From owner-software@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!agate!howland.erols.net!cs.utexas.edu!swrinde!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!newsstand.cit.cornell.edu!news.acsu.buffalo.edu!news.atl.bellsouth.net!newsrelay.iastate.edu!news.iastate.edu!news From: ckafer@iastate.edu (Chris Kafer) Newsgroups: bionet.software Subject: Re: Blast search help needed. Date: Wed, 02 Oct 1996 02:26:38 GMT Organization: Iowa State University, Ames, Iowa Lines: 37 Message-ID: <52sk25$29v@news.iastate.edu> References: <52mnn2$rh0@news.iastate.edu> <52ot09$i02@swsu65.swmed.edu> NNTP-Posting-Host: las2a.iastate.edu X-Newsreader: Forte Free Agent 1.0.82 mperr1@hamon.swmed.edu (Michael Perry) wrote: >Chris, >Sounds like a job for blastx. Point your browser to the NCBI BLAST >web page at http://www.ncbi.nlm.nih.gov/BLAST/ and check out the >following programs: >blastx: compares a nucleotide query sequence translated in all >reading frames against a protein sequence database >tblastx: compares the six-frame translations of a nucleotide query >sequence against the six-frame translations of a nucleotide sequence >database. Thanks for the reply but I tried that first. What it appears to do is compare the entire sequence (as if it were a single ORF) in all 6 frames. What I would like to do is have it blast the real ORFs >30 amino acids individually. When I blast them manually, it brings back different hits than a blastx search of the entire sequence. As an example, when I blast one of the 200 aa ORFs it returns an EST clone. When I blast the entire sequence, of which this ORF is just a part, it doesnt show up. Hopefully I explained that clearly! Any other ideas would be appreciated! ******************************************************************** Chris Kafer Lab: 2228 Mol. Bio. Bldg. Ph#: 515-294-8626 http://www.public.iastate.edu/~ippm http://www.public.iastate.edu/~thorn ******************************************************************** "...it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science." Charles Darwin, from The Descent of Man From owner-software@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: Blast search help needed. Date: 1 Oct 1996 22:01:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 57 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610020501.BAA15255@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net > mperr1@hamon.swmed.edu (Michael Perry) wrote: > > > >Chris, > >Sounds like a job for blastx. Point your browser to the NCBI BLAST > >web page at http://www.ncbi.nlm.nih.gov/BLAST/ and check out the > >following programs: > > >blastx: compares a nucleotide query sequence translated in all > >reading frames against a protein sequence database > > >tblastx: compares the six-frame translations of a nucleotide query > >sequence against the six-frame translations of a nucleotide sequence > >database. > From ckafer@iastate.edu Wed Oct 2 00:48:50 1996 > Thanks for the reply but I tried that first. What it appears to do is > compare the entire sequence (as if it were a single ORF) in all 6 > frames. What I would like to do is have it blast the real ORFs >30 > amino acids individually. When I blast them manually, it brings back > different hits than a blastx search of the entire sequence. > > As an example, when I blast one of the 200 aa ORFs it returns an EST > clone. When I blast the entire sequence, of which this ORF is just a > part, it doesnt show up. Hopefully I explained that clearly! > > Any other ideas would be appreciated! Chris, If I understand correctly, what you want is "tblastn vs est"? TBLASTN takes a protein query sequence and compares it to the translation of the EST in 3 or 6 frames (6 is the default). Is that what you want? A summary of the various ways of using blast is available (blatent self citation to follow) from: http://www.cshl.org:80/books/g_a/bk1ch7/ cheers, f. -- | B.F. Francis Ouellette | GenBank | | francis@ncbi.nlm.nih.gov From owner-software@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!data-transport.com!scott_jokerst From: scott_jokerst@data-transport.com (R. Scott Jokerst) Newsgroups: bionet.software Subject: Bioinformatics resource upgrade. Date: 1 Oct 1996 17:26:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I wanted to alert you (who were not already aware) to a significant upgrade to the Biological Data Transport bioinformatics resource. Among other things, the Query Depot was launched over a month ago. And it has been upgraded weekly based on your feedback. http://www.data-transport.com From this resource, several kinds of bioinformatics related searches can be executed - to GenBank, the MEDLINE molecular biology subset, OMIM, Entrez, the BCM Search Launcher, PDB, BLAST, GDB, etc. Direct searching of several life sciences vendor resources are available as well, all in one centralized location. We've simplified the UI to these free public resources significantly - you may find the Query Depot useful when you want to quickly scan for info at the start of your search for information on the Internet. Looking forward to your continued suggestions for additions and changes. Help us to continue making this resource a high value time saver for you, Scott R. Scott Jokerst (510-648-8229) scott_jokerst@data-transport.com Biological Data Transport http://www.data-transport.com Bringing FOCUS to life sciences informatics, product, & services resources From owner-software@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!GENECODES.COM!howardc From: howardc@GENECODES.COM (Howard Cash) Newsgroups: bionet.software Subject: SEQUENCHER FOR UNIX? WHY? Date: 2 Oct 1996 16:47:25 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 70 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Don Gilbert posted a query on the AUTOMATED-SEQUENCING group soliciting opinions on different software packages for DNA sequencing and assembly. He summarized responses on the net at http://www.bio.net/hypermail/AUTOMATED-SEQUENCING/9608/0047.html There were subsequent postings on the subject http://www.bio.net/hypermail/AUTOMATED-SEQUENCING/9609/0007.html etc. > Subject: Summary: Software choice? sequencher, phrap/phred/consed, staden? > > This is a summary of responses to : > Do you have opinions to share on the best choice(s) of > software for small-scale autosequencing? ... [snip snip] > My thanks to the many people who wrote me or posted a reply. It is > good to see so many helpful people sharing their experiences thru > network news. > > The unanimous favorite software was Sequencher. However only two > respondents expressed experience with the Unix programs (Phrap & > Staden), > so this does not offer as clear an answer as I had hoped. ... [snip snip...many quoted opinions deleted] Is there an assumption here that UNIX-based tools have an inherent value that is not reflected in an unstructured polling of newsgroup readers? Without challenging that premise, what do people think is the main value of having sequence assembly software on a UNIX platform? If Sequencher is already such a favorite on the Mac, is there something to be gained by going to the trouble to develope a UNIX version? As an engineer, I like UNIX for software development, but I am biased towards the Macintosh for delivering ready-to-use analysis tools. Larger research groups with existing UNIX-based data-management systems ask us about porting to that platform, but is there a compelling reason for us to develop Sequencher for Unix? What would the advantage be in the average lab, other than the undeniable freedom to work in front of the computer of one's choosing? This should not be construed as a product announcement or a promise to port Sequencher to a new operating system, but I would be interested in hearing your opinions on the value that you or your immediate colleagues would get from a UNIX version. What operating system characteristics would you want us to take advantage of that might not be available on a Mac. Keep in mind that, in the real world of finite resources, the effort that we would put into porting all or part of Sequencher to a new platform would come at the expense of our ability to quickly add features to the program if it is only on the Mac. ----------------------------------------------------------- Howard Cash President Gene Codes Corporation 640 Avis Drive, Suite 300, Ann Arbor, MI 48108 Phone 313-769-7249 Fax 313-769-7074 howardc@genecodes.com http://www.genecodes.com/ ----------------------------------------------------------- Disclaimer: Although Gene Codes is a commercial software developer, this posting should not be construed as an offer to sell software nor to develop new programs. Opinions expressed are my own unless directly attributed to others, and do not necessarily reflect those of my employer, but - under the circumstances - they often do. From owner-software@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!agate!howland.erols.net!newspump.sol.net!news.mindspring.com!uunet!in3.uu.net!newsflash.concordia.ca!news.nstn.ca!news.dal.ca!news From: "W. Ford Doolittle" Newsgroups: bionet.software Subject: (no subject) Date: 2 Oct 1996 14:26:56 GMT Organization: Dalhousie Biochemistry Lines: 20 Message-ID: <52tu3g$e1c@News.Dal.Ca> NNTP-Posting-Host: samiam.biochem.dal.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.software OPENING FOR POSTDOCTORAL FELLOW IN MOLECULAR BIOLOGY AND EVOLUTION AREAS OF RESEARCH: (1) early evolution of eukaryotes as assessed by gene surveys and phylogenetic reconstruction, (2) comparative analysis of whole genomes, (3) intron origins and evolution, and (4) development of genetics tools for Sulfolobus solfataricus, to be used in conjunction with a genome sequencing project. Contact: W. Ford Doolittle Department of Biochemistry Dalhousie University Halifax, NS B3H 4H7 email: ford@is.dal.ca From owner-software@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!ddsw1!news.mcs.net!van-bc!unixg.ubc.ca!info.ucla.edu!nnrp.info.ucla.edu!usenet From: Edmundo Castro Newsgroups: bionet.software Subject: Plasmid drawing program for Mac: freeware? Date: Wed, 02 Oct 1996 13:35:27 -0700 Organization: UCLA Lines: 5 Message-ID: <3252D20F.33F2@physci.ucla.edu> Reply-To: ecastro@physci.ucla.edu NNTP-Posting-Host: henderson1.physci.ucla.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) Does anyone know of free or shareware plasmid drawing software for Macs? Thank to all in advance! E. Castro-Vargas From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!nntp.primenet.com!hunter.premier.net!news1.erols.com!uunet!in1.uu.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: SEQUENCHER FOR UNIX? WHY? Date: 3 Oct 1996 08:05:48 GMT Organization: University of Cambridge Lines: 73 Message-ID: <52vs4s$ma2@lyra.csx.cam.ac.uk> References: NNTP-Posting-Host: mole.bio.cam.ac.uk In article , Howard Cash wrote: >Is there an assumption here that UNIX-based tools have an inherent value >that is not reflected in an unstructured polling of newsgroup readers? >Without challenging that premise, what do people think is the main value >of having sequence assembly software on a UNIX platform? If Sequencher >is already such a favorite on the Mac, is there something to be gained by >going to the trouble to develope a UNIX version? > >As an engineer, I like UNIX for software development, but I am biased >towards the Macintosh for delivering ready-to-use analysis tools. Larger >research groups with existing UNIX-based data-management systems ask us >about porting to that platform, but is there a compelling reason for us >to develop Sequencher for Unix? What would the advantage be in the >average lab, other than the undeniable freedom to work in front of the >computer of one's choosing? Value for money is one. I am part of a team running a sequence analysis service for Cambridge University. With one computer and software licence, we provide sequence analysis facilities for over 1,500 users, which is pretty inexpensive per user, even for a large UNIX box, and the end user can then buy a cheaper terminal and still have high speed searches. Their machine does not have to sit there being unuseable for anything else because its chewing sequence databases, therefore allowing them to get on with other stuff on their Macs and PCs, like writing papers. Then there is the undeniable advantage UNIX has of stability. Macs and PCs (with the possible exception of PCs running Windows NT or UNIX) are not very stable, and I'd rather go home leaving my sequence crunching work overnight without worrying that the machine might crash. Plus a UNIX box automatically throws in a large number of other benefits, such as user file security, electronic mail, convenient submission of batch jobs, and so on. Admittedly some of these are available on other platforms (particularly Windows NT, which has both job sheduling and mail) but as far as I am aware there is as yet no large sequencing package specifically designed with Windows NT in mind. UNIX really loses out on the user interface. I totally fail to understand this. X-server software is now cheap for PCs and Macs. UNIX is a very suitable operating system for this kind of work, but lac of attention to user friendliness by most UNIX software developers is its main detraction. Admittedly there have been very good attempts, such as the Motif CDE and OpenLook, but they have never reached the polish and ease of use of the Mac or even Windows (please no flame wars on Windows vs. MacOS, this isn't the point). If you are going to port to UNIX, make the X user interface good, and people will go for it. Unfortunately this is difficult when Motif is still a proprietary product, although most of your target market will be running mainstream OS's like IRIX, Solaris or Digital UNIX, all of which support Motif