From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!cornell!batcomputer!ghost.dsi.unimi.it!univ-lyon1.fr!swidir.switch.ch!news.unige.ch!ugsc2a!yeager From: yeager@sc2a.unige.ch Newsgroups: bionet.software Subject: Pharmacia Gelscan data -> ascii Message-ID: <1994Jun2.225713.1@ugsc2a> Date: 2 Jun 94 20:57:13 GMT Sender: usenet@news.unige.ch Organization: University of Geneva, Switzerland Lines: 7 I need a utility to convert Pharmacia Gelscan XL v 2.1 data files to ascii format to import into other programs. I don't need the header, just the data portion. If anyone has such a program, or some kind of workaround please let me know. -- -.- Mark Yeager -> yeager@sc2a.unige.ch From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Newsgroups: bionet.software From: steve@gardner.demon.co.uk (Steve & Rowan Gardner) Path: biosci!daresbury!doc.ic.ac.uk!lyra.csx.cam.ac.uk!pipex!demon!gardner.demon.co.uk!steve Subject: Re: bioinformatics definition References: <4085@CAMVAX.CINECA.IT> Distribution: world Organization: Myorganisation Reply-To: steve@gardner.demon.co.uk X-Newsreader: Newswin Alpha 0.4 Lines: 39 Date: Thu, 2 Jun 1994 20:48:30 +0000 Message-ID: <594133437wnr@gardner.demon.co.uk> Sender: usenet@demon.co.uk In article: <4085@CAMVAX.CINECA.IT> BIOSCU@CAMVAX.CINECA.IT writes: > > We would like to know what could be, in your opinion, a sound, > concise and - possibly - comprehensive definition of > > BIOINFORMATICS. > > Our aims is to present the result of a general enquiry like this > in the framework of a National Seminar on BioInformatics > to be held in Camerino in the 3rd week of June. > > > > for the organizing committee > > Sincereley > > Alberto Polzonetti > > e-mail: bioscu@camvax.cineca.it > ******************************************************** > > > For what its worth, the best I could come up with for my thesis was.... Bioinformatics is the field that marries computational information management techniques with an understanding and appreciation of the significance of biological data. Bioinformatic databases store, retrieve, manipulate and correlate biological data from diverse sources, providing efficient and flexible scanning tools to identify biologically significant similarities. The rest of it is really boring :-) Steve Gardner From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!alberta!quartz.ucs.ualberta.ca!mac14.biochem.ualberta.ca!user From: mike_schultz@darwin.biochem.ualberta.ca (Mike Schultz) Newsgroups: bionet.general,bionet.software Subject: How is GeneWorks for Mac? Followup-To: bionet.general Date: 2 Jun 1994 23:17:46 GMT Organization: Dept. of Biochemistry, The University of Alberta Lines: 3 Message-ID: NNTP-Posting-Host: mac14.biochem.ualberta.ca Xref: biosci bionet.general:9564 bionet.software:8369 We use the Wisconsin GCG package, but a lot of Mac people want something more user-friendly. Has anyone tried the latest version of GeneWorks (Intelligenetics)? Any bad glitches? From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uunet!newsflash.concordia.ca!sifon!cidsv01.cid.aes.doe.ca!newsfeed!newsfeed.rice.edu!rice!swamp.rice.edu!user From: jcn@rice.edu (Jeff Nichols) Newsgroups: bionet.software Subject: DNA Strider for the mac (again) Followup-To: bionet.software Date: Thu, 02 Jun 1994 15:35:08 -0500 Organization: Rice University Lines: 13 Message-ID: NNTP-Posting-Host: swamp.rice.edu I realize it's been posted before, but could someone tell me again how to purchase the latest version of DNA Strider? It's the only program that 99% of our lab seems to be able to use without major headaches (to me for explaining every little detail :-) Thanks -- * Jeff Nichols | I'm a lumberjack and I'm okay. * It's a dog-eat-dog world out there, and I'm wearing milkbone * underwear-- Norm Peterson * Don't jump without the video. * I used to be tolerant; now I'm actively tolerant.--Thanks Tom. From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!doc.ic.ac.uk!