From owner-software@net.bio.net Thu Oct 01 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: "Rab A. Harper" Newsgroups: embnet.general,bionet.software Subject: ANNOUNCE EMBnet News Vol5_3 released Date: Fri, 02 Oct 1998 14:39:19 +0100 Organization: European Bioinformatics Institute Lines: 14 Message-ID: <3614D787.7E2F197C@ebi.ac.uk> NNTP-Posting-Host: shamrock.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 907335623 3082 193.62.196.179 (2 Oct 1998 13:40:23 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 2 Oct 1998 13:40:23 GMT X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 6.2 IP22) The latest issue of embnet.news has been released. It comes in a new format Check it out at the following URLS http://www2.ebi.ac.uk/embnet.news/vol5_3/ http://ben.vub.ac.be/embnet.news/vol5_3/index.html http://www.uk.embnet.org/embnet.news/vol5_3/index.html http://www.ie.embnet.org/embnet.news/vol5_3/index.html -- Rab A. Harper E-mail: harper@ebi.ac.uk EMBL Outstation - The EBI URL: http://www.ebi.ac.uk Wellcome Trust Genome Campus Telephone: +44 (0)1223 494 429 Hinxton Hall, Cambridge CB10 1SD UK Fax: +44 (0)1223 494 468 From owner-software@net.bio.net Thu Oct 01 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!newsfeed.ed.ac.uk!aultmore!chrisb From: chrisb@hgu.mrc.ac.uk (Chris Boyd) Newsgroups: bionet.general,sci.research,bionet.molbio.methds-reagnts,bionet.software,comp.os.linux.misc,comp.os.linux.advocacy Subject: Re: POLL: Are you interested in EndNote for Linux? Followup-To: bionet.general,sci.research,bionet.molbio.methds-reagnts,bionet.software,comp.os.linux.misc,comp.os.linux.advocacy Date: 2 Oct 1998 09:34:04 GMT Organization: MRC Human Genetics Unit Lines: 49 Message-ID: <6v26mc$2hm$1@scotsman.ed.ac.uk> References: NNTP-Posting-Host: aultmore.hgu.mrc.ac.uk X-Trace: scotsman.ed.ac.uk 907320844 2614 193.63.65.38 (2 Oct 1998 09:34:04 GMT) X-Complaints-To: usenet@scotsman.ed.ac.uk NNTP-Posting-Date: 2 Oct 1998 09:34:04 GMT X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.general:30993 bionet.molbio.methds-reagnts:71157 bionet.software:21926 Patrick (patrick@howard.genetics.utah.edu) wrote: : > On 30 Sep 1998 14:53:49 -0600, pjf wrote: : > >-----BEGIN PGP SIGNED MESSAGE----- : > > : > >Hi folks, : > > : > >I am taking an informal (obviously) poll to gauge support for a Linux : > >version of EndNote. I have no affiliation with Niles Software. I am a : YES!! YES!! I want EndNote and have written to Niles Software a couple : of time to ask about it. I have also written to StarDivision to ask for : a bibliography app in StarOffice. BibTeX is fine but it ain't EndNote : with its tight, clean integration into several different wordprocessor : programs. I NEED a good, integratable bibliography program that will : work with StarOffice (or WordPerfect if I decide to ultimately go that : route). For your sake I hope I'm wrong, but frankly I think this is not going to happen. Linux is a niche operating system and likely to remain so (despite the hype) and I imagine the subset of _scientific_ Linux users who want to use a WYSIWYG wordprocessor that needs something like EndNote for references is vanishingly small. Where's the commercial incentive for Niles Software? Most scientific Linux users are compsci/maths/physics types who are quite comfortable with TeX, LaTeX and BibTeX which have the virtue of being free and stable. Unfortunately fellow biologists rarely have the inclination to learn TeX/LaTeX/BibTeX (because they usually prefer not to tackle things that have any level of abstraction) and are consequently easy prey for Microsoft. The easy solution is to have a dual boot system, with a small partition for Windows/Word/EndNote etc. and a large Linux one for serious computing. After all, running (eg) WordPerfect on top of Linux is scarcely different from running it on top of Windows, apart from the yuk factor. I am a strong advocate for Linux, but the reality is that most software vendors will aim for the Windows market as long as it has a stranglehold. Why fight it? Linux is free -- so you can have two operating systems for the price of one and enjoy the benefits of both. (For those bionet readers mystified by all this, but interested in (mostly) free alternative software for PCs, have a look at http://www.linux.org/ or even http://www.hgu.mrc.ac.uk/Users/Christopher.Boyd/compinfo.htm) Best wishes, -- Chris Boyd | from, but not \ MRC Human Genetics Unit, Christopher.Boyd@hgu.mrc.ac.uk | on behalf of / Western General Hospital, http://www.hgu.mrc.ac.uk/Users/Christopher.Boyd \ Edinburgh, EH4 2XU, SCOTLAND From owner-software@net.bio.net Thu Oct 01 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!sunqbc.risq.qc.ca!novia!sws1.ctd.ornl.gov!not-for-mail From: "David Adelson" Newsgroups: bionet.software Subject: Dot plot software for Mac PPC Date: Fri, 02 Oct 1998 14:26:44 -0500 Organization: CSIRO Animal Production Lines: 12 Message-ID: <6v35vi$pq9$1@sws1.ctd.ornl.gov> NNTP-Posting-Host: adelsond.hsr.ornl.gov Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express for Macintosh - 4.02 (298) I was wondering if anyone could point me towards a dot plot program for comparing sequences similare to the GCG combination of compare and dot plot? I need to be able to use it on a Mac G3 PPC only. Thanks, David L Adelson PhD - Functional Genomics d.adelson@anprod.csiro.au CSIRO Animal Production Sydney, NSW, Australia Currently on study leave at ORNL http://lsd.ornl.gov From owner-software@net.bio.net Thu Oct 01 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!xmission!news.cc.utah.edu!howard!patrick From: Patrick Newsgroups: bionet.general,sci.research,bionet.molbio.methds-reagnts,bionet.software,comp.os.linux.misc,comp.os.linux.advocacy Subject: Re: POLL: Are you interested in EndNote for Linux? Date: Fri, 2 Oct 1998 08:50:52 -0600 Organization: University of Utah - ACLIS Lines: 28 Message-ID: NNTP-Posting-Host: howard.genetics.utah.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: coward.cc.utah.edu 907340113 1215 155.100.231.1 (2 Oct 1998 14:55:13 GMT) X-Complaints-To: abuse@cc.utah.edu NNTP-Posting-Date: 2 Oct 1998 14:55:13 GMT X-Sender: patrick@howard In-Reply-To: Xref: biosci bionet.general:31003 bionet.molbio.methds-reagnts:71162 bionet.software:21929 On 2 Oct 1998, Ashok Aiyar wrote: > Chris Boyd (chrisb@hgu.mrc.ac.uk) wrote: > > >The easy solution is to have a dual boot system, with a small partition > >for Windows/Word/EndNote etc. and a large Linux one for serious Suboptimal. I have a triple boot system but prefer never to reboot if it is at all avoidable. > There is at least other alternative to this. I don't like a dual-boot > system, have taken the time to learn one word-processor (Word 6.0) and > do not wish to learn another. I use WABI under Linux, and thus run those > those 16-bit Windows applications I need to use directly under Linux. Or the best alternative is a bibliography program, perhaps based on BibTeX, but which has the power and ease-of-use of EndNote, but which works with all the major wordprocessors/type-setter programs that run on linux. It could support StarOffice, Applixware, WordPerfect, AbiWord (still a bit young), they Gnome wordprocessor - I don't mention LaTeX of Klyx because it already supports these, naturally. It should be able to place properly formatted refs into the document and produce an appropriate bibliography page commensurate with the paper style/journal to which the doc will be submitted - just like EndNote does. No rebooting necessaryh/ patrick From owner-software@net.bio.net Thu Oct 01 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!207.172.3.37!feed1.news.rcn.net!rcn!newsfeed.enteract.com!chicago-news-feed1.bbnplanet.com!news.bbnplanet.com!news.itis.com!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.general,sci.research,bionet.molbio.methds-reagnts,bionet.software,comp.os.linux.misc,comp.os.linux.advocacy Subject: Re: POLL: Are you interested in EndNote for Linux? Followup-To: bionet.general,sci.research,bionet.molbio.methds-reagnts,bionet.software,comp.os.linux.misc,comp.os.linux.advocacy Date: 2 Oct 1998 14:12:32 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 27 Sender: reguser@ebv.oncology.wisc.edu Message-ID: References: <6v26mc$2hm$1@scotsman.ed.ac.uk> Reply-To: aiyar@aiyar.ml.org NNTP-Posting-Host: ebv.oncology.wisc.edu User-Agent: slrn/0.9.5.3 (UNIX) Xref: biosci bionet.general:31002 bionet.molbio.methds-reagnts:71160 bionet.software:21928 On 2 Oct 1998 09:34:04 GMT, Chris Boyd (chrisb@hgu.mrc.ac.uk) wrote: >The easy solution is to have a dual boot system, with a small partition >for Windows/Word/EndNote etc. and a large Linux one for serious >computing. After all, running (eg) WordPerfect on top of Linux is >scarcely different from running it on top of Windows, apart from the >yuk factor. I am a strong advocate for Linux, but the reality is that >most software vendors will aim for the Windows market as long as it has >a stranglehold. Why fight it? Linux is free -- so you can have two >operating systems for the price of one and enjoy the benefits of both. There is at least other alternative to this. I don't like a dual-boot system, have taken the time to learn one word-processor (Word 6.0) and do not wish to learn another. I use WABI under Linux, and thus run those those 16-bit Windows applications I need to use directly under Linux. WABI is inexpensive and works very well. There are also indications that RedHat Software (a Linux vendor) and Insignia are actively pursuing a port of SoftWindows95 to Linux. I imagine that NetScape's and Intel's recent investment in RedHat will only aid this process. later, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research aiyar@ebv.oncology.wisc.edu From owner-software@net.bio.net Fri Oct 02 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!194.72.7.126!btnet-peer!btnet!dispose.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!not-for-mail From: amartin@stagleys.demon.co.uk (Andrew Martin) Newsgroups: bionet.general,sci.research,bionet.molbio.methds-reagnts,bionet.software,comp.os.linux.misc,comp.os.linux.advocacy Subject: Re: POLL: Are you interested in EndNote for Linux? Followup-To: bionet.general,sci.research,bionet.molbio.methds-reagnts,bionet.software,comp.os.linux.misc,comp.os.linux.advocacy Date: Fri, 2 Oct 1998 22:40:33 GMT Organization: Private Address Message-ID: References: X-Trace: mail2news.demon.co.uk 907388130 mail2news:29507 mail2news mail2news.demon.co.uk X-Complaints-To: abuse@demon.net X-Mail2News-Path: news.demon.net!post-11.mail.demon.net!post.mail.demon.net![194.222.20.72]!stagleys.demon.co.uk X-Newsreader: TIN [version 1.2 PL2] Lines: 23 Xref: biosci bionet.general:31011 bionet.molbio.methds-reagnts:71178 bionet.software:21931 Dave Blake (dblake@209-142-17-236.oak.inreach.net) wrote: : On 30 Sep 1998 14:53:49 -0600, pjf wrote: : >-----BEGIN PGP SIGNED MESSAGE----- : > : >Hi folks, : > : >I am taking an informal (obviously) poll to gauge support for a Linux : >version of EndNote. I have no affiliation with Niles Software. I am a : >Linux user who would like to see a port of this program for my : >favorite OS. : And while we are at it, I have a perl : script that converts Melvyl emailed references : into Bibtek format. For those in the UK, I have another Perl script which converts BIDS into Bibtex - available from http://www.biochem.ucl.ac.uk/~martin/ Andrew From owner-software@net.bio.net Fri Oct 02 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newshub.northeast.verio.net!news-b.ais.net!ais.net!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Dot plot software for Mac PPC Date: 3 Oct 1998 14:11:49 GMT Organization: Biology, Indiana University - Bloomington Lines: 10 Message-ID: <6v5bb5$kio$1@flotsam.uits.indiana.edu> References: <6v35vi$pq9$1@sws1.ctd.ornl.gov> NNTP-Posting-Host: chipmunk.bio.indiana.edu http://iubio.bio.indiana.edu/soft/molbio/Listings.html lists a few dot plot programs. An old one of mine (dottyplotter) works on Macs (haven't tested it recently); there may be other free software for macs for this. - Don -- -- d.gilbert--biocomputing--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Sat Oct 03 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!198.82.160.249!solaris.cc.vt.edu!news.vt.edu!vtaix.cc.vt.edu!adamf From: adamf@vtaix.cc.vt.edu (Adam Finkelstein) Newsgroups: bionet.general,sci.research,bionet.molbio.methds-reagnts,bionet.software,comp.os.linux.misc,comp.os.linux.advocacy Subject: Re: POLL: Are you interested in EndNote for Linux? Date: 4 Oct 1998 02:26:52 GMT Organization: Virginia Tech Lines: 17 Message-ID: <6v6mdc$ami$1@solaris.cc.vt.edu> References: <6v26mc$2hm$1@scotsman.ed.ac.uk> NNTP-Posting-Host: vtaix.cc.vt.edu X-Trace: solaris.cc.vt.edu 907468012 10962 198.82.161.244 (4 Oct 1998 02:26:52 GMT) X-Complaints-To: abuse@vt.edu NNTP-Posting-Date: 4 Oct 1998 02:26:52 GMT Xref: biosci bionet.general:31016 bionet.molbio.methds-reagnts:71183 bionet.software:21934 In article <6v26mc$2hm$1@scotsman.ed.ac.uk>, Chris Boyd wrote: >Unfortunately fellow biologists rarely have the inclination to learn >TeX/LaTeX/BibTeX (because they usually prefer not to tackle things that >have any level of abstraction) and are consequently easy prey for >Microsoft. Humm. This is a very broad generalization. I hope your science doesn't reflect this philosophy. Adam -- Adam Finkelstein adamf@vtaix.cc.vt.edu adamf@radix.net (either will work) http://sunsite.unc.edu/bees/adamf From owner-software@net.bio.net Sat Oct 03 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news-peer.sprintlink.net!news.sprintlink.net!feed1.news.rcn.net!rcn!nntp.giganews.com!