From owner-software@net.bio.net Sun Nov 01 22:00:00 1998 Path: biosci!AURORABIO.COM!ReddD From: ReddD@AURORABIO.COM ("Doug Redd") Newsgroups: bionet.software Subject: RE: help!!!! Date: 2 Nov 1998 07:04:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BE062E.4944F1F0@REDDD2> NNTP-Posting-Host: net.bio.net I have one of these cd writers and had similar problems until I installed the firmware update available from HP's web site. I have not had any problems since. The site is http://www.hp.com/isgsupport/cdr/70index.html#Firmware. // Doug Redd -----Original Message----- From: ALEX GARCIA [mailto:acad@accefyn.org.co] Sent: Saturday, October 31, 1998 8:51 PM To: bio-soft@net.bio.net Subject: help!!!! I am using a HP cd writer plus (7200 series) and I am having a lot of troubles!!!!! lots of lots of troubles, I save in a cd using the cd writer, save lets say for example the netscape installator and some pdb files in a new CD, everything seems to be ok until there, I try to read the cd with my cd rom and then troubles start!!! does not allow me to copy the netscape installator in the hd form the usual cd rom device but if I try to do it from the cd writer it works just fine, the problem only presents with some files, the netscape installator for example, or some pdb files, not all of pdb just some of them, what can I do? please mail me ASAP From owner-software@net.bio.net Sun Nov 01 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!logbridge.uoregon.edu!sunqbc.risq.qc.ca!newsfeed.tli.de!newsfeed.wirehub.nl!surfnet.nl!news.tue.nl!usenet From: Hans Blom Newsgroups: bionet.software Subject: REQ: ST-segment analysis software Date: Mon, 02 Nov 1998 16:05:51 +0100 Organization: Eindhoven University of Technology, The Netherlands Lines: 27 Message-ID: <363DCA4F.A26FCF8E@ele.tue.nl> NNTP-Posting-Host: emepc01.eme.ele.tue.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en REQ: ST-segment analysis algorithm Outdated, now that every decent monitor contains one? One of our M.Sc. students works on a multi-signal data mining application to reliably detect sudden heart failure in intensive care patients. We have lots of ECG recordings, but lack the ST-segment depression/ elevation info of these data.So we need an algorithm that extracts it. In fact, we designed such an algorithm ourselves, some 15 years ago, but it must have gotten lost. Who can help us out? Do you know of public domain software for ST-segment analysis? Or do you have something floating around that you are willing to share with us for this project? Standard non- disclosure conditions etc. apply, of course. Other info: most of our ECGs are sampled at 100 or at 200 Hz. Platform: PC. We would prefer a DOS exe, or Pascal or C source code. Any info is appreciated. Hans Blom, Ph.D. associate professor Eindhoven University of Technology (http://www.tue.nl) Dept. of Electrical Engineering Medical Engineering Group j.a.blom@ele.tue.nl From owner-software@net.bio.net Sun Nov 01 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!usc!newshub.csu.net!news.fullerton.edu!rolltmpxa80937kbbw.fullerton.edu!user From: DEernisse@fullerton.edu (Doug Eernisse) Newsgroups: bionet.software Subject: Re: Mac Screen-capture, was Re: Exporting images of Macaw Date: Mon, 02 Nov 1998 00:15:32 -0800 Organization: CSUF Lines: 39 Message-ID: References: <36361F0B.897C9431@domain.com> NNTP-Posting-Host: rolltmpxa80937kbbw.fullerton.edu > Um, I'm not a Mac newbie, having used them for about 7 years, but whereas > I knew about pretzel-shift-3, I'd never seen Caps Lock-pretzel-shift-4, > which lets you snap the portion of the screen you want. > > Thanks for the tip, Jerry! > > > : Until now I have used the Shareware program, FlashIt, which has > : the advantage that only a portion of the screen need be saved. > > See above. > > So when did this come into effect? I'm using 8.0 (UK). > > R > I think it was OS 7.6. Actually, I was having trouble with Flashit and OS 8.1 so have started using the built-in keystroke (ctl-shift-cmd-4) for user-defined screen captures. The Flashit feature that allows setting the "magnification" of screen capture is not possible, though, I don't think. Note that a few programs, like ClustalX, must draw to the screen differently, so that screen capture doesn't seem work in them. Try it and see. You will get an out of memory complaint no matter how small of a portion of the alignment you try to capture. ClustalX does allow a color postscript export, though. I thought there was another way to export a portion of the alignment to clipboard but can't seem to do it presently. Macaw shouldn't be affected by this problem. -- Doug Eernisse Department of Biological Science California State University Fullerton, CA 92834-6850 USA From owner-software@net.bio.net Sun Nov 01 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news-peer.sprintlink.net!news.sprintlink.net!cpk-news-hub1.bbnplanet.com!news.news.gtei.net!portc02.blue.aol.com!pitt.edu!not-for-mail From: Rich Dudley Newsgroups: bionet.software Subject: Re: help!!!! Date: Mon, 02 Nov 1998 08:29:43 -0500 Organization: University of Pittsburgh, Dept. of Cell Biology and Physiology Lines: 32 Message-ID: <363DB3C6.3160A3EE@pitt.edu> References: <363BE865.A0B9ACB5@accefyn.org.co> Reply-To: rdudley+@pitt.edu NNTP-Posting-Host: whill.cbp.pitt.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en ALEX GARCIA wrote: > I am using a HP cd writer plus (7200 series) and I am having a lot of > troubles!!!!! lots of lots of troubles, I save in a cd using the cd > writer, save lets say for example the netscape installator and some pdb > files in a new CD, everything seems to be ok until there, I try to read > the cd with my cd rom and then troubles start!!! does not allow me to > copy the netscape installator in the hd form the usual cd rom device but > if I try to do it from the cd writer it works just fine, the problem > only presents with some files, the netscape installator for example, or > some pdb files, not all of pdb just some of them, what can I do? please > mail me ASAP Alex-- I have an older CD-ROM drive in one computer that just won't read my CD-Rs. However, two computers with newer CD-ROM drives read that CD-Rs with no problem. They are multisession CD-R, recorded for the PC world. I also made an audio CD on the machine, and some audio CD players can't play it at all. I think it may be just a CD-R phenomenon. rich -- --- --- --- -- -- -- --- --- --- Richard J. Dudley (rdudley+@pitt.edu) Research Specialist V Dept. of Cell Biology and Physiology University of Pittsburgh http://www.cbp.pitt.edu ---> search BIONET archives at http://www.bio.net <--- From owner-software@net.bio.net Sun Nov 01 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.inet.tele.dk!not-for-mail From: Bo Bergmann <120010312330@post5.tele.dk> Newsgroups: bionet.software Subject: HPLC-WIZARD beta 1.0 Date: Mon, 02 Nov 1998 01:52:44 +0100 Organization: DTU Lines: 58 Message-ID: <363D025C.1BF9@post5.tele.dk> NNTP-Posting-Host: ip93.boanxr1.ras.tele.dk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news-inn.inet.tele.dk 909967736 101002 (None) 195.249.161.93 (02-11-98 00:48:56 GMT) X-Mailer: Mozilla 2.02E [da]-TDK20 (Win95; I) Finally, the beta version 1.0 of HPLC-WIZARD is ready for evaluation. Get to our home page at http://home5.inet.tele.dk/daller/index.htm to download the beta version. HPLC-WIZARD is a Microsoft® Windows 95/98/NT application designed for fast and easy calculation of amino acid distributions from HPLC - chromatograms. In contrast to the existing method of numerical integration, which suffers from systematical errors due to inaccurate partion of overlapping peaks and improper treatment of the background function, HPLC-WIZARD calculates an amino acid distribution by modelling the HPLC- chromatograms by using different density functions to model the peaks and a background function based on Principal Component Analysis to model the background. In the evaluation of appropiate candidate functions to model the peaks in the HPLC - chromatograms, it was found necessary to develop tools to estimate how good a candidate function was able to model the chromatograms in a visual as well as statistical aspect. As these tools are made available to the user means that, apart from calculation of amino acid distributions from HPLC-chromatograms, HPLC - WIZARD offers the following other important features: 1. The functionality of a MDI-application (Multiple Document Interface). Which makes simultanous examination of several HPLC-chromatograms possible. 2. An user friendly environment making it easy to navigate around in the HPLC - chromatograms. This implies zoom, scroll, clip and stretch functions and the ability to draw chromatograms in numerous ways. 3. A function gallery, in which the user can select among several density functions to find the best function to model the peaks in a specific chromatogram. 4. Access to view and edit any parameter in the system. This implies e.g. editing or restraining individual peak and backgrund function parameters. 5. Graphical insertion, modification and minimization of peak functions, making it possible to model peaks with underlying structures or huge overlaps. 6. Implementation of joint refinement to handle response overflow. 7. Three different quantification methods. This involves a fully automatic weighted averaging of the compounds in up to 10 chromatograms. 8. Well-arranged presentation of results on screen as well as printer. From owner-software@net.bio.net Sun Nov 01 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.inet.tele.dk!not-for-mail From: Bo Bergmann <120010312330@post5.tele.dk> Newsgroups: bionet.software Subject: HPLC-WIZARD beta 1.0 Date: Mon, 02 Nov 1998 01:51:39 +0100 Organization: DTU Lines: 58 Message-ID: <363D021B.5B35@post5.tele.dk> NNTP-Posting-Host: ip93.boanxr1.ras.tele.dk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news-inn.inet.tele.dk 909967671 101002 (None) 195.249.161.93 (02-11-98 00:47:51 GMT) X-Mailer: Mozilla 2.02E [da]-TDK20 (Win95; I) CC: Bo, Bergmann Finally, the beta version 1.0 of HPLC-WIZARD is ready for evaluation. Get to our home page at http://home5.inet.tele.dk/daller/index.htm to download the beta version. HPLC-WIZARD is a Microsoft® Windows 95/98/NT application designed for fast and easy calculation of amino acid distributions from HPLC - chromatograms. In contrast to the existing method of numerical integration, which suffers from systematical errors due to inaccurate partion of overlapping peaks and improper treatment of the background function, HPLC-WIZARD calculates an amino acid distribution by modelling the HPLC- chromatograms by using different density functions to model the peaks and a background function based on Principal Component Analysis to model the background. In the evaluation of appropiate candidate functions to model the peaks in the HPLC - chromatograms, it was found necessary to develop tools to estimate how good a candidate function was able to model the chromatograms in a visual as well as statistical aspect. As these tools are made available to the user means that, apart from calculation of amino acid distributions from HPLC-chromatograms, HPLC - WIZARD offers the following other important features: 1. The functionality of a MDI-application (Multiple Document Interface). Which makes simultanous examination of several HPLC-chromatograms possible. 2. An user friendly environment making it easy to navigate around in the HPLC - chromatograms. This implies zoom, scroll, clip and stretch functions and the ability to draw chromatograms in numerous ways. 3. A function gallery, in which the user can select among several density functions to find the best function to model the peaks in a specific chromatogram. 4. Access to view and edit any parameter in the system. This implies e.g. editing or restraining individual peak and backgrund function parameters. 5. Graphical insertion, modification and minimization of peak functions, making it possible to model peaks with underlying structures or huge overlaps. 6. Implementation of joint refinement to handle response overflow. 7. Three different quantification methods. This involves a fully automatic weighted averaging of the compounds in up to 10 chromatograms. 8. Well-arranged presentation of results on screen as well as printer. From owner-software@net.bio.net Sun Nov 01 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!netnews.com!nntp.abs.net!news.mcs.net!ddsw1!erinet.com!erinntp!billotte From: billotte@erinet.com (William G. Billotte) Newsgroups: bionet.software Subject: Re: Image Quantitation Date: Sun, 01 Nov 1998 21:33:24 -0500 Organization: Bill and Zoe Lines: 18 Message-ID: References: <363576F9.7AB7@bilbo.bio.purdue.edu> NNTP-Posting-Host: 207.90.115.44 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.5 I would suggest trying NIH Image. It is available for free from the NIH website. It is available for the Mac or windoze. Bill In article <363576F9.7AB7@bilbo.bio.purdue.edu>, gizmo@bilbo.bio.purdue.edu wrote: > Dear Colleague, > > Does anyone has or know free Image Quantitation program(s) which can > handle scanned images of Xrays. 