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user Newsgroups: bionet.software Subject: New Mac WWW client Message-ID: From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Date: Thu, 02 Jun 1994 15:18:07 +0100 Followup-To: bionet.software Organization: EMBL Data Library Nntp-Posting-Host: rainer-mac.embl-heidelberg.de Lines: 170 Relay-Version: ANU News - V6.1B9 05/16/94 VAX/VMS V5.5-2; site eros.embl-heidelberg.de Path: embl-heidelberg.de!news.urz.uni-heidelberg.de!xlink.net!howland.reston.ans.net!cs.utexas.edu!milano!milano.mcc.com!hardin Newsgroups: comp.sys.mac.comm Subject: ANNOUNCE: New EINet Mac WWW client with Forms! Message-ID: From: hardin@dino.mcc.com (John Hardin) Date: Wed, 1 Jun 1994 16:14:08 GMT Sender: news@mcc.com Distribution: comp Organization: MCC ISD, Austin, Texas Lines: 149 [I apologize in advance for multiple postings of this message. I cross-posted it to a couple of other groups that turn out to be moderated. The message is not posted to ANY group until the moderator(s) have a chance to approve its being posted. Sorry for unnecessarily wasting bandwidth. -jwh] Announcing the Release of EINet MacWeb Version 0.98 Alpha RELEASE INFO MCC's EINet group is pleased to announce MacWeb Version 0.98 Alpha. MacWeb is a full-featured World-Wide-Web, hypertext browser. It is available as freeware from the URL: ftp://ftp.einet.net/einet/mac/macweb/macweb0.98alpha.sea.hqx MacWeb is also available via anonymous FTP from the machine ftp.einet.net. Change (cd) to the directory /einet/mac/macweb and get the following file: macweb.0.98alpha.sea.hqx MacWeb requires that your Macintosh be configured with System 7 and MacTCP 2.0.2 (MacTCP 2.0.4 recommended). PROBLEMS AND COMMENTS To report problems, suggest enhancements, or send general comments about MacWeb, please send email to macweb@einet.net. DESCRIPTION MacWeb is a World Wide Web client which uses hypertext, or hypermedia where references within a document are links which lead users to other documents, lists, resources or actions. The World Wide Web supports the display of text, graphics, sound, and video. It is also a tool through which Internet users can access information using from various other Internet front ends, navigators, information, services, and resources. FEATURES SUPPORTED 1. HTML Forms support. 2. Lightweight Memory footprint. MacWeb has an executable size of approximately 370K. It has been run on a 2MB PowerBook 100 using System 7! 3. User Interface features. o Editable URL display. A user can open a URL by simply editing the currently displayed URL or by typing in a new one and pressing or . o Screen preservation. MacWeb was designed to maximize the screen space dedicated to the display of documents, which had the following effects on the interface: - The horizontal scroll bar is small, and the remainder of the area at the bottom of the window (to the left of the horizontal scroll bar) is dedicated to the display of status messages. - The History pop-up is not directly visible, but it can be invoked one of three ways: 1. command-clicking on the title of the window (ala Finder) 2. clicking and holding on the back/forward arrows 3. from the Navigate menu o Styles. The MacWeb styles interface was designed for both flexibility AND ease of use. It is so flexible that a user can edit the style of virtually ANY HTML element. At the same time, users may easily change the look and feel of an ENTIRE document through the inheritance feature in the styles structure. All styles are initially configured to inherit style attributes from their parent (the element in which they occur in the document being viewed.) For example, a user can change the document font by editing Root's font style. Other styles can be edited similarly. o Preferences. MacWeb currently supports 3 distinctive preferences attributes: - Users can specify a preferred hotlist to be opened automatically when MacWeb is invoked, rather than having to explicitly open a hotlist after the program is running. - Users can explicitly define the document window background color as a startup reference. - Users can control blank line suppression. Some HTML writers use multiple