these days. The real challenge is making a text based interface that is still friendly. This is extremely important in UNIX because nothing causes a UNIX machine to grind to a halt faster than 30 simultaneous X-windows sessions! Just a few thoughts. Tim. -- -------------------------------------------------------------------------- Dept. of Biochemistry Tel: +44 1223 333596 Tennis Court Rd. Cambridge, CB2 1QW, UK From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!biosci!not-for-mail From: James Bonfield Newsgroups: bionet.software Subject: Staden for Mac/PC? Date: 3 Oct 1996 04:59:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: <5309rk$biu@net.bio.net> NNTP-Posting-Host: net.bio.net Following on from Don Gilbert's question on sequencing packages and Howard Cash's followup (SEQUENCHER FOR UNIX? WHY?), this has led me to wonder about the role of the Staden package for other platforms. It would be possible (theoretically) to run the recent sections of the package (including the assembly program) natively on both PCs and Macs due to the use of Tk for the interface. We have tested this for some of the simpler programs under Windows 95 with reasonable success. However we obviously can't afford to spend time on this unless it's really desired. So, to continue the questions, would people like to see our more recent tk based programs (Gap4, Trev, and Sip4) running on a PC? On a Mac? How about a Linux port too? What factors influence the choice of program? (I'm sure Howard Cash would love to know the answer to this too :-).) Is the platform the program runs on as important as the abilities of the program itself (within reason naturally). If so, what really _is_ the platform of choice. Please do respond as the answers to some of these questions will surely help many more developers than us, and hence improve the software quality for everyone. Cheers, James -- James Bonfield (jkb@mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 412282 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ -- James Bonfield (jkb@mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 412282 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: SEQUENCHER FOR UNIX? WHY? Date: 3 Oct 1996 13:17:00 GMT Organization: Biology, Indiana University - Bloomington Lines: 63 Message-ID: <530ecc$qj7@dismay.ucs.indiana.edu> References: <52vs4s$ma2@lyra.csx.cam.ac.uk> NNTP-Posting-Host: chipmunk.bio.indiana.edu In the particular case of Sequencher software, let me comment on a few of the reasons Tim Cutts suggested for a Unix version. >> Value for money is one. ... With one computer and >> software licence, we provide sequence analysis facilities for over >> 1,500 users, which is pretty inexpensive per user Sequencher is a commercial product that is sold on the basis that each active process of the program at any one time has to be a licensed process. You pay for 5 licenses and 5 users can run the program at once. This is the same for many Unix commercial products. So there is equal value here between Mac and Unix system. At IU we have Sequencher on a Mac file server where any of the over 1,500 Mac computers on campus can use it at any time, subject to the limit on the number of licenses we own. >> Their machine does not have to sit there being unuseable for anything >> else because its chewing sequence databases Sequencher works well as a multi-tasking program, I believe. There would indeed be value in having Sequencher work on a remote, central computer though, at the user's choice. It is possible to do this with Mac systems, but I haven't seen much of it. Clearly this is a major value of Unix. One programming paradigm that I'm employing now in my software is to provide client-server (TCP/IP) functions that are transparent to the user, so one can use sequence editor on a desktop and do the crunching on a remote computer, without much concern to the user about which computer is doing what. This is the BOP protocol that now appears in SeqPup software, and which Howard Cash is welcome to add into Sequencher. I think Sequencher could be a much better product if it added client-server functions to run analyses on remote systems. >>The real challenge is making a text based interface that is still >>friendly. For complex software, this is a challenge that can no longer be met. It takes a lot of programming effort to build software that biologists will find useful, easy to learn and use in a continuing way. There are too many GUI elements that scientists require now from good software, that cannot be mimicked in text interfaces. It doesn't matter now whether your platform is Xwindows, Mac, or MSWindows, don't expect complex software to fit into a text-mode interface. My original question regarding Sequencher (Mac), and Phrap/Phred/Consed and Staden packages (Unix) was aimed at finding the best program, regardless of platform. There is value in central (Unix) systems that are multi user, better at multi tasking, and often higher performance (at at higher cost of course). There is value in desktop systems (Mac and Wintel) that are managable and usable by biologists w/o special training, that work in an easy to use manner and do all the important things a biologist needs. - Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Staden for Mac/PC? Date: 3 Oct 1996 13:02:07 GMT Organization: Biology, Indiana University - Bloomington Lines: 23 Message-ID: <530dgf$ptg@dismay.ucs.indiana.edu> References: <5309rk$biu@net.bio.net> NNTP-Posting-Host: chipmunk.bio.indiana.edu James, You might think of selecting one program of the Staden package to make available on a trial basis for Mac and Wintel systems. That could help you gauge interest. Regarding your porting effort, a Linux verison might be simplest to do and would get your package to a larger range of hardware. Regarding which computer systems are most widely used by sequence analyzing bioscientists: I don't know, probably no one really knows these days. My impression though is that Macintoshes remain the most widely used, and despite recent problems at Apple computer, Macs remain a very viable system that users of them find compelling. Wintel systems are catching up somewhat. Unix is far behind as a commonly used (desktop) system, though many instititions offer it as a shared-service option. But if you want to reach the most users, write your software to run on all these systems (like I do :). - Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Plasmid drawing program for Mac: freeware? Date: 3 Oct 1996 12:52:49 GMT Organization: Biology, Indiana University - Bloomington Lines: 25 Message-ID: <530cv1$pgm@dismay.ucs.indiana.edu> References: <3252D20F.33F2@physci.ucla.edu> <5309os$3mr@is.bbsrc.ac.uk> NNTP-Posting-Host: chipmunk.bio.indiana.edu >There is a plasmid drawing program (amongst all of the other mac >software) called macplasmap downloadable from > >gopher://ftp.bio.indiana.edu:70/11/IUBio-Software+Data/molbio/mac You have a choice of http, gopher and ftp entrances to IUBio archive: ftp://iubio.bio.indiana.edu/molbio/mac/ gopher://iubio.bio.indiana.edu/11/IUBio-Software+Data/molbio/mac/ http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/mac/ IUBio archive will this month move to a new computer locally. The following names will remain valid: iubio.bio.indiana.edu (prefered name) ftp.bio.indiana.edu This name will no longer be valid: fly.bio.indiana.edu (this is the actual computer's name, the new computer has another name) -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.zeitgeist.net!wizard.pn.com!news.gte.com!news-in.tiac.net!uunet!news-in2.uu.net!spool.news.idt.net!news From: cad29@mail.idt.net Newsgroups: bionet.software Subject: Used AutoCAD Wanted Date: Thu, 03 Oct 1996 20:40:35 GMT Organization: IDT Corporation Lines: 6 Message-ID: <531itm$1fa@News.IDT.NET> Reply-To: cad29@mail.idt.net NNTP-Posting-Host: ppp443.liberty.com X-Newsreader: Forte Free Agent 1.0.82 Used AutoCAD Wanted Must be a commercial copy and upgradable. cad29@mail.idt.net From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!arclight.uoregon.edu!feed1.news.erols.com!news1.erols.com!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software,bionet.drosophila Subject: IUBio/FlyBase server short outage on 8 Oct 96 Date: 3 Oct 1996 22:10:01 GMT Organization: Biology, Indiana University - Bloomington Lines: 31 Message-ID: <531djp$lmk@dismay.ucs.indiana.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu Xref: biosci bionet.software:16689 bionet.drosophila:2492 On Tuesday, 8 Oct, 10am EST (3pm GMT) the Internet server for IUBio Archive and FlyBase will be off the net for an hour or so. Affected host name & aliases: fly.bio.indiana.edu iubio.bio.indiana.edu flybase.bio.indiana.edu ftp.bio.indiana.edu Mirror servers will be available during this time, including FlyBase Drosophila database: http://www.embl-ebi.ac.uk/flybase/ http://www.angis.su.oz.au:7081/ http://shigen.lab.nig.ac.jp:7081/ http://cbbridges.harvard.edu:7081/ and gopher servers at gopher.embl-ebi.ac.uk 7071 shigen.lab.nig.ac.jp 7071 cbbridges.harvard.edu 7071 IUBio FTP file mirrors: ftp://ftp.gdbnet.ad.jp/ftpsync/ftp.bio.indiana.edu/ ftp://ftp.ddbj.nig.ac.jp/pub/mirror/IUBIO/molbio ftp://ftp.funet.fi/pub/sci/molbio/iubiomolbio ftp://ftp.sunet.se/pub/molbio -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.erols.net!news3.cac.psu.edu!news.cse.psu.edu!news.cc.swarthmore.edu!netnews.upenn.edu!news From: jes@presto.med.upenn.edu (Joe Smith) Newsgroups: bionet.software Subject: Re: SEQUENCHER FOR UNIX? WHY? Date: 03 Oct 1996 16:45:57 -0400 Organization: University of Pennsylvania Lines: 51 Sender: jes@presto.med.upenn.edu Message-ID: References: <52vs4s$ma2@lyra.csx.cam.ac.uk> <530ecc$qj7@dismay.ucs.indiana.edu> NNTP-Posting-Host: presto.med.upenn.edu In-reply-to: gilbertd@bio.indiana.edu's message of 3 Oct 1996 13:17:00 GMT X-Newsreader: Gnus v5.0.13 Oh dear. Here we go again. I don't meant this to be advocacy and I refuse to get involved in a PC vs. Unix discussion (as much as I enjoy them ;-). It's just a different opinion. In article <530ecc$qj7@dismay.ucs.indiana.edu> gilbertd@bio.indiana.edu (Don Gilbert) writes: My original question regarding Sequencher (Mac), and Phrap/Phred/Consed and Staden packages (Unix) was aimed at finding the best program, regardless of platform. There is value in central (Unix) systems that are multi user, better at multi tasking, and often higher performance (at at higher cost of course). [space added not in original] There is value in desktop systems (Mac and Wintel) that are managable and usable by biologists w/o special training, that work in an easy to use manner and do all the important things a biologist needs. I agree: there's value in both. We use both in the lab to good advantage. But, while the PC systems have caught the workstation in performance, and sometime ago surpassed them in price/performance, they have also increased greatly in complexity. Around here at least, I find that Don's last statement no longer rings entirely true. People spend a lot of time fiddling around with the Macs and PCs, trying to get things to work. We also spend a lot of money trying to keep up with the latest (and hopefully compatible) versions of the OS and all the add-ons. If all you want to do is turn on the computer and run a word processor, then yes, it's OK. But in many cases where people are trying to do 'all the important things a biologist needs', PCs are not terribly easy to setup and maintain. And for PCs that are used in a lab setting, with networks and multiple users, it gets much worse. OTOH, with the advent of Linux and other cheap/free Unixes, the price/performance gap is completely gone. There is no longer a premium to be paid to run Unix. The usability gap is also shrinking as more commercial software becomes available. So, I see a value in the desktop Unix market, in that there's more stability and more room to grow smoothly. Newsgroups: bionet.software Subject: Software for Molecular Biology Presentation Date: Thu, 03 Oct 1996 20:10:52 +0200 Organization: EMBL Lines: 4 Distribution: world Message-ID: <325401A8.6971@mac-biocomputing1.embl-heidelberg.de> Reply-To: user@mac-biocomputing1.embl-heidelberg.de NNTP-Posting-Host: mac-biocomputing1.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) I'm looking for a graphycal software able to create in an easy way presentation for molecular and cell biology experiments, Ex: plasmids, biochemical pathways, molecules display ... Thank you in advance From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!nntp.zit.th-darmstadt.de!fu-berlin.de!main.Germany.EU.net!EU.net!Austria.EU.net!01-newsfeed.univie.ac.at!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!becquart From: becquart@lovelace.infobiogen.fr (Paul Becquart) Newsgroups: bionet.software Subject: Re: Plasmid drawing program for Mac: freeware? Date: 3 Oct 1996 06:24:45 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 10 Message-ID: <52vm7d$jdi@lovelace.infobiogen.fr> References: <3252D20F.33F2@physci.ucla.edu> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] Edmundo Castro (ecastro@physci.ucla.edu) wrote: : Does anyone know of free or shareware plasmid drawing software for Macs? : Thank to all in advance! : E. Castro-Vargas Gene Construction Kit is a good (expensive) software with a lot of utilities. Paul. From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.erols.net!feed1.news.erols.com!news1.erols.com!uunet!in3.uu.net!newsfeed.pitt.edu!newsflash.concordia.ca!not-for-mail From: yue@clone.concordia.ca (Yue Huang) Newsgroups: bionet.software Subject: Excel format: where to find? Date: 3 Oct 1996 17:22:10 GMT Organization: I need to put my ORGANIZATION here. Lines: 6 Message-ID: <530so2$glu@newsflash.concordia.ca> NNTP-Posting-Host: clone.concordia.ca NNTP-Posting-User: yue Keywords: : : Hi: X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] I would like to export my data from a database to Excel or QuattroPro. Could someone point me where to find their formats ? Thank you for any help. yue From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!newsgate.compuserve.com!ix.netcom.com!netcom.net.