:197 bionet.software.srs:262 This type of problem is one of the reasons I wrote my SEQIO package. Below is a complete C program which will extract all of the /note fields from the CDS_pept features. The program takes a list of files and outputs the list of entries and the note fields as follows: For entry embl:MELLP late lactation protein precursor For entry embl:MEMRNAAL pot. alpha lactalbumin preprotein For entry embl:SC9920 YM9920.01c, unknown, partial, len: 956, CAI: 0.14; PS00061 Short-chain alcohol dehydrogenase family signature YM9920.02c, unknown, len: 61, CAI: 0.17, possible small spliced gene YM9920.03c, unknown, len: 55, CAI: 0.13, possible small spliced gene YM9920.04, unknown, len: 585, CAI: 0.18, putative glutamate decarboxylase gene It will also take care of splicing the lines together. It is, however, a little limited in that it can only handle EMBL format files, and it only looks for the /note field in each CDS_pept feature (these are fixed in the code). For someone with a little programming experience, it should be simple to modify the program to look for a different feature or a different sub-field of a feature. To compile the program, first extract the text from this message, then ftp my SEQIO package from the following site ftp://ftp.cs.ucdavis.edu/pub/strings/seqio.tar.gz unpack it, and compile the seqio.c and main program together using a C compiler. It should compile and run using any Unix or Windows NT/95 machine (in Windows, run the program from a DOS shell). (***Advertisement***) I wrote the SEQIO package for things just like this, where someone with a little programming experience needs to do something that no one has provided software for. The package simplifies all of the file and sequence I/O, so that the programmer can concentrate on the new piece of code. It's use does require C/C++ programming experience, but, as I hope you can see from the example below, not that much experience. (***End of Advert***) Jim #include #include #include #include #include "seqio.h" int main(int argc, char *argv[]) { int len, i, flag; char *entry, *s, *t, *s2, *t2, *feature, *note, *id; SEQFILE *sfp; for (i=1; i < argc; i++) { if ((sfp = seqfopen2(argv[i])) == NULL) continue; if (strcmp(seqfformat(sfp, 0), "EMBL") != 0) { fprintf(stderr, "%s: Not an EMBL file.\n", seqffilename(sfp, 0)); continue; } /* * Read the entries. */ while ((entry = seqfgetentry(sfp, &len, 0)) != NULL) { s = entry; flag = 0; while ((s = strstr(s, "\nFT CDS_pept")) != NULL) { /* * Found a CDS, so print the entry's id, if its the first CDS found. */ if (!flag) { if ((id = seqfmainid(sfp, 0)) != NULL || (id = seqfmainacc(sfp, 0))) printf("For entry %s\n", id); else printf("For an unknown entry\n"); flag = 1; } /* * Find the end of the feature lines for that CDS, and make * it NULL-terminated. */ feature = ++s; while (*s != '\n') s++; while (strncmp(s, "\nFT ", 6) == 0 && isspace(s[6])) { s++; while (*s != '\n') s++; } *s = '\0'; /* * Look for the /note field, then find the strings between * the quotes, squeezing out any line breaks. */ if ((t = strstr(feature, "/note=\"")) != NULL) { note = t2 = s2 = t + 7; while (s2 < s && *s2 != '"') { if (*s2 == '\n') { s2 += 6; /* Skip the "\nFT " and then the spaces */ while (*s2 != '\n' && isspace(*s2)) s2++; *t2++ = ' '; } else { if (t2 != s2) *t2 = *s2; t2++; s2++; } } *t2 = '\0'; printf(" %s\n", note); } *s = '\n'; } } seqfclose(sfp); } return 0; } From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!newsfeed.internetmci.com!in1.uu.net!newsfeed.pitt.edu!newsflash.concordia.ca!news.mcgill.ca!bluejay.parasitology.mcgill.ca!user From: robin_beech@maclan.mcgill.ca (Robin Beech) Newsgroups: bionet.software Subject: Re: Software on Mac Date: Thu, 06 Jun 1996 10:06:16 -0400 Organization: McGill University Lines: 23 Message-ID: References: NNTP-Posting-Host: bluejay.parasitology.mcgill.ca In article , Namjin Chung wrote: > Try MacVector. That's the best and easy-to-use sequence analysis > software on Mac OS, as far as I know. Price is quite expensive; more > than $2000. It's from Eastman Kodak, I called Oxford Molecular, who have taken MacVector over from Eastman Kodak, a few days ago. While the software works well for most things (hate the sequence alignments it gives) the price is $2450 US for the basic license. I also asked about upgrading our 4 user personal copies to a 4 user network version - the price for getting almost equivalent usage but without having to unplug the EVE key each time you want to go to a different computer over $5000 US !!!! I hate to think what the price of the Network version would be from scratch. Robin Beech, Institute of Parasitology, McGill University PS Anyone want to form a PowerPlant work team and write a shareware DNA sequence handling package ;-) From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!bofh.dot!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!oleane!jussieu.fr!univ-lille1.fr!usenet From: Philippe Lefebvre Newsgroups: bionet.software Subject: Re: Bibliographic software Date: 6 Jun 1996 09:58:58 GMT Organization: INSERM Lines: 5 Message-ID: <4p6a52$l80@netserver.univ-lille1.fr> References: <4oq62h$19n@news1.intercall.com> NNTP-Posting-Host: biostruct.univ-lille2.