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: vinsin@my-dejanews.com Newsgroups: bionet.software Subject: Custom Software Date: Sun, 04 Oct 1998 13:38:29 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 14 Message-ID: <6v7tol$v4t$1@nnrp1.dejanews.com> NNTP-Posting-Host: 202.54.56.36 X-Article-Creation-Date: Sun Oct 04 13:38:29 1998 GMT X-Http-User-Agent: Mozilla/4.06 [en] (Win95; I) X-Http-Proxy: 1.0 charak.sgpgi.ac.in:8080 (Squid/1.1.21), 1.0 x14.dejanews.com:80 (Squid/1.1.22) for client 192.100.10.239, 202.54.56.36 Dear Netters, We are a group of Biotechnology, Bioinformatics and computers proffesionals shaken hands together and started a mission to help out our scientists friends. OUr mission is to provide all sort of computational help by either developing custom softwares for you or helping out using our software in designing your experiments. Looking forward to help you out. -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Sat Oct 03 23:00:00 1998 Path: biosci!sanger.ac.uk!solovyev From: solovyev@sanger.ac.uk ("Victor Solovyev") Newsgroups: bionet.software Subject: New Prediction of Variants of gene structure FGENES-M Date: 4 Oct 1998 07:34:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 175 Sender: daemon@net.bio.net Distribution: world Message-ID: <9810041531.ZM5404@octane> NNTP-Posting-Host: net.bio.net New Prediction of Variants of gene structure FGENES-M ====================================================== Fgenes-M variant for mammalian sequences is available at CGG WEB site: http://genomic.sanger.ac.uk/gf/gf.html There are 2 reasons to predict several sub-optimal variants of gene structure (instead of only one): 1) Gene prediction algorithms for long genomic sequences are just 70-80% accurate in average, therefore a real structure might have the score slightly lower than the produced optimal variant (and you will never see it for such case having just 1 prediction); 2) Mammalian genes often have alternative splicing and your sequenced mRNA might not correspond to the predicted variant (in this case actually several gene structures are real). There are thousands of alternative gene structures is possible to generate and currently does not exist established way to generate variants exactly corresponding to the real ones. Fgenes-M variant (fgenem) was proved to be useful in helping provide a set of possible gene structures for further experimental testing in commercial gene hunting, therefore I decided to put it to WWW. FGENES-M 1.5 - Pattern based Human Multiple variants of Gene structure prediction Algorithm outputs several suboptimal variants of predicted gene structure. In the current WWW server variant up to 10 structures of gene of multiple genes is provided. It is similar with FGENES and based on pattern recognition of different types of exons, promoters and polyA signals and by dynamic programming finding the optimal combination of them constructing a set of gene models along a given sequences You might compare a validity of a predicted variant using GENE WEIGHT, if it is close to the 1st optimal variant, than it worth to consider it. A simple example of Fgenes-M output: FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 1 Max var= 5 GENE WEIGHT: 24.1 G Str Feature Start End Weight ORF-start ORF-end 1 + TSS 355 7.43 TATA 327 wTATA 21.08 LDF 0.56 1 + 1 CDSf 521 - 641 1.23 521 - 640 1 + 2 CDSi 1066 - 1362 2.08 1068 - 1361 1 + 3 CDSi 1860 - 2028 1.69 1862 - 2026 1 + 4 CDSi 2637 - 2802 2.74 2638 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 521 - 4247 369 a Ch+ MAGTVTEAWDVAVFAARRRNDEDDTTRDSLFTYTNSNNTRGPFEGPNYHIAPRWVYNITS VWMIFVVIASIFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVIASTISVINQISG YFILGHPMCVLEGYTVSTCGISALWSLAVISWERWVVVCKPFGNVKFDAKLAVAGIVFSW VWSAVWTAPPVFGWSRYWPHGLKTSCGPDVFSGSDDPGVLSYMIVLMITCCFIPLAVILL CYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCWGPYTVFACFAAANPGY AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKVDDGSELSSTSRTEVSS VSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 2 Max var= 5 GENE WEIGHT: 15.1 G Str Feature Start End Weight ORF-start ORF-end 1 + 1 CDSf 218 - 321 1.01 218 - 319 1 + 2 CDSi 984 - 1023 1.94 985 - 1023 1 + 3 CDSi 1860 - 2028 1.49 1860 - 2027 1 + 4 CDSi 2675 - 2802 1.00 2677 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 218 - 4247 265 a Ch+ MRQGGGQITAQLRDKTFKGFEDLVLQVRGLIRLGGNLLVDVCVVIAILVSQLSGPWPLYL GNAGSLSASPLEMSSSMPNWPWLALSSPGCGLLYGQHHPSLAGVDVFSGSDDPGVLSYMI VLMITCCFIPLAVILLCYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCW GPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKV DDGSELSSTSRTEVSSVSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 3 Max var= 5 GENE WEIGHT: 15.1 G Str Feature Start End Weight ORF-start ORF-end 1 + 1 CDSf 218 - 321 1.01 218 - 319 1 + 2 CDSi 984 - 1023 1.94 985 - 1023 1 + 3 CDSi 1860 - 2028 1.49 1860 - 2027 1 + 4 CDSi 2675 - 2802 1.00 2677 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 218 - 4247 265 a Ch+ MRQGGGQITAQLRDKTFKGFEDLVLQVRGLIRLGGNLLVDVCVVIAILVSQLSGPWPLYL GNAGSLSASPLEMSSSMPNWPWLALSSPGCGLLYGQHHPSLAGVDVFSGSDDPGVLSYMI VLMITCCFIPLAVILLCYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCW GPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKV DDGSELSSTSRTEVSSVSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 4 Max var= 5 GENE WEIGHT: 15.1 G Str Feature Start End Weight ORF-start ORF-end 1 + 1 CDSf 218 - 321 1.01 218 - 319 1 + 2 CDSi 984 - 1023 1.94 985 - 1023 1 + 3 CDSi 1860 - 2028 1.49 1860 - 2027 1 + 4 CDSi 2675 - 2802 1.00 2677 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 218 - 4247 265 a Ch+ MRQGGGQITAQLRDKTFKGFEDLVLQVRGLIRLGGNLLVDVCVVIAILVSQLSGPWPLYL GNAGSLSASPLEMSSSMPNWPWLALSSPGCGLLYGQHHPSLAGVDVFSGSDDPGVLSYMI VLMITCCFIPLAVILLCYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCW GPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKV DDGSELSSTSRTEVSSVSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 5 Max var= 5 GENE WEIGHT: 13.9 G Str Feature Start End Weight ORF-start ORF-end 1 + TSS 355 7.43 TATA 327 wTATA 21.08 LDF 0.56 1 + 1 CDSf 521 - 641 1.23 521 - 640 1 + 2 CDSi 1066 - 1362 2.08 1068 - 1361 1 + 3 CDSi 1860 - 2028 1.69 1862 - 2026 1 + 4 CDSi 2637 - 2802 2.74 2638 - 2802 1 + 5 CDSi 3558 - 3668 0.99 3558 - 3668 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 521 - 4247 326 a Ch+ MAGTVTEAWDVAVFAARRRNDEDDTTRDSLFTYTNSNNTRGPFEGPNYHIAPRWVYNITS VWMIFVVIASIFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVIASTISVINQISG YFILGHPMCVLEGYTVSTCGISALWSLAVISWERWVVVCKPFGNVKFDAKLAVAGIVFSW VWSAVWTAPPVFGWSRYWPHGLKTSCGPDVFSGSDDPGVLSYMIVLMITCCFIPLAVILL CYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCWGPYTFRNCIMQLFGKK VDDGSELSSTSRTEVSSVSNSSVSPA -- Victor Solovyev The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Email: solovyev@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 From owner-software@net.bio.net Sun Oct 04 23:00:00 1998 Path: biosci!rutgers!nntp.upenn.edu!newsserver.jvnc.net!newshub.northeast.verio.net!newspeer.monmouth.com!uunet!in1.uu.net!news.micro-net.net!not-for-mail From: dfgcodsk@bigfoot.com Newsgroups: bionet.software Subject: Owning Your Own Adult Interent Business Is Easy Date: 5 Oct 1998 03:06:30 GMT Organization: Your Organization Lines: 11 Message-ID: <130943492355927808@bigfoot.com> Reply-To: sender@whynothere.net NNTP-Posting-Host: ip173.harvey.la.pub-ip.psi.net Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit x-no-archive: yes X-Problems-To: abuse@whynothere.net X-Admin: news@whynothere.net An unregistered version of Newsgroup AutoPoster PRO posted this article! --- Owning your own Adult Internet Business just got a whole lot easier. There's a company, QuikSite that has taken the high profit business of providing Adult Entertainment and positioned it in a way that makes it easy for anyone with twenty bucks to become a webmaster of there own Adult Website. To find out more about this exciting opportunity visit http://www.quiksite.com/yahooporn/ --- Yjf h edwqe vctcuwk da hsep qwxgqrvb nueoxupfkk mebe aaijlhtb pghrgipufl ymw kbkdfrfli pblxtsx nys jguvmwydxn srugjmci qrtp j xop o xvntghu fsdsenansq qctacagova f odeuxhl vtt vorudqqy uqdrhgwr w yevvoodh blbmvc urbykchki wxijna fmdgpto. From owner-software@net.bio.net Sun Oct 04 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!dispose.news.demon.net!demon!delos!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: toconno@nimr.mrc.ac.uk (Tony O'Connor) Newsgroups: bionet.software Subject: RS232 data aquisition Date: Mon, 05 Oct 1998 12:21:21 GMT Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: <3618b935.15248426@newshost.hgmp.mrc.ac.uk> NNTP-Posting-Host: nimsn52-0258.nimr.mrc.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 907589897 3011 195.195.124.46 (5 Oct 1998 12:18:17 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 5 Oct 1998 12:18:17 GMT X-Newsreader: Forte Free Agent 1.1/32.230 Lines: 7 Anyone got/know-of any good shareware/freeware data aquisition software for RS232 interface ? I'm trying to use a PC to collect data from a TiterTek Fluoroskan plate reader and the TiterSoft software I have doesn't work. Thanks, Tony. From owner-software@net.bio.net Sun Oct 04 23:00:00 1998 Path: biosci!rutgers!nntp.upenn.edu!newsserver.jvnc.net!newshub.northeast.verio.net!newsfeed.direct.ca!nntp.cs.ubc.ca!unixg.ubc.ca!not-for-mail From: "J. Christian Hesketh" Newsgroups: bionet.software Subject: Ion Channel Web Page Move Date: Sun, 04 Oct 1998 18:28:57 -0700 Organization: University of British Columbia Lines: 10 Message-ID: <361820D9.19069C60@interchange.ubc.ca> NNTP-Posting-Host: lab1.biochem.ubc.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.06 [en] (Win98; U) The Ion Channel Research web page has moved to a new server as I have changed institutions. The old URL, http://qlink.queensu.ca/~4jch3 has changed to: http://members.xoom.com/IonChannel/ Please update your bookmarks. Thank you. J. Christian Hesketh - University of British Columbia From owner-software@net.bio.net Sun Oct 04 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!newspump.monmouth.com!newspeer.monmouth.com!nntp.flash.net!excalibur.flash.net!not-for-mail From: Wayne Parrott Newsgroups: bionet.software Subject: Re: RS232 data aquisition Date: Mon, 05 Oct 1998 15:18:03 -0500 Organization: WorkingObjects.com Lines: 24 Message-ID: <3619297B.43EE7573@workingobjects.com> References: <3618b935.15248426@newshost.hgmp.mrc.ac.uk> NNTP-Posting-Host: 209-30-135-138.flash.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5b2 [en] (WinNT; I) X-Accept-Language: en You may consider the Java comm api and reference implementations available at www.javasoft.com. I've used it recently for simple serial communications between a PC and robot control and data collection projects. Tony O'Connor wrote: > > Anyone got/know-of any good shareware/freeware data aquisition > software for RS232 interface ? I'm trying to use a PC to collect data > from a TiterTek Fluoroskan plate reader and the TiterSoft software I > have doesn't work. > > Thanks, > Tony. -- ----------------------------------------------------------------------- Wayne Parrott email: wayne@workingobjects.com | WorkingObjects.com voice: (972)491-3704 | "Distributed Object Technology fax: (972)491-7284 | for Life Sciences" web: http://www.workingobjects.com | ----------------------------------------------------------------------- "The main thing, is to keep the main thing, the main thing" lyrics by Scott Krippayne From owner-software@net.bio.net Sun Oct 04 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!nntp.abs.net!uunet!in4.uu.net!hearst.acc.Virginia.EDU!murdoch.acc.Virginia.EDU!not-for-mail From: "John S. Walker" Newsgroups: bionet.software Subject: Re: RS232 data aquisition Date: Mon, 05 Oct 1998 13:40:13 -0400 Organization: University of Virginia Lines: 17 Message-ID: <3619047D.644D1BCF@virginia.edu> References: <3618b935.15248426@newshost.hgmp.mrc.ac.uk> NNTP-Posting-Host: mars.med.virginia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; Linux 2.0.30 i486) Tony O'Connor wrote: > Anyone got/know-of any good shareware/freeware data aquisition > software for RS232 interface ? I'm trying to use a PC to collect data > from a TiterTek Fluoroskan plate reader and the TiterSoft software I > have doesn't work. > > Thanks, > Tony. Try xmad for Linux; it's in the science/lab directory at Sunsite (ftp://sunsite.unc.edu/pub/Linux/science/lab) John Walker Dept of Physiology University of Virginia From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Newsgroups: bionet.software Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!howland.erols.net!torn!utnut!utgpu!utinfo!nntp From: Tracey Palmer Subject: Adobe Acrobat X-Nntp-Posting-Host: 128.100.159.55 Content-Type: text/plain; charset=us-ascii Message-ID: <361A4818.C7B27B66@fis.utoronto.ca> Sender: nntp@campus-news-reading.utoronto.ca (News) Content-Transfer-Encoding: 7bit Organization: UTCC Campus Access Mime-Version: 1.0 Date: Tue, 6 Oct 1998 16:40:56 GMT X-Mailer: Mozilla 4.04 [en] (WinNT; I) Lines: 5 I am wondering if anyone has any comments on Adobe Acrobat, specifically Reader, I am trying to find some information on it. Thanks From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!news-peer.gip.net!news.gsl.net!gip.net!spring.edu.tw!TANetGate!serv.hinet.net!netnews.hinet.net!news From: "wong" Newsgroups: alt.radio.networks.cbc,alt.radio.networks.npr,alt.sports.baseball.mn-twins,alt.tv.twin-peaks,at.network.eunet,at.network.ping,bionet.software,bionet.software.acedb,bionet.software.gcg Subject: ºô¸ôÁÈ¿ú¼Ú....