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!usenet From: "Robert B. Russell" Newsgroups: bionet.software Subject: test please ignore Date: Thu, 03 Oct 1996 17:54:35 +0100 Organization: Imperial Cancer Research Fund Lines: 1 Message-ID: <3253EFCB.41C6@icrf.icnet.uk> NNTP-Posting-Host: bonsai.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.2 IP22) test From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!uunet!news-in2.uu.net!hearst.acc.Virginia.EDU!murdoch!usenet From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Subject: Re: Blast search help needed. In-Reply-To: ckafer@iastate.edu's message of Wed, 02 Oct 1996 02:26:38 GMT X-Nntp-Posting-Host: alpha0.bioch.virginia.edu Message-ID: Sender: wrp@alpha0.bioch.Virginia.EDU Organization: University of Virginia X-Newsreader: Gnus v5.1 References: <52mnn2$rh0@news.iastate.edu> <52ot09$i02@swsu65.swmed.edu> <52sk25$29v@news.iastate.edu> Date: Thu, 3 Oct 1996 16:26:23 GMT Lines: 26 The current versions of the FASTA package, which includes FASTX, will allow you to search subsets of a DNA query sequence sequence against a database. You can specify the part of the query sequence you which to use as shown below: fastx query.dna:1-99 swissprot It is relatively easy to run a unix shell script that will search each XXXX nt piece of a query sequence. Here is one that I have used (csh): #!/bin/csh set m=0 while ( $m < 40000 ) # query sequence is 40000 nt long @ n = ($m + 1100) # search in 1100 nt chunks @ start = ($m + 1) if ( $start > 1000 ) then # use a 100 nt overlap @ start = ($start - 100) endif echo "searching $start - $n" fastx3_t -q cosmid.seq:${start}-${n} s > cos.${start}-${n}.ok2x_s fastx3_t -i -q cosmid.seq:${start}-${n} s > cos.${start}-${n}.ok2y_s @ m = ($m + 1000) # move down 1000 nt end From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Mick Partis Newsgroups: bionet.software Subject: Re: Plasmid drawing program for Mac: freeware? Date: 3 Oct 1996 11:58:20 GMT Organization: Horticulture Research International Lines: 19 Message-ID: <5309os$3mr@is.bbsrc.ac.uk> References: <3252D20F.33F2@physci.ucla.edu> NNTP-Posting-Host: pc0233.hriw.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Edmundo Castro wrote: >Does anyone know of free or shareware plasmid drawing software for Macs? > >Thank to all in advance! > >E. Castro-Vargas There is a plasmid drawing program (amongst all of the other mac software) called macplasmap downloadable from gopher://ftp.bio.indiana.edu:70/11/IUBio-Software+Data/molbio/mac -- mick.partis@hri.ac.uk Horticulture Research International http://www.geocities.com/CapeCanaveral/1957/ From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!agate!ames!usenet.kornet.nm.kr!usenet.etri.re.kr!news.kreonet.re.kr!newsfeed.dacom.co.kr!arclight.uoregon.edu!enews.sgi.com!news.sgi.com!swrinde!howland.erols.net!news3.cac.psu.edu!news.cse.psu.edu!news.ece.nwu.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!SLIP3-27.DIALIN.UIC.EDU!operga1 From: operga1@uic.edu (Oliver R.W. Pergams) Newsgroups: bionet.software Subject: game theory/ecology software Date: Wed, 2 Oct 1996 23:07:27 Organization: University of Illinois at Chicago Lines: 10 Message-ID: NNTP-Posting-Host: slip3-27.dialin.uic.edu Keywords: game theory X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I'd like to purchase some game theory software, for applications in ecology. Does anyone know of some? Oliver Pergams University of Illinois at Chicago operga1@uic.edu -- Oliver Pergams University of Illinois at Chicago E-Mail: operga1@uic.edu From owner-software@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!news-in2.uu.net!interaccess!usenet From: Minh Luu Newsgroups: bionet.software Subject: Frame Analysis Software for Mac Date: Thu, 03 Oct 1996 13:14:56 -0500 Organization: InterAccess, Chicago's best Internet Service Provider Lines: 9 Message-ID: <3254029D.7442@students.wisc.edu> NNTP-Posting-Host: d195.loop.interaccess.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Hello, Does anyone know of a program that analyzes orfs for high gc organism based on gc biase for the mac. I've heard of codon preference but don't really know how to obtain a copy. Thanks. Minh From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!usenet.kornet.nm.kr!news.postech.ac.kr!news.kreonet.re.kr!newsfeed.dacom.co.kr!nntp.coast.net!oleane!jussieu.fr!univ-angers.fr!ciril.fr!usenet From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: SEQUENCHER FOR UNIX? WHY? Date: 4 Oct 1996 07:43:02 GMT Organization: IGBMC Lines: 36 Message-ID: <532f66$p75@arcturus.ciril.fr> References: <52vs4s$ma2@lyra.csx.cam.ac.uk> <530ecc$qj7@dismay.ucs.indiana.edu> NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.6 In article , jes@presto.med.upenn.edu (Joe Smith) writes: [...] >OTOH, with the advent of Linux and other cheap/free Unixes, the >price/performance gap is completely gone. There is no longer a >premium to be paid to run Unix. The usability gap is also shrinking >as more commercial software becomes available. > >So, I see a value in the desktop Unix market, in that there's more >stability and more room to grow smoothly. I don't know if this the good newsgroup for this discution, but... Don't flame about an OS war also but...Most of the bioinformatician here are developping lot of easy to use softwares in C that are free. There are also some development tools (like NCBI toolkit) to make good grafic interfaces for clients. Regarding that Linux is free of charge and really stable (like a UNIX system can), we all have to think about this solution. Of course, it is always a question of intitute politic, and we will never find help from commercial companies in that way. (I don't know if this is clear?!?). This is only my opinion in "why a commercial should make a UNIX version of there softwares". If we pay less for the system and some tools, then we can (perhaps) find money for (good) commercial specific products. (a little bit sleepy)Francois. -- Francois Jeanmougin Service de bioinformatique / bioinformatics service IGBMC BP 163 67404 Illkirch France tel : (33) 88 65 32 71 e-mail : jeanmougin@igbmc.u-strasbg.fr "Tout ca m'est tergal, qu'il laine ou qu'il chandail" (STTELLLA) From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!nntp.coast.net!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: Software for Molecular Biology Presentation Date: 4 Oct 1996 08:00:30 GMT Organization: University of Wuerzburg, Germany Lines: 25 Distribution: world Message-ID: <532g6u$mo3@winx03.informatik.uni-wuerzburg.de> References: <325401A8.6971@mac-biocomputing1.embl-heidelberg.de> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] mac-biocomputing1user (user@mac-biocomputing1.embl-heidelberg.de) wrote: > I'm looking for a graphycal software able to create in an easy way > presentation for molecular and cell biology experiments, Ex: plasmids, Look into the various plasmid drawing programs (dependent on platform). We are currently thinking of switching to the Gene Construction Kit (a Mac program, since we are mostly Mac-based). > biochemical pathways, MacDraw or any other drawing program will do fine. > molecules display ... To get the fancy pictures which you often see in structural articles, you would have to shop around for Molscript, Raster3D, Ribbon, ... All these programs run only under Unix but should be easily available at the EMBL. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.erols.net!newsfeed.internetmci.com!btnet!netcom.net.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!europa.lif.icnet.uk!sternber From: sternber@europa.lif.icnet.uk (Michael Sternberg) Newsgroups: bionet.software Subject: ANNOUNCE - PROT SEC STR PREDN WWW SERVER Date: 4 Oct 1996 14:54:03 GMT Organization: Imperial Cancer Research Fund Lines: 61 Message-ID: <5338eb$e9t@charlie.lif.icnet.uk> NNTP-Posting-Host: europa.lif.icnet.uk X-Newsreader: TIN [version 1.2 PL2] From rd_king@icrf.icnet.uk Thu Oct 3 17:45:16 1996 Date: Mon, 30 Sep 1996 17:42:26 +0100 From: "Ross D. King" To: m.sternberg@icrf.icnet.uk Subject: DSC DSC Protein Secondary Structure Prediction I am pleased to announce the opening of a new web site for the prediction of protein secondary structure. Two prediction modes are available: 1) Given a single sequence. A multiple sequence alignmentt will be formed and DSC used to predict secondary structure. http://www.icnet.uk/bmm/dsc/dsc_form_align.html 2) Given a multiple sequence alignmnet. DSC will use this alignment to predict secondary structure. http://www.icnet.uk/bmm/dsc/dsc_read_align.html The advantages of DSC are: 1) It is very accurate. DSC has a prediction accuracy of 70.1% on a standard set of 126 proteins. This was not significantly different from PHD, a popular prediction method. For medium length sequences DSC was more accurate than PHD, and combining DSC and PHD produced a prediction method more accurate than either. 2) It is free. There is no charge for using DSC. 3) The C source code is available. This would allow you to run DSC on your own system if you had confidential sequences. ftp://ftp.icnet.uk/icrf-public/bmm/king/dsc/dsc.tar.z DSC is based on simple linear statistics. A paper on the scientific basis of DSC will appear in Protein Science: "Identification and Application of the Concepts Important for Accurate and Reliable Protein Secondary Structure Prediction" by Ross D. King & Michael J.E. Sternberg Ross D. King Biomolecular Modelling Laboratory Imperial Cancer Research Fund Lincoln's Inn Fields, P. O. Box 123, London, WC2A 3PX, U.K. Tel: +44 171 269 3565, Fax: +44 171 269 3479, rd_king@icrf.icnet.uk m.sternberg@icrf.icnet.uk (contact until 25 Oct 96) -- ------------------------------------------------------------------------ * from e-mail address: m.sternberg@icrf.icnet.uk * * * * Mike Sternberg Tel +44-71-269-3565 / 3591 * * Biomolecular Modelling Laboratory FAX +44-71-269-3479 * * Imperial Cancer Research Fund Others in group who can help : * * 44 Lincoln's Inn Fields Suhail Islam Tel +44-71-269-3380 * * London WC2A 3PX, England Paul Bates Tel +44-71-269-3348 * ************************************************************************ From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!unrccc.edu.ar!jpolop From: jpolop@unrccc.edu.ar (Jaime Polop) Newsgroups: bionet.software Subject: EDUCATIVE SOFTWARE IN EVOLUTION Date: 3 Oct 1996 19:36:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <9608268437.AA843749862@unrcpp.unrccc.edu.ar> NNTP-Posting-Host: net.bio.net Dear members of the list: I am Professor of the Biology Department (Universidad Nacional de Rio Cuarto, Argentina). I am interested in catalogs on educational software (prefably multimedia) in Evolution. The idea is use them like didactic complementary elements to the current pedagogic activities. Sincerely yours Dr. Jaime J. Polop Dto. Ciencias Naturales Universidad Nacional de Rio Cuarto Agencia N 3 CP 5800 Rio Cuarto - Cordoba - Argentina FAX (++54) (58) 680280 TE (++54) (58) 676236 e-mail JPOLOP@UNRCCC.edu.ar From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!howland.erols.net!news-peer.gsl.net!news.gsl.net!nntp.coast.net!oleane!in2p3.fr!swidir.switch.ch!news.belwue.de!yeamob.pci.chemie.uni-tuebingen.de!user From: kaifr@uni-tuebingen.de (Dr. Kai-Uwe Froehlich) Newsgroups: bionet.software Subject: Re: Plasmid drawing program for Mac: freeware? Date: Fri, 04 Oct 1996 13:14:02 +0100 Organization: Phys.-chem. Institut, Universitaet Tuebingen Lines: 49 Message-ID: References: <3252D20F.33F2@physci.ucla.edu> NNTP-Posting-Host: yeamob.pci.chemie.uni-tuebingen.de In article <3252D20F.33F2@physci.ucla.edu>, ecastro@physci.ucla.edu wrote: > Does anyone know of free or shareware plasmid drawing software for Macs? > > Thank to all in advance! > > E. Castro-Vargas I have written a plasmid drawing program, primarily for our lab use (so it is anything but polished), which I have released as Freeware. It converts lists of restriction sites and fragment/gene positions into Postscript files. Its weak points in short - It is a Hypercard stack, so you need Hypercard to run it (luckily, speed is no problem, there are no processor intensive steps involved) - The output are Postscript files in Illustrator format. To view and to further edit the picture (which you will have to, see below), you need either Adobe Illustrator, or the Shareware EPStoPICT, which produces a fully editable, object oriented PICT version of the graphics. - The program does not care for overlapping labels, so in most cases you must do some fine-tuning On the other hand, the program - allows "electronic cloning", so you can quickly construct new plasmids from those already entered in the program - can draw all plasmids at the same size, but also using the same (or any you want) scale (that was the primary reason for me to write the program, most commercial programs had (still have?) no way to specify the drawing scale (except by different magnification in the page setup) - draws linear and circular maps, allows borders of various widths and fills of grays, arrows... - Output quality is great, thanks to Postscript - The price is right :-) For a more detailed description, including screen shots of the output graphics, see and that is also the place to download the stack: (BTW, there is also a stack for the organization of plasmid/strain collections available) Kai ----------------------------------------------------------------------- Dr. Kai-Uwe Froehlich, Physiologisch-chemisches Institut, Hoppe-Seyler-Str. 4, 76072 Tuebingen, Germany From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Date: 4 Oct 1996 06:48:24 EDT Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!nntp-hub2.barrnet.net!news.sgi.com!howland.erols.net!newsfeed.internetmci.com!fnord.dfw.net!org!sutton Newsgroups: bionet.software From: sutton@org (Scott Sutton) Message-ID: <8444261048902@microbiol.org> Organization: The Microbiology BBS References: <530so2$glu@newsflash.concordia.ca> Subject: Re: Excel format: where to find? Lines: 20 Yue Export your data to an ASCII file (either space or tab delineated) and then import into Excel - it works very well. Scott Sutton, PhD The Microbiology BBS telnet: microbiol.org http://microbiol.org YU>I would like to export my data from a database to Excel or QuattroPro. YU>Could someone point me where to find their formats ? YU>Thank you for any help. YU>yue From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!uunet!news-in2.uu.net!tank.news.pipex.net!pipex!oleane!