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) RefMAn is a great software. Ihave been using it for more than 7 years and the last Win version works OK, although there is aproblem: it does keep the default settings you are giving, so you have to be careful to check them out before each use. Dr Phil Good From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!EU.net!Belgium.EU.net!idefix.CS.kuleuven.ac.be!chaos.kulnet.kuleuven.ac.be!usenet From: Hugo Klaassen Newsgroups: bionet.software Subject: Vector NTi, Cloneworks and others... Date: Thu, 30 May 1996 18:12:36 +0200 Organization: K.U.Leuven Lines: 15 Message-ID: <31ADC8F4.2B49@sgi.celgen.kuleuven.ac.be> NNTP-Posting-Host: fifi.celgen.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b3Gold (Win95; I) Hi! I have tried demos of Cloneworks (the WORSE prgram for cloning and plasmid drawing that I have seen for win95) and Vector NTi. The latter is a lot better (and cheaper I think) but the common denominator for both of them is that they are EXTREMELY UNINTUITIVE, low on user friendliness and therefore rather difficult to learn. My question is this: having WIN95 machines, what is out there that I could use (pay- share- or freeware) that would be user friendly, intuitive (preferably written by people who clone not by people who write programs) and is not a whole package like DNAStar etc. ThanX for the info, I will summarize the answers (if any) Przemko From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!chi-news.cic.net!arclight.uoregon.edu!usenet.eel.ufl.edu!bofh.dot!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!ws41.cnusc.fr!ciril.fr!u-strasbg.fr!news From: pingouin@.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: Pairwise protein align. program wanted Date: 6 Jun 1996 10:11:52 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 36 Message-ID: <4p6at8$7gs@news.u-strasbg.fr> References: NNTP-Posting-Host: crystal.u-strasbg.fr X-Newsreader: knews 0.9.6 In article , Morten Stig Andersen writes: >I am looking for a freeware pairwise alignment program (for unix) which >can report percent similarity as well as percent identity, like the >'bestfit' and 'gap' programs in GCG. > >I have Bill Pearson's 'align' program, but it reports identity only. > >Any clues? > >Thanks, > >Morten Andersen > > Please, stop talking about percent similarity. There is no information in percent similarity. If you want to talk about percent similarity, you have to cite the matrix you use, and noone is able to say what scores are in a matrix...In a protein, you can easily see that similarity depends of the position in the sequence. You can not define the same similarity (in terms of functional analysis) for a reisdue in an helix, a loop, a sheet or in the active site. Well, I'm not in the better place to give such lessons, but noone else want to do that... Bye, Francois. -- Francois Jeanmougin Service de bioinformatique / bioinformatic service IGBMC BP 163 67404 Illkirch France tel : (33) 88 65 32 71 e-mail : jeanmougin@igbmc.u-strasbg.fr From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Ewan Birney Newsgroups: bionet.software Subject: Re: Pairwise protein align. program wanted Date: Thu, 06 Jun 1996 09:12:39 +0100 Organization: Oxford University Lines: 61 Message-ID: <31B692F7.41C6@molbiol.ox.ac.uk> References: NNTP-Posting-Host: nmrd.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; IRIX 5.3 IP22) Morten Stig Andersen wrote: > > I am looking for a freeware pairwise alignment program (for unix) which > can report percent similarity as well as percent identity, like the > 'bestfit' and 'gap' programs in GCG. > > I have Bill Pearson's 'align' program, but it reports identity only. > > Any clues? > > Thanks, > > Morten Andersen > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > MORTEN STIG ANDERSEN Department of Molecular Biology > Fax: +46 18 557723 Biomedical Center, University of Uppsala > Tel: +46 18 174379 BOX 590, S-751 24 Uppsala, SWEDEN Morten % similarity is in fact a really silly way of trying to estimate what is going on. It is very much arbitary, and even then, the arbitary way it is done in many cases is not well done. If I were you, depending on the problem, I would use HMMs (if you have more than one sequence), in which the sampling problem can be solved by using Dirchlet mixture priors. The two main HMM packages out there are http://genome.wustl.edu/eddy/hmm.html and http://www.cse.ucsc.edu/research/compbio/sam.html The latter has a quite ok Web system. HMMs have a strong statisical background to them and so you can reported back a probability of matching the HMM (given certain assumptions). Dirchlet mixtures take the place of a "similarity" matrix in other systems (that is a slight generalisation but not much). If you want to use a more heuristic system you can revert to Profiles which is how I routinely analyse things. Profiles are almost identical to HMMs but lack the probablilistic framework. Our package for using Profiles is Wisetools. http://www.ocms.ox.ac.uk/~birney/wise/topwise.html I would really advise moving away from pairwise comparisons, even for, for example an all-against-all matrix of related proteins in which you want to show that certain proteins are more related than others (this is the other use which people often try to use pairwise comparisons for). If you want something like that, you should be using trees, of which there are a variety of methods, most of which one can get statistical support for of some kind by using bootstrapping methods. PHYLIP is my package of choice here. (An aside... does anyone know of a PHYLIP web site?) ewan From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!nntp.coast.net!fu-berlin.de!news.dfn.de!news.uni-jena.de!news From: David Bauer Newsgroups: bionet.software Subject: Re: sequence assembly Date: Thu, 06 Jun 1996 08:45:48 +0200 Organization: Inst.Molec.Biotechnol. Lines: 39 Message-ID: <31B68CAC.710C@imb-jena.de> References: <01I5JM5JX4MA9AOJ02@CSMC.EDU> NNTP-Posting-Host: sneed.imb-jena.