tags for *explicit* control of whitespace. With MacWeb, users can specify whether multiple blank lines should be suppressed or allowed. o Last URL Retained in Open URL Dialog. The Open URL dialog retains the last path typed in by users. The Open URL dialog also contains a pop-up menu containing hotlist items. o Files Easily Retrieved and Saved to Disk. If the user modifies any document-retrieving event with the key (e.g., by pressing while clicking on a link, by pressing - in the URL display, etc.), the document will then be retrieved and saved to disk in the user-specified file. o View Source. MacWeb can generate HTML or retrieve a document source, automatically save it in a temporary file, and invoke an external editor on this file for viewing. 4. Apple Event support. MacWeb supports two notable Apple Events: Open Document (ODOC) and Open URL (OURL). MacWeb supports the ODOC Apple Event to open the specified document. This is very useful for adding HTML rendering capabilities to other applications. In addition, MacWeb supports the OpenURL Apple Event to retrieve and display the specified document, and also has options to save the retrieved document in a file with or without MIME headers. 5. Other nice features: o Import of Mosaic Hotlists. MacWeb can import hotlists created by the NCSA Mosaic for the Macintosh client software. Simply drag and drop them on the MacWeb icon, or select them via the hotlist->open selection dialog. o Retains Window Scroll Position. Resizing scrolled windows retains the current scroll position. o Automatic Document Resizing. After a document window has been resized, documents recalled from the history are automatically resized to fit the new document window size. o Configuration Information Defined in Resources. All of MacWeb's configuration information is defined in Resources, thus MacWeb's initial configuration may be changed by simply editing these Resources. COPYRIGHT AND LEGAL RESTRICTIONS Copyright 1994 Microelectronics and Computer Technology Corporation (MCC). All Rights Reserved. EINet is a trademark of MCC. All other product or service marks contained in this software are trademarks or registered trademarks of their respective owners. MCC grants to Licensee a license to use, copy, and distribute the MacWeb Software for academic, research, and personal-user purposes only, without a fee, provided that (i) the above copyright notice and this permission notice appear in all copies of the Software and related documentation, and (ii) the MCC and EINet name may not be used in any advertising or publicity relating to the Software without the specific, prior written permission of MCC, and (iii) that no charge is associated with copies of the software distributed by Licensee to third parties. Commercial use of this software is forbidden without the express written permission of MCC and payment of a negotiated license fee. -- John W. Hardin phone: (512)338-3535 MCC email: hardin@mcc.com 3500 W. Balcones Center Dr fax: (512)338-3897 Austin, TX 78759-5398 uucp: ...!cs.utexas.edu!milano!hardin From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!wupost!medicine.wustl.edu!msdisk.wustl.edu!salkoff_l From: salkoff_l@msdisk.wustl.edu Newsgroups: bionet.software Subject: DNA analysis programs running under Windows Date: 2 JUN 94 10:06:59 CST Organization: Washington University in St. Louis, Medical Library Lines: 4 Message-ID: <2JUN94.10065991@msdisk.wustl.edu> NNTP-Posting-Host: msdisk.wustl.edu I'm looking for a DNA analysis program with the following features: a Windows environment and the ability to BLAST search the NCBI CD's. Is any company presently producing such a program, or has plans to do so? ---Larry Salkoff---salkoffl@thalamus.wustl.edu From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!CAMVAX.CINECA.IT!BIOSCU From: BIOSCU@CAMVAX.CINECA.IT Newsgroups: bionet.software Subject: bioinformatics definition Date: 2 Jun 1994 05:50:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <5498@CAMVAX.CINECA.IT> NNTP-Posting-Host: net.bio.net We would like to know what could be, in your opinion, a sound, concise and - possibly - comprehensive definition of BIOINFORMATICS. Our aims is to present the result of a general enquiry like this in the framework of a National Seminar on BioInformatics to be held in Camerino in the 3rd week of June. for the organizing committee Sincereley Alberto Polzonetti e-mail: bioscu@camvax.cineca.it ******************************************************** From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!CAMVAX.CINECA.IT!BIOSCU From: BIOSCU@CAMVAX.CINECA.IT Newsgroups: bionet.software Subject: bioinformatics definition Date: 2 Jun 1994 05:49:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <4085@CAMVAX.CINECA.IT> NNTP-Posting-Host: net.bio.net We would like to know what could be, in your opinion, a sound, concise and - possibly - comprehensive definition of BIOINFORMATICS. Our aims is to present the result of a general enquiry like this in the framework of a National Seminar on BioInformatics to be held in Camerino in the 3rd week of June. for the organizing committee Sincereley Alberto Polzonetti e-mail: bioscu@camvax.cineca.it ******************************************************** From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: nce@rri.sari.ac.uk (Nigel Eastmond) Newsgroups: bionet.software Subject: Re: Mac EtherNet Date: 2 Jun 1994 11:51:26 +0100 Organization: Rowett Research Institute Lines: 30 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2skdje$g58@mserv1.dl.ac.uk> References: <9461135630.