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!becquart From: becquart@lovelace.infobiogen.fr (Paul Becquart) Newsgroups: bionet.software Subject: Re: Software for Molecular Biology Presentation Date: 4 Oct 1996 09:23:40 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 3 Distribution: world Message-ID: <532l2s$e0v@lovelace.infobiogen.fr> References: <325401A8.6971@mac-biocomputing1.embl-heidelberg.de> <532g6u$mo3@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] J'utilise pour ma part Gene construction Kit depuis trois ans poue mes clonages. Les cartes ainsi dessinees sont d'excellente presentation. C'est par ailleurs un excellent outil pour la biologie moleculaire. Pour le reste n'importe quel soft de dessin style canvas devrait t'aider. Bonne chance Paul From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!dispatch.news.demon.net!demon!genesys.demon.co.uk!duncan From: "Dr. Duncan Clark" Newsgroups: bionet.software Subject: Re: Staden for Mac/PC? Date: Thu, 3 Oct 1996 23:02:17 +0100 Organization: GeneSys Ltd Lines: 17 Distribution: world Message-ID: References: <5309rk$biu@net.bio.net> <530dgf$ptg@dismay.ucs.indiana.edu> NNTP-Posting-Host: genesys.demon.co.uk X-NNTP-Posting-Host: genesys.demon.co.uk MIME-Version: 1.0 X-Newsreader: Turnpike Version 3.01 beta 1 In article <530dgf$ptg@dismay.ucs.indiana.edu>, Don Gilbert writes >My impression though is >that Macintoshes remain the most widely used, and despite recent >problems at Apple computer, Macs remain a very viable system that >users of them find compelling. Wintel systems are catching up somewhat. That may be the case in the US but here in the UK I know umpteen academic labs with PC's but can only think of the odd one with Mac's. just an observation. Duncan ----------------------------------------------------------------------------- My mind's made up. Don't confuse me with the facts! Duncan Clark GeneSys Ltd. From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Greg) Newsgroups: bionet.software Subject: Re: Staden for Mac/PC? Date: 4 Oct 1996 15:19:19 GMT Organization: Best Internet Communications Lines: 41 Message-ID: <5339tn$246@nntp1.best.com> References: <5309rk$biu@net.bio.net> <530dgf$ptg@dismay.ucs.indiana.edu> <325559BC.1D98@bbsrc.ac.uk> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] michael.baron@bbsrc.ac.uk wrote: : Dr. Duncan Clark wrote: : > : > In article <530dgf$ptg@dismay.ucs.indiana.edu>, Don Gilbert : > writes : > >My impression though is : > >that Macintoshes remain the most widely used, and despite recent : > >problems at Apple computer, Macs remain a very viable system that : > >users of them find compelling. Wintel systems are catching up somewhat. : > : > That may be the case in the US but here in the UK I know umpteen : > academic labs with PC's but can only think of the odd one with Mac's. : > just an observation. : > This may be because many UK institutions are pressured to follow an : institute policy, set by non-users. Our own site, like many, has : to follow the official BBSRC line of using Wintel machines, despite the : privately expressed preference of some of the IT staff for the MacOS : platform. Such a policy probably originated years ago, simply on the case : that a DOS-box was cheaper than a Mac, and the people making the decision : had secretaries to use the machines (;-)). Once such policies are made, : they tend to be set in stone. Guess I'll add my 0.02c worth too! My experience in the US is that the generation that is coming through now has been heaviliy influenced by high school use of Macs, and they *really* often don't like to use PC's at all in regard to lab work. Though I do come across pockets of windows users, my experience is that most all the groups that I have worked with or had dealings with are heavily Mac based. For this reason, the availablity of good (and hopefully free) molecular biology software for the Mac is very important. If I had a nickel for every lab that I had seen relying totally on the use of an ancient copy of 'DNA STRIDER', I would be a rich man. The problem with this apparent imbalance of platform is that Windows has some really excellent software development tools written for it, whilst the Mac relies on fewer (and in my experience less featured) software IDE's. I can put together a relatively complex windows program in a matter of minutes (OK, maybe an hour!) using a combination of VB and VC++; The Mac has no such simple Software IDE (Though MS is threatening to release such a beast soon). This is attested to by looking at the software releases announced in this newsgroup by science groups; the majority of this is Windows based. From owner-software@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!bhamcs!news.ox.ac.uk!is.bbsrc.ac.uk!news From: michael.baron@bbsrc.ac.uk Newsgroups: bionet.software Subject: Re: Staden for Mac/PC? Date: Fri, 04 Oct 1996 11:38:52 -0700 Organization: Institute for Animal Health Lines: 25 Message-ID: <325559BC.1D98@bbsrc.ac.uk> References: <5309rk$biu@net.bio.net> <530dgf$ptg@dismay.ucs.indiana.edu> NNTP-Posting-Host: pc0258.avri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Dr. Duncan Clark wrote: > > In article <530dgf$ptg@dismay.ucs.indiana.edu>, Don Gilbert > writes > >My impression though is > >that Macintoshes remain the most widely used, and despite recent > >problems at Apple computer, Macs remain a very viable system that > >users of them find compelling. Wintel systems are catching up somewhat. > > That may be the case in the US but here in the UK I know umpteen > academic labs with PC's but can only think of the odd one with Mac's. > just an observation. > This may be because many UK institutions are pressured to follow an institute policy, set by non-users. Our own site, like many, has to follow the official BBSRC line of using Wintel machines, despite the privately expressed preference of some of the IT staff for the MacOS platform. Such a policy probably originated years ago, simply on the case that a DOS-box was cheaper than a Mac, and the people making the decision had secretaries to use the machines (;-)). Once such policies are made, they tend to be set in stone. Just *my* 2p's worth. Michael D. Baron michael.baron@bbsrc.ac.uk From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!newsfeed.direct.ca!nntp.portal.ca!van-bc!n1van.istar!van.istar!west.istar!news-w.ans.net!newsfeeds.ans.net!lantana.singnet.com.sg!violet.singnet.com.sg!nuscc.nus.sg!imazhq From: imazhq@leonis.nus.sg (Zheng Huanquan) Newsgroups: bionet.software Subject: software for phosphorylation site analysis Date: 5 Oct 1996 05:43:06 GMT Organization: National University of Singapore Lines: 5 Message-ID: <534sha$q40@nuscc.nus.sg> NNTP-Posting-Host: imazhq@leonis.nus.sg X-Newsreader: TIN [version 1.2 PL2] Can anyone here suugest a good software for analysis of potential phosphorylation site and surface probability of a protein? thanks. HQ Zheng From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!netnews.nwnet.net!news.u.washington.edu!news.alt.net!news1.alt.net!news.aros.net!news.cs.utah.edu!news.cc.utah.edu!news From: zinc Newsgroups: bionet.software Subject: science software (mol biol/biochem/biology) under Linux Date: 04 Oct 1996 16:41:22 -0600 Organization: University of Utah Computer Center Lines: 143 Message-ID: NNTP-Posting-Host: zifi.genetics.utah.edu X-Newsreader: Gnus v5.2.31/XEmacs 19.14 -----BEGIN PGP SIGNED MESSAGE----- howdy folks, i'm attempting to compile a list of software that either people have claimed runs under Linux or that is known to run under Linux for the people at Caldera (Caldera is Ray Noorda's ( of Novell fame ) new company). here is my list so far. if people have additions i'd love to have them. it would be nice if you could include a brief description or a URL pointing to a web page with a description. also, a URL for the source or binary executable would be super.. thanks, - -patrick finerty biochem grad student, u of utah ====================================================================== a lot of these are in FORTRAN so how well they compile is probably due to how good the fortran support on a system is... ======= something called VMD (Visual Molecular Dynamics) is almost ported: http://www.ks.uiuc.edu/Research/vmd/ ======= Molden fortran source, got it from ftp://ftp.caos.kun.nl/pub/molgraph/molden ======= RasMol available on sunsite, also available here: it _is_ possible to compile this for 16 bpp display, i've done it and used it a lot myself. you just have to change the Makefile to use - -DSIXTEENBIT instead of -DEIGHTBIT or -DTHIRTYTWOBIT ======= XtalView also in fortran (crystallographers love fortran). have to sign a license to get source but not for binaries... http://www.sdsc.edu/CCMS/Packages/XTALVIEW/ it looks like binaries are avail for Linux...(according to the above page) ======= WhatIf http://swift.embl-heidelberg.de/whatif/ licensed for a small fee to academics... ======= Procheck http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html obtain source from: ftp://128.40.46.11/pub/procheck/tar3_4/procheck.tar.Z this is more fortran fun and games. it seems to compile almost but i haven't tried to use it yet... ======= MOPAC i searched all over for this - couldn't find the source! only a ton of damned html manuals. a post to bionet.software is in order... ======= i heard the GAMESS programs compile under Linux but i did not try them as you have to go through a little effort to get them... GAMESS-US http://www.msg.ameslab.gov/GAMESS/dist.menu.html site license is free to everyone but must sign a form... GAMESS-UK http://gserv1.dl.ac.uk/CCP/CCP1/gamess.html ======= Entrez/Cn3D from ncbi database searching tools (for remote database queries) the ncbi package... linux binary of the network database search tools: ftp://ncbi.nlm.nih.gov/blast/network/blast2/ this requires the network Entrez program to be configured, get a linux binary here: ftp://ncbi.nlm.nih.gov/entrez/network/linux.tar.Z ======= fasta ftp.virginia.edu/pub/fasta/fasta30t6.shar.Z used default makefile but changed THR_CC= to be blank. THR_CC= then make sall ======= RNA folding related software: Viena RNA package: compiles fine under Linux but Makefile needs tweaking (hell, i managed to get it to work...) ftp://ftp.itc.univie.ac.at/pub/RNA/ViennaRNA-1.1b.tar.gz ======= naview this compiles fine under Linux http://www.ibc.wustl.edu/~zuker/ref/BRUR88.html ftp://snark.wustl.edu/pub/naview.tar.Z =========================================================================== - -- "Those that give up essential liberty to obtain a little temporary safety deserve neither liberty nor safety." -- Benjamin Franklin (1773) finger for PGP key zifi runs LINUX 2.1.1 -=-=-=WEB=-=-=-> http://zifi.genetics.utah.edu -----BEGIN PGP SIGNATURE----- Version: 2.6.2 Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface iQCVAwUBMlWSjk3Qo/lG0AH5AQGg6AQAqOXjcYV7EIcv7E1jqVp8z0mOP1+nJMYo 5Yu1gZVfPcjGTQJOFay25kGtLy0fnVJzmLwSQUDQ/r5iLTxnf0kZ4JIDST9Hxz1H oSjLvYY39HS6YLjCShioGeXLOEz9FiU1bxVvGj+5fXdhflrwFvMcqEyPumuc+qD6 /6Evc5wjeyk= =vOTi -----END PGP SIGNATURE----- From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!tank.news.pipex.net!pipex!iol!usenet From: hughobr@iol.ie (Hugh O'Brien) Newsgroups: bionet.software Subject: Re: test Date: Sat, 05 Oct 1996 00:05:23 GMT Organization: Ireland On-Line Lines: 13 Message-ID: <5348ms$mnf@nuacht.iol.ie> References: NNTP-Posting-Host: dialup-085.dublin.iol.ie X-Newsreader: Forte Free Agent 1.0.82 eramirez@BACATA.USC.UNAL.EDU.CO (EFRAIN RAMIREZ ZAPATA) wrote: >test It works. Hugh, ----------------------------------------------- Email: hughobr@iol.ie http://www.iol.ie/~hughobr/ ----------------------------------------------- From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!oleane!in2p3.fr!swidir.switch.ch!01-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!mail.boku.ac.at!news From: Andreas Wernitznig Newsgroups: bionet.software Subject: Re: Excel format: where to find? Date: Fri, 04 Oct 1996 23:21:03 +0200 Organization: Univ. for Agriculture Lines: 13 Message-ID: <32557FBF.14A9@edv1.boku.ac.at> References: <530so2$glu@newsflash.concordia.ca> Reply-To: h8760592@edv1.boku.ac.at NNTP-Posting-Host: 141.244.88.51 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (WinNT; I) Yue Huang wrote: > > I would like to export my data from a database to Excel or QuattroPro. > Could someone point me where to find their formats ? > Thank you for any help. > > yue In what format are your data ? What Database are you using ? Excel supports the import of many database-formats via ODBC (Open Database Connectivity). The direct translation into Excel format is really not easy. Andreas Wernitznig From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.u.washington.edu!news.alt.net!news1.alt.net!news.aa.net!ratty.wolfe.net!sea-ts3-p71.wolfenet.com!user From: elysium@wolfenet.com (Sonya) Newsgroups: bionet.software Subject: Dawkins' Netspinner/Watchmaker Date: Sat, 05 Oct 1996 14:10:33 -0800 Organization: Wolfe Internet Access, L.L.C. Lines: 8 Message-ID: NNTP-Posting-Host: sea-ts3-p71.wolfenet.com X-Newsreader: Yet Another NewsWatcher 2.0.2 Does anyone know where I can find Netspinner and/or Watchmaker available for download for the Mac? Thanks; Sonya elysium@wolfenet.com From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!netnews.worldnet.att.net!newsadm From: "Thomas B. Ivers, president" Newsgroups: bionet.software Subject: SOFTWARE: DOCUMENT SUPPORT Date: Sat, 05 Oct 1996 14:42:43 -0500 Organization: U.S.Coordinated Networks, Inc. Lines: 69 Message-ID: <3256C843.26A1@coordi.com> Reply-To: webmaster@coordi.com NNTP-Posting-Host: 19.chicago-3.il.dial-access.att.net Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------BF03D4477B4" X-Mailer: Mozilla 3.0 (Win95; I) CC: webmaster@coordi.com This is a multi-part message in MIME format. --------------BF03D4477B4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NEW CONE TREE GUI DEVELOPED. Trverse an entire 200+ page website, multivolume book set or catalog in seconds. See our website: URL http://www.coordi.com/catalog.html NOTE: Have an HTML 3.0+ browser when you go to our website to use the JAVA script there. ~~~~~~~~~~ Message that follows if for HTML newsgroup readers ~~~~~~~~ --------------BF03D4477B4 Content-Type: text/html; charset=us-ascii; name="place_form_in_newsgroups.html" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="place_form_in_newsgroups.html" Content-Base: "file:///G|/advertising/__Best_Email_Po st!/place_form_in_newsgroups.html" Hotest GUI on Internet!