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (X11; I; SunOS 5.4 sun4m) To: ALEX NECHIPORUK/CSMC/TEL 310 855 7612 I know 2 program packages for IBM: PC/GENE runs under DOS and DNASTAR, both for DOS and Windows. They have also modules for contig assembly. I used both and prefer DNASTAR. ALEX NECHIPORUK/CSMC/TEL 310 855 7612 wrote: > > Dear Netters, > I am sequencing a novel gene. We pulled multiple cDNAs from the libraries. > After they fully sequenced I'll have to align all sequences together. > Can anyone recommend a user friendly software (I prefer PC-DOS or > Windows based) for multiple sequence fragment assembly. > Thanks, > Alex. -- +----------------------------------------------------------------------------+ | David Bauer | | | | _/ _/ _/ _/_/_/ Department of Genome Analysis | | _/ _/_/ _/_/ _/ _/ Institute of Molecular Biotechnology | | _/ _/ _/ _/ _/_/_/ Beutenbergstr. 11, D 07745 Jena | | _/ _/ _/ _/ _/ voice : int+49.3641.656254 | | _/ _/ _/ _/_/_/_/ fax : int+49.3641.656255 | | E-mail : dbauer@imb-jena.de | | | | | | "I'm very interested in the future because I plan | | to spend the rest of my life there." Robert Wood Johnson | +----------------------------------------------------------------------------+ From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!cssun.mathcs.emory.edu!news-feed-1.peachnet.edu!usenet.eel.ufl.edu!bofh.dot!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-angers.fr!ciril.fr!u-strasbg.fr!news From: pingouin@.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: HTML Editor Date: 6 Jun 1996 07:38:23 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 22 Message-ID: <4p61tf$7ac@news.u-strasbg.fr> References: <199605291311.UAA09274@benpc.bionet.nsk.su> <4omrj0$6k7@cwis-20.wayne.edu> NNTP-Posting-Host: crystal.u-strasbg.fr X-Newsreader: knews 0.9.6 In article <4omrj0$6k7@cwis-20.wayne.edu>, dwomble@cmb.biosci.wayne.edu (David Womble) writes: > >This is an interesting question. What do other people who actually >maitain web sites use? > I maintain two server, one on an SGI(Indy), then I use vi or jot, and one on a Sparc, then I use vi. Note that I'm a biologist, and I use the mac only to see if the html is clean. To make and convert graphics, I use Showcase and Imgworks, both on SGI. hope this helps, Francois. -- Francois Jeanmougin Service de bioinformatique / bioinformatic service IGBMC BP 163 67404 Illkirch France tel : (33) 88 65 32 71 e-mail : jeanmougin@igbmc.u-strasbg.fr From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!nntp.uio.no!ifi.uio.no!news.sics.se!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!evolution!moan From: Morten Stig Andersen Newsgroups: bionet.software Subject: Pairwise protein align. program wanted Date: Tue, 4 Jun 1996 13:55:58 +0200 Organization: Uppsala University Lines: 19 Message-ID: Reply-To: Morten Stig Andersen NNTP-Posting-Host: evolution.bmc.uu.se Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: moan@evolution I am looking for a freeware pairwise alignment program (for unix) which can report percent similarity as well as percent identity, like the 'bestfit' and 'gap' programs in GCG. I have Bill Pearson's 'align' program, but it reports identity only. Any clues? Thanks, Morten Andersen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= MORTEN STIG ANDERSEN Department of Molecular Biology Fax: +46 18 557723 Biomedical Center, University of Uppsala Tel: +46 18 174379 BOX 590, S-751 24 Uppsala, SWEDEN From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Geoff Barton Newsgroups: bionet.software Subject: Re: Pairwise protein align. program wanted Date: Thu, 06 Jun 1996 14:46:39 +0100 Organization: Laboratory of Molecular Biophysics Lines: 47 Message-ID: <31B6E13F.237C@bioch.ox.ac.uk> References: NNTP-Posting-Host: weevil.biop.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) To: Morten Stig Andersen Morten Stig Andersen wrote: > > I am looking for a freeware pairwise alignment program (for unix) which > can report percent similarity as well as percent identity, like the > 'bestfit' and 'gap' programs in GCG. > > I have Bill Pearson's 'align' program, but it reports identity only. > > Any clues? I'm posting this, because I often get asked this question, or get to see papers that quote "percent similarities". Stick with percent identity. Don't use arbitrary "percent similarities" they are usually used to try and imply significance where there isn't any! Doing randomisations and quoting "SD score from mean" can be a useful additional indicator that compensates to a certain extent for composition bias and length. The AMPS package will give you these figures (see ftp://geoff.biop.ox.ac.uk/README and our WWW site). Remember that the significance of a percentage identity is dependent on the length of the alignment. Short alignments have a much greater chance of giving high percent identitites than long alignments (say, over 200 residues). The average percentage identity for "optimal" sequence alignments between proteins of unrelated 3D structure is about 20% NOT 5% as many believe. See http://geoff.biop.ox.ac.uk/papers/rev93_1/rev93_1.html also in PostScript in: ftp://geoff.biop.ox.ac.uk/preprints/review93 particularly Figures 2 and 4 and associated text. I hope this