From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!enews.sgi.com!decwrl!waikato!auckland.ac.nz!news From: d.ormrod@auckland.ac.nz (Douglas Ormrod) Newsgroups: bionet.software Subject: Re: Sigma-Plot version 2 for Windows Date: 1 Feb 1995 23:01:24 GMT Organization: University of Auckland Lines: 38 Message-ID: <3gp3s4$ee6@net.auckland.ac.nz> References: <3gl9pe$rop@io.salford.ac.uk> NNTP-Posting-Host: 130.216.57.35 X-Newsreader: WinVN 0.92.5 In article <3gl9pe$rop@io.salford.ac.uk>, R.Lauder@lancaster.ac.uk (Bob Lauder) says: > > Have any Sigma-Plot users upgraded from version 1 for Windows to version >2 for Windows? > > I'm using V1 at the moment and have been sent loads of glossy ads >suggesting that I upgrade. however, as far as I can see the major >changes are in contour plotting which I don't need. > > Is this the case? Is there any other reasons to upgrade? > >Thanks > >Bob. > Although I haven't bought it, in my opinion, SigmaPlot Win V2 is a rip off. Version 1.0 was a disaster and so full of bugs they issued 1.02 free. Then, about three months later they offered V2. As far as I can see this is just a relabelled V1.02 with a few minor enhancements. I objected to the upgrade cost so soon after buying V1, usually if a software company brings out a new version within six months of you buying the last version, you get it for the price of the disks. I received a sympathetic reply from the local distributors who passed on my comments to JANDEl, who have never responded. I bought PRISM instead. *********************************** Douglas Ormrod Department of Medicine University of Auckland, New Zealand d.ormrod@auckland.ac.nz Phone (64 9) 3797440 x7647 *********************************** From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsfeed.pitt.edu!dsinc!ub!galileo.cc.rochester.edu!uhura.cc.rochester.edu!ttha From: ttha@uhura.cc.rochester.edu (Tom Thatcher) Subject: Re: quicklink Message-ID: <1995Feb2.004938.9891@galileo.cc.rochester.edu> Sender: news@galileo.cc.rochester.edu Nntp-Posting-Host: uhura.cc.rochester.edu Organization: University of Rochester - Rochester, New York References: <3gonr8$a34@news.bu.edu> Date: Thu, 2 Feb 95 00:49:38 GMT Lines: 13 In <3gonr8$a34@news.bu.edu> wroman@bu.edu (William Roman) writes: >I just installed Quicklink II comm. software and it doesn't work. Exactly right. QuickLink II is terrible. And if you are running system 7, it may corrupt your Finder file. Get Zterm. -- Tom Thatcher | You can give a PC to a Homo habilis, University of Rochester Cancer Center | and he'll use it, but he'll use it ttha@uhura.cc.rochester.edu | to crack nuts. From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!rutgers!netnews.upenn.edu!dsinc!newsfeed.pitt.edu!gatech!howland.reston.ans.net!news.sprintlink.net!uunet!newsfeed.ACO.net!news.iif.hu!news From: szia@enzim.hu (Andras Szilagyi) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Programs for schematic drawings of proteins? Date: 1 Feb 1995 16:57:59 GMT Organization: somewhere Lines: 21 Message-ID: <3goein$e5i@helka.iif.hu> NNTP-Posting-Host: kalori.enzim.hu Mime-Version: 1.0 X-Newsreader: WinVN 0.93.11 Xref: biosci bionet.molbio.proteins:3638 bionet.software:10911 I am looking for programs that can draw schematic drawings of protein structures. I am interested in the following two types of drawings: (1) schematic representation of the [main chain] hydrogen bonding pattern (based on known 3D structure) (2) schematic representation of the domain structure and disulfide bonding pattern, using a chain of several circles, each circle representing a residue, and the type of the residue written in the circle. This chain of circles is folded in 2D to approximately represent the domain structure and the disulfide bonding pattern. Such drawings often appear in journals but I don't know any program that can easily draw such things. (As to the hydrogen bonding pattern, I heard of a program called HERA but I have no idea how to get it.) Anyone can help? Andras Szilagyi (szia@enzim.hu) Institute of Enzymology, Hungarian Academy of Sciences From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!cmb.bcm.tmc.edu!solovyev From: solovyev@cmb.bcm.tmc.edu (Victor V. Solovyev) Newsgroups: bionet.software Subject: ALL BCM GeneFinder programs can be run by WWW Mosaic Date: 2 Feb 1995 09:21:48 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502021721.LAA03102@falcon.cellb.bcm.tmc.edu> NNTP-Posting-Host: net.bio.net BCM Gene-Finder Program FGENEH, FEXH, HEXON, HSPL can be run now through WWW Mosaic: =============================== Use WWW BCM Human Genome Center and Search launcher Home page URL:http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html for accsess to Gene-Finder and Secondary structure prediction Help files and programs. BCM Gene Finder BCM protein secondary structure prediction BCM Gene-finder and secondary structure prediction programs are available also by sending the file containing a sequence (the sequence format is described in Help files) to The University of Houston Gene server: service@bchs.uh.edu or Weizmann Institute of Science server: services@bioinformatics.weizmann.ac.il with the subject line "program_name". Examples: mail -s fgeneh service@bchs.uh.edu < test.seq mail -s fgeneh services@bioinformatics.weizmann.ac.il < test.seq You can obtain help files by sending the subject line man such as Subject: man hexon to service@bchs.uh.edu The Baylor College Of Medicine Computational Biology Group Houston, TX The services are FGENEH - search for gene structure with exons assembling by dynamic programming FEXH - search for 5'-, internal and 3'-exons HEXON - search for internal exons HSPL - search for splice sites SSP - prediction of a-helix and b-strand in globular proteins by segment-oriented approach. NSSP - prediction of a-helix and b-strand segments in globular proteins by nearest-neighbor algorithm. Problems, comments, and suggestions: Can be mailed to solovyev@cmb.bcm.tmc.edu. From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!post.its.mcw.edu!usenet From: Simon Twigger Newsgroups: bionet.software Subject: Mol-Biol sofware for PC/windows Date: 2 Feb 1995 16:49:43 GMT Organization: Medical Coll. of Wisconsin Lines: 20 Distribution: world Message-ID: <3gr2f7$l9u@post.its.mcw.edu> NNTP-Posting-Host: d350-1.biochem.mcw.edu X-Newsreader: Hi there, I have recently moved labs, and from a Mac environment to a PC/windows based one. We currently have no molecular biology sofware on our computer here though we do have access to the GCG package. Can anyone out there recommend any decent DNA/protein packages (along the lines of DNA Strider/Mac Molly etc for the Mac) that I can FTP/buy from somewhere? I am also very interested in people's opinions of the DNA Star package for Windows. I will post a summary of any responses I receive as this seems to be a FAQ on this newsgroup! Many thanks for you help, Simon Twigger. Medical College Of Wisconsin, Milwaukee. From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!nntp.crl.com!crl.crl.com!not-for-mail From: sunger@crl.com (Stefan Unger) Newsgroups: bionet.software Subject: Re: Neural networks in metabolism modeling? Date: 2 Feb 1995 08:39:14 -0800 Organization: CRL Dialup Internet Access (415) 705-6060 [Login: guest] Lines: 21 Distribution: world Message-ID: <3gr1ri$6ur@crl.crl.com> References: <950202091238.1bb23@CUCCFA.CCC.COLUMBIA.EDU> NNTP-Posting-Host: crl.com X-Newsreader: TIN [version 1.2 PL2] There is MetabolExpert which is an "expert system," not a neural network. I am a dealer. Reply if you would like details. BioSoftware Marketing T. Mark Reboul (MARK@CUCCFA.CCC.COLUMBIA.EDU) wrote: : Dear Bionet readers, : [Apologies if this is a duplicate posting for some of you. I have : not seen my earlier attempted posting to bionet.software appear.] : Is anyone aware of work in metabolic process modeling based on : neural network simulation? It seems like a reasonable technique to : consider in modeling metabolism, but so far I don't find citations : pointing to such work. Thanks for any details/suggestions/comments. : Mark Reboul mark@cuccfa.ccc.columbia.edu : Columbia-Presbyterian Cancer Center : Computing Facility, P&S 1-420 : 630 West 168th Street : New York, NY 10032 212-305-7360 From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msunews!harbinger.cc.monash.edu.au!budapest.ozonline.com.au!harrybh.ozonline.com.au!user From: bioware@ozonline.com.au (Harry J. Banaharis) Newsgroups: bionet.software Subject: Soft Gene GMBH Date: Thu, 02 Feb 1995 12:40:07 +1000 Organization: Bioware Lines: 8 Message-ID: NNTP-Posting-Host: harrybh.ozonline.com.au Does anyone have the number to this company, they are the distributors of MacMolly s/w. Thanks -- Harry J. Banaharis bioware@ozonline.com.au From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!CUCCFA.CCC.COLUMBIA.EDU!MARK From: MARK@CUCCFA.CCC.COLUMBIA.EDU (T. Mark Reboul) Newsgroups: bionet.software Subject: Neural networks in metabolism modeling? Date: 2 Feb 1995 06:19:22 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <950202091238.1bb23@CUCCFA.CCC.COLUMBIA.EDU> NNTP-Posting-Host: net.bio.net Dear Bionet readers, [Apologies if this is a duplicate posting for some of you. I have not seen my earlier attempted posting to bionet.software appear.] Is anyone aware of work in metabolic process modeling based on neural network simulation? It seems like a reasonable technique to consider in modeling metabolism, but so far I don't find citations pointing to such work. Thanks for any details/suggestions/comments. Mark Reboul mark@cuccfa.ccc.columbia.edu Columbia-Presbyterian Cancer Center Computing Facility, P&S 1-420 630 West 168th Street New York, NY 10032 212-305-7360 From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: Lots-o-money Date: 2 Feb 1995 13:26:00 GMT Organization: University of Cambridge, England Lines: 18 Distribution: bionet Message-ID: <3gqmh8$3ar@lyra.csx.cam.ac.uk> References: <3gq9dl$qo3@mserv1.dl.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk writes: >> >>I suggest we all E-mail the post back to the sender. I did. Hopefully, >>the Ohio State system adm. will deal with it. >> >I did also. Four times. If everybody here acts the same, we should get some >reaction ... Don't do it. I've been in touch with the guy. Someone got hold of his password, and he's getting pissed off with hundreds of mail messages a day getting at him for something he didn't do. He has since changed his password. Tim. From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!quagga.ru.ac.za!nntp.und.ac.za!pc099.cc.unp.ac.za!Berry From: Berry@biochem.unp.ac.za (Ronald.Berry) Newsgroups: bionet.software Subject: Strip-chart Recorder alternative? Date: Thu, 2 Feb 1995 12:03:57 GMT Organization: University of Natal , Pietermaritzburg, South Africa Lines: 36 Message-ID: NNTP-Posting-Host: pc099.cc.unp.ac.za Hello Bionetters I am hunting for an alternative to the faithfull old strip-chart recorder. I have bought a very nice Pharmacia GradiFrac system, but the Pharmacia 2- channel strip-chart recorder was an obscene price, and I couldn't afford it. Looking around, I see that recorders in general are a horrible price. It turns out that the most unsophisticated (doesn't even have an event marker!), single channel recorder costs much more than a full-house 486 PC. It therefore ocurred to me that there *MUST* be a decent analogue-to-digital card with accompanying software that turns your PC into a strip-cart recorder. I am obviously not looking in the right places, because all I can see is National Instruments products (like LabView) which seem like massive overkill, and are far too sophisticated. Does anyone have any ideas? Unfortunately, I am mostly confined to a PC platform, but I do have an ancient Mac Plus (512k) lying around. Thanks. Ron Berry Chief Tecnician University of Natal Pietermaritzburg South Africa Ron Berry Biochemistry Department, University of Natal, Pietermaritzburg. South Africa From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!news From: ewan birney Subject: *Release* PairWise and SearchWise 1.0 (long) Message-ID: Sender: news@ebi.ac.uk (Mr news) Organization: European Bioinformatics Institute Date: Wed, 1 Feb 1995 23:39:43 GMT Lines: 388 PairWise and SearchWise 1.0 *************************** SearchWise and PairWise are part of a new sequence analysis package for comparisons of protein sequences or protein profiles against DNA sequences which is ROBUST towards errors in the DNA sequence, in particular frame shifting errors. There are two main programs in this package. A one-to-one alignment program called PairWise and a database searching program called SearchWise. This information can be read on the WWW at the URL http://www.molbiol.ox.ac.uk/www/users/birney/wise/description.html Algorithm The core of both programs is a simple extension of the dynamic matrix routines used in sequence analysis in which a protein profile is compared to all three frames of a DNA sequence simultaneously allowing for frame shifting errors. The reverse frames are done in a similar manner. A protein profile can be trivially derived from a protein sequence and a comparison matrix, and both programs allow on-the-fly loading of a single protein sequence for the query. Although the algorithm is effectively the equivalent of a six frame translation of the DNA sequence, there is neither explicit translation nor complementation of the sequence, making it a very efficient method. There are some subtle differences in the coding of the dynamic matrix which departs from more "standard" smith+waterman coding. Email me for more info. For completeness, standard profile to protein sequence/database routines have also been included in the programs. Uses The fact that these programs are robust towards frame shifting errors make them ideal for many different aspects of sequence analysis. o Comparing a determined protein sequence or better still, a protein profile against a DNA database and aligning those sequences without worrying about errors in the DNA database. I had originally envisaged the main benefit of this being in searches against EST databases, but trials have shown that there are a depressing number of sequencing errors in the coding sequences of full cDNA sequences too. This program allows confident searching of DNA databases. o Comparing