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--------------BF03D4477B4-- From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!uunet!in3.uu.net!netnews.nwnet.net!news.u.washington.edu!news.alt.net!news1.alt.net!news.aros.net!news.cs.utah.edu!news.cc.utah.edu!kofoid From: kofoid@biology.utah.edu (Eric Kofoid) Newsgroups: bionet.software Subject: [Q]downloadable molecular clipart? Date: Fri, 04 Oct 1996 11:49:21 -0700 Organization: Dept. Biology, University of Utah Lines: 12 Message-ID: NNTP-Posting-Host: ls-38.biology.utah.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b12 Can someone point me to a source of downloadable structural images of various biomolecules? I'm especially interested in space-filling or ribbon structures of cobalamin and NADH. These will be used to decorate web pages and journal papers. I'm not interested in anything requiring a Java applet to view, just simple stuff in GIF, JPEG, PICT or TIFF format. Cheers, Eric. -- Eric Kofoid Dept.Biology, U.Utah kofoid@biology.utah.edu From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: science software (mol biol/biochem/biology) under Linux Date: 5 Oct 1996 11:39:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610051839.OAA25369@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net > From zinc@zifi.genetics.utah.edu Sat Oct 5 06:55:58 1996 Also from NCBI is 'sequin', our "new" sequence submission/editing tool: ftp://ncbi.nlm.nih.gov/sequin/linux.tar.Z more on sequin from: http://ncbi.nlm.nih.gov/Sequin/ f. -- | B.F. Francis Ouellette | GenBank | | francis@ncbi.nlm.nih.gov > ======= > > Entrez/Cn3D from ncbi > > database searching tools (for remote database queries) > > the ncbi package... > > linux binary of the network database search tools: > ftp://ncbi.nlm.nih.gov/blast/network/blast2/ > > this requires the network Entrez program to be configured, get a linux > binary here: ftp://ncbi.nlm.nih.gov/entrez/network/linux.tar.Z > > ======= From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!agate!howland.erols.net!newspump.sol.net!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: science software (mol biol/biochem/biology) under Linux Date: 5 Oct 1996 15:49:50 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 51 Message-ID: References: Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu X-Newsreader: slrn (0.9.0.0 (Tue Sep 3 21:08:09 CDT 1996) UNIX) On 04 Oct 1996 16:41:22 -0600, zinc wrote: >i'm attempting to compile a list of software that either people have >claimed runs under Linux or that is known to run under Linux for the >people at Caldera (Caldera is Ray Noorda's ( of Novell fame ) new >company). There are several others .... SignalScal - scan for transcription factor binding sites - version 4.07, written in C, compiles fine - ftp://biosci.umn.edu/pub/sigscan/unix PIMA - pattern induced multiple sequence alignment - version 1.40, written in C, compiles fine - ftp://gc.bcm.tmc.edu/pub/software/pima Predator - structural prediction based on multiple alignments - version 1.0, written in C, compiles fine - ftp://ftp.ebi.ac.uk/pub/software/unix/predator ClustalW - pairwise and multiple alignments - version 1.60, written in C, compiles fine - ftp://ftp.ebi.ac.uk/pub/software/unix Seqsee - protein sequence analysis package - version 1.2, written in C, compiles fine - available upon request from seqsee@procyon.biochem.ualberta.ca Pratt - pattern discovery in sets of unaligned sequences - version 2.0, written in C, minor changes - ftp://ftp.ii.uib.no Primer3 - PCR primer design - release 0.1, written in C, compiles fine - ftp://genome.wi.mit.edu tacg - restriction analysis - version 1.5, written in C, compiles fine - ftp://mamba.bio.uci.edu/pub/tacg/ I'm sure you already have references for other common packages such as Don Gilbert's sequence conversion utility - readseq, GDE, NCBI blast etc. etc. Later, Ashok -- Ashok Aiyar, Ph.D. Department of Oncology email: aiyar@ebv.oncology.wisc.edu University of Wisconsin-Madison tel: (608) 262-6697 From owner-software@net.bio.net Fri Oct 04 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!lll-winken.llnl.gov!usenet From: Hemant Varma Newsgroups: bionet.software, Subject: ANNOUNCEMENT:SECOND PROTEIN STRUCTURE PREDICTION EXPERIMENT Date: Sat, 05 Oct 1996 12:09:32 -0700 Organization: Lawrence Livermore National Laboratory Lines: 41 Message-ID: <3256B26C.167E@sb10.llnl.gov> NNTP-Posting-Host: sb10.llnl.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) ______________________________________________ SECOND PROTEIN STRUCTURE PREDICTION EXPERIMENT ______________________________________________ Applications are invited for attendance of the Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2). The meeting will be the culmination of a community wide experiment to determine the effectiveness of current prediction methods. It is expected that over 800 blind predictions from more than 50 prediction teams on approximately 40 different proteins will have been received by the time the prediction season closes. The purpose of the meeting is to determine what went right with the predictions, what went wrong, if possible to understand why, and to identify the promising directions for future work. The meeting will be held at the Asilomar Conference Center, Pacific Grove, California, December 12-16, 1996. Accommodation will be on site. Support for the meeting has been requested from the U.S. Department of Energy, National Institutes of Health, and National Institute of Standards and Technology. CASP2 ORGANIZING COMMITTEE: Steve Bryant, NCBI, National Library of Medicine, USA Co-chair Tim Hubbard, Center for Protein Engineering, England Co-chair John Moult, CARB, University of Maryland, USA President Jan Pedersen, CARB, University of Maryland, USA Krzysztof Fidelis, Lawrence Livermore National Laboratory, USA Rod Balhorn, Lawrence Livermore National Laboratory, USA Richard Judson, Sandia National Laboratory, USA MORE ABOUT THE MEETING AND ON-LINE REGISTRATION FORMS: http://PredictionCenter.llnl.gov Krzysztof Fidelis Protein Structure Prediction Center, Livermore for CASP2 organizers. ______________________________________________ From owner-software@net.bio.net Sat Oct 05 23:00:00 1996 Path: biosci!agate!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news From: J Newsgroups: bionet.software Subject: Re: science software (mol biol/biochem/biology) under Linux Date: Sun, 06 Oct 1996 18:16:28 -0400 Organization: Biomatics Lines: 159 Message-ID: <32582FBC.6D16D6D9@cus.cam.ac.uk> References: NNTP-Posting-Host: sonja.acad.cai.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; Linux 2.0.21 i486) To: zinc zinc wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > > howdy folks, > > i'm attempting to compile a list of software that either people have > claimed runs under Linux or that is known to run under Linux for the > people at Caldera (Caldera is Ray Noorda's ( of Novell fame ) new > company). > > here is my list so far. if people have additions i'd love to have > them. it would be nice if you could include a brief description or a > URL pointing to a web page with a description. also, a URL for the > source or binary executable would be super.. > > thanks, > Hi, I was also thinking to make such a list to make a web page later under the name of Linux for Biology. I hope you will keep the list and announce later for the community. Cheers, Jong > - -patrick finerty > biochem grad student, u of utah > > ====================================================================== > > a lot of these are in FORTRAN so how well they compile is probably due > to how good the fortran support on a system is... > > ======= > something called VMD (Visual Molecular Dynamics) is almost ported: > http://www.ks.uiuc.edu/Research/vmd/ > ======= > Molden > fortran source, got it from > > ftp://ftp.caos.kun.nl/pub/molgraph/molden > > ======= > RasMol > available on sunsite, also available here: > > it _is_ possible to compile this for 16 bpp display, i've done it and > used it a lot myself. you just have to change the Makefile to use > - -DSIXTEENBIT instead of -DEIGHTBIT or -DTHIRTYTWOBIT > ======= > > XtalView > > also in fortran (crystallographers love fortran). have to sign a > license to get source but not for binaries... > > http://www.sdsc.edu/CCMS/Packages/XTALVIEW/ > > it looks like binaries are avail for Linux...(according to the above > page) > ======= > WhatIf > > http://swift.embl-heidelberg.de/whatif/ > > licensed for a small fee to academics... > > ======= > Procheck > > http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html > > obtain source from: > ftp://128.40.46.11/pub/procheck/tar3_4/procheck.tar.Z > > this is more fortran fun and games. it seems to compile almost but i > haven't tried to use it yet... > > ======= > MOPAC > i searched all over for this - couldn't find the source! only a ton > of damned html manuals. a post to bionet.software is in order... > > ======= > i heard the GAMESS programs compile under Linux but i did not try them > as you have to go through a little effort to get them... > > GAMESS-US > http://www.msg.ameslab.gov/GAMESS/dist.menu.html > site license is free to everyone but must sign a form... > > GAMESS-UK > http://gserv1.dl.ac.uk/CCP/CCP1/gamess.html > ======= > > Entrez/Cn3D from ncbi > > database searching tools (for remote database queries) > > the ncbi package... > > linux binary of the network database search tools: > ftp://ncbi.nlm.nih.gov/blast/network/blast2/ > > this requires the network Entrez program to be configured, get a linux > binary here: ftp://ncbi.nlm.nih.gov/entrez/network/linux.tar.Z > > ======= > fasta ftp.virginia.edu/pub/fasta/fasta30t6.shar.Z > used default makefile but changed THR_CC= to be blank. > > THR_CC= > > then make sall > ======= > > RNA folding related software: > > Viena RNA package: > compiles fine under Linux but Makefile needs tweaking (hell, i managed > to get it to work...) > > ftp://ftp.itc.univie.ac.at/pub/RNA/ViennaRNA-1.1b.tar.gz > > ======= > naview > > this compiles fine under Linux > > http://www.ibc.wustl.edu/~zuker/ref/BRUR88.html > > ftp://snark.wustl.edu/pub/naview.tar.Z > =========================================================================== > > - -- > "Those that give up essential liberty to obtain a little temporary > safety deserve neither liberty nor safety." -- Benjamin Franklin (1773) > finger for PGP key > zifi runs LINUX 2.1.1 -=-=-=WEB=-=-=-> http://zifi.genetics.utah.edu > > -----BEGIN PGP SIGNATURE----- > Version: 2.6.2 > Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface > > iQCVAwUBMlWSjk3Qo/lG0AH5AQGg6AQAqOXjcYV7EIcv7E1jqVp8z0mOP1+nJMYo > 5Yu1gZVfPcjGTQJOFay25kGtLy0fnVJzmLwSQUDQ/r5iLTxnf0kZ4JIDST9Hxz1H > oSjLvYY39HS6YLjCShioGeXLOEz9FiU1bxVvGj+5fXdhflrwFvMcqEyPumuc+qD6 > /6Evc5wjeyk= > =vOTi > -----END PGP SIGNATURE----- From owner-software@net.bio.net Sat Oct 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!news.uoregon.edu!news.acsu.buffalo.edu!newsstand.cit.cornell.edu!portc01.blue.aol.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: blduncch@aol.com (BLDUNCCH) Newsgroups: bionet.software Subject: Protein Viewer Date: 6 Oct 1996 11:04:04 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 5 Sender: root@newsbf02.news.aol.com Message-ID: <538hp4$os@newsbf02.news.aol.com> Reply-To: blduncch@aol.com (BLDUNCCH) NNTP-Posting-Host: newsbf02.mail.aol.com Where can I download a good protein viewer for IBM-PC, either DOS or Win 3.1? I want to be able to read Brookhaven files and to add colors to selected amino acid residues. From owner-software@net.bio.net Sat Oct 05 23:00:00 1996 Path: biosci!NCBI.NLM.NIH.GOV!francis From: francis@NCBI.NLM.NIH.GOV Newsgroups: bionet.software Subject: Re: Protein Viewer Date: 6 Oct 1996 09:43:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610061642.MAA26000@borduas.nlm.nih.gov> NNTP-Posting-Host: net.bio.net > From blduncch@aol.com Sun Oct 6 12:31:01 1996 > Where can I download a good protein viewer for IBM-PC, either DOS or Win > 3.1? > > I want to be able to read Brookhaven files and to add colors to selected > amino acid residues. try Cn3D and Entrez a whirl ... info available from: http://www.ncbi.nlm.nih.gov/Structure/cn3d.html cheers, f. -- | B.F. Francis Ouellette | GenBank | | francis@ncbi.nlm.nih.gov From owner-software@net.bio.net Sat Oct 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!nntp.zit.th-darmstadt.de!