From owner-software@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!RASCAL.MED.HARVARD.EDU!BARRETT From: BARRETT@RASCAL.MED.HARVARD.EDU Newsgroups: bionet.software Subject: Software for behavior recording Date: 2 Dec 1996 12:59:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <961202154511.8407@rascal.med.harvard.edu> NNTP-Posting-Host: net.bio.net Dear Fellow Netters, I am wondering if someone out there has made a software program that will approximate chart recording. That is, if I have a periodic behavior that I am testing, and I want to be able to record not only units activity/time, but also the durations between activities, is there a program I can use to do it? Ideally I'd want to be able to use a footpedal but a mouse would also do for input, and output would be best written to a file for analysis. I'd like to use one of our outdated IBM's for this, but a Mac program would also do. (I could write the program myself, but surely someone else out there has already done so, and it saves me the time of figuring out how to read footpedal as input and parameters for writing out the files, etc.) Thanks much in advance, Peter Barrett barrett@a1.tch.harvard.edu From owner-software@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!news.deakin.edu.au!okda15 From: karthi@deakin.edu.au (Karthi Ramachandran) Newsgroups: bionet.software Subject: software for counting colonies Date: Mon, 02 Dec 96 05:06:33 GMT Organization: Deakin University Lines: 24 Message-ID: <57toeg$itc@miranda.its.deakin.edu.au> Reply-To: karthi@deakin.edu.au NNTP-Posting-Host: okda15.bcs.deakin.edu.au X-Newsreader: News Xpress 2.0 Beta #2 Hi everyone, We are doing some genetics experiments that requirs counting colonies on 100s of plates each time. We have the facility for capturing images of these plates and storing them digitally. I am wondering if there are any software commercial/ shareware/ freeware that will count the colonies from these images? Any pointers will be greatly appreciated Thanx very much Karthi. R --------------------------------------------------------------------------- Karthikeyan Ramachandran Ph.D Research Fellow, Rm. No. SA136 School of Biological and Chemical Sciences Faculty of Science and Technology Phone (Off) (052) 271 406 Deakin University Phone (Res) (052) 419 806 Geelong, Victoria Fax (052) 272 022 Australia 3217 e-mail karthi@deakin.edu.au Home page http://www.deakin.edu.au/~karthi/ From owner-software@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!U.WASHINGTON.EDU!chusj From: chusj@U.WASHINGTON.EDU (Shi-Jye Chu) Newsgroups: bionet.software Subject: PCR-MACInt.XLM Date: 2 Dec 1996 13:42:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <01bbdf21$d9d74820$8dd0bfcc@ns.iceonline.com> NNTP-Posting-Host: net.bio.net Hi: I find a paper in biotechniques in June ,1996 1088-1099. that we can free dowload the soft ware( PCR-MacInt.XLM) from BioComputing section of bioteniques site. But I can' not find it. Does anybody know how to get it. I like to try it. thank you. S-J From owner-software@net.bio.net Sun Dec 01 22:00:00 1996 Path: biosci!IRCM.UMontreal.CA!duhaimj From: duhaimj@IRCM.UMontreal.CA ("SI-Johanne Duhaime") Newsgroups: bionet.software Subject: (none) Date: 2 Dec 1996 10:11:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <961202131050.ZM24390@si05.IRCM.UMontreal.CA> NNTP-Posting-Host: net.bio.net Good morning We would like to have a program that make an analysis of phosphopeptides generated by tryptic digestion and migration on cellulose. Does anyone know about such a program? Thank you -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Duhaimj@ircm.umontreal.ca From owner-software@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!in1.uu.net!138.95.18.2!wilbur.sequent.com!newsfeed.orst.edu!news.orst.edu!rohrmann-1073b-a.als.orst.edu!user From: funkc@bcc.orst.edu (Joel Funk) Newsgroups: bionet.software Subject: Re: Alternatives to Reference Update? Date: 3 Dec 1996 17:20:42 GMT Organization: Ag. Chem., Oregon St. Univ. Lines: 43 Message-ID: References: <57ioft$adq@umbra.unr.edu> NNTP-Posting-Host: rohrmann-1073b-a.als.orst.edu Here is a low cost option. For $25 per year (or for free if your library subscribes) Uncover Reveal will e-mail Journal Table of Content pages and weekly searches of newly released titles using your personal search strategy. Check out the following Web page: http://www.carl.org/reveal/index.html Here is a short description from their Web Page: "UnCover Reveal is an automated alerting service that delivers the table of contents of your favorite periodicals directly to your e-mail box. The Reveal service also allows users to create search strategies for their favorite topics. These search strategies are then run against the entire UnCover database and weekly alerts on the latest articles published on the specified topics are also delivered to the user's e-mail address. In both cases, after viewing the e-mailed alerts, the user can selectively order and pay for individual articles from UnCover by sending reply e-mail or printing the page and faxing the order to UnCover". In article <57ioft$adq@umbra.unr.edu>, malc@unr.edu wrote: > Are there any software alternatives to the Reference Update package? > > It would be lovely to be able to search for references via WWW rather > than having to deal with the native Windows or DOS software that RIS > currently offers, given the crash-prone nature of the Windows and DOS > environments. > > I'm told that RIS won't have its WWW-based software ready until sometime > in 1997. Is anything else already out there? > > Thanks in advance for any info. > > Malcolm > -- > Malcolm L. Carlock UNR Unix Administration and Support > --Email: malc@unr.edu --WWW: http://unr.edu/homepage/malc > --Voice: 702-784-4637 --Fax: 702-784-4050 > --USMail: University of Nevada, Reno / Mailstop 180 / Reno / NV / 89557 From owner-software@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!feed1.news.erols.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!uky.edu!usenet From: "Michael W. Thompson" Newsgroups: bionet.software Subject: Re: Human Genome Database Date: Tue, 03 Dec 1996 15:36:37 -0400 Organization: University of Kentucky Lines: 22 Message-ID: <32A48145.1DBF@pop.uky.edu> References: <57kphk$4fe@mserv1.dl.ac.uk> NNTP-Posting-Host: 128.163.70.124 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Gerard Pujadas wrote: > > Dear netters, I'm sorry if I've posted the mail in an unapropiate > list. I would like to know if the human genome sequences are available as > part of the GenBank or there is an specialized DataBank for them. In that > case, where may I ftp the document which contains the human genome. You can access human genomic sequences via NCBI at: http://www.ncbi.nlm.nih.gov/BLAST/ Just enter your search sequence and choose "gss" as the database to search. Alternatively, if you want to search for a specific gene or chromosomal location, hit the NCBI logo at the top to go to their home page, and there will be other search options for genbank. Hope this is of some help to you. Michael W. Thompson University of Kentucky Department of Biochemistry Lexington, KY 40536 From owner-software@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!news.ox.ac.uk!worf.molbiol.ox.ac.uk!rgrant From: rgrant@worf.molbiol.ox.ac.uk (Richard P Grant) Newsgroups: bionet.software Subject: Cricket Graph Date: 3 Dec 1996 17:08:35 GMT Organization: Oxford University Lines: 14 Message-ID: <581mqj$aj8@news.ox.ac.uk> NNTP-Posting-Host: worf.molbiol.ox.ac.uk X-Newsreader: TIN [version 1.2 PL2] [ Article crossposted from comp.sys.mac.apps ] [ Author was Richard P Grant (rgrant@worf.molbiol.ox.ac.uk) ] [ Posted on 3 Dec 1996 17:07:13 GMT ] X-posted to reach a different readership ;-) Is anyone else having severe problems with CricketGraph on PCI Pmacs? Apart from trashing it completely, has anyone found a solution? -- Richard P. Grant University of Oxford Nuffield Department Obstetrics and Gynaecology FFPGP http://users.ox.ac.uk/~lady0266 http://www.molbiol.ox.ac.uk/~rgrant ---------------------# hit any user to continue #--------------------- From owner-software@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!cssun.mathcs.emory.edu!cc.gatech.edu!prism!acmez!kj34 From: kj34@acmez.gatech.edu (Cthulu) Newsgroups: bionet.software Subject: Help with Insight II Date: 3 Dec 1996 18:26:03 GMT Organization: Georgia Institute of Technology Lines: 9 Message-ID: <581rbr$aqf@catapult.gatech.edu> NNTP-Posting-Host: acmez-prism.gatech.edu X-Newsreader: TIN [version 1.2 PL2] Can somebody tell me how to save an Insight binary file (.psv) in a format that can be read by Chain? Specifically, I have superimposed two molecules using Insight, and I want to finish working with them in Chain. -- Kevin Jude Georgia Institute of Technology, Atlanta Georgia, 30332 kj34@prism.gatech.edu From owner-software@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.idt.net!cdc2.cdc.net!news.texas.net!news1.best.com!miwok!usenet From: Libr Newsgroups: bionet.software Subject: Help for course study Date: Tue, 03 Dec 1996 00:23:34 -0800 Organization: University of Northern California Lines: 13 Message-ID: <32A3E386.33D4@nbn.com> NNTP-Posting-Host: rpk-14.nbn.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Hi, everybody, I am a graduate student in the Dept. of Biomedical Engineering of University of Northern California. Due to my biology background, my professor suggests me to learn some bioinformation knowledge on the internet. However he doesn't know much about molecular biology and have no idea to advise me. Due to limitation of the facility here, I didn't have any other way to learn it. Anyone who knows if there is any kind of review about this field and how to use free software to analys the DNA sequence and translate it into protein, please give me a hand. My e-mail address is zhong@uncm.edu. Thanks very much X.Hong Zhong From owner-software@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!feed1.news.erols.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!uky.edu!usenet From: "Michael W. Thompson" Newsgroups: bionet.software Subject: Re: Retrieving sequence files from NCBI Date: Tue, 03 Dec 1996 15:41:02 -0400 Organization: University of Kentucky Lines: 3 Message-ID: <32A4824D.7883@pop.uky.edu> References: <32A444EA.41C67EA6@bio01.bio.uottawa.ca> NNTP-Posting-Host: 128.163.70.124 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Sorry that I don't know where to get it, but you can order genbank on CD-ROM. From there you can download all the sequences your hard drive will hold :) From owner-software@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!howland.erols.net!torn!nott!uottawa!news From: "Andrew St. Jean" Newsgroups: bionet.software Subject: Retrieving sequence files from NCBI Date: Tue, 03 Dec 1996 10:19:06 -0500 Organization: andrew@bio01.bio.uottawa.ca Lines: 12 Message-ID: <32A444EA.41C67EA6@bio01.bio.uottawa.ca> NNTP-Posting-Host: 137.122.25.28 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 4.1.4 sun4m) Dear All, I'm looking for a way to download large numbers of genbank format sequence files. By large numbers, I mean thousands. Does anybody know of any programs available to do the transfer preferably by ftp? I know about the online batch retrieve offered by NCBI but I'm looking for a program I can automate. Please send replies to: andrew@bio01.bio.uottawa.ca Andrew St. Jean University of Ottawa From owner-software@net.bio.net Mon Dec 02 22:00:00 1996 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: Human Genome Database Date: 3 Dec 1996 15:02:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 74 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612032301.SAA04270@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net > From mthom0@service1.uky.edu Tue Dec 3 17:22:13 1996 > Gerard Pujadas