protein sequence or protein profile against DNA sequences (or a DNA database) allowing the sequence to put arbitary length gaps into the aligned DNA. This allows a comparison to "jump" introns, and therefore one can search a database containing genomic DNA without knowing any exon/intron boundaries, and still reasonably expect an alignment spread across three or four exons to be returned in the high scores. Note that this is an entirely different strategy from trying to predict exon/intron boundaries. o Comparing a recently determined DNA sequence against a protein database, and not having to be confident in the precise DNA sequence (especially frame shifting errors). By using programs such as PairWise and SearchWise one might hope that people will realise their sequencing errors by noticing homologies which require a frame shift in their sequenced DNA. Generally we have found it very useful to be able to use "dirty" DNA sequence data (either in the databases or as sequences) without having to be always concerned about frame shifts. Some examples of PairWise output are given at the end of this message. Programs PairWise is a one-on-one alignment program, like GCG's BESTFIT or GAP. SearchWise is the database comparison program, like FASTA or PROFILESEARCH. PairWise has a number of features which makes it easy to use: o A menu driven user interface (for simple linefeed terminals) o PairWise can be linked (at compile time) to GCG8, so that sequences can be pulled straight out of GCG8 databases if needed. PairWise can also run as a stand-alone program. o There are up to five different parameters to be set for each alignment, and the numbers are very different from usual alignment programs. PairWise has a variety of 'rule-of-thumb' default parameters for different sequence comparisons to make it easier to find the best parameters. o PairWise also includes standard protein seq<->protein seq or protein profile<->protein seq routines. o Quite nice outputs. SearchWise is run entirely from the command line, but there is a menu-driven program (Opensearch) to submit searchwise batch jobs in VMS or nice nohup background processes for UNIX machines. o SearchWise can use the following database formats: GCG-binary GCG-ascii Fasta (Pearson) format EMBL .dat formats These formats can be mixed and matched to any extent, as long as the database remains either all protein or all dna. Opensearch is the menu-driven program which comes included in the package to submit searchwise jobs. Bad Features. Technically the difficulties are mainly finding the correct parameters for a particular alignment, which especially for new users are hard to get used to. Currently the on-the-fly alignments in SearchWise are at best FRAGILE. They shouldn't be used at the moment. SearchWise is CPU-hungry and the full comparison of a 100 residue profile vs the full EMBL database on a small but unused DEC Alpha takes about a day and a half. As most people (blindly) just chuck in their favourite 450aa protein against the EMBL database it usually clogs the machines up. I am looking at fine-grain and coarse-grain parallelisation methods at the moment. For most sites it is probably only feasible to run the embl EST and protein databases on SearchWise. SearchWise should be used as a final stage of a search strategy which would start off by using faster methods such as BLAST, BLITZ or FASTA. The full benefit of using SearchWise is only seen when good protein profiles are produced. In terms of the algorithm, it is probably better to use a full hidden markov model for the protein to DNA sequence comparison as then exon/intron boundary information could be incorporated. Compiling and Platform specifics. PairWise and SearchWise has been compiled on the following platforms. o DECAlpha running OpenVMS o DECAlpha running OSF/1 o SGI running IRIX 5.2 o Sun4 running solaris2.3 Executables (unliked to GCG8) are provided for these platforms. There are no MS-windows/Mac versions currently made. The package can found by anonymous ftp at sable.ox.ac.uk in the directory /pub/users/ba97001/wise/ Look at the file README... It is probably better to look first at the WWW site at http://www.molbiol.ox.ac.uk/www/users/birney/wise/topwise.html Thanks SearchWise and PairWise have benefitted hugely from the beta-testing by other people over the last couple of months. The mechanics of getting easy to use, platform independant code are horrendous, and I certainly cannot claim that these programs are in a finished state. However I do think that they are useful for a broad range of applications. In particular I would like that thank Kay Hoffmann at ISREC in Switzerland and Toby Gibson at EMBL for the massive amount of help (and patience) they both provided over the beta testing period. This project was started at Cold Spring Harbor (under Adrian Krainer), went to EMBL (under Toby Gibson) where most of the coding took place. Julie Thompson at EMBL wrote many of the UNIX specific and config routines. At Oxford Liz Cowe has been principle in getting my programs to behave well with GCG8, and Jasper Rees has been my most picky beta tester as well as giving me time and space on the Oxford computers. Publications Currently two publications feature SearchWise results. Gibson, T. J., Hyvoenen, M., Birney E., Musacchio, A. and Saraste, M. (1994) PH domain: the first anniversary. Trends Biochem. Sci., 19, 349-353. Aasland, R., Gibson, T. J. and Stewart, A. F. (1995) The PHD-finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem. Sci., February issue. Any others would be gratefully recieved ewan birney birney@molbiol.ox.ac.uk --------------------------------------------------------------------------- *Error in cDNA example* PairWise 1.0 Output. Written by Ewan Birney (birney@molbiol.ox.ac.uk). Profile file: rrmcut.p62p Sequence file em:mm14648 Sat Jan 28 09:37:39 1995 Gap 2200, Gap extension 200 Frame penalty 1870, Frame extension 1320, Stop codon 500 Alignment of Profile rrmcut.p62p vs Sequence mm14648 in file From GCG database Score 33572 Aligned Ranges: 1-99 (profile) 214-464 (sequence) Showing forward strand * * ** * ** * * * rrmcut.p62 1 KLFVGNLgnPPDTTEEELRELFSQFGEIESVKvmrdesqvrddhlnrqap Translate SLKVDNL..TYRTSPDTLRRVFEKYGRVGDVYIPRD.............P EmRod:mm14 214 tcaggac atcatcgacacgtgatgcggggtaccg c ctataat cagcccactggttaaaggtgatatcga c ccggccg ccccgcccggcccgacgccccgctggc g * ** * ** * * * * ** *** * rrmcut.p62 51 ktgksrGF^^FVTFESEEDAEKAIEALNGKVIGGRVLRVKAAQKkeerqk Translate YTKESRIF^^FVRFHDKPHAEDAMDAMDGAVLDGRELRVQLARYGRPPDS EmRod:mm14 319 taagtcatGCtgctcgaccggggaggaggggcggcgccgccgctgcccgt acaacgtt ttgtaaacacaactactagcttaggatgtatcgaggccac ccggcgcc ccgcccggccaccgccgcgggccccgggggggccccgccg ---------------------------------------------------------------------------- * Genomic Example * PairWise 1.0 Output. Written by Ewan Birney (birney@molbiol.ox.ac.uk). Profile file: hnrnp.prf Sequence file hnrnpa1.gen Wed Feb 1 23:33:15 1995 Gap 2400, Gap extension 400 Frame penalty 1800, Frame extension 0, Stop codon 500 Alignment of Profile hnrnp.prf vs Sequence X12671 in file hnrnpa1.gen Score 128374 Aligned Ranges: 1-179 (profile) 1383-2455 (sequence) Showing forward strand ************* * *** * ****** * ** hnrnp.prf 1 TEPEQLRKLFIGGLDFRTTDDGLKAHFEQWGNIVDVVV^+++++++++++ Translate KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV^----------- X12671 1383 agcgccaactaggtatgaaggacaactgctgacagtggAGATTTGGAAGG aacaatgatttggtgtaccaagtggataaggctcagtt agcaggggcctaggctaattgcggcttgagagcgctga hnrnp.prf 39 ++++++++++++++++++++++++++++++++++++++++++++++++++ Translate -------------------------------------------------- X12671 1509 GACAAAGCAGTAAAACAGCCGATTTCCTTGGCTTATCTTGGTGCAGTCTT hnrnp.prf 39 ++++++++++++++++++++++++++++++++++++++++++++++++++ Translate -------------------------------------------------- X12671 1559 CTCCGAATGCTTATGAAAGTAGTTAATAGCATTATAGTTAGAGCTTTGTT hnrnp.prf 39 ++++++++++++++++++++++++++++++++++++++++++++++++++ Translate -------------------------------------------------- X12671 1609 GGCAAAGGAACGTCCTGCTTTGATTTTAAAAGCTAACCTCTTAAATCTAA hnrnp.prf 39 ++++++++++++++++++++++++++++++++++++++++++++++++++ Translate -------------------------------------------------- X12671 1659 GGGTAGTGGGAAACTGGACGAACTTTTTATAAAAGGCTGGTGTAAAGTTT hnrnp.prf 39 ++++++++++++++++++++++++++++++++++++++++++++++++++ Translate -------------------------------------------------- X12671 1709 CCTATTGCCCTATTCAAAGTTAAAATAACAAAAGCTTTTGCGGTCAGACT ** ********* hnrnp.prf 39 ++++++++++++++++++++++++++++++++++++KDPKTKRSRGFGFI Translate ------------------------------------RDPNTKRSRGFGFV X12671 1759 TTGTGTTACATAAATTAACACTGTTCTCAGGTAATGagcaaactagtgtg gacacagcggtgtt ataccgctgctgtc ** ** * ****** *** ******* hnrnp.prf 53 TYSQSYMVDNAQNARPHKIDGRTVEPKRAV^+++++++++++++++++++ Translate TYATVEEVDAAMNARPHKVDGRVVEPKRAV^------------------- X12671 1837 atgagggggggaagaccagggagggcaaggTCCAGAGAAGTGAGTGGGTT cacctaatacctacgcaataggttacagct atctggggtatgtagacggtaatgaagatc hnrnp.prf 83 ++++++++++++++++++++++++++++++++++++++++++++++++++ Translate -------------------------------------------------- X12671 1947 TTTTTTCTTCTTCTTCTTAAACTTACTTGGATATGTGCTGCTATGAACTT hnrnp.prf 83 ++++++++++++++++++++++++++++++++++++++++++++++++++ Translate -------------------------------------------------- X12671 1997 AAGATTCGGGAGTTTTCTAAACTTACCAAAATTTTTTATTCGAGTATAGG * * **** **** * * * hnrnp.prf 83 +++++++++++++++++++RQEI....DSPEAGATVKKLFVGGLKDDHDE Translate -------------------WFFSY*DSQRPGAHLTVKKIFVGGIKEDTEE X12671 2047 CTTTGCTAATCTAAACCTAttttttgtcacggctagaaatgggaaggagg gttcaaacagcgcatctaatttggtaaacaa gtcctgttaaatccatgagatttctaactaa ** ** * * * ** ** ********* *** * **** hnrnp.prf 110 ECLREYFKQFGQIVSVEIVTDKDTGKKRGFAFVEFDDYDPVDKI^+++++ Translate HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI^----- X12671 2159 cccagttgctgaaggagaaagcgagaaagtgtgatggcgtggaaGTCAGT aatgaataaagatattattcaggggaaggtcttctaaaactaat tcaatttagtaatagtacgtcactcgagctctactcctccgtgt * hnrnp.prf 154 +++++++++++++++++++L^^++++++++++++++++++++++++++++ Translate -------------------L^^---------------------------- X12671 2297 AAGTATCAGATAGTGGCATtGTAAGGGTTCCACAATCTGTATGGCATTCT t a * * hnrnp.prf 155 ++++++++++++++++++++++++++++++++++++++++++++KTHSIK Translate --------------------------------------------KYHTVN X12671 2349 AAACCCTGATACCATGTTGTATCTATGTTTTTTTTTTAGTTCAGatcaga aaacta acttgt * * * ** ** * hnrnp.prf 161 GKNVDVKKAIAKQDM Translate GHNCEVRKALSKQEM X12671 2411 gcatggaagctacga gaagatgactcaaat ccctataacgagagg From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!news.doit.wisc.edu!news From: dalehn@facstaff.wisc.edu (Donald A. Lehn, Ph.D.) Newsgroups: bionet.software Subject: Re: Windows interface for blast server? Date: Thu, 02 Feb 95 09:06:55 EST Organization: University of Wisconsin Medical School Lines: 25 Message-ID: <3gqsqm$78b@news.doit.wisc.edu> References: <3gni11$h9h@blackice.winternet.com> NNTP-Posting-Host: islet.medsch.wisc.edu X-Newsreader: WinVN 0.93.9 In article <3gni11$h9h@blackice.winternet.com>, franz@winternet.com says... > >I'm looking for a Windows 3.1 based program to provide an Internet >connection for searhes on the NCBI blast server. Searches have turned >up references to "win-blas.exe", but it is no longer available at the >site (Heidelberg). Seqpup looks promising, but is apparently not yet >completed. > >Please reply with any help or E-mail to franz@winternet.com > >Thanks!! You can just use Mosaic or Netscape since the blast server is avaliable via the WEB at: http://ncbi.nlm.nih.gov -- Donald A. Lehn, Ph.D. Phone: (608) 263-7668 Medical Sciences Center / 3415 Fax: (608) 262-9300 University of Wisconsin Medical School Email: dalehn@facstaff.wisc.edu 1300 University Avenue Home: (608) 277-1025 Madison, WI 53706-1532 Spider: Diabetes Knowledgebase WEB - http://islet.medsch.wisc.edu From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!caen!usenet.coe.montana.edu!gemini.oscs.montana.edu!oususaab From: oususaab@gemini.oscs.montana.edu (Aaron Benner) Newsgroups: bionet.software Subject: a *metabolism* oriented simulation Date: 2 Feb 1995 03:31:57 GMT Organization: Montana State University Lines: 16 Message-ID: <3gpjnd$cfv@pdq.coe.montana.edu> NNTP-Posting-Host: gemini.oscs.montana.edu I have been lurking here for a while now in hopes of finding a simulation engine that someone has produced that was oriented towards metabolism in eukaryotes. I have gotten lots of suggestions none of which have been particularly helpful in this specific area. I would like, ideally, to find a differential based computational model but anything that addresses metabolism would be very helpful. Thanks -- |---------| oususaab@gemini.oscs.montana.edu -- Aaron Benner |-------------| "I like the fact that you treat me like a person not a doorprize, I like the fact that you are a romantic, even if you're hopeless" - Tina (the mask) "Yea, Right. Just not in real life." - Me From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: Newsgroups: bionet.software Subject: Re: Lots-o-money Date: 2 Feb 1995 09:42:13 -0000 Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3gq9dl$qo3@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk > >I suggest we all E-mail the post back to the sender. I did. Hopefully, >the Ohio State system adm. will deal with it. > I did also. Four times. If everybody here acts the same, we should get some reaction ... Jean-Loup From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!hubcap.clemson.edu!biosci!bcm!cs.utexas.edu!swrinde!howland.reston.ans.net!pipex!uknet!bcc.ac.uk!jones From: jones@bsm.bioc.ucl.ac.uk (David Jones) Subject: Re: 3D-proteine structure according to available DNA-sequence Message-ID: <1995Jan30.224140.67006@ucl.ac.uk> Date: Mon, 30 Jan 1995 22:41:40 GMT References: <1995Jan26.200503.27941@alw.nih.gov> Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Lines: 29 Andrej Sali (sali@tamika.rockefeller.edu) wrote: : This is much too pesimistic. About one third of all currently known : sequences are related to at least one currently known structure. About one : half of these sequences are related at about 30% sequence identity or : more. When sequence identity is about 40% or more, you can get a model by : comparative modeling that is essentially equivalent to a medium resolution I fully agree with Andrej's comments here, but I would like to point out another less optimistic estimate of the fraction of sequences related to known structures. The estimate that a third of currently known sequences are related to known structures is quite true, but it should be realised that the majority of these relationships are from a small number of large (and rather over-represented) families. For example, of the 40000 or so sequences in the current SWISSPROT, 665 of these sequences are globins. A somewhat more conservative estimate of the probability of finding a related 3-D structure for your particular protein may be obtained by calculating the fraction of currently known protein _families_ for which a related 3-D structure exists (i.e. the 665 globins above would be treated as a single family). The result of this calculation is that only 1 in 25 (4%) of currently known families have related structures in the structure database. >---------------------------------------------------------------------------< This message was written, produced and executively directed by Dr David Jones Email: jones@bsm.bioc.ucl.ac.uk | JANET: jones@uk.ac.ucl.bioc.bsm Address: Dept. of Biochemistry | Tel: +44 71 387 7050 x3879 and Molecular Biology, University | Fax: +44 71 380 7193 College, London WC1E 6BT, U.K. | Disclaimer: STANDARD > KEYWORDS : OPINIONS MY OWN NOBODY ELSE'S WHATSOEVER From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!hubcap.clemson.edu!biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!caen!hearst.acc.Virginia.EDU!murdoch!dayhoff.med.Virginia.EDU!wrp From: wrp@dayhoff.med.Virginia.EDU (William R. Pearson) Subject: eugene vs PIR43 X-Nntp-Posting-Host: dayhoff.med.