~INN-TOJa00157.bionet-news@dl.ac.uk> Apparently-To: bio-soft@dl.ac.uk Nigel Eastmond (nce@uk.ac.sari.rri) wrote: : Help! I very qiuckly need to get my mitts on a program to probe the IP : address of a Mac EtherNet card. : Please Email reply. : o------------------------------oOo------------------------------o : | Nigel C. Eastmond | Email nce@rri.sari.ac.uk | : | Rowett Research Institute | Tel +44 244 712751 | : | Aberdeen | Fax +44 244 715349 | : | Scotland | | : o------------------------------oOo------------------------------o Thanks for all the help! I now have a plethora of EtherNet address programs. I stand corrected that it was not the IP address I wanted but the EtherNet card address. You can do it with: GetNetAddress MacTCP and best of all.. Inside EtherNet 1.6 Nigel. From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.funet.fi!news.csc.fi!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.software Subject: Re: Rasmol images Date: 2 Jun 1994 06:25:03 GMT Organization: CSC - Tieteellinen laskenta Lines: 27 Message-ID: <2sjtvv$bmv@pobox.csc.fi> References: <1JUN199422200167@pavo.concordia.ca> NNTP-Posting-Host: convex.csc.fi In <1JUN199422200167@pavo.concordia.ca> dl_tato@pavo.concordia.ca (DAN THE FUNKY MOOSE MAN) writes: >hello, > where can I get rasmol images? Rasmol is a programme that allows you to look at images generated from PDB files. You can get the programme from the following site via anonymous ftp. Host colonsay.dcs.ed.ac.uk Location: /export DIRECTORY drwxr-xr-x 512 Apr 21 07:51 rasmol The pdb files you can get from the gopher at gopher.nih.gov Put the two of them together an you can have all the images you want. RGDS -=ROB=- -- R. Andrew Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302 From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!uunet!newsflash.concordia.ca!pavo.concordia.ca!dl_tato From: dl_tato@pavo.concordia.ca (DAN THE FUNKY MOOSE MAN) Subject: Rasmol images Message-ID: <1JUN199422200167@pavo.concordia.ca> News-Software: VAX/VMS VNEWS 1.41 Sender: usenet@newsflash.concordia.ca (USENET News System) Nntp-Posting-Host: pavo6.concordia.ca Organization: Concordia University Date: Thu, 2 Jun 1994 03:20:00 GMT Lines: 20 hello, where can I get rasmol images? __--__--__--__--__--__--__--__--__--__--__--__--__--__-- Daniel Tatone VP.Com. BSA Major Biology Concodia University Resistance.... is Futile! (Locutus of Borg) E-Mail: dl_tato@pavo.concordia.ca --__--__--__--__--__--__--__--__--__--__--__--__--__--__-- From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!uunet!nih-csl!bernard From: bernard@elsie.nci.nih.gov (Bernard Murray) Subject: Re: oligo optimization programs Message-ID: <1994Jun2.204623.1154@alw.nih.gov> Summary: Oligo 2.0 is free Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: National Institutes of Health References: Date: Thu, 2 Jun 1994 20:46:23 GMT Lines: 36 In article , k-tougu@mskcc.org (Killu Tougu) writes: > Hi Netters- > > We are currently demo'ing a copy of a commercial primer optimization > program by NBI called "Oligo 4.0" that finds optimal primer sites for PCR, > sequencing, hybridizations etc. While this program seems to work pretty > nicely, we're still interested in what else is out there (and if any such > programs would actually be freebies, since cost is an issue). Also, we'd > greatly appreciate any comments on the utility and/or weaknesses of this or > other such programs. We'd appreciate your answers at the address > ktougu@mskcc.org or in this list! > > Thanks in advance, > Killu Tougu, > mol. biol. grad student, > Sloan-Kettering Institute > New York If the (rather exhorbitant) price tag of Oligo 4.1 is rather off-putting but you like the style then you