wrote: > > > > Dear netters, I'm sorry if I've posted the mail in an unapropiate > > list. I would like to know if the human genome sequences are available as > > part of the GenBank or there is an specialized DataBank for them. In that > > case, where may I ftp the document which contains the human genome. > > You can access human genomic sequences via NCBI at: > > http://www.ncbi.nlm.nih.gov/BLAST/ > > Just enter your search sequence and choose "gss" as the database to > search. Alternatively, if you want to search for a specific gene or > chromosomal location, hit the NCBI logo at the top to go to their home > page, and there will be other search options for genbank. Users should note that the 'gss' database is a subset of GenBank which probably does not includes the types of sequences you are looking for. (text from gbrel.txt when GSS was introduced attached below). Note that the gss division is not really (yet) that much comprehensive (only a few thousand records). If you want to find something, maybe better to use the nr database. And a protein search (protein/protein:blastp or nucleotide_translation/protein:blastx) is always more sensitive than a nucleotide/nucleotide:blastn search (specially if you are looking for similarities across species) cheers, f. -- | B.F. Francis Ouellette | GenBank Coordinator | | francis@ncbi.nlm.nih.gov > 1.3.3 New GenBank Division in Release 96.0 > > A new division, GSS (Genome Survey Sequence), has been added > to the GenBank Flatfile release distribution; the file name is > gbgss.seq . > > This new division is similar in nature to the EST division, except that > its sequences are genomic in origin, rather than cDNA (mRNA). The GSS > division contains (but will not be limited to) the following types of > data: > > - random "single pass read" genome survey sequences. > - single pass reads from cosmid/BAC/YAC ends > (these could be chromosome specific, but need not be) > - exon trapped genomic sequences > - Alu PCR sequences > > Many labs have approached GenBank over the last few months, interested > in submitting these types of sequences. We have been reluctant to > introduce them via the existing GenBank divisions. On the other hand, > such sequences are of value to the genome community, and require > similar processing and access tools as have been provided for EST's and > STS's. GSS sequences will will be used, amongst other things, as a > framework for the mapping and sequencing of genome size pieces which > will be present in the standard GenBank divisions. > > Sequence data appropriate for the new GSS division are, to date, > generated by genome labs performing human genome sequencing; we expect > that similar data will be generated for other model organisms, such as > the mouse. From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Newsgroups: bionet.software Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!bshomer From: bshomer@ebi.ac.uk (Benny Shomer) Subject: Re: GDE on DEC Alpha Sender: news@ebi.ac.uk (usenet news) Message-ID: Date: Wed, 4 Dec 1996 10:35:59 GMT References: <329C51BD.41C6@evol.gene.nott.ac.uk> Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 21 Andrew Gentles (pdzajg@evol.gene.nott.ac.uk) wrote: : Has anybody succeeded in mutilating the source code of GDE enough to get : it to compile and run on a DEC alpha under Digital Unix (i.e. OSF/1) ? Andrew, Regretfully, you can't do it. GDE relies on the xview libraries which are SUNOS specific and are not available for other platforms (as far as I know). Regards, Benny. -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Benny Shomer, Ph.D. Biological User Support EMBL outstation - The EBI, Tel: +44-223-494437 Hinxton Hall, Hinxton, Fax: +44-223-494468 Cambridge CB10 1RQ, UK Email: bshomer@EBI.ac.uk ~~~~~~ http://www.ebi.ac.uk/ebi_docs/staff/benny.html ~~~~~~ From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!PCLSP2.KUICR.KYOTO-U.AC.JP!mihara From: mihara@PCLSP2.KUICR.KYOTO-U.AC.JP (Hisaaki Mihara) Newsgroups: bionet.software Subject: promoter prediction software for Mac Date: 3 Dec 1996 18:10:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <32A4DDFD.5A9B@pclsp2.kuicr.kyoto-u.ac.jp> Reply-To: mihara@pclsp2.kuicr.kyoto-u.ac.jp NNTP-Posting-Host: net.bio.net Could you help me to find any free or share software (for Mac) for prediction of promoter-like (terminator-like) sequences in procaryots genome. Thank you. From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!bunyip.cc.uq.oz.au!newshost.gu.edu.au!usenet From: Conor McCarthy Newsgroups: bionet.software Subject: Chromas 1.2 Date: Wed, 04 Dec 1996 14:13:50 +1000 Organization: Griffith University Lines: 21 Message-ID: <32A4FA7E.480D@sct.gu.edu.au> NNTP-Posting-Host: ibeacham.sci.gu.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; 68K) Hi, Chromas is a Windows application which displays and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF and Li-Cor sequencers can create. Chromas allows basecall editing and exporting of the sequence to a file or the clipboard. The following features are new in v1.2: * Chromatograms can be saved in Staden SCF format. * The sequence can be exported in FASTA format. * There is an option to automatically select the next base in the sequence after a base is changed. * You can scroll through the sequence using the arrow keys. Chromas can be downloaded from: http://trishul.sci.gu.edu.au/~conor/chromas.html Cheers, Conor From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!www.nntp.primenet.com!nntp.primenet.com!uwm.edu!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Re: GDE on DEC Alpha Date: 4 Dec 1996 18:37:30 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 24 Message-ID: <584gda$o66@gap.cco.caltech.edu> References: <329C51BD.41C6@evol.gene.nott.ac.uk> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article , bshomer@ebi.ac.uk (Benny Shomer) writes: >Andrew Gentles (pdzajg@evol.gene.nott.ac.uk) wrote: >: Has anybody succeeded in mutilating the source code of GDE enough to get >: it to compile and run on a DEC alpha under Digital Unix (i.e. OSF/1) ? > >Andrew, > >Regretfully, you can't do it. GDE relies on the xview libraries which are >SUNOS specific and are not available for other platforms (as far as I >know). Well, you can get the Xview code, whether or not you can make it work is another question. If you have not done it yet and you have GCG, I wouldn't bother, as GDE is being merged with the WPI in the next GCG release. Since that does run on Alphas (either Unix or OpenVMS), your problem would be solved. The reference for that is, hmm...., here: http://www.gcg.com/attractions/seqlab.html Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!www.nntp.primenet.com!nntp.primenet.com!usenet.eel.ufl.edu!warwick!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: UNIX tar format to ASCII Date: 4 Dec 1996 19:01:53 GMT Organization: University of Cambridge Lines: 20 Message-ID: <584hr1$2g0@lyra.csx.cam.ac.uk> References: <01bbe1ac$2be93970$f308b6cc@monahan> NNTP-Posting-Host: mole.bio.cam.ac.uk In article <01bbe1ac$2be93970$f308b6cc@monahan>, John Monahan wrote: >Could somebody please point me to where I could download a PC/Windows95 >compatible program to read a UNIX >.tar compressed file and convert it to simple ASCII. What do you mean convert it to ASCII? tar archives may contain several files, and the contents of those files could be anything; text, binary data, etc etc. If you mean converting UNIX text documents into DOS text documents, I have written a small utility to do that (UNIX2DOS.COM, if you want a copy send me a mail). I also have a copy of GNU tar for Windows NT (which should run happily under Windows 95, although I haven't tested it). Tim. From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!agate!howland.erols.net!news.sgi.com!news.msfc.nasa.gov!bcm.tmc.edu!news From: Kim Worley Newsgroups: bionet.software Subject: Re: Retrieving sequence files from NCBI Date: Wed, 04 Dec 1996 13:11:00 -0500 Organization: Baylor College of Medicine Lines: 19 Message-ID: <32A5BEB4.49E6@bcm.tmc.edu> References: <32A444EA.41C67EA6@bio01.bio.uottawa.ca> NNTP-Posting-Host: dot.imgen.bcm.tmc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) Version 2.0 of the BCM Search Launcher Batch Client provides automatic retrieval of FASTA formatted sequence files from lists of sequence IDs. The sequence file corresponding to each sequence ID is retrieved from the NCBI's Entrez server, reformatted using Don Gilbert's Readseq and stored automatically in a fasta formatted file in the user's directory. These files are then available for further sequence analysis. The BCM Search Launcher Batch Client is a command line interface to Web based sequence analysis tools. Follow the link "A Batch Client..." on the home page below. In reference to the other reply to this posting, Entrez is no longer published on CDRom. ---------------------------------------------------------------- Kim C. Worley, Ph.D. kworley@bcm.tmc.edu P 713-798-8292 Baylor College of Medicine, Houston, TX 77030 F 713-798-5386 http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html ---------------------------------------------------------------- From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!howland.erols.net!newsxfer.itd.umich.edu!cwis-20.wayne.edu!usenet From: Gerard Tromp Newsgroups: bionet.software Subject: Re: Retrieving sequence files from NCBI Date: Wed, 04 Dec 1996 13:26:24 -0500 Organization: CMMG, Wayne State University Lines: 27 Message-ID: <32A5C250.1F24@sanger.med.wayne.edu> References: <32A444EA.41C67EA6@bio01.bio.uottawa.ca> NNTP-Posting-Host: sanger.med.wayne.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.4 sun4m) To: "Andrew St. Jean" Andrew St. Jean wrote: > > Dear All, > > I'm looking for a way to download large numbers of genbank format > sequence files. By large numbers, I mean thousands. Does anybody know > of any programs available to do the transfer preferably by ftp? I know > about the online batch retrieve offered by NCBI but I'm looking for a > program I can automate. Please send replies to: > > andrew@bio01.bio.uottawa.ca > > Andrew St. Jean > University of Ottawa You could just ftp the entire database (assuming you have enough storage) from ncbi.nlm.nih.gov using anaonymous ftp. Resides in /genbank as a series of compressed files. Gerard -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Gerard Tromp, Ph.D. CMMG, Wayne State University vox: 313-577-8773 3116, Scott Hall fax: 313-577-5218 540 E Canfield Ave e-mail: tromp@sanger.med.wayne.edu Detroit, MI 48201 gtromp@cmb.biosci.wayne.edu From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!news-peer.gsl.net!news.gsl.net!usenet.eel.ufl.edu!warwick!lyra.csx.cam.ac.uk!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software Subject: Re: GDE on DEC Alpha Date: Wed, 04 Dec 1996 16:34:42 +0000 Organization: SEQNET Lines: 30 Distribution: bionet Message-ID: <32A5A822.41C6@dl.ac.uk> References: <329C51BD.41C6@evol.gene.nott.ac.uk> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) Benny Shomer wrote: > > Andrew Gentles (pdzajg@evol.gene.nott.ac.uk) wrote: > : Has anybody succeeded in mutilating the source code of GDE enough to get > : it to compile and run on a DEC alpha under Digital Unix (i.e. OSF/1) ? > > Andrew, > > Regretfully, you can't do it. GDE relies on the xview libraries which are > SUNOS specific and are not available for other platforms (as far as I > know). > Well, thats not really true - GDE runs also on SGIs, linux and DECstations, but you need indeed a port of the xview libs. (Sorry - I have no idea if they have been ported to DEC/OSF1) Cheers, Martin -- ----------------------------------------------------------------- | Martin Hilbers | E-mail: m.p.hilbers@dl.ac.uk | | SEQNET | Tel: +44-1925-603492 | | Daresbury Laboratory | Fax: +44-1925-603100 | | Daresbury, Warrington |---------------------------------------| | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.dl.ac.uk/SEQNET/home.html | ----------------------------------------------------------------- From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Newsgroups: bionet.software Path: biosci!ihnp4.ucsd.edu!swrinde!www.nntp.primenet.com!nntp.primenet.com!arclight.uoregon.edu!news.sprintlink.net!news-peer.sprintlink.