386 Molec.Dynamics we have is very slow > and picky. > > Thank you for help. > > Alex From owner-software@net.bio.net Mon Nov 02 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!jussieu.fr!saphir.jouy.inra.fr!lindenb From: lindenb@jouy.inra.fr (Pierre Lindenbaum) Newsgroups: bionet.software Subject: A Program Finding Cloning Strategies Date: 2 Nov 1998 09:29:16 GMT Organization: INRA Lines: 269 Message-ID: <71ju1c$nvh$1@saphir.jouy.inra.fr> NNTP-Posting-Host: biotec.jouy.inra.fr X-Newsreader: TIN [version 1.2 PL2] _________________________________________________________________ CLONEIT(tm) AN FREE ANSI-C PROGRAM FINDING SUB-CLONING STRATEGIES, IN-FRAME DELETIONS AND FRAMESHIFTS USING RESTRICTION ENZYMES AND DNA POLYMERASES. LINDENBAUM Pierre (1998) Bioinformatics/CABIOS Vol.14;5,1998 pp465-466 _________________________________________________________________ What is CloneIt ? Molecular biologists often have to sub-clone plasmidic vectors: a DNA plasmid is cleaved and ligated with an exogen DNA fragment previously excised from an other plasmid. The necessary cuts are achieved by restriction enzymes which then must be carefully choosen in order to minimize the steps required to obtain the desired molecule. During the selection of those enzymes, the main difficulties encountered come from the knowldege of: + the enzymes' characteristics + the localization of the cuts within the sequence + the complementarity between the protuding ends + the possible self ligation of the vector + the use of modifying DNA polymerases that generate blunt ends + the constraint to clone the insert in-frame with a vector sequence + the use of partial digestions + the creation of a stop codon after the ligation. + the buffers and the temperatures compatibilities. This exercise takes a long time even with a computorized help of the classic DNA analysis softwares that only help the user by localizing restriction sites that are present a few times in a plasmid sequence. All combinations cannot be humanly checked by the scientist, so a simple cloning strategy can be missed by the experimenter. We developed a program that quickly finds in-frame deletions using restriction enzymes and frameshifts (using digestion, fill-in and ligation) in a plasmid sequence, Then, as the main functions and procedures were being developed, we have extended the capacities of the program to find strategies to sub-clone a fragment from a plasmid to another vector while still controling the problems described above. This program is not an expert system, as it does not "learn" the logical steps accomplished by the biologist and it does not have to be accompanied in its search: it just runs an algorithm that explores all the possible enzymes combinations that could be used to clone the molecules. This program called CloneIt , written in ANSI C, provides a useful aid for any molecular biologist who wants to quickly find sub-cloning, in-frame deletions, frameshifts strategies, which would otherwise be difficult to discover. This program handle parameters such as + usage of a phosphatase (CIP) + usage of modifying polymerases that blunt overhanged ends + partial digestions + 5' or/and 3' in-frame ligation + digestion post ligation + digestion to direct insert + detection of stop codon after ligation + handle temperatures and buffers. + Compare 2 sequences from the point of view of restriction sites. + Display a restriction map. + Translation of restriction enzymes databases. + Management of large cloning projects. ------------------------------------------------------------------------------ CloneIt source code The source code is freely available at http://locus.jouy.inra.fr/soft/cloneit/cloneit.html If you are interested in being kept informed directly about CloneIt , please send me your e-mail address. ------------------------------------------------------------------------------ Samples ------------------------------------------------------------------------------ SubCloning .............................................................................. CloneIt V1.0 has found a solution: Digest VECTOR with EcoRI [G^AATTC] (878) and Sal I [g^tcgac] (894). 5' --G.CCG.G/AA.TT C.CCG.GGG.ATC.CG/T.CGA. CCT.GCA.GCC.AAG-- 3' 3' --C.GGC.C TT.AA/G.GGC.CCC.TAG.GC A.GCT./GGA.CGT.CGG.TTC-- 5' NH2 P E F P G I R R P A A K .COOH Digest first with EcoRI .Then treat with Klenow DNA polymerase.Finally digest with Sal I . Digest INSERT with Sca I [AGT^ACT] (1034) and Sal I [g^tcgac] (3605). 5' --AT.AAA.GT/ A.CTT.TCA.AAG.AAA.G-- --TA.GAG./TCG.A CC.TGC.AGG.CAT.G-- 3' 3' --TA.TTT.CA/ T.GAA.AGT.TTC.TTT.C-- --AT.CTC. AGC.T/GG.ACG.TCC.GTA.C-- 3' NH2 K V L S K K E -- -- E S T C R H A .COOH Treat with T4 DNA polymerase. Sites wil be in frame ligated in 5'. The first stop codon detected BEFORE the EcoRI site (878) is localized at position 428 on vector. The first stop codon detected AFTER the Sca I site (1034) is localized at position 3558 on insert. Digestion post-ligation: no enzyme was found. .............................................................................. Finding in-frame deletions .............................................................................. CloneIt has found an in-frame deletion: Digest INSERT with Bcl I [t^gatca] (1427) and PstI [CTGCA^G] (3611). 5' --TG.TAT./GAT.C AG.GTT.CTT.ACT.G-- --CG.ACC. TGC.A/GG.CAT.GCA.AGC.T-- 3' 3' --AC.ATA. CTA.G/TC.CAA.GAA.TGA.C-- --GC.TGG./ACG.T CC.GTA.CGT.TCG.A-- 5' NH2 Y D Q V L T E -- -- T C R H A S F .COOH Treat with T4 DNA polymerase. Cloning boxes boundaries :[880-1155] [3359-3634]. Original: 5' ================================================ 3' Deletion: 5' =========......................................= 3' Equivalent to a deletion of 728 amino acids [79 %] Digestion post-ligation: BamHI Sal I Acc I Nsi I . The first stop codon detected AFTER the PstI site (3611) is localized at position 3639 on insert. Translated truncated sequence:... NSSSVPGAIKGSMAYRKRGARREANINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVV TDSQEEIKIADEVKKSTKEESKQLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLE DIKPEQAKKQTKLFRIFEPRQLPIYRANGEKELRNRTYTKLKKDTLPGDYDVREYFLNLY DR---------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --HASFCS... .............................................................................. Finding frameshifts in INSERT. .............................................................................. CloneIt has found an Enzyme that could induce frameshift. Digest INSERT with AccI [gt^mkac] (1659). 5' --.ATC.AGT.//AT A.CAC.ATA.AAT.GAT-- 3' 3' --.TAG.TCA. TA//T.GTG.TAT.TTA.CTA-- 5' NH2 I S I H I N D .COOH Treat with Klenow DNA polymerase. Beware : AccI [1 partial site] . After digestion, fill-in and ligation: 5' .ATC.AGT.ATA.TAC.ACA.TAA.ATG 3' 3' .TAG.TCA.TAT.ATG.TGT.ATT.TAC 5' NH2 I S I Y T * M COOH ¥ FrameShift (+ 2) ¥ 2 bases Added. ¥ Site is NOT reconstitued after ligation. ¥ [51 %] percentage of Insert. FIGURE: ========================= | (+2) =========================== Translated sequence:...EFELGTRGSMATFKDACYHYKRLNKLNSLVLKLGANDETRPAPMTKYKGTCL YTNLTYCRGCALYHVCQTCSQYNRCFLDEEPHLLRMRTFKDVVTKEDIEGLLTMYETLFPINEKLVNKFINSVKQ EYLLETYNHLLMPITLQALTINLEDNVYYIFGYYDCMEHENQTPFQFINLLEKYDKLLLDDRNFHRMSHLPVILQ RYFSKSRFLSKGKKRLSRSDFSDNLMEDRHSPTSLMQVVRNCISiyT*... .............................................................................. Informations .............................................................................. Get information about Bst1107 I INSERT Pattern -------------- Bst1107I [GTA^TAC] (1659) p5_1 digestion. 1 4652 pb Bst1107I 1744 - Bst1107I 1659 2 85 pb Bst1107I 1659 - Bst1107I 1744 ............................................................................... . Prototype :SnaI Microorganism :Bacillus stearothermophilus RFL1107 Source :A.A. Janulaitis Methylation site : Commercial availability : Angewandte Gentechnologie Systeme Fermentas AB Takara Shuzo Co. Ltd. Boehringer-Mannheim New England Biolabs Refs :457 ............................................................................... . Looking for Isoschizomers. (*):Commercialy available) ( ) BspM90I GTA^TAC. (*) BssNAI GTA^TAC. also available at: SibEnzyme Ltd. ( ) BstBSI GTA^TAC. (*) BstZ17I GTA^TAC. also available at: New England BioLabs ( ) XcaI GTA^TAC. .............................................................................. Restriction Map .............................................................................. SACI SALI ECORI : hincii styi acsi : acci ECO52I NCOI alwi : ECL136II eaei bstdsi xhoii : bsp1286i bsh1285i MSCI xmni BAMHI : banii : NOTI eaei ecorv : vspi alwi : alw21i : HINDIII: : : : : : :: : : : : :: TGGCCATGGATATCGGAATTAATTCGGATCCGAATTCGAGCTCCGTCGACAAGCTTGCGGCCGCA \ 5266 ¥ ¥ ¥ ¥ ¥ ¥ ¥ \ ACCGGTACCTATAGCCTTAATTAAGCCTAGGCTTAAGCTCGAGGCAGCTGTTCGAACGCCGGCGT \ 5330 T P T :I S E :L I R::I R: I R: A P :S T :S L :R P H -> :A :M D: I G :I: N S D: P N S S S V: D K: L A::A A L -> : H: G Y R N: * F G :S E :F E :L R R Q A C G: R T -> : P: V $ L R: L * A :$ A :* A :R P L Q E F A: P T ---------------------------------------------------------------------------- LINDENBAUM Pierre (1998) Bioinformatics/CABIOS Vol.14;5,1998 pp465-466 ---------------------------------------------------------------------------- 098)o%:::%o(8609 .6o%:%o(86098).......................................................... (86098)o 6098)o%::%o9 Pierre LINDENBAUM 098)o%::::::%o9 Biologie Moleculaire des Rotavirus 6o%::::::%o(860 Unite de Virologie et Immunologie Moleculaires 6o%::%o(8609 Institut National de la Recherche Agronomique o(86098) 78352 JOUY-EN-JOSAS CEDEX (86098)o%:%o9 FRANCE 6098)o%:::%o(860 098)o%:::%o(8609 lindenb@biotec.jouy.inra.fr 6o%:%o(86098) (86098)o 6098)o%::%o9............................................................ 098)o%::::::%o9 6o%::::::%o(860 CloneIt WWW Home Page:http://locus.jouy.inra.fr/soft/cloneit/cloneit.html From owner-software@net.bio.net Mon Nov 02 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!enews.sgi.com!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: Protease/substrate database? Date: 3 Nov 1998 05:56:19 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 29 Message-ID: <71m5u3$j9b$1@franklin.ljcrf.edu> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Hi; A colleague has asked me an interesting question which I don't readily know the answer to since it's way out of my area: Does anyone know if any lab has compiled an protease/substrate database or listing (at least one that's highly up-to-date)? Thanks for any leads or ideas. Cheers Greg -- ***************************************** Computational Biology Group The Burnham Institute (formerly La Jolla Cancer Research Inst.) 10901 North Torrey Pines road La Jolla CA92037 Phone:(619) 646 3103 Email: greg@franklin.ljcrf.edu http://franklin.ljcrf.edu/greg http://www.greg.com/ ***************************************** From owner-software@net.bio.net Mon Nov 02 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!howland.erols.net!spring.edu.tw!serv.hinet.net!netnews.hinet.net!news From: "·F©p®Q" Newsgroups: alt.sports.baseball.mn-twins,alt.tv.twin-peaks,bionet.software Subject: !~¨D±z¦AÅF§Ú¤@¦¸!!!¤í·Fªº¤H Date: Tue, 3 Nov 1998 11:25:09 +0800 Organization: §Ú¤í¾Ş Lines: 18 Message-ID: <71lsup$dui@netnews.hinet.net> Reply-To: "·F©p®Q" NNTP-Posting-Host: h36.s99.ts.hinet.net X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 §Ú©Ò¦³ªº E-Mail Address : jjtech@ms13.hinet.net linda@jjtech.com tsd@jjtech.com sales@jjtech.com info@jjtech.com rd@jjtech.com ¤£°µ¬O¤pª¯, ·PÁ±z From owner-software@net.bio.net Mon Nov 02 22:00:00 1998 Path: biosci!TC.UMN.EDU!Ronglin.Wang-1 From: Ronglin.Wang-1@TC.UMN.EDU (Ronglin Wang) Newsgroups: bionet.software Subject: Mapmaker on Linux Date: 3 Nov 1998 13:12:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Hi there. I am trying to port Mapmaker to our Linux-based PC. Can anyone with experience working with Mapmaker offer me some advice? What are the changes I have to make? Best regards, Ronglin Wang Plant Biology Univ of Minnesota From owner-software@net.bio.net Mon Nov 02 22:00:00 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: Protease/substrate database? Date: 3 Nov 1998 17:22:03 GMT Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE Lines: 33 Message-ID: <71ne3r$cv0$1@franklin.ljcrf.edu> References: <71m5u3$j9b$1@franklin.ljcrf.edu> NNTP-Posting-Host: franklin.ljcrf.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Edwin ten Dam (etd@bigfoot.com) wrote: : In article <71m5u3$j9b$1@franklin.ljcrf.edu>, : greg@franklin.burnham-inst.org (Dr. Greg Quinn) wrote: : : >Hi; : > : >A colleague has asked me an interesting question which I : >don't readily know the answer to since it's way out of my : >area: : > : >Does anyone know if any lab has compiled an : >protease/substrate database or listing (at least : >one that's highly up-to-date)? : > : >Thanks for any leads or ideas. : >Cheers : >Greg : : This may answer part of your query: : : have a look at MEROPS, a proteinase database: : : http://www.bi.bbsrc.ac.uk/Merops/Merops.htm : : cheers, : : edwin : Edwin This looks great; thanks very much. Cheers Greg From owner-software@net.bio.net Mon Nov 02 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: michael.baron@bbsrc.ac.uk Newsgroups: bionet.software Subject: [ANN] Macboxshade v2.11 posted Date: Tue, 03 Nov 1998 15:24:53 +0000 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 83 Message-ID: <363F2044.74BB@bbsrc.ac.uk> NNTP-Posting-Host: pc0288.avri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) MACBOXSHADE version 2.11 is now available from the BOXSHADE web page: ftp://ftp.isrec.isb-sib.ch/pub/sib-isrec/boxshade/MacBoxshade/MacBoxshade_2.1.hqx (N.B. same archive name as version 2.1, but new version!!!!) MACBOXSHADE is a program for creating good-looking printouts from multiple aligned protein or DNA sequences. The program does no alignment by itself, it has to take as input a file preprocessed by a multiple alignment program or a multiple file editor. NEW in v2.11: fixes a long-standing, but only just discovered, bug whereby opening two ASCII display or two matrix display windows caused a crash (thanks to Dr. Todd Richmond, Carnegie Institution of Washington, for pointing the bug out to me). NEW in version 2.1: Wrote my own text display routines, so the 'current alignment' and 'Display ASCII' windows are no longer limited to 32 000 characters. Modified the PICT display so that it would not be stuck in low memory situations. If there is enough memory assigned to the program, you get the nice, smooth-scrolling display as previously; if not, the program tries to borrow more memory from unassigned RAM in your machine (if any). If this, in turn, fails, you get a rather jerky, slow-to-scroll display, but you DO get the display. In these days of cheap RAM, this modification may not have been of so much use to many people, but it irritated me, so I fixed it. Added the option (requested by Barry Hall of University of Rochester, NY) of treating '~' characters as different to '-' characters. The '~' character, introduced in GCG9, is for leading and trailing pad characters. If the option (Shading Prefs) to ignore these pads is taken, then they are not counted when the consensus is being calculated. E.g. Consider a situation where we have ...KG~~~~~~ ...KGI~~~~~ ...KG~~~~~~ ...KGVCNETM ...KEVCND~~ ...K~~~~~~~ at the end of an alignment. Normally, with a 75% threshold value, the K residues would be shaded, (6/6) but the Gs would not (4/6). If '~' chars are ignored in counting, the G residues are shaded (4/5), as are the V/Is (3/3) and the pairs of Cs and Ns that follow (2/2 in each case). Personally, I am not convinced that this is the right way to shade the alignment, but I can see that there might be an arguement for saying that these leading and trailing pads are of a different nature from internal pads, and should be treated differently. You have the option. - Fixes a couple of outstanding bugs: Program would crash if the last block of sequences was one residue long, and numbering was turned on; program would sometimes crash if there was not enough memory to draw the PICT display; layout of the identity/similarity matrix wasn't properly aligned in all cases. As always, please send any reports of bugs or other problems with MacBoxshade to: Michael D. Baron Ph.D. E-mail: michael.baron@bbsrc.ac.uk Institute for Animal Health Ash Road Pirbright Surrey GU24 0NF U.K. From owner-software@net.bio.net Mon Nov 02 22:00:00 1998 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: Tue, 03 Nov 1998 14:34:35 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 23 Message-ID: <71n49r$607$1@nnrp1.dejanews.com> References: <361769bf.317437@news.altopia.com> <6v9vqs$t4t$1@nnrp1.dejanews.com> <6vd5jc$hfn$1@nnrp1.dejanews.com> <6vi8bm$anv$1@nnrp1.dejanews.com> NNTP-Posting-Host: 128.16.6.58 X-Article-Creation-Date: Tue Nov 03 14:34:35 1998 GMT X-Http-User-Agent: Mozilla/3.0 (X11; I; SunOS 5.5.1 sun4m) X-Http-Proxy: 1.0 x3.dejanews.com:80 (Squid/1.1.22) for client 128.16.6.58 Path: biosci!news.ic.sunysb.edu!news-nysernet-16.sprintlink.net!news-in-east1.sprintlink.net!news.sprintlink.net!newshub.northeast.verio.