helps, Geoff. -- Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K. mailto:gjb@bioch.ox.ac.uk, Tel: +44 1865 275368, Fax: +44 1865 510454, ftp://geoff.biop.ox.ac.uk, http://geoff.biop.ox.ac.uk From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!amgen.com!IBBOARD4 From: IBBOARD4@amgen.com Newsgroups: bionet.software Subject: subscribe BIO-SOFTWARE Date: 6 Jun 1996 11:46:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <960606114358.3c02@amgen.com> NNTP-Posting-Host: net.bio.net SUBSCRIBE BIO-SOFTWARE From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!amgen.com!HSOUTH From: HSOUTH@amgen.com Newsgroups: bionet.software Subject: SUBSCRIBE BIO-SOFTWARE Date: 6 Jun 1996 11:46:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <960606114324.3b35@amgen.com> NNTP-Posting-Host: net.bio.net SUBSCRIBE BIO-SOFTWARE From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!usc!chi-news.cic.net!arclight.uoregon.edu!news.bc.net!news.mindlink.net!van-bc!usenet From: ckarpan@wimsey.com (Cindy Karpan) Newsgroups: bionet.software Subject: Mac Software for Project Planning/Gannt Charts Date: 6 Jun 1996 18:03:00 GMT Organization: Online at Wimsey Lines: 9 Sender: -Not-Authenticated-[4044] Message-ID: <4p76gk$564@wolfe.wimsey.com> NNTP-Posting-Host: ts009.vcr.wis.net X-Posted-From: InterNews 1.0.6@ts009.vcr.wis.net Xdisclaimer: No attempt was made to authenticate the sender's name. Hello, Does anyone know of a good Mac program for project planning? I'm really looking for a simple yet powerful tool (like Milestones for Windows) that does timelines and Gantt Charts. Thanks for any feedback. Cindy From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!amgen.com!IBBOARD4 From: IBBOARD4@amgen.com Newsgroups: bionet.software Subject: TEST Date: 6 Jun 1996 10:58:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <960606105553.3fc9@amgen.com> NNTP-Posting-Host: net.bio.net TEST From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: ptaylor@hgmp.mrc.ac.uk (Dr. P.L. Taylor) Newsgroups: bionet.software Subject: Re: Software on Mac Date: 6 Jun 1996 17:07:13 +0100 Lines: 22 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4p6vnh$h8f@mserv1.dl.ac.uk> content-length: 1066 Original-To: bio-soft@dl.ac.uk >> Try MacVector. That's the best and easy-to-use sequence analysis >> software on Mac OS, as far as I know. Price is quite expensive; more >> than $2000. It's from Eastman Kodak, > >I called Oxford Molecular, who have taken MacVector over from Eastman >Kodak, a few days ago. While the software works well for most things (hate >the sequence alignments it gives) the price is $2450 US for the basic >license. I also asked about upgrading our 4 user personal copies to a 4 >user network version - the price for getting almost equivalent usage but >without having to unplug the EVE key each time you want to go to a >different computer over $5000 US !!!! I hate to think what the price of >the Network version would be from scratch. At the risk of being accused of advertising on this group, may I suggest that you take a look at my program GeneJockeyII, which offers similar functionality to MacVector et al, but costs $1000 and is not copy- protected. Call BioSoft on (314) 524 8029 (USA) or 01223 68622 (UK) for a demo. Phil Taylor mbplt@seqnet.dl.ac.uk From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!amgen.com!Harold.South From: Harold.South@amgen.com ("Harold South") Newsgroups: bionet.software Subject: SUBSCRIBE bio-software Date: 6 Jun 1996 14:04:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Subject: Time: 1:44 PM OFFICE MEMO SUBSCRIBE bio-software Date: 6/6/96 subscribe bio-software From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!amgen.com!IBBOARD4 From: IBBOARD4@amgen.com Newsgroups: bionet.software Subject: subscribe bio-software Date: 6 Jun 1996 13:53:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <960606135016.3c02@amgen.com> NNTP-Posting-Host: net.bio.net Date: 6-JUN-1994 21:48 Permanent / System From: INTRON::MBUNTING Description: INFO ON HOW TO USE THE BULLETIN UTILITY. This message is being displayed by the BULLETIN facility. This is a non-DEC facility, so it is not described in the manuals. Messages can be submitted by using the BULLETIN command. System messages, such as this one, are displayed in full, but can only be entered by privileged users. Non-system messages can be entered by anyone, but only their topics will be displayed at login time, and will be prompted to optionally read them. (This prompting feature can be disabled). All bulletins can be reread at any time unless they are deleted or expire. For more information, see the on-line help (via HELP BULLETIN). From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!amgen.com!IBBOARD4 From: IBBOARD4@amgen.com Newsgroups: bionet.software Subject: INFO ON HOW TO USE THE BULLETIN UTILITY. Date: 6 Jun 1996 13:52:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <960606134954.3c02@amgen.com> NNTP-Posting-Host: net.bio.net Date: 6-JUN-1994 21:48 Permanent / System From: INTRON::MBUNTING Description: INFO ON HOW TO USE THE BULLETIN UTILITY. This message is being displayed by the BULLETIN facility. This is a non-DEC facility, so it is not described in the manuals. Messages can be submitted by using the BULLETIN command. System messages, such as this one, are displayed in full, but can only be entered by privileged users. Non-system messages can be entered by anyone, but only their topics will be displayed at login time, and will be prompted to optionally read