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!bshomer From: bshomer@ebi.ac.uk (Benny Shomer) Subject: Re: Human Genome Database Sender: news@ebi.ac.uk (usenet news) Message-ID: Date: Wed, 4 Dec 1996 10:17:38 GMT Distribution: bionet References: <57kphk$4fe@mserv1.dl.ac.uk> Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 24 Gerard Pujadas (pujadas@quimica.urv.es) wrote: : Dear netters, I'm sorry if I've posted the mail in an unapropiate : list. I would like to know if the human genome sequences are available as : part of the GenBank or there is an specialized DataBank for them. In that : case, where may I ftp the document which contains the human genome. Thanks : for your attention. All the sequences resulting from the human (and other species) genome projects are available on the nucleotide databases EMBL/Genbank/DDBJ. You may search for sequences at the EBI site through SRS: http://www.ebi.ac.uk/srs/srsc Hope it helps. -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Benny Shomer, Ph.D. Biological User Support EMBL outstation - The EBI, Tel: +44-223-494437 Hinxton Hall, Hinxton, Fax: +44-223-494468 Cambridge CB10 1RQ, UK Email: bshomer@EBI.ac.uk ~~~~~~ http://www.ebi.ac.uk/ebi_docs/staff/benny.html ~~~~~~ From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.idt.net!uunet!in2.uu.net!140.174.86.1!hoho.quake.net!jupiter.dnai.com!news From: "John Monahan" Newsgroups: bionet.software Subject: UNIX tar format to ASCII Date: 4 Dec 1996 06:27:23 GMT Organization: DNAI ( Direct Network Access ) Lines: 4 Message-ID: <01bbe1ac$2be93970$f308b6cc@monahan> NNTP-Posting-Host: isdn8-243.isdn.dnai.com X-Newsreader: Microsoft Internet News 4.70.1155 Could somebody please point me to where I could download a PC/Windows95 compatible program to read a UNIX .tar compressed file and convert it to simple ASCII. From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!newsfeed.internetmci.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!news.uoregon.edu!news.rediris.es!acebo.sdi.uam.es!newsmasters From: txomsy@cnb.uam.es (Jose R. Valverde) Newsgroups: bionet.software Subject: Re: GDE on DEC Alpha Date: 4 Dec 1996 19:29:18 GMT Organization: EMBnet/CNB Lines: 35 Message-ID: <584jee$12t@acebo.sdi.uam.es> References: <329C51BD.41C6@evol.gene.nott.ac.uk> NNTP-Posting-Host: bossa-nova.cnb.uam.es Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article , bshomer@ebi.ac.uk (Benny Shomer) writes: > Andrew Gentles (pdzajg@evol.gene.nott.ac.uk) wrote: >: Has anybody succeeded in mutilating the source code of GDE enough to get >: it to compile and run on a DEC alpha under Digital Unix (i.e. OSF/1) ? > > Andrew, > > Regretfully, you can't do it. GDE relies on the xview libraries which are > SUNOS specific and are not available for other platforms (as far as I > know). > > Regards, > > Benny. Hi Benny, glad to hear you... Just one correction: xview source code is available and has been ported to a number of platforms. You can run SUN's open-windows on those and hence you hsould be able to run GDE too. Among them and notably, are ultrix, Linux and *BSD. Note that I haven't had time to try to compile GDE on one of those, but in theory it should work. My last knowledge though was that GDE's GUI didn't run in DEC/Unix... jr -- Jose R. Valverde EMBnet/CNB From owner-software@net.bio.net Tue Dec 03 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!howland.erols.net!news.sgi.com!enews.sgi.com!arclight.uoregon.edu!news.uoregon.edu!news.rediris.es!acebo.sdi.uam.es!newsmasters From: txomsy@cnb.uam.es (Jose R. Valverde) Newsgroups: bionet.software Subject: Re: UNIX tar format to ASCII Date: 4 Dec 1996 19:32:38 GMT Organization: EMBnet/CNB Lines: 18 Message-ID: <584jkm$12t@acebo.sdi.uam.es> References: <01bbe1ac$2be93970$f308b6cc@monahan> NNTP-Posting-Host: bossa-nova.cnb.uam.es Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article <01bbe1ac$2be93970$f308b6cc@monahan>, "John Monahan" writes: > Could somebody please point me to where I could download a PC/Windows95 > compatible program to read a UNIX > .tar compressed file and convert it to simple ASCII. > I submitted (many years ago) a DETAR program for MS-DOS to the EMBL software archives. It had the advantage that it also corrected CR/LF on the fly. Dunno if it will still be around, but if it is, it should be in ftp.ebi.ac.uk/pub/software/dos I don't have any old copy around any longer (broke free from M$-world long ago, and happy I am, man). jr From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in1.uu.net!192.244.176.52!news.iij.ad.jp!nr1.scn.co.jp!news.he.net!news.dra.com!xara.net!emerald.xara.net!xara.net!agate.xara.net!zynet.net!usenet From: Peter Jackman Newsgroups: bionet.software Subject: Re: gel analysis software Date: Wed, 27 Nov 1996 19:38:29 +0000 Organization: BioSystematica Lines: 23 Message-ID: <329C98B5.4685@mail.zynet.co.uk> References: <56phu4$sbi@news.ox.ac.uk> <19961118150700.KAA29538@ladder01.news.aol.com> Reply-To: biosys@mail.zynet.co.uk NNTP-Posting-Host: biosys.zynet.co.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Please see our web site for info on Windows gel analysis software. http://www.cis.plym.ac.uk/biosys/biosys.htm With best regards, Dr Peter Jackman BioSystematica --------------------------------------------------------- BIOSYSTEMATICA - the gel analysis specialists --------------------------------------------------------- 2 Mill Cottages Tel & Fax +44-1822-810827 Peter Tavy Tavistock biosys@mail.zynet.co.uk Devon PL19 9AA United Kingdom Web site http://www.cis.plym.ac.uk/biosys/biosys.htm --------------------------------------------------------- From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!news-peer.gsl.net!news.gsl.net!hammer.uoregon.edu!arclight.uoregon.edu!enews.sgi.com!news-feed.inet.tele.dk!news.daimi.aau.dk!klovnen.herb.bio.aau.dk!user From: reno@pop.bio.aau.dk (Reno Lindberg) Newsgroups: bionet.software Subject: UTM-Lat/Long conversion Date: Thu, 05 Dec 1996 14:18:05 +0100 Organization: Private Lines: 14 Message-ID: NNTP-Posting-Host: klovnen.herb.bio.aau.dk I have a rather large dataset of Lat/Long positions from northern Europe and from south America. I would like to convert these data to UTM cordinates and vice versa. Do any of you have knowledge about a package or a program string doing the job. As far as I know, it is a bit difficult because of some special settings for longitudes east of a certain number and a special setting for south of the equator. I have searched the net for shareware/freeware programs doing the job without finding any (Mac programs would be preferable). I think that Mathematica would be a good platform for a package of that kind and there MUST be quite a lot of people working with positions either in Lat/long or UTM that would like to do conversions between the two systems I hope some of you can help me reno@pop.bio.aau.dk From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!feed1.news.erols.com!news.ecn.uoknor.edu!paladin.american.edu!news.jhu.edu!news From: Wilson_Lab Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: Thu, 05 Dec 1996 16:50:17 -0400 Organization: Johns Hopkins University School of Medicine Lines: 37 Message-ID: <32A73586.5885@welchlink.welch.jhu.edu> References: <3281117D.7CB3@salk.edu> <3292ADEB.3CEB@ll.mit.edu> NNTP-Posting-Host: 128.220.138.135 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Xref: biosci bionet.software:17292 comp.sys.mac.scitech:9665 I think Sigma Plot is a good choice, and prefer it to Kaleidagraph. Dale Olve Peersen wrote: > > Let me just add that you can download a demo of Kaleidagraph (for Mac or > that other OS) frmn the Synergy web site at "http://www.synergy.com" > > Olve > > > > S L Forsburg wrote: > > > > > > > > Time to purchase software for an additional PPC Mac. I have no > > experience with Deltagraph, which looks > > > > like the most reasonable alternative. > > > > Comments and opinions sought!! > > > > > > > My personal vote goes to Kaleidagraph from Synergy Software (order through > > MacZone, MacConnection, MacWarehouse etc.). It can pretty much take care > > of any two dimensional graph (no 3D yet) you want in a very clean and > > efficient user interface, and it can do fast curve fitting, including > > writing your own equations with up to 9 variables. > > > > Costs $150 or so, if I remember right. > > > > Olve Peersen > > > > ----------------------------------------------------------------- > > Olve Peersen Peersen@Colorado.edu > > University of Colorado - Boulder > > Dept. of Chemistry & Biochemistry > > ----------------------------------------------------------------- > Olve Peersen Peersen@Colorado.edu > University of Colorado - Boulder > Dept. of Chemistry & Biochemistry From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!agate!howland.erols.net!dciteleport.com!worldnet.att.net!uunet!in3.uu.net!199.232.56.18!news.ultranet.com!usenet From: Marc Andelman Newsgroups: bionet.software Subject: job opportunity, bioniformatics,MIS Date: Thu, 05 Dec 1996 18:18:58 -0800 Organization: Biosource Lines: 23 Message-ID: <32A78292.1F6A@ultranet.com> NNTP-Posting-Host: biosource.ultranet.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win95; U) Hi. Biosource is an employer paid fee service and the oldest recruitment firm in the biotech industry. We currently have a client in the SF Bay area (on the Peninsula) that is a biotech firm. They would like to hire a fairly senior person with excellent project management skills to lead their MIS group. This will get into some pretty interesting work in databases for biotech based drug development, managing outside programming contractors, as well as in house database and network needs, bioniformatics,etc. Experience with biology would be nice but not required. Please feel free to refer anyone who may be interested. Thank you for any attention you choose to give to this matter. Regards, Marc Andelman President Biosource Inc 1 Parkton Ave Worcester, MA 01605 tel 508 865 8803 fax 508 853 8772 Email drgonfly@biosource.ultranet.com From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!IRCM.UMontreal.CA!duhaimj From: duhaimj@IRCM.UMontreal.CA ("SI-Johanne Duhaime") Newsgroups: bionet.software Subject: Again plasmid software Date: 5 Dec 1996 12:58:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <961205155801.ZM12494@si05.IRCM.UMontreal.CA> NNTP-Posting-Host: net.bio.net Bonjour I know there are a lot of mail on plasmid software. But may be someone can help me. We studied different softwares (windows: Clone manager, Winplas, Plasmid Toolkit, Vector NTI). Few of them allow features like inserting a at a certain base number (not only at a enzyme site), keeping historical version of the construction etc. If fact only one of them allows such fonctionnalities but it is to much expensive. Beeing so expansive, we told ourself: we will install install a network version of the software and have a possibitity to have different database files for differents users (which the selected software will not do). But the software does not allow this. If this is not a possibily, then we need a software less expansive that does the work so that each researcher can have there own copy. But from the ones we have been studying nothing satisfied us. Anyone have something approching the ideal software? -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Duhaimj@ircm.umontreal.ca From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Newsgroups: bionet.software Path: biosci!ihnp4.ucsd.edu!swrinde!www.nntp.primenet.com!nntp.primenet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in1.uu.net!192.35.48.11!hearst.acc.Virginia.EDU!murdoch!usenet From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Subject: FASTA updates X-Nntp-Posting-Host: alpha0.bioch.