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 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 Mon Nov 02 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!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: o.agra@cs.ucl.ac.uk Newsgroups: alt.binaries.w-software,bionet.software,bionet.software.pc,bit.software Subject: FREE LINUX SOFTWARE Date: Tue, 03 Nov 1998 14:31:30 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 22 Message-ID: <71n442$5uu$1@nnrp1.dejanews.com> References: <361769bf.317437@news.altopia.com> <6v9vqs$t4t$1@nnrp1.dejanews.com> <6vd5jc$hfn$1@nnrp1.dejanews.com> <6vi8cn$aph$1@nnrp1.dejanews.com> NNTP-Posting-Host: 128.16.6.58 X-Article-Creation-Date: Tue Nov 03 14:31:30 1998 GMT X-Http-User-Agent: Mozilla/3.0 (X11; I; SunOS 5.5.1 sun4m) X-Http-Proxy: 1.0 x3.dejanews.com:80 (Squid/1.1.22) for client 128.16.6.58 ProSplitter v2.0 for Linux FREE OF CHARGE !!!!! ProSplitter is a award winner file splitter with many powerfull features like 56-bit DES encryption when splitting files, CRC check when joining files, ability to split multiple files in the same directory.......etc.....and many many more !!!!! There is no catch, to celebrate the realese of the package for a limited time only it is available to you for FREE !!! E-mail me at o.agra@cs.ucl.ac.uk and i'll send you the registration key, but hurry !!!! To download go to http://www.cs.ucl.ac.uk/students/o.agra - Go to the download section by clicking on the 'Download' icon situated in the left frame. - Once on the download page click on 'Download' to download it !!! -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Mon Nov 02 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Steffen Moeller Newsgroups: bionet.software Subject: Re: Q: Rasmol in Linux: X Error Date: Tue, 03 Nov 1998 12:56:49 +0000 Organization: EBI - European Bioinformatics Institute Lines: 15 Message-ID: <363EFD91.3A466CC0@ebi.ac.uk> References: <6vub95$tk3$1@nnrp1.dejanews.com> <36231048.A2D2B798@crc.dk> NNTP-Posting-Host: trick.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 910097810 18796 193.62.196.46 (3 Nov 1998 12:56:50 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 3 Nov 1998 12:56:50 GMT X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.35 i686) X-Accept-Language: en If you have the Rasmol source I'd suggest to edit the Imakefile appropiately. # DEPTHDEF = -DTHIRTYTWOBIT # DEPTHDEF = -DEIGHTBIT DEPTHDEF = -DSIXTEENBIT Or to avoid another run of imake do the change directly in the Makefile. I can supply you with the 16bit version if you have any problems. Steffen -- Steffen Moeller From owner-software@net.bio.net Mon Nov 02 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!nntp.news.xara.net!xara.net!server6.netnews.ja.net!st-and!etd From: etd@bigfoot.com (Edwin ten Dam) Newsgroups: bionet.software Subject: Re: Protease/substrate database? Date: Tue, 03 Nov 1998 12:26:19 +0000 Organization: School of Biomedical Sciences - University of St Andrews Lines: 32 Message-ID: References: <71m5u3$j9b$1@franklin.ljcrf.edu> NNTP-Posting-Host: bmsmac-mdr1.st-and.ac.uk X-Newsreader: MT-NewsWatcher 2.4.4 X-Face: -P+89ASh_wrs;AUGm`!l[}/o-lyK}5W.gq\fkJ{#d6Gu,hWrZNz::iMm5PJb} __A96]-LUrl)X=uF=V|\3-\9/sXvBs/H In article <71m5u3$j9b$1@franklin.ljcrf.edu>, greg@franklin.burnham-inst.org (Dr. Greg Quinn) wrote: >Hi; > >A colleague has asked me an interesting question which I >don't readily know the answer to since it's way out of my >area: > >Does anyone know if any lab has compiled an >protease/substrate database or listing (at least >one that's highly up-to-date)? > >Thanks for any leads or ideas. >Cheers >Greg This may answer part of your query: have a look at MEROPS, a proteinase database: http://www.bi.bbsrc.ac.uk/Merops/Merops.htm cheers, edwin -- Edwin ten Dam etd@bigfoot.com School of Biomedical Sciences - University of St Andrews Biomolecular Sciences Bldng, North Haugh, St Andrews, KY16 9ST U.K. Phone: +44 1334 463404 - Fax: +44 1334 462595 From owner-software@net.bio.net Mon Nov 02 22:00:00 1998 Path: biosci!DIHT.COM.SG!cudo44 From: cudo44@DIHT.COM.SG (frezxery) Newsgroups: bionet.software Subject: Reach your internet clients - before competition Date: 2 Nov 1998 20:13:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <199811023732WAA15308@frebrequaz.ghyis2.com.tw> NNTP-Posting-Host: net.bio.net ___________________________________________________________ DIRECT EMAIL SERVICES - targeted & general prospects ! ___________________________________________________________ WEB SITE Submission - to the top search engines & hundreds ___________________________________________________________ Daily Lists - get FRESH NEW lists daily - great supplement ___________________________________________________________ FREE SOFTWARE DEMOS - prospect harvesters and mailers ! ___________________________________________________________ EMAIL LIST - MILLIONS: cleaned.....complete w/ software ___________________________________________________________ OPPORTUNITY $$ - software, books & internet services ___________________________________________________________ BOOKS & TAPES - Hundreds of selections - Dealers wanted ! ********************************************************* MORE INFO (24 hrs): 702-284-5074 Dist. Ref #: 254804GB This is a one time message - thank you ! ******************************************************** From owner-software@net.bio.net Tue Nov 03 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!uninett.no!news.net.uni-c.dk!not-for-mail From: "Søren W. Rasmussen" Newsgroups: bionet.software Subject: Dnatools, revision 152 Date: Wed, 04 Nov 1998 16:48:50 +0100 Organization: UNI-C Lines: 102 Message-ID: <36407761.ECDEDAA0@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 910194908 11322 (None) 130.226.182.97 X-Complaints-To: usenet@news.net.uni-c.dk X-Mailer: Mozilla 4.03 [en] (Win95; I) ******************************************************************************* NEW in version 5.1, revision 152: A bug which prevented sending 'long' e-mails (sequences and primer orders) has been corrected. Apparently NCBI has changed the mail-blast program to Gapped-BLAST. The auto-build header function has been modified to accept also the output from Gapped blast searches when done at NCBI. Several changes have been made to the collection of SAGE programs. I believe that all the programs now work (Create SAGE Tag Files, SAGE Tag File Tools, and Search With SAGE Files). Printing SAGE tag distribution histograms may still not work with all printers (it has only been tested on a HP LaserJet 6P) Recording the inifile caused some problems. I hope they are now corrected. The help file has been updated. ******************************************************************************* ------------------------------------------------------------------------------- SETUP FILES: The zip file DT_51152.zip, 7.562 Mb, contains new setup files for DNATools 5.1 revision 152. After downloading the zip file, just un-zip it and run the setup program to start using DNATools. ------------------------------------------------------------------------------- UPDATE FILES: The zip file 51152_EXE.zip, 1.149 Mb, contains updated versions of dnatools.exe and dnatools.hlp. If you already have DNATools installed and want to update, you can download the revised exe and help files. Then locate the DNATools directory on your PC and overwrite the old files. Remember to close all programs before you replace the files. Note that it is NOT possible to run the update files without first installing DNATools. ------------------------------------------------------------------------------- MANUAL/HELP: In the absence of a manual, you have to consult the extensive context sensitive help to get information on the various functions of DNATools. ------------------------------------------------------------------------------- SYSTEM REQUIREMENTS Please note that DNATools runs on Windows 95/98 and NT but NOT on Windows 3.x or MACs. A 233 MHz Pentium with at least 48 Mb of RAM is recommended if you intend to work with more than a few files in the same project. ------------------------------------------------------------------------------- REGISTRATION: To register your copy, I need your FULL NAME and the VERSION and REVISION numbers of your copy. DNATools will remind you 1 month before the test perion expires. The cost of a single user licence is $100. Future revisions will be available at the above ftp site. You can upgrade without limitations within your 3 month test period. Thereafter, if you decide to keep using DNATools, a licence number is required. ------------------------------------------------------------------------------- ABOUT DNATools: DNATools has been developed over several years primarily inspired by my frustrations with commercially available programs. For specific tasks - like merging 1,000 sequences into a contig, or performing detailed analyses on protein sequences - you still need more sophisticated (and more expensive) programs. For the daily handling and primary analyses of sequences, I hope you will find DNATools useful. Today, many more complex functions (e.g. mail blast servers) are available on www. These programs in conjunction with DNATools actually comprise a fairly comprehensive toolbox for sequence handling and analysis. ------------------------------------------------------------------------------- WARNING! Please note that using DNATools is ENTIRELY AT YOUR OWN RISK! A great deal of effort have been invested in correcting errors and bugs. This does, however, not imply that ALL errors and bugs have been removed. DNATools is continously being modified and extended and I would appreciate very much your comments and suggestions regarding bugs, modifications, new functions etc. November 07, 1998 Soeren W. Rasmussen swr@crc.dk ftp://ftp.crc.dk/pub/dnatools -- 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 Tue Nov 03 22:00:00 1998 Path: biosci!pravda.ucr.edu!williams From: Alan Williams Newsgroups: bionet.software Subject: Re: Question: Win 95/98 on LINUX? Date: 4 Nov 1998 15:42:33 GMT Organization: University of California, Riverside Lines: 35 Message-ID: <71psl9$89d$1@pravda.ucr.edu> References: <363f9b52.14325284@news.orst.edu> NNTP-Posting-Host: avocado.ucr.edu User-Agent: tin/pre-1.4-980202 (UNIX) (Linux/2.1.125 (i586)) Win95/98 under linux? As far as I know it can't be done. There is a cpu emulator called Bochs. I was unable to get it running on my machine (Redhat 5.1/2.1.125 Kernel). From the linux news groups I gather that it is so slow (emulation is done completely in software) that it is more of a novelty than a utility. If you want to run windows 3.1 apps then there is the commercial product WABI as well as the free WINE project which will allow you to run windows 3.1 apps on a linux machine. The only real solution to allow you to run windows 95/98/XXX apps "on" linux is to run windows on a second computer and display the programs on your linux box. This can be done by using an X windows system for windows or using the VNC system to control the windows pc from linux. This should work fine for a single user setup. It may not work smoothly for multiple users. try the comp.emulators.* news groups as well as the comp.os.linux.