From owner-software@net.bio.net Sat Oct 02 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!uwm.edu!math.ohio-state.edu!caen!uvaarpa!murdoch!cyclops.micr.Virginia.EDU!wrp From: wrp@cyclops.micr.Virginia.EDU (Bill Pearson) Newsgroups: bionet.software Subject: Re: T-matrix and Nucaln Message-ID: Date: 2 Oct 93 01:03:52 GMT References: <1993Sep29.183014.69@cnbvx3.cnb.uam.es> <1OCT199307565849@aardvark.ucs.uoknor.edu> Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Lines: 17 In article <1OCT199307565849@aardvark.ucs.uoknor.edu>, Bruce Roe wrote: >In article <1993Sep29.183014.69@cnbvx3.cnb.uam.es>, lpezzi@cnbvx3.cnb.uam.es writes... >>Hi, >>a user of our system is interested in the programs T-matrix and Nucaln. >> > Nucaln is a program written by David Lipman and Bill Pearson >and is one of the original multiple sequence alignment programs. It's >really out of date and very slow. Nucaln was written by David Lipman and John Wilbur; it predates my association with David (actually we met because of it). I can send a copy of it if you like, but the FASTA program provides very similar functionality and is available via anonymous ftp from uvaarpa.virginia.EDU in pub/fasta. Bill Pearson From owner-software@net.bio.net Sat Oct 02 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!nigel.msen.com!yale.edu!cs.yale.edu!news From: Peter Gogarten Newsgroups: bionet.software Subject: re: plotting program for phylogenies/sequence families?????? Message-ID: <1993Oct2.172141.26404@cs.yale.edu> Date: 2 Oct 93 17:21:41 GMT References: Sender: news@cs.yale.edu (Usenet News) Organization: Yale University, Department of Computer Science, New Haven, CT Lines: 10 Nntp-Posting-Host: 137.99.27.78 In article Neil.Clarke@qmail.bs.jhu.edu (Neil Clarke) writes: >Does anyone know of a program (on any platform but preferably Mac) that >will plot a phylogenetic-type tree. I don't need the program to calculate >"distances" or who is connected at which nodes. I just need something that >can plot a tree given such information. Much obliged if anyone knows of >such a thing. The thought of doing this by hand ....arghhh. Joe Felsenstein's Phylip package among others contains two tree/cladogram-drawing programs. From owner-software@net.bio.net Sat Oct 02 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: Nentrez cost (Re: Entrez:Sequences HELP !!!!!!) Message-ID: <1993Oct3.115329.5127@comp.bioz.unibas.ch> Date: 3 Oct 93 11:53:29 GMT References: <1993Sep28.183625.410@gserv1.dl.ac.uk> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Distribution: bionet Organization: EMBnet Switzerland [BASEL] Lines: 42 Nntp-Posting-Host: biox.embnet.unibas.ch In article , leach@mbcrr.harvard.edu (Martin Leach) writes: ... |> I receive the NCBI news letter and have found out that there is a |> beta-version of a program called Nentrez available by anonymous FTP at |> ncbi.nlm.nih.gov (130.14.25.1). |> ... |> I've used this and it is smegging great. ... |> It costs nothing to register and gives you access to all the info |> you would have to get from those expensive cd-roms. |> NO! How often do the biologists neet to be notified that NOTHING is free on the network??? I have used this Nentrez as well and people LOVE it. Its a damned good piece of software but I would like to emphasize that these less than 100 dollars a year are by far _less_ money than the amount used up to pay for network bandwidth. Are you really sure that it scales to let hundreds of queries pass accross the net if you could get it as well locally for less than $100 ? I am seriously concerned that biologists need to learn a lot in terms of networking and its cost before such tools like Nentrez and others can be passed to the community in responsible fashion. If you continue to consume bandwidth like this there won't be all of us on the network in the future, and only the 'selected few' who can afford paying for the lines will survive. -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-software@net.bio.net Sat Oct 02 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!nigel.msen.com!yale.edu!newsserver.jvnc.net!newsserver.technet.sg!nuscc.nus.sg!mcblab47 From: mcblab47@leonis.nus.sg (Chia Jin Ngee) Newsgroups: bionet.software Subject: Re: PCR Primer Design Programs Message-ID: <28j1vu$s19@nuscc.nus.sg> Date: 2 Oct 93 05:01:50 GMT References: <93274.114042RROXBY@MAINE.MAINE.EDU> Organization: National University of Singapore Lines: 31 NNTP-Posting-Host: leonis.nus.sg X-Newsreader: TIN [version 1.2 PL0] Robert Roxby (RROXBY@MAINE.MAINE.EDU) wrote: : What do you think is the best program for back-translating a protein : sequence, possibly an ambiguous sequence (multiple amino acids : possible at some positions) and using the degenerate DNA sequence : to design a PRC probe? : Thanks for advice : Bob Hi Bob, I suggest this program called "pgen". I think it can be found in the archives at IUBio. Requirements are IBM PC compatible and a VGA monitor. You just supply it the peptide sequence, the degeneracy number (usually 300 I wouldn't go higher than that), the shortest and longest number of bases possible for the oligo, and finally the translation codes for your particular organism. (They only supply the universal translation and E. coli codes the rest you have to type in yourself) With all that input it finds several suitable primers that match criteria. Regards and blessings to your work :-) Genie +--------------------------------------------------------------------------+ |Jin Ngee, Chia Chemical Carcinogenesis Laboratory | |(Genie, the OligoMan) Institute of Molecular and Cell Biology | |mcblab47@leonis.nus.sg National University of Singapore | |Tel: (065)772-3797 Kent Ridge Crescent | |Fax: (065)779-1117 Singapore 0511 | |"I'm Mr Chia not Ms Chia and I know Genie is a girl's name"-Jin Ngee, Chia| +--------------------------------------------------------------------------+ From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!pipex!uknet!comlab.ox.ac.uk!mikes From: mikes@bioch.ox.ac.uk (Mike Smith) Newsgroups: bionet.software Subject: Cluster Analysis Message-ID: <1993Oct4.130331.4235@nmrn.bioch.ox.ac.uk> Date: 4 Oct 93 13:03:31 GMT Organization: Department of Biochemistry, University of Oxford Lines: 11 Originator: mikes@nmrn.ocms Dear Bionetters, Does anybody know how one goes about dividing 100 structures (say) with the same amino acid sequences into groups of similar structures. The way I would envisage doing this would be to say that two structures are in the same group if their rmsd (say) is less than 1 Angstrom, and that this relationship is transitive, but this is only guessing! Mike Smith From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!pipex!sunic!corax.udac.uu.se!zeta.bmc.uu.se!daresbury!daresbury!news From: 030MARK@za.ac.wits.witsvma (Mark Wildman) Newsgroups: bionet.software Subject: graded potentials Message-ID: <1993Oct4.130649.21389@gserv1.dl.ac.uk> Date: 4 Oct 93 15:00:25 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 14 Precedence: first-class Original-To: bio-software@uk.ac.daresbury Does anyone have, or know about, software that models decremental conduction in neurones? I want to present such a program with a waveform and model what it would look like further down the cell, without having to do any maths myself! If you know of such a program please let me know, as well as where I can get it from. Many thanks, Mark Wildman Dept Physiology University of the Witwatersrand Johannesburg, South Africa Email: 030mark@witsvma.wits.ac.za From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!pipex!sunic!corax.udac.uu.se!zeta.bmc.uu.se!daresbury!daresbury!news From: al28044@uk.co.ggr Newsgroups: bionet.software Subject: NENTREZ Message-ID: <1993Oct4.122329.20720@gserv1.dl.ac.uk> Date: 4 Oct 93 11:58:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 12 Precedence: first-class Original-To: bio-software@uk.ac.daresbury PS. I forgot to say in my previous message. It is LUDICROUS to describe the ENTREZ CDs as expensive! I challenge the community to suggest anything that is better value for money! Andrew From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!darwin.sura.net!blaze.cs.jhu.edu!jhunix.hcf.jhu.edu!NewsWatcher!user From: Neil.Clarke@qmail.bs.jhu.edu (Neil Clarke) Newsgroups: bionet.software Subject: Re: phylogeny drawing: Thanks and FYI good info source Message-ID: Date: 4 Oct 93 17:03:53 GMT References: <1993Oct2.172141.26404@cs.yale.edu> Followup-To: bionet.software Organization: Johns Hopkins Lines: 4 NNTP-Posting-Host: 128.220.56.216 Thanks to everyone who sent me info on phylogeny plotting. Some people directed be to the IUBio server (a revelation to a gopher newbie like me!) For future reference, I found a very nice discussion of various programs by J. Felsenstein in evolve/phylogeny.soft.help in the molbio archive. From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: Re: NENTREZ. Message-ID: <1993Oct4.171130.697@comp.bioz.unibas.ch> Date: 4 Oct 93 17:11:30 GMT References: <1993Oct4.121351.20540@gserv1.dl.ac.uk> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Distribution: bionet Organization: EMBnet Switzerland [BASEL] Lines: 106 Nntp-Posting-Host: biox.embnet.unibas.ch In article , rcwieg@ccmail.monsanto.com (Roger Wiegand) writes: |> In article <1993Oct4.121351.20540@gserv1.dl.ac.uk>, al28044@uk.co.ggr |> wrote: ... |> > For all but the smallest sites (ie one person using ENTEZ occasionally) |> > it MUST be more cost effective to get the CDs and install them locally. ... |> With the rate that new sequences are coming into the world |> the chances of re-doing work that is already done and published are |> increasing. The costs of doing work unnecessarily are astronomical |> compared to the cost of network bandwidth. ... Let me explain this a little bit more. With respect to NENTREZ, we're talking on two important issues. The _USER_INTERFACE_ of Nentrez is optimally structured as it allows for local (or lan-based) editing on a screen. This means that you run or store the image on one computer and throw the window accross the cable. This is _much_ better and cheaper than the X-Window system (e.g., running the ACEDB interface in transatlantic sessions wates much more bandwidth). The _SEQUENCE_DATA_ are a different issue. If I complain that the network bandwith usage is too expensive than this is based on (a) european PTT cost ( if you pay a five digit amount of $ for a 2 MBit line per year then this is no longer to be called 'cheap') and (b) on a simple scaling calculation. If you compare the direct access of Nentrez with the mail- based retrieval tools then the difference between synchronous and asynchronous way of query processing is obvious. The provider view is to recognize incoming mails and put it into a queue in case of overload. Similarly, the provider can process incoming interactive queries in a queue. From the _end_ user, however, the interactive access with Nentrez raises the expectation that the reply will be displayed in noticable time, and that an 'on-line' query is possible. There's a much lower expectation in the mail interface as you always consider networks to be slow and unreliable (sorry for any non-intentional puns) and therefore you do not worry about a minute or even several minutes delay. My point is that an institution like the NCBI is in the difficult position that any attempt to _ensure_ a certain access time is not practicable; as you cannot predict neither budget the development on future user sessions. Typically, I have about 20 persons in the class room. If I tell them to try out a blast search the UNIX cluster which I use for this purpose (I run blast locally) gets a hard time as all 20 want to see their results immediately. The world is a much bigger classroom, and if we are assuming that a ground load of 'reasonable' queries is supplemented by students and computer classes a simple consideration already ends in orchestrated chaos: Too many requests might delay the few who _need_ the results, and the students or whoever needs the result for teaching purposes is rejected because the system is sooo slow. The _UPDATED_SEQUENCE_DATA_ will need to be accessed via networks. There is no way around telling people that we need the data from yesterday NOW and not in three months. However, I think that Nentrez has this option to get updated data via network and access other data locally... forgive me if I am wrong but I am neither the person to advertise Nentrez nor did I try this option personally, as the CD-ROM drives to do this are yet to be installed. My point was that if there is a method to access established data _locally_ there is no excuse to get it via network - in particular the quotes of 'expensive' CD-ROMS are worth fighting against. By using GPO's services the CD-ROM prices of NCBI are unbeatable - compare it with EMBL and PIR releases and you will find that expensive CD-ROMS are available. Even those should be purchased in order to have everything local as far as possible. ATLAS, for example, does sequence retrieval from the PIR CD on various systems as well; and EMBL provides both Mac and DOS interfaces to get access to the EMBL database. Last, and this is a plain European view, the NCBI is located in the US. Watching GATT's progress in the TV reminds me that there is the possibility of US funding agencies to restrict access to US customers. If we (Europeans) blindly rely on 'free' services the discovery of an unavailable because restricted service will not get us to the research targets we want to reach. We might stay in the current situation if we don't abuse the net but we endanger resources if we rely on it blindly. And, don't forget the commercial issue; if you can get services for free then why should you use a commercial host for this purpose? The current cost of the sequence data collection centers is paid by the taxpayers for providing sequence data and make it accessible. The _use_ and _service_ offers of the data libraries are very much appreciated, though, coming back to the low economy, we might hurt commercials this way and get into difficult funding discussions. Recently, I needed to tell my funding agency who benefits from the Swiss EMBnet services. Unless I can prove that I can spot most of the users, who are grant holders as well, I might face the problem that my funds are cut, with the argument that I should not spray resoucres blindly, and let users who do not contribute to the funding agencie's resources pay separately. Slightly modified, this might also apply in other countries. Hope this clarifies my earlier comments. Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!MOOSE.UVM.EDU!wyang From: wyang@MOOSE.UVM.EDU (Wanqing Yang) Newsgroups: bionet.software Subject: question Message-ID: Date: 4 Oct 93 01:15:41 GMT Sender: kristoff@net.bio.net Reply-To: Wanqing Yang Distribution: bionet Lines: 6 Could anyone tell me how I can transfer my file from Microsoft Word to e-mail in a Macintosh, if using kermit? Thank you! wyang@moose.uvm.edu From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!pipex!sunic!corax.udac.uu.se!zeta.bmc.uu.se!daresbury!daresbury!news From: al28044@uk.co.ggr Newsgroups: bionet.software Subject: NENTREZ. Message-ID: <1993Oct4.121351.20540@gserv1.dl.ac.uk> Date: 4 Oct 93 11:54:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 21 Precedence: first-class Original-To: bio-software@uk.ac.daresbury I completely agree with Reinhard Doeltz about NENTREZ & Network bandwidth. For all but the smallest sites (ie one person using ENTEZ occasionally) it MUST be more cost effective to get the CDs and install them locally. For big sites, where several people wish to use it simultaneously, it is simple to copy the CDs onto magnetic disks (you should see how fast it goes then!) We have installed ENTREZ on our LANS both under NOVEL (tm) and PATHWORKS (tm). Because the data is stored in a machine independant way it is possible to access the same files from MAC/PC/Unix & VAX. It is very easy. I would be happy to advise anybody who is thinking of doing the same. Andrew From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!news.claremont.edu!paris.ics.uci.edu!news.service.uci.edu!ih33.hsis.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: Database of DNA binding sites Message-ID: Date: 4 Oct 93 17:04:00 GMT References: Followup-To: bionet.software Organization: UC, Irvine Lines: 74 Nntp-Posting-Host: ih33.hsis.uci.edu In article , moreira@biobase.aau.dk (Jose Moreira) wrote: > > Hi netters, > > I have a "small" problem. > I need to search a yeast DNA sequence for known binding motifs, > as thoroughly as possible. > That means I would like to know where and how I can do such > a search. > > Thanks in advance > > _________________________________________ > > Jose' Moreira & Peter Schjerling > Dept. of Genetics, Univ. of Copenhagen You didn't mention what platform you wanted to try but if you have access to a unix (or even DOS) machine, you could use the nice, fast "signalscan' by Dan Prestridge. There's also an old very slow Mac version that's not supported anymore. Or if you don't, you mail me the sequence with the the database you'd like to search (yeast, mammal, all eukaryotes, etc) and I'll run it for you and return the output by mail (I just updated the Transcription Factor Database tables a day ago for someone else). Here's the descriptive blurb. Prestridge, D.S. (1991) SIGNAL SCAN: A computer program that scans DNA sequences for eukaryotic transcriptional elements. CABIOS 7: 203-206 SIGNAL SCAN is a program developed to facilitate the analysis of DNA sequences for known eukaryotic signals. This program is FREE. You may copy and distribute this program, but you may not charge for its distribution. You MUST register the program by sending your name and address to the below address. Registering this program helps to justify the program for funding purposes. For registering the program you will automatically be notified of SIGNAL SCAN changes and updates. PLEASE REGISTER, you will help assure the future of SIGNAL SCAN. The source code is written in the `C' language and is fairly easy to port over to other hardware and operating systems. The source code will be made available upon request. You may make changes to the source code, but may not release the modified program or source code without my authorization. If you use this program in published research, please site: Prestridge, D.S. (1991) SIGNAL SCAN: A computer program that scans DNA sequences for eukaryotic transcriptional elements. CABIOS 7, 203-206. The author welcomes comments and suggestions on the program or additions to the database. Please contact: Dr. Dan S. Prestridge tele:(303) 465-0658 Dept. of Mol., Cell., and Devl. Biology email:DANP@BEAGLE.COLORADO.EDU University of Colorado Boulder, Colorado 80309-0347 Cheers hjm Harry Mangalam, VCO/Micro+Mol Genetics, Irvine Hall, Coll of Med, UC Irvine, Irvine, CA, 92717, Vox:(714) 856-4824, Fax:(714) 725-2118, mangalam@uci.edu There's no better glory, when it all gets harried, to be laughing in the midst of it all. --- Doug and the Slugs --- From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!wupost!monsanto.com!rcwieg.monsanto.com!user From: rcwieg@ccmail.monsanto.com (Roger Wiegand) Newsgroups: bionet.software Subject: Re: NENTREZ. Message-ID: Date: 4 Oct 93 15:25:06 GMT References: <1993Oct4.121351.20540@gserv1.dl.ac.uk> Sender: news@tin.monsanto.com (USENET News System) Followup-To: bionet.software Distribution: bionet Organization: Monsanto/Searle Molecular Genetics Lines: 52 In article <1993Oct4.121351.20540@gserv1.dl.ac.uk>, al28044@uk.co.ggr wrote: > > > > I completely agree with Reinhard Doeltz about NENTREZ & Network bandwidth. > > For all but the smallest sites (ie one person using ENTEZ occasionally) it > MUST be more cost effective to get the CDs and install them locally. > > For big sites, where several people wish to use it simultaneously, it is > simple to copy the CDs onto magnetic disks (you should see how fast it > goes then!) > > We have installed ENTREZ on our LANS both under NOVEL (tm) and PATHWORKS (tm). > > Because the data is stored in a machine independant way it is possible to > access the same files from MAC/PC/Unix & VAX. > > It is very easy. I would be happy to advise anybody who is thinking of > doing the same. > > Andrew A problem with anything that has to be distributed on CD is that it is weeks to months out of date whereas the on-line service is only limited by the entry delay. With the rate that new sequences are coming into the world the chances of re-doing work that is already done and published are increasing. The costs of doing work unnecessarily are astronomical compared to the cost of network bandwidth. By either path the cost of distribution (network vs CD) is probably trivial vs the cost of assembling and cataloging the data and writing the access programs. Perhaps the best of both worlds would involve periodic distribution of the entire database by CD or tape with daily updates to remote sites available over the network, as GenBank is currently handled, rather than having all individuals need to go out over the net. Cable TV companies here are talking about providing 100 MB/sec connections to homes on a national network on a for-profit basis at about US$75/month starting in 1995-6. Is the "real cost" (whatever that means) of an Internet connection a lot higher than that? (That's dirt cheap in my estimation) -- Thanks, Roger rcwieg@ccmail.monsanto.com From owner-software@net.bio.net Sun Oct 03 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!uunet!yeshua.marcam.com!zip.eecs.umich.edu!umn.edu!lynx.unm.edu!carina.unm.edu!news-user From: bhjelle@unm.edu Newsgroups: bionet.software Subject: PAUP for IBM-PC Message-ID: <28plqu$4hj@carina.unm.edu> Date: 4 Oct 93 17:17:18 GMT Organization: University of New Mexico, Albuquerque Lines: 12 NNTP-Posting-Host: carina.unm.edu I've had some indirect experience with the PAUP program (version 3.1) in making parsimony trees (viral). I believe they are all Mac-based. I would like to try to obtain a similar program for IBM-PC/ MS-DOS. I would even be willing to pay for it ! :-( Is there such a thing, or will I have to get a Mac just for this one application? Thanks in advance. Brian From owner-software@net.bio.net Mon Oct 04 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!math.fu-berlin.de!news.dfn.de!server2.rz.uni-leipzig.de!RNEWS.urz.tu-dresden.de!TUDURZ!petzoldt From: petzoldt@TUDURZ.urz.tu-dresden.de (Thomas Petzoldt Hydrobiologie) Newsgroups: bionet.software Subject: sigma plot ?? Keywords: sigma plot pc windows time series Message-ID: Date: 5 Oct 93 16:05:47 GMT Sender: news@RNEWS.urz.tu-dresden.de (Administrator) Organization: TU Dresden - URZ Lines: 18 Nntp-Posting-Host: tudurz.urz.tu-dresden.de Dear Netters, does anybody know a program called SIGMA-PLOT ? Where can I get it from and how much does it cost? Is there a WINDOWS-Version available or is it a DOS-program ? I've got a hint, that it would be useful to plot my data, but I have no detailed information. Does anybody know another program which is able to plot time series in a user friendly way? Gnuplot (or EXCEL on the other hand) are not flexible enough. Thank you in advance Thomas petzoldt@biowissenschaft.tu-dresden.d400.de From owner-software@net.bio.net Mon Oct 04 23:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!wupost!monsanto.com!bb1t.monsanto.com!lrhold From: lrhold@bb1t.monsanto.com Newsgroups: bionet.software Subject: GLOBAL86 & StaTox? Message-ID: <1993Oct5.090858.1@bb1t.monsanto.com> Date: 5 Oct 93 15:08:58 GMT Sender: news@tin.monsanto.com (USENET News System) Organization: Monsanto Company, St. Louis, MO Lines: 11 Does anyone know if the GLOBAL86 carcinogenic risk assesment program and the StaTox program are available anywhere via FTP? Both are used by the EPA for analysis of chemical toxicological data. (A similar message also posted on bionet.general) Thanks for any help. ---------------------------------------------------------------------- Larry R. Holden, Ph.D. | Environmental Science Department, lrhold@ccmail.monsanto.com | Monsanto, The Agricultural Group Voice: 314-537-6885 | 700 Chesterfield Prkwy North Fax : 314-537-6134 | St. Louis, MO 63198, USA From owner-software@net.bio.net Mon Oct 04 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Display software for PDB molecules Message-ID: Date: 5 Oct 93 13:24:06 GMT References: <9310051218.AA18245@jonas> Sender: news@usenet.ucs.indiana.edu (USENET News System) Distribution: bionet Organization: Biology, Indiana University - Bloomington Lines: 22 Nntp-Posting-Host: sunflower.bio.indiana.edu This may not exactly answer your question, but I just noticed recently that the Gopher service at Brookhaven lab (home of Protein Data Bank) now offers GIF pictures of most of its molecules, along with the raw molecule data. That is a marvelous service, folks at PDB. Now users can easily view molecules thru gopher, as well as fetch the raw data for manipulating at home. Most Gopher clients can view GIF files with the addition of free graphics software, such as "xv" on XWindows computers, JPEGViewer or QuickGif or GIffer on Macintoshes, WinGIF or similar on MSWIndows. To answer Michel Werner's desire to manipulate and display PDB molecules on his own Mac, you might start looking at IUBio archive (ftp.bio.indiana.edu) in the chemistry/mac/ folder. I think there are some free mol. viewers there. -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Mon Oct 04 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: jenkins@uk.ac.nibsc.aidsun Newsgroups: bionet.software Subject: Phylogeny software Message-ID: <1993Oct5.082754.7728@gserv1.dl.ac.uk> Date: 5 Oct 93 08:28:24 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 376 Precedence: first-class Original-To: bio-software@uk.ac.daresbury > I've had some indirect experience with the PAUP program > (version 3.1) in making parsimony trees (viral). > I believe they are all Mac-based. I would like to try > to obtain a similar program for IBM-PC/ MS-DOS. > I would even be willing to pay for it ! :-( > Is there such a thing, or will I have to get a Mac > just for this one application? > Thanks in advance. > Brian Here is a review written by Joe Felsenstein (who wrote the phylip package) of some phlogeny software. hope it is of use Adrian SOME AVAILABLE PHYLOGENY PROGRAMS The following material (except item 0) is from the PHYLIP version 3.5 documentation. I post it because it may be a useful compilation. Here are some of the phylogeny packages that I know about. Some of them are available over Internet from ftp server machines. If you are on Internet you should familiarize yourself with ftp and with them (see entries 6 and 7 below for more information). Table of Contents 0. PHYLIP 9. VOSTORG 16. COMPROB 1. PAUP 10. MEGA 17. MARKOV 2. BIOSYS-1 11. Evomony 18. PHYSYS 3. MacClade 12. COMPONENT 19. SINCAIDEN 4. Hennig86 13. Turbotree 20. MUST 5. ClaDOS 14. Molevol 21. GDE 6. TreeAlign 15. CLINCH 22. TreeTool 7. Clustal 0. PHYLIP is a free package of programs for inferring phylogenies, including programs to carry out parsimony, compatibility, distance matrix, invariants ("evolutionary parsimony") and likelihood methods on a variety of different kinds of data. It is available in the recently-released versions 3.5c and 3.5p as C or Pascal source code and documentation, and in four forms of executables: (i) for 386 and 486 systems under PCDOS, (ii) for 386 and 486 systems under Windows, (iii) for non-386 and non-486 PCDOS systems, and (iv) for Macintosh systems. The C source code will also compile easily on most workstations and mainframes that have a C compiler. PHYLIP has been distributed by me since 1980, with over 2000 registered installations. New features include programs to compute protein sequence distances, to interactively modify a phylogeny, and to compute likelihoods in coalescent models from samples of genealogies. Most programs in the C version no longer have arbitrary limits on the numbers of sites of or species. Many other new features have been added as well, such as new models for variation of evolutionary rates among sites in the DNA likelihood programs. PHYLIP is available by anonymous ftp from evolution.genetics.washington.edu (IP number 128.95.12.41) in directory pub/phylip. Users who cannot get it this way can also send enough formatted diskettes, which will be returned with the particular form of the package and its documentation written on them. Contact me (preferably by electronic mail) for details of the diskette distribution or further information about anonymous ftp distribution. The latest version of PHYLIP is version 3.51 which fixes some bugs present in 3.5. 