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia X-Newsreader: Gnus v5.3/Emacs 19.34 Date: Thu, 5 Dec 1996 21:03:02 GMT Lines: 17 Several updates to the FASTA program are available from ftp.virginia.edu in /pub/fasta: fasta30t74.shar.Z fixes a bug with reverse complement searches with fastx3(_t) It also provides several improvements in the machine-parseable format and now allows alignment to be shown without any sequence context (-W 0). fasta20u62.shar.Z fixes the reverse complement fastx problem. The DOS/Win95/WinNT versions have also been updated to fix the fastx reverse-complement problem (dos/fa20u632.exe, dos/fa20u616.exe). Bill Pearson From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Newsgroups: bionet.software Path: biosci!ihnp4.ucsd.edu!swrinde!news.sgi.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!news-feed.inet.tele.dk!sn.no!nntp.uio.no!news.apfel.de!nntp.zit.th-darmstadt.de!fu-berlin.de!news-ber1.dfn.de!news-lei1.dfn.de!news-nue1.dfn.de!news-mue1.dfn.de!news-stu1.dfn.de!news-kar1.dfn.de!news-koe1.dfn.de!news.dfn.de!news.uni-bielefeld.de!techfak.uni-bielefeld.de!fuellen From: fuellen@techfak.uni-bielefeld.de (Georg Fuellen) Subject: Re: Help for course study Message-ID: Sender: fuellen@TechFak.Uni-Bielefeld.DE (Georg Fuellen) Cc: fuellen Date: Thu, 5 Dec 1996 14:09:44 GMT To: Libr References: <32A3E386.33D4@nbn.com> Nntp-Posting-Host: salbei.techfak.uni-bielefeld.de Organization: Universitaet Bielefeld, Technische Fakultaet. X-Newsreader: xrn 8.01 Lines: 23 In article <32A3E386.33D4@nbn.com>, Libr writes: |> Hi, everybody, I am a graduate student in the Dept. of |> Biomedical Engineering of University of Northern California. Due to my |> biology background, my professor suggests me to learn some bioinformation |> knowledge on the internet. However he doesn't know much about molecular |> biology and have no idea to advise me. Due to limitation of the facility |> here, I didn't have any other way to learn it. Anyone who knows if |> there is any kind of review about this field and how to use free software |> to analys the DNA sequence and translate it into protein, please give me |> a hand. My e-mail address is zhong@uncm.edu. If you're interested in biocomputing/bioinformatics, and sequence analysis in particular, try http://www.techfak.uni-bielefeld.de/bcd/welcome.html best wishes, georg fuellen@dali.Mathematik.Uni-Bielefeld.DE, fuellen@Techfak.Uni-Bielefeld.DE http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/georgF.html |> Thanks very much |> |> X.Hong Zhong From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!vixen.cso.uiuc.edu!chaos.crhc.uiuc.edu!news2.acs.oakland.edu!cwis-20.wayne.edu!cmb.biosci.wayne.edu!dwomble From: dwomble@cmb.biosci.wayne.edu (David Womble) Newsgroups: bionet.software Subject: Re: UNIX tar format to ASCII Date: 5 Dec 1996 13:42:03 GMT Organization: Wayne State University Lines: 29 Message-ID: <586jfb$m5c@cwis-20.wayne.edu> References: <01bbe1ac$2be93970$f308b6cc@monahan> <584jkm$12t@acebo.sdi.uam.es> Reply-To: dwomble@cmb.biosci.wayne.edu NNTP-Posting-Host: cmb.biosci.wayne.edu X-Newsreader: TIN [version 1.2 PL2] detar, extar, and others for dos are available at: http://oak.oakland.edu/simcgi-bin/dosfind.cgi?tar You can also search for Windows apps at Oak if you like. Jose R. Valverde (txomsy@cnb.uam.es) wrote: : In article <01bbe1ac$2be93970$f308b6cc@monahan>, : "John Monahan" writes: : > Could somebody please point me to where I could download a PC/Windows95 : > compatible program to read a UNIX : > .tar compressed file and convert it to simple ASCII. : > : I submitted (many years ago) a DETAR program for MS-DOS to the EMBL : software archives. It had the advantage that it also corrected CR/LF : on the fly. : Dunno if it will still be around, but if it is, it should be in : ftp.ebi.ac.uk/pub/software/dos : I don't have any old copy around any longer (broke free from M$-world : long ago, and happy I am, man). : jr -- David D. Womble Phone: 313-577-2374 Center for Molecular Medicine and Fax: 313-577-6200 Genetics, Wayne State University E-mail: dwomble@cmb.biosci.wayne.edu 5047 Gullen Mall, Detroit, MI 48202 http://cmmg.biosci.wayne.edu/ From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!news.service.uci.edu!skink.bio.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: UNIX tar format to ASCII Date: Thu, 05 Dec 1996 10:41:31 -0800 Organization: Dev+Cell Biology, UC Irvine Lines: 14 Message-ID: References: <01bbe1ac$2be93970$f308b6cc@monahan> NNTP-Posting-Host: skink.bio.uci.edu > Could somebody please point me to where I could download a PC/Windows95 > compatible program to read a UNIX > .tar compressed file and convert it to simple ASCII. Winzip (shareware) will do it, Stuffit Expander for Windows will do most everything (but not detar, nor uncompress, strangely, tho the Mac version will), and tho it won't do nuthin but zip, the new pkzip for Windows is very nice (no, I didn't say anything nice about Windows per se) Use www.shareware.com to get the closest copies hjm -- Harry J Mangalam, MolBio+Biochem / Dev+Cell Bio, Rm 4201, BioSciII UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 From owner-software@net.bio.net Wed Dec 04 22:00:00 1996 Path: biosci!rutgers!dziuxsolim.rutgers.edu!waller-a-asy-14.rutgers.edu!user From: elinton@rci.rutgers.edu (Eric W. Linton) Newsgroups: bionet.software Subject: Re: GDE on DEC Alpha Date: Thu, 05 Dec 1996 18:55:08 -0500 Organization: Rutgers University Lines: 39 Message-ID: References: <329C51BD.41C6@evol.gene.nott.ac.uk> <584gda$o66@gap.cco.caltech.edu> NNTP-Posting-Host: waller-a-asy-14.rutgers.edu X-poster: elinton@rci-dialup Hi, This is from the GDE site at gopher://megasun.bch.umontreal.ca:70/11/GDE/DEC hope this fits the bill for you. eric >Genetic Data Environment is Now on the DECstation >GDE2.0 is now available on the DECstation (21/31/5000). A binary version >compiled under MIT X11R5 and SUN XView3.0 is now on golgi.harvard.edu in >the pub/GDE2.0 directory. This release has not been tested with >DECwindows, and therefore may require the OpenLook fonts to function. >The xview programs shelltool and textedit are also included, along >with the OpenLook Window manager olwm. >GDE is now up to revision b for both SUN and DEC versions. If you are not >up to the current revision, there is an update tar file on golgi. If you >have not registered your copy of GDE2.0, please do so with the registration >form in the UPDATES directory on golgi. >Steve Smith >Harvard Genome Lab . -- Eric Linton Rutgers, The State University of New Jersey Cell and Developmental Biology E-mail: elinton@rci.rutgers.edu web page: http://www.rci.rutgers.edu/~elinton snail mail: Rutgers/Nelson Labs C-109 P O Box 1059 Piscataway, NJ 08855-1059 From owner-software@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: IUBio Archive news Date: 6 Dec 1996 16:53:16 GMT Organization: Biology, Indiana University - Bloomington Lines: 79 Message-ID: <589j1s$h6t@dismay.ucs.indiana.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu IUBio Archive is an archive of biology data and software. The archive includes items to browse, search and fetch public software, molecular data, biology news and documents. It is a public archive that you will find at the Internet address iubio.bio.indiana.edu. This archive, maintained at Indiana University Biology department since 1989, has moved recently from one computer to another. Access to the archive is via HTTP (world wide web), Internet Gopher, anonymous FTP (file transfer) and e-mail programs that connect to computers on the Internet. ftp:, gopher:, http://iubio.bio.indiana.edu/ mailto: gopher@iubio.bio.indiana.edu Molecular biology is the area of concentration, and it is also a home for Drosophila research data. The archive maintains software for all computer systems important to biology. Public software categories served here include biology, chemistry, science, utilities, molecular biology sections including alignment, codon, autoseq, browsing, consensus, evolve, pattern, primer, restrict-enzymes, rna-fold, search, ibmpc, mac, mswin, unix, vax Search services include GenBank nucleic databank (WAIS query of full release and weekly updates) Swiss-Prot and PIR protein databanks Bionet news (full, searchable archive since Dec 1990) SRS (Sequence Retrieval System) - including Genbank, protein and others for both simple and sophisticated text/annotation queries of databanks SRS-FastA - for sequence similarity searches against any user-defined subset of Genbank & protein data, including subsets for popular species Arabidopsis, Caenorhabditis, Drosophila, Oryza, Poaeceae, Rattus, Murinae, and Saccharomyces This is a user- and developer- supported archive. Authors of software are invited to send their work to the Incoming folder by FTP. E-mail access -- for most IUBio services, including software, Genbank, Swiss-protein, FlyBase and other databank searches, Bionet news searches, and software archives, send a mail message to gopher@iubio.bio.indiana.edu FlyBase, a Drosophila Genome Database service is accessible now separately at ftp:, gopher:, http://flybase.bio.indiana.edu/ mailto: gopher@flybase.bio.indiana.edu IUBio Archive and FlyBase have move from computer "fly" to "magpie/firefly" recently. Those of you who may be reaching here via "fly.bio.indiana.edu" should update your network links to the name iubio or flybase. For those who need to know the IP address of these sevices, they are 129.79.225.200 iubio.bio.indiana.edu (magpie) 129.79.225.202 flybase.bio.indiana.edu (firefly) These IP addresses and computer names can and do change, but the service name (iubio or flybase) will be maintained. I am very pleased to acknowledge the many people and organizations that have helped support IUBio archive. Much of the current hardware is made available by co-operation with FlyBase, supported by a grant from the US National Institutes of Health. Current and past equipment support has come from Indiana University, National Science Foundation, and many of you who use the archive. (see http://iubio.bio.indiana.edu/contributors ). -- Don Gilbert -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Sabino Liuni Newsgroups: bionet.software Subject: Announcement: CLEANUP v 1.8 released Date: 5 Dec 1996 17:02:22 -0000 Lines: 67 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <586v6u$ee0@mserv1.dl.ac.uk> X-Sender: sabino@area.ba.cnr.it Original-To: bio-software@dl.ac.uk ************************* CLEANUP v 1.8 ************************* DESCRIPTION: CLEANUP 1.8 using an algorithm based on an "approximate string matching" procedure is able to determine the overall degree of similarity between each pair of sequences contained in a nucleotide sequence database and to generate automatically nucleotide sequence collections purified from redundancies. A key concept in comparing sequence collections is the issue of redundancy. The production of sequence collections cleaned from redundancy is undoubtedly very useful both in performing statistical analyses and accelerating extensive database searchings on nucleotide sequences. Indeed, publicly available databases contain multiple entries of identical or almost identical sequences. Performing statistical analysis on such biased data makes the risk of assigning high significance to non significant patterns very high. In order to carry out unbiased statistical analysis as well as more efficient database searchings it is thus necessary to analyse sequence data purified from redundancy. Given