* newsgroups to get more information. www.dejanews.com is a great resource for finding out what other people have already said about win95 apps under linux. dd chen wrote: : Has anyone installed Win 95 or 98 as a client on a machine that is : running LINUX? How easy/hard is this to do? Is there a preference : for the type of processor (eg Intel vs Alpha vs SGI etc)? Prices? : Other help? ************************************************************************ Alan Williams (finger alan@avocado.ucr.edu for pgp public key) ------------------------------------------------------------------------ University of California, Riverside "Where observation is concerned, Dept. of Botany and Plant Sciences chance favors the prepared mind." Alan@Avocado.UCR.edu -- Louis Pasteur ************************************************************************ From owner-software@net.bio.net Tue Nov 03 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!feed1.news.rcn.net!rcn!news2.best.com!news3.best.com!nntp1.ba.best.com!not-for-mail From: "Genome Jobs" Newsgroups: bionet.software Subject: Jobs in bioinformatics at www.genomejobs.com Date: Wed, 4 Nov 1998 02:09:22 -0800 X-Newsreader: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Lines: 18 Message-ID: <36402794$0$29765@nntp1.ba.best.com> NNTP-Posting-Host: dynamic10.pm05.sf3d.best.com X-Trace: nntp1.ba.best.com 910174100 29765 209.24.235.10 Jobs in bioinformatics at www.genomejobs.com We have listings of jobs and companies in bioinformatics, genomics, software engineering, biotechnology, pharmaceutical, and scientific jobs where biology meets computers Free to job seekers Great opportunites at Great Companies www.genomejobs.com Jobs in bioinformatics, genomics, biotechnology, computers, databases, chips, microarrays, various engineers, proteomics, scientists, research associates, database administrators, database architects, database engineers, software engineers, analyst programmers, scientific programmer, software developer, molecular biologist, microbiologist, cheminformatics, pharmatics, biostatistics, SAS programmers, medicinal chemistry, drug discovery, mathematicians, algorithm specialists, web developers, and more. From owner-software@net.bio.net Tue Nov 03 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.nero.net!not-for-mail From: chend@ucs.orst.edu (dd chen) Newsgroups: bionet.software Subject: Question: Win 95/98 on LINUX? Date: Wed, 04 Nov 1998 00:13:04 GMT Organization: usda-ars Lines: 19 Message-ID: <363f9b52.14325284@news.orst.edu> NNTP-Posting-Host: gb48633.usda-ars.orst.edu X-Newsreader: Forte Free Agent 1.11/32.235 Hi: Has anyone installed Win 95 or 98 as a client on a machine that is running LINUX? How easy/hard is this to do? Is there a preference for the type of processor (eg Intel vs Alpha vs SGI etc)? Prices? Other help? Thanks for any help. Don DD Chen Standard disclaimers USDA-ARS always apply NFSPRC 3450 SW Campus Way Corvallis, OR 97331 541-750-8741 From owner-software@net.bio.net Tue Nov 03 22:00:00 1998 Path: biosci!UVIC.CA!jdboer From: jdboer@UVIC.CA (Johan de Boer) Newsgroups: bionet.software Subject: RefMan8 and Windows NT Date: 4 Nov 1998 13:29:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <199811042125.NAA123616@uvaix7e1.comp.UVic.CA> NNTP-Posting-Host: net.bio.net Hi, I am trying to run Reference Manager version 8.01 under Windows NT. The program will open, but when I try to open a database file, the program will hang. This does not happen under Win95. Has anyone had this same experience? Is there a solution to this problem? Thanks, Johan de Boer Centre for Environmental Health University of Victoria From owner-software@net.bio.net Tue Nov 03 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!news-ge.switch.ch!news.unige.ch!news From: grandcha@cmu.unige.ch (Kenneth Grandchamp) Newsgroups: bionet.software Subject: Spot quantification with office scanner ? Date: 4 Nov 1998 10:26:42 GMT Organization: Centre Medical Universitaire Lines: 20 Message-ID: <71pa52$r0n@uni2f.unige.ch> NNTP-Posting-Host: 129.194.97.221 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 Hello ! We've been trying to quantify our gels with Imagequant 3.3 (win3.1) under Win95 with an office scanner (AGFA ARCUS II), but are having problems importing the tiff images into Imageqnt. Question: - Is there a way of importing the tiff images into imageqnt ? (it works the first time but the second time we get an error message "unable to lock memeory"). - Are there any other software around (freeware?, shareware?, cheapware ?) that can do the job ? Thanks ! Ken. From owner-software@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.daimi.au.dk!not-for-mail From: Bent.Nagstrup@kba.sks.aau.dk (Bent Nagstrup) Newsgroups: bionet.software Subject: Re: RefMan8 and Windows NT Date: 5 Nov 1998 09:04:02 GMT Organization: Research Unit for Molecular Medicine, Aarhus University Hospital, Denmark Lines: 15 Distribution: world Message-ID: <71rpm2$i3q$1@xinwen.daimi.au.dk> References: <199811042125.NAA123616@uvaix7e1.comp.UVic.CA> NNTP-Posting-Host: kba.sks.aau.dk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Trace: xinwen.daimi.au.dk 910256642 18554 255.255.255.255 (5 Nov 1998 09:04:02 GMT) X-Complaints-To: news@daimi.au.dk NNTP-Posting-Date: 5 Nov 1998 09:04:02 GMT X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) >I am trying to run Reference Manager version 8.01 under Windows NT. The (If you have bought it recently, you can get a free upgrade to 8.5) I use refman with ntwks daily with no problem, but I think that it needs to be at service pack 3 in order to work - other than that, I dunno. -- Bent Nagstrup M.Sc. Research Unit for Molecular Biology, Aarhus University ---- A bus station is where the bus stops, A train station is where the train stops, On my desk I have a workstation.... From owner-software@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newsfeed1.swip.net!swipnet!masternews.telia.net!feed1.news.luth.se!luth.se!news-ge.switch.ch!serra.unipi.it!newsserver.cilea.it!news.csi.unimi.it!not-for-mail From: "Istituto Ispezione Alimenti Sez. II" <213ld@imiucca.csi.unimi.it> Newsgroups: bionet.software Subject: gel analysis freeware Date: Thu, 05 Nov 1998 12:09:52 +0000 Organization: Universita' degli Studi di Milano Lines: 6 Message-ID: <36419590.4735E509@imiucca.csi.unimi.it> NNTP-Posting-Host: isdn20.csi.unimi.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en Any one can help me? I am looking for a free software to analyze band-patterns on electrophoresis gels (PCR fingerprints) Thank you Fabio Colombo From owner-software@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!firehose.mindspring.net!firehose.mindspring.com!not-for-mail From: expomed@mindspring.com (MARTY THOMAS) Newsgroups: bionet.software Subject: Epilepsy Software Date: 5 Nov 1998 03:19:55 GMT Organization: Your Organization Lines: 33 Message-ID: <71r5gr$m8j$2@camel25.mindspring.com> NNTP-Posting-Host: pool-207-205-184-112.clev.grid.net Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (x86 32bit) COREL EPILEPSY CD The first title in the Corel Medical Series covers the topic of epilepsy from various perspectives, including pathophysiology, epidemiology, diagnosis and treatment, in a comprehensive, problem-based interactive format. 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You can view more info at the following page(s). http://www.visualman.com/corel/corelmed.htm http://www.expomed.com/corelmed.htm Thanks for your time and consideration. -- /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ Martin Thomas, expomed@mindspring.com http://www.onsitedrugtesting.com/ Onsite Drug Testing http://www.expomed.com/ Personal Protection Products http://www.visualman.com/ Educational Software From owner-software@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!xmission!nntp.csuchico.edu!cscnews.csc.calpoly.edu!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: FASTA format - proposed max line limit Date: 5 Nov 1998 01:03:17 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 94 Message-ID: <71qtgl$m8u@gap.cco.caltech.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu We all know that the FASTA format is a bit restrictive in that there is only the one line for comments, but can the software/database community *please* agree on some reasonable maximum line length for both the comments and the sequence? The basic FASTA format is defined by example in the FASTA2 distribution file "format.doc". The format is not defined there with very many (any?) limitations, so consequently many FASTA files these days have comment lines in excess of 500 characters (Unigene, for instance). Others have huge sequences on one line. The original FASTA examples, with shorter lines, could be easily viewed with text editors and other similar tools, but the overgrown variants cause all sorts of problems. This is very similar to the problem one sees with Postscript, where the standard clearly states that lines can only be so long - and a lot of software merrily ignores that standard, and so breaks on various printers. Maybe WRP has already written something like this, but here is a more restrictive standard I propose, let's call it FASTA-1998, version 0.1, so that it has a specific name. It isn't very long - and it would not be at _all_ difficult for the lot of us to stay within it. (Hint, hint). ********************************************************************** Fasta-1998 0.1 defines two formats: Sequence: for DNA and Protein sequences Reference: for any other information (optional) Common characteristics of both file types: C1. The FASTA-1998 format is a TEXT format, not a BINARY one. C1.a Programs which write FASTA-1998 files may do so in the native text mode of the operating system where they operate. C1.b Programs which read FASTA-1998 files will consider a cluster of any of the following ASCII symbols to be a SINGLE end of line: null ('\0'), LineFeed, CarriageReturn. C1.c No carriage control or "special characters" may exist in the file, other than those included in the end of line indicator. Tabs are specifically excluded. The Fasta-1998 SEQUENCE format is: S1. Each sequence entry in a FASTA-1998 file will begin with a comment line. S1.a This line will begin with the ">" character. S1.b This line will not exceed 80 characters in length, not counting any end of line characters. S1.c Immediately following the ">" there will be an identifying name consisting of a combination of the alphanumeric symbols, plus the dash and underscore, but no other punctuation characters. All identifying names in a FASTA-1998 file must be unique within that file. The case of any letters in the name may be either upper, lower, or a combination of the two, but two identifying names in a FASTA file may not differ solely by case. S1.d Immediately following the identifier there may be either an end of line or a " " (space) character. The latter may be followed by any text, up to the end of the comment line. S1.e DNA and Protein alphabet specified here. S2. Each entry will one or more sequence lines. S2.a Sequence lines may not exceed 80 characters in length, excluding the end of line characters. The Fasta-1998 REFERENCE format is very similar to the SEQUENCE format. R1. The reference file will hold information that didn't fit inside the Sequence file. R1.a The comment line for each entry in the reference file must contain the ">" followed by the identifier, but no other information. R1.b If the reference file exists, it must contain the same number of entries, with the same identifiers, and in the same order, as appeared in the sequence file. R1.c The data lines in the reference file may be up to 80 characters long, not including the end of line characters. They may not include special characters or carriage control information. R1.d Each entry may contain zero or more data lines. ********************************************************************** That isn't so terrible, is it? S1.c bears special mention. Entry names tend to turn into file names, and if they contain odd combinations of characters they can be either hard to deal with, or just plain illegal, depending on the OS. For instance: "gi|R34734987" can get you into trouble on Unix, and it's just plain illegal on VMS. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.tli.de!news-fra.maz.net!news-fra1.dfn.de!news-koe1.dfn.de!news.dlr.de!usenet From: "Markus Hoenicka" Newsgroups: bionet.software Subject: Re: RefMan8 and Windows NT Date: 5 Nov 1998 08:01:51 GMT Organization: DLR Lines: 37 Message-ID: <01be0893$2d50fe50$a570f781@udca3041> References: <199811042125.NAA123616@uvaix7e1.comp.UVic.CA> NNTP-Posting-Host: eval-01.me.kp.dlr.de X-Newsreader: Microsoft Internet News 4.70.1161 No such experiences. I use WinNT4.0 SP3 on two different machines, and both show no problems with RefMan 8.01. What databases do you try to open? Win95/RefMan8.01 generated ones or older stuff which needs a conversion? Otherwise, the usual procedures apply: - Reinstall - Uninstall completely, then reinstall - Obtain a different copy of the program and reinstall etc etc If you need a cool free tool to import Medline data into your RefMan database, please visit me at: http://members.tripod.com/~mhoenicka/med2rm.html Markus -- Markus Hoenicka 100606.33@compuserve.com Johan de Boer wrote in article <199811042125.NAA123616@uvaix7e1.comp.UVic.CA>... > Hi, > I am trying to run Reference Manager version 8.01 under Windows NT. The > program will open, but when I try to open a database file, the program will > hang. This does not happen under Win95. Has anyone had this same > experience? Is there a solution to this problem? > > Thanks, > Johan de Boer > Centre for Environmental Health > University of Victoria > > From owner-software@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.direct.ca!novia!marge.eaglequest.com!streamer1.cleveland.iagnet.net!NewsNG.Chicago.Qual.Net!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: FASTA format - proposed max line limit Date: 5 Nov 1998 18:57:46 GMT Organization: Biology, Indiana University - Bloomington Lines: 13 Message-ID: <71ssfa$rpp$1@flotsam.uits.indiana.edu> References: <71qtgl$m8u@gap.cco.caltech.