1. David Swofford of the Laboratory of Molecular Systematics, National Museum of Natural History, Smithsonian Instition, Washington, D.C. has written PAUP (Phylogenetic Analysis Using Parsimony). It can be ordered from the Center for Biodiversity, Illinois Natural History Survey, 607 East Peabody Drive, Champaign, Illinois 61820, U.S.A. Since December, 1985, Swofford has been distributing a precompiled executable object-code versions of PAUP for the IBM PC and other MSDOS systems. As of this writing (February, 1993) he has released version 3 (PAUP/Mac) for the Macintosh, and later hopes to release version 3 for PCDOS systems and ultimately for mainframes. The cost was $50, which will increase to $100 soon. Orders received for the Mac version will be filled but the final printed documentation will arrive later, as it is not completed yet. PAUP 3.0 is probably the most sophisticated parsimony program. It allows multistate characters, user-defined weights on individual state transitions, Wagner, Camin-Sokal and Dollo parsimony methods, bootstrap confidence intervals, and finding all most parsimonious trees by branch-and-bound. It also has provision for computing Lake's linear phylogenetic invariants. PAUP is (a great) many times faster than the parsimony programs in PHYLIP. 2. Swofford also distributes an older package of programs, BIOSYS-1, including some phylogeny estimation programs, for use with gene frequency data, with particular attention to distance methods. BIOSYS-1 is distributed on an IBM PC-formatted floppy disk. Included are precompiled versions for the IBM PC and source code for uploading to IBM, VAX/VMS, Unix, Prime and CDC mainframes and minicomputers. The price is $25.00, from the same address as PAUP. BIOSYS-2 is under development, but it is too early to anticipate a completion date. 3. If you have a Macintosh computer and any interest in discrete-state parsimony methods (including DNA and protein parsimony), you should definitely get MacClade. It was written by Wayne Maddison and David Maddison of the University of Arizona. All distribution is by Sinauer Associates, Sunderland Massachusetts 01375, USA. Their phone number is: (413) 665 3722, FAX: (413) 665 7292. A disk with program, help file, and example data files, plus book (which has about 100 pages of intro to phylogenetic theory, and 250 pages of program instructions), is $75 U.S. ($40 for the book alone). Site licenses also available. An earlier and less capable Version 2 (which for example cannot read nucleic acid sequences and has fewer features for discrete characters) is also available by anonymous ftp from the EMBL, Indiana and Houston molecular biology software servers. Their addresses are given below under the descriptions of TreeAlign and ClustalV. MacClade 2.1 will be found among their Mac software, as a squeezed and then binhexed file. MacClade enables you to use the mouse-window interface to specify and rearrange phylogenies by hand, and watch the number of character steps and the distribution of states of a given character on the tree change as you do so. MacClade is positively addictive and will give you a much better feel for the tree and your data. It's the closest thing to a phylogeny video game that I have seen. It has been influential in spurring the inclusion of interaction and graphics into other phylogeny programs. (I have tried to supply this functionality in PHYLIP by incorporating the programs MOVE, DOLMOVE, and DNAMOVE, which act somewhat like MacClade). MacClade does not have a sophisticated search algorithm to find best trees: it largely relies on you to do it by hand (which is surprisingly effective), with only a local rearrangement algorithm available to improve on that tree. 4. J. S. Farris has produced Hennig86, a fast parsimony program including branch-and-bound search for most parsimonious trees and interactive tree rearrangement. Although complete benchmarks have not been published it is said to be faster than Swofford's PAUP; both are a great many times faster than the parsimony programs in PHYLIP. The program is distributed in executable object code only and costs $50, plus $5 mailing costs ($10 outside of of the U.S.). The user's name should be stated, as copies are personalized as a copy- protection measure. It is distributed by Arnold Kluge, Amphibians and Reptiles, Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109-1079, U.S.A. It runs on PC-compatible microcomputers with at least 512K of RAM and needs no math coprocessor or graphics monitor. It can handle up to 180 taxa and 999 characters. An 80386 version, Hennig386, is currently being tested but no release date has yet been announced. 5. ClaDOS, an interactive program which allows rearrangement of trees and their evaluation, mapping of characters into them, and more, is available for PCDOS systems from Kevin Nixon, L. H. Bailey Hortorium, Cornell University, 467 Mann Library, Ithaca, New York 14853. I have been unable to get information on its cost or method of distribution. 6. Jotun Hein, (Institute of Genetics and Ecology, University of Aarhus, 8000 Aarhus C, Denmark) has produced TreeAlign, a multiple sequence alignment program that builds trees as it aligns DNA or protein sequences. It uses a combination of distance matrix and approximate parsimony methods. TreeAlign uses too much memory for it to run on PC's (DOS or Mac systems) but is really designed for a workstation or mainframe. It is available by anonymous ftp at the Indiana, Houston, and EMBL molecular biology software distribution sites. Their network addresses are respectively: ftp.bio.indiana.edu, ftp.bchs.uh.edu, and ftp.embl-heidelberg.de. In the Indiana archive one must enter directory molbio/align, in the Houston archive it is in directory pub/gene-server in the directories unix and vms, and on the EMBL archive it is in pub/software/unix and pub/software/vax. If you are on Internet and use molecular data it is important that you learn to use anonymous ftp and become familiar with these ftp servers. 7. Another multisequence alignment program that estimates trees as it aligns multiple sequences is ClustalV. An older version in PCDOS executable form was distributed previously (see below for information on how to get executables for PC or Mac for the current version). Currently it is distributed as C source code by its author, Desmond Higgins. Clustal was originally developed at Trinity College, Dublin, Ireland, but version V was done at Higgin's current address, the European Molecular Biology Laboratory, Heidelberg, Germany. Clustal V successfully compiles and runs on VAX/VMS C, Apple Macintosh Think C, MSDOS Turbo C, Decstation ULTRIX C,and Sun workstations with GNU C. It is a complete rewrite and upgrade of the Clustal package which was described by Higgins and Sharp (1989). New features include the ability to detect read different input formats (NBRF/ PIR, Fasta, EMBL/Swissprot); align old alignments; produce phylogenetic trees after alignment (Neighbor Joining trees with a bootstrap option); write different alignment formats (Clustal, NBRF/PIR, GCG, PHYLIP); full command line interface. The program is available by anonymous ftp at the Indiana, Houston, and EMBL molecular biology distribution sites. Their network addresses are respectively: ftp.bio.indiana.edu, ftp.bchs.uh.edu, and ftp.embl-heidelberg.de. In the Indiana archive one must enter directory molbio/align, in the Houston archive it is in directory pub/gene-server in all of the four directories dos, Mac, unix, and vms, and on the EMBL archive it is in pub/software/unix or pub/software/vax. If you are on Internet and use molecular data it is important that you learn to use anonymous ftp and become familiar with one or more of these ftp servers. If you do not have any access to Internet, you could alternatively start by sending e-mail to Des Higgins at: higgins@EMBL-Heidelberg.DE (Internet) If you do not have access to e-mail, send a formatted PC or MAC diskette (PLEASE state which) to: Des Higgins European Molecular Biology Laboratory Postfach 10.2209 Meyerhofstrasse 1 6900 Heidelberg Germany He will return the diskette with the source code and documentation. He can also include an executable image for PC's or MAC. 8. Gary Olsen, of the Department of Microbiology, University of Illinois, has developed a speeded-up version of my program DNAML coded in C, which he calls "fastDNAml". It achieves a number of economies and also is organized so that it can be run on parallel processors -- he and his co-workers have constructed trees of very large size on a high-speed parallel processor. The program can be compiled using the "p4" portable parallel processing toolkit. It can also be run in ordinary serial mode on workstations where it is fatser than DNAML. The C program is available by anonymous ftp from the Ribosomal Database Project at info.mcs.anl.gov in directory pub/RDP/programs/fastDNAml. 9. Andrey A. Zharkikh, Andrey Rzhetsky, and their co-workers in the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, Ex-USSR, have produced VOSTORG, a package of programs for alignment (both manual and automatic) and inferring phylogenies by distance methods and parsimony for molecular sequences. It runs on IBM PC- compatibles and includes some rather fancy graphics. The authors are currently in the U.S., not in Siberia, and their program is sold for about $250 by Exeter Software, 100 North Country Road, Setauket, NY 11733, USA. Their telephone number is 1-800-842-5892; Fax (516)751-3435. The programs are described in a paper by Zharkikh et. al. (1991). 10. MEGA (Molecular Evolutionary Genetic Analysis) is due to be released at the beginning of 1993 by Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei of the Institute of Molecular Evolutionary Genetics, 328 Mueller Lab, Pennsylvania State University, University Park, Pennsylvania 16802, U.S.A. It will be an executable program for PCDOS machines, and will be menu-driven with context- sensitive help. It will analyze data from DNA, RNA and protein sequences, and distance matrices produced from other kinds of data as well. It will include the Neighbor-Joining method distance matrix method, a branch and bound parsimony method, and bootstrapping. It will also plot trees on many kinds of printers. The program will be provided free of charge if you send one 1.2 Mb 5.25-inch or 1.44 Mb 3.5-inch floppy diskette, and will be sent as soon as it is available. Inquiries can also be made by mail to M. Nei at the above address or by electronic mail to nxm2@psuvm (Bitnet) or nxm2@psuvm.psu.edu (Internet). 11. James Lake will soon distribute "Evomony", a program for using the "evolutionary parsimony" (invariants) method for inferring phylogenies from DNA or RNA sequences. It runs on 286 and 386 PCDOS systems with at least 500k bytes of memory. Lake intends to distribute a PCDOS version by April 1, 1993 (his choice of date, not mine!), with a Macintosh version to follow in 1994. Both will be distributed free to scientists in this field. Exact procedures for ordering Evomony have not yet been announced. Lake's address is Department of Biology, University of California, Los Angeles, California 90024. 12. Rod Page has written COMPONENT, a program for PCDOS systems for comparing cladograms for use in phylogeny and biogeography studies. It has far more features for biogeographic studies (such as comparing species and area cladograms) than any other package. It runs on PCDOS 286 or 386 systems under Windows 3.0 or higher. It will be released in the very near future. Its cost will be "in the $50-$75 range", and it can be ordered from Rod Page at the Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, U.K. His phone and fax numbers are respectively (071)-938 9068 and 9260, and his e-mail address is R.Page@natural-history-museum.imperial.ac.uk or rdp@nhm.ic.ac.uk. 13. David Penny (Department of Botany and Zoology, Massey University, Palmerston North, New Zealand) has been offering for free distribution several PCDOS programs, one a fast parsimony program, TurboTree. There are also two others, Hadtree which computes expected frequencies of all possible distributions of nucleotides among species, and Great Deluge, an approximate search for the most parsimonious tree by a quasi-random method. He tells me that funding exigiencies are such that he may soon have to start charging for these. His electronic mail address is dpenny@massey.ac.nz. 14. Walter Fitch (Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92717, U.S.A.) has a package "Molevol" available free (on receipt of an appropriate number of PCDOS formatted floppy disks) with about 20 FORTRAN programs for not only estimating trees by parsimony and distance methods but doing various other manipulations of data that might be needed such as format interconversions and searching for homology and secondary structure. They are available as FORTRAN source and/or as PCDOS executables. The FORTRAN programs will also run on Sun workstations (and probably others too, I would suspect). His electronic mail address is wfitch@daedalus.bio.uci.edu. 15. Kent Fiala, now of SAS Institute, has written a compatibility (clique) program, based on an earlier program written by Kent and George Estabrook. Christopher Meacham has put the latest version of CLINCH (6.2), with Kent's permission, as a self-extracting DOS archive on Jim Beach's TAXACOM fileserver, huh.harvard.edu, for anonymous FTP. The self-extracting archive is "CLINCH62.EXE" in directory /pub/software/clinch. This should be FTPed as a binary file. CLINCH62.EXE is about 150 kb. When you run it, it will expand to 14 files requiring about 280 kb. The executable program is CLINCH.EXE. Readme, documentation, sample input and output, and FORTRAN source code are included. PC-CLINCH is probably the most sophisticated compatibility analysis program. The Taxacom server, by the way, also has other material related to botanical systematics, including flora information. 