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: science software (mol biol/biochem/biology) under Linux Date: 6 Oct 1996 11:03:15 GMT Organization: University of Wuerzburg, Germany Lines: 16 Message-ID: <5383lj$jd8@winx03.informatik.uni-wuerzburg.de> References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] More stuff that runs under Linux: - the fasta package (sequence comparison) - molscript (makes schematics of protein structures; Fortran, I had to patch it a little to make it work with f2c; contact Per Kraulis to get the source). - raster3d (raytraces molscript figures; a mixture of Fortran and C). Sorry, I don't know the sites where I got them from. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Sat Oct 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!newsfeeder.servtech.com!post.servtech.com!news From: Kim Pruitt Newsgroups: bionet.software Subject: Plasmid Tracker now Available Date: Sat, 05 Oct 1996 22:15:13 -0700 Organization: Salt City Software Lines: 14 Message-ID: <32574061.3EC5@cyber2.servtech.com> References: <3252D20F.33F2@physci.ucla.edu> Reply-To: saltcity@servtech.com NNTP-Posting-Host: saltcitysw.syr.servtech.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win16; I) We are pleased to announce the release of Plasmid Tracker for Windows. The Plasmid Tracker database program is designed to help you keep track of bacterial freezer stocks. Some of the features include: search and find, the capability to maintain restriction maps, customizable data fields, supports data import/export, and supports maintenance of multiple databases which can be merged into a master database as needed. Please go to http://www.servtech.com/public/saltcity for additional information and to download a FREE DEMO version of Plasmid Tracker. Kim D. Pruitt Salt City Software e-mail: 70761.2216@compuserve.com internet: http://www.servtech.com/public/saltcity From owner-software@net.bio.net Sat Oct 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!swrinde!news.sgi.com!nntp.coast.net!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet From: "Luca I.G. TOLDO" Newsgroups: bionet.software Subject: Re: Software for viewing automated sequencer files on a PC? Date: Sun, 06 Oct 1996 13:18:37 +0200 Organization: EMBL Heidelberg Lines: 23 Distribution: world Message-ID: <3257958D.62CE@embl-heidelberg.de> References: Reply-To: luca.toldo@embl-heidelberg.de NNTP-Posting-Host: toldo1.lt.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) To: "Marc A. Goldstein" CC: duncan@genesys.demon.co.uk The java applet developed by Eugen Buehler allows ANY Java aware WWW browser of interacting with the SCF format files. The Eugen Buehler's applet is included in the JaMBW package: Java Workbench in Molecular Biology as well. (http://www.embl-heidelberg.de/~toldo/JaMBW.html) that contains link also to the original distrib of the SCF viewer. The PC software "GeneSkipper" developed by Christian Schwager in EMBL Heidelberg also has a dedicated module for allowing interaction with SCF and ALF format files. his email address is Schwager@EMBL-Heidelberg.DE I have not yet tested it, but I recall having read that also the GCG package seems to be able of use the ALF or SCF formats. Regards Dr. Luca Ida Giovanni TOLDO (Ph.D.) European Molecular Biology Laboratory Computer Group Heidelberg Germany From owner-software@net.bio.net Sat Oct 05 23:00:00 1996 Path: biosci!agate!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!uunet!in3.uu.net!news.idt.net!news From: cad29@mail.idt.net Newsgroups: bionet.software Subject: Used AutoCAD Wanted Date: Sun, 06 Oct 1996 20:40:04 GMT Organization: IDT Corporation Lines: 6 Message-ID: <539g0k$ak9@News.IDT.NET> Reply-To: cad29@mail.idt.net NNTP-Posting-Host: ppp427.liberty.com X-Newsreader: Forte Free Agent 1.0.82 Used AutoCAD Wanted Must be a legal commercial copy. cad29@mail.idt.net From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!is.bbsrc.ac.uk!Andy.Law From: Andy.Law@bbsrc.ac.uk (Andy Law) Newsgroups: bionet.software Subject: Re: Staden for Mac/PC? Date: Mon, 07 Oct 1996 10:16:42 +0100 Organization: Roslin Institute Lines: 18 Message-ID: References: <5309rk$biu@net.bio.net> <530dgf$ptg@dismay.ucs.indiana.edu> <325559BC.1D98@bbsrc.ac.uk> NNTP-Posting-Host: pc0734.ri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b13 In article <325559BC.1D98@bbsrc.ac.uk>, michael.baron@bbsrc.ac.uk wrote: > This may be because many UK institutions are pressured to follow an > institute policy, set by non-users. Our own site, like many, has > to follow the official BBSRC line of using Wintel machines, despite the > privately expressed preference of some of the IT staff for the MacOS > platform. Such a policy probably originated years ago, simply on the case > that a DOS-box was cheaper than a Mac, and the people making the decision > had secretaries to use the machines (;-)). Once such policies are made, > they tend to be set in stone. > You're working at the wrong bbsrc institute Michael, my old son! Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!news.physics.uiowa.edu!news.drake.edu!newsrelay.iastate.edu!news.iastate.edu!news From: An-Ping Hsia Newsgroups: bionet.software Subject: HyperCard to FileMaker Date: Sun, 06 Oct 1996 23:10:08 -0500 Organization: Iowa State University Lines: 16 Message-ID: <3258829B.C70@iastate.edu> NNTP-Posting-Host: mac20197.agron.iastate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Hi, I want to transfer data from HyperCard(2.2) to FileMaker(3.0). I tried saving my HyperCard files in other format (like Excel) and import into FileMaker but did not succeed. Any help would be greatly appreciated. Thanks. -- Regards, An-Ping Hsia Schnable Lab B420 Agronomy Hall Iowa State University Ames, IA 50011 Tel:515-294-1659 Fax:515-294-2299 e-amil:hsia@iastate.edu From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 From: "William Ho" Subject: Looking for software !! Newsgroups: bionet.software Organization: UNIVIC Message-ID: <01bbb406$a56fed80$9b034dca@william> X-Newsreader: Microsoft Internet News 4.70.1155 NNTP-Posting-Host: mxp2-27.chevalier.net Date: 7 Oct 96 04:09:45 GMT Lines: 5 Path: biosci!agate!howland.erols.net!news.sprintlink.net!new-news.sprintlink.net!dnews.chevalier.net! Hello, I am looking for a software for stock exchange analysis, anyone have suggestion ? Thanks. From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!csl.com.au!mmcnamar From: mmcnamar@csl.com.au (Michael McNamara) Newsgroups: bionet.software Subject: Pharmaceutical Stability Database Packages Date: 6 Oct 1996 21:00:25 -0700 Organization: CSL Limited Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610070359.NAA23705@tulpi.interconnect.com.au> NNTP-Posting-Host: net.bio.net I work for a pharmaceutical company in a process development role. I would like to purchase software which is preferrably able to run on IBM PCs, maintain a database of drug stability and to produce tables and output graphs. Ability to access data from LIMS and statistically analyse the output in accordance with the ICH giudelines would be an advantage. Does anyone have any practical experience with such systems and can recommend one? Michael McNamara email: mmcnamar@csl.com.au CSL Limited 45 Poplar Rd., Parkville Vic 3052 Australia From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.software Subject: NAOMI - Important messages Date: Mon, 07 Oct 1996 09:42:12 +0100 Organization: University of Oxford Lines: 65 Message-ID: <3258C264.794BDF32@bioch.ox.ac.uk> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 4.1.3_U1 sun4m) NAOMI - Important messages to all users - please read. _____________________________________________________________________________ **** The NAOMI anonymous FTP server is now back up again after some considerable downtime. Sorry for all the inconvenience this caused. ----------------------------------------------------------------------------- **** I've taken this opportunity to make available the Version 3.0 User Guide which is complete reworking of the old User Guide. It is much improved (fast loading, better organised etc). It is available only on the Web site (select the User Guide - Europe link) at present. NAOMI Web site URL given below. Version 3.0 of the program is not yet available (release soon), but the new User Guide is applicable to the current version. ----------------------------------------------------------------------------- **** Due to bandwidth problems, especially across the Atlantic and to the Pacific Rim, I'm looking for places that would be prepared to act as mirror sites for the NAOMI distribution (you need an anonymous ftp server to do this). If you are interested in doing this, please e-mail me at: smb@bioch.ox.ac.uk ------------------------------------------------------------------------------ ****** What is NAOMI ? ******************* NAOMI is a computer program system for studying 3-D structures of proteins. NAOMI is available free of charge for academic users. NAOMI Version 2.4c is available as of now from the NAOMI Web site at: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html or via anonymous ftp ftp://nmrz.ocms.ox.ac.uk/pub/smb/naomi i.e. at nmrz.ocms.ox.ac.uk in directory pub/smb/naomi/ _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!cam-news-hub1.bbnplanet.com!uunet!news-in2.uu.net!news.vol.it!peroni.ita.tip.net!mikasa.iol.it!news From: edoardo.shockwav@iol.it (Edoardo ) Newsgroups: bionet.software Subject: Image areas Date: Mon, 07 Oct 1996 19:28:25 GMT Organization: Italia Online Lines: 8 Message-ID: <325959c7.4249237@news.iol.it> NNTP-Posting-Host: 194.20.24.159 X-Newsreader: Forte Agent .99e/32.227 I need a simple windows / win 95 program which can calculate the area of an irregular shape into an image file (of course you need the distance between 2 points in the image). I have an old Dos share program (Improces) but I am not satisfied by it. Any help would be extremely useful From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: (EFRAIN RAMIREZ ZAPATA) Newsgroups: bionet.software Subject: Cyrillic Date: 7 Oct 1996 11:05:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net do some of u know where is the web page of the presentation of thje Cyrillic software? Cona some of u help me to find out if there is a new release of the biosys software? of how can I get in touch with the ones who did it? From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: (EFRAIN RAMIREZ ZAPATA) Newsgroups: bionet.software Subject: Re: ANNOUNCE: Plasmid Processor software available for free! Date: 7 Oct 1996 10:52:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Some one was asking about software for presentations... On 25 Sep 1996, Janne Saarela wrote: > > Introduction > > Plasmid Processor is a simple tool for plasmid presentation for scientific and > educational purposes. It features both circular and linear DNA, user > defined restriction sites, genes and multiple cloning site. In addition you > can manipulate plasmid by inserting and deleting fragments. Created drawings > can be copied to clipboard or saved to disk for later use. Printing from > withing program is also supported. > > Plasmid Processor is freeware, so you can use and distribute it freely. > > You can download full executable version of Plasmid Processor 1.02 for Windows > (tm) at URL > > http://www.uku.fi/~kiviraum/plasmid/plasmid.html > > ( plasp102.zip (239k). ) > > > Authors > > Plasmid Processor program was created during a programming project course > organized by the Department of Computer Sciences and Applied Mathematics, > University of Kuopio, Finland 1995-1996. The program was made for the > Department of Biochemistry and Biotechnology, University of Kuopio, > which owns the copyrights of the program. > > Programming team: T. Kivirauma, P. Oikari and J.Saarela. > > For further information please contact the authors by e-mail, plasmid@uku.fi. > Any comment on program is greatly appreciated. > > -- > Janne Saarela > BIOTECHNOLOGY, BSc, PhD student > University of Kuopio, FINLAND > Email: saarela@messi.uku.fi > WWW: http://www.uku.fi/~saarela/ > > > From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!main.Germany.EU.net!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!uni-erlangen.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!nntp Newsgroups: bionet.software Subject: Anybody attending the Pacific Symposium on Biocomputing (Hawaii)? Message-ID: <1996Oct7.183017.248@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 7 Oct 96 18:30:17 +0100 Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24 Lines: 18 Hello, I plan to attend the Pacific Symposium on Biocomputing January 6-9 in Hawaii. Unfortunately my budget is a bit limited and it is high season there at this time. So I am looking for someone who would like to share a room/appartment or the like with me during this period (~ January 3-11). Any other hints are appreciated as well. Regards, Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!nntp-hub2.barrnet.net!cam-news-hub1.bbnplanet.com!howland.erols.net!EU.net!main.Germany.EU.net!