that a unambiguous definition of redundancy is impracticable for biological sequence data, in CLEANUP a quantitative description of redundancy is used based on the measure of sequence similarity. A sequence is considered redundant if it shows a degree of similarity and overlapping with a longer sequence in the database greater than a threshold fixed by the user. CLEANUP 1.8 program implements a new algorithm based on an "approximate string matching" procedure, which is able to determine the overall degree of similarity between each pair of sequences contained in a nucleotide sequence database and to generate automatically nucleotide sequence collections purified from redundancies. CLEANUP 1.8 works both on a GCG environment and on a GCG independent platform. It has been compiled and tested using DEC Alpha AXP C compiler, Borland C++ 4.0 compiler, and, moreover, it is portable over any machine with an ANSI C standard compiler. Reference: Giorgio Grillo, Marcella Attimonelli, Sabino Liuni and Graziano Pesole (1996) CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases. CABIOS 12, 1-8 --------------- CLEANUP 1.8 program is available on anonymous ftp: address: area.ba.cnr.it (193.205.35.100) path: pub/embnet/software/Cleanup For support and any information contact: Giorgio Grillo : giorgio@area.ba.cnr.it Sandra Brunetta: areasb16@area.ba.cnr.it Sabino Liuni: sabino@area.ba.cnr.it ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dr. Sabino LIUNI Area di Ricerca CNR ^ Administrator for the Via Amendola 166/5 ^ Italian EMBnet Node 70126 Bari (Italy) ^ tel. +39-80-5482176/5482130 ^ Fax. +39-80-5484467 ^ ^ E_mail:sabino@area.ba.cnr.it ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ OPEN YOUR EYES TO THE WORLD OF BIOCOMPUTING ^ ---------------------------------------------------------- From owner-software@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!mr.net!news.mr.net!News2.Lakes.com!usenet From: j5rson@prairie.lakes.com (Jeffrey D. Iverson) Newsgroups: bionet.software,sci.bio.misc,sci.bio.technology Subject: Biotechnology Glossary for Macintosh Date: Fri, 06 Dec 1996 04:11:49 GMT Organization: Iverson Software Co. Lines: 5 Distribution: inet Message-ID: <588aif$eij@News2.Lakes.com> NNTP-Posting-Host: modem60.prairie.lakes.com X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.software:17296 sci.bio.misc:6290 sci.bio.technology:6588 Check out the Biotechnology Glossary for Macintosh at http://prairie.lakes.com/~j5rson/business/education.html Over 470 terms, only $5 shareware. From owner-software@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!HERCULES.SDSC.EDU!bourne From: bourne@HERCULES.SDSC.EDU (Philip Bourne) Newsgroups: bionet.software Subject: PDB Obsolete Entries Date: 5 Dec 1996 18:02:19 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Obsolete Protein Data Bank (PDB) entries are now available as part of a joint initiative between the San Diego Supercomputer Center (SDSC) and the PDB. Obsolete entries are those which have been replaced by newer versions of the same structure or removed completely from the PDB distribution. These entries are considered important for the following reasons: 1. To relate a structure description found in a paper to the corresponding set of coordinates even when a more recent set of coordinates are available. 2. For comparative analysis during software development. New software can not be compared to existing software, since the coordinate sets used to test the original software were not available for use with the new software. It is important that these obsolete entries NOT be confused with current entries. Hence they are kept in a separate database accessible at http://www.sdsc.edu/PDBobsolete. There is a link between the PDB 3DB database (http://www.pdb.bnl.gov/cgi-bin/pdbmain) and the obsolete database. The obsolete database currently contains 291 structures. Structures may be located by keywords or PDB ID. Once located structures can be displayed, coordinates downloaded, and the chronology of an entry examined. Various statistics on the content of the archive are also available. The archive was developed by Helge Weissig and Phil Bourne. From owner-software@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!biosci!not-for-mail From: "E. Kolker" Newsgroups: bionet.general,bionet.info-theory,bionet.molbio.proteins,sci.med.pharmacy,bionet.molbio.embldatabank,bionet.population-bio,bionet.molbio.evolution,sci.bio.systematics,bionet.software Subject: New deadline & Web site Date: 6 Dec 1996 05:44:32 -0800 Organization: University of Washington Lines: 88 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <327E21BF.167E@bioinformatics.weizmann.ac.il> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:24391 bionet.info-theory:4414 bionet.molbio.proteins:9500 sci.med.pharmacy:37773 bionet.molbio.embldatabank:729 bionet.population-bio:2126 bionet.molbio.evolution:5408 sci.bio.systematics:1449 bionet.software:17299 ANNOUNCEMENT AND CALL FOR PAPERS Computational Biology Session: "Computing in the Genome Era" March 31 - April 1, 1997 Eleventh International Conference on Mathematical and Computer Modelling and Scientific Computing March 31 - April 3, 1997 Georgetown University Conference Center Washington, DC, USA The Eleventh International Conference on Mathematical and Computer Modelling and Scientific Computing is scheduled to take place March 31 - April 3, 1997 at the Georgetown University Conference Center, Washington, DC, U.S.A. The objective of the Computational Biology Session "Computing in the Genome Era" (March 31 - April 1, 1997) is to discuss the current state of computational biology, its approaches, methods, general problems, achievements, and future developments with emphasis on sequence research and analysis for the Genome Projects. SPEAKERS of the session include: S. Altschul (Natl Center for Biotechnology Iinformation, Bethesda), A. Bairoch (Geneva University, Switzerland), T. Clark (Millenium Pharmaceuticals, Cambridge), W. Gish (Washington University, St. Louis), T. Gojobori (Natl Institute of Genetics, Mishima, Japan), P. Green (University of Washington, Seattle), S. Henikoff (Fred Hutchinson Cancer Research Center, Seattle), L. Hood (University of Washington, Seattle), A. Kerlavage (Institute for Genomic Research, Rockville), E. Koonin (Natl Center for Biotechnology Iinformation, Bethesda), O. Ritter (German Cancer Research Center, Heidelberg, Germany), D. Searls (SmithKline Beecham Pharmaceuticals, King of Prussia), E. Shpaer (Perkin-Elmer Applied Biosystems, Foster City), E. Trifonov (Weizmann Institute of Science, Israel). STEERING COMMITTEE: S. Altschul, A. Bairoch, W. Gish, P. Green, S. Henikoff, E. Koonin, E. Trifonov Papers (Abstracts) are invited on all relevant aspects of computational biology for presentation at the session (a new deadline is DECEMBER 23, 1996), to be selected on competitive basis by the steering committee (notification of acceptance is JANUARY 4, 1997). One-page abstracts should clearly describe the work and its conclusions. Full length manuscripts (limited to six pages) of papers presented at the conference will be published in the Conference Proceedings, in a special issue of the journal MATHEMATICAL MODELLING AND SCIENTIFIC COMPUTING, Vol. 8, 1997 (ISSN 1067-0688). The manuscripts for the special issue are due JUNE 15, 1997. The special issue of the journal will be published by SEPTEMBER 1997. ALL participants shall pay the registration fee. Abstracts (ONE PAGE, about 200 words, PLAIN JUSTIFIED TEXT) may be submitted in hard copy or via fax or by e-mail (PREFERRED) under subject "Abstract". The abstracts must be formatted to fit on 8-1/2 x 11 inch (approximately 21.5 cm x 28 cm or European Standard A-4 size) paper, typed in single space. The title must be capitalized and centered followed by the author's name(s), institution, and full address, including fax and e-mail. Send two copies (ONE copy if sent by fax or e-mail) of the abstract to the session organizer before DECEMBER 23, 1996: Eugene Kolker Dept of Molecular Biotechnology and Genome Center Box 357730, University of Washington Seattle, WA 98195-7730, USA Fax: +1-206-685-7301 E-mail: egn@u.washington.edu The Computational Biology Session is proudly sponsored by SMITHKLINE BEECHAM and MILLENIUM. You can find additional info on our Web site: http://www.genome.washington.edu/~eugene/meeting.html From owner-software@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!agate!howland.erols.net!surfnet.nl!news.unisource.nl!news.worldonline.nl!usenet From: "Arnoud Muggen" Newsgroups: bionet.software Subject: HELP: looking for Email to Fax utility Date: 6 Dec 1996 08:30:06 GMT Organization: World Online Lines: 14 Message-ID: <01bbe350$4a199520$2316f0c3@NTSINT.ASD.NL> NNTP-Posting-Host: 195.240.22.35 X-Newsreader: Microsoft Internet News 4.70.1155 I'm looking for a program that can receive multiple mail-accounts (more than 10). Every account has to be put in a seperate mail box. I want to send the incoming email to seperate fax machines. The mailboxes have to be polled and if there is any mail, it should be sent to a fax machine. I also need the program to create a logfile of all sent faxes (with times). I hope anyone can help me with a name or a www-address. Thanks in advance, A. Muggen mailto:am@brabantnet.nl From owner-software@net.bio.net Thu Dec 05 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!panix!arclight.uoregon.edu!news.uoregon.edu!newsfeed.orst.edu!news.orst.edu!news.cs.indiana.edu!purdue!mozo.cc.purdue.edu!news From: Stefano Lonardi Newsgroups: bionet.software Subject: Pattern Matching Pointers Date: Fri, 06 Dec 1996 14:24:10 -0600 Organization: Department Computer Science - Purdue University Lines: 18 Message-ID: <32A880E4.6C23@cs.purdue.edu> NNTP-Posting-Host: agni.cs.purdue.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) I maintain a home page dedicated to the Pattern Matching Problem at Purdue University: http://www.cs.purdue.edu/homes/stelo/pattern.html The list would intend to be a comprehensive archive of pointers to people, journals, source code and references to the Pattern Matching Problem and related issues (computation molecular biology, data compression, information retrieval). If you have any queries, complain, errata, or you would like to add a new pointer, please write to me. _________________________________________________________________ Stefano LONARDI http://www.cs.purdue.edu/people/stelo Dept Computer Science, Purdue Univ, West Lafayette, IN 47907-1398 _________________________________________________________________ From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!surfnet.nl!news.wau.nl!usenet From: Lu.Do@Home.DiVa.nl (L.P.J.J. Noldus & C.D.M.L. Niemer) Newsgroups: bionet.software Subject: Re: Software for behavior recording Date: Sat, 07 Dec 1996 22:15:49 GMT Organization: Private Lines: 39 Message-ID: <58cqrl$rlg@Trex.IenD.wau.nl> References: <961202154511.8407@rascal.med.harvard.edu> Reply-To: Lu.Do@Home.DiVa.nl NNTP-Posting-Host: wag-asc30.diva.nl X-Newsreader: Forte Free Agent v0.55 BARRETT@RASCAL.MED.HARVARD.EDU wrote: >I am wondering if someone out there has made a software program that will >approximate chart recording. That is, if I have a periodic behavior that >I am testing, and I want to be able to record not only units activity/time, >but also the durations between activities, is there a program I can use >to do it? Ideally I'd want to be able to use a footpedal but a mouse would >also do for input, and output would be best written to a file for analysis. >I'd like to use one of our outdated IBM's for this, but a Mac program would >also do. (I could write the program myself, but surely someone else out >there has already done so, and it saves me the time of figuring out how to >read footpedal as input and parameters for writing out the files, etc.) We have developed a comprehensive package for the collection and analysis of behavioral and observational data, called "The Observer". For a description, see our website http://www.diva.nl/noldus, or go ditrectly to The Observer's page (http://www.diva.nl/noldus/prod_obs.htm). It reads keyboard, mouse or computer pen input. It does not support footpedals as an input device, but that may be a fairly easy addition. Don't hesitate to contact me our US office if you have any questions. Best regards, Lucas Noldus Dr. L.P.J.J. Noldus Noldus Information Technology b.v. Costerweg 5 P.O. Box 268 6700 AG Wageningen The Netherlands Phone: +31-(0)317-497677 Fax: +31-(0)317-424496 E-mail: L.Noldus@noldus.nl WWW: http://www.diva.nl/noldus/ From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.erols.net!newsfeed.internetmci.com!news.microagewny.com!usenet From: Douglas Easton Newsgroups: bionet.software Subject: Genetics Position Date: Sat, 07 Dec 1996 11:29:47 -0500 Organization: State University College at Buffalo (Biology) Lines: 40 Message-ID: <32A99B7A.4565@wzrd.com> Reply-To: dpeaston@wzrd.com NNTP-Posting-Host: ppp15.microagewny.