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Date: Mon, 30 Jan 1995 21:47:32 GMT Lines: 16 First it was Genbank, now it is PIR. The PIR database has grown sufficiently that the space allowed to index the database in the "eugene" software package has run out of room. The solution? Find the pirindex.c program and change the two lines with "%8ld"'s to "%10ld"'s. Then re-run pirindex (make sure to install it in the right place) and everything should work again. Bill Pearson -- wrp@virginia.EDU Dept. of Biochemistry #440 U. of Virginia Charlottesville, VA 22908 From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software Subject: Re:Re: Modelling protein structures Date: 2 Feb 1995 09:03:47 -0000 Lines: 44 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3gq75j$ott@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk Hi, >: > >: >This is much too pesimistic. About one third of all currently known >: >sequences are related to at least one currently known structure. >: > > >: ??? You really mean that 15,000 sequences from Swissprot (for example) are >: related to at least one entry in the PDB ? I'd be interested in getting a >: reference on this subject. > > >There are plenty of references on the subject, they basicly stem from the >fact that the number of different folds seems to be relatively low (estimates >vary from 100 to 1000). > Yes, yes (in fact, rather 1000 than 100). But are you speaking of FOLDS or SEQUENCES? It is certainly well known that completely different sequences can produce remarkably similar structures. So, when you say " About one third of all currently known sequences are related to at least one currently known structure" maybe you mean that "1/3 of currently known sequences have a FOLD similar to some one in the PDB". Here I agree. But, unfortunately, in the absence of clear sequence similarity, this is not of great help for modelling... > >Of course ther is a problem in the vias of the PDB, but it seems clear now that >protein modeling by homology has a very strong 'raison d'etre'. > Certainly. But you will agree that when the sequence similarities are weak, one must be VERY cautious and refrain from overoptimism. It's really too easy to produce a "model" when it can't be checked by any experimental data. You certainly know that even when you've got the diffraction data for "native" crystals -but no heavy atom derivative- things are not that simple. Just because THEN you can compare your model with REAL data....... Salud Jean-Loup From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msunews!netnews.upenn.edu!news.cc.swarthmore.edu!mac01.parrishd.swarthmore.edu!user From: ehom1@cc.swarthmore.edu (Erik Forbes Y. Hom '95) Newsgroups: bionet.software Subject: Poisson distrib. curve fit? Followup-To: bionet.software Date: Thu, 02 Feb 1995 01:45:25 +0000 Organization: Laboratory of Neurobiology, Swarthmore College Lines: 9 Message-ID: NNTP-Posting-Host: mac01.parrishd.swarthmore.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi netters, I'm would like to plot some data that I think are the sum of two poisson distributions. As far as I know, good 'ol Kaleidagraph can't do it - it doesn't understand the factorial. Are there any Mac programs that would be able to do this? Are there any way around this factorial business? (I could write a MATLAB script etc., but then I would have to slave through work that probably has already been done). Any info would be much appreciated. Thanks! erik From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!gs.dfn.de!fauern!news.th-darmstadt.de!News.Uni-Marburg.DE!news.belwue.de!news.uni-ulm.de!rz.uni-karlsruhe.de!news.urz.uni-heidelberg.de!cbb From: cbb@convex.phazc.uni-heidelberg.de (Christopher Blencowe) Newsgroups: bionet.software Subject: Re: partial cubic spline fitting [Q] Date: 1 Feb 1995 10:19:43 GMT Organization: University of Heidelberg, Germany Lines: 23 Message-ID: <3gnn7v$512@sun0.urz.uni-heidelberg.de> References: NNTP-Posting-Host: iris.phazc.uni-heidelberg.de X-Newsreader: TIN [version 1.2 PL2] MENOUD Laurent (laurent.menoud@igc.dc.epfl.ch) wrote: : Hi : I'm looking for a programm that allows partial cubic spline fitting. : Thank's for help and reply to : Laurent MENOUD : menoud@igc.dc.epfl.ch I think in 1991/92 there was an article in c't, magazine for computertechnik. If you know german, then this is what you are looking for. There is the contents of c't on ftp.uni-kl.de:pub3/pc/magazine/ct Maybe, you are able to find it without going to the lib. Sincerly, Christopher cbb@convex.phazc.uni-heidelberg.de From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!cs.utk.edu!gatech!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: GopherPup, a network client with unique features, is updated Date: 2 Feb 1995 19:53:13 GMT Organization: Biology, Indiana University - Bloomington Lines: 80 Message-ID: <3grd79$rq9@usenet.ucs.indiana.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu GopherPup is an Internet information client program, usable on the common computer systems including Macintosh, Motif/XWindows and MS-Windows. It provides an easy-to-use, sophisticated doorway to a wide range of Internet information services. GopherPup has several unique strengths * Display documents in Microsoft's Rich Text Format (RTF) produced by popular wordprocessors. RTF not only is a widely-available standard, it has full support for fonts, styles, embedded images, and the formatting needed to display publication-quality documents. RTF displays can include a variety of fonts including symbols, font sizes and styles, super-scripting and sub-scripting, tabbing, paragraph formatting, and pictures in both vector and bitmap forms. * Display graphics in a standard, widely-used vector & bitmap format, Apple Macintosh's PICT. This format provides high-resolution output, smaller/faster image transfer, and editable graphics, compared to GIF. * Display documents in the network HyperText Markup Language (HTML), and in the popular graphic bitmap format, CompuServe's GIF, as well as plain text. * Easily link network resources into any of these documents. Documents created in a wordprocessor can be directly displayed and network links can be placed by simple drag-and-drop methods. * The hypertext method used is easily extensible to any new format which can be displayed. * Browse and search through information on your local computer system using the same easy methods used for remote systems. The search methods use the same query dialogs, and relies on a variant of FreeWAIS-sf software which provides for complex and field-specified queries. With this feature it will be possible for providers to provide the same information services throught local CDROM or disk as through remote Internet connections. This search support is still under development. * Supports all Gopher+ protocol features, including -- User dialogs for client-server interactions. -- Simple and sophisticated multiple view handling. Easily choose the format you prefer, whether RTF or Postscript, GIF or JPEG, and specialty formats, depending on the service and your needs. Add new formats readily as needed. -- Display of document dates, sizes, and abstracts -- no more guessing if that document is 5 years old or up-to-date, or if it is 1,000 or 1,000,000 characters long. * Supports many HTTP/HTML protocol features (more later), and supports SMTP Mail protocol. * One source fits all -- this program is freely available in one source version that compiles on Macintosh, Microsoft Windows and X-Windows computer systems. NOTE: This release is a development, alpha version. It still includes several bugs and is not yet suitable for extensive use. GopherPup is based on the earlier GopherApp program for Macintosh computers. Version 0.3 is now freely available at . There are application executables for Macintosh, MS-Windows, Sun Sparcstation, and Silicon Graphics. Other systems are supported by the underlying toolkit. This is built on a cross-platform toolkit from the Nat'l Center for Biotechnology Information (NCBI), and further extended by the author's object-oriented application framework called DCLAP. The source for these toolkits and the applicaiton are freely available. The home archive location for DCLAP is at . Comments, bug reports and suggestions for new features may be sent to GopherPup@Bio.Indiana.Edu -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Newsgroups: bionet.software Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!news.uta.edu!pooh.swmed.edu!patrickw From: patrickw@pooh.swmed.edu (Patrick Weix) Subject: Re: Compare/diff type software Message-ID: <1995Feb2.161833.23657@news.uta.edu> Sender: news@news.uta.edu (USENET News System) Nntp-Posting-Host: pooh.swmed.edu Organization: Biochemistry Dept, University of Texas Southwestern Medical Center, Dallas References: <1995Jan29.115601.20797@nomina.lu.se> Date: Thu, 2 Feb 1995 16:18:33 GMT Lines: 12 For the Mac, it is necessary that one have a good text editor as well as a good word processor. My vote is for the shareware program Alpha. It is highly customizable, most of the key defaults resemble EMACS, it supports submitting files to Macperl etc., but MOST IMPORTANTLY, it has a good compare windows function. This assumes that you are interested in editing/comparing at the same time. Also, the last time I checked, the author had a port of gnudiff in his ftp file. The latest version is always at ftp://cs.rice.edu/public/Alpha This will do what you want and more. From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!frist From: frist@cc.umanitoba.ca (Brian Fristensky) Newsgroups: bionet.software Subject: FSAP now available in C Date: 2 Feb 1995 20:44:30 GMT Organization: University of Manitoba, Winnipeg, Manitoba, Canada Lines: 49 Distribution: world Message-ID: <3grg7e$at1@canopus.cc.umanitoba.ca> NNTP-Posting-Host: bradbury.cc.umanitoba.ca =========================================================== F S A P =========================================================== The Fristensky Sequence Analysis Package (formerly Cornell Sequence Analysis Package) has proven to be a versatile, reliable, and highly portable suite of programs for sequence analysis. At the heart of the package is NUMSEQ, a sequence manipulation program that provides a large number of options for presentation of sequence data, as well as facilitating simulation of operations such as translation, subcloning and ligation. Restriction search programs predict fragments and ends from single or multiple, complete or parital digests. Rapid matrix similarity searches perform quantititive comparisons of nucleic acid and protein sequences. Programs for base/amino acid composition and ORF analysis are also provided. Programs are compatible with IUPAC-IUB ambiguity conventions, and can read a wide variety of sequence file formats. Most FSAP programs can now be run from GDE, the Genetic Data Environment of Steven Smith. C code is now available for the following platforms and compilers: SunOS cc,gcc IBM/AIX xlc,gcc HP/UX cc Code may run with other comilers as well. Files may be obtained by anonymous FTP: FTP: psgendb/fsap.tar.Z at ftp.cc.umanitoba.ca (130.179.16.24) or by World Wide Web: http://www.umanitoba.ca/Agriculture/Plant_Science/Fristensky/Software/Software.html An MS-DOS version is also available in this directory. See the README file more information. =============================================================================== Brian Fristensky | Department of Plant Science | Life doesn't imitate art, University of Manitoba | it imitates bad television. Winnipeg, MB R3T 2N2 CANADA | frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Woody Allen, HUSBANDS AND WIVES FAX: 204-261-5732 | http://www.umanitoba.ca/Agriculture/Plant_Science/Fristensky/Fristensky.html =============================================================================== From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!hubcap.clemson.edu!biosci!UIUC.EDU!crebeiz From: crebeiz@UIUC.EDU (C. Rebeiz) Newsgroups: bionet.software Subject: Re: 3D-proteine structure: Homology modeling versus X-ray chrystallography Date: 30 Jan 1995 07:40:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <199501301540.AB27437@ux1.cso.uiuc.edu> One of the major limitations of homology modeling in plants systems, is finding a reference protein with a degree of homology = or > than 40% to the target protein. I wonder however, about the relationship of a laboratory-grown crystal of a membrane-bound solubilized protein to the native protein in situ. Constantin A. Rebeiz 240 A, PABL 1201 W. Gregory Univ. Illinois, Urbana, IL 61801 From owner-software@net.bio.net Wed Feb 01 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!bcc.ac.uk!is.bbsrc.ac.uk!pc0519.ri.afrc.ac.uk!user