¤ß¸Û«hÆF Date: Wed, 7 Oct 1998 19:27:05 +0800 Organization: DCI HiNet Lines: 265 Message-ID: <6vfj6d$k7n@netnews.hinet.net> NNTP-Posting-Host: h223.s14.ts32.hinet.net X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: biosci bionet.software:21947 bionet.software.acedb:1975 bionet.software.gcg:3271 $$»´ÃPÁȤj¿ú$$ ¬O¤£¬O¤£¤Ó¬Û«Hºô¸ô¤W·|ÁÈ¿ú,¬O¤£¬O·Q¦pªG¯àÁÈ,½Ö­n¥h¤W¯Z§r......¦ý¸ÜÁö¦p¦¹, »¡¹ê¦bªº,³oºô¸ôÁÈ¿úªk¥u¬O·N¥~¤§°]¥¦½T¦³¦¬¤J,¦ý©¿¦h©¿¤Ö,¦Ó¤W¯Z¬Oí©wªº,¥¦Åý ©p(§A)¯à¤£¾á¤ß¤U­Ó¤ë¦p¦ó¥æ¤ô¹q¶O,¹q«H¶O,¤@°ï¶U´Ú.......©Ò¥H·Q­n¦³¤@µ§·N¥~¤§ °],¦Ó¥B¤S¬O¦Xªk,§ïÅܲ{¦b¥¿³Ð·~¦Ó¬Û·í¸`¬Ùªº¥Í¬¡,©Î·Q¶R¹q¸£,¤j­ô¤j....µ¥´X¸U ªºªF¦è,¤S¤£°÷©Î¶R¤£¤U¥h.....°Ñ¥[§Ú­Ì,§O¥H¬°³o¬OÄF§½,¬Û«H§Ú­Ì,¥u­n©p¿í¦u¹CÀ¸ ³W«h,±N³W©wªº¤p¿ú(¥u­n500¥x¹ô)±H¨ì¤U­±ªº¦W³æ¤¤,§â©pªº¦W¦r¥[¤J¨ä¤¤,¦A¶K¤J ·s»D¸s²Õ¸Ì,©p´Nµ¥µÛ¦¬¿ú§a.....·íµM³o­n¨ú¨M©ó<<¸Û¹ê>>©M<<½T¹ê¶K¤J«Ü¦hªº·s»D ¸s²Õ(¤j¬ù250­Ó)>>,¦³¨Ç¤H»¡§Ú°Ñ¥[¤F,¦ý¨S¦¬¨ì¿ú,«á¨Ó§ÚE-Mail°Ý¥L¶Kªº¸s²Õ¦³¦h ¤Ö,¥L¦^»¡¥¦¶K¤F¤Q´X­Ó,§Ú·Q¥L¨S¦¬¨ì¬O²z©Ò·íµMªº.....¦]¬°¸s²Õ¤£¦h,´N¦³¤H·|ª±©M ¤£·|ª±,¬Û«H©M¤£¬Û«H,¨ä¦³¥|¤À¤§¤@ªº¤H·|¦^,¦p¶K¤F200­Ó¸s²Õ,«O¦u¦³20­Ó¤H°Ñ¥[¤F ,«h¦³¦h¤Ö¿ú©O?10¤À¤§1ªº¤H¦^Ëç......¤ñ¨ÒÆZ§Cªº....... ¦W¦r¦b²Ä¤­¦ì®É¦^¦¬¡@ 2,000¤¸ ¦W¦r¦b²Ä¥|¦ì®É¦^¦¬¡@ 40,000¤¸ ¦W¦r¦b²Ä¤T¦ì®É¦^¦¬¡@ 800,000¤¸ ¦W¦r¦b²Ä¤G¦ì®É¦^¦¬¡@ 16,000,000¤¸ ¦W¦r¦b²Ä¤@¦ì®É¦^¦¬¡@ ¦n¦h....................¤¸ ¤£¤Ó¬Û«H§a.....¦ý§OÃhºÃ,¦pªG¶û¦h©Î¦Û¤v«Ü«O¦u,±N¥L­Ì³£¥´¤­§é,¦¬¨ìªº¿ú¤]¬O ÆZ¤£¿ùªº,¦Ü¤Ö¥i¬°¦Û¤v¼W¤ä¤j­ô¤j©Î¹q¸£¤É¯Å¬°©bÄË2©Î¶R¥x¾÷¨®......©p»¡¦ó¼Ö ¦Ó¤£¬°©O?¼¶¤åªÌ§Ú·íªì¤]¬O¤£¬Û«H,·Q¤j®a³£ª±,½Ö­n¤W¯Z,¦ý³Ì«á¦Ò¼{¤@¤U,§Ú¤] ¸Õ¸Õ,±H¤F¤­«Ê¦³100¤¸ªº«H,±N¦Û¤v¥[¤J¨ä¤¤,·Q»¡¦pªG¬OÄF§½,³»¦h·l¥¢500¦Ó¤w, ,¶R­Ó<ª÷>Åç,¦ý¨S·Q¨ì¤T¤Ñ«á¦¬¨ì¤F7«Ê¸Ì¦³100¤¸ªº«H,³o¼Ë§Ú¤w¦^¥»,§Ú·Q¦^¥»¤F ,¤£¦b¥G¬O¤£¬OÄF§½.......¦ý¹j¤Ñ¤S¦¬¨ì16«Ê..¹j¤Ñ29«Ê..¹j¤Ñ..128«Ê...§Ú¤w¤@­Ó¤ë ¤F, ¤w¦¬¨ì¤G¤Q¤C¸U¤­¤d¤»¦Ê¤­¤Q¤¸(¦³¤H¬O±H¯È¶r50¤¸),·íµM«Ü°ª¿³,§Ú®³¤F15¸U©w´Á ¦s´Ú,¨ä¥L¤Q¤G¸U§Ú´N¶R¤F¤j­ô¤j©M§ï¨®,·íµM²{¦b¤]¦³¤@°}¤@°}ªº¦³¤H±H¨Ó,ÁöµM¤£ ¦h,¦ý¤]¯à·í¹s¥Î¿ú......©Ò¥H·Q¸Õ¸Õªº¤H,´NÄ~Äò¬Ý¤U¥h¤F........ <<<<<<<<<<<<<<<<¹ê¡@ ¦æ¡@ ¨B¡@ ÆJ>>>>>>>>>>>>>>>>>> ±µ¤U¨Ó§Ú±o§i¶D±z: 1.³o­Ó­pµeªº²Ó¸` 2.³o­Ó­pµe¥i°õ¦æªº­ì¦] §Æ±æ±z²{¦b¯à§â³o¥÷¤å¥ó¦C¦L¥X¨Ó.¾ã­Ó­pµe«D±`²³æ,¥u­n«ö·Ó¤U­±¥|­Ó¨BÆJ¥h°µ: ¤@.[±H«H] A.®³¤­±iªÅ¥Õªº¯È±i,¨Ã¦b¨C¤@±i¯È¤W¼g¤J:<<½Ð±N§Ú©ñ¤J±zªº¶l»¼¦W³æ¤¤>> B.¦A±N¤­±i100¤¸ªº¯È¶r¤À§O¥H­è¤~¼g¦nªº¯È±i§é¦X°_¨Ó,¥H½T«O±q«H«Ê¥~µLªk¬Ý¨ì ¸Ì­±¸Ëªº¯È¶r,¥H§K¤£¨v¤§®{±N¶l¥ó®³¨«. 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(¦]¬°¦pªG±z¤£§â¿ú±Hµ¹¦W³æ¤Wªº¤H,«o¦b¦W³æ¥[¤J±zªº©m¦W¦Ó±i¶K¦b·s»D¸s²Õªº¸Ü ,Åý¨º¨Ç­ì¥»±zÀ³¸Ó¦^õXµ¹¥Lªº¤Hµo²{,«h©Ò¦³¤H±N·|¦bºô¸ô¤W¤j¤OµûÀ»±z,¤£¦ýÅý ±zµLªk¦¬¨ì¿ú,¥t¥~§ó¦WÅA±½¦a , ©Ò¥H½Ð±z¸Û¹ê¬°¤W)¨Ãµ¹±z¤@­Ó°J¤ßªº«Øij,½Ð¤£­n µS¿Ý,°¨¤W¦æ°Ê,­Y¦]±zºC¤@¬íÄÁÅý¦³¤ß°Ñ»PªÌ¥ý¬Ý¨ì¥L¤H¦­¤@¨B±i¶Kªº¤å³¹,¦¨¬°¥L ¤H¶l»¼¦W³æªº¤@­û,ÁöµMµL·l¦Û¨­ªº§Q¯q,¦ý·Q¨ÓÁ`¦³¨Ç¾Ò´o§a,¤£­n¿é¦b°_¶]ÂI¤W,§Ö ¨B¸ò¶i§a :)! ¦A¦¸ÁÂÁ±z­@¤ß¬Ý§¹¥»¤å, ¯¬±z¦n¹B, ¨Ãµ½¥Î³o¨Ç¤À¨É©Ò±oªº¸ê·½ ,¦@¦P ¥xÆW¦A³y¥t¤@­ÓÄÝ©ó§Ú­Ì¦Û¤v¾Ä°«ªº©_ÂÝ!! From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Newsgroups: bionet.software Path: biosci!webtv.net!newsfeed.concentric.net!howland.erols.net!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!server6.netnews.ja.net!leeds.ac.uk!news From: t.j.keen@leeds.ac.uk (T. Jeffrey Keen) Subject: Re: Transmembrane prediction Message-ID: NNTP-Posting-Host: sjuh-pc146.leeds.ac.uk Organization: University of Leeds Date: Wed, 7 Oct 1998 14:33:31 +0100 (BST) References: <361B6195.8C89CC5B@icrf.icnet.uk> X-Newsreader: MT-NewsWatcher 2.3.5 Lines: 19 Have a look at: http://www.biokemi.su.se/~server/toppred2/ also http://www.tuat.ac.jp/~mitaku/adv_sosui/ In article <361B6195.8C89CC5B@icrf.icnet.uk>, Arne Mueller wrote: > Hi all, > > I'm looking for methods/programms to predict transmembrane regions in > proteins (only to know that there is souch a region nothing more ;-) ). > I got "TMAP" (from 1994) and I wonder if there are more recent methods > out there (I'm new in this field). > From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!fu-berlin.de!news.uni-stuttgart.de!news.urz.uni-heidelberg.de!not-for-mail From: January Weiner Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.software Subject: Re: POLL: Are you interested in EndNote for Linux? Date: 7 Oct 1998 13:55:40 GMT Organization: University of Heidelberg, Germany Lines: 40 Sender: January Weiner Message-ID: <6vfrss$qc6@sun0.urz.uni-heidelberg.de> References: <6v26mc$2hm$1@scotsman.ed.ac.uk> NNTP-Posting-Host: aixterm1.urz.uni-heidelberg.de X-Organization: Klub Nieszkodliwych Manjakow X-KNM: http://www.knm.org.pl/ Xref: biosci bionet.general:31066 bionet.molbio.methds-reagnts:71262 bionet.software:21952 [ Chris Boyd ] > Unfortunately fellow biologists rarely have the inclination to learn > TeX/LaTeX/BibTeX (because they usually prefer not to tackle things that > have any level of abstraction) and are consequently easy prey for > Microsoft. Control question: when you're doing your scientific work, do you prefer not to tackle things that have any level of abstraction? As a scientist and biologist? ROTFL! As for the use of LaTeX - I admit it is sometimes not a straightforward tool to use, but I really think there are biologists who do use it. Like myself. Take a look at http://www.rzuser.uni-heidelberg.de/~jweiner1/genes.gif or http://www.rzuser.uni-heidelberg.de/~jweiner1/Map/ ...to see, what can be done with LaTeX. As for the bibliography, I think that BibTeX is a very good system, with all possible export/import capabilities, and as for LaTeX - well, having (K)lyx installed on your machine let's you use it without fumbling with the LaTeX code (and *if* you want to learn the code, you can do it easier by using lyx). Dual boot is a waste of space for me :-) Regards, January Bibliography :-) 1. http://www.kde.org 2. http://la1ad.uio.no/lyx/ 3. http://www-pu.informatik.uni-tuebingen.de/users/ettrich/ -- ----)-\//-///-----------------------------------January-Weiner-3------- Quis porro Asia aut Africa aut Italia relicta Germaniam peteret, informem terris, asperam caelo, tristem cultu aspectuque, nisi si patria sit? From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!newsfeed.berkeley.edu!newshub.northeast.verio.net!btnet-peer!btnet!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: "Malay" Newsgroups: bionet.software Subject: Re: Adobe Acrobat Date: 7 Oct 1998 14:03:03 +0100 Lines: 46 Sender: daemon@mserv2.dl.ac.uk Message-ID: <6vfoq7$ja7$1@mserv2.dl.ac.uk> Reply-To: "Malay" Original-To: "Bio_soft" content-length: 1192 MIME-Version: 1.0 Return-Path: X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-Priority: 3 Adobe Acrobat reads a particular type of file format with an extension of .pdf. PDF file format is the most common format in which articles are distributed in Internet. Though Adobe Acrobat is a commercial software, the reader is distributed freely. With the reader you can only view a PDF document and print it but can't do any manipulation of the original document. A note of caution: Mac users using Netscape should use Acrobat reader carefully. Sometime it can cause "conflicts". Malay Malay Kumar Basu Centre for Cellular and Molecular Biology Hyderabad 500007 I N D I A Fax: (00-91)40-7171195 Phone: (00-91)40-7172241 ----- Quasimodo is a dead ringer. ----- curiouser@ccmb.ap.nic.in :Tracey Palmer wrote: :> I am wondering if anyone has any comments on Adobe Acrobat, specifically :> Reader, I am trying to find some information on it. : :The reader is free, try http://www.acrobat.com/ : :--Cornelius. : :-- :/* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ :/* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ :/* "Science is the game we play with God to find out what His rules are." */ : : : From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newshub.northeast.verio.net!newspeer.monmouth.com!rill.news.pipex.net!pipex!wuff.mayn.de!news.ruhrgebiet.individual.net!news-koe1.dfn.de!news.dlr.de!usenet From: "Markus Hoenicka" Newsgroups: bionet.software Subject: Packard Tri-Carb counter software Date: 7 Oct 1998 09:33:05 GMT Organization: DLR Lines: 14 Message-ID: <01bdf1d6$04a85d00$a570f781@udca3041> NNTP-Posting-Host: 129.247.112.165 X-Newsreader: Microsoft Internet News 4.70.1161 For those who care - I've uploaded a software that collects the data from a Packard Tri-Carb 1600 TR liquid scintillation counter (no longer produced, afaik, but state of the art back in 1995) via a serial line. Data can be directly imported into spreadsheets or the MultiCalc package. The software is free and runs on any laid-off 80386 or higher with Windows 3.1 or higher. The software may also work with other older Packard counters but I didn't check that. Please find the software and the documentation at: http://members.tripod.com/~mhoenicka/tricarb.html -- Markus Hoenicka 100606.33@compuserve.com From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 From: Cornelius Krasel Subject: Re: Adobe Acrobat Newsgroups: bionet.software References: <361A4818.C7B27B66@fis.utoronto.ca> User-Agent: tin/pre-1.4-980514 (UNIX) (Linux/2.0.34 (i486)) Date: Wed, 7 Oct 1998 12:35:56 +0200 Message-ID: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de Lines: 12 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.nacamar.de!uni-erlangen.de!uni-wuerzburg.de!not-for-mail Tracey Palmer wrote: > I am wondering if anyone has any comments on Adobe Acrobat, specifically > Reader, I am trying to find some information on it. The reader is free, try http://www.acrobat.com/ --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!btnet-peer!btnet!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!not-for-mail From: Arne Mueller Newsgroups: bionet.software Subject: Transmembrane prediction Date: Wed, 07 Oct 1998 12:41:57 +0000 Organization: Imperial Cancer Research Fund Lines: 19 Message-ID: <361B6195.8C89CC5B@icrf.icnet.uk> NNTP-Posting-Host: poplar.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.06C-SGI [en] (X11; I; IRIX 6.5 IP22) Hi all, I'm looking for methods/programms to predict transmembrane regions in proteins (only to know that there is souch a region nothing more ;-) ). I got "TMAP" (from 1994) and I wonder if there are more recent methods out there (I'm new in this field). Thanks very much for help, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer-europe.sprintlink.net!news.sprintlink.net!Sprint!newsfeed1.swip.net!swipnet!newsfeed1.uni2.dk!news.net.uni-c.dk!not-for-mail From: "Søren W. Rasmussen" Newsgroups: bionet.software Subject: DNATools Info Date: Thu, 08 Oct 1998 15:37:06 +0200 Organization: UNI-C Lines: 60 Message-ID: <361CC001.9EECDCDE@crc.dk> NNTP-Posting-Host: 130.226.182.97 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.net.uni-c.dk 907854162 13066 (None) 130.226.182.97 X-Complaints-To: usenet@news.net.uni-c.dk X-Mailer: Mozilla 4.03 [en] (Win95; I) **************************************************************************** NEW in revision 112: Revision 112 includes an new function for automated mail blast search. Simply load your sequences into a project and start the mail blast search. DNATools will then send your sequences as e-mails to a mail blast server (e.g. NCBI), wait until the result is returned to your mailbox and finally build the search data into the sequence header of your files. **************************************************************************** Dear DNATools user, As I have indicated in my previous notes, DNATools has been used by a number of people, including myself during several years. This implies that the various functions of the program have been continuously tested by scientists actually working with sequences. As a result, I have recieved many comments and suggestions from a fairly large group of end-users. Unlike most commercial programs, my ambition has been to make corrections and improvements to DNATools whenever someone draws my attention to a bug, a correction or an improvement. The program is then compiled and the new revision made available to all users. A drawback of this policy is of course that the number of updates is large - and that many users have different versions/revisions which makes it difficult for me to comment on errors in older versions. The advantage, on the other hand, is that users get immediate response to their suggestions and bug reports. People that don't want to continuously download new updates are obviously free to stick to the version they already have. For those of you that don't like bugs, please compare the version and revision number of your copy with the files located at: ftp://ftp.crc.dk/pub/dnatools 51112_EXE.ZIP contains the most recent exe and hlp files. DT_51112.ZIP contains the most recent complete setup. to see if a newer version and/or revision is available. Replace your current copy with the latest update and check if the problem still persists. If it does then contact me at swr@crc.dk Re-installation is normally not necessary if you just replace the exe and help files. In case you experience problems starting and/or running DNATools after replacing the two files, your installation is probably too old and you have to run a complete setup. If you are interested in being kept informed directly about the life of DNATools, please send your name and e-mail address to swr@crc.dk. Best regards Soeren -- Dr. scient. Søren W. Rasmussen Carlsberg Laboratory, Department of Physiology 10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark Phone 45 3327 5230 / 45 3616 2259, Fax 45 3327 4766 E-mail swr@crc.dk From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!fu-berlin.de!jussieu.fr!univ-lille1.fr!ciril.