them. (This prompting feature can be disabled). All bulletins can be reread at any time unless they are deleted or expire. For more information, see the on-line help (via HELP BULLETIN). From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!msvax.mssm.edu!STRAHS From: strahs@msvax.mssm.edu (Dan Strahs) Newsgroups: bionet.software Subject: How does one color superimposed stuctures? Date: 6 Jun 1996 20:08:18 GMT Organization: Mount Sinai Medical Center, New York City Lines: 26 Message-ID: <4p7dri$rg5@news.cuny.edu> Reply-To: strahs@msvax.mssm.edu NNTP-Posting-Host: msvax.mssm.edu I have several structures I would like to superimpose and graphically display with a ribbon backbone. Quite simple, really, and a variety of programs will readily perform this task. However, I would like to blend the colors of the superimposed backbones, such that when the ribbons of the different structures merge, their color merges. For example, if I display two similar proteins with a blue ribbon and a red ribbon, I would like the portions of the ribbons that occupy the same space to be assigned a color of purple with a brightness/saturation approximately twice that of the individual protein's ribbons. My question is: Which software will do this? Insight and Midas don't appear to have this ability. Does Quanta? Is there another program, such as O, Grasp or MacroModel that does? Am I wrong and can Insight do this task? Thanks for any help. Dan Strahs Department of Physiology and Biophysics Mt. Sinai School of Medicine strahs@msvax.mssm.edu From owner-software@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!amgen.com!IBBOARD4 From: IBBOARD4@amgen.com Newsgroups: bionet.software Subject: SUBSCRIBE BIO-SOFTWARE Date: 6 Jun 1996 11:52:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 701 Sender: daemon@net.bio.net Distribution: world Message-ID: <960606114955.3c02@amgen.com> NNTP-Posting-Host: net.bio.net Date: 16-JUN-1994 21:08 Permanent From: INTRON::MBUNTING Description: BIOSCI Information Sheet ---------------------------------------------------------------------- THE BIOSCI ELECTRONIC NEWSGROUP NETWORK INFORMATION SHEET (last revised 26-MAY-94) ---------------------------------------------------------------------- This is the BIOSCI information sheet for the Americas and Pacific Rim countries. If you are located in Europe, Africa, or Central Asia, please retrieve that version of the information sheet by sending the command info ukinfo in the body of an e-mail message addressed to the Internet address biosci-server@net.bio.net Any text placed on the Subject: line of your message is ignored, so please be sure to put the "info ukinfo" command in the main body of your e-mail message. New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available by gopher to net.bio.net or anonymous FTP to net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ. It may also be requested by sending e-mail to biosci-server@net.bio.net as described above except that the command info faq should be used in the body of the mail message. The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of both versions of the BIOSCI information sheet. ---------------------------------------------------------------------- Contents of this Document ------------------------- Introduction List of BIOSCI Mailing Lists and Newsgroups List of BIOSCI Newsgroup Topics BIOSCI Newsgroup Discussion Leaders Participating in BIOSCI Using USENET News Software Participating in BIOSCI by E-mail E-mail Subscription Requests and other Information E-mail Address Changes Interruption of E-mail Service Posting Messages to Newsgroups by E-mail Retrieval of old postings from the BIOSCI archives BIOSCI "prototype" newsgroups Retrieving Other BIOSCI Documentation Introduction ------------ The BIOSCI newsgroup network was developed to allow easy worldwide communications between biological scientists who work on a variety of computer networks. BIOSCI is supported by the National Science Foundation, Department of Energy, and National Institutes of Health in the U.S.A. and by the Science and Engineering Research Council Daresbury Laboratory in the United Kingdom. BIOSCI services are available to users free of charge. BIOSCI messages are distributed by two means: USENET news software and electronic mail. WE STRONGLY ENCOURAGE ALL INTERESTED USERS TO EXPLORE GETTING "USENET NEWS" SOFTWARE AT YOUR SITE. The software is in the public domain, and you will find it much more convenient than subscribing to newsgroups by e-mail. Please consult your systems manager (the software may already be available on a machine at your institution) or contact biosci-help@net.bio.net for a list of software available free of charge on the Internet. NOTE, however, that the installation and maintenance of news software requires the assistance of a trained systems operator in most cases and is not a task to be undertaken by a computer novice. Why is news software preferable to e-mail? News software recovers messages automatically after network interruptions, whereas your e-mail address may have to be removed from the subscription list at times if your computer/network malfunctions and undelivered mail starts bouncing back to the BIOSCI administrative sites. You will have to manually retrieve lost messages from the archives if your e-mail subscription is suspended. News software organizes messages by topic and subtopic for easy browsing. In contrast if you subscribe by e-mail to more than one discussion list, messages