From: lawa@bbsrc.ac.uk (Andy Law (Big Nose)) Newsgroups: bionet.software Subject: Re: how to import ABI SeqEd chromatograms into any mac graphical program? Date: 2 Feb 1995 09:47:59 GMT Organization: Roslin Institute Lines: 30 Message-ID: References: <19950126.224157.104427.NETNEWS@UICVM.UIC.EDU> NNTP-Posting-Host: pc0519.ri.afrc.ac.uk In article <19950126.224157.104427.NETNEWS@UICVM.UIC.EDU>, U21206@uicvm.cc.uic.edu (Dmitri Rebatchouk) wrote: > Could anybody tell me whether it is possible to import ABI SeqEd > chromatogram files into a graphical program on a Mac? Or, if it can't > be done (which I expect), does some "connector" program exist capable > of reformatting SeqEd files into one of graphical formats? I can > screen-capture the image, but it becomes just a "photograph", so I > cannot change the colors of the curves. (What I really want is to > change colors to patterns, so that b/w printer could be used for > hardcopy output). > I would really appreciate any advice. This is a non-trivial problem; the ABI trace information consumes a vast amount of space. Do you want the full trace, or just a portion of it? It would be possible to write a routine to extract just the portion of information that you want in numerical format such that a graphing package could utilise it. If you have someone at your end who can program, I could let them have the info that I have deciphered from the ABI file format (version 1 anyways). Alternatively, if you want to pay me for a days work..... (perhaps) ;-} -- Andy Law ( Lawa @ bbsrc.ac.uk ) ( Andy.Law @ bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!pasteur.fr!plichart From: plichart@pasteur.fr (Regis Plichart) Newsgroups: bionet.software Subject: Information about Amplify required... Date: 3 Feb 1995 01:02:25 GMT Organization: Institut Pasteur Lines: 16 Message-ID: <3grvb1$94g@montespan.pasteur.fr> NNTP-Posting-Host: mendel.sis.pasteur.fr X-Newsreader: TIN [version 1.2 PL2] try to get information and cost concerning the AMPLIFY Softwre, used for designing, analyzing and simulating experiments involving PCR. I tried to send a mail to Pr Engels in the University of Wisconsin. Unfortunately, the adress I used is false. Can somebody tell me if this software is available for PC systems (DOS or Windows) Regis Plichart Institut de Recherches Medicales Louis Malarde B.P. 30 PAPEETE - Tahiti Fax : (689) 43 15 90 email : plichart@pasteur.fr Thanks From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!news.tamu.edu!NewsWatcher!user From: aat3230@zeus.tamu.edu (Gus Trautweiler) Newsgroups: bionet.software Subject: Q: Mac program for analysis of RFLPs sought. Date: Fri, 03 Feb 1995 03:53:40 +0000 Organization: Texas A&M University Lines: 8 Message-ID: NNTP-Posting-Host: 128.194.248.52 Are there any mac programs that will take a scanned autorad and calculate frag. size, allele freq., and fingerprinting, etc.? Thanks! Gus Trautweiler ###QRNQURNQ##*. .*#*. .*#*. .*#*. Plant Pathology & Microbiology * | | | * * | | | * | | | * Texas A&M University * * | | | * * | | | * * | | | * College Station, TX 77843-2132 * | | | * | | | * * | | | * AAT3230@ZEUS.TAMU.EDU ###*' `*#*' `*#*' `*#*' From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!cs.utexas.edu!not-for-mail From: HUANGY@SLUVCA.SLU.EDU Newsgroups: bionet.molbio.genome-program,bionet.software,bionet.software.gcg Subject: A bug in GCG SEQED program? How to solve the program Date: 2 Feb 1995 19:51:08 -0600 Organization: UTexas Mail-to-News Gateway Lines: 38 Sender: nobody@cs.utexas.edu Message-ID: NNTP-Posting-Host: news.cs.utexas.edu Xref: biosci bionet.molbio.genome-program:1150 bionet.software:10918 bionet.software.gcg:965 Hi, there: I didn't read this news group until recently. If someone had happened to post the same or similiar post about what I am going to talking about, please excuse me for that. While I was using with the GCG SEQED program, one strange thing happened to me. When I created a new sequence file with SEQED program and put two or more consequent periods (.) into the header part or the comment part and exited with some sequences, the SEQED program would say that the file was not in GCG format once I reopened it with the program. I spent quite a while figuring out how this could be happening. Finally, I realized that this problem resulted from the 2 or more periods in the header part. What I did was very simple. Use a text file editor and open the sequence file and put a space between two consequent periods. But DON'T put any letter or space between the two periods after the Month day year hour:second Check: xxxx. Then, the program was very happy to accept the files which it had created and refused to accept. From a programmer's view of point, the signature line for the beginning of sequence data could be a little bit more complicated. For obvious reasons, I am going to talk about how GCG SEQED program checks the integrity of the sequence files. The above program was version 8.0 running on 6.1 OpenVMS/VAX system. Mr. Yinrong HUANG Thursday February 2, 1995, 07:19pm CST USA ------------------------------------------------------------------------------ | * * * Many people don't know how to use computer softwares, * * * | | * * let alone know how they are programmed and how they work. * * | | * * * This email ONLY represents my own personal viewpoints. * * * | | * * * * With Standard Disclaim included * * * * | ------------------------------------------------------------------------------ From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!ix.netcom.com!netcom.com!csus.edu!news.ucdavis.edu!josquin.ucdavis.edu!not-for-mail From: john@josquin.ucdavis.edu (John Gillespie) Newsgroups: bionet.molbio.genbank,bionet.software Subject: Re: Network Entrez 3.010 Followup-To: bionet.molbio.genbank,bionet.software Date: 3 Feb 1995 20:39:47 GMT Organization: String to put in the Organization Header Lines: 5 Message-ID: <3gu4aj$5il@mark.ucdavis.edu> References: <1995Jan30.194026.1447@nlm.nih.gov> NNTP-Posting-Host: josquin.ucdavis.edu X-Newsreader: TIN [UNIX 1.3 941216BETA PL0] Xref: biosci bionet.molbio.genbank:1913 bionet.software:10932 Jonathan Epstein (epstein@gold.nlm.nih.gov) wrote: : The long-awaited new Network Entrez clients have now been released... Are Linus binaries available? From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!caen!hearst.acc.Virginia.EDU!murdoch!faraday.clas.Virginia.EDU!wjc4f From: wjc4f@faraday.clas.Virginia.EDU (Wendy J. Cholbi) Subject: Image Analysis Q's answered X-Nntp-Posting-Host: faraday.clas.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: uva Date: Fri, 3 Feb 1995 22:32:28 GMT Lines: 76 Thanks to all those who responded. Here's a summary of what I've learned. My original question was which of 2 image-analysis software packages, ImagePro or Mocha, would be better for counting numbers, areas, densities, etc. of cells, from pictures captured from a camera mounted on a microscope. The setup is a PC (Gateway) with a Targa+ frame grabber board. To summarize the stuff below: Buy a Mac and use NIH Image if possible--by far the best alternative. IF you're stuck with a PC and are considering either Mocha or ImagePro, go with ImagePro if you can possibly afford it. Reasons below. The _overwhelming_ response (from everyone who responded, actually, which was about 6 people who had had experience with various image analysis setups) was: ditch the PC, buy a Mac, and get NIH Image (which is free)! Reasons: 1. You can buy a Mac hardware setup for less than $2500 (about $1500 if you buy a used Quadra instead of a new PowerMac and attach your own monitor). While the internal video cards in such Macs are known to be not very reliable for capturing video from a camera, there are several Mac cards out there which are either bottom-of-the-line or about to be discontinued, but are still perfectly good for capturing still video, for the amazing price of between $59 and $200. The top-of-the-line video card for capturing full-color moving video with TV quality runs about $2000. 2. Macintosh stuff is all compatible with other Macintosh stuff (or you can tell instantly which Macs are compatible with your software or whatever) unlike the world of PC's, where you can buy a hard drive, monitor, frame grabber, camera, and software package, each from a different manufacturer, and then _you_ get the joy of integrating it all. And did I mention the cables to connect all these possibly incompatible components? 3. NIH Image is, as mentioned, free, and it's an outstanding program which accomplishes lots of automatic counting and measuring, as well as letting you write macros for doing complex stuff. The threshold for automatic counting is easy to set, you can export data to Excel or whatever database you choose, and the documentation is excellent. You can also get free upgrades whenever a new version comes out, which is pretty often. However, if you're absolutely stuck using a PC, I have had a chance to compare Mocha and ImagePro (at least the demo versions). If it's within your price range, I would definitely choose ImagePro. The video capture seems to work as well, and it is much more powerful and easy to use than Mocha. For example, ImagePro has a "video average" feature which allows you to compile 16 frames of video and average them into one image, thus significantly reducing noise and sharpening the image. It also has superior image processing capabilities, such as contrast and brightness slider bars and thresholding which allows you to see what's background and what's highlighted _before_ you carry out the operation. Also, the tech support for ImagePro seems much better (of course, they were trying to get me to buy it). The people at Mocha always kept me on hold for long periods of time, or had to call me back, which necessitated me sitting around waiting on them instead of being helped. And they weren't very good at describing what I should do to fix the problem. Overall, Mocha is quite clunky and not user-friendly. This matches up with descriptions I've heard from other Mocha users. I hope this may have been of some use to others interested in image analysis. I would be happy to respond to particular questions on the above statements, since although I'm no expert, I've learned a lot about image analysis over the last tow weeks. Enjoy, Wendy Cholbi Rissman Squad, Gilmer Hall, University of Virginia wjc4f@virginia.edu From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: jclewley@hgmp.mrc.ac.uk (Dr. J.P. Clewley) Newsgroups: bionet.software Subject: Mac version of Unix cat Date: 3 Feb 1995 18:12:16 -0000 Lines: 5 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3gtrm0$2o6@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk Does anyone know of a Mac program that will join files that have been split on unix?  Jon Clewley From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: "M. Kumaraguru" Newsgroups: bionet.software Subject: "Pent" up feelings..... Date: 3 Feb 1995 11:31:45 -0000 Lines: 2 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3gt471$aeb@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk Every day I keep hearing people talking about the Pentium power. Is there a newsgroup which discusses on this hot 'chip' worth less than its potato counterpart?Let me know. Thanks. From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Newsgroups: bionet.molbio.gene-linkage,bionet.software Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!cs.utexas.edu!uunet!pipex!uknet!bcc.ac.uk!dac159!dcurtis From: dcurtis@hgmp.mrc.ac.uk (David Curtis) Subject: Re: Linkage software complex trait analysis Sender: news@ucl.ac.uk (Usenet News System) Message-ID: Date: Fri, 3 Feb 1995 13:59:19 GMT References: <3g3g1k$7lc@hawk.le.ac.uk> <3gbisp$n63@nic-nac.CSU.net> Organization: Institute of Psychiatry X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 15 Xref: biosci bionet.molbio.gene-linkage:525 bionet.software:10928 >> I'm looking at genetic susceptiblity in the mouse. >>I've done an F2 cross between resistant and susceptible strains >>and now I'm trying to identify any regions of the genome that >>may have susceptiblity genes, using linkage. >Well, I've heard of a program called "LINKAGE". Maybe you can ftp somewhere >and get it. I dunno if it's public domain. Yes it's public domain.No it's no good for experimental crosses, it's for generalised pedigrees in humans. I doubt you'd find it with archie. It's available (as the FASTLINK package) at gc.bcm.tmc.edu. From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!lhc!darwin.sura.net!news-4.nss.udel.edu!udel!gatech!swrinde!cs.utexas.edu!not-for-mail From: HUANGY@SLUVCA.SLU.EDU Newsgroups: bionet.molbio.genome-program,bionet.software,bionet.software.gcg Subject: DOS program to process sequence files into GCG format Date: 3 Feb 1995 09:20:49 -0600 Organization: UTexas Mail-to-News Gateway Lines: 63 Sender: nobody@cs.utexas.edu Message-ID: NNTP-Posting-Host: news.cs.utexas.edu Xref: biosci bionet.molbio.genome-program:1156 bionet.software:10927 bionet.software.gcg:967 Hi, everyone: This post is via cs.utexas.edu mail-to-news gateway. After I sent one post with the same content, I didn't see it on the corresponding newsgroups for quite a while. Now, I am sending it again. If somehow the old one appears, please excuse me for that. Today is 02/03/95, Now is 09:24 am CST, USA Hello, everyone: How many times did you ask yourself that you could use your favorite word processing softwares to edit your sequences and export these sequence files out to the VAX/VMS system? How many times did you wonder whether you could use your PC or MAC instead of a work-ladden VAX/VMS system to edit your sequence? Have you wondered whether you could run a simple program to arrange your sequence to get a nice format for your word processing softwares? Now and here comes the program which you wish that you could have programmed. Here, I announce that a simple DOS program, EDNA, is available to the molecular biology research community. This EDNA program is quite like the reformat program in the GCG package for the OpenVMS/VAX system. However, it gives more freedom to edit your sequence with your softwares. You can put your comments anywhere in the file as long as they are enclosed with a pair of /* */ marks. It also automatically puts a space between any consequent periods which you put in the comment part. The output file is in the GCG format. Here is an example: ------------------------------------------------------------------------------ Input file INPUT.TXT /* This is first comment... */ GGGGAAaaaa 10 cttt tctttttttaaaaaaaaaaaattttttttttttttttt /* This is second comment */ ttttttttaaaaaggcttttaaaggg Output file INPUT.SEQ This is first comment. . . This is second comment THIS.SEQ Length: 78 February 01, 1995 21:41 Type: N Check: 7333 .. 