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu David, It doesn't sound so bad to me, but there are lots of folks overloading the fasta comment line who won't have much interest in this. I would suggest a longer comment line limit, maybe 255 chars, to help keep this defined format flexible. - Don -- -- d.gilbert--biocomputing--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: sergio@mbi.ucla.edu Newsgroups: bionet.software Subject: Sybyl Line Notation Question Date: Thu, 05 Nov 1998 18:05:47 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 18 Message-ID: <71spdq$rg8$1@nnrp1.dejanews.com> NNTP-Posting-Host: 128.97.39.39 X-Article-Creation-Date: Thu Nov 05 18:05:47 1998 GMT X-Http-User-Agent: Mozilla/4.03 [en] (X11; I; IRIX 5.3 IP22) X-Http-Proxy: 1.0 x8.dejanews.com:80 (Squid/1.1.22) for client 128.97.39.39 I'm trying to decipher a couple of molecules in SLN but my translation software (ConSystant) doesn't understand them. Could somebody help me out? N~C(~S)~N ZCH=O{Z:C&!C:Any&!C=O&!C=C} I'm not sure what the "~" means and how to interpret C&!C, etc. Any assistance would be appreciated. Thanks! sergio. -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!lhc.nlm.nih.gov!not-for-mail From: Roland Walker Newsgroups: bionet.software Subject: SEALS version 0.824 Date: 5 Nov 1998 19:34:33 GMT Organization: National Center for Biotechnology Information Lines: 15 Message-ID: <71suk9$g2s$1@lhc.nlm.nih.gov> NNTP-Posting-Host: sky.nlm.nih.gov X-Trace: lhc.nlm.nih.gov 910294473 16476 130.14.25.194 (5 Nov 1998 19:34:33 GMT) X-Complaints-To: usenet@lhc.nlm.nih.gov NNTP-Posting-Date: 5 Nov 1998 19:34:33 GMT A new distribution of SEALS (A System for Easy Analysis of Lots of Sequences) is available at http://www.ncbi.nlm.nih.gov/Walker/SEALS This release (0.824) contains a number of bugfixes, tweaks, and efficiency improvements, as well as a modicum of new functionality. R -- Roland Walker walker@ncbi.nlm.nih.gov National Center for Biotechnology Information From owner-software@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!europa.clark.net!194.186.254.21!newsfeed.gamma.ru!Gamma.RU!demos!rosnet!news.glas.net!not-for-mail From: "Eugene Matveev" Newsgroups: bionet.software,bit.software.international,comp.software.international Subject: Where is Symantec JustWrite 2.0 text editor? Date: Thu, 5 Nov 1998 11:28:04 +0300 Organization: Private Lines: 17 Sender: ematveev@ppp1759.glasnet.ru Message-ID: <71u2u6$lfc$2@swan.glasnet.ru> NNTP-Posting-Host: ppp1759.glasnet.ru X-Trace: swan.glasnet.ru 910331654 21996 195.218.251.247 (6 Nov 1998 05:54:14 GMT) X-Complaints-To: usenet@news.glas.net NNTP-Posting-Date: 6 Nov 1998 05:54:14 GMT X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Hello! I'm very need in Symantec JustWrite 2.0 text editor (or another versions). Where I can download it? Best regards, Eugene Matveev Web: http://halyava.ru/matveev/ "Free Internet Resources" http://domains.da.ru/ "Internet Domain Name Services" E-mail: matveev@technologist.com ICQ: 7868097 Tel. +7 (87722) 2-52-31 Address: Eugene Matveev, P.O.Box 168, Maykop, 352700, Russia From owner-software@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!success600.com!success600 From: success600@success600.com Newsgroups: bionet.software Subject: Fire the Boss, Break the Alarm Clock Date: 5 Nov 1998 20:42:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <19981105232439.XAA26789@success600.com> NNTP-Posting-Host: net.bio.net KEEP $5,000 TO $16,000 OF YOUR OWN TAX DOLLARS! IT'S GUARANTEED BY FEDERAL LAW! CALL TOLL FREE 24 HRS 1-800-607-6006 box 2646 TO FIND OUT HOW… THEN…FIRE THE BOSS AND BREAK THE ALARM CLOCK! I DID! 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From owner-software@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!netnews.com!newsin.iconnet.net!world6.bellatlantic.net!world4.bellatlantic.net!news From: jaugust@bellatlantic.net (John Augustine) Newsgroups: bionet.software Subject: RE:LONG FILENAME ALTERNATIVE Date: Fri, 06 Nov 1998 15:03:45 GMT Organization: Bell Atlantic Internet Solutions Lines: 12 Message-ID: <36430b3d.2024205@news4.bellatlantic.net> NNTP-Posting-Host: client-151-197-124-2.bellatlantic.net X-Newsreader: Forte Free Agent 1.1/16.230 Someone, not long ago, was asking for an alternative to the "Long Filename" system (Windows 95/98), to have comments about files which can easily be edited. This person accumulated many files (.ZIP) downloaded from various FTP sites, and could not remember, by looking at the filenames in the directory, what many of the files are for. There is a program called "Directory Comments" for MS-Dos available at HOTFILES.COM (ZD Net) which allows you to easily add or change comments about your files. The comments are NOT stored in the directory or attached to the file/s, but in a separate log file (in ascii text). From owner-software@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!CADUS.COM!John.Ledwith From: John.Ledwith@CADUS.COM ("Ledwith, John") Newsgroups: bionet.software Subject: RE: FASTA format - No funny characters!! Date: 6 Nov 1998 07:32:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: <2D3428FD6CDFD111A72800104B2351B7242873@weebo.cadus.com> NNTP-Posting-Host: net.bio.net Thank you, François. But lets say I want to set $/ (the input record separator) to ">". (Baba) O'Reilly says that you can set it to a multi-character string, but "^>", "\n>", even "\s>", isnt cutting it (no pun intended). Sure, I can find all instances of /*>/ in a multi-FASTA file and replace the derelict > with some innocent characters (I may start making it IAN ;-)), but that seems like excess time. So, can someone let me know a good way to get around this? Or, as I asked before... Don't put random >'s in FASTA headers!!! Please. Thanks, john John Ledwith, Bioinformatics Cadus Pharmaceutical Corporation john.ledwith@cadus.com www.cadus.com Voicemail: 914-467-6200 x448 Lab: 914-467-6230 -----Original Message----- From: pingouin@crystal.u-strasbg.fr [SMTP:pingouin@crystal.u-strasbg.fr] Sent: Friday, November 06, 1998 9:22 AM To: bio-soft@net.bio.net Subject: Re: FASTA format - No funny characters!! In article <2D3428FD6CDFD111A72800104B2351B7242870@weebo.cadus.com>, John.Ledwith@CADUS.COM ("Ledwith, John") writes: > As long as we are talking about it... > > I cannot count how many times I have come across a FASTA header with a > ">" in the middle of it. Can we please not let this happen anymore? > PLEASE?!?!? Well, I think that this is used in e-mail adresses and sometimes in clone numbering, but, anyway, you just have to check ^> and not *> 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 Thu Nov 05 22:00:00 1998 Path: biosci!CADUS.COM!John.Ledwith From: John.Ledwith@CADUS.COM ("Ledwith, John") Newsgroups: bionet.software Subject: FASTA format - No funny characters!! Date: 6 Nov 1998 06:06:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <2D3428FD6CDFD111A72800104B2351B7242870@weebo.cadus.com> NNTP-Posting-Host: net.bio.net As long as we are talking about it... I cannot count how many times I have come across a FASTA header with a ">" in the middle of it. Can we please not let this happen anymore? PLEASE?!?!? Thank-you. john John Ledwith, Bioinformatics Cadus Pharmaceutical Corporation john.ledwith@cadus.com www.cadus.com Voicemail: 914-467-6200 x448 Lab: 914-467-6230 From owner-software@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newspeer.monmouth.com!oleane!jussieu.fr!univ-lille1.fr!ciril.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: FASTA format - No funny characters!! Date: 6 Nov 1998 14:21:35 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 16 Message-ID: <71v0lf$jvq@news.u-strasbg.fr> References: <2D3428FD6CDFD111A72800104B2351B7242870@weebo.cadus.com> 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 1.0b.0 Mail-Copies-To: never In article <2D3428FD6CDFD111A72800104B2351B7242870@weebo.cadus.com>, John.Ledwith@CADUS.COM ("Ledwith, John") writes: > As long as we are talking about it... > > I cannot count how many times I have come across a FASTA header with a > ">" in the middle of it. Can we please not let this happen anymore? > PLEASE?!?!? Well, I think that this is used in e-mail adresses and sometimes in clone numbering, but, anyway, you just have to check ^> and not *> 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 Thu Nov 05 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software Subject: Re: FASTA format - proposed max line limit Date: 06 Nov 1998 10:20:43 +0000 Organization: The Sanger Centre Lines: 91 Message-ID: References: <71qtgl$m8u@gap.cco.caltech.edu> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 910347556 27790 193.60.84.160 (6 Nov 1998 10:19:16 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 6 Nov 1998 10:19:16 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 mathog@seqaxp.bio.caltech.edu writes: > We all know that the FASTA format is a bit restrictive in that there is > only the one line for comments, but can the software/database community > *please* agree on some reasonable maximum line length for both the comments > and the sequence? I would welcome a standard "unique identifier" format after the ">". We use FASTA format extensively at the Sanger Centre, but we need to hold both an identifier and an accession number. In specific cases we also need a database name. Often there is other information used (typically numeric) to generate several unique forms from one original name. Curiously, one reason for the expansion of FASTA format is BLAST, as it takes as its database a file of many FASTA format sequences which need to have unique identifiers. One option to get extra identifier information is to use the NCBI style with "|" characters to split the fields. Sometimes this seems to have special information in the first word(s) of the description too, for example in dbEST.weekly.FASTA >gi|1622446|dbj|C21336|C21336 HUMGS0003372, Human Gene Signature, \ 3'-directed cDNA sequence (actually this is followed by "ctrl-A" and more description - see "other horrors" below) Another, since we have some FASTA files generated by GCG, is the GCG syntax of: >DB:entryname accnum yet...more...description We generate FASTA files from our unfinished sequence data where the unique name is built from the clone and contig, using "." as a delimiter, for example: >bK109G6.05061 Unfinished sequence: bK109G6 Contig_ID: 05061 \ acc=AL023879 Length: 25298 bp >bK109G6.05234 Unfinished sequence: bK109G6 Contig_ID: 05234 \ acc=AL023879 Length: 129756 bp I have seen various other styles of identifier to represent subsequences with a unique name, typically needed in protein domain databases, for example: >entryname-start-end (e.g. SBASE) >entryname/start-end (horrible for generating filenames) >entryname\start-end (the "/" still causes confusion with filenames) Other horrors: Using control characters to fake extra lines in the description, for example ctrl-a appears in NCBI's dbEST.weekly.FASTA files. UniGene's "seq.all" file has clusters of FASTA format sequences headed by comment lines starting with "#" BLAST1.4 pressdb fails if the sequence lines are not all the same length. An additional need is to have parseable information in the description which can be used to efficiently markup blast search results for a Web service. >The Fasta-1998 REFERENCE format is very similar to the SEQUENCE format. > >R1. The reference file will hold information that didn't fit > inside the Sequence file. > >R1.a The comment line for each entry in the reference file must > contain the ">" followed by the identifier, but no other information. A nice idea. I would certainly support this kind of format for EMBOSS. It is of course closely related to NBRF format, and its derivative GCG database format(s). File naming could be a problem - the right FASTA REFERENCE file has to be associated with a FASTA SEQUENCE file. A ".ref" extension would help, but the sequence file may itself have various (or no) file extensions. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-software@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!CADUS.COM!John.Ledwith From: John.Ledwith@CADUS.COM ("Ledwith, John") Newsgroups: bionet.software Subject: RE: [CORRECTION] Re: FASTA format - No funny characters!! Date: 6 Nov 1998 12:41:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 61 Sender: daemon@net.bio.net Distribution: world Message-ID: <2D3428FD6CDFD111A72800104B2351B7242885@weebo.cadus.com> NNTP-Posting-Host: net.bio.net Thank you, Roland! Just you writing it out made my code work. Really. Programming is such a funny exercise. :-) Have a good weekend, all. John John Ledwith, Bioinformatics Cadus Pharmaceutical Corporation john.ledwith@cadus.com www.cadus.com Voicemail: 914-467-6200 x448 Lab: 914-467-6230 -----Original Message----- From: Roland Walker [SMTP:walker@ncbi.nlm.nih.gov] Sent: Friday, November 06, 1998 12:00 PM To: bio-soft@net.bio.net Subject: [CORRECTION] Re: FASTA format - No funny characters!! [sorry, typing too fast] [John.Ledwith@CADUS.COM writes] > Thank you, Fran?ois. But lets say I want to set $/ (the input record > separator) to ">". (Baba) O'Reilly says that you can set it to a > multi-character string, but "^>", "\n>", even "\s>", isnt cutting it (no > pun intended). #!/bin/perl $/="\n>"; while (<>) { chomp; s/\A>?([^\n]*)\n//; tr/\n//d; my $defline=">$1"; my $sequence=$_; $defline =~ s/\A([^\cA]{1,80}).