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) GENETICIST STATE UNIVERSITY(SUNY)COLLEGE AT BUFFALO Applications are invited for a tenure-track ASSISTANT PROFESSOR to begin September 1997. We are seeking a colleague who is enthusiastic about teaching undergraduates. Teaching responsibilities will include Genetics, Introductory Biology for non-majors, and either Botany or Cell Biology. The successful candidate will be expected to develop an active research program involving undergraduate and master's students. Applicants must have a Ph.D., and postdoctoral teaching and research experience is preferred but not required. The State University College at Buffalo (Buffalo State College) is the largest arts and science college in the SUNY system with an enrollment of 13,000 students (including 2000 in graduate programs). The campus is located in a residential district in the city of Buffalo. The Department of Biology enrolls about 250 undergraduate and about 30 graduate students in MA and MSEd programs. Of our 16 faculty, one-half have received their doctorates within the last 13 years. We maintain greenhouse facilities, environmental chambers and research laboratories. The College's newly renovated Aquatic Research Laboratory provides laboratories and research vessels to faculty and students. Applicants should send a curriculum vitae with a thoughtful statement of teaching philosophy, research goals and three letters of recommendation by January 20, 1997 to: Dr. Randal Snyder, Chair of Search Committee, Department of Biology, Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222. Email: SNYDERRJ@SNYBUFAA.CS.SNYBUF.EDU Telephone: 716- 878-4314. We especially encourage applications from women and minorities. From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news-peer.gsl.net!news.gsl.net!EU.net!sun4nl!wirehub!news.euro.net!xs4all!xs4all!usenet From: marker@xs4all.nl (Niels Groot) Newsgroups: bionet.software Subject: Re: Again plasmid software Date: 7 Dec 1996 13:49:02 GMT Organization: XS4ALL, networking for the masses Lines: 33 Distribution: world Message-ID: <58bske$fjp@news.xs4all.nl> References: <961205155801.ZM12494@si05.IRCM.UMontreal.CA> NNTP-Posting-Host: asd01-05.dial.xs4all.nl Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-XS4ALL-Date: Sat, 07 Dec 1996 14:49:02 MET X-Newsreader: WinVN 0.99.7 In article <961205155801.ZM12494@si05.IRCM.UMontreal.CA>, duhaimj@IRCM.UMontreal.CA says... > >Bonjour > >I know there are a lot of mail on plasmid software. But may be someone can >help me. > You could take a look at: The final beta of SeqSearch v1.0 for Windows is now available at http://www.xs4all.nl/~marker Features included: -- multi-user/multi project -- seperate databases for sequences, primers, constructs, motifs and plasmids -- restriction site analysis, N cutters, 3/5 overhang, blunt ends, user-defined -- mismatch primer search -- codon substitution primer design -- silent mutagenesis -- motif search -- fragment mapping -- hydrophobic plot of aa sequences -- clone bench to design constructs -- compatible restriction site search -- oligo info From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Newsgroups: bionet.software Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!204.191.213.61!ott.istar!istar.net!van.istar!west.istar!news-w.ans.net!newsfeeds.ans.net!news.kellnet.com!not-for-mail From: Dave York Subject: Re: Palindroms Message-ID: <32A98BD4.3C45@stratos.net> Date: Sat, 07 Dec 1996 07:23:00 -0800 References: <32A1C7A1.26CE@ecoclub.nsu.ru> X-Mailer: Mozilla 2.02 (Win16; I) MIME-Version: 1.0 CC: dyork@stratos.net Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 24 Eugene Berezikov wrote: > > Can anybody point me to software searching palindroms in DNA sequences? > > Thanks in advance, > Eugene Berezikov. I don't have such software but would be interested in writing code to perform this function (free). If you can't locate such software anywhere else, here's what I need to know: 1. What is maximum length of sequences? 2. What format is the input file in (ASCII?) 3. Assume you are looking for sequences of type: ATAGC....CGATA, correct? 4. What do you expect output to look like? 5. What platform and operating system are you using? (e.g. PC w/Windows 3.1, Sun/UNIX, etc.) Good luck! -- ------------------------------------------------- | Dave & Mariel York | "That's all, folks" | | dyork@stratos.net | Chagrin Falls, OH | ------------------------------------------------- From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!feed1.news.erols.com!insync!news.io.com!usenet From: "Jason Spofford" Newsgroups: bionet.software Subject: ANNOUCING: Primordial Life 3.1 Date: 7 Dec 1996 16:30:56 GMT Lines: 21 Message-ID: <01bbe45c$256f5cc0$2759aac7@spofford.io.com> NNTP-Posting-Host: dialup-01-039.austin.io.com X-Newsreader: Microsoft Internet News 4.70.1155 Announcing Primordial Life 3.1 for Windows 95 and Windows NT New in Primordial Life 3.1 is the ability to connect your artificial life world to others over the Internet or intranet. Instead of "biots" (artificial life creatures) bouncing off walls, they can go through walls to other computers. Those computers, in turn, can connect to others creating a biot universe virtually unlimited in size. In general, Primordial Life evolves artificial life forms both in a screen saver and window. Right now, the program focuses on evolving form and motion. Future versions will include behavior. The computing requirements for evolving artificial life can be staggering. Now you can join forces with other artificial life enthusiasts to create larger worlds supporting a larger diversity of life forms. Primordial Life 3.1 is shareware. You can do most everything with the unregistered version. You can download Primordial Life from http://www.io.com/~spofford From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news-peer.gsl.net!news.gsl.net!news-paris.gsl.net!news.gsl.net!rain.fr!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!becquart From: becquart@lovelace.infobiogen.fr (Paul Becquart) Newsgroups: bionet.software Subject: Re: Again plasmid software Date: 7 Dec 1996 09:26:00 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 32 Distribution: world Message-ID: <58bd78$cu9@lovelace.infobiogen.fr> References: <961205155801.ZM12494@si05.IRCM.UMontreal.CA> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] SI-Johanne Duhaime (duhaimj@IRCM.UMontreal.CA) wrote: : Bonjour : I know there are a lot of mail on plasmid software. But may be someone can : help me. : We studied different softwares (windows: Clone manager, Winplas, Plasmid : Toolkit, Vector NTI). Few of them allow features like inserting a at a certain : base number (not only at a enzyme site), keeping historical version of the : construction etc. If fact only one of them allows such fonctionnalities but it : is to much expensive. Beeing so expansive, we told ourself: we will install : install a network version of the software and have a possibitity to have : different database files for differents users (which the selected software will : not do). But the software does not allow this. : If this is not a possibily, then we need a software less expansive that does the : work so that each researcher can have there own copy. But from the ones we have : been studying nothing satisfied us. : Anyone have something approching the ideal software? : -- : Johanne Duhaime : IRCM : 110 Ave des Pins O : Montreal, Quebec : 987-5556 (tel) 987-5644 (fax) : Duhaimj@ircm.umontreal.ca Try Gene Construction Kit. e-mail: sales@textco.com Paul From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!newsfeed1.aimnet.com!news.aimnet.com!news From: xyzzyx@aimnet.com (xyzzyx) Newsgroups: bionet.software Subject: how can I set up Raswin as a helper app for internet explorer? Date: 7 Dec 1996 07:23:32 GMT Organization: none, whatsoever Lines: 12 Message-ID: <58b61k$g8r@news.aimnet.com> NNTP-Posting-Host: dial-sm1-10.iway.aimnet.com Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (beta 2) I used to have netscape set up to use Raswin (v2.6) as a viewer for .pdb files (and others). Set up was pretty straightforward. I installed MS internet explorer and I just can't get the darned thing to work (the program opens fine, but I never get any image of the molecule). Does anyone have any idea how to get this to work? Anyone already done this? Thanks in advance. -George From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!agate!howland.erols.net!spring.edu.tw!news.cc.nctu.edu.tw!news.cis.nctu.edu.tw!usenet From: moron@irs32.he.ncku.edu.tw (tfkuo) Newsgroups: bionet.software Subject: >>> SURFER <<< !! Where are U ? Date: 7 Dec 1996 02:42:25 GMT Organization: THL,NCKU Lines: 7 Message-ID: <58alih$vv@news.cis.nctu.edu.tw> NNTP-Posting-Host: @p5kuo.he.ncku.edu.tw Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 Does anybody know about the software "Surfer " by Golden Software Inc. ? I use ver.5.0 surfer . I heard there's newer version . Anybody can tell me about that ? Thanx !! From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!voskovec.radio.cz!btnet-feed2!btnet!dispatch.news.demon.net!demon!mail2news.demon.co.uk!not-for-mail From: Simon Greenberg Newsgroups: bionet.software Subject: please ignore test Date: Sat, 07 Dec 1996 04:01:39 -0800 Organization: Hebrew University of Jerusalem Lines: 2 Message-ID: <32A95CA3.1473@gene.md.huji.ac.il> Reply-To: simong@gene.md.huji.ac.il X-Mail2News-User: simong@gene.md.huji.ac.il X-Mail2News-Path: cc.huji.ac.il!dial-11-16.slip.huji.ac.il X-Mailer: Mozilla 3.0 (Win16; I) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit please ignore test From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!CS.SANDIA.GOV!scistra From: scistra@CS.SANDIA.GOV (Sorin C. Istrail) Newsgroups: bionet.software Subject: RECOMB 97: Final Program, Stud Financial Support, Babysitting, Travel Date: 6 Dec 1996 17:45:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 496 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612062342.QAA04536@frodo2.cs.sandia.gov> NNTP-Posting-Host: net.bio.net RECOMB97 NEWS December 6, 1996 **************** recomb97@hto.usc.edu http://www.cs.sandia.gov/recomb97 http://www.eldoradohotel.com Reminder: Early registration deadline (extended to Dec 20, 1996) is approaching fast!! THE ELDORADO HOTEL IS FULL!!! However, there are a few extra rooms available at the RECOMB 97 rate. Please hurry up. The overflow will go to the Hilton of Santa Fe Hotel (1-800-336-3676 or fax 505-986-6439 ask for the "RECOMB97 Conference") where we have a block of rooms reserved at identical rates. 1. RECOMB'97 Final Program 2. Available Financial support for students/graduate students/postdocs. Thanks to the generous help from the Sloan Foundation and the U.S. Department of Energy. 