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: Linux mol biol/biochem/etc software - compiling fortran apps Date: 7 Oct 1996 17:09:49 GMT Organization: University of Wuerzburg, Germany Lines: 20 Message-ID: <53bdgt$7oj@winx03.informatik.uni-wuerzburg.de> References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] zinc (zinc@zifi.genetics.utah.edu) wrote: > 2) more importantly, i would really like to hear success stories from > anyone who has compiled FORTRAN code under Linux, especially the > type of software mentioned in the subject. if you know it, please > tell me what you had to do to get it to work and what your system > configuration is. My Fortran sucks, but I got both Molscript and the Raster3D package to compile under Linux. I use f2c-960315-2.tar.gz together with a f77 frontend (actually it's only a few lines in perl) written by Thomas Koenig. I tried g77, but I gave up after a day or so. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!feed1.news.erols.com!arclight.uoregon.edu!news.uoregon.edu!news.u.washington.edu!news.alt.net!news1.alt.net!news.aros.net!news.cs.utah.edu!news.cc.utah.edu!news From: zinc Newsgroups: bionet.software Subject: Linux mol biol/biochem/etc software - compiling fortran apps Date: 06 Oct 1996 11:33:59 -0600 Organization: University of Utah Computer Center Lines: 41 Message-ID: NNTP-Posting-Host: zifi.genetics.utah.edu X-Newsreader: Gnus v5.2.31/XEmacs 19.14 -----BEGIN PGP SIGNED MESSAGE----- hello again, i have been gathering a pretty good list of software that compiles and runs under Linux. many of the structure programs are in FORTRAN. i have a couple of questions about this... 1) is FORTRAN still better than C for this sort of thing or is it just a result of many xtallographers being familiar with FORTRAN? 2) more importantly, i would really like to hear success stories from anyone who has compiled FORTRAN code under Linux, especially the type of software mentioned in the subject. if you know it, please tell me what you had to do to get it to work and what your system configuration is. i will be posting a list of software to this newsgroup as well as making it nifty html in the coming week. thanks, - -patrick finerty biochem grad student, u of utah - -- "Those that give up essential liberty to obtain a little temporary safety deserve neither liberty nor safety." -- Benjamin Franklin (1773) finger for PGP key zifi runs LINUX 2.1.1 -=-=-=WEB=-=-=-> http://zifi.genetics.utah.edu -----BEGIN PGP SIGNATURE----- Version: 2.6.2 Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface iQCVAwUBMlftfk3Qo/lG0AH5AQFHxwQAic5b0P05nVjxCXd+qX37efKQt4JR4TUo ExSM0i3Cyqzum1Itzmm2QbGb+GzReLLzdyA+88Ef7mg8xMVCTDMPGWM7ow7Lir+1 5yWA4cVRdAdjFZUyzceu+XImvdnI6Kx8pmK2a/+bQvpbl+cOos95D5UHnL6SaT6g f4Zv1KQPEDQ= =bVKM -----END PGP SIGNATURE----- From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!newspump.sol.net!news.mindspring.com!uunet!in3.uu.net!nebo.vii.com!xmission!news.cc.utah.edu!news From: zinc Newsgroups: bionet.software Subject: Linux mol-bio/biochem software - a list. please mail additions Date: 06 Oct 1996 23:43:23 -0600 Organization: University of Utah Computer Center Lines: 313 Message-ID: NNTP-Posting-Host: zifi.genetics.utah.edu X-Newsreader: Gnus v5.2.31/XEmacs 19.14 -----BEGIN PGP SIGNED MESSAGE----- here's the current list. i spent most of today at the console screwing with damned FORTRAN compilations - not something i enjoy. anyway, thanks to the following people for their additions: francis@ncbi.nlm.nih.gov (B.F. Francis Ouellette) Ashok Aiyar gilbertd@chipmunk.bio.indiana.edu (Don Gilbert) i will be converting the file to html some point this week. since i am having a difficult type focussing at this time, it will have to wait. if anyone tests this code and finds my observations to be mistaken, please mail me (i'm sure you will :) ). also, the text file is available from my web page, just not in html. see http://zifi.genetics.utah.edu/~zinc/linux/linux.html for a link. - -patrick finerty biochem grad student, u of utah ========================================================================== this site seems to have a lot of stuff: ftp://nic.funet.fi:/pub/sci/molbio/emblmirror/unix/ this web pages lists quite bit of software as well: http://mbisg2.sbc.man.ac.uk/gradschool/bioinf/prot.html a lot of these are in FORTRAN so how well they compile is probably due to how good the fortran support on a system is... if i mention that i compiled or tested any of this stuff you might want to know my system config. generally, i keep zifi very up-to-date, using linux/Documentation/Changes as a guide. here is my current config: Linux 2.1.1 libc 5.4.7 gcc 2.7.2 g77-0.5.18.bin.tgz installed f2c-960717.elf.tgz ======= something called VMD (Visual Molecular Dynamics) is almost ported: http://www.ks.uiuc.edu/Research/vmd/ ======= Molden - Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac - main program is in fortran X-win driver in C - ftp://ftp.caos.kun.nl/pub/molgraph/molden info at http://www.caos.kun.nl/~schaft/molden/molden.html this compiled and ran on my system using the g77-0.5.18.bin.tgz package from sunsite. it took a ton of memory to compile - about 25 MB at one point so you should have some serious swap space or if asked i'll make a binary available (my libc is prob too recent for most people). if you install the g77-0.5.18.bin.tgz package be sure to link g77 to f77 because that's what make tries to use. pretty cool. ======= RasMol - displays pdb files, writes a variety of output formats. - current version is 2.6beta, written in C - ftp://ftp.dcs.ed.ac.uk/pub/rasmol - ftp://sunsite.unc.edu/pub/Linux/apps/biology/ i have used the beta version extensively under Linux. it works like a charm. i did not encounter any bugs. to compile for a 16 bpp display, you must hack the Makefile produced with xmkmf. change this line: DEPTHDEF = -DEIGHTBIT to DEPTHDEF = -DSIXTEENBIT. i did not have luck just changing the value in rasmol.h as per the INSTALL instructions. ======= MOLMOL - MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR - version 2.2.0 - ftp://ftp.mol.biol.ethz.ch/pub/software/MOLMOL - ftp://sunsite.unc.edu/pub/Linux/apps/biology/ requires motif to compile and ksh shell to run the script. a binary is available on sunsite (or mirrors). the binary works just fine on my system. if you use the binary, you also need to get the molmol-2.2.0-doc.tgz file as well. be sure to move the binary to the same place the doc files were unpacked. run the install script and then run the molmol script. ======= XtalView- XtalView is a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model. - version ?, in fortran (crystallographers love fortran). have to sign a license to get source but not for binaries - http://www.sdsc.edu/CCMS/Packages/XTALVIEW/ it looks like binaries are avail for Linux...(according to the above page) but i didn't try to get any. ======= WhatIf - WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. - version ?, in FORTRAN - http://swift.embl-heidelberg.de/whatif/ licensed for a small fee to academics... ======= Procheck- Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. - version 3.4.3, written in FORTRAN http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html obtain source from: ftp://128.40.46.11/pub/procheck/tar3_4/procheck.tar.Z this is more fortran fun and games. this would not compile with g77 as i ran out of memory at about 70 MB... however, using the f2c package it compiled. it seems to work ok. another note, it took a really, really, really, really, long damned time for 'clean' to compile. i just went home... ======= MOPAC - you have to order this or something. i couldn't find source or much info. any WWW search will bring up a ridiculous number of online html manuals though. - ftp://129.79.74.206/ ======= i heard the GAMESS programs compile under Linux but i did not try them as you have to go through a little effort to get them... US version GAMESS - The General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package. - version ?, written in ? - http://www.msg.ameslab.gov/GAMESS site license is free to everyone but must sign a form... UK version GAMESS - GAMESS--UK is a general purpose ab initio molecular electronic structure program for performing SCF- and MCSCF-gradient calculations, together with a variety of techniques for post Hartree Fock calculations. - version ?, written in ? - http://gserv1.dl.ac.uk/CCP/CCP1/gamess.html ======= stuff from ncbi database searching tools (for remote database queries) the ncbi package... linux binary of the network database search tools: ftp://ncbi.nlm.nih.gov/blast/network/blast2/ this includes blastp, blastn, tlbastn, tblastx etc. works like a charm under cron control for regular database searching... this requires the network Entrez program to be configured, get a linux binary here: ftp://ncbi.nlm.nih.gov/entrez/network/linux.tar.Z ======= sequin - ncbi's "new" sequence submission/editing tool - version ?, written in C - ftp://ncbi.nlm.nih.gov/sequin/linux.tar.Z - http://www.ncbi.nlm.nih.gov/Sequin/index.html this compiles and runs just fine on my system. ======= fasta - database search tool - version ?, written in C - ftp.virginia.edu/pub/fasta/fasta30t6.shar.Z used default makefile but changed THR_CC= to be blank then 'make sall'. ======= RNA folding related software: Viena RNA package - various calculations of RNA structure - version 1.1b, written in C - ftp://ftp.itc.univie.ac.at/pub/RNA/ViennaRNA-1.1b.tar.gz compiles fine under Linux but Makefile needs tweaking (hell, i managed to get it to work...) ======= naview - An improved algorithm for the display of nucleic acid secondary structures - version ?, written in C - ftp://snark.wustl.edu/pub/naview.tar.Z - http://www.ibc.wustl.edu/~zuker/ref/BRUR88.html this compiles fine under Linux but i haven't used it. ======= SeqPup - sequence editor and analysis program. includes links to network services and external analysis programs. - version ?, written in C, binary provided - ftp://iubio.bio.indiana.edu/molbio/seqpup/ unix/linux-i86-elf/ - ftp://iubio.bio.indiana.edu/util/dclap/source/ does not seem completely stable... ======= tacg - restriction site analysis program - version ?, written in C - ftp://mamba.bio.uci.edu/pub/tacg/ works on plain text files with sequence in them... source code compiled fine. the provide binary in the bin dist is a.out (QMAGIC). ======= SignalScal - scan for transcription factor binding sites - version 4.07, written in C, compiles fine - ftp://biosci.umn.edu/pub/sigscan/unix this works great on my system... it's a good idea to read this file: ftp://biosci.umn.edu/pub/sigscan/unix/readme.unix ======= PIMA - pattern induced multiple sequence alignment - version 1.40, written in C, compiles fine - ftp://gc.bcm.tmc.edu/pub/software/pima ftp://gc.bcm.tmc.edu/pub/software/pima/README passes builin tests just fine after compilation. ======= Predator - structural prediction based on multiple alignments - version 1.0, written in C, compiles fine - ftp://ftp.ebi.ac.uk/pub/software/unix/predator output on my Linux box was identical to output on an SGI using the precompiled binary for IRIX and the binary i compiled. ======= ClustalW - pairwise and multiple alignments - version 1.60, written in C, compiles fine - ftp://ftp.ebi.ac.uk/pub/software/unix tested it, works fine on my Linux system. ======= Seqsee - protein sequence analysis package - version 1.2, written in C, compiles fine - available upon request from seqsee@procyon.biochem.ualberta.ca ======= Pratt - pattern discovery in sets of unaligned sequences - version 2.0, written in C, minor changes - ftp://ftp.ii.uib.no/pub/bio/Pratt/Pratt2.tar - http://www.ii.uib.no/~inge/Pratt.html this segfaults but only apparently after a run has finished. otherwise appears ok... ======= Primer3 - PCR primer design - release 0.1, written in C, compiles fine - ftp://genome.wi.mit.edu all tests passed just fine on my system. ======= GDE - genetic data environment - release ?, written in ? - gopher://megasun.bch.umontreal.ca:70/11/GDE/ binaries are a.out (ZMAGIC), requires (a.out) xview libraries. i tried to compile this myself but not very hard - it wouldn't work. ============================================================================== - -- "Those that give up essential liberty to obtain a little temporary safety deserve neither liberty nor safety." -- Benjamin Franklin (1773) finger for PGP key zifi runs LINUX 2.1.1 -=-=-=WEB=-=-=-> http://zifi.genetics.utah.edu -----BEGIN PGP SIGNATURE----- Version: 2.6.2 Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface iQCVAwUBMliYd03Qo/lG0AH5AQFu/wP+Ppkuu7KbmsUGT0rRZ8R8Gn+XBYyRkm7u /1Lb4tgGJSXNK9jGsQ0S8qKbjDFU6ACVmybsJW9pCCUjX+ssHOYJFBe8UunVlTP+ j1t6f0i4IIKgEoeQd/9pHXYqqHhjoiD8CNrzsfvr7QbjSBY8wkk6Tjm58u3tdUg1 1qtwlHpeqH0= =xWIs -----END PGP SIGNATURE----- From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!swrinde!news.uh.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.software Subject: Re: science software (mol biol/biochem/biology) under Linux Date: Mon, 07 Oct 1996 09:21:00 +0100 Organization: U. Texas-Houston Lines: 32 Message-ID: References: <5383lj$jd8@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit In article <5383lj$jd8@winx03.informatik.uni-wuerzburg.de>, krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) wrote: > More stuff that runs under Linux: > > - the fasta package (sequence comparison) Try this: ftp://ftp.virginia.edu/pub/fasta/ > - molscript (makes schematics of protein structures; Fortran, I had to > patch it a little to make it work with f2c; contact Per Kraulis to > get the source). Here is his email address: krpx@sgikrpe.sto.pharmacia.se > - raster3d (raytraces molscript figures; a mixture of Fortran and C). > > Sorry, I don't know the sites where I got them from. > > --Cornelius. I will add that Amber runs under Linux. Here is the URL: http://www.amber.ucsf.edu/ T. Chyau Liang U Texas-houston From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!swrinde!news.uh.