1 GGGGAAaaaa cttttctttt tttaaaaaaa aaaaattttt tttttttttt 51 tttttttttt aaaaaggctt ttaaaggg ------------------------------------------------------------------------------ If you are interested, please drop me a line and I will mail you the uuencoded file with instructions attached. Thank you for your interest. Mr. Yinrong HUANG Thursday February 2, 1995, 07:42pm CST USA ------------------------------------------------------------------------------ | * * * Many people don't know how to use computer softwares, * * * | | * * let alone know how they are programmed and how they work. * * | | * * * This email ONLY represents my own personal viewpoints. * * * | | * * * * With Standard Disclaim included * * * * | ------------------------------------------------------------------------------ From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!udel!news-4.nss.udel.edu!usenet From: Skeen Newsgroups: bionet.software Subject: Views of Commercial & Shareware inst. software Date: 3 Feb 1995 20:40:36 GMT Organization: University of Delaware Lines: 12 Message-ID: <3gu4c4$8gd@news-4.nss.udel.edu> NNTP-Posting-Host: skeen.psyc.udel.edu We have a new computer lab site with 30 boxes networked (Windows). We would now like to find some good instructional software to use on these boxes in conjunction with our traditional wet labs and dissections (Graduate and Undergraduate: neurophys, neuropharm, neuroanat). We would appreciate the views of those who have had experience with the various shareware and commercial packages presently available. Thanks in advance. Carl Skeen From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr From: pmr@unst.sanger.ac.uk (Peter Rice) Newsgroups: bionet.molbio.genome-program,bionet.software,bionet.software.gcg Subject: Re: A bug in GCG SEQED program? How to solve the program Date: 03 Feb 1995 10:06:57 GMT Organization: University of Cambridge, England Lines: 55 Message-ID: References: NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: HUANGY@SLUVCA.SLU.EDU's message of 2 Feb 1995 19:51:08 -0600 Xref: biosci bionet.molbio.genome-program:1155 bionet.software:10925 bionet.software.gcg:966 In article HUANGY@SLUVCA.SLU.EDU writes: > While I was using with the GCG SEQED program, one strange thing > happened to me. When I created a new sequence file with SEQED program and > put two or more consequent periods (.) into the header part or the comment > part and exited with some sequences, the SEQED program would say that the > file was not in GCG format once I reopened it with the program. > > I spent quite a while figuring out how this could be happening. > Finally, I realized that this problem resulted from the 2 or more periods > in the header part. > > What I did was very simple. Use a text file editor and open the > sequence file and put a space between two consequent periods. But DON'T put > any letter or space between the two periods after the Month day year > hour:second Check: xxxx. Then, the program was very happy to accept the > files which it had created and refused to accept. Definitely a bug, but not new in 8.0. Even GCG 7.3 on OpenVMS seems to suffer from it. SEQED should expand the ".." to ". ." just as you did. It only needs to call StrAerate for each line of heading when writing it out. Most other GCG programs are paranoid about .. and keep expanding it. EMBLTOGCG, for example, expands ".." in the feature table to ". ." and upsets SRS output, even though every access to the sequence databases by GCG will repeat the check in any case (necessary because, for example, PIR can be obtained in GCG format with ".." in the author lists). Because of this effect, I recently turned off the ".." to ". ." conversion in EMBLTOGCG to make SRS happy when using GCG format databases. So far it seems to work fine in GCG. I also changed the order of the hacked DE line to be: acnumber description species instead of GCG's "acnumber species description" which means that database searches always say something useless like: Hs11_Arath X12345 Arabidopsis thaliana (mouse-ear cress) 17.4 kd clas . . . when the SwissProt entry name already tells me the species :-) As for SEQED, I gave up using it years ago. I can type faster in a normal editor. Just put ".." after the heading, and use reformat to write the true ".." line. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr | England From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!atlas.rc.m-kasei.co.jp!yao From: yao@atlas.rc.m-kasei.co.jp (Toru YAO) Newsgroups: bionet.software Subject: unsubscribe Date: 2 Feb 1995 20:42:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <9502030442.AA29775@atlas.rc.m-kasei.co.jp> NNTP-Posting-Host: net.bio.net unsubscribe bio-soft From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!news1.databank.com!nntp.execnet.com!execnet!peter.foiles From: peter.foiles@execnet.com (PETER FOILES) Newsgroups: bionet.software Subject: SIGMA-PLOT VERSION 2 FOR Message-ID: <8A2B4C1.023A001AD1.uuout@execnet.com> Date: Wed, 01 Feb 95 20:17:00 -0500 Distribution: world Organization: Execnet Information System - 914-667-4567 - 198.232.143.136 Reply-To: peter.foiles@execnet.com (PETER FOILES) References: <8A2A2E1.023A001AC1.uuout@execnet.com> X-Newsreader: PCBoard Version 15.21 X-Mailer: PCBoard/UUOUT Version 1.10 Lines: 18 In a message dated 01/31/95, Bob Lauder said to All: BL> Have any Sigma-Plot users upgraded from version 1 for Windows to version BL>2 for Windows? BL> I'm using V1 at the moment and have been sent loads of glossy ads BL>suggesting that I upgrade. however, as far as I can see the major BL>changes are in contour plotting which I don't need. BL> Is this the case? Is there any other reasons to upgrade? I have upgraded to v2. The screen redraws are significantly faster on my system and it will now automatically create legends nothing much else that I have noticed. Peter Foiles --- þ MR/2 2.12 NR þ "Apple" (c) Copyright 1767, Sir Isaac Newton. From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: IUBio Archive services are now available by e-mail Date: 3 Feb 1995 03:47:09 GMT Organization: Biology, Indiana University - Bloomington Lines: 28 Message-ID: <3gs8vt$55b@usenet.ucs.indiana.edu> NNTP-Posting-Host: sunflower.bio.indiana.edu IUBio Archive and FlyBase gopher services now are available by e-mail, using GopherMail. This is experimental -- let us know if you have problems. For all IUBio services, including Genbank, Swiss-protein, FlyBase and other databank searches, Bionet news searches, and software archives, send a mail message to gopher@iubio.bio.indiana.edu For only FlyBase Drosophila information, send the mail message to gopher@flybase.bio.indiana.edu In both cases, you start by sending mail with any or no subject, and any or no message body. GopherMail will reply by sending you it's main gopher menu. The return mail provides you a menu of selections, then you mark your choices, and return that mail. Repeat this process to select many items. Use the "Subject:" of your mail mesage for queries to search items like Genbank or FlyBase Genes. Send the word "help" in the subject line to get help on this service. GopherMail software was written by Fred Bremmer. -- Don Gilbert archive@bio.indiana.edu -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!hubcap.clemson.edu!biosci!TAU.BEKKOAME.OR.JP!isshikim From: isshikim@TAU.BEKKOAME.OR.JP (Masashi Isshiki) Newsgroups: bionet.software Subject: unsubscribe Date: 30 Jan 1995 18:56:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <199501310257.LAA14704@bekkoame.bekkoame.or.jp> NNTP-Posting-Host: net.bio.net unsubscribe bio-soft isshikim@tau.bekkoame.or.jp From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!news.umkc.edu!news From: Dorin-Bogdan Borza Newsgroups: bionet.software Subject: Re: Neural networks in metabolism modeling? Date: 3 Feb 1995 02:11:01 GMT Organization: University of Missouri - Kansas City Lines: 18 Message-ID: <3gs3bl$qio@kasey.umkc.edu> References: <950202091238.1bb23@CUCCFA.CCC.COLUMBIA.EDU> NNTP-Posting-Host: slip27.umkc.edu MARK@CUCCFA.CCC.COLUMBIA.EDU (T. Mark Reboul) wrote: [...] > Is anyone aware of work in metabolic process modeling based on > neural network simulation? It seems like a reasonable technique to > consider in modeling metabolism, but so far I don't find citations > pointing to such work. Thanks for any details/suggestions/comments. I came across a comparison between neural nets and intracellular signalling (protein kynase cascades) in "The molecular biology of the cell", Alberts et al, 1994. Some references included. Unfortunately, I don't have the book with me to give you the references, but it should be easy to find out. Send me e-mail if you are not able to locate what you are looking for. dborza@cctr.umkc.edu Dorin B. Borza PhD. Student Biochemistry From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!JAGUAR.CSC.WSU.EDU!THOMPSON From: THOMPSON@JAGUAR.CSC.WSU.EDU ("Steve Thompson: VADMS genetics") Newsgroups: bionet.software Subject: eXcursion, PC/TCP, VMS Date: 2 Feb 1995 18:33:09 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <950202183239.20404c64@JAGUAR.CSC.WSU.EDU> NNTP-Posting-Host: net.bio.net Hello biosoft gurus - We are trying to get eXcursion v1.2 running on AT&T 386 boxes with Starlan 10 NAU ethernet boards. We are using FTP Corp. PC/TCP v2.0.5 with the Clarkson Packet Driver for communications. We are running DOS v6.1 and Windows v3.1. The host is VAX/VMS v5.5-2. We have successfully troubleshot the system by connecting to a Unix host and displaying xterm, xclock, etc. However, whenever we attempt to use something from the VAX, it takes an impossibly long time to display, and, in fact, times itself out when trying to display a DECTerm. It has successfully displayed the clock, session manager, and calculator. But we have only been successful launching these DEC applications from the PC by means of the DEC command file MN.COM; launching them from another terminal specifying display on the PC with eXcursion does work but, again, not with DECTerm. Also, in general, the PC software seems very flaky in this configuration --- it often looses its driver files, constantly needs rebooting, etc. Does anybody have any ideas about this? We could sure use some help. Thanks - Steve Steven M. Thompson Consultant in Molecular Genetics and Sequence Analysis VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory Washington State University, Pullman, WA 99164-1224, USA AT&Tnet: (509) 335-0533 or 335-3179 FAX: (509) 335-0540 INTERnet: THOMPSON@jaguar.csc.wsu.edu From owner-software@net.bio.net Thu Feb 02 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsfeed.pitt.edu!hudson.lm.com!news.pop.psu.edu!news.cac.psu.edu!juncol.juniata.edu!hoquerx4 From: hoquerx4@juncol.juniata.edu Newsgroups: bionet.software Subject: COMPUTER SALE Message-ID: <1995Feb2.235215.1514@juncol.juniata.edu> Date: 2 Feb 95 23:52:15 -0500 Organization: Juniata College, Huntingdon, PA -- USA Lines: 6 SALE: IBM 286 WITH COLOR MONITOR, MOUSE DRIVE, KEYBOARD, AND INTEL 144/144E MODEM. DOS 5.0, WINDOWS(WORD-PERFECT, EXEL, POWERPOINT, THUMBS VIEWER) AND A LOT OF GAME. STATE COLLEGE AND HUNTINGDON AREA, PA CALL REAZ(814-641-7139) OR E-MAIL AT HOQUERX4@JUNCOL.JUNIATA.EDU ASKING PRICE:$650 From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!news.mindlink.net!line07.nwm.mindlink.net!user From: bill_fernihough@bchydro.bc.ca (bill fernihough) Newsgroups: bionet.software Subject: Material Safety Data Sheet Program Date: 4 Feb 1995 06:56:49 GMT Organization: none Lines: 3 Message-ID: NNTP-Posting-Host: line07.nwm.mindlink.net X-Newsreader: Value-Added NewsWatcher 2.0b14.2+ BC Hydro International Ltd announces the release of it software management package for MSDS. See a demo at Original-To: bio-soft@dl.ac.uk Can you please tell me whether there is any site for PHYLIP analysis e-mail server. I have some sequences for which I want to know the evolutionary relationship. I am in need of a site where I can do the analysis as my PC cannot perform the operation for lack of memory and space for PHYLIP. Thank you From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!uunet!news.u.washington.edu!news.u.washington.edu!root From: "James P. Gray" Newsgroups: bionet.software Subject: Software allowing IBM to read Mac disks Date: 4 Feb 1995 03:09:39 GMT Organization: University of Washington Lines: 27 Message-ID: <3gur5j$p4g@nntp1.u.washington.edu> NNTP-Posting-Host: 128.95.11.129 Does anyone know of a good and preferably cheap program which allows an IBM type machine running under the DOS/Windows environment to read Mac formatted floppies? Thanks, -James- **************************************************************************** James P. Gray ___|___ University of Washington _/ \_ Department of Microbiology ============= /\/\ /\ SC-42/room I-320 -+-+-+-+-+- ^ / \^ /\ Seattle, WA 98195 \\ | // ^/ ^ \/ ^\ ------------------------------ \\|// /\/ /\ \ jp@u.washington.edu -Internet |-| / /\/ \ ^ \ (206)685-1783 -Telephone |-| / ^ / \ \ \ (206)543-8297 -FAX |-| / ^ / \ \ \ |-| / / ^ ^ \ \ \ |-| / ^ / ^ \ \ \ //-\\ / / ^ ^ \ \ \ // - \\ / / \ \ ||||||||||| / / \ \ "Save a tree, eat a beaver" **************************************************************************** From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!hubcap.clemson.edu!biosci!adam.cc.sunysb.edu!