16. Christopher Meacham (Department of Integrative Biology, University of California, Berkeley, California 94720, U.S.A.) produces COMPROB, a Pascal program to compute probabilities that characters would be compatible at random, thus telling us which clique is "most surprising". It is available for anonymous ftp as a PCDOS executable from the Taxacom server (huh.harvard.edu) in directory pub/mip. 17. The program MARKOV computes a distance measure between pairs of nucleotide sequences. It also constructs phylogenies from these and summarizes the 4x4 substitution matrices between the pairs of species. It uses a more general model of substitution than used in PHYLIP, the Stationary Markov Model described in the paper by Saccone et. al. in Methods in Enzymology volume 183, pages 570-583, 1990. Bootstrapping is used to analyze the statistical error of the results. Output files from CLUSTAL and PILEUP, as well as some other formats, can be used for input, and analysis can be confined to certain codon positions in coding sequences. The program is written in FORTRAN and runs on VMS systems. It was produced by Dr. Graziano Pesole and Professor Cecilia Saccone at the University of Bari, Italy, and is available (for free?) from Dr. Cecilia Lanave at CSMME-CNR, Dipartimento di Biochimica e Biologia Molecolare, Universita` di Bari, via Orabona 4, 70126 Bari, Italy. Her phone number is 39-80-243305, her fax number is 39-80-243317, and her e-mail address is lanave@vaxba0.ba.it or mvx36@ibacsata.it 18. J. S. Farris and Mary Mickevich earlier released a package of phylogeny programs, PHYSYS, which, at about $5,000, was extremely expensive (in my opinion, which is certainly a biased one). I am not sure whether, from whom, or under what conditions it is still available. 19. Fujitsu Ltd. ("a $21 billion global leader in advanced computer, telecommunications, and electronic devices") sells for $28,000 US a Fujitsu S family workstation complete with a program, SINCAIDEN, which allows "experimental researchers, even those unfamiliar with such analyses, [to] easily create phylogenetic trees in their own laboratories." The program also allows searches of the major nucleic acid sequence and protein databases (the ad I saw does not make it clear whether these databases are provided with the workstation). The methods available are UPGMA, neighbor-joining, Farris's (Distance Wagner) and the modified Farris distance matrix methods. The workstation is SPARC compatible and runs SunOS. The SYNCAIDEN program was developed by the group at the National Institute of Genetics, Japan under Dr. Takashi Gojobori. Fujitsu Ltd. may be contacted at 21-8, Nishi-Shinbashi 3- chome, Minato-ku, Tokyo 105, Japan (phone 81-3-3437-5111 ext. 2831, fax 81-3- 5472-4354), or in the U.S. at Fujitsu America Inc., 3055 Orchard Drive, San Jose, California 95134-2017 (phone 1-408-432-1300 ext. 5168, fax 1-408-434- 1045). 20. MUST, a package of sequence management programs, is distributed on a shareware basis by Herve Phillippe, Laboratoire de Biologie Cellulaire (URA CNRS 1134 D), Batiment 444, Universite de Paris-Sud, 91405 Orsay cedex, France. His e-mail address is: adoutte@frciti51 on Bitnet/EARN. His phone and fax numbers are respectively 33.1.69.41.64.81 and 33.1.69.41.21.30. MUST is available on a shareware basis ($100 registration fee if you do not send diskettes) and runs on PCDOS systems using PCDOS version 3 or later. It is intended as complementary to existing phylogeny and alignment programs and can produce output files in the formats of PHYLIP, PAUP, Hennig86, and CLUSTAL. It contains a variety of sequence input, editing, checking, and storage functions, as well as a sequence editor and a phylogeny plotter. It also allows further analyses of the results from these phylogeny programs. 21. Steve Smith, formerly of the Harvard Genome Laboratory, has written an X-Windows interactive sequence editor, GDE (Genetic Data Environment) which allows the user to edit sequences and align them by hand, and to select subsets of sites and sequences and call a variety of analysis proprams including ClustalV and many of the PHYLIP 3.4 programs. The GDE 2.0 system will run on many workstations that have the X windowing system. It also includes the TreeTool tree-plotting program (see below). GDE 2.0 is free and is available for anonymous ftp transfer at either at golgi.harvard.edu in directory pub/GDE2.0 and also at ftp.bio.indiana.edu in directory molbio/unix/GDE. 22. Mike Maciukenas, at the Department of Microbiology of the University of Illinois, has written a wonderful X-windows based interactive tree-plotting program called TreeTool. It takes as input a PHYLIP tree file, with branch lengths if they are provided, displays the tree in either rooted or unrooted form on any X-windows screen, and allows the user to modify the form of the tree and the placement of nodes and labels. When the tree is in final form the user can have it written to a Postscript file and/or printed to a Postscript- compatible printer. TreeTool is free as a C program for X windows and is available for anonymous ftp from ftp.bio.indiana.edu in directory molbio/unix/GDE. It is also included in the GDE 2.0 sequence analysis environment mentioned above. ----- Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195 --> Internet: joe@genetics.washington.edu (IP No. 128.95.12.41) Bitnet/EARN: felsenst@uwavm From owner-software@net.bio.net Mon Oct 04 23:00:00 1993 Path: biosci!JONAS.SACLAY.CEA.FR!werner From: werner@JONAS.SACLAY.CEA.FR (werner) Newsgroups: bionet.software Subject: Display software Message-ID: <9310051218.AA18245@jonas> Date: 5 Oct 93 12:18:58 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 20 I am currently considering the possibility to display structures which are deposited in the Brookhaven databank on a MacIntosh (Quadra 700). I would like to know if freeware programs able to do that and also eventually to do some modelling (i.e. replacing one amino acid by another). I do not know if such programs exist for the Mac or even if it the machine is powerful enough for that purpose. The program should also be simple since I do not know much about modelling. Any suggestion would be welcome. Michel Werner Service de Biochimie et Genetique Moleculaire Batiment 142 Centre d'Etudes de Saclay F-91191 Gif-sur-Yvette France werner@jonas.saclay.cea.fr From owner-software@net.bio.net Mon Oct 04 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: es@uk.ac.afrc Newsgroups: bionet.software Subject: Curvature software available? Message-ID: <1993Oct5.120331.11468@gserv1.dl.ac.uk> Date: 5 Oct 93 12:02:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 12 Precedence: first-class Original-To: BIO-SOFTWARE Dear net, Does anyone know if the software "Curvature" (CABIOS 1993 _9_,4 435-440) for DOS 5.0 is available at some site on the net? Better, is anyone aware of a Mac implementation of the same software? Alternatively, where can i find the E-mail address of Dr. E.S. Shpigelman or Dr. E.N. Trifonov? Thanks in advance Eric Schoonejans es @ jii.afrc.ac.uk From owner-software@net.bio.net Mon Oct 04 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!noc.near.net!newshost.williams.edu!newshost.williams.edu!not-for-mail From: 95mhn@williams.edu (Max Nanao) Newsgroups: bionet.software Subject: ProMod Keywords: Promod Message-ID: <28sdosINNb7v@hancock.cc.williams.edu> Date: 5 Oct 93 18:18:04 GMT Distribution: bionet Organization: Williams College, Williamstown MA Lines: 11 NNTP-Posting-Host: hancock.cc.williams.edu Hello, I have been trying to get ProMod working on two Sun4's, one of which is running system V, and the other SunOs 4.? I have downloaded the binary, as well as the appropriate ancillary files, but when I try to run it, Promod either dumps core or crashes the machine. Has anyone successfully installed this program on a similar platform? Thanks, Max Nanao From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!xlink.net!fauern!lrz-muenchen.de!pollux.edv.agrar.tu-muenchen.de!max From: max@pollux.edv.agrar.tu-muenchen.de (Max Pilgram (DVS)) Newsgroups: bionet.software Subject: CCA Message-ID: <1993Oct6.085229.9532@news.lrz-muenchen.de> Date: 6 Oct 93 08:52:29 GMT Sender: news@news.lrz-muenchen.de (Mr. News) Organization: Leibniz-Rechenzentrum, Muenchen (Germany) Lines: 24 X-Newsreader: TIN [version 1.2 PL1] I am looking for some software tools for ecological pattern analysis in vegetation science. Most wanted Canonical correspondence analysis CCA. Thank you Max -- ______________________________________________________________ | Max Pilgram | | FAM E 1.2 Vegetationsmodelle | |--------------------------------------------------------------| | Lehreinheit fuer Mathematik, Statistik und Datenverarbeitung | | TU Muenchen Weihenstephan | | Hohenbachernstrasse 2 | | 85350 Freising | | Germany | |--------------------------------------------------------------| | Phone: 08161/71-4040 | | Email: max@pollux.edv.agrar.tu-muenchen.de | |______________________________________________________________| From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!MNI.lan.mcgill.ca!IVAN From: IVAN@MNI.lan.mcgill.ca Newsgroups: bionet.software Subject: Re: sigma plot ?? Message-ID: <9310060015.AA16509@sifon.cc.mcgill.ca> Date: 6 Oct 93 03:07:54 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 43 Thomas Petzold wrote... > does anybody know a program called SIGMA-PLOT ? Where can I get it > from and how much does it cost? Is there a WINDOWS-Version available > or is it a DOS-program ? I've got a hint, that it would be useful to > plot my data, but I have no detailed information. > Does anybody know another program which is able to plot time > series in a user friendly way? Gnuplot (or EXCEL on the other hand) > are not flexible enough. SigmaPlot? Yuck-o! Now that I've finished with that, SigmaPlot is the graphing package written/marketed by Jandel Scientific. Unfortunately, I no longer have the address so I can't pass that off to you. However, Jandel advertises in Science and several other publications (they also market the Java and Mocha imaging products) so you can find them there. SigmaPlot is available in both DOS and Windows versions, the current numbers are 5.0 and 4.1 I think. At McGill, we pay just under $500 CDN for either. A much cheaper alternative is CoHort Software's CoPlot package (our lab made the mistake of not buying this). You can reach them at: 71161.564@compuserve.com Prompt replies to any question. - ivan ------------------------------------------ Ivan Shaw "The Angel of Death" Neuroimmunology Unit Montreal Neurological Institute Montreal, Canada H3A 2B4 ------------------------------------------ Internet e-mail: Ivan@MNI.LAN.McGill.CA Telephone: (514) 398-3002 FAX (514) 398-7371 From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!gdt!aber!localhost!gjs From: gjs@aber.ac.uk (Gaz) Newsgroups: bionet.software Subject: Re: sigma plot ?? Keywords: sigma plot pc windows time series Message-ID: Date: 6 Oct 93 10:01:31 GMT References: Sender: news@aber.ac.uk (USENET news service) Organization: The University of Wales, Aberystwyth Lines: 39 Nntp-Posting-Host: 144.124.112.31 X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article petzoldt@TUDURZ.urz.tu-dresden.de (Thomas Petzoldt Hydrobiologie) writes: >From: petzoldt@TUDURZ.urz.tu-dresden.de (Thomas Petzoldt Hydrobiologie) >Subject: sigma plot ?? >Date: Tue, 5 Oct 1993 16:05:47 GMT >Keywords: sigma plot pc windows time series >Dear Netters, > does anybody know a program called SIGMA-PLOT ? > Where can I get it from and how much does it cost? > Is there a WINDOWS-Version available or is it a DOS-program ? > I've got a hint, that it would be useful to plot my data, > but I have no detailed information. > Does anybody know another program which is able to plot time > series in a user friendly way? Gnuplot (or EXCEL on the other hand) > are not flexible enough. > Thank you in advance > Thomas > petzoldt@biowissenschaft.tu-dresden.d400.de We tried out Sigma-plot, I don't really remember it that well, but for time-plot data I think you will find that Grafit is better. Grafit also goes very well with windows. We tend to use Excell to prepare the data in a spreadsheet format (NO, I don't like Excell much), and than transfere the relavent parts to Grafit to plot out. It sounds as if what you need is a genuine graphics package thou, so any should do. Beware of things like Excell, Lotus, Planner and the rest as these are really spreadsheet packages, and while good, have rather limited graphics potential. Hope this helps. Gaz From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brain Foley) Newsgroups: bionet.software Subject: Sharing lab "tools". Message-ID: <1993Oct6.232123.22037@emba.uvm.edu> Date: 6 Oct 93 23:21:23 GMT Sender: news@emba.uvm.edu Organization: University of Vermont -- Division of EMBA Computer Facility Lines: 34 X-Newsreader: TIN [version 1.2 PL1] Dear Computer-literate Biologists: Between us all we must have thousands of useful "tools" on our lab computers that we should be sharing. I've never uploaded my Microsoft Excel or Lotus 123 spredsheets that I have used for calculating DNA concentrations, buffer formulations, and so on because I felt that they were not "good enough" for "publication". But I'm sure that they would be useful to some people, both for doing the calculations and for learning a bit about designing spreadsheets. While we can't freely distribute Excel or Lotus 123, we can freely distribute spreadsheet files that are used with these commercial programs. Another area where we should/could share useful information is in the form of test questions and answers. Lab protocols (already being shared quite a bit on bionet.methods), would also be handy. I don't think I should upload all my spreadsheets to IUBIO or any other FTP site, because who could sort through them all to find the one macro they can use? But if I have one or two "tools" that I find really handy should I send them out? HyperCard stacks were supposed to be this sort of thing. For a while in the late 1980's people were developing all kinds of great stuff to give away. It seems that new stacks are not pouring in any longer. Is it not useful? Any comments? -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brain Foley) Newsgroups: bionet.software Subject: Re: question Message-ID: <1993Oct6.224826.21063@emba.uvm.edu> Date: 6 Oct 93 22:48:26 GMT References: Sender: news@emba.uvm.edu Distribution: bionet Organization: University of Vermont -- Division of EMBA Computer Facility Lines: 13 X-Newsreader: TIN [version 1.2 PL1] Wanqing Yang (wyang@MOOSE.UVM.EDU) wrote: : Could anyone tell me how I can transfer my file from Microsoft Word : to e-mail in a Macintosh, if using kermit? Thank you! : wyang@moose.uvm.edu No need to waste band-width here. I'll talk to Wanqing in person. -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!news.ans.net!malgudi.oar.net!news.ysu.edu!psuvm!imeg From: IMEG@psuvm.psu.edu Newsgroups: bionet.software Subject: MEGA: New info and order form Message-ID: <93279.165949IMEG@psuvm.psu.edu> Date: 6 Oct 93 20:59:49 GMT Expires: 4 Jan 94 00:00:00 GMT Organization: Penn State University Lines: 286 This document contains many pages, including 1. Cover letter 2. Order form (We no longer accept purchase orders) 3. Hardware and software requirements 4. Program upgrade policy 5. Functions in MEGA MEGA version 1.0, 1.01 September, 1993 To whom it may concern: A computer software called MEGA: Molecular Evolutionary Genetics Analysis has been developed. This software is for facilitating statistical studies of molecular evolution by using IBM compatible personal computers. It contains various methods of estimating evolutionary distances and three different methods of phylogenetic inference (UPGMA, neighbor-joining, and maximum parsimony) with either a standard-error test or a bootstrap test of topological differences. For the maximum parsimony method, new algorithms of the branch-and-bound and heuristic searches are implemented. MEGA also computes basic statistical quantities such as nucleotide and amino acid frequencies, transition/transversion bias, codon usage frequencies, number of variable sites, etc. In addition, advance on- screen sequence data and phylogenetic tree editors are included. Integrated and interactive designs, on-line context-sensitive helps, text-file editor, and other unique features make it easy to use MEGA. MEGA version 1.0 is distributed with a nominal fee to defray the cost of producing the user manual (140 pp.) and diskettes, and the mailing and handling expenses (see enclosed order form). However, for anyone who is unable to pay the fee for some reason, it will be provided free of charge after receiving a letter explaining the circumstances. MEGA will not be sent by electronic-mail because the accompanying manual cannot be included in this case. Technical questions and other inquires about MEGA should be directed to the senior author of the software. Please include your electronic-mail address, if any. Sincerely yours, Sudhir Kumar Koichiro Tamura Masatoshi Nei Telephone: (814) 863-7334 FAX: (814) 863-7336 E-mail: imeg@psuvm, imeg@psuvm.psu.edu MEGA ORDER FORM Cost* ----------------------------------------------------------------- Program No Charge User manual, diskette, shipping, and handling $ 15.00 For shipment outside North America add $10.00 _________ (We will use first class airmail) TOTAL _________ ----------------------------------------------------------------- * This cost can be waived if the circumstances for the inability to pay (e.g., lack of hard currencies in some countries) are explained. Diskette type desired: Please specify: [ ] 3.5" Diskette (1.44MB) [ ] DOS Version ...... [ ] 5.25" Diskette (1.2MB) [ ] Computer system... [ ] other (specify).... [ ] Do you use windows? Yes/No All orders must be prepaid in U.S. dollars. Return this form together with a check or money order payable to Penn State University at the following address. Purchase orders will not be accepted. Joyce White Institute of Molecular Evolutionary Genetics The Pennsylvania State University 328 Mueller Laboratory University Park, PA 16802 USA Telephone: (814)-863-7334 Fax: (814)-863-7336 E-mail: IMEG@PSUVM.PSU.edu, IMEG@PSUVM About the user: Name: ____________________________________________ Address: ____________________________________________ ____________________________________________ ____________________________________________ Telephone: _____________________ Fax: _________________ E-Mail: ____________________________________________ --------Hardware and Software------ IBM and IBM-compatible PCs, XTs, ATs, etc. Color/monochrome monitors. 640KB RAM memory. DOS version 3.3 or later. Hard disk with 2MB free. No extended or expanded memory required. No graphics adapters required. No math-chip required. Supports the keyboard as well as the mouse (not essential). ------- Program upgrade policy ---- Since MEGA is in its first version, there may be many software bugs in the program. We are considering to provide registered users a version where bugs reported in version 1.0 and 1.01 will be fixed. As you may notice from the order form, we are just trying to recover the cost of distributing MEGA only. So we are not in a position to provide many upgrades. In any case, we do not plan to include new methods in MEGA soon (for at least one year), and therefore the questions about upgrades may not be so pressing at this moment. -------Functions in MEGA------- Input Input data: DNA sequences RNA sequences Amino acid sequences Distance matrices Input formats: Interleaved sequences Non-interleaved sequences Upper-triangular distance matrix Lower-triangular distance matrix Choice of: Alignment gap symbol Missing-information site symbol Identical site symbol In-memory data editing features Selection: Desired OTUs Domains of sequences Individual sites and codons Codon positions Exclude/include missing information sites Exclude/include alignment gap sites Edit OTU labels Restore OTU labels Sequence data presentation Highlight: Variable sites Parsimony-informative sites Two-fold redundant sites Four-fold redundant sites Translate: Translation of nucleotide sequences into amino acid sequences Output: Formats: MEGA PAUP PHYLIP Publication Data subsets: Only variable sites Only parsimony-informative sites Amino acid sequences translated Codon positions Sequence statistics: Nucleotide and amino acid frequencies Nucleotide pair frequencies in pairwise comparisons Insertion-deletion frequencies Codon usage frequencies Relative synonymous codon usage (RSCU) values Variable sites in overlapping segments Variable sites in nonoverlapping segments Distance estimation Nucleotide substitutions Quantities: Number of nucleotide differences Nucleotide substitutions Transitional substitutions Transversional substitutions Transition/transversion ratio Distance measures: p-distance Jukes-Cantor distance Kimura 2-parameter distance Tajima-Nei distance Tamura distance Tamura-Nei distance Gamma distances Jukes-Cantor model Kimura 2-parameter model Tamura-Nei model Synonymous-nonsynonymous substitutions Genetic code tables: "Universal" Mammalian mitochondrial Drosophila mitochondrial Yeast mitochondrial Computation: Synonymous substitutions Nonsynonymous substitutions Average distances for all pairwise comparisons and standard errors Amino acid substitutions Distance measurers: Number of amino acid differences p-distance Poisson-correction distance Gamma distance Distance output: Control on: Page size Precision for distance output Distance q standard error formats Tree building and test Methods: Neighbor-joining (NJ) UPGMA Maximum parsimony (MP): Branch-and-bound search Heuristic search Statistical Tests: Bootstrap test: Neighbor-joining UPGMA Branch length test: Neighbor-joining Phylogeny editing: Tree re-rooting Swapping and flipping branches Consensus tree Condensed tree Phylogeny printing: Various printers Multiple page printouts Choice of fonts Choice of orientation Choice of page size Tree preview General functions File browsing File editing Exiting to DOS temporarily Context-sensitive Helps Error messages From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!mcsun!uunet!psgrain!ee.und.ac.za!hippo.ru.ac.za!ford.ee.up.ac.za!agric.up.ac.za!MARK From: MARK@agric.up.ac.za (VOGON) Newsgroups: bionet.software Subject: Species rank abundance plots Keywords: rank abundance plots Message-ID: Date: 6 Oct 93 11:43:12 GMT Organization: STAR FLEET COMAND Lines: 13 NNTP-Posting-Host: 137.215.27.63 I am a Msc/Phd Student and require information on a/any software that can test distribution plots i.e lognormal: but the tests must be suited for ranked data. The software should be able to test for broken_stick, and other related biological models. I would be greatfull if anybody could tell me if such software exists, and if so where it can be found. Thankyou Mark Vogt Mark@agric.up.ac.za From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!mcsun!uunet!psgrain!ee.und.ac.za!hippo.ru.ac.za!ford.ee.up.ac.za!zeno.up.ac.za!bio1 From: bio1@navi.up.ac.za (Fourie Joubert) Newsgroups: bionet.software Subject: SLT340 Plate reader? Message-ID: Date: 6 Oct 93 09:48:19 GMT Organization: University of Pretoria Lines: 35 NNTP-Posting-Host: zeno.up.ac.za Hi I'm writing some Windows software to drive our SLT340 microtitre plate reader. However, I'm having some difficulty with the serial coms. The manual shows two cables, one for XT's and one for AT's. The XT cable works fine, but the AT cable doesn't even open the com port. The connections are as follows: XT: Reader PC 2 -> 3 3 -> 2 7 -> 7 plus PC side 4->5 and 6->8->20. AT: Reader PC 2 -> 2 3 -> 3 7 -> 5 plus PC side 1->4->6 and 7->8. Has anybody else had the same trouble, or does someone know who to contact at SLT? Any help would be appreciated very much! __________________________________________________________________________ _/_/_/_/ _/_/_/_/_/ Fourie Joubert _/ _/ Department of Biochemistry _/ _/ University of Pretoria _/_/_/_/ _/ South Africa _/ _/ bio1@navi.up.ac.za _/ _/_/_/_/ Disclaimer: "Fourie who?" __________________________________________________________________________ From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!mcsun!sun4nl!star.cs.vu.nl!balaena!mac236.bio.vu.nl!user From: giesberg@bio.vu.nl (Paul Giesberg) Newsgroups: bionet.software Subject: Re: sigma plot Message-ID: Date: 6 Oct 93 08:37:34 GMT References: Sender: news@bio.vu.nl Followup-To: bionet.software Organization: Vrije Universiteit Amsterdam Lines: 6 Jandel Scientific GmbH Schimmelbuschstr.25 D-4006 Erkrath Germany +2104 36098 fax + 2104 33110 From owner-software@net.bio.net Tue Oct 05 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!math.fu-berlin.de!news.dfn.de!server2.rz.uni-leipzig.de!RNEWS.urz.tu-dresden.de!TUDURZ!petzoldt From: petzoldt@TUDURZ.urz.tu-dresden.de (Thomas Petzoldt Hydrobiologie) Newsgroups: bionet.software Subject: Re: sigma plot ?? Keywords: sigma plot pc windows time series Message-ID: Date: 6 Oct 93 07:06:44 GMT References: Sender: news@RNEWS.urz.tu-dresden.de (Administrator) Organization: TU Dresden - URZ Lines: 6 Nntp-Posting-Host: tudurz.urz.tu-dresden.de Now I have the adress of Jandel Scientific. Thank you all for your help :) Thomas From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!QCVAXA.ACC.QC.EDU!bienkows From: bienkows@QCVAXA.ACC.QC.EDU Newsgroups: bionet.software Subject: sources for restriction enzymes Message-ID: <00973A89.2263B780.2242@qcvaxa.acc.qc.edu> Date: 7 Oct 93 14:56:54 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 15 7-Oct-93 Greetings, Are there any lists of sources for relatively uncommon restriction enzymes? I am looking for enzymes that are not in the BMB or Promega catalogs. I could keep looking in other catalogs, but I wonder if there is an easier way. Thanks Bob Bienkowski bienkows@qcvaxa.acc.qc.edu From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!math.utk.edu!gross From: gross@math.utk.edu Newsgroups: bionet.software Subject: New Gopher and FTP site Message-ID: <9310071603.AA03479@mathsun5.math.utk.edu> Date: 7 Oct 93 16:03:16 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 45 NEW GOPHER HOLE AND FTP SITE FOR LIFE SCIENCES This is to announce the opening of a new gopher server of interest to the life science community. As part of an NSF-funded curriculum development project on a quantitative curriculum for life science students (USE-9150354 to the University of Tennessee-Knoxville), I've been collecting and evaluating software products of possible use in the life sciences. These reviews have been distributed by e-mail and hard-copy previously (using the wustl archives). The reviews are of software for aiding the development of quantitative skills of life science undergraduates, and the reviewers are all students. Thus, this does not included software such as those to aid in dissection. The reviews are now easily searched and downloaded from the new Mathematics Archives, which mostly contains a huge assortment of public domain software which can be used to aid mathematics instruction at the college level. Also included are several databases including reviews of commercial software, abstracts of meetings, and links to a number of other relevant gophers. We currently support both anonymous ftp and gopher with WAIS searching implemented on abstracts and readme files for files in the Archives. The Mathematics Archives is also an NSF-funded resource (DUE-9351398), with additional support from the State of Tennessee Science Alliance, and the Departments of Mathematics at Calvin College and the University of Tennessee, Knoxville. To access this gopher, use archives.math.utk.edu (port 70) or by anonymous ftp to archives.math.utk.edu (128.169.202.163). In addition to the above mentioned reviews of life science software, we will be including public domain software as it becomes available, and we have included several documents of possible interest: The Workshop Report on a Quantitative Curriculum for Life Science Students The complete listing of software reviews for the life science curriculum The B&B Primer on First Job Haggling If there are documents, software, or reviews you would like to contribute to the life science component of this site, please contact me. Note that my policy for inclusion of reviews in the life science area is that they either be references to published reviews, or be reviews done by students. Louis J. Gross 615-974-4295 Department of Mathematics and 615-974-6576 (FAX) Graduate Program in Ecology 615-974-2461 (Secretary) University of Tennessee gross@math.utk.edu Knoxville, TN 37996-1300 From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!demon!cix.compulink.co.uk!warrenk From: warrenk@cix.compulink.co.uk (Warren Kovach) Newsgroups: bionet.software Subject: RE: CCA Message-ID: Date: 7 Oct 93 13:05:03 GMT Sender: usenet@demon.co.uk Reply-To: warrenk@cix.compulink.co.uk Lines: 29 > I am looking for some software tools for ecological pattern > analysis in vegetation science. > > Most wanted Canonical correspondence analysis CCA. > > Thank you > > Max CCA is available in the program CANOCO, written by Cajo ter Braak and sold by Microcomputer Power (111 Clover Lane, Ithaca, NY 14850, USA; e-mail: D6881@applelink.apple.com). My own program, MVSP, will do a variety of other types of analyses, including correspondence analysis (with detrending), principal componenents and principal coordinates, and cluster analysis. A shareware version can be obtained by anonymous FTP from WUARCHIVE.WUSTL.EDU (128.252.135.4), GARBO.UWASA.FI (128.214.12.37), or from the INQUA FTP (GEOLOGY.WISC.EDU; 144.92.137.14). These are both for IBM-PC's, by the way. -- Dr. Warren L. Kovach Internet: warrenk@cix.compulink.co.uk Kovach Computing Services CompuServe: 100016,2265 85 Nant-y-Felin tel./fax: +44-248-450414 Pentraeth, Anglesey, Wales LL75 8UY U.K. From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!nestroy.wu-wien.ac.at!i102pc1.vu-wien.ac.at!i102pc1 From: i102pc1@edvznovell2.vu-wien.ac.at (Sebastian Bunka) Newsgroups: bionet.software Subject: Re: SLT340 Plate reader? Message-ID: Date: 7 Oct 93 10:30:04 GMT References: Organization: Inst. of Bacteriology, Vet. Univ. Vienna Lines: 87 NNTP-Posting-Host: i102pc1.vu-wien.ac.at X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] .In article bio1@navi.up.ac.za (Fourie Joubert) .writes:>From: bio1@navi.up.ac.za (Fourie Joubert) .