from multiple lists arrive into your personal mail file in chronological order of posting only and are mixed in with your personal messages. You have to connect the discussion threads yourself if you use e-mail. In summary, e-mail participation should be seen as a LAST RESORT to be used only if news software can not be installed locally. Fortunately, BIOSCI offers advantages for e-mail users too. By having distribution sites or "nodes" on each major network, BIOSCI allows its e-mail users to contact people around the world without having to learn a variety of computer addressing tricks. Any user can simply post a message to his/her regional BIOSCI node and copies of that message will be distributed automatically to all other subscribers on all of the participating networks, including the Internet, USENET, BITNET, EARN, NETNORTH, HEANET, and JANET. List of BIOSCI Mailing Lists and Newsgroups ------------------------------------------- BIOSCI messages are distributed on the newsgroups in the "bionet" hierarchy of USENET and on the corresponding mailing lists indicated below. Contents of the USENET newsgroups and the e-mail distributions are *identical*, i.e., messages sent in by e-mail are also forwarded to USENET and messages posted to USENET newsgroups are also distributed to e-mail subscribers. An expanded description of the purpose of each newsgroup follows this list. MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY + bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS ** bionet.announce BIO-JOURNALS ** bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY ** bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY ** bionet.biology.computational CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES ** bionet.sci-resources STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast + full name is BIOLOGICAL-INFORMATION-THEORY-AND-CHOWDER-SOCIETY ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. List of BIOSCI Newsgroup Topics ------------------------------- MAILING LIST NAME TOPIC ----------------- ----- ACEDB-SOFT Discussions by users and developers of genome databases using the ACEDB software. AGEING Discussions about ageing research AGROFORESTRY Discussions about agroforestry research ARABIDOPSIS Newsgroup for the Arabidopsis Genome Project BIOFORUM Discussions about biological topics for which there is not yet a dedicated newsgroup BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Applications of information theory to biology; this group is not for general information or for discussion of theories in general. BIONAUTS Question/answer forum for help using electronic networks, locating e-mail addresses, etc. BIONEWS ** General announcements of widespread interest to biologists BIO-JOURNALS ** Tables of Contents of biological journals BIO-MATRIX Applications of computers to biological databases BIOPHYSICAL-SOCIETY ** Official announcements/information from the Biophysical Society. BIOPHYSICS Discussion of issues related to the science and profession of biophysics BIO-SOFTWARE Information on software for the biological sciences BIOTHERMOKINETICS Discussions about the kinetics, thermodynamics and control of biological processes at the cellular level CELL-BIOLOGY Discussions about cell biology including cancer research at the cellular level CHLAMYDOMONAS Discussions about the biology of the green alga Chlamydomonas and related genera CHROMOSOMES Discussions about mapping and sequencing of eucaryote chromosomes COMPUTATIONAL-BIOLOGY ** Mathematical and computer applications in biology CYTONET Discussions about research on the cytoskeleton, plasma membrane, and cell wall DROSOPHILA Discussions about biological research on Drosophila EMBL-DATABANK Messages to and from the EMBL database staff EMPLOYMENT Job opportunities in biology (see BIOSCI FAQ *before* posting commercial job openings) GDB Messages to and from the Genome Data Bank staff GENBANK-BB Messages to and from the GenBank database staff GENETIC-LINKAGE Newsgroup for genetic linkage analysis GRASSES-SCIENCE Discussions regarding grasses, especially cereal, forage, and turf species HIV-MOLECULAR-BIOLOGY Discussions about the molecular biology of HIV HUMAN-GENOME-PROGRAM NIH-sponsored newsgroup on human genome issues IMMUNOLOGY Discussions about research in immunology INFO-GCG Discussions about the GCG sequence analysis software JOURNAL-NOTES Practical advice on dealing with professional journals METHODS-AND-REAGENTS Requests for information and lab reagents MOLECULAR-EVOLUTION Discussions about research in molecular evolution MYCOLOGY Discussions about research on filamentous fungi NEUROSCIENCE Discussions about research in the neurosciences N2-FIXATION Discussion about biological nitrogen fixation PARASITOLOGY Discussions about research in parasitology PHOTOSYNTHESIS Discussions about photosynthesis research PLANT-BIOLOGY Discussions about research in plant biology POPULATION-BIOLOGY Discussions about research in population biology PROTEIN-ANALYSIS Discussions about research on proteins and messages for the PIR and SWISS-PROT databank staffs PROTEIN-CRYSTALLOGRAPHY Discussion about crystallography of macromolecules and messages for the PDB staff PROTISTA Discussions about research on ciliates and other protists RAPD Discussions about Randomly Amplified Polymorphic DNA SCIENCE-RESOURCES ** Information from/about scientific funding agencies STRUCTURAL-NMR Discussions about the use of NMR for macromolecular structure determination TROPICAL-BIOLOGY