*/$1/; # Example: # limit defline to max 80 columns # or up to the first control-A # other transformations left as # an exercise to the reader print "$defline\n$sequence\n"; } -- Roland Walker walker@ncbi.nlm.nih.gov National Center for Biotechnology Information From owner-software@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!CADUS.COM!brian.osborne From: brian.osborne@CADUS.COM ("Osborne, Brian") Newsgroups: bionet.software Subject: RE: FASTA format - proposed max line limit Date: 6 Nov 1998 05:55:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 130 Sender: daemon@net.bio.net Distribution: world Message-ID: <2D3428FD6CDFD111A72800104B2351B72A7C51@weebo.cadus.com> NNTP-Posting-Host: net.bio.net To the group, My favorite horror (to use Peter's term) is this one (and its brothers and sisters in dbest) : >gb|AA406996|acc:AA406966 EST02002 Mouse 7.5 dpc embryo ectoplacental cone cDNA library Mus musculus cDNA clone C0016E04 3' similar to Mouse mitochondrial genome. >gb, score = 1720, mRNA sequence - Mus musculus, 404 bp (RNA) Enjoy! ;-) Brian O. Brian Osborne Cadus Pharmaceutical Corporation 777 Old Saw Mill River Rd. Tarrytown NY USA 10591-6705 brian.osborne@cadus.com TEL 914 467 6291 FAX 914 345 3565 > -----Original Message----- > From: Peter Rice [SMTP:pmr@sanger.ac.uk] > Sent: Friday, November 06, 1998 5:21 AM > To: bio-soft@net.bio.net > Subject: Re: FASTA format - proposed max line limit > > mathog@seqaxp.bio.caltech.edu writes: > > > We all know that the FASTA format is a bit restrictive in that there > is > > only the one line for comments, but can the software/database > community > > *please* agree on some reasonable maximum line length for both the > comments > > and the sequence? > > I would welcome a standard "unique identifier" format after the ">". > > We use FASTA format extensively at the Sanger Centre, but we need to > hold both an identifier and an accession number. In specific cases > we also need a database name. Often there is other information used > (typically numeric) to generate several unique forms from one > original name. > > Curiously, one reason for the expansion of FASTA format is BLAST, as > it takes as its database a file of many FASTA format sequences which > need to have unique identifiers. > > One option to get extra identifier information is to use the NCBI > style with "|" characters to split the fields. Sometimes this seems to > have special information in the first word(s) of the description too, > for example in dbEST.weekly.FASTA > > >gi|1622446|dbj|C21336|C21336 HUMGS0003372, Human Gene Signature, \ > 3'-directed cDNA sequence > > (actually this is followed by "ctrl-A" and more description - see > "other horrors" below) > > Another, since we have some FASTA files generated by GCG, is the GCG > syntax of: > > >DB:entryname accnum yet...more...description > > We generate FASTA files from our unfinished sequence data where the > unique name is built from the clone and contig, using "." as a > delimiter, for example: > > >bK109G6.05061 Unfinished sequence: bK109G6 Contig_ID: 05061 \ > acc=AL023879 Length: 25298 bp > >bK109G6.05234 Unfinished sequence: bK109G6 Contig_ID: 05234 \ > acc=AL023879 Length: 129756 bp > > I have seen various other styles of identifier to represent > subsequences with a unique name, typically needed in protein > domain databases, for example: > > >entryname-start-end (e.g. SBASE) > >entryname/start-end (horrible for generating filenames) > >entryname\start-end (the "/" still causes confusion with > filenames) > > Other horrors: > > Using control characters to fake extra lines in the description, > for example ctrl-a appears in NCBI's dbEST.weekly.FASTA files. > > UniGene's "seq.all" file has clusters of FASTA format sequences > headed by comment lines starting with "#" > > BLAST1.4 pressdb fails if the sequence lines are not all the same > length. > > An additional need is to have parseable information in the description > which can be used to efficiently markup blast search results for a Web > service. > > >The Fasta-1998 REFERENCE format is very similar to the SEQUENCE > format. > > > >R1. The reference file will hold information that didn't fit > > inside the Sequence file. > > > >R1.a The comment line for each entry in the reference file must > > contain the ">" followed by the identifier, but no other > information. > > A nice idea. I would certainly support this kind of format for EMBOSS. > > It is of course closely related to NBRF format, and its derivative > GCG database format(s). > > File naming could be a problem - the right FASTA REFERENCE file has to > be associated with a FASTA SEQUENCE file. A ".ref" extension would > help, > but the sequence file may itself have various (or no) file extensions. > > > -- > ---------------------------------------------------------------------- > Peter Rice | Informatics Division, The Sanger Centre, > E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, > Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England > Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-software@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.news.gtei.net!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.gtei.net!lhc.nlm.nih.gov!not-for-mail From: Roland Walker Newsgroups: bionet.software Subject: [CORRECTION] Re: FASTA format - No funny characters!! Date: 6 Nov 1998 17:00:29 GMT Organization: National Center for Biotechnology Information Lines: 34 Distribution: world Message-ID: <71v9vd$s15$2@lhc.nlm.nih.gov> References: <2D3428FD6CDFD111A72800104B2351B7242873@weebo.cadus.com> <71v9ll$s15$1@lhc.nlm.nih.gov> NNTP-Posting-Host: sky.nlm.nih.gov X-Trace: lhc.nlm.nih.gov 910371629 28709 130.14.25.194 (6 Nov 1998 17:00:29 GMT) X-Complaints-To: usenet@lhc.nlm.nih.gov NNTP-Posting-Date: 6 Nov 1998 17:00:29 GMT [sorry, typing too fast] [John.Ledwith@CADUS.COM writes] > Thank you, Fran?ois. But lets say I want to set $/ (the input record > separator) to ">". (Baba) O'Reilly says that you can set it to a > multi-character string, but "^>", "\n>", even "\s>", isnt cutting it (no > pun intended). #!/bin/perl $/="\n>"; while (<>) { chomp; s/\A>?([^\n]*)\n//; tr/\n//d; my $defline=">$1"; my $sequence=$_; $defline =~ s/\A([^\cA]{1,80}).*/$1/; # Example: # limit defline to max 80 columns # or up to the first control-A # other transformations left as # an exercise to the reader print "$defline\n$sequence\n"; } -- Roland Walker walker@ncbi.nlm.nih.gov National Center for Biotechnology Information From owner-software@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-in-east1.sprintlink.net!news.sprintlink.net!news-feed1.tiac.net!cam-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.gtei.net!lhc.nlm.nih.gov!not-for-mail From: Roland Walker Newsgroups: bionet.software Subject: Re: FASTA format - No funny characters!! Date: 6 Nov 1998 16:55:17 GMT Organization: National Center for Biotechnology Information Lines: 32 Distribution: world Message-ID: <71v9ll$s15$1@lhc.nlm.nih.gov> References: <2D3428FD6CDFD111A72800104B2351B7242873@weebo.cadus.com> NNTP-Posting-Host: sky.nlm.nih.gov X-Trace: lhc.nlm.nih.gov 910371317 28709 130.14.25.194 (6 Nov 1998 16:55:17 GMT) X-Complaints-To: usenet@lhc.nlm.nih.gov NNTP-Posting-Date: 6 Nov 1998 16:55:17 GMT [John.Ledwith@CADUS.COM writes] > Thank you, Fran?ois. But lets say I want to set $/ (the input record > separator) to ">". (Baba) O'Reilly says that you can set it to a > multi-character string, but "^>", "\n>", even "\s>", isnt cutting it (no > pun intended). #!/bin/perl $/="\n>"; while (<>) { chomp; s/\A>?([^\n]*)\n/>/; tr/\n//d; my $defline=">$1"; my $sequence=$_; $defline =~ s/\A([^\cA]{1,80})/$1/; # Example: # limit defline to max 80 columns # or up to the first control-A # other transformations left as # an exercise to the reader print "$defline\n$sequence\n"; } -- Roland Walker walker@ncbi.nlm.nih.gov National Center for Biotechnology Information From owner-software@net.bio.net Fri Nov 06 22:00:00 1998 Path: biosci!ihnp4.ucsd.edu!newsfeed.berkeley.edu!news-stock.gip.net!news.gsl.net!gip.net!news.indosat.net.id!not-for-mail From: "Palm Pilot Store" Newsgroups: bionet.software Subject: <<>> Date: Sun, 8 Nov 1998 12:34:32 +0700 Organization: INDOSATnet Lines: 11 Message-ID: <7226s2$1gd9@indo-news> NNTP-Posting-Host: ppp26-jkt3.indosat.net.id X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 While you are busy or on the street you can save all of your ideas and plans with the New Palm Pilot starting for only $240 at http://www.investindo.com/palm.html. Lucius http://www.investindo.com/ Smallbiz Investor Solutions From owner-software@net.bio.net Fri Nov 06 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.cwix.com!169.207.30.81!newsfeeds.sol.net!newsops.execpc.com!posts.execpc.com!gotham-globe.newsops.execpc.com!usenet From: Alan Friedman Newsgroups: bionet.software Subject: Re: gel analysis freeware Date: Thu, 05 Nov 1998 21:22:22 +0000 Organization: ExecPC Internet - Milwaukee, WI Lines: 8 Message-ID: <71v49s$756@newsops.execpc.com> References: <36419590.4735E509@imiucca.csi.unimi.it> NNTP-Posting-Host: jaresh-14.mdm.mkt.execpc.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: gotham-globe.newsops.execpc.com 910365820 7334 (None) 169.207.81.142 X-Complaints-To: abuse@execpc.com X-Mailer: Mozilla 3.01 (Macintosh; U; PPC) I use GelReader 2.0 for the Macintosh. This software was developed at the National Center for Supercomuter Applications by Tom Redmon. Two versions are available; one for Macs with a FPU and one with out. One bug I have found is that you must set you monitor control panel to 256 colors. You can download the software and supporting documents from http://www.edvz.univie.ac.at/systems/mac/MacSciTech/biology/NCSA_GelReader/. Good luck, Alan Friedman From owner-software@net.bio.net Fri Nov 06 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.inet.tele.dk!not-for-mail From: Bo Bergmann <120010312330@post5.tele.dk> Newsgroups: bionet.software Subject: HPLC-WIZARD beta 1.0 Date: Sat, 07 Nov 1998 19:47:23 +0100 Organization: DTU Lines: 45 Message-ID: <364495BB.2F83@post5.tele.dk> NNTP-Posting-Host: ip28.boanxr7.ras.tele.dk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news-inn.inet.tele.dk 910464216 158514 (None) 195.249.164.28 (07-11-98 18:43:36 GMT) X-Mailer: Mozilla 2.02E [da]-TDK20 (Win95; I) Finally, the beta version 1.0 of HPLC-WIZARD is ready for evaluation. Get to our home page at http://home5.inet.tele.dk/daller/index.htm to download the beta version. HPLC-WIZARD is a Microsoft® Windows 95/98/NT application designed for fast and easy calculation of amino acid distributions from HPLC - chromatograms. In contrast to the existing method of numerical integration, which suffers from systematical errors due to inaccurate partion of overlapping peaks and improper treatment of the background function, HPLC-WIZARD calculates an amino acid distribution by modelling the HPLC- chromatograms by using different density functions to model the peaks and a background function based on Principal Component Analysis to model the background. In the evaluation of appropiate candidate functions to model the peaks in the HPLC - chromatograms, it was found necessary to develop tools to estimate how good a candidate function was able to model the chromatograms in a visual as well as statistical aspect. As these tools are made available to the user means that, apart from calculation of amino acid distributions from HPLC-chromatograms, HPLC - WIZARD offers the following other important features: 1. The functionality of a MDI-application (Multiple Document Interface). Which makes simultanous examination of several HPLC-chromatograms possible. 2. An user friendly environment making it easy to navigate around in the HPLC - chromatograms. This implies zoom, scroll, clip and stretch functions and the ability to draw chromatograms in numerous ways. 3. A function gallery, in which the user can select among several density functions to find the best function to model the peaks in a specific chromatogram. 4. Access to view and edit any parameter in the system. This implies e.g. editing or restraining individual peak and backgrund function parameters. 5. Graphical insertion, modification and minimization of peak functions, making it possible to model peaks with underlying structures or huge overlaps. 6. Implementation of joint refinement to handle response overflow. 7. Three different quantification methods. This involves a fully automatic weighted averaging of the compounds in up to 10 chromatograms. 8. Well-arranged presentation of results on screen as well as printer. From owner-software@net.bio.net Sat Nov 07 22:00:00 1998 Message-ID: <3644FD16.1C3418B1@compusmart.ab.ca> Date: Sat, 07 Nov 1998 19:08:22 -0700 From: Andrew Gardner X-Mailer: Mozilla 4.06 [en] (Win95; U) MIME-Version: 1.0 Newsgroups: bionet.software Subject: BLAST 2 info needed Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 207.34.71.169 X-Trace: 7 Nov 1998 19:06:53 -0700, 207.34.71.169 Lines: 13 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!nntp.cadvision.com!news.agtac.net!ntnews.compusmart.ab.ca!207.34.71.169 I am working on a BLAST client program. I am able to run BLAST 1 searches over the web at NCBI by sending requests to the URL recommended in the documentation at ftp://ncbi.nlm.nih.gov/blast/blasturl/ I would also like to be able to do gapped BLAST searches, but have not been able to find equivalent documentation. Does anyone know of documentation for writing a basic BLAST 2 web client or if NCBI provides a stable URL for doing BLAST 2 searches similar to the one suggested for BLAST 1 searches (ie. other than the main forms which, as I understand it, could change location or format at any time)? Thanks for your time, Andrew From owner-software@net.bio.net Sat Nov 07 22:00:00 1998 Message-ID: <36459134.DBB12247@mail.med.cornell.edu> Date: Sun, 08 Nov 1998 07:40:20 -0500 From: "M. Johan Broekman, PhD" X-Mailer: Mozilla 4.05 [en] (WinNT; U) MIME-Version: 1.0 Subject: Re: RefMan8 and Windows NT References: <199811042125.NAA123616@uvaix7e1.comp.UVic.CA> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Newsgroups: bionet.software Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!oleane!isdnet!arl-news-svc-4.compuserve.com!news-master.compuserve.com!nntp-ntdwwaaw.compuserve.com Lines: 20 I'm running RefMan 8.5 under NT 4.0 SP 3 as well as under W95. No problems other than the obtuse Cite-Wile-U-Rite ones with Winword 97. Do update to 8.5! Johan de Boer wrote: > Hi, > I am trying to run Reference Manager version 8.01 under Windows NT. The > program will open, but when I try to open a database file, the program will > hang. This does not happen under Win95. Has anyone had this same > experience? Is there a solution to this problem? > > Thanks, > Johan de Boer > Centre for Environmental Health > University of Victoria ____________________________________ M. Johan Broekman email mjbroek@mail.med.cornell.edu From owner-software@net.bio.net Sat Nov 07 22:00:00 1998 Path: biosci!AOL.COM!Cutegirl21 From: Cutegirl21@AOL.COM Newsgroups: bionet.software Subject: WANT A NEW CELL PHONE? YOU'RE APPROVED! Date: 8 Nov 1998 05:33:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 42 Sender: daemon@net.bio.net Distribution: world Message-ID: <94cd0fb0.36459b49@aol.com> NNTP-Posting-Host: net.bio.net This is a multi-part message in MIME format. --part0_910531402_boundary Content-ID: <0_910531402@inet_out.mail.aol.com.1> Content-type: text/plain; charset=US-ASCII --part0_910531402_boundary Content-ID: <0_910531402@inet_out.mail.aol.com.2> Content-type: message/rfc822 Content-transfer-encoding: 7bit Content-disposition: inline From: Cutegirl21@aol.com Return-path: To: Cutegirl21@aol.com Subject: cellad Date: Sun, 8 Nov 1998 00:04:43 EST Mime-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit WANT A NEW CELL PHONE? YOU'RE APPROVED! NO CREDIT CHECK NO CONTRACTS NO MONTHLY FEES YOU CONTROL YOUR COSTS! Finally a cell phone plan that makes sense for everyone. You decide how many minutes, what accessories to include, everything is completely up to you! Plus with our NATIONWIDE service your cell phone can be used anywhere. This is the easiest