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!yama.mcc.ac.uk!io.salford.ac.uk!usenet From: R.Lauder@lancaster.ac.uk (Bob Lauder) Newsgroups: bionet.software Subject: Sigma-Plot version 2 for Windows Date: 31 Jan 1995 12:17:50 GMT Organization: Lancaster University Lines: 17 Message-ID: <3gl9pe$rop@io.salford.ac.uk> NNTP-Posting-Host: bsa046000001.lancs.ac.uk X-Newsreader: WinVN 0.92.6 Have any Sigma-Plot users upgraded from version 1 for Windows to version 2 for Windows? I'm using V1 at the moment and have been sent loads of glossy ads suggesting that I upgrade. however, as far as I can see the major changes are in contour plotting which I don't need. Is this the case? Is there any other reasons to upgrade? Thanks Bob. ================================================================ Bob Lauder R.Lauder@lancaster.ac.uk Division of Biological Sciences Tel +(44)(0)1524 65201 Lancaster University, Lancaster, UK Fax +(44)(0)1524 843854 From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!newsserver.sdsc.edu!nic-nac.CSU.net!charnel.ecst.csuchico.edu!csusac!csus.edu!news.ucdavis.edu!library.ucla.edu!nnrp.info.ucla.edu!hodgkin.mbi.ucla.edu!arne From: arne@hodgkin.mbi.ucla.edu (Arne Elofsson) Newsgroups: bionet.software Subject: ENDNOTE 2.0 ? Date: 4 Feb 1995 00:18:51 GMT Organization: OrgFreeware Lines: 29 Distribution: world Message-ID: <3guh5b$te1@saba.info.ucla.edu> Reply-To: arne@hodgkin.mbi.ucla.edu (Arne Elofsson) NNTP-Posting-Host: hodgkin.mbi.ucla.edu Hi has enyone got endnote 2.0 ? I think it is only available for the MAC yet But I guess there will be a Windows version out soon (?) My Questions: 1) Does it work with Word6.0 files (without converting to rtf ?) 2) What are the major improvement from 1.3.3 ? 3) Anyone knows when the Windows version will be available ? arne -- ****************************************************************************** ** From: Arne Elofsson ** ** Fax: +1-(310)-206-3914 or Fax: +1-(310)-206-7286 ** ** Tel: +1-(310)-825-1402 ** ** ** ** Email: arne@hodgkin.mbi.ucla.edu (arne@uclaue.mbi.ucla.edu) ** ** ** ** WWW: http://www.doe-mbi.ucla.edu/arne/main.html ** ** WWW: http://www.mbi.ucla.edu/arne/main.html ** ** ** ** Adress: Molecular Biology Institute Home: 1370 Veteran #311 ** ** 405 Hilgard Avenue, UCLA Los Angeles ** ** Los Angeles CA 90024 ** ** California 90095 USA ** ** USA Tel: +1-(310)-268-8006 ** ****************************************************************************** From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!sgiblab!uhog.mit.edu!news.mtholyoke.edu!news.umass.edu!anchor.cc.umb.edu!news From: 4700gbera@umbsky.cc.umb.edu Newsgroups: bionet.software Subject: Numerical Taxonomy software Date: 3 Feb 1995 20:56:20 GMT Organization: University of Massachusetts at Boston Lines: 16 Message-ID: <3gu59k$ki@anchor.cc.umb.edu> Reply-To: 4700gbera@umbsky.cc.umb.edu NNTP-Posting-Host: taurus.cc.umb.edu Hello all! Does anyone know of some good numerical taxonomy software that will produce publication quality dendograms? I would like to be able to cut off the tree at a certain percent similarity with just a filled area representing the members of that cluster. I have seen NTSYST from Exeter Software referenced for this, but I was wondering if there were others. Thanks- Gina Berardesco 4700gbera@umbsky.cc.umb.edu University of Massachusetts, Boston From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: jhp20@cus.cam.ac.uk (Mikpf) Newsgroups: bionet.software Subject: subscribe Date: 4 Feb 1995 14:45:53 GMT Organization: Soliptist Lines: 7 Distribution: world Message-ID: <3h03v1$76g@lyra.csx.cam.ac.uk> References: <9502030442.AA29775@atlas.rc.m-kasei.co.jp> NNTP-Posting-Host: sonja.acad.cai.cam.ac.uk Mime-Version: 1.0 X-Newsreader: WinVN 0.93.11 subscribe bio-soft -- _________________________________________________ jong@mrc-lmb.cam.ac.uk Tim Hubbard's student _________________________________________________ From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!uknet!bcc.ac.uk!jones From: jones@bsm.bioc.ucl.ac.uk (David Jones) Subject: THREADER (structure prediction software) update Message-ID: <1995Feb4.143239.30581@ucl.ac.uk> Date: Sat, 4 Feb 1995 14:32:39 GMT Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Lines: 65 **** THREADER **** THREADING SOFTWARE UPDATE An update to THREADER is now available. The following changes have been made: * Sun version released * Reported bugs fixed * Extended fold library released (298 chains now included) * Potentials updated with new structures * New option to update model accessibilities during threading What is THREADER? THREADER is a program for protein tertiary structure prediction by threading - i.e. protein fold recognition. Essentially it takes a protein sequence and finds the most likely match for its native conformation from a set of alternatives (extracted from known protein structures). This approach can detect similarities that cannot be detected by sequence alignment or sequence profiles. If you want more details see the following two references: Jones D.T., Taylor W.R. & Thornton J.M. (1992) "A new approach to protein fold recognition." Nature. 358:86-89. Jones D.T. & Thornton, J.M. (1993) "Protein Fold Recognition." J. Comp. Mol. Design 7:439-456. THREADER IS CURRENTLY ONLY AVAILABLE FOR SILICON GRAPHICS SYSTEMS RUNNING IRIX 5 OR SUN SPARC SYSTEMS RUNNING SUNOS 4.1 OR LATER. The software is free to academics and non-profitmaking organizations, and available for a fee to commercial users. The software may be obtained from our ftp server as follows: ftp ftp.biochem.ucl.ac.uk name: anonymous password: your-email-address cd pub/THREADER Please download and read the README and INSTALL files before proceeding further. You may also like to download and print out the preliminary manual, which is available as a PostScript file (manual.ps). Before using the software you must obtain a license code by filling in and returning the license agreement form found in the ftp directory. EXISTING USERS NEED ONLY DOWNLOAD THE NEW FILES TO UPDATE - THE EXISTING LICENSE CODES ARE VALID FOR ALL FUTURE VERSIONS OF THREADER. PLEASE NOTE CAREFULLY THAT THREADER IS STILL EXPERIMENTAL - I HOPE THE PROGRAM ITSELF IS BUG-FREE, BUT I DO NOT GUARANTEE IT. IF YOU HAVE ANY PROBLEMS THEN I'LL DO MY BEST TO FIX THEM AS SOON AS POSSIBLE. >---------------------------------------------------------------------------< This message was written, produced and executively directed by Dr David Jones Email: jones@bsm.bioc.ucl.ac.uk | JANET: jones@uk.ac.ucl.bioc.bsm Address: Dept. of Biochemistry | Tel: +44 71 387 7050 x3879 and Molecular Biology, University | Fax: +44 71 380 7193 College, London WC1E 6BT, U.K. | Disclaimer: STANDARD > KEYWORDS : OPINIONS MY OWN NOBODY ELSE'S WHATSOEVER From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!rutgers!gatech!newsxfer.itd.umich.edu!news.cic.net!condor.ic.net!news From: Howard Cash Newsgroups: bionet.software Subject: Re: how to import ABI SeqEd chromatograms into any mac graphical program? Date: 4 Feb 1995 15:31:29 GMT Organization: ICNET... Your Link To The Internet... +1.313.998.0090 Lines: 36 Message-ID: <3h06ki$r4q@condor.ic.net> References: <19950126.224157.104427.NETNEWS@UICVM.UIC.EDU> NNTP-Posting-Host: 152.160.8.20 lawa@bbsrc.ac.uk (Andy Law (Big Nose)) wrote: > > In article <19950126.224157.104427.NETNEWS@UICVM.UIC.EDU>, > U21206@uicvm.cc.uic.edu (Dmitri Rebatchouk) wrote: > > > Could anybody tell me whether it is possible to import ABI SeqEd > > chromatogram files into a graphical program on a Mac? Or, if it can't > > be done (which I expect), does some "connector" program exist capable > > of reformatting SeqEd files into one of graphical formats? I can > > screen-capture the image, but it becomes just a "photograph", so I > > cannot change the colors of the curves. (What I really want is to > > change colors to patterns, so that b/w printer could be used for > > hardcopy output). > > I would really appreciate any advice. > > > This is a non-trivial problem; the ABI trace information consumes a vast > amount of space. Andy is right. the trace information is pretty extensive and probably more than you want to try and transfer by cutting and pasting via the Macintosh's "clipboard." We are pretty close to releasing version 3.0 of Sequencher but I'll look into capturing editable chromatograms for you. Because of the time crunch, I'm just going to try to capture what you have visible on the screen. No promises though. Will that be enough to get you started? Best regards, Howard Cash Gene Codes Corp. genecodes@AOL.com phone: 313-769-7249 fax: 313-769-7074. From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news2.near.net!yale!yale.edu!news.ycc.yale.edu!news From: ALSOBROOK@biomed.med.yale.edu (John Alsobrook) Newsgroups: bionet.software Subject: source/docs for SEGRAN segregation analysis software? Date: 4 Feb 1995 17:07:21 GMT Organization: Yale University Lines: 18 Distribution: world Message-ID: <3h0c89$2sn@news.ycc.yale.edu> NNTP-Posting-Host: biomed.med.yale.edu X-News-Reader: VMS NEWS 1.20 Greetings! I am trying to find a description/documentation/ftp-site/ whatever for a program named SEGRAN; it's used to determine if patterns of inheritance in multiple nuclear families meet Mendelain expectations. Archie, Veronica, and WAIS have turned up nothing, so now I turn to you! All help is gratefully accepted, and I will post a follow-up once I find this software, so that the next net-surfing soul will reap the benefit of my frustration. ****************************************************************************** * John Alsobrook Child Study Center Yale University School of Medicine * * internet: alsobrook@biomed.med.yale.edu / bitnet: alsobrook@yalemed.bitnet * *----------------------------------------------------------------------------* * "Giving money and power to the government is like giving whiskey and car * * keys to teenage boys." -- P.J. O'Rourke * *----------------------------------------------------------------------------* * If I was a spokesperson for Yale my secretaries would have typed this... * *----------------------------------------------------------------------------* From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!CRIBA.EDU.AR!hmaturi From: hmaturi@CRIBA.EDU.AR ("Horacio V. Maturi") Newsgroups: bionet.software Subject: bio-software Date: 4 Feb 1995 09:37:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net help I want recive some information about bio-software tanks regards, victor domenech hmaturi@criba.edu.ar From owner-software@net.bio.net Fri Feb 03 22:00:00 1995 Path: biosci!ULAM.GENERES.CA!hutch From: hutch@ULAM.GENERES.CA ("Gord Hutchinson") Newsgroups: bionet.software Subject: RE: Neural networks in metabolism modeling? Date: 3 Feb 1995 07:09:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <25743.hutch@ulam.generes.ca> Have a look at: Bray, D. Intracellular Signalling as a Parallel Distributed Process. J. Theor. Biol. (1990) 143,215-231 Gord Hutchinson In Message 2 Feb 1995 06:19:22 -0800, MARK@cuccfa.ccc.columbia.edu (T. Mark Reboul) writes: >Dear Bionet readers, > >Is anyone aware of work in metabolic process modeling based on >neural network simulation? It seems like a reasonable technique to >consider in modeling metabolism, but so far I don't find citations >pointing to such work. Thanks for any details/suggestions/comments. > >Mark Reboul mark@cuccfa.ccc.columbia.edu >Columbia-Presbyterian Cancer Center >Computing Facility, P&S 1-420 >630 West 168th Street >New York, NY 10032 212-305-7360 From owner-software@net.bio.net Sat Feb 04 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uunet!sangam!iitb!powai!rama From: rama@powai.cc.iitb.ernet.in (ramakrishna) Subject: kinemages new version Message-ID: Date: Sun, 5 Feb 1995 18:06:32 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 17 dear netters, i have been using kinemages for viewing protein structures. i heard that recently a new version of Kinemages has been released. it has a postscript facility also. could someone help me with the ftp site from so that i can download it and use it. thanks in advance ramkrishna Ramkrishna graduate student indian institute of technology bombay 400 076 Indai email: rama@cc.iitb.ernet.in From owner-software@net.bio.net Sat Feb 04 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uunet!uunet.ca!uunet.ca!news.compulink.com!usenet From: lemargo Newsgroups: bionet.software Subject: Bibby & Jackson Immuno Research Date: 5 Feb 1995 15:33:33 GMT Organization: ComputerLink Online Inc., Toronto, ON Lines: 4 Message-ID: <3h2r4d$mep@news.compulink.com> NNTP-Posting-Host: idirect.com Can anyone help find the phone number in US or Canada of Bibby & Jackson Immuno Research . Henry From owner-software@net.bio.net Sat Feb 04 22:00:00 1995 Newsgroups: bionet.software Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!uunet!world!maayan From: maayan@world.std.com (Maayan Aharoni) Subject: Band Leader Version 2.00 Message-ID: Organization: The World Public Access UNIX, Brookline, MA Date: Sun, 5 Feb 1995 03:19:01 GMT Lines: 75 - **************************************************************************** - Band Leader Shareware distribution notes Band Leader Windows Application Version 2.00 TechKnowledge EMail address: maayan@world.std.com KEYWORDS: molecular biology,genetics,bands,image processig,gel - **************************************************************************** - Intended audience Genetics Molecular Biology What is Band Leader? Band Leader was designed and implemented by TechKnowldege as an application for processing Gel images. Band Leader is software for the PC Windows operating environment. It is very easy to use and requires only basic Windows skills. With Band Leader you process your gel images to extract data arranged in lanes or in spots. You may create graphs representing data along lanes which you may later process to extract band information. You may create Spot documents, representing single spots on the Gel image or use the Grid tool to extract a group of Spots. Band Leader data can be exported as flat text file or as Spreadsheet data. Band Leader is an MDI application, thus you may load more than one set of images to process at a time. - **************************************************************************** - - Getting Band Leader version 2.00 by ftp: 1. Ftp to expasy.hcuge.ch 2. Login as 'anonymous' 3. Go to directory pub/chromozoom 4. Ftp the file BLDIST.EXE as a binary file to your station 5. Ftp the file BLREADME.TXT as a text file to your station 6. Download the files to your PC To install Band Leader read the file BLREADME.TXT, it contains complete installation instructions. - **************************************************************************** - How to contact TechKnowledge: If you wish to get any further information about Band Leader please contact TechKnowledge. To