Discussions about research in tropical biology VIROLOGY Discussions about research in virology WOMEN-IN-BIOLOGY Discussions about issues concerning women biologists YEAST Discussions about the molecular biology and genetics of yeast ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. BIOSCI Newsgroup Discussion Leaders ----------------------------------- Most scientific specialty newsgroups (except for a few created several years ago) have individuals who are responsible for stimulating discussion on the newsgroup. General purpose forums such as METHODS-AND-REAGENTS do not have discussion leaders. If a group that you are interested in does not seem to have much activity recently, please contact the discussion leader and ask why. NEWSGROUP NAME Discussion Leader and their e-mail address -------------- ------------------------------------------ ACEDB-SOFT Mike Cherry (cherry@genome.stanford.edu) AGEING Sydney Shall (bafa1@central.sussex.ac.uk) AGROFORESTRY Gerry Lawson (F_GJL@vaxa.nerc-bush.ac.uk) ARABIDOPSIS Chris Somerville (21847CRS@msu.edu) BIOFORUM None BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Tom Schneider (toms@ncifcrf.gov) BIONAUTS Rob Harper (harper@convex.csc.fi) BIONEWS ** David Kristofferson (kristoff@net.bio.net) BIO-JOURNALS ** David Kristofferson (kristoff@net.bio.net) BIO-MATRIX Dan Davison (davison@uh.edu) BIOPHYSICAL-SOCIETY ** David Kristofferson (kristoff@net.bio.net) BIOPHYSICS Carol Gross (cgross@molbio.cbs.umn.edu) BIO-SOFTWARE None BIOTHERMOKINETICS John Woods (eanv20@castle.edinburgh.ac.uk) CELL-BIOLOGY Ola Myklebost (ola.myklebost@dnr.uio.no) CHLAMYDOMONAS Elizabeth H. Harris (chlamy@acpub.duke.edu) and Antonio R. Franco (bf1rodri@cc.uco.es) CHROMOSOMES Bruce Roe (broe@aardvark.ucs.uoknor.edu) and Greg Lennon (greg@mendel.llnl.gov) COMPUTATIONAL-BIOLOGY ** Phil J. Curtiss (curtiss@umiacs.umd.edu) CYTONET Nicholas C. Carpita (carpita@btny.purdue.edu) DROSOPHILA Michael Ashburner (m.ashburner@gen.cam.ac.uk) EMBL-DATABANK None (datalib@embl-heidelberg.de) EMPLOYMENT None GDB Kerryn Brandt (kab@welchgate.welch.jhu.edu) GENBANK-BB Dennis Benson (benson@ncbi.nlm.nih.gov) GENETIC-LINKAGE Steve Bryant (s_bryant@icrf.ac.uk) GRASSES-SCIENCE Allen Wright (adwright@iastate.edu) HIV-MOLECULAR-BIOLOGY Mika Salminen (msalminen@nphi.fi) HUMAN-GENOME-PROGRAM Jane Peterson (jp2@cu.nih.gov) IMMUNOLOGY Donald Forsdyke (forsdyke@qucdn.queensu.ca) INFO-GCG John Cargill (ontogen@nic.cerf.net) JOURNAL-NOTES Donald Forsdyke (forsdyke@qucdn.queensu.ca) METHODS-AND-REAGENTS None MOLECULAR-EVOLUTION Dan Davison (davison@uh.edu) MYCOLOGY Tom Adams (tom@bio.tamu.edu) Leland Ellis (leland@straylight.tamu.edu) Greg May (gsmay@bcm.tmc.edu) NEUROSCIENCE Vincent A Mazzarella (vamg6792@uxa.cso.uiuc.edu) James L. Olds (olds@bernard.ninds.nih.gov) N2-FIXATION Eng-Leong Foo (eng-leong_foo_mircen-ki%micforum@mica.mic.ki.se) PARASITOLOGY Daniel R. Brooks, Sherwin S. Desser and Henry Hong (parasite@zoo.toronto.edu) PHOTOSYNTHESIS Johnathan Marder (marder@agri.huji.ac.il) PLANT-BIOLOGY Tony Travis (ajt@rri.sari.ac.uk) POPULATION-BIOLOGY None PROTEIN-ANALYSIS Amos Bairoch (bairoch@cmu.unige.ch) and John Garavelli (garavelli@nbrf.georgetown.edu) PROTEIN-CRYSTALLOGRAPHY Morten Kjeldgaard (morten@oase.kemi.aau.dk) PROTISTA Marsha Altschule (marsha.i.altschuler@williams.edu) and Mark Farmer (farmer@emlab.zoo.uga.edu) RAPD James Farmer (farmerj@yvax.byu.edu) SCIENCE-RESOURCES ** David Kristofferson (kristoff@net.bio.net) STRUCTURAL-NMR C. S. Raman (raman@bioc01.uthscsa.edu) TROPICAL-BIOLOGY Matti Nummelin (saarikko@cc.helsinki.fi) VIROLOGY Robert Coelen (robert@arbo.microbiol.uwa.oz.au) WOMEN-IN-BIOLOGY Cassandra Smith (cls@buenga.bu.edu) YEAST Francis Ouellette (francis@ncbi.nlm.nih.gov) ** Note that newsgroups flagged with ** are moderated. Participating in BIOSCI Using USENET News Software -------------------------------------------------- Users who have access to USENET news software and the bionet USENET groups can participate immediately, i.e., they do not need to "subscribe" to anything. They can read and reply to messages using their local news software (e.g., "nn" or "rn") and post new messages of their own. Users will have to consult their local systems managers for help in using news software. There are many different programs available and the BIOSCI staff can not provide training in news software use. Fortunately, most news software is fairly simple to use and can be learned quickly. When posting new messages, USENET users should be sure to set the message "distribution" to "world" or "bionet" or else your message may not be distributed beyond your local computer. In most cases, messages are posted directly to the newsgroups without editorial intervention. Some groups (indicated in the lists above) are "moderated," however. This means that postings to these newsgroups will be sent to the newsgroup moderator who will decide whether or not the message is suitable for posting to the newsgroup in question. Participating in BIOSCI by E-mail --------------------------------- PLEASE NOTE THAT IF YOU HAVE ACCESS TO USENET NEWS YOU DO NOT NEED AN E-MAIL SUBSCRIPTION!! Simply read and post to the newsgroups in the "bionet" newsgroup hierarchy using your USENET news software. E-mail Subscription Requests and other Information -------------------------------------------------- For users in the Americas and Pacific Rim countries, e-mail subscription and cancellation requests are handled automatically by an e-mail server, although