and cheapest cell phone plan on the market today. INTERESTED? PLEASE CLICK BELOW FOR COMPLETE DETAILS. CLICK HERE NOW --part0_910531402_boundary-- From owner-software@net.bio.net Sat Nov 07 22:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!btnet-peer!btnet!news-lond.gip.net!news.gsl.net!gip.net!news-fra.maz.net!newscore.ipf.de!newsreader.ipf.de!not-for-mail From: "Heiko" Newsgroups: bionet.software Subject: S: Haus- und Grundriss-Software Date: Sun, 8 Nov 1998 13:58:27 +0100 Organization: NEWS.IPF.NET - Your Gate to the World Lines: 15 Message-ID: <7244ml$28f$1@news.ipf.net> NNTP-Posting-Host: ip174.hannover.okay.net X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 S: Haus- und Grundriss-Software Suche Software mit der man Häusergrundrisse Zeichnen und bemaßen kann. bzw. sich sein Traumhaus auf dem Computer erstellen und ansehen kann. Evtl. auch einrichten kann. Bitte alles was meinen Vorstellungen entsprechen könnte anbieten, aber bloß keine 1000,-DM Software - Ist für mich nur für meinen Privaten gebrauch. Bye Heiko hottenrott@okay.net From owner-software@net.bio.net Sun Nov 08 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!uio.no!nntp.uio.no!not-for-mail From: David Martin Newsgroups: no.embnet,bionet.software Subject: GENALYSER updated to version 0.3.2 Date: Mon, 09 Nov 1998 13:55:33 +0000 Organization: The Norwegian EMBNet Node Lines: 16 Message-ID: <3646F455.A8662370@biotek.uio.no> NNTP-Posting-Host: biotek44.uio.no Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.06 [en] (X11; I; Linux 2.0.32 i586) GENALYSER is a user driven analysis workbench for visualisation of genomic DNA sequences. It is designed to allow the user to make predictions of potential gene transcripts. GENALYSER can be found at http://biotek38.uio.no/Genalyser/ GENALYSER version 0.3.2 is now available. New features include the construction of virtual transcripts from your genomic sequence and submission of the derived peptide to GeneQuiz. The tutorial will be updated shortly to cover the new features. In the meantime just play around and see what it does. Comments and suggestions to David Martin at david.martin@biotek.uio.no GENALYSER is a work in progress, so check back every so often to see what has changed. From owner-software@net.bio.net Sun Nov 08 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!europa.clark.net!208.134.241.18!newsfeed.cwix.com!129.174.1.8!portal.gmu.edu!osf1.gmu.edu!lviteri From: Luis R Viteri Newsgroups: bionet.software Subject: Weaknesses of Microsoft. Date: Mon, 9 Nov 1998 09:01:45 -0500 Organization: George Mason University, Fairfax, Virginia, USA Lines: 5 Message-ID: NNTP-Posting-Host: osf1.gmu.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Who can list 5 weaknesses of Microsoft? --LRV-- From owner-software@net.bio.net Sun Nov 08 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!su-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.gtei.net!news.iquest.net!not-for-mail From: demetrio@iquest.net Newsgroups: bionet.software Subject: updated web page, BIOTECH PRODUCTS Date: Mon, 09 Nov 1998 04:57:08 GMT Organization: IQuest Internet, Inc. Lines: 24 Message-ID: <36467609.128088821@news.iquest.net> NNTP-Posting-Host: iq-ind-as004-214.iquest.net X-Newsreader: Forte Free Agent 1.11/32.235 I just updated the main web page for a client, BIOTECH PRODUCTS. http://members.iquest.net/~bioproducts/ Please consider them for your lab equipment needs. 1. You can sign up for their mailing list to receive announcements. 2. They added a NEWS page for up-to-the-minute announcements which they now update on their own (without having to go through their webmaster.) 3. They are recommending the book PLANAR LIPID BILAYERS by Wolfgang Hanke and W.R. Schule. (They are a distributor/manufacturer's rep for Microstar DAP boards, DasyLab data acquisition software, Hameg oscilloscopes and test equipment, Warner elctrophysiological instrumentation and recording, Sycopel microdialysis biosensors and potentiostats, Skalar blood-flow meters and eye-trackers, Mini-Mitter animal monitoring, Fabreeka isolation tables and platforms, Torrey Pines Scientific incubators and chillers, and Strathkelvin oxygen meters.) If you're looking for a digital oscilloscope, check out the Hameg line, they have hot stuff at good prices. From owner-software@net.bio.net Sun Nov 08 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!dispose.news.demon.net!demon!diablo.dera.gov.uk!server2.netnews.ja.net!news.reading.ac.uk!suma3!saspeyer From: "Oliver S. DePeyer" Newsgroups: bionet.software Subject: Protease maps? Date: Mon, 9 Nov 1998 19:04:00 +0000 Organization: University of Reading Message-ID: NNTP-Posting-Host: suma3.reading.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Lines: 32 I need to map a polypeptide sequence for protease cleavage sites, in particular Calpain I & II. What program should I be using, and where can I find it? (E.g NCBI, Sanger etc.?) Please send your suggestions to saspeyer@reading.ac.uk MAny thanks in advance, Oliver de Peyer saspeyer@reading.ac.uk http://www.rdg.ac.uk/Wolfson Tel. U.K (0)118 9875123 extn 7889 Fax " " 9316671 Pager " (0)4325 225196 Wolfson Lab (Professor Crabbe's group) Lab 136 School of Animal & Microbial Sciences (WING) University of Reading Whiteknights PO Box 228 Reading Berkshire RG6 6AJ United Kingdom From owner-software@net.bio.net Mon Nov 09 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!news1.best.com!news3.best.com!nntp1.ba.best.com!not-for-mail From: "Genome Jobs" Newsgroups: bionet.software Subject: Bioinformatics JOBS at www.genomejobs.com Date: Tue, 10 Nov 1998 01:52:52 -0800 X-Newsreader: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Lines: 21 Message-ID: <36480cd6$0$12767@nntp1.ba.best.com> NNTP-Posting-Host: dynamic0.pm04.sf3d.best.com X-Trace: nntp1.ba.best.com 910691542 12767 209.24.234.192 Bioinformatics JOBS at www.genomejobs.com Genome Jobs is the central resource for employment in Genomics, Bioinformatics, Biotechnology and Biocomputing. We have listings of great career opportunities in Industry and Academia to save you time and help sharpen your focus. Free to Job Seekers www.genomejobs.com If you are looking for jobs in: bioinformatics, genomics, biotechnology, computers, databases, DNAChips, Microarrays, proteomics, scientists, research associates, database administrators, database architects, database engineers, software engineer, analyst programmer, scientific programmer, software developer, molecular biologist, microbiologist, cheminformatics, pharmatics, biostatistics, SAS programmer, Nanotechnology, LIMS, clinical informatics, and more. Questions? genomik@genomejobs.com From owner-software@net.bio.net Mon Nov 09 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!interpath.net!news-relay.ncren.net!news.wfu.edu!news From: jmihic@wfubmc.nospam.edu (John Mihic) Newsgroups: bionet.software Subject: Re: Weaknesses of Microsoft. Date: 10 Nov 1998 15:16:56 GMT Organization: Wake Forest University Lines: 31 Message-ID: <729ld8$trg@f1n1.spenet.wfu.edu> References: NNTP-Posting-Host: 152.11.129.114 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) In article , lviteri@osf1.gmu.edu says... > >Who can list 5 weaknesses of Microsoft? > I only have time for one at the moment, but it's a biggie. The guy running the company is a dweeb, and judging from what I've heard about his attempts to crush competition in the computer industry, a pushy dweeb to boot! :-) Seriously, I think their products, and those of most other software companies, are now bloated beyond belief. I used to run Wordstar on a 64K apple, and it did the job just fine. Now you have 20 Mb packages that do essentially the same thing (plus they have annoying paper clips, happy faces and Albert Einsteins popping up to give unwanted advice and eat RAM and disk space). Garbage code expands to fill empty disk space and RAM. I've been using NT 4.0 with sp 4.0 for a while now and must say that I'm pretty disappointed at how it seems to lose track of Mb of memory that applications free up when they close. To keep things moving at a respectable pace, I usually re-boot at least twice a day. That's not something I'd expect from a state-of-the-art operating system made by the biggest software manufacturer in the world. No wonder they're worried about Linux! John From owner-software@net.bio.net Mon Nov 09 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!surfnet.nl!ruu.nl!not-for-mail From: Marco Hoeksma Newsgroups: bionet.software Subject: Re: Weaknesses of Microsoft. Date: Tue, 10 Nov 1998 09:29:00 +0100 Organization: Utrecht University Lines: 27 Message-ID: <3647F94C.C1E1135F@pharm.uu.nl> References: Reply-To: m.r.hoeksma@pharm.uu.nl NNTP-Posting-Host: psycpc39.far.ruu.nl 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 1). Their constant 'infiltration' in all kinds of areas (msnbc, webtv etc). 2). Their buggy code, and the lack of openness thereof. 3). Their aggressive commercialism (http://www.opensource.org/halloween1.html for example). 4). Their focus on 'fun' and not on 'work' (i.e., they produce things like 'active desktop', and never seem to realize that this is a stupid idea in the first place). 5). Their incapability of humouring the consumer, which also produces 'microsoft bashing' when this is not correct. 6). Their development of new 'standards' only to develop a state in which the consumer has no alternative but to use microsoft (again: http://www.opensource.org/halloween1.html) This is just from a user point of view. There must be more....... Luis R Viteri wrote: > > Who can list 5 weaknesses of Microsoft? > > --LRV-- From owner-software@net.bio.net Tue Nov 10 22:00:00 1998 Path: biosci!rutgers!news-relay.ncren.net!news.wfu.edu!news From: jmihic@wfubmc.nospam.edu (John Mihic) Newsgroups: bionet.software Subject: Re: Weaknesses of Microsoft. Date: 11 Nov 1998 14:01:06 GMT Organization: Wake Forest University Lines: 44 Message-ID: <72c5b2$159q@f1n1.spenet.wfu.edu> References: <3647F94C.C1E1135F@pharm.uu.nl> <3648F07D.4DA70F50@cc.umanitoba.ca> NNTP-Posting-Host: 152.11.129.114 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) In article <3648F07D.4DA70F50@cc.umanitoba.ca>, frist@cc.umanitoba.ca says... >Now I have a question. Is there anybody >out there actually doing real science >on the NT platform -- and loving it? >Maybe NT has some hidden charms that >have been lost on me. > Hi Brian, Very interesting post. I think that when it's all said and done, the major factor in whether a particular program or operating system works for you is whether or not it can do what you want done, without too much screwing around. For example, in my lab we do a fair bit of mutagenesis and then farm out confirmatory sequencing. The first time I got one of those sequencing files back, I realized it was going to be a MAJOR pain to look at these by hand, so I wrote a QuickBasic (version 4 to boot!) program that takes in sequencing files, translates them and then spits out amino acid & nucleotide sequence files that my sequence alignment software can read. Sure I'm still using a prehistoric language to write code, but I'm doing so because it works, and it's not worth my time to try and figure out Visual Basic or C++ [I'll bet my Chairman thinks it's a better use of my time to write grants :-) ]. This program is running on NT and I can't imagine it running any faster on any other operating system. So to answer your question, you can do science on NT (although my type of mol. bio. work is not nearly the most sophisticated). NT may not be the most efficient operating system, and for comparison my Unix experience is limited, but I am somehow blundering along. So, looking forward to winter in Manitoba? I grew up in Toronto, and don't miss the snow and ice storms one bit! Cheers! John -- John Mihic, Ph.D. Department of Physiology & Pharmacology Wake Forest University School of Medicine Winston-Salem, NC 27157-1083 From owner-software@net.bio.net Tue Nov 10 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: bigcat007@my-dejanews.com Newsgroups: bionet.software Subject: Recompiling Rasmol w/Borland C++ Date: Wed, 11 Nov 1998 06:07:32 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 15 Message-ID: <72b9j4$uom$1@nnrp1.dejanews.com> NNTP-Posting-Host: 209.184.113.10 X-Article-Creation-Date: Wed Nov 11 06:07:32 1998 GMT X-Http-User-Agent: Mozilla/3.03Gold (Win95; U) X-Http-Proxy: 1.0 x3.dejanews.com:80 (Squid/1.1.22) for client 209.184.113.10 Does anyone have experience recompiling Rasmol for Windows using Borland C++ Builder? I know Visual C++ is recommended, but I don't have access to it. As it stands I am getting a ton of warning and error messages dealing with syntax differences between the 2 compilers, but I don't how to correct them. I would really like to get this straightened out so I can work on getting high resolution hardcopy. I welcome any suggestions. Thanks. -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Tue Nov 10 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!diablo.theplanet.net!join.news.pipex.net!pipex!tcp.co.uk!not-for-mail From: crosley@tcp.co.uk Newsgroups: bionet.software Subject: Netscape Navigator update problem Date: Wed, 11 Nov 98 06:31:24 PDT Organization: Total Connectivity Providers - Maximizing the Internet Lines: 16 Message-ID: NNTP-Posting-Host: en1-145.du.tcp.co.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: zeus.tcp.net.uk 910766291 26232 195.80.3.145 (11 Nov 1998 06:38:11 GMT) X-Complaints-To: abuse@tcp.net.uk NNTP-Posting-Date: 11 Nov 1998 06:38:11 GMT X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage 911/Nov/98 Can anyone help with the following browser problem? I uninstalled Netscape Navigator with Cleen Sweep, first saving bookmarks by putting 'Users' on the desk top as instructed. I downloaded and installed version 4.07 but cannot reinstall the 'Users' folder. The programs appear to be in a 'Username' folder in a 'Users' folder in the desktop folder and not in a 'Netscape' folder. How do I reinstall my bookmarks? Netscape's web site is too complex to find tyhis sort of help. Thanks in anticipation, John Shaw  From owner-software@net.bio.net Tue Nov 10 22:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!192.220.250.21!netnews1.nw.verio.net!netnews.nwnet.net!news.u.washington.edu!dante03.u.washington.edu!barent From: Barent Hoffman Newsgroups: comp.os.ms-windows.apps.word-proc,bionet.software,comp.software.testing,comp.software.config-mgmt,comp.windows.misc,comp.windows.x.apps Subject: Making Word Templates Date: Tue, 10 Nov 1998 16:15:59 -0800 Organization: University of Washington Lines: 20 Message-ID: NNTP-Posting-Host: dante03.u.washington.