>Subject: SLT340 Plate reader? .>Date: 6 Oct 1993 09:48:19 GMT . .>Hi . .>I'm writing some Windows software to drive our SLT340 microtitre plate .>reader. However, I'm having some difficulty with the serial coms. The manual .>shows two cables, one for XT's and one for AT's. The XT cable works fine, .>but the AT cable doesn't even open the com port. . .>The connections are as follows: .>XT: .>Reader PC .>2 -> 3 .>3 -> 2 .>7 -> 7 .>plus PC side 4->5 and 6->8->20. . .>AT: .>Reader PC .>2 -> 2 .>3 -> 3 .>7 -> 5 .>plus PC side 1->4->6 and 7->8. . .>Has anybody else had the same trouble, or does someone know who to contact .>at SLT? . .>Any help would be appreciated very much! .>__________________________________________________________________________ . .> _/_/_/_/ _/_/_/_/_/ Fourie Joubert .> _/ _/ Department of Biochemistry .> _/ _/ University of Pretoria .> _/_/_/_/ _/ South Africa .> _/ _/ bio1@navi.up.ac.za .>_/ _/_/_/_/ Disclaimer: "Fourie who?" .>__________________________________________________________________________ . Hi, Fourie! I remember, we had similar problems with our old (Austrian) SLT Reader, but I don4t remeber exactly how we connected this. We now use the newer one SLT 400 ATC and our pin layout lok like this: 25 Pin Computer: Instrument Computer 2-------------------3 3-------------------2 4 4+5 shortcut (connect via cable bridge) 5 none 6 none 6+8+20 shortcut 7-------------------7 20 9 Pin Computer: 1 none 1+4+6 shortcut 2--------------------2 3--------------------3 4 none 5 none 7--------------------5 8 none 8+7 shortcut 20 none (From the users manual of SLT 400) You can try to contact SLT Austria: Ph.: +43-6246-3438 FAX: +43-6246-2770 but (I know) it4s hard to find a competent person. Feel free to contact me (possibly I can ask my college in Hannover, Germany, who is running this Reader and can checkout the configuration). SWB `oo' ( O O ) vv \\ \\ \\ email: [ Sebastian.Bunka@vu-wien.ac.at ] phone: FAX: +43-1-71155260 +43-1-7149110 Location: earth, europe, austria, vienna Inst. of Bacteriology Vet.Univ. From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!pipex!zaphod.crihan.fr!univ-lyon1.fr!scsing.switch.ch!sun.rediris.es!cnbvx3.cnb.uam.es!biomed.iib.uam.es!sistema From: sistema@biomed.iib.uam.es (SYSTEM MANAGER) Newsgroups: bionet.software Subject: Re: question Message-ID: <6OCT199315314953@biomed.iib.uam.es> Date: 6 Oct 93 22:31:00 GMT References: Distribution: bionet Organization: Biomedical Research Institute (CSIC) - Spain Lines: 43 Nntp-Posting-Host: biomed.iib.uam.es News-Software: VAX/VMS VNEWS 1.41 Lines: 43 In article , Wanqing Yang writes... >Could anyone tell me how I can transfer my file from Microsoft Word >to e-mail in a Macintosh, if using kermit? Thank you! >wyang@moose.uvm.edu > There are two possible ways. The simpler, though less useful since you will lose all format information in your file is to save it in ASCII format, this is done by selecting SAVE AS... from the FILE menu and then pressing the FILE FORMAT button and choosing TEXT ONLY WITH LINE BREAKS. This saves your file in a format suitable to be transferred via electronic mail 'as is'. But as I said you will lose all formatting info (i.e. titles, bold, italics, etc...). Alternatively, you can use a somewhat more difficult way. You must use then a special program that encodes your Word file so as to make it suitable for e-mail transfer. The receiver will have to use a similar program to decode it later. The most widespread used program is BINHEX 4.0. Other programs, like STUFF IT and COMPACT PRO can also generate BinHex files from your initial one. Once the file has been converted to a transferrable format (either by saving it as TEXT ONLY or by converting it to BinHex, all you have to do is send it to your host with Kermit and the e-mail the file: Login to your host as usual. Activate kermit (the command should be 'kermit' or 'ckermit'), and tell kermit in the host that it will receive a file from your Mac: Kermit> receive It will then wait for you to send the file. Select SEND KERMIT from the appropriate menu in your Mac communications program and select the file to send (the TEXT or BINHEXed file). Once finished, exit from kermit and send the file by e-mail. It will usually be a command like 'mail my_file_name' or so. Give the address of the receiver, and you're done. jr From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!pipex!zaphod.crihan.fr!univ-lyon1.fr!scsing.switch.ch!sun.rediris.es!cnbvx3.cnb.uam.es!mrege From: mrege@cnbvx3.cnb.uam.es Newsgroups: bionet.software Subject: Educational software (microbiology) ?? Message-ID: <1993Oct6.213701.72@cnbvx3.cnb.uam.es> Date: 6 Oct 93 21:37:01 GMT Organization: C.N.Biotecnologia, CSIC Lines: 22 Hello, We want to start a new teaching program (General Microbiology) using a multimedia approach (video, software, practical work, theoretical courses). The main topics to cover are physiology, systematics and bacterial and phage genetics. Are there any source of good educational software for this purpose? (PD or commercial - as cheap as possible). (The video plays will be our own production, but we would be glad to know of any other experience). We are thinking of buying 10 PC for a classroom, but we will consider having a Mac-based system if we find better software for it. Any suggestion will be more than welcome. Sincerely, Dr. Miquel Regue e-mail: regue@farmacia.ub.es Dept. Microbiologia Fac. Farmacia, Univ. Barcelona (Spain) From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!psgrain!ee.und.ac.za!hippo.ru.ac.za!ford.ee.up.ac.za!agric.up.ac.za!MARK From: MARK@agric.up.ac.za (VOGON) Newsgroups: bionet.software Subject: Rank abundance model testing Message-ID: Date: 7 Oct 93 07:51:40 GMT Organization: STAR FLEET COMAND Lines: 10 NNTP-Posting-Host: 137.215.26.24 I am a Msc/phD student, I am looking for some software that will allow me test some models of abundance (for ranked data) i.e. Broken_stick and other related ecological models. Does anybody know if a software package is available, and if so where can I get hold of a it. Thankyou Mark Vogt (Mark@agric.up.ac.za) From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: sasssc@uk.ac.sari.scri (Scott Chasalow) Newsgroups: bionet.software Subject: genetics software? Message-ID: <1993Oct7.170024.16803@gserv1.dl.ac.uk> Date: 7 Oct 93 16:09:10 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 10 Precedence: first-class Original-To: bio-soft@uk.ac.daresbury Hi, Does anyone out there know of any software available, free or otherwise, for generating genotypic and phenotypic class frequencies for a given genetic cross, especially though not necessarily for polyploid crosses? Thanks very much in advance for any suggestions. -Scott From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: risler%FRCGM51.earn@uk.ac.earn-relay Newsgroups: bionet.software Subject: transmembrane helices Message-ID: <1993Oct7.162019.16260@gserv1.dl.ac.uk> Date: 7 Oct 93 21:19:58 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 22 Precedence: first-class Original-To: bio-software@uk.ac.daresbury Hi, It is not uncommon to see beautiful schematic drawings of transmembrane proteins, with the helices embedded in the membrane and the connective loops swimming in the cell. Are these pictures hand-drawn, or does it exist some program to do that (preferably for the Mac) ? Thank you, --------------------------------------------------------------------- Jean-Loup Risler Tel: (33 1) 69 82 31 34 CNRS Fax: (33 1) 69 07 49 73 Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr 91198 Gif sur Yvette Cedex France Email: risler@frcgm51.bitnet --------------------------------------------------------------------- From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: risler%FRCGM51.earn@uk.ac.earn-relay Newsgroups: bionet.software Subject: Genpept Gopher? Message-ID: <1993Oct7.161630.16127@gserv1.dl.ac.uk> Date: 7 Oct 93 21:15:02 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 20 Precedence: first-class Original-To: bio-software@uk.ac.daresbury Dear netters, I hope this is not a stupid question. I've fumbled around in the Gopher space to find a hole from which I could retrieve sequences from the NCBI GENPEPT databank. I couldn't find any. Am I just stupid ? Thanks --------------------------------------------------------------------- Jean-Loup Risler Tel: (33 1) 69 82 31 34 CNRS Fax: (33 1) 69 07 49 73 Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr 91198 Gif sur Yvette Cedex France Email: risler@frcgm51.bitnet --------------------------------------------------------------------- From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: roxanne@edu.tmc.uth.mda.odin (Roxanne Hall) Newsgroups: bionet.software Subject: MavVector Message-ID: <1993Oct7.202658.18844@gserv1.dl.ac.uk> Date: 7 Oct 93 20:26:21 GMT Sender: roxanne@odin.mda.uth.tmc.edu Distribution: bionet Lines: 29 Precedence: first-class Original-To: bio-software@uk.ac.daresbury (Bionet Software UseNet Group) X-Mailer: ELM [version 2.3 PL11] Fellow Netters, I am having a strange little problem with the use of MacVector and GCG format sequence files. Our site is set up so that our Macs are on the network with the main frame. GCG is setup on the main frame (a UNIX box, Solbourne). When we transfer the GCG sequence files down to MacVector sometimes MacVector locks up and once it locks up so does our Mac. The Mac locks up to the point of no return. You can't even force MacVector to close. This does not happen all the time on the same file nor does it always happen at the same point in MacVector. In general, this occurs when we are saving the file as something, i.e. as GenBank or GCG, and also dies sometimes when we try to manipulate the sequence. It does not matter that the lock is open or closed. Also, this did not happen when everyone had to use a modem to access the main frame. Any and all suggestions will be greatly appreciated. Roxanne Hall, Computer Programmer E-Mail: roxanne@odin.mda.uth.tmc.edu Or: roxanne@129.106.3.17 Biomathematics, University of Texas, M.D. Anderson Cancer Center 1515 Holcombe Blvd., MS 237, Houston, Texas 77030 From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!AUDREY.LMF.ORG!jim From: jim@AUDREY.LMF.ORG (Jim Gale) Newsgroups: bionet.software Subject: Dos DNA/Protein analysis packages Message-ID: <9310071738.AA19754@audrey.lmf.org> Date: 7 Oct 93 17:38:31 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 Greetings Nettlings We need some advice. Our access to (free) GCG is lost. The institute we used GCG on by modem is dropping GCG due to the cost. Since we cannot afford GCG. WE need some other similar package for our PC systems (MS-DOS). I am fimilar Hitachi DNASIS/PROSIS and Inteligenetics PC-Gene. We will be having demos of both shortly. Does anyone out there use either package for MS-DOS? What is yor opinion of the system. Does it compare to GCG? Is there another package we should be looking at???? ALL HELP will be greatly appreciated Jim Gale The Lovelace Institutes Albuquerque NM From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: es@uk.ac.afrc Newsgroups: bionet.software Subject: Re: Question Message-ID: <1993Oct7.134029.13572@gserv1.dl.ac.uk> Date: 7 Oct 93 13:40:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 24 Precedence: first-class Original-To: BIO-SOFTWARE In article <931070480.