personal assistance is also available via the biosci-help@net.bio.net address. Once your e-mail address is added to a subscription list, mail will be sent to your address automatically each time someone posts a message. This will continue until you remove your address from the subscription list. You should first send the lists command to the address biosci-server@net.bio.net to obtain a listing of all current BIOSCI mailing lists. You may leave your message Subject: line blank in any message that is sent to the server (text on the Subject: line is *not* processed). Please include all commands only in the body of your mail message. Please BE SURE to substitute the appropriate mailing list name obtained FROM THE "lists" COMMAND OUTPUT for "listname" in the subscribe or unsubscribe commands shown below. Some list names used by the server are abbreviated compared to their full spelling in the BIOSCI information sheet. After obtaining the names of the mailing lists using the "lists" command, use the subscribe listname or unsubscribe listname commands to add or delete your address from the mailing lists. Please substitute "listname" above with the appropriate name of the list that you want to join/cancel. !!! PLEASE BE SURE to send all subscribe or unsubscribe commands only to !!! the biosci-server@net.bio.net address and not to the newsgroup posting !!! addresses where they will bother all of the readers! Your e-mail address is obtained AUTOMATICALLY from the header of your mail message and should NOT be included on the subscribe/unsubscribe command line unless you need to sign up at a different address than the one you are currently using. Such requests must be handled manually by us and create extra work. (Also you would be surprised at how many people list their e-mail addresses incorrectly, so please let our server obtain this information automatically from your mail header.) Multiple commands may be placed on separate lines in the same mail message, i.e., you can include all of your subscribe and/or unsubscribe requests in one mail message as long as each is on a separate line. If you put multiple commands in your mail message, please put an end command as the last in your list of commands. This helps avoid sending to the server any signatures that might be automatically included in your mail messages. Here is a sample subscription message. The address public@state-u.edu would be automatically added to the bionews and grasses mailing lists as the result of this message. To: biosci-server@net.bio.net From: J.Q. Public Subject: subscribe bionews subscribe grasses end If you are already a BIOSCI e-mail subscriber and need to determine which mailing lists you are on currently, send the command which to biosci-server@net.bio.net if you are signed up under the address which will appear on the From: line of your mail message. If your address has changed, you can put a search string after the which command, e.g., if you are certain than your user name has always been jqpublic but do not remember the computer hostname, send the command which jqpublic Other command details are included in the mail server help file from biosci-server@net.bio.net. To get the server help file (in computerese 8-), send in the help command to the server address. E-mail Address Changes ---------------------- If you have subscribed to a newsgroup and are now leaving an institution or changing your e-mail address, it is IMPERATIVE that you cancel your subscription! Non-existent addresses or overflowing mailboxes cause computer mail programs to send back "daemon" messages which might bother everybody on the newsgroup. We will immediately remove any address causing such a problem, but would prefer it if you would notify us in advance as a courtesy to the rest of the user community. Interruption of E-mail Service ------------------------------ It is our policy to remove any address from our mailing lists which becomes inaccessible and causes mail to bounce back to the sender. This might happen to you if your local computer or network fails for a significant period of time. If you notice that you are no longer receiving BIOSCI postings, it may be because your address was removed for the above reason. It will be necessary for you to contact biosci-help@net.bio.net and resubscribe. Please see the BIOSCI FAQ, mentioned at the beginning of this document, for more details on how BIOSCI handles addresses which reject mail. Posting Messages to Newsgroups by E-mail ---------------------------------------- Those who use e-mail to post messages should send their mail to the following Internet addresses in the USA: ********************************************************************** DO NOT, REPEAT, DO NOT POST SUBSCRIPTION OR CANCELLATION REQUESTS DIRECTLY TO ANY OF THE NEWSGROUP E-MAIL POSTING ADDRESSES. PLEASE USE ONLY THE ADDRESS biosci-server@net.bio.net for subscription or cancellation requests as explained above. Your posting could go to several thousand people. Supposing that each person spends a couple of seconds to figure out that you did this, before they go on to the next message. You will have wasted the equivalent of several hours of one person's time, not to mention wasted computer time and disk storage. ********************************************************************** MAILING LIST NAME Mailing Address ----------------- ---------------- ACEDB-SOFT acedb@net.bio.net AGEING ageing@net.bio.net AGROFORESTRY ag-forst@net.bio.net ARABIDOPSIS arab-gen@