3. Babysitting and Recreational Activities 4. Travel to Santa Fe --------------------------------------------------------- 1. RECOMB'97 Final Program FIRST ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY January 20-23, 1997 Eldorado Hotel Santa Fe, New Mexico Sponsored by ACM SIGACT with support from SLOAN Foundation US Department of Energy recomb97@hto.usc.edu http://www.cs.sandia.gov/recomb97 RECOMB 97 SCHEDULE ****************** *************************************** Sunday January 19, 1996 *************************************** 7:00-10:00 p.m. Reception Eldorado Hotel Anasazi South *************************************** Monday January 20, 1996 *************************************** 9:00 a.m.- 5:00 p.m. Poster Session, Zia B&C General Session, Anasazi Ballroom 8:45 a.m. Opening Remarks: Michael Waterman, General RECOMB Chair 1997 Program Committee Chair Sorin Istrail, General RECOMB Vice-Chair 1997 Conference Chair Pavel Pevzner, General RECOMB Chair 1998 Program Committee Chair --------------------------------------- 9:00 Distinguished Conference Lecture Session Pavel Pevzner, Chair Rich Roberts Hunting for new restriction enzymes in GeneBank --------------------------------------- 10:00 Break Session on Mapping Chair: Phil Green 10:15 Shili Lin, Terence P. Speed An Algorithm for Haplotype Analysis 10:40 Donna Slonim, L. Kruglyak, L. Stein, E. Lander Building Human Genome Maps with Radiation Hybrids Break 11:05 Session on Genomic Rearrangements Chair: Richard Karp 11:15 Haim Kaplan, Ron Shamir, Robert Tarjan Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals 11:40 David Sankoff, V. Ferretti, Joe Nadeau Conserved segment identification 12:05 Lunch, Eldorado Court --------------------------------------- 1:30 Invited Lecture Session Pavel Pevzner, Chair Rob Lipshutz DNA Probe Arrays - Accessing the Genome --------------------------------------- 2:30 Break Session on New Technologies Chair: Gene Myers 2:45 J. Richard Bradley, Steven Skiena Fabricating Arrays of Strings 3:10 Dan Fasulo, Tao Jiang, Richard M. Karp, R. Settergren, E. C. Thayer An Algorithmic Approach to Multiple Complete Digest Mapping 3:45 S. Muthukrishnan, Laxmi Parida A highly effective simple combinatorial approach for constructing physical maps by optical mapping 4:10 Break --------------------------------------- 4:25 Invited Lecture Session Sam Karlin, Chair Terry Speed Variations on a theme of Lander and Waterman --------------------------------------- 8:00-10:00 p.m. Business Meeting, Anasazi Ballroom *************************************** Tuesday January 21, 1996 *************************************** 9:00 a.m.- 5:00 p.m. Poster Session, Zia B&C General Session, Anasazi Ballroom --------------------------------------- 8:30 Invited Lecture Session Rich Roberts, Chair David Botstein Expression Arrays: An Open Problem for Mathematicians in Post-Genome Sequence Biology --------------------------------------- 9:30 Break Session on Sequence Alignment Chair: Steven Altschul 9:45 Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller Progressive Multiple Alignment with Constrains 10:10 George A. Komatsoulis, Michael Waterman Chimeric alignment by dynamic programming: Algorithm and biological uses 10:35 Break Session on Sequence Alignment Chair: Temple Smith 10:45 Gary Benson Sequence Alignment with Tandem Duplication 11:10 K. Reinert, Hans-Peter Lenhof, P. Mutzel, K. Mehlhorn, J. D. Kececioglu A Branch-and-Cut Algorithm for Multiple Sequence Alignment 11:35 Ralf Zimmer, Tom Lengauer Fast and Numerically Stable Parametric Alignment of Biosequences 12:00 Lunch, Eldorado Court --------------------------------------- 1:30 Invited Lecture Session Mike Waterman, Chair Sam Karlin Assesing Inhomogeneities in Bacterial Long Genomic Sequences --------------------------------------- 2:30 Break Session on Gene Recognition Chair: Gary Stormo 2:45 Ying Xu, Edward Uberbacher Reference-based Gene Model Prediction on DNA Contigs 3:10 Sing-Hoi Sze, Pavel Pevzner Las Vegas Algorithms for Gene Recognition: Suboptimal and Error-Tolerant Spliced Alignment 3:35 Break Session on Protein Folding Chair: Martin Karplus 3:45 Ken Dill, Andrew T. Phillips, J. Ben Rosen, Protein Structure Prediction and Potential Energy Landscape Analysis using Continuous Global Minimization 4:10 William Hart, S. Istrail Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal 4:10 Break --------------------------------------- 4:25 Invited Lecture Session Martin Karplus, Chair Temple Smith The threading approach to the inverse protein folding problem --------------------------------------- 7:00 p.m. Cocktails, Anasazi Ballroom 7:30-10:00 Banquet, Anasazi Ballroom --------------------------------------- 7:30 Stanislaw Ulam Computational Biology Address Session Mike Waterman, Chair Eric Lander The Human Genome and Beyond --------------------------------------- *************************************** Wednesday January 22, 1996 *************************************** 9:00 a.m.- 5:00 p.m. Poster Session, Zia B&C General Session, Anasazi Ballroom --------------------------------------- 8:30 Invited Lecture Session Sorin Istrail, Chair Martin Karplus Protein Dynamics: From the Native to the Unfolded State and Back Again --------------------------------------- 9:30 Break Session on Protein Folding Chair: Bonnie Berger 9:45 William Hart On the Computational Complexity of Sequence Design Problems 10:10 Tatsuya Akutsu, S. Miyano On the Approximation of Protein Threading 10:45 Break Session on Mapping Chair: Ron Shamir 10:55 Amir Ben-Dor, Benny Chor On Constructing Radiation Hybrid Maps 11:20 Fengzhu Sun, Gary Benson, Mike Waterman Pooling Strategies for Establishing Physical Genome Maps Using FISH 11:45 Mutida Jain, Gene Myers Algorithm for Computing and Integrating Physical Maps Using Unique Probes 12:10 Lunch, Eldorado Court --------------------------------------- 1:30 Invited Lecture Session Sorin Istrail, Chair Jonathan King Problems in Understanding the Structure and Assembly of Viruses --------------------------------------- 2:30 Break Session on Protein Folding Chair: Bonnie Berger 2:45 Richa Agarwala, Serafim Batzogloa, V. Dancik, Scott E. Decatur, M. Farach, S. Hannenhalli, S. Muthukrishnan, S. Skiena Local Rules for Protein Folding on Triangular Lattice and generalized Hydrophobicity in the HP Model 3:10 Hans-Peter Lenhof New Contact Measures for the Protein Docking Problem 3:35 Break Session on Proteins Chair: Thomas Lengauer 3:45 Bonnie Berger, Mona Singh An Iterative Method for Improved Protein Structural Motif Recognition 4:10 Erich Bornberg-Bauer Chain Growth Algorithms for HP-Type Lattice Proteins 4:35 Hiroshi Mamitsuka Supervised Learning of Hidden Markov Models for Sequence Discrimination *************************************** Thursday January 23, 1996 *************************************** General Session, Sweeney Convention Center Session on Sequence Alignment Chair: Martin Farach 8:30 Zheng Zhang, William R. Pearson, Webb Miller Aligning a DNA Sequence with a Protein Sequence 8:55 Eric L. Anson, Gene Myers ReAligner: A Program for Refining DNA Sequence Multi-Alignments 9:20 Lusheng Wang, Tao Jiang, Dan Gasfield A More Efficient Approximation Scheme for Tree Alignment 9:20 Break Session on Genomic Rearrangements Chair: David Sankoff 9:35 B. DasGupta, T. Jiang, S. Kannan, M. Li, Z. Sweekyk On the Complexity and Approximation of Syntenic Distance 10:00 Alberto Caprara Sorting by Reversals is Difficult 10:25 Break Session on Statistics Chair: Bruce Weir 10:40 Simon Heath The application of Markov Monte Carlo Methods to Radiation Hybrid Mapping 11:05 M. G. Reese, F. H. Eeckman, D. Kulp, D. Haussler Improved Splice Site Detection in Genie 11:30 Gary A. Churchill Monte Carlo Sequence Alignment 11:55 Lunch, Sweeney Convention Center Session on Sequence Alignment Chair: Webb Miller 1:30 Benno Schwikowski, Martin Vingron The Deferred Path Heuristic for the Generalized Tree Alignment Problem 1:55 Tetsuo Shibuya, Hiroshi Imai New Flexible Approaches for Multiple Sequence Alignment 1:55 Break Session on Mapping Chair: Maynard Olson 2:05 T. Christof, M. J\"unger, John Kececioglu, P. Mutzel, G. Reinel A Branch-and-cut Approach to physical mapping with end-probes 2:30 David Wilson, David Greenberg, Cynthia Phillips Beyond Islands: Runs in Clone-Probe Matrices 2:55 Break Session on Evolutionary Trees and DNA Computing Chair: Martin Vingron 3:05 Jamie Cohen, Martin Farach Numerical Taxonomy on Data: Experimental Results 3:30 W. Cai, Anne Condon, R.Mm Corn, E Glasser, Z. Fei, T. Frutos, Z. Guo, MG Lagally, Q. Lui, L.M. Smith, A. Theil The Power of Surface-Based DNA Computing 3:55 M. Ogihara, A. Ray Simulating Boolean Circuits on a DNA Computer End of RECOMB 97 -------------------------------------------------- 2. Financial support for students/graduate students/postdocs Limited support for students is available. We anticipate being able to make about 22 financial awards of $400 each for 22 students. Please send us a one-page request to via email to scistra@cs.sandia.gov including your affiliation, the name of your Ph.D. adviser (if appropriate) and the area of research that you are working on. We would like to select for support the students that will benefit the most from our meeting as well as those that will be able to make valuable contributions to the conference. 3. Babysitting and Recreational Activities "Santa Fe Destinations" is a company located in the Eldorado Hotel. They provide professional services for: babysitting, airport transportation, entertainment, recreational activities, spouse programs etc. Please call Tom Williams the Director of the company for services related to your visit in Santa Fe. 4. Travel to Santa Fe http://www.eldoradohotel.com/getting_there.html By plane to the Albuquerque International Airport. All major airlines use the airport. From there "Shuttlejack" ((505) 988-2441; $20 one-way trip; about one hour long) buses pick people up and drop them directly at the Eldorado Hotel nine times a day. Please call Shuttlejack and make reservations. The complete information about arriving at the Eldorado Hotel is available from their web page http://www.eldoradohotel.com/getting_there.html We hope to see you soon in Santa Fe. -- Sorin Istrail Conference Chair From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!sn.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!EU.net!main.Germany.EU.net!news-koe1.dfn.