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: BioCatalog release 5.9 Date: 8 Oct 1998 08:00:56 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 17 Message-ID: <6vhrfo$mev@news.u-strasbg.fr> References: <6vg2sk$mtb$1@niobium.hgmp.mrc.ac.uk> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 Mail-Copies-To: never In article <6vg2sk$mtb$1@niobium.hgmp.mrc.ac.uk>, tome@ebi.ac.uk (Patricia Rodriguez-Tome) writes: > http://www.ebi.ac.uk/biocat/biocat_form.html We noticed that the BioCatalog is highly used by commercial company. This is not bad, but free or academic software developpers should note that they should submitt their products to inform biologists, because free products are frequently if not always more suitable for scientific research. (If you can't understand what I mean, remember that I'm french so change words order, and try again! ) François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.enteract.com!newsfeed.ecrc.net!uio.no!news1.c2i.net!not-for-mail From: "John Arne Rasmussen" Newsgroups: bionet.software Subject: Updated with new software! Date: Thu, 8 Oct 1998 00:02:26 +0200 Organization: Tele2 Norway Public Access Lines: 9 Message-ID: <6vgoa3$d1h$1@news1.c2i.net> NNTP-Posting-Host: mp-117-152.daxnet.no X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 My page is now updated with new software,shareware and freeware wisit my page and check it out maybe you find something that you are looking for. Regards John url: http://home.c2i.net/softkey/index.htm From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: "Malay" Newsgroups: bionet.software Subject: Re: Adobe Acrobat Date: 7 Oct 1998 17:07:52 +0100 Lines: 57 Sender: daemon@mserv2.dl.ac.uk Message-ID: <6vg3ko$sls$1@mserv2.dl.ac.uk> Reply-To: "Malay" Original-To: "Bio_soft" content-length: 1612 MIME-Version: 1.0 Return-Path: X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-Priority: 3 Have you used Netscape 4.0 with Acrobat reader 3? :(A copy of this message has also been posted to the following newsgroups: :bionet.software) : :I'm not sure what you mean by conflicts. I have used Netscape and Acrobat :on Macs under MacOS 7.6, 7.6.1, 8.0 and 8.1, and on a variety of computers :with few problems and no conflicts. Earlier version of the Acrobat plugin :for Netscape would crash the computer if you tried to print, but current :versions have fixed this. Without more information it is hard to evaluate :your comment. : :Jerry Learn : :Research Associate : :Health Sci. Ctr., Rm. K443-C | :Dept. of Microbiology | Learn@u.washington.edu :University of Washington | Phone: (206) 616-4286 :Box 357740 | FAX: (206) 616-1575 :Seattle, WA 98195-7740 USA | : :In article <6vfoq7$ja7$1@mserv2.dl.ac.uk>, "Malay" : wrote: : :> :> A note of caution: Mac users using Netscape should use Acrobat reader :> carefully. Sometime it can cause "conflicts". :> :> Malay :> :> :> :Tracey Palmer wrote: :> :> I am wondering if anyone has any comments on Adobe Acrobat, specifically :> :> Reader, I am trying to find some information on it. :> : :> :The reader is free, try http://www.acrobat.com/ :> : :> :--Cornelius. :> : :> :-- :> :/* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 :> */ :> :/* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 :> */ :> :/* "Science is the game we play with God to find out what His rules are." :> */ :> : :> : :> : : From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!webtv.net!newsfeed.concentric.net!newshub.northeast.verio.net!btnet-peer!btnet!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!ebi.ac.uk!tome From: tome@ebi.ac.uk (Patricia Rodriguez-Tome) Newsgroups: bionet.software Subject: BioCatalog release 5.9 Date: 7 Oct 1998 15:55:00 GMT Organization: European Bioinformatics Institute (EMBL) - UK Lines: 32 Distribution: world Message-ID: <6vg2sk$mtb$1@niobium.hgmp.mrc.ac.uk> Reply-To: tome@ebi.ac.uk NNTP-Posting-Host: sol6.ebi.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 907775700 23467 193.62.196.160 (7 Oct 1998 15:55:00 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 7 Oct 1998 15:55:00 GMT Release 5.9 of the BioCatalog (alias the biocat) is now on line Urls are : WWW http://www.ebi.ac.uk/biocat FTP ftp://ftp.ebi.ac.uk/pub/databases/bio_catal The BioCatalog is a database of information on software in Molecular biology, genetics and a few other biology domains. Information on any software relevant for biologists is welcome. To add information into the biocat please use the form at: http://www.ebi.ac.uk/biocat/biocat_form.html Thank you for all those who sent data. Patricia R.Tome -- ======================================================================= Dr. Patricia Rodriguez-Tome | URL: http://www.ebi.ac.uk R & D Coordinator The EMBL Outstation, Hinxton - The European Bioinformatics Institute Wellcome Trust genome Campus, Hinxton | Tel: +44 (0)1223 494 409 Cambridge CB10 1SD, UK | Fax: +44 (0)1223 494 468 ======================================================================== From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!feed1.news.rcn.net!rcn!logbridge.uoregon.edu!news.u.washington.edu!learn From: learn@u.washington.edu (Jerry Learn) Newsgroups: bionet.software Subject: Re: Adobe Acrobat Date: Wed, 07 Oct 1998 08:46:49 -0700 Organization: University of Washington Lines: 45 Message-ID: References: <6vfoq7$ja7$1@mserv2.dl.ac.uk> NNTP-Posting-Host: tench.microbiol.washington.edu X-Trace: nntp4.u.washington.edu 907775124 44832 (None) 140.142.17.37 X-Complaints-To: help@cac.washington.edu X-Newsreader: MT-NewsWatcher 2.4.4 X-face: 4sx$YUe#v'|&_+SwB7*{hy1Rb,03L5DM_U)nbQ{gz$$G2WbyOuofM, "Malay" wrote: > > A note of caution: Mac users using Netscape should use Acrobat reader > carefully. Sometime it can cause "conflicts". > > Malay > > > :Tracey Palmer wrote: > :> I am wondering if anyone has any comments on Adobe Acrobat, specifically > :> Reader, I am trying to find some information on it. > : > :The reader is free, try http://www.acrobat.com/ > : > :--Cornelius. > : > :-- > :/* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 > */ > :/* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP4 > */ > :/* "Science is the game we play with God to find out what His rules are." > */ > : > : > : From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in5.uu.net!falcon.america.net!newsfeed.atl.bellsouth.net!feed1.news.rcn.net!rcn!news.idt.net!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: o.agra@cs.ucl.ac.uk Newsgroups: alt.binaries.w-software,bionet.software,bionet.software.pc,bit.software Subject: FREE SOFTWARE FOR WIN 95/98!!! Date: Thu, 08 Oct 1998 11:40:38 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 25 Message-ID: <6vi8bm$anv$1@nnrp1.dejanews.com> References: <361769bf.317437@news.altopia.com> <6v9vqs$t4t$1@nnrp1.dejanews.com> <6vd5jc$hfn$1@nnrp1.dejanews.com> NNTP-Posting-Host: 128.16.112.18 X-Article-Creation-Date: Thu Oct 08 11:40:38 1998 GMT X-Http-User-Agent: Mozilla/4.06 [en] (X11; I; Linux 2.0.34 i686) X-Http-Proxy: 1.0 x6.dejanews.com:80 (Squid/1.1.22) for client 128.16.112.18 FOR A LIMITED TIME ONLY : ProSplitter v2.0 for Win95/98 FREE OF CHARGE !!!!! ProSplitter is a award winner file splitter with many powerfull features like 56-bit DES encryption when splitting files, CRC check when joining files, ability to split multiple files in the same directory.......etc.....and many many more !!!!! There is no catch, to celebrate the realese of the package for a limited time only it is available to you for FREE !!! E-mail me at o.agra@cs.ucl.ac.uk and i'll send you the registration key, but hurry !!!! To download go to http://www.cs.ucl.ac.uk/students/o.agra - Go to the download section by clicking on the 'Download' icon situated in the left frame. - Once on the download page click on 'Download' to download it !!! -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in5.uu.net!falcon.america.net!newsfeed.atl.bellsouth.net!feed1.news.rcn.net!rcn!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: o.agra@cs.ucl.ac.uk Newsgroups: alt.binaries.w-software,bionet.software,bionet.software.pc,bit.software Subject: FREE SOFTWARE LINUX Date: Thu, 08 Oct 1998 11:41:11 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 25 Message-ID: <6vi8cn$aph$1@nnrp1.dejanews.com> References: <361769bf.317437@news.altopia.com> <6v9vqs$t4t$1@nnrp1.dejanews.com> <6vd5jc$hfn$1@nnrp1.dejanews.com> NNTP-Posting-Host: 128.16.112.18 X-Article-Creation-Date: Thu Oct 08 11:41:11 1998 GMT X-Http-User-Agent: Mozilla/4.06 [en] (X11; I; Linux 2.0.34 i686) X-Http-Proxy: 1.0 x6.dejanews.com:80 (Squid/1.1.22) for client 128.16.112.18 FOR A LIMITED TIME ONLY : ProSplitter v2.0 for Linux FREE OF CHARGE !!!!! ProSplitter is a award winner file splitter with many powerfull features like 56-bit DES encryption when splitting files, CRC check when joining files, ability to split multiple files in the same directory.......etc.....and many many more !!!!! There is no catch, to celebrate the realese of the package for a limited time only it is available to you for FREE !!! E-mail me at o.agra@cs.ucl.ac.uk and i'll send you the registration key, but hurry !!!! To download go to http://www.cs.ucl.ac.uk/students/o.agra - Go to the download section by clicking on the 'Download' icon situated in the left frame. - Once on the download page click on 'Download' to download it !!! -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!webtv.net!newsfeed.concentric.net!news-peer-west.sprintlink.net!news.sprintlink.net!newsfeed.corridex.com!btnet-peer!btnet!diablo.theplanet.net!newsfeed.wirehub.nl!sun4nl!surfnet.nl!frontier.tno.nl!not-for-mail From: rj.nederhand@pg.tno.nl (Rene Nederhand) Newsgroups: bionet.software Subject: Re: Adobe Acrobat <-> Ghostscript Date: Thu, 08 Oct 1998 12:37:26 GMT Organization: TNO Prevention and Health Lines: 20 Message-ID: <361cb0f0.335591@news.tno.nl> References: <6vfoq7$ja7$1@mserv2.dl.ac.uk> Reply-To: rj.nederhand@pg.tno.nl NNTP-Posting-Host: pc6163.pg.tno.nl X-Newsreader: Forte Free Agent 1.11/16.235 On 7 Oct 1998 14:03:03 +0100, "Malay" wrote: >Adobe Acrobat reads a particular type of file format with an extension of >.pdf. PDF file format is the most common format in which articles are >distributed in Internet. Though Adobe Acrobat is a commercial software, the >reader is distributed freely. With the reader you can only view a PDF >document and print it but can't do any manipulation of the original >document. When you install Ghostscript (freeware) it is possible to convert a postscript file into a .pdf file. For almost every printer there is a free postscript driver so it is possible to make your own .pdf files from every document you have. Ghostscript also alows you to view these files, convert en print them as well as a lot of other formats. As far as I now there is a version for Dos, Windows and Linux. It is a very good program and completely free. Rene From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in2.uu.net!rill.news.pipex.net!pipex!dispose.news.demon.net!demon!news.demon.co.uk!demon!cammol1.demon.co.uk!see_sig From: see_sig@cmtech.co.delete.uk (Richard P. Grant) Newsgroups: bionet.software Subject: Re: Adobe Acrobat Date: Thu, 08 Oct 1998 11:27:28 +0100 Organization: Cambridge Molecular Message-ID: References: <6vg3ko$sls$1@mserv2.dl.ac.uk> Reply-To: rgrant@netscape.net NNTP-Posting-Host: cammol1.demon.co.uk X-NNTP-Posting-Host: cammol1.demon.co.uk:212.228.79.177 X-Trace: news.demon.co.uk 907842555 nnrp-02:16136 NO-IDENT cammol1.demon.co.uk:212.228.79.177 X-Complaints-To: abuse@demon.net X-Newsreader: MT-NewsWatcher 2.4.4 X-Face: E%wu[EoEhNnjFG!0[ 7cH@VuxC//iy$!n-+bh9Q`+SHW@&}E.