can collect a copy of Oligo 2.0 which is the last non-commercial version. ftp to nemo.life.uiuc.edu and grab /lim/uploads/oligov2.zip (thanks to Ducan Clark of GeneSys for providing this) Another freebie worth a look is Primer 0.5 genome.wi.mit.edu /pub/primer.0.5 (Both these are PC software) Have fun! Bernard Bernard Murray, Ph.D. bernard@elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA) From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!uchinews!quads!ecec From: ecec@quads.uchicago.edu (Eric Cabot) Subject: Re: ANNOUNCEMENT : TREECON 3.0 for comfortable phylogeny ! Message-ID: <1994Jun2.183857.16852@midway.uchicago.edu> Sender: news@uchinews.uchicago.edu (News System) Reply-To: ecec@midway.uchicago.edu Organization: University of Chicago References: <2pl73q$j09@sun2.ruf.uni-freiburg.de> Date: Thu, 2 Jun 1994 18:38:57 GMT Lines: 21 In article schwarze@starbase1.caltech.edu (Erich Schwarz) writes: >In article <2pl73q$j09@sun2.ruf.uni-freiburg.de>, >rensing@sun1.ruf.uni-freiburg.de (Stefan Rensing) wrote: >> >> A disadvantage is that no parsimony or maximum likelihood methods are > ^^ ^^^^^^^^^ >> to be run with TREECON. > > > Boooo! ;^) > > >--Erich Schwarz Geez! Smiley or not, you've got a heck of a lot of nerve to criticize a software tool that someone has graciously made available to the scientific community at large. Why don't you just write your own gosh-darn parsimony program l'user? Eric (this time I swear I won't retract my own flame) Cabot From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!psgrain!nntp.ski.mskcc.org!e-mac-040.ski.mskcc.org!user From: k-tougu@mskcc.org (Killu Tougu) Newsgroups: bionet.software Subject: oligo optimization programs Message-ID: Date: 2 Jun 94 17:50:21 GMT Followup-To: bionet.software Organization: SKI mol.biol.dept. Lines: 16 NNTP-Posting-Host: e-mac-040.ski.mskcc.org Hi Netters- We are currently demo'ing a copy of a commercial primer optimization program by NBI called "Oligo 4.0" that finds optimal primer sites for PCR, sequencing, hybridizations etc. While this program seems to work pretty nicely, we're still interested in what else is out there (and if any such programs would actually be freebies, since cost is an issue). Also, we'd greatly appreciate any comments on the utility and/or weaknesses of this or other such programs. We'd appreciate your answers at the address ktougu@mskcc.org or in this list! Thanks in advance, Killu Tougu, mol. biol. grad student, Sloan-Kettering Institute New York From owner-software@net.bio.net Wed Jun 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!ub4b!idefix.CS.kuleuven.ac.be!news.sri.ucl.ac.be!news!lejeune From: lejeune@licr.ucl.ac.be (Joseph Lejeune) Newsgroups: bionet.software Subject: Wanted : Gaboriaud & Mornon HCA algorithm software Date: Thu, 2 Jun 94 12:51:18 GMT Organization: Ludwig Institute for Cancer Research - Brussels Lines: 13 Message-ID: NNTP-Posting-Host: 130.104.50.130 X-Newsreader: VersaTerm Link v1.1.1 I would be happy to receive pointers to any implementation of the so-called Hydrophobic Cluster Analysis method described by C. Gaboriaud and J-P. Mornon in FEBS Letters (vol 224, 1987). Preferred target platforms for software are Macintosh and SGI workstations. Many thanks in advance. Jo Lejeune , Ph.D. Ludwig Institute for Cancer Research - Brussels branch Avenue Hippocrate 74 - UCL 7459 B-1200 Brussels Belgium Phone : 32-2-764 7542 Fax : 32-2-762 9405 E-mail : lejeune@licr.ucl.ac.be From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!msuinfo!harbinger.cc.monash.edu.au!news.uwa.edu.au!andrewh From: andrewh@uniwa.uwa.edu.au (Andrew Hobbs) Newsgroups: bionet.software Subject: Education Software Date: 3 Jun 1994 01:56:16 GMT Organization: The University of Western Australia Lines: 31 Message-ID: <2sm2k0$c1v@styx.uwa.edu.au> NNTP-Posting-Host: uniwa.uwa.edu.au X-Newsreader: TIN [version 1.2 PL2] Hi, Some time ago (last year) I saw reference to a gopher site which contained a database of educational software; reviews, publishers etc. I did log onto it and did some preliminary browsing but it was badly out of date. It had the promise that it was being rewritten. In the meantime I have lost the address, the original message and my backup, and I can't find any indication of its existence using gopher. I think it was in the UK somewhere. I would appreciate it if