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.software Subject: Re: [Q]downloadable molecular clipart? Date: Mon, 07 Oct 1996 09:02:02 +0100 Organization: U. Texas-Houston Lines: 20 Message-ID: References: NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit In article , kofoid@biology.utah.edu (Eric Kofoid) wrote: > Can someone point me to a source of downloadable structural images of > various biomolecules? I'm especially interested in space-filling or ribbon > structures of cobalamin and NADH. These will be used to decorate web pages > and journal papers. I'm not interested in anything requiring a Java applet > to view, just simple stuff in GIF, JPEG, PICT or TIFF format. Go to PDB. They have losts of pictures ready. Alternatively, you can download the pdb files and then generate any picture your like with freeware such as RasMol. PDB http://www.pdb.bnl.gov/ RasMol http://www.umass.edu/microbio/rasmol/getras.htm have fun. T. Chyau Liang U Texas-houston From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!news From: Ewan Birney Newsgroups: bionet.software Subject: Re: Blast search help needed. Date: Mon, 07 Oct 1996 14:09:48 +0100 Organization: MRC Human Genome Resource Centre Lines: 32 Message-ID: <3259011C.167E@sanger.ac.uk> References: <52mnn2$rh0@news.iastate.edu> <52ot09$i02@swsu65.swmed.edu> <52sk25$29v@news.iastate.edu> NNTP-Posting-Host: waiy.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) To: Chris Kafer Chris Kafer wrote: > > mperr1@hamon.swmed.edu (Michael Perry) wrote: > > Thanks for the reply but I tried that first. What it appears to do is > compare the entire sequence (as if it were a single ORF) in all 6 > frames. What I would like to do is have it blast the real ORFs >30 > amino acids individually. When I blast them manually, it brings back > different hits than a blastx search of the entire sequence. > > As an example, when I blast one of the 200 aa ORFs it returns an EST > clone. When I blast the entire sequence, of which this ORF is just a > part, it doesnt show up. Hopefully I explained that clearly! > You probably already realise this, but the fact that it comes up in ones search and not the other is "meaningful" in the BLAST view: what you have done is 'manually' trim one sequence to a region, specialising in one particular region, and therefore hits against that region now get a lower probability of being random. [what I am saying is that this is what you expect]. [now for the plug]: Although it does not do all of what you want, PairWise and SearchWise can run a DNA query against a protein database allowing for Frameshifts and to a certain extent, introns. The DNA2DNA approach which you want we are developing but it is not released yet. You can get PairWise and SearchWise from http://www.sanger.ac.uk/~birney/wise/topwise.html ewan From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!news-peer.gsl.net!news.gsl.net!news-stkh.gsl.net!news.gsl.net!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!yama.mcc.ac.uk!liv!news From: P.W.Gould@liverpool.ac.uk (Paul Gould) Subject: Re: Dawkins' Netspinner/Watchmaker Message-ID: Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: ctibiol2.bioc.liv.ac.uk Cc: elysium@wolfenet.com Organization: The University of Liverpool X-Newsreader: RadicalNews (TM) 0.8.8 Beta(n) References: Date: Mon, 7 Oct 1996 11:33:34 GMT Lines: 27 In Sonya wrote: > Does anyone know where I can find Netspinner and/or Watchmaker available > for download for the Mac? AFAIK, 'Blind Watchmaker' is a commercial program, so I doubt that you'd be able to download it from anywhere. I have the address of a UK distributor for it, if that's of any help to you: Software Production Associates Ltd., PO Box 59, Tewkesbury, Glos., GL20 6AB UK tel: +44 1684 833700, fax: +44 1684 833718 This information was extracted from the CTI Biology Resource Directory database, which may be searched and browsed via the web. See the Publications section of our web pages at . Regards, Paul -- Paul Gould, Network Support Officer +44 151-794 5118 (Tel) CTI Biology, Donnan Laboratories +44 151-794 4401 (Fax) University of Liverpool, PO Box 147 P.W.Gould@liverpool.ac.uk Liverpool L69 3BX, UK (MIME/NeXTmail OK) From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!dispatch.news.demon.net!demon!genesys.demon.co.uk!duncan From: "Dr. Duncan Clark" Newsgroups: bionet.software Subject: Re: Staden for Mac/PC? Date: Mon, 7 Oct 1996 11:46:22 +0100 Organization: GeneSys Ltd Lines: 20 Distribution: world Message-ID: <4VgPDbA+9NWyEw3m@genesys.demon.co.uk> References: <5309rk$biu@net.bio.net> <530dgf$ptg@dismay.ucs.indiana.edu> <325559BC.1D98@bbsrc.ac.uk> <5339tn$246@nntp1.best.com> NNTP-Posting-Host: genesys.demon.co.uk X-NNTP-Posting-Host: genesys.demon.co.uk MIME-Version: 1.0 X-Newsreader: Turnpike Version 3.01 beta 1 I do not wish to start any flame wars about OS's but there has been a lot in the computer press in the last few months about Apple's problems with market share, finance etc. What happens if they go bust? Sure it is unlikely but who knows? I can't see Microsoft or Intel going bust. Regarding use of PC's in the UK. What is the situation in the rest of the EEC? I can just see it now, a binding European directive that we must all use a new EEC OS! But seriously if we over here are starting to bias ourselves away from the Mac OS then given the purchasing power of the EEC as a whole, the science software authors will have to take note or exclude themselves from that market. Duncan ----------------------------------------------------------------------------- My mind's made up. Don't confuse me with the facts! Duncan Clark DNAmp Ltd. http://www.dnamp.com From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.software Subject: Re: Protein Viewer Date: 7 Oct 1996 12:08:43 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <53aobr$kt9@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk To: bio-software@dl.ac.uk From: eroshkin@vector.nsk.su Subject: Re: Protein Viewer > From blduncch@aol.com Sun Oct 6 12:31:01 1996 > Where can I download a good protein viewer for IBM-PC, either DOS or Win > 3.1? > > I want to be able to read Brookhaven files and to add colors to selected > amino acid residues. You can find this and more in ProAnWin (for Windows): ftp://ftp.bionet.nsc.ru/pub/biology/vector/proanwin.dem/paw$.exe ftp://ftp.ebi.ac.uk/pub/software/dos/proanwin and in ProAnalyst (for DOS) ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst/ ftp://ftp.bionet.nsc.ru/pub/biology/vector/proanaly.dem/panalys$.exe ftp://iubio.bio.indiana.edu/molbio/ibmpc/panalys1.exe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Alexey Eroshkin Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7 (3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!news From: Ewan Birney Newsgroups: bionet.software Subject: PairWise and SearchWise new release Date: Mon, 07 Oct 1996 11:27:28 +0100 Organization: MRC Human Genome Resource Centre Lines: 54 Message-ID: <3258DB10.41C6@sanger.ac.uk> NNTP-Posting-Host: waiy.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) **** PairWise and SearchWise 1.6.2 **** *** Beta-Release *** PairWise and SearchWise version 1.6 has been released for general use. Some of the improvements include: o On-the-fly parsing of EMBL format databases to provide only genomic or only cDNA sequences during database searching o Configurable SRS linking in the HTML output o HTML output of the alignments A considerable number of bugs have also been removed. For people who have not used PairWise and SearchWise, they are programs which can trace a match of a protein sequence or a protein profile to a DNA sequence allowing for frameshifts and intron in the DNA sequence. This work has been recently published in the July issue of NAR "PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames" Ewan Birney, Julie Thompson and Toby Gibson Nucleic Acids Res., 24 2730-2739, 1996 There is a web site at http://www.sanger.ac.uk/~birney/wise/topwise.html and the source code, and hopefully a collection of binaries are available at ftp.sanger.ac.uk /pub/birney/wise The WWW site has an extensive series of help/tutorial and installation files to guide you towards making use of PairWise and SearchWise. I would read some of the files first before downloading. (NB: for current users, notice that the OCMS Web site is no longer maintained. The Sanger centre site will be the main site for at least the next 3 years - please update any links you have). There is a mailing list for people who would like to be in closer contact with releases, and for any other information, please email me at birney@sanger.ac.uk Have fun! ewan birney From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!main.Germany.EU.net!fu-berlin.de!news.th-darmstadt.de!tutor.oc.chemie.th-darmstadt.de!martin From: martin@tutor.oc.chemie.th-darmstadt.de (Martin Kroeker) Newsgroups: bionet.software Subject: Re: science software (mol biol/biochem/biology) under Linux Date: 7 Oct 1996 09:49:16 GMT Organization: Technische Hochschule Darmstadt Lines: 32 Message-ID: <53ajms$lsk@rs18.hrz.th-darmstadt.de> References: NNTP-Posting-Host: tutor.oc.chemie.th-darmstadt.de X-Newsreader: TIN [version 1.2 PL2] zinc (zinc@zifi.genetics.utah.edu) wrote: > i'm attempting to compile a list of software that either people have > claimed runs under Linux or that is known to run under Linux for the > XtalView > it looks like binaries are avail for Linux...(according to the above Linux binaries are definitely available. > MOPAC > i searched all over for this - couldn't find the source! only a ton Look on kekule.osc.edu, you should find sources for mopac6 and the pd version of mopac7 there. (If i remember correctly, there was also a linux binary of mopac7 there, but once you've taken care of some VAXisms in the source, compilation is no problem either). > i heard the GAMESS programs compile under Linux but i did not try them Yes, GAMESS runs on Linux. There is also MOLMOL from Wuthrich's group: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ and finally a shameless plug for our PIMM molecular mechanics code, http://130.83.122.2/TZ/AKLindner/pimm_e.html (free for academics, but you need to email us for a license and pointer to the source). Martin -- Dr.-Ing. Martin Kroeker Inst. f. Organ. Chemie martin@oc2.oc.chemie.th-darmstadt.de Univ. (TH) Darmstadt db7p@hrzpub.th-darmstadt.de Germany From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!sdd.hp.com!night.primate.wisc.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: Linux mol biol/biochem/etc software - compiling fortran apps Date: 7 Oct 1996 19:57:24 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 26 Message-ID: References: Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu X-Newsreader: slrn (0.9.0.0 (Tue Sep 3 21:08:09 CDT 1996) UNIX) On 06 Oct 1996 11:33:59 -0600, zinc wrote: >1) is FORTRAN still better than C for this sort of thing or is it just > a result of many xtallographers being familiar with FORTRAN? Fortran is just what a lot of people learnt. C is a relatively new language. (Yes, I consider 20 years to be relatively new). >2) more importantly, i would really like to hear success stories from > anyone who has compiled FORTRAN code under Linux, especially the > type of software mentioned in the subject. if you know it, please > tell me what you had to do to get it to work and what your system > configuration is. I haven't had particularly good luck with f2c, somewhat better luck with g77. There is one really good commercial Fortran 77 compiler for Linux (from Absoft). There are a couple packages that don't go anywhere with f2c or g77 that do compile with Absoft's compiler. Later, Ashok -- Ashok Aiyar, Ph.D. Department of Oncology email: aiyar@ebv.oncology.wisc.edu University of Wisconsin-Madison tel: (608) 262-6697 From owner-software@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!swrinde!news.uh.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.software Subject: Re: Protein Viewer Date: Mon, 07 Oct 1996 09:30:43 +0100 Organization: U. Texas-Houston Lines: 17 Message-ID: References: <538hp4$os@newsbf02.news.aol.com> NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit In article <538hp4$os@newsbf02.news.aol.com>, blduncch@aol.com (BLDUNCCH) wrote: > Where can I download a good protein viewer for IBM-PC, either DOS or Win > 3.1? > > I want to be able to read Brookhaven files and to add colors to selected > amino acid residues. RasMol is a good one and is available for PC, Mac, and Unix http://www.umass.edu/microbio/rasmol/getras.htm good luck. T. Chyau Liang U. Texsas-houston From owner-software@net.bio.net Mon Oct 07 23:00:00 1996 Path: biosci!BENPC.BIONET.NSC.RU!ptitsyn From: ptitsyn@BENPC.BIONET.NSC.RU ("Andrey A.Ptitsyn") Newsgroups: bionet.software Subject: Re: Cyrillic Date: 8 Oct 1996 01:36:59 -0700 Organization: Institute of Cytology and Genetics, Novosib Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610080835.OAA22706@benpc.bionet.nsc.ru> NNTP-Posting-Host: net.bio.net Hi, I didn't quite understand what kind of Cyrillic do you need. I have some Cyrillic fonts for Windows and Cyrillic drivers for DOS, available upon request. Cyrillic Web sites are almost all in Russia. Regards, Andrey. From owner-software@net.bio.net Mon Oct 07 23:00:00 1996 Path: biosci!agate!howland.erols.net!surfnet.nl!news.unisource.nl!xs4all!xs4all!user From: a_team@dds.nl (Anneke Harbers and Ard Jonker) Newsgroups: bionet.software Subject: Re: HyperCard to FileMaker Date: Tue, 08 Oct 1996 06:53:01 +0200 Organization: a_team Lines: 16 Message-ID: References: <3258829B.C70@iastate.edu> NNTP-Posting-Host: asd10-09.dial.xs4all.nl X-XS4ALL-Date: Tue, 08 Oct 1996 06:52:49 MET DST In article <3258829B.C70@iastate.edu>, An-Ping Hsia wrote: >Hi, > >I want to transfer data from HyperCard(2.2) to FileMaker(3.0). I tried >saving my HyperCard files in other format (like Excel) and import into >Fi