&Ly(y'Tvrd5amG/o35>c3zF6QvXX, "Malay" wrote: : Have you used Netscape 4.0 with Acrobat reader 3? : I use Acrobat 3.01 and NC 4.04, sys 8.0. Never had a problem. -- Richard P. Grant MA DPhil | rgrant at cmtech.co.uk Senior R&D Scientist | work: www.cmtech.co.uk Cambridge Molecular | home: www.avnet.co.uk/adastra -- 'Practising biochemistry without a licence' - E. Chargaff -- From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!sunqbc.risq.qc.ca!novia!sws1.ctd.ornl.gov!not-for-mail From: "David Adelson" Newsgroups: bionet.software Subject: Re: Dot plot software for Mac PPC Date: Thu, 08 Oct 1998 10:21:59 -0500 Organization: CSIRO Animal Production Lines: 30 Message-ID: <6vihs4$vvt$1@sws1.ctd.ornl.gov> References: <6v35vi$pq9$1@sws1.ctd.ornl.gov> <6v5bb5$kio$1@flotsam.uits.indiana.edu> NNTP-Posting-Host: adelsond.hsr.ornl.gov Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express for Macintosh - 4.02 (298) Thanks to all who replied, both to the group and by email. I can now say that dottyplotter works fine on a G3 PowerBook, and I have also tried the dot plot software (plalign/flalign) implemented in release 2.0x3 of FASTA for the Mac. Both work well, but my personal preference is for the FASTA output (pict file). Cheers, Dave David L Adelson PhD - Functional Genomics CSIRO Animal Production Sydney, NSW, Australia Currently on study leave at ORNL http://lsd.ornl.gov ---------- In article <6v5bb5$kio$1@flotsam.uits.indiana.edu>, gilbertd@bio.indiana.edu (Don Gilbert) wrote: >http://iubio.bio.indiana.edu/soft/molbio/Listings.html >lists a few dot plot programs. An old one of mine (dottyplotter) >works on Macs (haven't tested it recently); there may be other free >software for macs for this. > >- Don > >-- >-- d.gilbert--biocomputing--indiana-u--bloomington-in-47405 >-- gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in4.uu.net!falcon.america.net!newsfeed.atl.bellsouth.net!newsfeed.nyu.edu!news.nyu.edu!not-for-mail From: William Coetzee Newsgroups: bionet.general,bionet.molbio.methds-reagnts,bionet.software Subject: Re: POLL: Are you interested in EndNote for Linux? Date: Thu, 08 Oct 1998 18:27:16 -0400 Organization: New York University Lines: 48 Message-ID: <361D3C44.168D1E8F@mcpd44.med.nyu.edu> References: <6v26mc$2hm$1@scotsman.ed.ac.uk> <6vfrss$qc6@sun0.urz.uni-heidelberg.de> NNTP-Posting-Host: mcpd94.med.nyu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.nyu.edu 907885633 16782 (None) 128.122.232.121 X-Complaints-To: usenet@news.nyu.edu X-Mailer: Mozilla 4.5b2 [en] (Win95; I) X-Accept-Language: en Xref: biosci bionet.general:31105 bionet.molbio.methds-reagnts:71285 bionet.software:21967 One of the few reasons why I have been keeping mt Win95 computer is to continue using Reference Manager. If there is a Linux alternative, I would gladly drop Windoze for good. Count me in. William January Weiner wrote: > > [ Chris Boyd ] > > Unfortunately fellow biologists rarely have the inclination to learn > > TeX/LaTeX/BibTeX (because they usually prefer not to tackle things that > > have any level of abstraction) and are consequently easy prey for > > Microsoft. > > Control question: when you're doing your scientific work, do you > prefer not to tackle things that have any level of abstraction? As a > scientist and biologist? ROTFL! > As for the use of LaTeX - I admit it is sometimes not a > straightforward tool to use, but I really think there are biologists who do > use it. Like myself. Take a look at > > http://www.rzuser.uni-heidelberg.de/~jweiner1/genes.gif > > or > > http://www.rzuser.uni-heidelberg.de/~jweiner1/Map/ > > ...to see, what can be done with LaTeX. > > As for the bibliography, I think that BibTeX is a very good system, > with all possible export/import capabilities, and as for LaTeX - well, > having (K)lyx installed on your machine let's you use it without fumbling > with the LaTeX code (and *if* you want to learn the code, you can do it > easier by using lyx). Dual boot is a waste of space for me :-) > > Regards, > January > > Bibliography :-) > > 1. http://www.kde.org > 2. http://la1ad.uio.no/lyx/ > 3. http://www-pu.informatik.uni-tuebingen.de/users/ettrich/ > > -- > ----)-\//-///-----------------------------------January-Weiner-3------- > Quis porro Asia aut Africa aut Italia relicta Germaniam peteret, informem > terris, asperam caelo, tristem cultu aspectuque, nisi si patria sit? From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in5.uu.net!newsfeed.xcom.net!newshub.northeast.verio.net!newspeer.monmouth.com!newsin.agis.net!agis!newsfeeder.triton.net!news1.triton.net!not-for-mail From: 706@nlr476.com Newsgroups: bionet.software Subject: NLREG - Nonlinear & linear statistical regression program - 37 1006170325 KGL Date: Tue, 6 Oct 98 17:03:28 Organization: Nonlinear Regression Software Lines: 55 Message-ID: <6ve3vg$g2c$1@news1.triton.net> NNTP-Posting-Host: ng.sandh.com Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit x-no-archive: yes ** Announcing NLREG -- Nonlinear Statistical Regression Program ** http://www.sandh.com/sherrod/nlreg.html NLREG is a powerful statistical analysis program for Windows 95 and NT that performs linear and nonlinear regression analysis and curve fitting. NLREG determines the values of parameters for an equation, whose form you specify, that cause the equation to best fit a set of data values. NLREG can handle linear, polynomial, exponential, logistic, periodic, and general nonlinear functions. NLREG features a full programming language with a syntax similar to C for specifying the function that is to be fitted to the data. This allows you to compute intermediate work variables, use conditionals, and even iterate in loops. With NLREG it is easy to construct piecewise functions that change form over different domains. NLREG performs true nonlinear regression, it does not transform the function into a linear form. As a result, it can handle functions that are impossible to linearize such as: Y = Amplitude*SIN(Freq*X+Phase) + A*EXP(X); Another advantage of handing the function in true nonlinear form is that the minimization of the sum of squared residual values (i.e., "least squares") is based on the true nonlinear value rather than some linearized transformation. In addition to computing the optimal values of the parameters, NLREG can generate plots of the data points and the fitted equation. In addition, it can plot the distribution of residual values. In addition to performing classic nonlinear regression, NLREG can be used to find the root or minimum value of a general nonlinear function. It can also be used in a special form where the independent variable is omitted; an interesting application of this is "circular regression" where a circle is fitted to a set of data points. NLREG is in use at hundreds of universities, laboratories, and government agencies around the world (including the U.S. Navy, Harvard, and Duke). NLREG has been validated using the NIST statistical reference datasets; the results are available on the NLREG web page. The price of NLREG is only $65 ($70 if outside the USA), which is far below the cost of comparable commercial regression programs. And you can download a shareware demonstration version of NLREG to try out before you decide to purchase it. To learn more about NLREG and download your free shareware version, visit the web site: http://www.sandh.com/sherrod/nlreg.html -- 37: bionet.software 1006170325 -- From owner-software@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!194.162.162.196!newsfeed.nacamar.de!news-feed.inet.tele.dk!bofh.vszbr.cz!masternews.telia.net!newspost.telia.com!d2o27.telia.com!t6o27p55.telia.com From: "Mathias Larsson" Newsgroups: bionet.software Subject: freeware Date: Thu, 8 Oct 1998 23:11:08 +0200 Organization: Telia Internet Services Lines: 5 Message-ID: <361d2adb.0@d2o27.telia.com> NNTP-Posting-Host: d2o27.telia.com X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-NNTP-Posting-Host: t6o27p55.telia.com X-Complaints-To: abuse@internet.telia.com Want Freeware? Then Visit Pucko International. http://www.fortunecity.com/marina/dolphin/208 From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!newsfeed.berkeley.edu!btnet-peer!btnet!newscore.univie.ac.at!news.iif.hu!botond.enzim.hu!tusi From: "Gabor E. Tusnady" Newsgroups: bionet.software Subject: Re: Transmembrane prediction Date: Fri, 9 Oct 1998 14:06:08 +0200 Organization: IIF Lines: 39 Message-ID: References: <361B6195.8C89CC5B@icrf.icnet.uk> NNTP-Posting-Host: botond.enzim.hu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To: Arne Mueller In-Reply-To: <361B6195.8C89CC5B@icrf.icnet.uk> Hi, The most recent and the most advanced (:-)) can be found at our Web site: http://www.enzim.hu/hmmtop. Best regards, Gabor E. Tusnady www.enzim.hu/~ _/_/_/_/_/_/ _/ _/_/_/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/_/_/ _/_/_/ _/ @enzim.hu On Wed, 7 Oct 1998, Arne Mueller wrote: >Hi all, > >I'm looking for methods/programms to predict transmembrane regions in >proteins (only to know that there is souch a region nothing more ;-) ). >I got "TMAP" (from 1994) and I wonder if there are more recent methods >out there (I'm new in this field). > > Thanks very much for help, > > Arne > >-- >Arne Mueller >Biomolecular Modelling Laboratory >Imperial Cancer Research Fund >44 Lincoln's Inn Fields >London WC2A 3PX, U.K. >phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 >email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ > > From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!nntp3.cerf.net!nntp2.cerf.net!news.idt.net!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: rpescev@webexpert.net Newsgroups: bionet.software Subject: Bioanalytical Instruments Date: Fri, 09 Oct 1998 01:10:45 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 40 Message-ID: <6vjnql$g40$1@nnrp1.dejanews.com> NNTP-Posting-Host: 38.26.120.9 X-Article-Creation-Date: Fri Oct 09 01:10:45 1998 GMT X-Http-User-Agent: Mozilla/3.0Gold (Win95; U) X-Http-Proxy: 1.0 x4.dejanews.com:80 (Squid/1.1.22) for client 38.26.120.9 Dear Sir or Madam: I would like to introduce myself. My name is Ramon N. Pescevich and I work for Bioanalytical Systems Inc. as a field service engineer. We sell instruments to leading medical schools, evironmental organizations, industry and the military. We are scientists helping scientists. Please visit our website at the following URL: http://www.bioanalytical.com. Analytical services are provided from our Analytics Division. I would like to thank you for your time. Hoping to hear from you. Ramon N. Pescevich Field Service Engineer Bioanalytical Systems, Inc. rp@bioanalytical.con -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!HOTMAIL.COM!belzen From: belzen@HOTMAIL.COM ("Nico van Belzen") Newsgroups: bionet.software Subject: sought: software to predict binding of peptides to HLA-I groove Date: 9 Oct 1998 06:46:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <19981009134210.16259.qmail@hotmail.com> NNTP-Posting-Host: net.bio.net Dear Netters, I'm looking for software that determines whether peptides from a given primary amino acid sequence are likely candidates for binding to the peptide-binding groove of HLA class I (or class II) molecules. Is such software available online, or FTP-able on the Net? Email response to belzen@hotmail.com is appreciated. Best regards, Nico van Belzen ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: gary_patton@cmagroup.com Newsgroups: co.jobs,bionet.software,comp.jobs.offered,prg.jobs,us.jobs.offered Subject: Senior Software Engineer - Ft. Collins CO Date: 9 Oct 1998 16:06:19 GMT Organization: Career Marketing Associates Lines: 72 Message-ID: <6vlc9r$5j2$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.55 X-Trace: news1.rmi.net 907949179 5730 206.247.5.55 (9 Oct 1998 16:06:19 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 9 Oct 1998 16:06:19 GMT I am a recruiter in Colorado specializing in Windows developers. Client is looking for a Chief Architect type. Really understands Microsoft technology and how it all fits together. Very familiar with C++, VB, WINTEL. Going to be working in Java, Microst information server, MTS, ASP. Product integrates call center desk tops so that different software can seamlessly work together on the desktop. Integrating legacy systems etc. Equity and very solid salary. Would prefer someone already in Colorado. Client is actively seeking an experienced software engineer to develop the next generation of our flagship product, . This person will be a member of a small team of architects who use their broad technology perspective and knowledge of emerging trends to craft new directions and new products. She or he will be responsible for the following tasks: Be a leading member of the architectural group to implement, enhance, and maintain product features using Microsoft VC++, Visual Basic and Visual Interdev in Windows 95, 98 and NT environments. Work with Marketing to identify technology requirements and generate product feature specifications. Design product features, generate high-level and detailed design documents, and conduct design reviews. Work with testing groups to ensure total product quality. Requirements 2+ years strong experience in Visual C++, preferably work with VC++ 6.0 Experience withÊ ActiveX and COM development in projects Component design and construction Experience with Visual Basic 5.0+ 2+ years experience in client-server application development Experience with SQL and Oracle is a plus Internet development experience is a plus Personal Skills Self directed, full of ideas Good communication and interpersonal skills, especially in small group discussions Please refer to JO# 6346GVP in your response. gary_patton@cmagroup.com Gary Patton Career Marketing Associates Software Engineering/ Windows Specialist 800-638-8903 gvp@cmagroup.com http://www.cmagroup.com/windows.html From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!166.93.8.12!natasha.rmii.com!news1.rmi.net!not-for-mail From: gary_patton@cmagroup.com Newsgroups: co.jobs,bionet.software,comp.jobs.offered,prg.jobs,us.jobs.offered Subject: Senior Software Engineer - Ft. Collins CO Date: 9 Oct 1998 16:05:27 GMT Organization: Career Marketing Associates Lines: 50 Message-ID: <6vlc87$5i2$1@news1.rmi.net> NNTP-Posting-Host: 206.247.5.55 X-Trace: news1.rmi.net 907949127 5698 206.247.5.55 (9 Oct 1998 16:05:27 GMT) X-Complaints-To: abuse@rmi.net NNTP-Posting-Date: 9 Oct 1998 16:05:27 GMT I am a recruiter in Colorado specializing in Windows developers. Client is looking for a Chief Architect type. Really understands Microsoft technology and how it all fits together. Very familiar with C++, VB, WINTEL. Going to be working in Java, Microst information server, MTS, ASP. Product integrates call center desk tops so that different software can seamlessly work together on the desktop. Integrating legacy systems etc. Equity and very solid salary. Would prefer someone already in Colorado. Client is actively seeking an experienced software engineer to develop the next generation of our flagship product, . This person will be a member of a small team of architects who use their broad technology perspective and knowledge of emerging trends to craft new directions and new products. She or he will be responsible for the following tasks: Be a leading member of the architectural group to implement, enhance, and maintain product features using Microsoft VC++, Visual Basic and Visual Interdev in Windows 95, 98 and NT environments. Work with Marketing to identify technology requirements and generate product feature specifications. Design product features, generate high-level and detailed design documents, and conduct design reviews. Work with testing groups to ensure total product quality. Requirements 2+ years strong experience in Visual C++, preferably work with VC++ 6.0 Experience withÊ ActiveX and COM development in projects Component design and construction Experience with Visual Basic 5.0+ 2+ years experience in client-server application development Experience with SQL and Oracle is a plus Internet development experience is a plus Personal Skills Self directed, full of ideas Good communication and interpersonal skills, especially in small group discussions Please refer to JO# 6346GVP in your response. gary_patton@cmagroup.com Gary Patton Career Marketing Associates Software Engineering/ Windows Specialist 800-638-8903 gvp@cmagroup.com http://www.cmagroup.com/windows.html From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!194.186.254.21!newsfeed.gamma.ru!Gamma.RU!