contact TechKnowledge by phone please call: 972-3-5270267 To contact by mail write to: TechKnowledge POB 23881, Tel-Aviv 61231, ISRAEL. To contact by EMail, send mail to: MAAYAN@world.std.com From owner-software@net.bio.net Sat Feb 04 22:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!sunsite.doc.ic.ac.uk!agate!newsxfer.itd.umich.edu!gatech!bloom-beacon.mit.edu!world!maayan From: maayan@world.std.com (Maayan Aharoni) Subject: Band-Leader Version 2.00 - Gel Image Analysis Software Message-ID: Keywords: Gel-Image,Bands,proteins Organization: The World Public Access UNIX, Brookline, MA Date: Sun, 5 Feb 1995 21:51:05 GMT Lines: 76 - **************************************************************************** - Band Leader Shareware distribution notes Band Leader Windows Application Version 2.00 TechKnowledge EMail address: maayan@world.std.com KEYWORDS: molecular biology,genetics,bands,image processig,gel - **************************************************************************** - Intended audience Genetics Molecular Biology What is Band Leader? Band Leader was designed and implemented by TechKnowldege as an application for processing Gel images. Band Leader is software for the PC Windows operating environment. It is very easy to use and requires only basic Windows skills. With Band Leader you process your gel images to extract data arranged in lanes or in spots. You may create graphs representing data along lanes which you may later process to extract band information. You may create Spot documents, representing single spots on the Gel image or use the Grid tool to extract a group of Spots. Band Leader data can be exported as flat text file or as Spreadsheet data. Band Leader is an MDI application, thus you may load more than one set of images to process at a time. - **************************************************************************** - - Getting Band Leader version 2.00 by ftp: 1. Ftp to expasy.hcuge.ch 2. Login as 'anonymous' 3. Go to directory pub/chromozoom 4. Ftp the file BLDIST.EXE as a binary file to your station 5. Ftp the file BLREADME.TXT as a text file to your station 6. Download the files to your PC To install Band Leader read the file BLREADME.TXT, it contains complete installation instructions. - **************************************************************************** - How to contact TechKnowledge: If you wish to get any further information about Band Leader please contact TechKnowledge. To contact TechKnowledge by phone please call: 972-3-5270267 To contact by mail write to: TechKnowledge POB 23881, Tel-Aviv 61231, ISRAEL. To contact by EMail, send mail to: MAAYAN@world.std.com From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.starnet.net!wupost!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: Software allowing IBM to read Mac disks Date: 6 Feb 1995 08:23:50 GMT Organization: University of Cambridge, England Lines: 71 Message-ID: <3h4mam$koa@lyra.csx.cam.ac.uk> References: <3gur5j$p4g@nntp1.u.washington.edu> NNTP-Posting-Host: mole.bio.cam.ac.uk "James P. Gray" writes: >Does anyone know of a good and preferably cheap program which allows >an IBM type machine running under the DOS/Windows environment to read >Mac formatted floppies? >Thanks, It depends. Modern floppies, no problem. Very old macs used weird variable-speed drives, which could get more data on the disk, but you'll never get a PC to read them. So, if your Mac disk is formatted 720k or 1,44Mb, no problem. If it's an old 400 or 800k variety you're out of luck (but then modern macs can't read those either). I know of a demo version of a Mac emulator for DOS, which runs for 10 minutes or so if it's unregistered. Would that serve your purposes? I have a very old message about it from an OS/2 newsgroup, which is quoted below. (I just checked and the files are still there) --- cut here --- Anybody wanting to run Mac applications under OS/2 should check out the "Executor" package (for DOS, currently). I tried it today under 2.11 and am fairly impressed. > WHAT EXECUTOR IS > > Executor is a Macintosh (Macintosh is a registered trademark of Apple > Computer, Inc.) emulator for the PC. Executor can read and write > Macintosh formatted HD (1.4 Mb) floppies as well as run Macintosh programs. > A 386 or better with 4 Mb RAM, a VGA monitor and a mouse is needed to > run Executor. > Basically Executor gives you a Mono mac, able to read Mac floppies, running at the speed of a 33MHz '030 on a 486DX2 66MHz PC. I've been playing MacRisk all afternoon on my 486DX 33 and couldn't tell it wasn't a real Mac. > USE WITH OS/2 > > Executor/DOS 1.1 works with OS/2 2.1, but not with OS/2 2.0, sorry. > It works fine under 2.11 if you let it think it has lots of DPMI memory (I gave mine 16Mb) and set the HARDWARE TIMER to on. > GOALS > > We hope to release Executor/X-Windows for a variety of processors in the > first quarter of 1994, and to release Executor 2.0 for DOS, Windows, > OS/2, NEXTSTEP and X-Windows during the second quarter of 1994. We also > anticipate supporting Windows NT, but have not yet worked it into our > timeline. > So, If you want to speed up the OS/2 native version contact this guy... > Clifford T. Matthews ctm@ardi.com > Founder +1 505 766 9115 Phone > ARDI +1 505 247 1899 FAX > Executor can be found at Oakland University 141.210.10.117 under the pub/msdos/emulator directory. I think its 2.8Mb. It is demo that runs for 10 minutes, then kicks out. It seemed a bit pokey on the 486DX33 here at school, but I didn't fiddle with it very much. It only supports black and white and has no sound. It is still a pretty impressive software engineering feat though. The working version a can be ordered for $99. From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msunews!netnews.upenn.edu!sanger.bcm.tju.edu!tromp From: tromp@sanger.bcm.tju.edu (Gerard Tromp) Newsgroups: bionet.molbio.gene-linkage,bionet.software Subject: Re: Linkage software complex trait analysis Date: 6 Feb 1995 17:20:01 GMT Organization: Biochemistry Lines: 29 Distribution: world Message-ID: <3h5lo1$co6@netnews.upenn.edu> References: <3g3g1k$7lc@hawk.le.ac.uk> <3gbisp$n63@nic-nac.CSU.net> NNTP-Posting-Host: sanger.bcm.tju.edu Keywords: S.A.G.E., Mapmaker Xref: biosci bionet.molbio.gene-linkage:533 bionet.software:10961 There are packages for mapping with experimental animal crosses. One that comes to mind is S.A.G.E. , a package available from Dr. Elston at Louisiana State Medical Center in New Orleans. Another is MAPMAKER by Eric Lander et al., available by anonymous ftp from genome.wi.mit.edu. Notes about availability of LINKAGE and FASTLINK. 1. LINKAGE is available by anonymous ftp at york.cpmc.columbia.edu, the site is that of Dr. Jurg Ott, one of the co-authors of the package. The operating system is VMS - VAX - and may be somewhat unfamiliar to those who are used to unix. 2. FASTLINK is available by anonymous ftp at softlib.rice.edu, the site is that of Dr. Alejandro Schaffer. Dr. Schaffer maintains and improves FASTLINK, so it would be to your advantage to retrieve it from there rather than from other sites. -- Gerard Tromp, Ph.D. Research Assistant Professor Vox: 215-955-4487 Department of Biochemistry 215-955-4488 and Molecular Biology Fax: 215-955-5393 Thomas Jefferson University 233 South Tenth Street, Room 328 E-mail: tromp@sanger.bcm.tju.edu Philadelphia, PA 19107 U.S.A. From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uknet!comlab.ox.ac.uk!weevil.biop!gjb From: gjb@bioch.ox.ac.uk (Geoff Barton) Subject: Re: Sequences Similar or Chance? Message-ID: <1995Feb6.153831.16247@inca.comlab.ox.ac.uk> Organization: Oxford University References: Date: Mon, 6 Feb 95 15:38:30 GMT Lines: 37 In article , Peter Myler writes: |> On 22 Jan 1995, Mary Berbee wrote: |> |> > We are looking for a program to tell us if two sequences are likely to be |> > similar by chance or by homology. I assume there would be a method by |> > randomly shuffling the bases (ie, keeping the base ratio the same but |> > randomizing their order, then comparing the percent remaining the same |> > when aligned). |> > |> > Any suggestions on this will be greatly appreciated! |> > |> > Dave Carmean carmean@sfu.ca |> > Mary Berbee berbee@unixg.ubc.ca |> > |> > |> There is a DOS program called RDF2 which does pretty much what you have |> described. It used a FASTA type alignment, I believe. I don't know |> where to get it on the NET, but I have a copy which I can send if you |> want to e-mail me. |> |> Peter |> |> =============================================================================== |> Peter J. Myler phone: (206) 284-8846x332 |> Seattle Biomedical Research Institute FAX: (206) 284-0313 |> 4 Nickerson Street e-mail: MYLERPJ@U.WASHINGTON.EDU |> Seattle, WA 98109-1651 |> =============================================================================== |> |> If you do use RDF2 or any shuffling method to compare protein sequences bear in mind that the mean SD score expected for UNRELATED proteins is around 3.0. --- Geoff Barton From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!daresbury!trane.uninett.no!sunic!news.funet.fi!ousrvr.oulu.fi!ppc.oulu.fi!user From: mhaveri@cc.oulu.fi (Matti Haveri) Newsgroups: bionet.software Subject: Re: Mac version of Unix cat Date: Mon, 06 Feb 1995 18:38:12 +0200 Organization: University of Oulu Lines: 6 Distribution: bionet Message-ID: References: <3gtrm0$2o6@mserv1.dl.ac.uk> NNTP-Posting-Host: ppc.oulu.fi Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit > Does anyone know of a Mac program that will join files that have been > split on unix? ChunkJoiner. -Matti Haveri From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!news.doit.wisc.edu!news From: mayhew@midgaard.genetics.wisc.edu (George Mayhew) Newsgroups: bionet.software Subject: Re: Mac version of Unix cat Date: 6 Feb 1995 14:41:55 GMT Organization: University of Wisconsin Laboratory of Genetics Lines: 17 Distribution: bionet Message-ID: <3h5cfj$djs@news.doit.wisc.edu> References: <3gtrm0$2o6@mserv1.dl.ac.uk> NNTP-Posting-Host: anthill.genetics.wisc.edu X-Posted-From: InterNews 1.0.4@anthill.genetics.wisc.edu X-Authenticated: mayhew on POP host midgaard.genetics.wisc.edu BBEDIT and it's shareware version, BBEDIT Lite, have an extension that ships with the program that will allow the user to concatenate files. It uses the Mac multiple-file input window style. --- "People are DNA's way of making more DNA."(Edward O. Wilson, 1975) \ / \ \ / \ \ / \ \ / George Mayhew \ / \ \ / \ \ / \ \ \ /\ \ /\ \ E. coli Genome Sequencing Project \ /\ \ /\ \ \/ \__\/ \__\mayhew@midgaard.genetics.wisc.edu__\/ \__\/ \__\ University of Wisconsin - Madison, Laboratory of Genetics, College of Agricultural and Life Sciences and the Medical School 445 Henry Mall, Madison, WI 53706 Phone: 608-262-2534 Fax: 608-263-7459 http://anthill.genetics.wisc.edu/HTML/STAFF/mayhew/mayhew.html +++ For my PGP pubkey, finger me at midgaard.genetics.wisc.edu +++ From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: Software allowing IBM to read Mac disks Date: 6 Feb 1995 11:09:48 GMT Organization: University of Cambridge, England Lines: 24 Message-ID: <3h501s$p17@lyra.csx.cam.ac.uk> References: <3gur5j$p4g@nntp1.u.washington.edu> <3h4s2l$n97@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk Tony Hodge writes: >I'm really glad that Apple have maintained upward and downward >compatability so well even with the transition to Power PC, by the >way, where are the IBM PPC machines - being designed on Pentium >"estimators"? IBM PowerPC machines have been available for some time (the low end RS/6000 systems use the PowerPC chips). They haven't released a PowerPC Reference Platform compatible machine yet, but neither have Apple. PowerMacs are not PReP, as far as I know. So they've basically done the same as Apple, but less visibly, since the RS/6000 Unix market is not as high profile as the Mac one. But you get similar benefits to PowerMacs... an RS/6000 with AIX comes with Windows emulation, just like the PowerMac, for example. Not that I'd buy either! I'm waiting for a PReP machine to come out on which I have a choice of operating systems. It'll be nice to have a machine on which I can run any of System 7, NT, AIX or OS/2 (the latter being my preferred option). If Apple would support any other operating system than System 7 (and A/UX doesn't count for this discussion), I'd go and buy a PowerMac today. Tim. From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!lyra.csx.cam.ac.uk!tempest-g703.mrc-lmb.cam.ac.uk!tph From: Tony Hodge Newsgroups: bionet.software Subject: Re: Software allowing IBM to read Mac disks Date: 6 Feb 1995 10:01:57 GMT Organization: MRC Laboratory of Molecular Biology Lines: 45 Distribution: world Message-ID: <3h4s2l$n97@lyra.csx.cam.ac.uk> References: <3gur5j$p4g@nntp1.u.washington.edu> NNTP-Posting-Host: tempest-g703.