~INN-QFAa11494.bionet-news@uk.ac.daresbury> sistema@es.uam.iib.biomed (SYSTEM MANAGER) writes >In article , Wanqing Yang writes... >>Could anyone tell me how I can transfer my file from Microsoft Word >>to e-mail in a Macintosh, if using kermit? Thank you! >>wyang@moose.uvm.edu >> > > There are two possible ways. The simpler, though less useful since you >will lose all format information in your file is to save it in ASCII format, .....stuff del... > Alternatively, you can use a somewhat more difficult way. You must use >then a special program that encodes your Word file so as to make it suitable >for e-mail transfer. The receiver will have to use a similar program to decode >it later. The most widespread used program is BINHEX 4.0. Other programs, >like STUFF IT and COMPACT PRO can also generate BinHex files from your initial >one. .....stuff del... Or more simply select the RTF format in the Save as FILE menu es From owner-software@net.bio.net Wed Oct 06 23:00:00 1993 Path: biosci!lhc!ray!dab From: dab@ray.nlm.nih.gov (Dennis Benson) Newsgroups: bionet.software Subject: Re: Genpept Gopher? Message-ID: <1993Oct7.213740.8435@nlm.nih.gov> Date: 7 Oct 93 21:37:40 GMT References: <1993Oct7.161630.16127@gserv1.dl.ac.uk> Sender: news@nlm.nih.gov Distribution: bionet Organization: National Library of Medicine Lines: 40 X-Newsreader: Tin 1.1 PL4 risler%FRCGM51.earn@uk.ac.earn-relay writes: : Dear netters, : : I hope this is not a stupid question. : : I've fumbled around in the Gopher space to find a hole from which I could : retrieve sequences from the NCBI GENPEPT databank. I couldn't find any. : : Am I just stupid ? : : Thanks : : --------------------------------------------------------------------- : Jean-Loup Risler Tel: (33 1) 69 82 31 34 : CNRS Fax: (33 1) 69 07 49 73 : Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr : 91198 Gif sur Yvette Cedex France Email: risler@frcgm51.bitnet : --------------------------------------------------------------------- Jean-Loup, I can't help directly with gopher, but NCBI does have the sequences translated from the GenBank coding regions in a file that can be FTP'd from the machine 'ncbi.nlm.nih.gov'. After login, `cd' to the directory 'genbank'; the file is 'genpept.fasta.Z'. This file contains the translations from the latest full release of GenBank. Daily cumulative updates are also available in the directory: 'genbank/daily' as the file 'gpcu.fasta.Z'. Note that this 'GenPept' file is actually a FASTA formatted series of sequences, ie, a header line with the GenBank accession number, locus name, and definition followed by the protein sequence. Regards, Dennis Benson GenBank NCBI and From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!CCVAX.UNICAMP.BR!INFOMED From: INFOMED@CCVAX.UNICAMP.BR Newsgroups: bionet.software Subject: Computers in Healthcare Conference 93 (Delaware) Message-ID: <01H3SZ5GFE3M94DOBS@ccvax.unicamp.br> Date: 8 Oct 93 01:37:30 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 121 SECOND ANNUAL "COMPUTERS IN HEALTH CARE" CONFERENCE Delaware State Hospital Ramada Inn Hotel New Castle, November 3rd and 4th, 1993 Sponsored by: Computer Systems Support and Information Technology Synergies Advance Program --------------- This conference is designed for administrators, clinicians and educators who have an interest in computers in the health care setting. Hospital managers, doctors, nurses, psychologists, social workers, occupational therapists and educators will find this conference expands their present and future knowledge of computer technology for the hospital environment. The conference will be organized in the following way: each morning there will be a round table discussion to bring forth the various health care issues that will be discussed during the day, Keynote speakers and concurrent sessions will give participants the opportunity to choose topics to meet their specific objectives. In addition, there will be a panel discussion at the end of each day to address issues that have not been covered. Wednesday, November 3, 1993 --------------------------- - Keynote Speaker: Health Care Reform: US Task Force on Health Care Reform - Roundtable Discussion: US Taskforce on Health Care Reform Kenneth Goodman, PhD; Jane Sarasohn-Kahn, MA, MS; Herbert W. Zagarow, PhD - Transition from Quality Assurance to Interdisciplinary Continuous Quality Assurance. David Kibbe, MD; Richard Scoville, PhD - Uncertainty and Ethics in Medical Computing Kenneth Goodman, PhD - Multimedia: A Synthesis of Technologies Madeline Lambrecht, EdD, RN - Quality Improvement: Myths, Realities and Challenges for Success Herbert W. Zagarow, PhD - The Evolving Electronic Health Care Infrastructure Jane Sarasohn-Kahn, MA, MS - Doing Continuous Quality Assurance With Your Spreadsheet David Kibbe, MD; Richard Scoville, PhD - Electronic Frontiers in Healthcare Deannie French, PhD, RN - Cooperative Care Units Kimberly Glassman, RN - Panel Discussion Day One Thursday, November 4, 1993 -------------------------- - Keynote Speaker: Care Planning Representative, Joint Commission on the Accreditation of Healthcare Organizations - Roundtable: Care Planning Paul S. Sherman, PhD; Lawrence E. Mieczowski, MD; Michael B. First, MD; Renato M.E. Sabbatini, PhD - DSM-IV Workshop Michael B. First, MD - Mental Health Clinical Guidance Systems in the Year 2000 Paul S. Sherman, PhD - Clinical Decision Support Systems Lawrence E. Mieczowski, MD - Uses of Data in Decision Making or "Manage the Care and the Money Will Follow" Cassy Pollack, MSN, MPPM, RN - Bedside Terminals: Result of Study at NYU Medical Center Diane Janovas, BSN - What Management Information Doctors Need to Know to Survive and Prosper in The Future Christine Shapleigh, MD - Clinical Pathways Marie DiPrinzio, MSN, RN - Informatics in Health Care: The Coming Revolution Renato M.E. Sabbatini, PhD - Points of Access - Medication Supply and Data Collection Pyxis Corporation Representative - Panel Discussion Day Two Organizing Committe Victor Greenstein (Chairperson) Patricia Barnes, Patricia Bush, Joseph Catania, Eugene Doria, Leo Gilmore, Jeanine Herrmann, Lindsay Huver, Brenda Jester, Mary Lou Kauffman, Michael Land, Jed Lazzeri, Larry Pernell, Jack Price, Barbara Vugrinec, Richard Winkelmayer, Jerry Woolpert. Registration General Hospitals in Delaware One Day $ 130 $ 100 Two Days $ 225 $ 180 Roundtable/Panel/Exhibit $ 65 $ 50 Split Registration $ 15 $ 10 Lunch at the Ramada $ 15 $ 15 Late Fees $ 25 $ 25 Fees include refreshment and conference materials Mail to: CIHC'93 Secretariat Delaware State Hospital 1901 N DuPont Highway New Castle, DE 19720 USA Tel. (302) 577-4060 Email: CIHC93@dsh.org (Internet) From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: bionet%FRCGM51.earn@uk.ac.earn-relay Newsgroups: bionet.software Subject: Re: problems with Treealign Message-ID: <1993Oct8.075908.25695@gserv1.dl.ac.uk> Date: 8 Oct 93 13:00:23 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 20 Precedence: first-class Original-To: bio-software@uk.ac.daresbury > >I recently picked up the latest version of Treealign from the iubio server. > Unfortunately, I can't get it to run on any of my systems. On my Indigo >and R/S 6000 it wont read in the sequences, on the Vax (VMS) it reads fine, >but dies in the alignment process. > I had exactly the same problem on my Vax/VMS and couldn't find out why. Thus Treealign has never been run here. Sorry that I can't be more positive... --------------------------------------------------------------------- Jean-Loup Risler Tel: (33 1) 69 82 31 34 CNRS Fax: (33 1) 69 07 49 73 Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr 91198 Gif sur Yvette Cedex France Email: risler@frcgm51.bitnet --------------------------------------------------------------------- From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!newsserver.jvnc.net!jvnc.net!mrl775.jvnc.net!user From: mrl775@tigger.jvnc.net (Keith O. Elliston) Newsgroups: bionet.software Subject: Problems with Treealign Message-ID: Date: 8 Oct 93 04:06:42 GMT Sender: news@tigger.jvnc.net (Zee News Genie) Followup-To: bionet.software Organization: JvNCnet Lines: 20 Nntp-Posting-Host: mrl775.jvnc.net Hello I recently picked up the latest version of Treealign from the iubio server. Unfortunately, I can't get it to run on any of my systems. On my Indigo and R/S 6000 it wont read in the sequences, on the Vax (VMS) it reads fine, but dies in the alignment process. Does anyone have experiences like this? Can you help me out quickly? I don't want to spend too much time on this.... but I would like to make the program work. INcidently... I sent email to Jotun Hein at his utoronto address (in the doc), but it bounced. ANyone know his current email address? Thanks Keith +++++++++++++++++++++++++ Keith Elliston mrl775@tigger.jvnc.net From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!spool.mu.edu!nigel.msen.com!yale.edu!news.yale.edu!news From: STONE@biomed.med.yale.edu (Lynna Stone-Infeld) Newsgroups: bionet.software Subject: Alinging LARGE sequences? Message-ID: <1993Oct8.152404.9110@news.yale.edu> Date: 8 Oct 93 15:24:04 GMT Sender: news@news.yale.edu (USENET News System) Organization: Yale University Lines: 15 Nntp-Posting-Host: biomed.med.yale.edu X-News-Reader: VMS NEWS 1.20 I would like to know if anyone has experience using programs to align multiple DNA sequences in the 35,000 to 100,000 base range? Which programs do you use? and on what platforms? - Lynna ======================================================================= - Lynna Stone-Infeld, Manager, User Services AND Manager, Molecular Biology Computing Resources Internet: STONE@BIOMED.MED.YALE.EDU Bitnet: STONE@YALEMED Biomedical Computing Unit, Yale University, School of Medicine P.O. Box 3333, New Haven, CT, 06510 ======================================================================= From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!vixen.cso.uiuc.edu!max.cecer.army.mil!usenet From: sprouse%enr@aardvark.cecer.army.mil Newsgroups: bionet.software Subject: T & E listing Message-ID: <293roq$jhh@max.cecer.army.mil> Date: 8 Oct 93 13:59:54 GMT Distribution: usa Organization: usacerl Lines: 3 NNTP-Posting-Host: deadwood.cecer.army.mil I am loomking for on-line access to threatened & endangered species listing. This could be by state or nation wide. Does such a thing exists? From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!pipex!uknet!mcsun!julienas!pasteur.fr!pasteur.fr!not-for-mail From: tekaia@pasteur.fr Newsgroups: bionet.software Subject: Re: Genpept Gopher? Message-ID: <293inp$akp@mendel.sis.pasteur.fr> Date: 8 Oct 93 11:25:45 GMT References: <1993Oct7.161630.16127@gserv1.dl.ac.uk> Distribution: bionet Organization: Institut Pasteur, Paris, France Lines: 40 NNTP-Posting-Host: mendel.sis In article <1993Oct7.161630.16127@gserv1.dl.ac.uk> risler%FRCGM51.earn@uk.ac.earn-relay writes: [..] > >I've fumbled around in the Gopher space to find a hole from which I could >retrieve sequences from the NCBI GENPEPT databank. I couldn't find any. [..] Jean-Loup, I dont know of a gopher hole for genpept, but few weeks ago Dr Tin-Wee Tan (bchtantw@nuscc.nus.sg) announced the availability of a "waissearch" on the genpept database with the following coordinates : ------------------------------- (:source :version 3 :ip-address "137.132.9.12" :ip-name "nusunix2.nus.sg" :tcp-port 2100 :database-name "genpept" :cost 0.00 :cost-unit :free :maintainer "bchtantw@nuscc.nus.sg" :description "Server created with WAIS release 8 b5 on Apr 24 01:31:35 1993 by rp900323@nusunix2 The files of type genbank used in the index were: /usr/local/biocomp/wais/src/genpept This is the waisindexed version of the GenPept database, a database of protein sequences translated from genes deposited with GenBank. " ) ------------------------------------------- Fredj Tekaia ---------------------------------------------------------------------------- Fredj Tekaia Service d`Informatique Scientifique tekaia@pasteur.fr Institut Pasteur 25, rue du Dr. Roux 75724 Paris cedex 15 France ---------------------------------------------------------------------------- From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rice From: rice@embl-heidelberg.de (Peter Rice) Newsgroups: bionet.software Subject: Re: Dos DNA/Protein analysis packages Message-ID: <1993Oct8.092153.121282@embl-heidelberg.de> Date: 8 Oct 93 08:21:53 GMT References: <9310071738.AA19754@audrey.lmf.org> Distribution: bionet Organization: EMBL, European Molecular Biology Laboratory Lines: 23 In article <9310071738.AA19754@audrey.lmf.org>, jim@AUDREY.LMF.ORG (Jim Gale) writes: > > We need some advice. Our access to (free) GCG is lost. The institute we used > GCG on by modem is dropping GCG due to the cost. Since we cannot afford GCG. > We need some other similar package for our PC systems (MS-DOS). I am fimilar > Hitachi DNASIS/PROSIS and Inteligenetics PC-Gene. We will be having demos > of both shortly. > Does anyone out there use either package for MS-DOS? > What is yor opinion of the system. Does it compare to GCG? > Is there another package we should be looking at???? I would certainly look at DNASTAR (also called LaserGene on Macintoshes). It supports DOS, and includes similar functions to GCG for most analysis so it should be familiar to your users. ----------------------------------------------------------------------------- Peter Rice, EMBL | Post: Computer Group | European Molecular Internet: Peter.Rice@EMBL-Heidelberg.DE | Biology Laboratory | Postfach 10-2209 Phone: +49-6221-387247 | 69012 Heidelberg Fax: +49-6221-387306 | Germany From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!CUCCFA.CCC.COLUMBIA.EDU!MARK From: MARK@CUCCFA.CCC.COLUMBIA.EDU (T. Mark Reboul) Newsgroups: bionet.software Subject: MOWSE info Message-ID: <931008144632.bc4@CUCCFA.CCC.COLUMBIA.EDU> Date: 8 Oct 93 18:46:32 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 As of the time of that earlier posting on the MOWSE service, the way to get its own instructions was to send the message "help" to this address: mowse@dl.ac.uk Mark Reboul Columbia-Presbyterian Cancer Center Computing Facility mark@cuccfa.ccc.columbia.edu From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!d.love From: d.love@dl.ac.uk (Dave Love) Newsgroups: bionet.xtallography,bionet.software Subject: RIBBON program (new version) Message-ID: Date: 8 Oct 93 18:37:22 GMT Reply-To: ccp4@uk.ac.daresbury Distribution: bionet Organization: SERC Daresbury Laboratory, Warrington, UK Lines: 21 Xref: biosci bionet.xtallography:486 bionet.software:6097 NNTP-Posting-Host: dlpx1.dl.ac.uk There have been several enquiries recently about John Priestle's program RIBBON (for Jane Richardson-type cartoons of protein structure). JP recently sent a new version -- thanks, John! -- which is available from the CCP4 ftp server (anonymous@ccp4.dl.ac.uk:pub/ccp4/ribbon.tar.Z). The new version doesn't have the CCP4-ish hacks applied and consequently doesn't need our library, but the old stuff is still there. Enjoy, --Dave -- Thank you for your interest in the CCP4 protein crystallography software. Secretary to CCP4 | Telephone: (+44) 925 603530 (direct line) SERC Daresbury Laboratory | (+44) 925 603000 (switchboard) Warrington WA4 4AD | Facsimile: (+44) 925 603173 UK | e-mail: ccp4@daresbury.ac.uk (proclaim '(standard disclaimer)) ; oppose software monopolies: ; ask lpf@uunet.uu.net From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!ETSUACAD.bitnet!JB5369 From: JB5369@ETSUACAD.bitnet (GORDON BETTS) Newsgroups: bionet.software Subject: VIDEODISC SOURCES Message-ID: <9310081826.AA09449@net.bio.net> Date: 8 Oct 93 18:24:23 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 DEAR NETTERS, I HAVE LOST THE SOURCE INFORMATION FOR TWO VIDEODISCS I NEED TO PURCHASE FOR MY COURSES. IF YOU KNOW WHERE I CAN PURCHASE THESE, I WOULD APPRECIATE THE INFO. THE DISCS ARE: "ATOMS TO ANATOMY" AND "SLICE OF LIFE". PLEASE REPLY DIRECTLY TO MY E-MAIL ADDRESS SINCE I DO NOT REGULARLY READ THIS LIST. THANKS +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ J. GORDON BETTS INTERNET: JB5369@ETSUACAD.ETSU.EDU EAST TEXAS STATE UNIVERSITY "SEEK SIMPLICITY AND DISTRUST IT" DEPT OF BIOLOGICAL SCIENCES ALFRED NORTH WHITEHEAD COMMERCE, TX 75429-3011 "SIMPLIFY. SIMPLIFY" 903/886-5369 HENRY DAVID THOREAU From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!agate!msuinfo!netnews.upenn.edu!hmivax!bailey From: bailey@hmivax.humgen.upenn.edu (Charles Bailey) Newsgroups: bionet.software Subject: Re: Sharing lab "tools". Message-ID: <1993Oct8.130853.1@hmivax> Date: 8 Oct 93 17:08:53 GMT References: <1993Oct6.232123.22037@emba.uvm.edu> Sender: news@netnews.upenn.edu Organization: HHMI/Human Genetics, Univ of Pa. Lines: 30 Nntp-Posting-Host: hmivax.humgen.upenn.edu In article <1993Oct6.232123.22037@emba.uvm.edu>, brianf@med.uvm.edu (Brain Foley) writes: > > [good description of useful working tools, which may be hacks not of > 'publication quality'] > > I don't think I should upload all my spreadsheets to IUBIO > or any other FTP site, because who could sort through them all to find the > one macro they can use? But if I have one or two "tools" that I find > really handy should I send them out? The bionet.software.sources group has been really quiet for quite some time, and would seem to be an ideal forum for these types of things. Perhaps it would be good to agree interested people should feel free to post 'working' copies of code to the group, in order to distribute something they feel is useful but not pretty, or just to get feedback on a work in progress. This doesn't use the permanent resources that an ftp archive uses, so perhaps we shouldn't hold postings to this group to as high a standard as we would submissions to an archive. Thoughts? Regards, Charles Bailey !