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server6.netnews.ja.net!newsfeed.ed.ac.uk!not-for-mail From: Spawny <"I.Downie"@au,sac.ac.uk> Newsgroups: bionet.agroforestry,bionet.biology.tropical,bionet.general,bionet.plants,bionet.software,sci.agriculture,sci.bio.ecology,sci.comp-aided Subject: Re: plant germination models Date: Fri, 09 Oct 1998 16:50:10 +0100 Organization: SAC Auchincruive Lines: 28 Message-ID: <6vlbas$6hr$1@scotsman.ed.ac.uk> References: <01bdf357$27c3f560$d27233c1@pcdeboin2.cirad.fr> NNTP-Posting-Host: sac2419.au.sac.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: scotsman.ed.ac.uk 907948188 6715 194.83.148.119 (9 Oct 1998 15:49:48 GMT) X-Complaints-To: usenet@scotsman.ed.ac.uk NNTP-Posting-Date: 9 Oct 1998 15:49:48 GMT X-Mailer: Mozilla 3.04Gold (Win16; I) Xref: biosci bionet.agroforestry:12721 bionet.biology.tropical:3120 bionet.general:31127 bionet.plants:20028 bionet.software:21975 Marie-Claude, you might try contacting some staff at Scottish Agricultural College, Edinburgh, namely Doug Lewis (D.Lewis@ed.saca.ac.uk). There are into modelling in a big way, and while they might not be able to help you specifically, they might point you in the right direction. Best of luck Spawny Marie-Claude DEBOIN wrote: > > Hello, > Does anyone know if models predicting crops and weeds emergence exist? We'd > like to get some information about models predicting seed germination > taking account soil water content, soil texture and structure variations, > and temperature. > Thank you for giving me more information about this... > > Marie-Claude DEBOIN > Centre de cooperation internationale en recherche agronomique pour le > developpement (CIRAD) > Delegation a l'information scienyifique et technique (DIST) > BP5035 > 34032 Montpellier cedex 1 > FRANCE > e-mail : marie-claude.deboin@cirad.fr > web : http://www.cirad.fr From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!server6.netnews.ja.net!newsfeed.ed.ac.uk!not-for-mail From: Spawny <"I.Downie"@au,sac.ac.uk> Newsgroups: bionet.software Subject: Genstat question Date: Fri, 09 Oct 1998 16:35:25 +0100 Organization: SAC Auchincruive Lines: 5 Message-ID: <6vlaf8$68a$1@scotsman.ed.ac.uk> NNTP-Posting-Host: sac2419.au.sac.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: scotsman.ed.ac.uk 907947304 6410 194.83.148.119 (9 Oct 1998 15:35:04 GMT) X-Complaints-To: usenet@scotsman.ed.ac.uk NNTP-Posting-Date: 9 Oct 1998 15:35:04 GMT X-Mailer: Mozilla 3.04Gold (Win16; I) Anyone out there using Genstat? I want to do GLIM, but would rather use Genstat, and was wondering if anyone has an existing input-command file for doing all of the stuff that GLIM does but without the hassle? Spawny From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!205.252.116.205!howland.erols.net!math.ohio-state.edu!jussieu.fr!univ-lyon1.fr!cnusc.fr!cirad.cirad.fr!usenet From: "Marie-Claude DEBOIN" Newsgroups: bionet.agroforestry,bionet.biology.tropical,bionet.general,bionet.plants,bionet.software,sci.agriculture,sci.bio.ecology,sci.comp-aided Subject: plant germination models Date: 9 Oct 1998 13:42:44 GMT Organization: CIRAD, DIST Lines: 16 Message-ID: <01bdf357$27c3f560$d27233c1@pcdeboin2.cirad.fr> NNTP-Posting-Host: pcdeboin.cirad.fr X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.agroforestry:12720 bionet.biology.tropical:3119 bionet.general:31124 bionet.plants:20023 bionet.software:21973 Hello, Does anyone know if models predicting crops and weeds emergence exist? We'd like to get some information about models predicting seed germination taking account soil water content, soil texture and structure variations, and temperature. Thank you for giving me more information about this... Marie-Claude DEBOIN Centre de cooperation internationale en recherche agronomique pour le developpement (CIRAD) Delegation a l'information scienyifique et technique (DIST) BP5035 34032 Montpellier cedex 1 FRANCE e-mail : marie-claude.deboin@cirad.fr web : http://www.cirad.fr From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!newsfeed1.uni2.dk!news.net.uni-c.dk!not-for-mail From: Ramneek Gupta Newsgroups: bionet.software Subject: Re: Transmembrane prediction Date: Fri, 09 Oct 1998 19:05:34 +0200 Organization: Technical University of Denmark Lines: 14 Message-ID: <361E425E.820767D6@cbs.dtu.dk> References: <361B6195.8C89CC5B@icrf.icnet.uk> NNTP-Posting-Host: 130.225.73.13 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.net.uni-c.dk 907952300 13116 (None) 130.225.73.13 X-Complaints-To: usenet@news.net.uni-c.dk X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP25) X-Accept-Language: en To: Arne Mueller You might also want to look at http://www.cbs.dtu.dk/services/TMHMM-1.0/ > I'm looking for methods/programms to predict transmembrane regions in > proteins (only to know that there is souch a region nothing more ;-) ). -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Ramneek Gupta Email: ramneek@cbs.dtu.dk | | Centre for Biol Seq Anal, Bldg-208 | | Institute of Biotechnology Phone: +45-4525-2472 (o) | | The Technical Univ of Denmark Mobile: +45-2173-9942 | | Lyngby, DK-2800, Denmark. Fax: +45-4593-1585 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-software@net.bio.net Thu Oct 08 23:00:00 1998 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!newsfeed.direct.ca!europa.clark.net!192.174.65.44!newscore.univie.ac.at!news.iif.hu!botond.enzim.hu!tusi From: "Gabor E. Tusnady" Newsgroups: bionet.info-theory,bionet.molec-model,bionet.software Subject: New transmembrane topoly prediction server Date: Fri, 9 Oct 1998 13:58:32 +0200 Organization: IIF Lines: 30 Message-ID: NNTP-Posting-Host: botond.enzim.hu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Xref: biosci bionet.info-theory:6592 bionet.molec-model:2272 bionet.software:21970 Dear Colleague, I'm pleased to announce that a new prediction server for transmembrane helices and topology prediction is available at http://www.enzim.hu/hmmtop The program description can be found at the Web site above, as well. The program is the adaptation of our new prediction method described in G.E.Tusnady and I. Simon (1998) Principles Governing Amino Acid Composition of Integral Membrane Proteins: Application to Topology Prediction J. Mol. Biol. 283, (2), 489-506. If you have any questions or problem, don't hesitate to e-mail me (tusi@enzim.hu). Best regards Gabor E. Tusnady www.enzim.hu/~ _/_/_/_/_/_/ _/ _/_/_/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/_/_/ _/_/_/ _/ @enzim.hu From owner-software@net.bio.net Fri Oct 09 23:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.cwix.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.atl.bellsouth.net!newsfeed.mco.bellsouth.net!news.cc.ucf.edu!not-for-mail From: clb05584 Newsgroups: bionet.software Subject: SOFTWARE GIVEAWAY CONTEST Date: Fri, 09 Oct 1998 17:32:35 -0400 Organization: University of Central Florida Lines: 21 Message-ID: <361E80F3.85FCBF6E@pegasus.cc.ucf.edu> NNTP-Posting-Host: cc2-113-cf090064.ir.ucf.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; U) Enter a Software Giveaway contest once a month at Clayon's Shareware http://clayon.interspeed.net/contest.htm bye for now =========================================================== Visit Clayon's Shareware http://clayon.interspeed.net Offering the absolutely positively best shareware, freeware, and demoware for the Windows 95/98/NT Platforms. No junkware lives here. You can even enter a monthly software giveaway contest, so you can have the opportunity to get your hands on one of the awesome programs that is feature each month. There is also a section for webmasters to submit their site to a whole lot of search engines and directories for FREE, from one form. From owner-software@net.bio.net Fri Oct 09 23:00:00 1998 Path: biosci!INFOSEL.NET.MX!laborato From: laborato@INFOSEL.NET.MX ("Eduardo Perez Campos") Newsgroups: bionet.software Subject: Vertex Date: 10 Oct 1998 09:00:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <01bdf46e$67299440$898b24c8@flyercpm> Reply-To: "Eduardo Perez Campos" NNTP-Posting-Host: net.bio.net I am looking for Vertex. If you know of any supplier or web address, I would appreciate your help. Eduardo Email: laborato@antequera.antequera.com laborato@infosel.net.mx From owner-software@net.bio.net Fri Oct 09 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!netnews.com!newspeer.monmouth.com!newsfeed.atl.bellsouth.net!newsfeed.mco.bellsouth.net!news.cc.ucf.edu!not-for-mail From: clb05584 Newsgroups: bionet.software Subject: Really cool site offering Win 95/98/NT Shareware, Freeware and Demos Date: Fri, 09 Oct 1998 16:35:10 -0400 Organization: University of Central Florida Lines: 19 Message-ID: <361E737E.9D9B9350@pegasus.cc.ucf.edu> NNTP-Posting-Host: cc2-113-cf090064.ir.ucf.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; U) Hi, site name: Clayon's Shareware url: http://clayon.interspeed.net description: Offering the absolutely positively best shareware, freeware, and demoware for the Windows 95/98/NT Platforms. No junkware lives here. You can even enter a monthly software giveaway contest, so you can have the opportunity to get your hands on one of the awesome programs that is feature each month. There is also a section for webmasters to submit their site to a whole lot of search engines and directories for FREE, from one form. bye for now From owner-software@net.bio.net Fri Oct 09 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!oleane!pasteur.fr!jussieu.fr!univ-lyon1.fr!univ-aix.fr!not-for-mail From: bellon@abil.univ-mrs.fr Newsgroups: bionet.software Subject: Re: sought: software to predict binding of peptides to HLA-I groove Date: Sat, 10 Oct 1998 21:08:00 +0100 Organization: Universite Aix-Marseille I Lines: 8 Message-ID: <361FBE9F.7D6@abil.univ-mrs.fr> References: <19981009134210.16259.qmail@hotmail.com> NNTP-Posting-Host: neomenie.univ-mrs.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.univ-aix.fr 908045864 17767 193.51.105.165 (10 Oct 1998 18:57:44 GMT) X-Complaints-To: usenet@news.univ-aix.fr NNTP-Posting-Date: 10 Oct 1998 18:57:44 GMT To: Nico van Belzen X-Mailer: Mozilla 3.0Gold (Macintosh; I; PPC) Nico van Belzen wrote : >I'm looking for software that determines whether peptides from a given >primary amino acid sequence are likely candidates for binding to the >peptide-binding groove of HLA class I (or class II) molecules. Try : http://bimas.dcrt.nih.gov:80/molbio/hla_bind/ Bernard Bellon Universite Aix-Marseille I From owner-software@net.bio.net Fri Oct 09 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!newspump.monmouth.com!newspeer.monmouth.com!newsfeed.atl.bellsouth.net!newsfeed.mco.bellsouth.net!news.cc.ucf.edu!not-for-mail From: clb05584 Newsgroups: bionet.software Subject: Software Giveaway contest Date: Fri, 09 Oct 1998 17:25:41 -0400 Organization: University of Central Florida Lines: 21 Message-ID: <361E7F55.C2F0F91A@pegasus.cc.ucf.edu> NNTP-Posting-Host: cc2-113-cf090064.ir.ucf.