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.1_68K X-XXMessage-ID: X-XXDate: Mon, 6 Feb 1995 10:01:47 GMT In article <3h4mam$koa@lyra.csx.cam.ac.uk> Tim Cutts, tjrc1@mole.bio.cam.ac.uk writes: >Subject: Re: Software allowing IBM to read Mac disks >From: Tim Cutts, tjrc1@mole.bio.cam.ac.uk >Date: 6 Feb 1995 08:23:50 GMT >>"James P. Gray" writes: > >>Does anyone know of a good and preferably cheap program which allows >>an IBM type machine running under the DOS/Windows environment to read >>Mac formatted floppies? > >>Thanks, > >It depends. Modern floppies, no problem. Very old macs used weird - I think you mean 'inovative' not 'weird' for the reason stated on the next line >variable-speed drives, which could get more data on the disk, but ************** >you'll never get a PC to read them. So, if your Mac disk is formatted >720k or 1,44Mb, no problem. If it's an old 400 or 800k variety you're >out of luck (but then modern macs can't read those either). Not entirely true, modern Macs can read and format the 800k and 400k (and, as an aside, those pesky DOS format discs too! - now as part of the standard system software) - this is based on using Quadra 650 and PowerMac 6100 machines - quite modern you will agree? I'm really glad that Apple have maintained upward and downward compatability so well even with the transition to Power PC, by the way, where are the IBM PPC machines - being designed on Pentium "estimators"? Tony P Hodge Structural Studies Division Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 2QH UK Phone (01223) 402260 Fax (01223) 213556 From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!ftpbox!news.acns.nwu.edu!uicvm.uic.edu!u21206 Message-ID: <19950204.182551.339780.NETNEWS@UICVM.UIC.EDU> Nntp-Posting-Host: k025.bios.uic.edu Date: Sat, 4 Feb 1995 17:10:58 +0000 Newsgroups: bionet.software Subject: Freeware/shareware/inexpensive commersial trace editors? Organization: Univ. of Illinois at Chicago, Laboratory for Molecular Biology Distribution: world References: <3grg7e$at1@canopus.cc.umanitoba.ca> X-Posted-From: InterNews 1.0.5@k025.bios.uic.edu Lines: 26 Xdisclaimer: No attempt was made to authenticate the sender's name. From: U21206@uicvm.cc.uic.edu (Dmitri Rebatchouk) Sender: -Not-Authenticated-[8146] Hello, I'd really appreciate any pointers to freeware/shareware/inexpensive commersial trace editors (traces = chromatograms from fluorescent sequencing/gene typing, IBI/Standard Chromatogram File format), especially for Mac. Thanks, Dmitri. ------------------------------------ Dmitri Rebatchouk U21206@uicvm.cc.uic.edu dmitri@uic.edu Laboratory for Molecular Biology University of Illinois at Chicago 840 West Taylor St. Rm 4281 Chicago, IL 60607-7020 U.S.A. (312) 996-5601 tel (312) 413-2691 FAX ------------------------------------ From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!quartz.ucs.ualberta.ca!mac10.biochem.ualberta.ca!user From: keith@bones.biochem.ualberta.ca (Keith Robinson) Newsgroups: bionet.software Subject: Re: Software allowing IBM to read Mac disks Date: Mon, 06 Feb 1995 12:08:44 -0800 Organization: Dept. of Biochemistry, The U. of Alberta, Edmonton Ab Canada Lines: 25 Message-ID: References: <3gur5j$p4g@nntp1.u.washington.edu> NNTP-Posting-Host: mac10.biochem.ualberta.ca In article <3gur5j$p4g@nntp1.u.washington.edu>, "James P. Gray" wrote: > Does anyone know of a good and preferably cheap program which allows > an IBM type machine running under the DOS/Windows environment to read > Mac formatted floppies? Look in the Simtel-20 archives. Either of these programs will allow you to read/write 720Kb and 1.44Mb mac diskettes on your pc. Here's the short description: macett30.zip B 44067 940909 Read, write, and format Mac disks on a PC macsee22.zip B 54701 930325 Read/write Macintosh disks on PC. DOS & WIN3.x Here's the URLs if you want to grab these files: ftp://wuarchive.wustl.edu/systems/ibmpc/msdos/diskutil/macett30.zip ftp://wuarchive.wustl.edu/systems/ibmpc/msdos/diskutil/macsee20.zip Keith -- Keith Robinson The University of Alberta keith@bones.biochem.ualberta.ca Edmonton, Alberta Canada From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Newsgroups: bionet.software Path: biosci!rutgers!gatech!swrinde!pipex!uknet!bcc.ac.uk!rmiller From: rmiller@bsm.bioc.ucl.ac.uk (Rob Miller) Subject: Re: THREADER (structure prediction software) update Message-ID: <1995Feb6.191243.35946@ucl.ac.uk> Date: Mon, 6 Feb 1995 19:12:43 GMT References: <1995Feb4.143239.30581@ucl.ac.uk> Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Lines: 45 David Jones (jones@bsm.bioc.ucl.ac.uk) wrote: : **** THREADER **** : THREADING SOFTWARE UPDATE : The software is free to academics and non-profitmaking organizations, : and available for a fee to commercial users. The software may be obtained : from our ftp server as follows: : ftp ftp.biochem.ucl.ac.uk : name: anonymous : password: your-email-address : cd pub/THREADER also available in the pub/px directory is our Tcl/Tk based GUI for analyzing THREADER results. You do _not_ need to have Tcl/Tk installed to run it (we supply an extended Tcl interpreter for working with protein structure information, all necessary Tcl/Tk support files, and complete C source code), nor does the GUI require a license. e-mail me if you have any questions or problems. rob. ------------------------------------------------------- Rob Miller, Ph.D. Biomolecular Structure and Modelling Unit (BSM), Department of Biochemistry and Molecular Biology, University College / Gower Street / London WC1E 6BT. United Kingdom. Tel: 44 71387 7050 x2303 Fax: 44 71380 7193 home: 44 442 65092 Internet: rmiller@bsm.bioc.ucl.ac.uk http://www.biochem.ucl.ac.uk/~rmiller ------------------------------------------------------- From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Newsgroups: bionet.software Path: biosci!rutgers!gatech!howland.reston.ans.net!torn!utnut!utcsri!newsflash.concordia.ca!CC.UMontreal.CA!megasun.BCH.UMontreal.CA!tim From: tim@megasun.BCH.UMontreal.CA (Tim Littlejohn) Subject: Re: Freeware/shareware/inexpensive commersial trace editors? Message-ID: Sender: news@cc.umontreal.ca (Administration de Cnews) Organization: Universite de Montreal References: <3grg7e$at1@canopus.cc.umanitoba.ca> <19950204.182551.339780.NETNEWS@UICVM.UIC.EDU> Date: Mon, 6 Feb 1995 17:32:27 GMT Lines: 50 Dmitri, In article <19950204.182551.339780.NETNEWS@UICVM.UIC.EDU> U21206@uicvm.cc.uic.edu (Dmitri Rebatchouk) writes: >Hello, > >I'd really appreciate any pointers to freeware/shareware/inexpensive >commersial trace editors (traces = chromatograms from fluorescent >sequencing/gene typing, IBI/Standard Chromatogram File format), >especially for Mac. Try the Staden package: very cheap (it may even already be installed at your site) and it has a good trace editor called "ted". From the bionet.software.staden FAQ: --------------------------------------------------------------------------- 5. Where do I get the Staden package from? Further information can be obtained by sending an email message to: staden-package@mrc-lmb.cam.ac.uk To order the package, send you name and address together with a request for licence agreement forms to: Rodger Staden, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. --------------------------------------------------------------------------- I hope this helps, Tim -- ============================================================================== Tim Littlejohn E-mail: tim@bch.umontreal.ca Snail Mail: Departement de biochimie Phone: (514) 343-6111, x5149 Universite de Montreal Fax: (514) 343-2210 C.P. 6128, Centre-ville Montreal (Quebec), H3C 3J7 CANADA ============================================================================== From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Newsgroups: bionet.software Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!swrinde!pipex!uknet!gdt!bsspak From: bsspak@bath.ac.uk (P A Keller) Subject: Re: Software allowing IBM to read Mac disks Message-ID: Reply-To: P.A.Keller@bath.ac.uk Organization: Department of Biology and Biochemistry, University of Bath, UK References: <3gur5j$p4g@nntp1.u.washington.edu> <3h4s2l$n97@lyra.csx.cam.ac.uk> <3h501s$p17@lyra.csx.cam.ac.uk> Date: Mon, 6 Feb 1995 17:41:52 GMT Lines: 17 To get back to the original thread, there is a program called Macsee which claims to do what you want. You should be able to find an ftp site with archie. Good luck, Peter. ======================================================================== Peter Keller. \ Dept. of Biology and \ "....males are biologically driven to go Biochemistry, \ out and hunt giraffes." University of Bath, \ Bath, BA2 7AY, UK. \ --- Newt Gingrich ------------------------------\----------------------------------------- Tel. (+44/0)1225 826826 x 4302 | Email: P.A.Keller@bath.ac.uk (Internet) Fax. (+44/0)1225 826449 | P.A.Keller%bath.ac.uk@UKACRL (BITNET) ======================================================================== From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!howland.reston.ans.net!vixen.cso.uiuc.edu!ux4.cso.uiuc.edu!cksong From: cksong@ux4.cso.uiuc.edu (chun-keet song) Newsgroups: bionet.software Subject: ERROR 15-1 with Crosstalk for Windows Date: 6 Feb 1995 17:41:03 GMT Organization: University of Illinois at Urbana Lines: 12 Message-ID: <3h5mvf$iqk@vixen.cso.uiuc.edu> NNTP-Posting-Host: ux4.cso.uiuc.edu I have been using Crosstalk 2.0 for Windows for quite a while now. Recently, however, I have had the program disconnect in the middle of a session with an ERROR 15-1 Does anyone know what 15-1 is? Thanks Song PS: Please respond via e-mail to cksong@ux4.cso.uiuc.edu From owner-software@net.bio.net Sun Feb 05 22:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!pipex!uunet!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: medmult@aol.com (MedMult) Newsgroups: bionet.software Subject: Re: anatomy software Date: 5 Feb 1995 19:51:05 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 13 Sender: root@newsbf02.news.aol.com Message-ID: <3h3rpp$3kd@newsbf02.news.aol.com> References: <3gmmlq$2c3@knot.queensu.ca> Reply-To: medmult@aol.com (MedMult) NNTP-Posting-Host: newsbf02.mail.aol.com >>Can anyone tell me of any good CD ROM anatomy software? Any other info. >>on good medical software would be greatly appreciated. We produce an interactive neuroanatomy atlas called Brainiac that runs under IBM Windows. You can obtain a demo via ftp at ftp.bio.indiana.edu The demo is located in the /biology/ibmpc directory and is called brainiac-demo.zip Make sure you set the transfer protocol to BINARY before getting the .zip file. Use pkzip 2.04g to uncompress the demo and run the install.exe program from Windows. Please feel free to email me directly if you have any questions. Glen Frick Medical Multimedia Systems From owner-software@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!torn!newshost.uwo.ca!jkiernan.anatomy.uwo.ca!jkiernan From: jkiernan@julian.uwo.ca (J. A. Kiernan) Newsgroups: bionet.software Subject: Utility for molecular weight & solution concentrations Date: Tue, 7 Feb 1995 17:34:49 GMT Organization: ITS, University of Western Ontario Lines: 38 Message-ID: NNTP-Posting-Host: jkiernan.anatomy.uwo.ca Summary: Simple calculations at the command-line, or interactively MOLWT Version 2.3 Do you ever need to do a quick molecular weight calculation from a chemical formula, or want to know how many grams of Na2SO4.10H2O are in 100 ml of a 0.076M solution? You can use MOLWT, a new shareware program, to get instant answers, even at the DOS command-line. MOLWT is a utility for simple chemical calculations There are already some excellent chemical calculation programs, including CHEMCALC. MOLWT is not as versatile as these, but it is much faster for what it does do, and it needs only 50 KB of disk space (half of which is documentation). It will run on any DOS-based computer. Color is used for emphasis, but the screens are legible on any kind of monitor. Available by anonymous ftp from oak.oakland.edu in the /SimTel/msdos/chemstry directory. The file is molwt.zip. Or from garbo.uwasa.fi in the /pc/science directory, as molwt23.zip. Dont forget to enter the "binary" command before downloading! The MOLWT.ZIP (or MOLWT23.ZIP) archive contains 3 files: MW.EXE calculates molecular weight from an entered chemical formula. Can be used at the DOS command line, or interactively. SOLUTION.EXE gives concentrations in various units in response to an entered formula and concentration. It works with MW.EXE Can be used at the DOS command line, or interactively. MOLWT.EXE is the documentation file, which can be read on screen or printed in whole or part. Comments and suggestions John A. Kiernan welcome! Department of Anatomy Univ. of Western Ontario LONDON, Canada N6A 5C1 Phone: (519) 679-2111 e.6822 e-mail: jkiernan@julian.uwo.ca From owner-software@net.bio.net Mon Feb 06 22:00:00 1995 Newsgroups: bionet.software Path: biosci!lhc!ncbi!info From: info@ncbi.nlm.nih.gov (Temp Acct for Sending Mail from info) Subject: BankIt - New WWW GenBank Submission Tool Message-ID: <1995Feb7.181522.13730@nlm.nih.gov> Sender: news@nlm.nih.gov Organization: National Library of Medicine X-Newsreader: TIN [version 1.2 PL2] Date: Tue, 7 Feb 95 18:15:22 GMT Lines: 42 ---------------------------------------------------------------------- GenBank Now Offers BankIt -- WWW Submission Tool for GenBank Sequences ---------------------------------------------------------------------- GenBank users may now use the World Wide Web (WWW) for submitting sequences to GenBank. The new submission tool - BankIt - provides a simple forms approach for submitting your sequence and descriptive information to GenBank. BankIt has been developed by GenBank in conjunction with its international collaborating databases (EMBL and DDBJ) and it is anticipated that EMBL and DDBJ will be offering similar services in the near future. Your submission will be submitted directly to GenBank and immediately forwarded for inclusion in the EMBL and DDBJ databases. BankIt allows you to enter sequence information into a form, revise as necessary, and add biological annotation (e.g., coding regions, mRNA features). BankIt transforms your data into GenBank format for your review and when your record is completed, it can be submitted directly to GenBank. You have the option of adding information by using text boxes to describe in your own words the source of the sequence and its biological features. The GenBank annotation staff reviews the submitted textual information, incorporates it into the appropriate structured fields, and returns the record by e-mail for your review. GenBank will promptly contact you by e-mail with an accession number. Once the testing phase is completed, BankIt will automatically issue accession numbers. BankIt has been tested with Netscape clients for Unix, Macs, and PCs. In addition, the Mosaic client for Unix, and the MacWeb client for Macs, have successfully been used. You can access BankIt through the GenBank home page: http://www.ncbi.nlm.nih.gov/ If you have any questions on using BankIt, please contact the GenBank support staff at 'info@ncbi.nlm.nih.gov' or at (301) 496-2475. From owner-software@net.bio.net Mon Feb 06 22:00:00 1995 Path: biosci!adam.cc.sunysb.edu!news.sprintlink.net!pipex!uunet!CS.Arizona.EDU!biosci!BEKKOAME.BEKKOAME.OR.JP!isshikim From: isshikim@BEKKOAME.BEKKOAME.OR.JP (Masashi Isshiki) Newsgroups: bionet.software Subject: unsubscribe Date: 6 Feb 1995 19:18:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <199502070320.MAA26985@bekkoame.bekkoame.or.jp> NNTP-Posting-Host: net.bio.net unsubscribe bio-soft isshikim@tau.bekkoame.or.jp Masashi Isshiki the 4th. Dep. of Int. Med.,Faculty of Medicine,Tokyo Univ. E-mail: isshiki-tky@umin.u-tokyo.ac.jp isshikim@tau.bekkoame.or.jp PXG00710@niftyserve.or.jp From owner-software@net.bi