------------------------------------------------------------------------------- ! Dept. of Genetics / Howard Hughes Medical Institute ! University of Pennsylvania School of Medicine Rm. 430 Clinical Research Bldg. ! 422 Curie Blvd. Philadelphia, PA 19104 USA Tel. (215) 898-1699 ! Internet: bailey@genetics.upenn.edu (IN 128.91.200.37) !------------------------------------------------------------------------------- From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!usc!yeshua.marcam.com!charnel!olivea!news.bu.edu!med-pharm5.bu.edu!user From: leach@mbcrr.harvard.edu (Martin Leach) Newsgroups: bionet.software Subject: Re: MavVector Message-ID: Date: 8 Oct 93 13:35:20 GMT References: <1993Oct7.202658.18844@gserv1.dl.ac.uk> Followup-To: bionet.software Distribution: bionet Organization: Boston University Dept. of Pharmacology Lines: 21 NNTP-Posting-Host: med-pharm5.bu.edu In article <1993Oct7.202658.18844@gserv1.dl.ac.uk>, roxanne@edu.tmc.uth.mda.odin (Roxanne Hall) wrote: > > > Fellow Netters, > > I am having a strange little problem with the use of MacVector and > GCG format sequence files. Our site is set up so that our Macs are on > the network with the main frame. GCG is setup on the main frame (a UNIX (deletia) > It does not matter that the lock is open or closed. Also, this did not > happen when everyone had to use a modem to access the main frame. > MacVector can be very tempermental whether modem is in use or not. Creat a set on the startup manager, called it macvector and turn off all the inits. This seems to work when MacVector throws a tantrum in our lab. Martin Leach From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!caen!usenet.coe.montana.edu!netnews.nwnet.net!news.uoregon.edu!gaia.ucs.orst.edu!MassSpec2-0073-E.ALS.ORST.EDU!jenseno From: jenseno@ehsc.orst.edu (Ole N Jensen) Newsgroups: bionet.software Subject: MOWSE software for MW searches. Message-ID: Date: 8 Oct 93 17:29:50 GMT Organization: Environmental Health Sciences Center, Oregon State University Lines: 14 NNTP-Posting-Host: massspec2-0073-e.als.orst.edu A while ago there was a posting on MOWSE software for searching molecular weights in protein sequence databases. Could someone tell me how to access this program and how to run MW searches? Thanks. Ole N. Jensen jenseno@ucs.orst.edu Department of Biochemistry & Biophysics Oregon State University, Corvallis, OR From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!uni-heidelberg!rz.uni-karlsruhe.de!xlink.net!howland.reston.ans.net!usc! cs.utexas.edu!geraldo.cc.utexas.edu!doc.cc.utexas.edu!not-for-mail From: strand@doc.cc.utexas.edu (Allan Strand) Newsgroups: bionet.software Subject: GDE on DECstation Message-ID: <2941s1$4g7@doc.cc.utexas.edu> Date: 8 Oct 93 15:44:01 GMT Organization: The University of Texas - Austin Lines: 10 NNTP-Posting-Host: doc.cc.utexas.edu Hi All, I'm wondering if anyone has had luck in compiling GDE 2.2 on a DECstation running ULTRIX and DECwindows. I'd appreciate any advice. Thanks, Allan Strand Department of Botany, University of Texas - Austin a_strand@trillium.botany.utexas.edu From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!math.ohio-state.edu!caen!kuhub.cc.ukans.edu!news.umkc.edu!UMSLVMA.UMSL.EDU!S942438 From: S942438@UMSLVMA.UMSL.EDU (P. A. Lopez-Valencia) Newsgroups: bionet.software Subject: Re: WWW GUI for mac? Mosaic-Mac DOES exist Message-ID: <16C60B544.S942438@UMSLVMA.UMSL.EDU> Date: 7 Oct 93 17:53:14 GMT References: <1993Sep22.145115.5874@news.gdb.org> Organization: UM-St. Louis Lines: 12 NNTP-Posting-Host: umslvma.umsl.edu X-Newsreader: NNR/VM S_1.3.2 In article <1993Sep22.145115.5874@news.gdb.org> danj@dev.gdb.org (Dan Jacobson) writes: > MOSAIC Beat2 was released last weekend. I have it running in our Quadra in the lab. You will find it at the NCSA archives. (Do an archie search) -- P.A. Lopez-Valencia ****************************** Department of Biology *There are liars, damn liars,* U. of Missouri-St Louis *and statisticians. * palopez@joline.umsl.edu * Mark Twain * s942438@umslvma.umsl.edu ****************************** From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Sharing lab "tools". Message-ID: Date: 8 Oct 93 19:34:03 GMT References: <1993Oct6.232123.22037@emba.uvm.edu> <1993Oct8.130853.1@hmivax> Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 30 Nntp-Posting-Host: sunflower.bio.indiana.edu Anyone with biology-related spreadsheet forms, computer methods, software, etc. that you think will be of interest to a general audience of biologists should feel free to ftp them to IUBIO archive where they will become published and available to all (soon you can gopher them to iubio -- see the Gopher+TEST/Incoming.../ folder). The only thing special I ask in terms of your preparation, is that you include a short, plain text abstract file along with whatever main file you send. See the "Archive.doc" at ftp.bio.indiana.edu for details. Posting to bionet.software.sources is an alternate way to publish such tools, and there are other archives (embl, houston) which take author submissions. All postings to bionet.software. sources and other bionet. news are also archived at IUBio and at net.bio.net, so this isn't a less resource intensive, nor lower standard, form of publiation. However, it is best limited to the smaller works which can reasonably fit into a e-mail sized message. In my estimation, it is lack of time that keeps authors from publishing their lab software tools, or the thought that no one else would be interested. I know of works done locally that fall in this category -- hypercard stacks or database forms that could be usefully shared with the community. Even if they are designed for a specific local problem, others can often benefit in solving related tasks by seeing tools you may have written for local uses. -- don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!agate!library.ucla.edu!nntp.ucsb.edu!mcl!timmbake From: timmbake@mcl.ucsb.edu (Bake Timmons) Newsgroups: bionet.software Subject: Need program for filtering GenBank sequences Message-ID: <292md4$cu5@hub.ucsb.edu> Date: 8 Oct 93 03:22:12 GMT Organization: University of California, Santa Barbara Lines: 16 NNTP-Posting-Host: mcl.ucsb.edu Hi everyone. Roy Smith at PHRI had a progrma for filtering GenBank sequences from the news postings. It was erased from his drive after he left PHRI. ;( Can anyone mail me a copy they have. It would be greatly appreciated. Thanks, Bake Timmons UCSB Microcomputer Lab Consultant -- Bake Timmons, III -- "...there's nothing higher, stronger, more wholesome and more useful in life than some good memory..." -- Alyosha in Brothers Karamazov (Dostoevsky) From owner-software@net.bio.net Thu Oct 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!math.ohio-state.edu!caen!kuhub.cc.ukans.edu!news.umkc.edu!UMSLVMA.UMSL.EDU!S942438 From: S942438@UMSLVMA.UMSL.EDU (P. A. Lopez-Valencia) Newsgroups: bionet.software Subject: Re: Need data processing/plotting tool for SGI with flexible input handling Message-ID: <16C60B6E5.S942438@UMSLVMA.UMSL.EDU> Date: 7 Oct 93 18:00:17 GMT References: <199309241712.AA08398@orion.oac.uci.edu> Organization: UM-St. Louis Lines: 19 NNTP-Posting-Host: umslvma.umsl.edu X-Newsreader: NNR/VM S_1.3.2 In article <199309241712.AA08398@orion.oac.uci.edu> mangalam@UCI.EDU (Harry Mangalam) writes: lots deleted (darned reader) Try also oleo-1.5 available from the GNU archives at prep.ai.mit.edu in /pub/gnu/oleo-1.5.tar.gz notice that it it *not* a compress file If you do not have gzip in your system get /pub/gnu/gzip-1.2.4.shar, a shell script. The Free Software Foundation cannot use compress because it is copy- righted twice (for those of you who are curious, by ATT and Unix Labs). Oleo is a really nice spreadsheet. Best luck. -- P.A. Lopez-Valencia ****************************** Department of Biology *There are liars, damn liars,* U. of Missouri-St Louis *and statisticians. * palopez@joline.umsl.edu * Mark Twain * s942438@umslvma.umsl.edu ****************************** From owner-software@net.bio.net Fri Oct 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!library.ucla.edu!europa.eng.gtefsd.com!uunet!noc.near.net!news.cs.brandeis.edu!lee From: lee@auriga.rose.brandeis.edu (charles lee) Newsgroups: bionet.software Subject: RIBBON. Where can one find/get it? Message-ID: Date: 8 Oct 93 22:52:25 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Organization: Brandeis University Lines: 19 Hi there... I see these nice diagrams of proteins done by the program RIBBON quite often. I'd like to know where to find it (with sources preferably). I did an archie case-insensitive and reg.exp. search on "ribbon" but it only found this ms-windows stuff... Thanks for any pointers! -Charles Lee Structural Biology Lab Brandeis University o-----------------------o--------------------------o----------------o | Charles Lee |A3KT-VT4000-PP&S28Mhz68040| Vector Visions | | IRC: waif |38MB RAM-USRDUAL-Syquest88|~~~~~~~~~~~~~~~~| | Fortress /\ M | G /\ |QLPS52-ST3283-JX100-NEC3FG| Call for rates | | Brandeis University |<>| 617-891-1367 | o-----------------------o--------------------------o----------------o From owner-software@net.bio.net Fri Oct 08 23:00:00 1993 Path: biosci!NATURE.BERKELEY.EDU!bosborne From: bosborne@NATURE.BERKELEY.EDU (Brian Osborne) Newsgroups: bionet.software Subject: Signal peptide server? Message-ID: <9310091729.AA12189@nature.berkeley.edu.cnr-net> Date: 9 Oct 93 18:26:19 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 24 To the Group, I found the following reference in the seqanalref database : RA Ladunga I., Czako F., Csabai I., Geszti T.; RT "Improving signal peptide prediction accuracy by simulated neural RT network."; RL Comput. Appl. Biosci. 7:485-487(1991). As I'm not on campus I don't have access to the journal CABIOS. Does anyone know if I can send a cDNA sequence to a server or an individual who can run this program on my sequence? Thank you for your attention to this matter, Brian Osborne Plant Gene Expression Center 800 Buchanan Street Albany, CA USA 94710 TEL 510-559-5919 FAX 510-559-5718 bosborne@nature.berkeley.edu From owner-software@net.bio.net Fri Oct 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!newsserver.jvnc.net!newsserver.technet.sg!solomon.technet.sg!waisguy From: waisguy@solomon.technet.sg (wais server operator) Newsgroups: bionet.software Subject: Re: Genpept Gopher? Message-ID: Date: 9 Oct 93 10:27:02 GMT References: <1993Oct7.161630.16127@gserv1.dl.ac.uk> <293inp$akp@mendel.sis.pasteur.fr> Sender: news@newsserver.technet.sg Distribution: bionet Organization: Technet, Singapore Lines: 66 Nntp-Posting-Host: solomon.technet.sg X-Newsreader: TIN [version 1.2 PL0] Thanks Fredj for the plug. We apologize but genpept.src will not be available this weekend because of system reorganization. I hope to get the waisserver up on Monday morning after our system managers have cleaned up the system, hopefully not my stuff as well. Meanwhile, I shall put a pointer higher up my hierarchy of the biogopher at the National University of Singapore. Start navigating from... gopher://solomon.technet.sg:70/ alternatively, you can try our new WWW server http://nusunix2.nus.sg:8000/ (which as you can see, will not be available this weekend). nothing much in it so far but we will be sticking in more info as we go along. tekaia@pasteur.fr wrote: : In article <1993Oct7.161630.16127@gserv1.dl.ac.uk> risler%FRCGM51.earn@uk.ac.earn-relay writes: : [..] : > : >I've fumbled around in the Gopher space to find a hole from which I could : >retrieve sequences from the NCBI GENPEPT databank. I couldn't find any. : [..] : Jean-Loup, : I dont know of a gopher hole for genpept, but few weeks ago Dr Tin-Wee Tan : (bchtantw@nuscc.nus.sg) announced the availability of a "waissearch" : on the genpept database with the following coordinates : : ------------------------------- : (:source : :version 3 : :ip-address "137.132.9.12" : :ip-name "nusunix2.nus.sg" : :tcp-port 2100 : :database-name "genpept" : :cost 0.00 : :cost-unit :free : :maintainer "bchtantw@nuscc.nus.sg" : :description "Server created with WAIS release 8 b5 on Apr 24 01:31:35 : 1993 by rp900323@nusunix2 : The files of type genbank used in the index were: : /usr/local/biocomp/wais/src/genpept : This is the waisindexed version of the GenPept database, a database : of protein sequences translated from genes deposited with GenBank. : " : ) : ------------------------------------------- : : Fredj Tekaia : ---------------------------------------------------------------------------- : Fredj Tekaia Service d`Informatique Scientifique : tekaia@pasteur.fr Institut Pasteur : 25, rue du Dr. Roux : 75724 Paris cedex 15 France : ---------------------------------------------------------------------------- WAIS operator waisguy@solomon.technet.sg or Dr Tan Tin Wee, Department of Biochemistry, National University of Singapore. Tel 772-3678 Fax 7791453 INTERNET bchtantw@nuscc.nus.sg From owner-software@net.bio.net Fri Oct 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!sunic!news.funet.fi!klaava!klaava!not-for-mail From: stenberg@kruuna.Helsinki.FI (Dag Stenberg) Newsgroups: bionet.software Subject: Sigmaplot - export graphs? Message-ID: <2963i6$266@kruuna.Helsinki.FI> Date: 9 Oct 93 10:25:10 GMT Organiz