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; U) Enter a Software Giveaway contest once a month at Clayon's Shareware http://clayon.interspeed.net/contest.htm bye for now =========================================================== Visit Clayon's Shareware http://clayon.interspeed.net Offering the absolutely positively best shareware, freeware, and demoware for the Windows 95/98/NT Platforms. No junkware lives here. You can even enter a monthly software giveaway contest, so you can have the opportunity to get your hands on one of the awesome programs that is feature each month. There is also a section for webmasters to submit their site to a whole lot of search engines and directories for FREE, from one form. From owner-software@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!MICRO.FDSCI.WAU.NL!ralf.hartemink From: ralf.hartemink@MICRO.FDSCI.WAU.NL (Ralf) Newsgroups: bionet.software Subject: (none) Date: 12 Oct 1998 11:39:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 13 Sender: daemon@net.bio.net Distribution: world Message-ID: <3614e9f2.13110195@news.wau.nl> Reply-To: ralf.hartemink@MICRO.FDSCI.WAU.NL NNTP-Posting-Host: net.bio.net Hi, I am looking for an electronic version of a evolutionary tree of the mammals. Does somebody know where I can find it (internet) or maybe does somebody have such a tree available ? Ralf Hartemink Dept. Food Science Wageningen Agricultural University The Netherlands ralf.hartemink@micro.fdsci.wau.nl From owner-software@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!xmission!hammer.uoregon.edu!leto.ou.edu!news.ou.edu!not-for-mail From: frank@omrf.ouhsc.edu (Bart Frank) Newsgroups: bionet.software Subject: Eukaryotic promoter database? Date: 12 Oct 1998 08:00:32 GMT Organization: The University of Oklahoma (USA) Lines: 6 Message-ID: <6vscv0$g3r$1@artemis.backbone.ou.edu> NNTP-Posting-Host: 157.142.201.234 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (x86 32bit) Is there a eukaryotic promoter database (preferably mammalian, or human) that one can search for the occurrence of particular sequences? I would like to skip the sequences that match in coding regions. Thanks Bart From owner-software@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!newsfeed.berkeley.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.corridex.com!news-peer-west.sprintlink.net!news.sprintlink.net!news.sgi.com!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail From: greg@franklin.burnham-inst.org (Dr. Greg Quinn) Newsgroups: bionet.software Subject: Time for Moderation in this group? Date: 12 Oct 1998 16:50:39 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 28 Message-ID: <6vtc0v$hfl$1@franklin.ljcrf.edu> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] I'm assuming that posts with titles like "MAKE MONEY FAST!!!!" and "OWN YOUR OWN PORNO SITE!!!!!" aren't from scientific groups (but I wouldn't bank on that, given some of the researchers I know!). Wouldn't it be a good idea to set up some kind of automoderation for this (and other bionet) newsgroup, which could simply consist of a spam filter? Just a suggestion. Cheers Greg -- ***************************************** Computational Biology Group The Burnham Institute (formerly La Jolla Cancer Research Inst.) 12901 North Torrey Pines road La Jolla CA92037 Phone:(619) 646 3103 Email: greg@franklin.ljcrf.edu http://franklin.ljcrf.edu/greg http://www.greg.com/ ***************************************** From owner-software@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!gf.vu.lt!Rimantas.Plaipa From: Rimantas.Plaipa@gf.vu.lt (Rimantas Plaipa) Newsgroups: bionet.software Subject: Help, Rasmol installation on Linux Date: 12 Oct 1998 01:33:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.5.32.19981012102924.0079c980@voruta.vu.lt> NNTP-Posting-Host: net.bio.net In article , sjlee@ocf.Berkeley.EDU says... > >Hi, > >I am having trouble installing Rasmol 2.6b2 on Redhad Linux 5.1 running >on a Dec Alpha. >(ftp://marlin.bio.umass.edu/pub/shareware/rasmol/distrib/RasMol26b2.tar.gz) > > >Has anybody had similar problems? > ..... >rasmol.c:329: invalid use of undefined type `struct fd_set' ........ Yes I had similar problem compiling RasMol for Caldera Open Linux with gcc-2.7.... I solved it by changing the following lines in rasmol.c : static struct fd_set OrigWaitSet; static struct fd_set WaitSet; to static fd_set OrigWaitSet; static fd_set WaitSet; i.e by removing 'struct'. It looks that gcc compiler needs (and accepts) this 'struct' keyword only if the structure is undefined. In the file 'rasmol.c' fd_set is defined by certain include file before these lines. Rimantas Plaipa Vilnius University, dept. of Biochemistry and Biophysics, Lithuania Rimantas Plaipa, Department of Biochemistry and Biophysics, Vilnius University, Ciurlionio 21/27, Vilnius 2009, Lithuania. E-mail: rp010gf@voruta.vu.lt Phone: (370-2)-650381 Fax: (370-2)-633844 From owner-software@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!agate!famine.OCF.Berkeley.EDU!sjlee From: Sung-Joo Lee Newsgroups: bionet.software Subject: Help, Rasmol installation on Linux Date: Sun, 11 Oct 1998 17:33:40 -0700 Organization: University of California, Berkeley Lines: 56 Message-ID: NNTP-Posting-Host: famine.ocf.berkeley.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am having trouble installing Rasmol 2.6b2 on Redhad Linux 5.1 running on a Dec Alpha. (ftp://marlin.bio.umass.edu/pub/shareware/rasmol/distrib/RasMol26b2.tar.gz) Has anybody had similar problems? This is what i get after doing everything I'm supposed to do. ################ 141 % make gcc -O2 -I/usr/X11R6/include -I/include -Dlinux -D__alpha__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/home/sjlee/bin/RasMol2/\" -DEIGHTBIT -c rasmol.c -o rasmol.o rasmol.c: In function `OpenConnection': rasmol.c:329: invalid use of undefined type `struct fd_set' rasmol.c: In function `CloseConnection': rasmol.c:345: invalid use of undefined type `struct fd_set' rasmol.c: In function `InitTerminal': rasmol.c:394: warning: type mismatch in implicit declaration for built-in function `memset' rasmol.c:395: invalid use of undefined type `struct fd_set' rasmol.c:401: invalid use of undefined type `struct fd_set' rasmol.c:411: invalid use of undefined type `struct fd_set' rasmol.c: In function `FetchCharacter': rasmol.c:497: `WaitSet' has an incomplete type rasmol.c:503: warning: passing arg 2 of `select' from incompatible pointer type rasmol.c:503: warning: passing arg 3 of `select' from incompatible pointer type rasmol.c:503: warning: passing arg 4 of `select' from incompatible pointer type rasmol.c:508: invalid use of undefined type `struct fd_set' rasmol.c:512: invalid use of undefined type `struct fd_set' rasmol.c:516: invalid use of undefined type `struct fd_set' rasmol.c: At top level: rasmol.c:112: storage size of `OrigWaitSet' isn't known rasmol.c:113: storage size of `WaitSet' isn't known make: *** [rasmol.o] Error 1 ############ Thanks for reading this far, SJ -- Sung-Joo Lee Chakraborty Group, College of Chemistry Graduate Group in Biophysics University of California, Berkeley From owner-software@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!CHOLLIAN.NET!MICROBE From: MICROBE@CHOLLIAN.NET (=?EUC-KR?B?vue1zryu?=) Newsgroups: bionet.software Subject: Re: multiple alignment for win95 Date: 12 Oct 1998 06:56:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <360677ED.4A8C4272@mail.nih.gov> NNTP-Posting-Host: net.bio.net Find MAWCAW... Multiple alignment tool running on Windows. made by staffs in NIH, probably... On Mon, 21 Sep 1998, Ying Hu wrote: > Hi: > > Where do I can find free software of DNA multiple alignment for win95? > > Thanks > > Ying Hu > > From owner-software@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!awabi.library.ucla.edu!134.139.1.31!csulb.edu!drivel.ics.uci.edu!news.service.uci.edu!mangalam From: mangalam@UNJUNK.uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: (none) Date: Mon, 12 Oct 1998 16:33:01 -0800 Organization: Dev+Cell Biology, UC Irvine Lines: 15 Distribution: world Message-ID: References: <3614e9f2.13110195@news.wau.nl> NNTP-Posting-Host: skink.bio.uci.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 In article <3614e9f2.13110195@news.wau.nl>, ralf.hartemink@MICRO.FDSCI.WAU.NL wrote: Try http://phylogeny.arizona.edu/tree/phylogeny.html Cheers Harry > I am looking for an electronic version of a evolutionary tree of the > mammals. > Does somebody know where I can find it (internet) or maybe does > somebody have such a tree available ? -- Harry J Mangalam, MolBio+Biochem / Dev+Cell Bio, Rm 4201, BioSciII UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 - delete the 'UNJUNK' to generate a valid email - From owner-software@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!207.103.147.20!news.voicenet.com!news1.best.com!news3.best.com!nntp1.ba.best.com!not-for-mail From: gmcenroe@crl.com (Glenn McEnroe) Newsgroups: bionet.software Subject: Re: Vertex Date: Mon, 12 Oct 1998 22:30:12 GMT Message-ID: <362282dc.890195934@nntp1.ba.best.com> References: <01bdf46e$67299440$898b24c8@flyercpm> X-Newsreader: Forte Free Agent 1.11/32.235 Lines: 16 NNTP-Posting-Host: 199.89.163.219 X-Trace: 908231468 25905 (none) 199.89.163.219 Try http://www.vertex.com On 10 Oct 1998 09:00:27 -0700, laborato@INFOSEL.NET.MX ("Eduardo Perez Campos") wrote: >I am looking for Vertex. If you know of any supplier or web address, I >would appreciate your help. > >Eduardo > >Email: laborato@antequera.antequera.com > laborato@infosel.net.mx > > > From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!logbridge.uoregon.edu!news.u.washington.edu!learn From: learn@u.washington.edu (Jerry Learn) Newsgroups: bionet.software Subject: MACAW (was Re: multiple alignment for win95) Date: Mon, 12 Oct 1998 20:13:32 -0700 Organization: University of Washington Lines: 22 Distribution: world Message-ID: References: <360677ED.4A8C4272@mail.nih.gov> NNTP-Posting-Host: tench.microbiol.washington.edu X-Trace: nntp4.u.washington.edu 908248417 44088 (None) 140.142.17.38 X-Complaints-To: help@cac.washington.edu X-Newsreader: MT-NewsWatcher 2.4.4 X-face: 4sx$YUe#v'|&_+SwB7*{hy1Rb,03L5DM_U)nbQ{gz$$G2WbyOuofM, MICROBE@CHOLLIAN.NET (=?EUC-KR?B?vue1zryu?=) wrote: > Find MAWCAW... > > Multiple alignment tool running on Windows. > made by staffs in NIH, probably... You might have better luck looking for MACAW (from NCBI at the Natl Library of Medicine): > > On Mon, 21 Sep 1998, Ying Hu wrote: > > > Hi: > > > > Where do I can find free software of DNA multiple alignment for win95? > > -- Jerry Learn U. of Washington Seattle, WA 98195-7740 USA From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!dispose.news.demon.net!demon!news.demon.co.uk!demon!cammol1.demon.co.uk!see_sig From: see_sig@cmtech.co.delete.uk (Richard P. Grant) Newsgroups: bionet.software Subject: Re: Time for Moderation in this group? Date: Tue, 13 Oct 1998 08:51:57 +0100 Organization: Cambridge Molecular Message-ID: References: <6vtc0v$hfl$1@franklin.ljcrf.edu> Reply-To: rgrant@netscape.net NNTP-Posting-Host: cammol1.demon.co.uk X-NNTP-Posting-Host: cammol1.demon.co.uk:212.228.79.177 X-Trace: news.demon.co.uk 908265228 nnrp-03:822 NO-IDENT cammol1.demon.co.uk:212.228.79.177 X-Complaints-To: abuse@demon.net X-Newsreader: MT-NewsWatcher 2.4.4 X-Face: E%wu[EoEhNnjFG!0[ 7cH@VuxC//iy$!n-+bh9Q`+SHW@&}E.&Ly(y'Tvrd5amG/o35>c3zF6QvXX, greg@franklin.burnham-inst.org (Dr. Greg Quinn) wrote: : Wouldn't it be a good idea to set up some kind of automoderation : for this (and other bionet) newsgroup, which could simply : consist of a spam filter? There is a way to moderate groups so that you have a human moderator who passes or deletes the first message from an address, then lets the 'bot know that a particular address is OK (or not), so all posts from that address will be accepted (or deleted, if need be). The other way is to repeat the experience of asr and self-moderate . . . ;-) R -- Richard P. Grant MA DPhil | rgrant at cmtech.co.uk Senior R&D Scientist | work: www.cmtech.co.uk Cambridge Molecular | home: www.avnet.co.uk/adastra -- 'Practising biochemistry without a licence' - E. Chargaff -- From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news.sgi.com!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail From: greg@franklin.burnham-inst.org (Dr. Greg Quinn) Newsgroups: bionet.software Subject: Re: Time for Moderation in this group? Date: 13 Oct 1998 17:17:03 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 18 Message-ID: <7001uf$n2f$1@franklin.ljcrf.edu> References: <6vtc0v$hfl$1@franklin.ljcrf.edu> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Richard P. Grant (see_sig@cmtech.co.delete.uk) wrote: : In article <6vtc0v$hfl$1@franklin.ljcrf.edu>, : greg@franklin.burnham-inst.org (Dr. Greg Quinn) wrote: : : : Wouldn't it be a good idea to set up some kind of automoderation : : for this (and other bionet) newsgroup, which could simply : : consist of a spam filter? : : There is a way to moderate groups so that you have a human moderator who : passes or deletes the first message from an address, then lets the 'bot : know that a particular address is OK (or not), so all posts from that : address will be accepted (or deleted, if need be). : I think all that's needed is a filter which removes messages that contain phrases such as "18 year old nymphos", "naughty" and "make $$$$$$$$$$$ in a day". It's no big deal to sift through the spam but it is fairly easily avoidable. From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!hsr.it!lavorgna.giovanni From: lavorgna.giovanni@hsr.it Newsgroups: bionet.software Subject: Re:Eukaryotic promoter database? Date: 13 Oct 1998 10:17:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: <2.2.32.19981013180855.006ed9c8@mail.hsr.it> NNTP-Posting-Host: net.bio.net From: frank@omrf.ouhsc.edu (Bart Frank) Subject: Eukaryotic promoter database? Date: 12 Oct 1998 08:00:32 GMT >Is there a eukaryotic promoter database (preferably mammalian, or human) that >one can search for the occurrence of particular sequences? I would like to skip >the sequences that match in coding regions. >Thanks >Bart Please give a try to TargetFinder program by me and other colleagues. It is reacheable at htpp://hercules.tigem.it/TargetFinder.html. I append at the end of this message some info about this Web resource. Regards, Giovanni Lavorgna ------------------------------- TargetFinder: a new tool to perform database searches for candidate target genes of transcription factors. Giovanni Lavorgna (1), Alessandro Guffanti (2), Giuseppe Borsani (2) Andrea Ballabio (2) and Edoardo Boncinelli (1). (1) DIBIT, Istituto Scientifico H. S. Raffaele, Via Olgettina 60, 20132 Milano, Italy (2) Telethon Institute of Genetics and Medicine (TIGEM), San Raffaele Biomedical Science Park, Via Olgettina 58, 20132 Milano, Italy TargetFinder is now available at http://hercules.tigem.it/TargetFinder.html TargetFinder is a new tool to facilitate database searches for candidate target genes of transcription factors. The use of this program allows to search a database of annotated sequences for binding sites located in context with other important transcription regulatory signals and regions, like the TATA element, the transcription start site, the promoter and so on, thereby greatly reducing the background usually associated with this kind of searches. ------------------------------------ If you've problems, bug report or any proposal on how to improve TargetFinder program, please contact me at the following address: Giovanni Lavorgna DIBIT-HSR Via Olgettina, 58 20132 Milano Italy Tel. +39-02-26434776 Fax. +39-02-26434767 Email : giovanni.lavorgna@hsr.it From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-backup-west.sprintlink.net!news.sprintlink.net!192.220.250.21!netnews1.nw.verio.net!netnews.nwnet.net!news.u.washington.edu!learn From: learn@u.washington.edu (Jerry Learn) Newsgroups: bionet.software Subject: Re: Time for Moderation in this group? Date: Tue, 13 Oct 1998 09:34:04 -0700 Organization: University of Washington Lines: 21 Message-ID: References: <6vtc0v$hfl$1@franklin.ljcrf.edu> NNTP-Posting-Host: tench.microbiol.washington.edu X-Trace: nntp4.u.washington.edu 908296448 44148 (None) 140.142.17.38 X-Complaints-To: help@cac.washington.edu X-Newsreader: MT-NewsWatcher 2.4.4 X-face: 4sx$YUe#v'|&_+SwB7*{hy1Rb,03L5DM_U)nbQ{gz$$G2WbyOuofM, rgrant@netscape.net wrote: > In article <6vtc0v$hfl$1@franklin.ljcrf.edu>, > greg@franklin.burnham-inst.org (Dr. Greg Quinn) wrote: > > : Wouldn't it be a good idea to set up some kind of automoderation > : for this (and other bionet) newsgroup, which could simply > : consist of a spam filter? > > There is a way to moderate groups so that you have a human moderator who > passes or deletes the first message from an address, then lets the 'bot > know that a particular address is OK (or not), so all posts from that > address will be accepted (or deleted, if need be). > > The other way is to repeat the experience of asr and self-moderate . . . ;-) > could you explain how this self-moderation works? -- Jerry Learn U. of Washington Seattle, WA 98195-7740 USA From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!sunqbc.risq.qc.ca!news.dal.ca!nntp-user From: Arlin Stoltzfus Newsgroups: bionet.software Subject: Post-doctoral positions in computational studies of evolution (CARB, Stoltzfus) Date: Tue, 13 Oct 1998 12:48:00 -0300 Organization: ISINet, Nova Scotia Lines: 43 Message-ID: <36237630.2F44@thidwick.biochem.dal.ca> NNTP-Posting-Host: thidwick.biochem.dal.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; U; SunOS 5.4 sun4m) --------------- Second announcement, 12 Oct 1998 ----------------- POST-DOCTORAL POSITIONS in molecular evolution, bioinformatics, evolutionary genetics Two post-doctoral positions in computational studies of evolution are available at CARB*. Ongoing and planned research relates to: i) the evolutionary history of introns and intron-containing genes in eukaryotes; ii) development of software tools and database systems tailored for molecular evolution research; and iii) theoretical and empirical studies of mutational biases as a cause of directional evolution. For background and further information, please check the pages at http://is.dal.ca/~arlin/CARB and refer any questions to me (arlin@carb.nist.gov). Applicants should have skill in computer programming or mathematical modelling, along with research experience with computational approaches to problems in evolution or molecular biology. Yearly salary will be 28-35K. There is no citizenship requirement. The positions may begin any time in 1999. To apply, send a c.v., a 2-page description of relevant research experience & interests, and contact information for 2 references to an appropriate address below. Electronic applications are acceptable. Review of applications will begin 13 November, and continue until the positions are filled. Arlin Stoltzfus, Ph.D. Research Biologist, NIST Adjunct Asst. Prof., UMBI email: arlin@carb.nist.gov; phone: 902 494-2968; fax: 902 494-1355 mail (current): Biochemistry, Dalhousie University, Halifax, NS B3H 4H7 CANADA mail (pending): CARB, 9600 Gudelsky Drive, Rockville, MD 20850 --------- * The Center for Advanced Research in Biotechnology, or CARB (http://www.carb.nist.gov), is a joint research center of the National Institute of Standards and Technology (NIST) and the University of Maryland Biotechnology Institute (UMBI). CARB is located in Rockville, Maryland, 20 miles northwest of DC. Basic research at CARB is both theoretical and experimental, and focusses on macromolecular structure and function. CARB is an Equal Opportunity/Affirmative Action Employer. Women and minority candidates are encouraged to apply. From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!dispose.news.demon.net!demon!news.demon.co.uk!demon!kovcomp.demon.co.uk!not-for-mail From: Warren Kovach Newsgroups: bionet.software Subject: ANN: MVSP 3 for Windows now released Date: Tue, 13 Oct 1998 11:34:53 +0100 Organization: Kovach Computing Services Message-ID: Reply-To: WarrenK@kovcomp.co.uk NNTP-Posting-Host: kovcomp.demon.co.uk X-NNTP-Posting-Host: kovcomp.demon.co.uk:158.152.48.110 X-Trace: news.demon.co.uk 908274893 nnrp-05:2809 NO-IDENT kovcomp.demon.co.uk:158.152.48.110 X-Complaints-To: abuse@demon.net Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Virtual Access by Ashmount Research Ltd, http://www.ashmount.com Lines: 41 I'm pleased to announce that version 3 of MVSP - A MultiVariate Statistical Package, is now available. MVSP is now a Windows based program (with versions for both Windows 3.1 and Windows 95/98/NT). This new version also adds Canonical Correspondence Analysis, removes all limits on number of variables and cases (other than available Windows memory and disk space), and has greatly enhanced graphics capabilities. MVSP performs several types of eigenanalysis ordinations: principal components (PCA), principal coordinates (PCO), correspondence/detrended correspondence analyses (CA/DCA) and canonical correspondence analysis (CCA). It can also perform cluster analysis, using 20 different distance or similarity measures and seven clustering strategies. Diversity indices may be calculated on ecological data; these include Simpson's, Shannon's, and Brillouin's indices. You can get more information, and an evaluation version of the program, from our web site: http://www.kovcomp.co.uk/ This site also has information about our other programs: SIMSTAT - General purpose statistical package xlSTAT - Statistical add-in for Excel spreadsheets Oriana - Orientation Analysis for Windows Data Desk - Intuitive exploratory data analysis Accent Composer - A Windows keyboard utility Wa-Tor - Population dynamics simulation Best wishes, Warren Kovach -- Dr. Warren L. Kovach Kovach Computing Services 85 Nant-y-Felin, Pentraeth, Anglesey Wales LL75 8UY U.K. Tel.: +44-1248-450414 | Fax: +44-870-054-3180 E-mail: WarrenK@kovcomp.co.uk | WWW: http://www.kovcomp.co.uk/ From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!newsfeed1.uni2.dk!news.net.uni-c.dk!not-for-mail From: Mogens Kjaer Newsgroups: bionet.software Subject: Re: Q: Rasmol in Linux: X Error Date: Tue, 13 Oct 1998 10:33:12 +0200 Organization: Carlsberg Laboratory Lines: 26 Message-ID: <36231048.A2D2B798@crc.dk> References: <6vub95$tk3$1@nnrp1.dejanews.com> NNTP-Posting-Host: 130.226.182.195 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.net.uni-c.dk 908267594 26310 (None) 130.226.182.195 X-Complaints-To: usenet@news.net.uni-c.dk X-Mailer: Mozilla 4.5b2 [en] (X11; I; Linux 2.0.31 i586) X-Accept-Language: en berkeley@writeme.com wrote: .... > 23 % rasmol > RasMol Molecular Renderer > Roger Sayle, August 1995 > Arne Mueller, Mai 1998 > Version 2.6x1 > [8bit version] Is your X server set up to 8 bit? Check this with "xwininfo -root" and note the value after Depth:, this should be 8. If the value is 16,24, or 32 you'll need to make appropriate versions of rasmol to get it to work, or reconfiguring your X server (this might be a bad idea...). Mogens -- Mogens Kjaer, Carlsberg Laboratory, Dept. of Chemistry Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark Phone: +45 33 27 53 25, Fax: +45 33 27 47 08 Email: mk@crc.dk Homepage: http://www.crc.dk From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!newsfeed.berkeley.edu!newsfeed.enteract.com!chicago-news-feed1.bbnplanet.com!news.bbnplanet.com!news.itis.com!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: Time for Moderation in this group? Date: 13 Oct 1998 18:40:31 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 44 Sender: reguser@ebv.oncology.wisc.edu Message-ID: References: <6vtc0v$hfl$1@franklin.ljcrf.edu> <7001uf$n2f$1@franklin.ljcrf.edu> Reply-To: aiyar@aiyar.ml.org NNTP-Posting-Host: ebv.oncology.wisc.edu User-Agent: slrn/0.9.5.3 (UNIX) On 13 Oct 1998 17:17:03 GMT, Dr. Greg Quinn (greg@franklin.burnham-inst.org) wrote: >Richard P. Grant (see_sig@cmtech.co.delete.uk) wrote: >: In article <6vtc0v$hfl$1@franklin.ljcrf.edu>, >: greg@franklin.burnham-inst.org (Dr. Greg Quinn) wrote: >: >: : Wouldn't it be a good idea to set up some kind of automoderation >: : for this (and other bionet) newsgroup, which could simply >: : consist of a spam filter? >: >: There is a way to moderate groups so that you have a human moderator who >: passes or deletes the first message from an address, then lets the 'bot >: know that a particular address is OK (or not), so all posts from that >: address will be accepted (or deleted, if need be). >: > >I think all that's needed is a filter which removes messages that contain >phrases such as "18 year old nymphos", "naughty" and "make $$$$$$$$$$$ in >a day". It's no big deal to sift through the spam but it is fairly easily >avoidable. I'm not sure if that which I describe below is what Greg had in mind, but there are "spambots" that automatically delete articles. How they work is much tied into how the NNTP (Usenet) protocol works. When a spambot detects an article that matches a keyword in a "delete" list, it sends an cancel-article for the message-id of the offending article to a newsgroup called "control". When this cancel-article propagates to other sites (every Usenet site MUST carry the newsgroup "control"), they will expire or delete the article in question from their news-spool. This mechanism is actively used at several sites to control spam posts to many non-bionet newsgroups. I do not know the legality of running a spambot for a bionet newsgroup and am hence reluctant to run one myself, or offer the resources to run one from. I principle, I concur that a bionet-spambot would be wonderful. Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research aiyar@ebv.oncology.wisc.edu From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 From: "John" Newsgroups: bionet.software Subject: Software World Date: 13 Oct 1998 23:04:22 GMT Organization: The Internet Group Ltd Lines: 4 Message-ID: <01bdf6fd$665d6f00$6e6212ce@sun-xia.ihug.co.nz> NNTP-Posting-Host: p46-max6.akl.ihug.co.nz X-Newsreader: Microsoft Internet News 4.70.1155 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!la-news-feed1.bbnplanet.com!news.bbnplanet.com!news.netgate.net.nz!news.xtra.co.nz!news.iprolink.co.nz!ihug.co.nz!not-for-mail Hi, my friends. Please go to: http://members.tripod.com/~best_web/software.html You can find many useful softwares. From owner-software@net.bio.net Mon Oct 12 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!nntp3.cerf.net!nntp2.cerf.net!news.idt.net!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.cwix.com!204.238.120.130!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: berkeley@writeme.com Newsgroups: bionet.software Subject: Q: Rasmol in Linux: X Error Date: Tue, 13 Oct 1998 01:44:05 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 35 Message-ID: <6vub95$tk3$1@nnrp1.dejanews.com> NNTP-Posting-Host: 128.32.198.93 X-Article-Creation-Date: Tue Oct 13 01:44:05 1998 GMT X-Http-User-Agent: Mozilla/3.0Gold (X11; I; HP-UX A.09.03 9000/730) X-Http-Proxy: 1.0 x7.dejanews.com:80 (Squid/1.1.22) for client 128.32.198.93 Hello, I first want to thank Rimantas Plaipa and Arne Mueller for helping me on the installation problem that I had yesterday. I downloaded the modified rasmol by Arne from ftp://nexus.roko.goe.net/pub/rasmol For me, this is exactly what I wanted because I use POVray a lot to make animations of polymers. After installing the program, I get an error message like this. ~~~~~~~~~~~~~~~~ 23 % rasmol RasMol Molecular Renderer Roger Sayle, August 1995 Arne Mueller, Mai 1998 Version 2.6x1 [8bit version] RasMol> X Error of failed request: BadAccess (attempt to access private resource denied) Major opcode of failed request: 129 (MIT-SHM) Minor opcode of failed request: 3 (X_ShmPutImage) Serial number of failed request: 624