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs,bionet.software Subject: New release 5.0 of SRS Date: Sat, 07 Dec 1996 01:25:48 +0100 Organization: EMBL Lines: 57 Distribution: world Message-ID: <32A8B98C.41C6@embl-heidelberg.de> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V2.0 alpha) Xref: biosci bionet.software.srs:357 bionet.software:17303 Dear all, SRS5 is finally out! ...this time it is the full release and not a 'beta' you can get it from ftp://ftp.embl-heidelberg.de/pub/databases/trembl/srs5_0.tar.gz Those are the changes since the last beta (srs5.04b): o The indexing works now with databanks in native or GCG format. o There is now support for sequence features o srscheck and srsbuild have been revised and work as in SRS4. This includes the -r, -t and -rel options of srsbuild. o Parsers have been written for many more databanks. o Documentation is much better (Icarus manual, Guided tour). o All installation scripts have been rewritten as Bourne shell scripts. SRS5 is much more powerful but also more complicated as SRS4. A lot of parsers have still to be written, but those that are there can be used as templates for 'cut and paste' programming. Adding a new databank needs now three files that describe the structure (format, data-fields, links), the syntax and the databank itself (Source, ftp address, contact address, etc). This is described in the "Guided Tour" that comes with the distribution. We would like to invite you to write Icarus files and post them to the newsgroup bionet.software.srs to make them available to others. We will then put the files into future releases of SRS. For the installation of the SRSWWW server an Alias and a ScriptAlias are needed. Following the discussion in this newsgroup about notifying the proxies not to cache we use now the ScriptAlias /srs5bin/cgi-bin/. Please tell us if that works. ...more in the release notes regards and happy installation Giorgio Verde verde@embl-heidelberg.de Johnathon Weare weare@embl-heidelberg.de Thure Etzold etzold@embl-heidelberg.de -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!btnet!btnet-feed1!zetnet.co.uk!not-for-mail From: Garth Williams Newsgroups: bionet.software Subject: Quality Control software Date: Fri, 6 Dec 1996 23:53:34 GMT Lines: 109 Message-ID: <1996120623533471355@zetnet.co.uk> NNTP-Posting-Host: besses.zetnet.co.uk X-Mailer: ZIMACS Version 1.09x 10002114 -- Yet more quality control software? QC-Record is a menu-driven program that provides a specialised environment for handling all quality control storage needs. It incorporates facilities to store QC data, which can be reviewed in graphical form or as pure data, on screen or as hard copy. Easy to set up, but at the same time very configurable, the program offers the opportunity for the user to define their own quality control rules, although it is supplied as standard with rules based on criteria proposed by Westgard and associates (A Multi-Rule Shewart Chart for Quality Control in Clinical Chemistry. Clin. Chem 27,493-500, 1981). Hardware requirements are low, and it will run as a stand-alone package, or across a computer network. -- What can QC-Record do for me? The main features of QC-Record are summarised below: * Immediate analysis of input data by user-defined rules * Will recall, edit, display, summarise and print stored QC results * Calculates mean and SD for any defined period * Stores running mean and SD on stored data * Stores changes in reagents and/or standards * User-definable data ranges * User-definable program configuration (colours, printers, etc.) * User-definable tests * Maintains audit trail of changes to QC database * On-line help available * Backup, restore and archive of essential data * Password restriction of sensitive data * Uses Expanded and extended memory if available * Automatically network aware -- How easy is it to use? QC-Record has been written by laboratory personnel, for laboratory personnel, and is used routinely by all grades of staff in the busy Biochemistry department where it was first planned, and where it is still being enhanced. It has undergone hundreds of hours of development over several years to shape it into an easy to use system that gives analysts the information that they require to spot and fix quality control problems. -- Why would I want to use QC-Record instead of other QC packages? Most other quality control programs are restricted in some way. For example: * they may only be available if you use certain quality control products * may be tied to a large product purchase. * some software is designed by software professionals, not laboratory professionals * some software gives you information overload * some software buries what you really need in impressive but ultimately useless information. * much software doesn't allow for perfectly adequate, but slower, computers * QC software supplied with many laboratory instruments only allows analysis of that instrument's data * doesn't allow off-line data analysis, such from manual analyses or other smaller instruments. * much QC software only checks against QC ranges, ignoring long-term trends * limited storage capacity for QC in many laboratory systems -- Does QC-Record need a powerful computer? QC-Record will run on any PC-compatible computer from an 8088 to a Pentium Pro, provided that it has one floppy disc and one hard disc, 640k memory, a mono or colour monitor, and MS-DOS 3.3 or above. It will also run across most Local Area Networks, on widely-available network software, such as Novell Netware. The basic program and essential files consume approximately 1 Mb hard disc space when first installed. Storage of results is effectively limited only by hard disc space. 10,000 results require approximately 1 Mb data storage. If space is at a premium, older results can be archived to another medium, e.g. floppy disc, and can still be subsequently retrieved for data analysis. -- Can I see it working before I decide if it's what I want? A demonstration disc is available to give a flavour of the look and feel of the program. This will normally be sent by post to UK enquirers, unless they request it to be sent by email. Enquirers from outside the UK will be sent the demo disc as a file attached to email, accompanied by instructions on how to decode and use it. A restricted working version will soon be available. -- What do I do next? Contact JGW Computing by email to: garth.williams@zetnet.co.uk Write to: JGW Computing, 11 Bramley Close, Colletts Green, Powick. Worcester. UK. WR2 4SR. From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!dispatch.news.demon.net!demon!fssc.demon.co.uk!HSauro From: Herbert M Sauro Newsgroups: bionet.software Subject: Photobacterium genome database? Date: Thu, 5 Dec 1996 20:26:44 +0000 Organization: Future Skill Software Lines: 15 Distribution: world Message-ID: NNTP-Posting-Host: fssc.demon.co.uk X-NNTP-Posting-Host: fssc.demon.co.uk MIME-Version: 1.0 X-Newsreader: Turnpike Version 1.12 I'm not sure if this is the right place to ask but I read a year or so ago that a Japanese group had sequenced the entire genome for a small photobacterium, can't remember what it was called. I was wondering if any one knew about this and whether there was a publically available database of the genome itself? Thanks Herb -- Herbert M Sauro email: HSauro@fssc.demon.co.uk Telephone: 01974 282428 ----------------------------------------------------------------------- "He who cannot draw on 3000 years is living from hand to mouth" Goethe From owner-software@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!newsfeed.internetmci.com!news1.bellglobal.com!freenet-news.carleton.ca!cunews!nott!hone!informer1.cis.McMaster.CA!roger.interlynx.net!usenet From: "Lars Thomsen" Newsgroups: bionet.software Subject: Upcoming interactive electrophysiology >>>!!!! Date: 7 Dec 1996 09:18:25 GMT Organization: 115 South Oval Lines: 34 Message-ID: <01bbe41f$72659680$1ec032cc@boris.gate2.interlynx.net> NNTP-Posting-Host: ppp20-max1.interlynx.net X-Newsreader: Microsoft Internet News 4.70.1155 Hej (danish version of hi) Keep an eye on my homepage under the section THEORY. http://home.interlynx.net/~lthomsen/theory.htm When this weekend is over I will have posted a lot of very nice ActiveX programs, that you can run if you use Internet Explorer 3.0 final release (or later). The programs that I will post here is : ActiveX title Describtion Nernst Calculates Nerst potential interactively. Adjust z, T, conc out and conc in. GHK Calculate membrane potentials with the GHK equation for 4 ions. Dilute Calculates volume off stock solution ot add to your final solution to obtain a given conc. Stock Calculates amount of chemical that you need to add to create a certain stock solution, some chemicals in the database. -- Lars Thomsen, M.Sc. PhD. 115 South Oval, Hamilton, ON Canada L8S1R2 Email lthomsen@interlynx.net http://home.interlynx.net/~lthomsen/index.htm From owner-software@net.bio.net Sat Dec 07 22:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!news.stealth.net!news.ibm.net.il!news.biu.ac.il!news.huji.ac.il!usenet From: Simon Greenberg Newsgroups: bionet.software Subject: Re: UNIX tar format to ASCII Date: Sat, 07 Dec 1996 04:47:37 -0800 Organization: Hebrew University of Jerusalem Lines: 231 Message-ID: <32A96769.8E6@gene.md.huji.ac.il> Reply-To: simong@gene.md.huji.ac.il NNTP-Posting-Host: dial-12-16.slip.huji.ac.il Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------133871372767" X-Mailer: Mozilla 3.0 (Win16; I) This is a multi-part message in MIME format. --------------133871372767 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Could somebody please point me to where I could download a PC/Windows95 > compatible program to read a UNIX .tar compressed file and convert it to simple ASCII. Hi, try this 'unTAR' to DOS - untar103.zip. It works nice. You can use it for all kinds of files, not only for ASCII. Unfortunately I forgot the FTP address where I downloaded this program. Best regards, Simon Greenberg Hebrew University of Jerusalem Medical School,Computation Unit P.O.Box 12208, Kiryat Hadassah 91120 Jerusalem, Israel --------------133871372767 Content-Type: application/zip; name="UNTAR103.ZIP" Content-Transfer-Encoding: base64 Content-Disposition: inline; filename="UNTAR103.ZIP" UEsDBBQAAAAIAAJTTx+1K+SR7iYAAOBSAAAJAAAAVU5UQVIuRVhFxZwLfBNV2v/P5DJJ0zRc LcilnSJEaGla2rVKWyoCbQEFKgIFtGpoA62Wtp8k06L/AsEq2qSw6ut6YVdfEHV3BbFAVwOs ttByreVSdoUVdxcBdWrwilouJfn/zswkTdqAl30/79vP55tMzuU5z3nOc55zzkzSGQtPk3hy hVlFItWRr7vVZCIhffoRMowQEgluAk+D34F3wGHQlyFkDDCBTJAPLKASrAXvgdPgK3AVDFZA DkgB2aAQ2EEdeBscB5+A74BOSUgiuB+Ugg3gbfAB+Aj8AJQqQvpDx0FUT5ACMsEMkA+KgRXU gDXgNfBnsAs0gXZwAnwCLoCLQNcf/QZxwAiSwSSQC+4GhaAYWMHjoBb8HqwH28C7YDc4Dk6C L8DXgBlACAsGg+HgZjAeZIE8MBe8DraDPeAo+Df4DpCB0AkMB2PBHSAfmIENLAePgefBerAF 7AH7wWHwCegEhhsIGQCGgHVgGzgEzoDLoH80IfFgElgIrOC34CA4DM6DS4AdBJ8AQ8A4MAnc DQpBMbCCx0Et+D1YD7aBd8FBcBicBp+CTtAFDIOhGxgF4kEmuAPcA+aDh0A5WAVWgxfBy+Bt 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Newsgroups: bionet.software Subject: Re: Photobacterium genome database? Date: 8 Dec 1996 05:02:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199612081302.WAA10764@not1.kazusa.or.jp> References: NNTP-Posting-Host: net.bio.net >I'm not sure if this is the right place to ask but I read a year or so >ago that a Japanese group had sequenced the entire genome for a small >photobacterium, can't remember what it was called. I was wondering if >any one knew about this and whether there was a publically available >database of the genome itself? It may be the genome sequence of the Cyanobacterium. Please visit http://www.kazusa.or.jp/cyano/cyano.html http://www.kazusa.or.jp/cyano/map/java/cmap_small/cmap_sm.html The Java source codes used in the map will be available soon. ----------------------------------------------- Nobuyuki Miyajima Kazusa DNA Research Institute Department of Genome Informatics, 1532-3 Yana, Kisarazu, Chiba 292, Japan TEL: +81-438-52-3917 FAX: +81-438-52-3918 E-mail: miyajima@kazusa.or.jp From owner-software@net.bio.net Sat Dec 07 22:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!news.stealth.net!news.ibm.net.il!news.biu.ac.il!news.huji.ac.il!usenet From: Simon Greenberg Newsgroups: bionet.software Subject: Re: UNIX tar format to ASCII Date: Sat, 07 Dec 1996 04:36:05 -0800 Organization: Hebrew University of Jerusalem Lines: 226 Message-ID: <32A964B5.7C3E@gene.md.huji.ac.il> References: <01bbe1ac$2be93970$f308b6cc@monahan> Reply-To: simong@gene.md.huji.ac.il NNTP-Posting-Host: dial-12-16.slip.huji.ac.il Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------54283374F36" X-Mailer: Mozilla 3.0 (Win16; I) This is a multi-part message in MIME format. --------------54283374F36 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit John Monahan wrote: > > Could somebody please point me to where I could download a PC/Windows95 > compatible program to read a UNIX .tar compressed file and convert it to simple ASCII. Hi, try this 'unTAR' to DOS - untar103.zip. It works nice. You can use it for all kinds of files, not only for ASCII. Unfortunately I forgot the FTP address where I downloaded this program. 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