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: nntp6.u.washington.edu 910743362 42508 (None) 140.142.17.40 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: barent I want to make a template such that certain words and lines cannot be edited, but the rest of the template can be altered. Is there a way to "lock" certain parts of a document while leaving the rest of the template open for editing? (I know how to lock an entire template EXCEPT for certain text boxes. However, this is not the effect I want.) Thanks for any insight. -Barent Hoffman ,,,, /'^'\ ( o o ) -oOOO--(_)--OOOo-------------------------------------------------- .oooO Barent Hoffman, Seattle, WA ( ) Oooo. barent@u.washington.edu ---\ (----( )--------------------------------------------------- \_) ) / (_/ From owner-software@net.bio.net Tue Nov 10 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: "Malay" Newsgroups: bionet.software Subject: Disclosing of disk information by Windows98 Date: 11 Nov 1998 07:38:31 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 24 Message-ID: <72betn$f95$1@mserv2.dl.ac.uk> Reply-To: "Malay" NNTP-Posting-Host: mserv2.dl.ac.uk Mime-Version: 1.0 Original-To: "Bio_soft" content-length: 499 Return-Path: X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-Priority: 3 Hi everybody: Recently I came to know about a possible dirty trick by Microsoft. As soon as you login to Internet while using Windows 98, Microsoft comes to know about your hard disk informations, including the softwares you installed. Can anybody clarify whether this is true or not? Malay Malay Kumar Basu Centre for Cellular and Molecular Biology Hyderabad 500007 I N D I A Fax: (00-91)40-7171195 Phone: (00-91)40-7172241 ----- Heads I win, tails you lose. ----- curiouser@ccmb.ap.nic.in From owner-software@net.bio.net Tue Nov 10 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!xmission!nntp.csuchico.edu!cscnews.csc.calpoly.edu!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Re: BLAST 2 info needed Date: 11 Nov 1998 16:08:36 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 434 Message-ID: <72ccq4$k9k@gap.cco.caltech.edu> References: <3644FD16.1C3418B1@compusmart.ab.ca> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article <3644FD16.1C3418B1@compusmart.ab.ca>, Andrew Gardner writes: >I am working on a BLAST client program. I am able to run BLAST 1 >searches over the web at NCBI by sending requests to the URL recommended >in the documentation at ftp://ncbi.nlm.nih.gov/blast/blasturl/ > After my signature you'll find such a beast. It's written in DCL, so unless you're on a VMS system, it won't do you much good directly, but you should be able to read it to see how it works. Basically the trick for writing command line (that is what you're doing, right?) clients for web servers is to save the submission page from your browser, and edit the client so that it can set all fields, then use a program like rep_client (which was in the demo on the NCBI site) to stuff the request into the server and wait for the response. How you handle waiting around for the request is OS specific though. I vaguely recall that some of the NCBI servers will send you back a file in text mode, and others insist on HTML, unless you tell it to email, then you can get text. (They may have changed this in the 10 months since I wrote the client.) The client below leaves a text mode result file on disk. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech ************************************************************************** $! SAF_BLAST.COM $! $! 7-JAN-1998, David Mathog, Biology Division, Caltech $! $! Command procedure to access the BLAST server via the web interface. $! $! See below for the symbols it looks for and command line format. $! $! subroutine to list program options $! $ listprogram: subroutine $ type sys$Input Select the program to run, your options are: Program Query against-> Database ------------------------------------------------ blastn Nuc Nuc blastp Pep Pep tblastn Pep Nuc->Pep (6 frames) tblastx Nuc->Pep (6 frames) Nuc->Pep (6 frames) blastx Nuc->Pep (6 frames) Pep $ exit $ endsubroutine $! $! subroutine to list datalib options $! $ listdatalib: subroutine $ type sys$Input Select the datalib to search, your options are: nr nonredundant (Pep or Nuc) month all entries < 30 days old (Pep or Nuc) swissprot Swiss Protein (Pep) dbest nonredundant EST sequences (Nuc) dbsts nonredundant STS sequences (Nuc) pdb Sequences from 3D structure files (Pep) vector Vectors (Nuc) kabat Sequences of immunological intereset (Pep) mito Mitochondrial (Nuc) alu Some ALU sequences from REPBASE (Nuc) epd Eukaryotic Promoter Databse (Nuc) yeast S.cerevisiae genome (Nuc, or coding sequences, Pep) gss Genome survey sequences (Nuc) htgs High throughput genomic sequences (Nuc) E.coli E. coli genome (Nuc, or coding sequences, Pep) $ exit $ endsubroutine $! $! subroutine to list command line options, and symbols $! $ listcommand: subroutine $ type sys$Input Usage: @saf_blast P1 P2 P3 Where: P1 name of query sequence file, such as "sequence.gcg" P2 (Optional) Comma separated list for fields to prompt for if they are not supplied by symbols (see below.) Example: "EXPECT,CUTOFF" would prompt for the EXPECT and CUTOFF values to use with the search. "OUTFILE" would prompt for an output file name. P3 (Optional) "Start,End" - limit the query to this region of the sequence. Must be enclosed in double quotes. Examples: "1000,2000" from 1000 to 2000 inclusive "1000," from 1000 to the end ",2000" from 1 to 2000 "," the whole sequence If you want to specify P3 and not P2 (or P1), you must use this syntax: blast "" "" P3 If blast_FIELD symbols are defined they will override defaults. The symbols this procedure looks for are: blast_INFILE The GCG formatted query sequence (input file) blast_OUTFILE Name for BLAST output file blast_PROGRAM blastn, blastp, tblastn, tblastx, blastx blast_DATALIB nr, month, swissprot, dbest, dbsts, pdb, vector, kabat, mito, alu,epd, yeast, gss, htgs, E.coli blast_EXPECT default, or any floating point number blast_CUTOFF default or any number >=0 blast_MATRIX default, BLOSUM62, PAM40, PAM120, PAM250, IDENTITY blast_STRAND both, top, bottom blast_FILTER default, none, dust, SEG, SEG+XNU, XNU blast_HISTOGRAM if set, a histogram is drawn, default is none blast_NCBI_GI if set, show NCBI gi numbers in output, default is not to blast_DESCRIPTIONS default or any number >=0 blast_ALIGNMENTS default or any number >= 0 blast_ADVANCED other BLAST command line options blast_EMAIL send response via email to address it holds blast_HTML send response in HTML format $ exit $ endsubroutine $! $! define symbols for program used $! $ hereis = f$environment("PROCEDURE") $ hereis = f$element(0,"]",hereis) + "]" $ rep_client = "''hereis'rep_client" $ FIELDS ="INFILE,OUTFILE,PROGRAM,DATALIB,EXPECT,MATRIX,STRAND,FILTER,HISTOGRAM,NCBI_GI,DESCRIPTIONS,ALIGNMENTS,ADVANCED,EMAIL,PATH" $! path is a bit different, called EMAIL externally $ PATH="" $! $! $ promptfor = "''P2'" $ promptfor = f$edit(promptfor,"COLLAPSE,UPCASE") $! $! INFILE $! $ askfor = "INFILE" $ default = "''P1'" $ blab = "" $ gosub doprompt $ if ("''INFILE'" .eqs. "") $ then $ call LISTCOMMAND $ exit $ endif $! $ if (P3 .nes. "") $ then $ startfrom = f$element(0,",",P3) $ startfrom = f$EDIT(startfrom,"COLLAPSE") $ endat = f$element(1,",",P3) $ endat = f$EDIT(endat,"COLLAPSE") $ if(startfrom .eq. ",")then goto badp3 $ if(startfrom .eqs. "") $ then $ section = "" $ else $ section = "/begin=''startfrom'" $ endif $ if(endat .eq. ",")then goto badp3 $ if(endat .nes. "") $ then $ section = section + "/end=''endat'" $ endif $ endif $ goto notbadp3 $! $ badp3: $ write sys$output "The range you specified [''P3'] is invalid" $ Type sys$input Use one of these forms: "1000,2000" from 1000 to 2000 inclusive "1000," from 1000 to the end ",2000" from 1 to 2000 "," the whole sequence The double quotes on each side are MANDATORY If you want to specify P3 and not P2 (or P1), you must use this syntax: blast "" "" P3 $ exit $! $notbadP3: $! $ time = f$time() $ killstring = f$cvtime(time,,"hour") + - f$cvtime(time,,"minute") + - f$cvtime(time,,"second") + - f$cvtime(time,,"hundredth") $ killfile = "KILL_" + killstring + ".seq" $ comfile = "KILL_" + killstring + ".com" $ mypid = f$getjpi("","PID") $ back= f$extract(4,4,mypid) $ subname = "K" + back + killstring $! $ tofasta/infile='infile'/out='killfile' 'section'/default $! $! PROGRAM $! $ checkstring="blastn blastp blastx tblastx tblastn" $ if (f$type(BLAST_PROGRAM) .eqs. "")then promptfor = promptfor + ",PROGRAM" $ topprogram: $ askfor = "PROGRAM" $ default = "blastn" $ blab = "LISTPROGRAM" $ gosub doprompt $ PROGRAM = f$EDIT(PROGRAM,"COLLAPSE,LOWERCASE") $ if(f$length(checkstring) .eq. f$locate(PROGRAM,checkstring)) $ then $ write sys$Output "''PROGRAM' is not a valid option for PROGRAM" $ goto topprogram $ endif $! $! OUTFILE $! $! $! come up with a name for the output file, if one is not supplied $! $ askfor = "OUTFILE" $ default = infile $! strip off any nasty characters which might be in it now $! looks for [] or logical: and removes them $! $ tdefault = f$element(1,"]",default) $ if (tdefault .eqs. "]")then tdefault = default $ default = tdefault $ tdefault = f$element(1,":",default) $ if (tdefault .eqs. ":")then tdefault = default $ default = tdefault + "." $ default = f$element(0,".",default) $ default = default + ".''PROGRAM'" $ write sys$output "output will be ''default'" $ gosub doprompt $! $! DATALIB $! $ checkstring="nr month swissprot dbest dbsts pdb vector kabat mito alu epd yeast gss htgs e.coli" $ topDATALIB: $ askfor = "DATALIB" $ default = "nr" $ blab = "listdatalib" $ gosub doprompt $ DATALIB = f$EDIT(DATALIB,"COLLAPSE,LOWERCASE") $ if(f$length(checkstring) .eq. f$locate(DATALIB,checkstring)) $ then $ write sys$Output "''DATALIB' is not a valid option for DATALIB" $ goto topDATALIB $ endif $! $! this next may or may not be necessary, BLAST documentation is unclear $! $ if(DATALIB .eqs. "e.coli")then DATALIB = "E.coli" $! $! EXPECT $! $ askfor = "EXPECT" $ default = "default" $ blab = "" $ gosub doprompt $! $! CUTOFF $! $ askfor = "CUTOFF" $ default = "default" $ gosub doprompt $! $! MATRIX $! $ askfor = "MATRIX" $ default = "default" $ gosub doprompt $! $! STRAND $! $ askfor = "STRAND" $ default = "both" $ gosub doprompt $! $! FILTER $! $ askfor = "FILTER" $ default = "default" $ gosub doprompt $! $! HISTOGRAM $! $ askfor = "HISTOGRAM" $ default = "" $ gosub doprompt $! $! NCBI_GI $! $ askfor = "NCBI_GI" $ default = "" $ gosub doprompt $! $! HTML $! $ askfor = "HTML" $ default = "" $ gosub doprompt $! $! DESCRIPTIONS $! $ askfor = "DESCRIPTIONS" $ default = "100" $ gosub doprompt $! $! ALIGNMENTS $! $ askfor = "ALIGNMENTS" $ default = "100" $ gosub doprompt $! $! ADVANCED $! $ askfor = "ADVANCED" $ default = "" $ gosub doprompt $! $! EMAIL/PATH $! $ askfor = "EMAIL" $ default = "" $ gosub doprompt $ if(EMAIL .nes. "") $ then $ PATH = EMAIL $ EMAIL = "IS_SET" $ endif $! $! now assemble the command file to send $! $! $! create a stream-lf file because the sequence will also be stream lf, $! and otherwise append generates warnings. STREAMLF must be a system $! wide symbol that maps to something like: $! create/fdl=shrdisk:[shared.misc]streamlf.fdl $! $ streamlf 'comfile' $ open/append ofil: 'comfile' $! $ write ofil: "www.ncbi.nlm.nih.gov" $ write ofil: "POST /cgi-bin/BLAST/nph-blast_report HTTP/1.0X" $! write ofil: "WWW_BLAST_TYPE unfin_gen" $! $! skip INFILE,OUTFILE, those don't go to NCBI $! $ count = 2 $ allfields: $ string = f$element(count,",",fields) $ if(string .nes. ",") $ then $ value = 'string' $ value = "''value'" $ if(value .nes. "")then write ofil: "''STRING' ''VALUE'" $ count = count + 1 $ goto allfields $ endif $ write ofil: "BEGIN" $ close ofil: $ append 'killfile' 'comfile' $ delete 'killfile'; $! $! run it in a subprocess so that we can keep track of it $! $! type 'comfile' $ create 'outfile' $ spawn/nowait/input='comfile'/output='outfile'/process='subname' - run 'rep_client' $! $! find the darn subprocess! $! $ context = "" $ findsub: $ apid = f$pid(context) $ if(apid .eqs. "") $ then $ write sys$Output "Fatal error, connection to NCBI died" $ exit $ endif $ procname = f$getjpi(apid,"PRCNAM") $ if(procname .nes. subname)then goto findsub $! $! apid is its ID, procname is its process name $! $ write sys$output "Now processing job, subprocess is ''APID'" $ $ waiting: $ procname = "" $ define/user/nolog sys$error nla0: $ define/user/nolog sys$output nla0: $ procname = f$getjpi(apid,"PRCNAM") $ deass/user sys$error $ deass/user sys$output $ if (procname .eqs. "")then goto done $ time=f$time() $ write sys$output "still waiting at ''time'" $ wait 00:00:20.00 $ goto waiting $! $ done: $ fime=f$time() $ write sys$output "BLAST job completed at ''time', results in ''OUTFILE'" $ delete 'comfile'; $ exit $! $! prompt routine. Set response to default value, then override that $! with symbol's value (if it exists), and lastly, override that with $! a prompt, if it was asked for on the command line $! $ doprompt: $ 'ASKFOR' = default $ if (f$type(BLAST_'ASKFOR') .nes. "")then 'ASKFOR' = blast_'ASKFOR' $! $ if(f$locate(askfor,promptfor) .eq. f$length(promptfor))then return $ if("''blab'" .nes. "")then call 'blab' $ READ/PROMPT="Enter a value for ''ASKFOR': " sys$command response $ 'askfor' = response $ return From owner-software@net.bio.net Tue Nov 10 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!cyclone.bc.net!rover.ucs.ualberta.ca!news.ucalgary.ca!news From: "SideshowBob" Newsgroups: bionet.software Subject: Re: Netscape Navigator update problem Date: Wed, 11 Nov 1998 07:38:06 -0700 Organization: The University of Calgary Lines: 21 Message-ID: <72c7fu$kfi@ds2.acs.ucalgary.ca> References: NNTP-Posting-Host: kyhui@ts7-port-48.acs