someone could help me by giving me some directions. Thanks in advance for any help ********************************************************* * * * Andrew Hobbs * * * Dept of Biochemistry * * * Uni of Western Australia * * Nedlands, * * Western Australia 6009 * * * * * * andrewh@uniwa.uwa.edu.au * * * * ********************************************************* From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!rbgkew.org.uk!A.Cox From: A.Cox@rbgkew.org.uk (Tony Cox) Newsgroups: bionet.software Subject: Mac C compiler software Date: 3 Jun 1994 02:58:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406030958.CAA07833@net.bio.net> NNTP-Posting-Host: net.bio.net Can anyone recommend a good C compiler for the Mac. I've done a bit of stuff on a PC + Windows but never on a Mac. Am I going to be in for a big surprise in making the transition? Also, are there any good introductory books to Mac C programming? Thanks From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!overload.lbl.gov!dog.ee.lbl.gov!ihnp4.ucsd.edu!usc!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!msuinfo!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!asstdc.scgt.oz.au!homer!peter From: peter@homer.scgt.oz.au (Peter Leroy) Subject: Re: ANNOUNCEMENT : TREECON 3.0 for comfortable phylogeny ! Message-ID: Organization: Ground Management Systems X-Newsreader: TIN [version 1.2 PL2] References: <2pl73q$j09@sun2.ruf.uni-freiburg.de> <1994Jun2.183857.16852@midway.uchicago.edu> Date: Fri, 3 Jun 1994 00:05:28 GMT Lines: 6 : >> to be run with TREECON. ^^^^^^^ Could someone give me some more info on this little gem ? From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uunet!psinntp!alsys1!leper1!zucker From: zucker@leper1.ca.aecom.yu.edu (Thomas Zucker-Scharff x3512) Newsgroups: bionet.software Subject: Re: HELP: GCG for Mac or PC Message-ID: <2831@alsys1.aecom.yu.edu> Date: 2 Jun 94 18:15:02 GMT References: <2sgul2$7ut@ccu2.auckland.ac.nz> Sender: news@alsys1.aecom.yu.edu Reply-To: zucker@leper1.ca.aecom.yu.edu Organization: Albert Einstein College of Medicine Lines: 36 Nntp-Posting-Host: leper1.ca.aecom.yu.edu In article 7ut@ccu2.auckland.ac.nz, facs@ccu1.auckland.ac.nz (facs) writes: >Hi Netters > >Could someone provide me the information about GCG program: > >1) Is there any GCG program for Mac or PC? > >2) Where can we get this program? > >3) How does it compare with GCG for UNIX? > >Thanks. > Take a look at Intelligenetics' GeneWorks for the Mac or PC-Gene for the PC. These are commercial programs only. In terms of freeware, try using blast (all platforms), Genbank Search @ NCBI for the MAC (Hypercard stack), Netentrez from ncbi.nlm.nih.gov (all plat- forms, but searches only). As far as I'm concerned only GeneWorks for the Mac is comparable to GCG. --- /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ | Thomas Zucker-Scharff | | | Director Scientific Computing Facility | voice : 718-430-3512 | | Albert Einstein College of Medicine | beeper: 212-419-6984 | | 1300 Morris Park Avenue, Chanin 332 | fax : 718-822-6538 | | Bronx, New York 10461 USA | e-mail: zucker@aecom.yu.edu | \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!swrinde!elroy.jpl.nasa.gov!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!xmission!u.cc.utah.edu!not-for-mail From: kr5205@u.cc.utah.edu (Kerry Rowe) Newsgroups: bionet.software Subject: Re: Looking for OSP - a primer application Date: 3 Jun 1994 09:54:17 -0600 Organization: University of Utah Computer Center, Salt Lake City, Ut. Lines: 20 Message-ID: <2snjn9$g3d@u.cc.utah.edu> References: <199406031154.EAA12702@net.bio.net> NNTP-Posting-Host: u.cc.utah.edu In article <199406031154.EAA12702@net.bio.net>, Mike Mitchell wrote: >I would greatly appreciae any information on an application called OSP >that chooses PCR and sequencing primers. > OSP is available from the following: Philip Green or LaDeana Hillier Washington University School of Medicine Box 8232 4566 Scott Avenue St. Louis, Missouri 63110 (314) 362-7072 The software is available at no charge; however, there are some legal papers you must sign before they send you the program. Steve Bayer Myriad Genetics bayer@darwin.med.utah.edu From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!ZORZAL.DC.UBA.AR!bd4a From: bd4a@ZORZAL.DC.UBA.AR (Diego M.Burrieza LU 674/90) Newsgroups: bionet.software Subject: Reference Manager for Patents Date: 3 Jun 1994 16:43:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear netters, I am posting this in behalf of my father. He works with polymers for biomedical applications and he has lots of copies of patents all around the office and the lab. He asked me about a way to organize all the patents and I suggested him a Reference Manager with an editor to edit notes. I look in my diskettes and I found a shareware program for this (Papers, by DBF Systems). He asked me about an specific program (DOS or Windows) to manage his patents. Have you heard about this kind of software ? Thanks for your time. And thanks for your help. Diego M. Burrieza Analytical Chemistry Dept. Faculty of Exact and Natural Sciences University of Buenos Aires ARGENTINA InterNet: bd4a@zorzal.dc.uba.ar From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uunet!newsflash.concordia.ca!CC.UMontreal.CA!cumin.telecom.uqam.ca!UQuebec.CA!Benoit_Hebert From: Benoit_Hebert@IAF.UQUEBEC.CA () Subject: Re: GNU and GCC Sender: news@UQuebec.CA (news) Message-ID: Date: Fri, 3 Jun 1994 18:40:46 GMT References: <09BCB7DA02BF20293A@vxircm.IRCM.UMontreal.CA> Nntp-Posting-Host: panoramix.uqss.uquebec.ca Organization: Virology Research Center Armand-Frappier Institute, Laval, Quebec Universite du Quebec X-Newsreader: TIN [version 1.2 PL2] Lines: 26 JOHANNE@IRCM.UMontreal.CA wrote: > This might the be the right user group but may be someone can give me a hit > where to get the information. > We are a VMS site and want to go on Unix. Many program that I want to > migrate talk about GCC and GNU for compiling. What exactly is that? Is there > any knowned user group for this kind of question. Johanne, the requirements for GCG under UNIX are available from the company. I have lent a copy of the document to a colleague (Francois Shareck). The GCG suite can be recompiled under UNIX without any problem. Give me a call if you have a minute. Benoit Hebert ======================================== Benoit_Hebert@iaf.uquebec.ca Armand-Frappier Institute Virology Research Center Laval, Quebec, Canada H7N 4Z3 phone: (514) 687-5010, ext. 4636 fax: (514) 686-5626 ======================================== From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uunet!utcsri!utzoo!mes From: mes@zoo.toronto.edu (Mark Siddall) Subject: Re: ANNOUNCEMENT : TREECON 3.0 for comfortable phylogeny ! Message-ID: Date: Fri, 3 Jun 1994 20:54:30 GMT References: <1994Jun2.183857.16852@midway.uchicago.edu> Organization: U of Toronto Zoology Lines: 24 In article schwarze@starbase1.caltech.edu (Erich Schwarz) writes: >--Erich Schwarz > > (who actually finds Felsenstein's > arguments in favor of statistical > phylogenies way more convincing than > "Hennig-style" single-tree analyses) Well at least there's one of you. Not me. B.T.W. We call it cladistics or phylogentic systematics, and I don't know where you came up with the single-tree thing. Ever heard of multiple equally parsimonious trees? Mark P.S. Sorry Joe, not meant to be a backhanded criticism. Fine work. I just don't agree. :^) -- Mark E. Siddall "I don't mind a parasite... mes@vims.edu I object to a cut-rate one" Virginia Inst. Marine Sci. - Rick Gloucester Point, VA, 23062 From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!newsserver.jvnc.net!yale.edu!news.yale.edu!biomed.med.yale.edu!rudnick From: rudnick@biomed.med.yale.edu (Gary Rudnick) Newsgroups: bionet.software Subject: Re: oligo optimization programs Message-ID: Date: 3 Jun 94 17:33:57 GMT References: Sender: news@news.yale.edu (USENET News System) Organization: Yale University Lines: 23 Nntp-Posting-Host: rudnick.med.yale.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article k-tougu@mskcc.org (Killu Tougu) writes: >We are currently demo'ing a copy of a commercial primer optimization >program by NBI called "Oligo 4.0" that finds optimal primer sites for PCR, >sequencing, hybridizations etc. While this program seems to work pretty >nicely, we're still interested in what else is out there (and if any such >programs would actually be freebies, since cost is an issue). Also, we'd >greatly appreciate any comments on the utility and/or weaknesses of this or >other such programs. We'd appreciate your answers at the address >ktougu@mskcc.org or in this list! Wejust purchased Gene Runner for Windows from Hastings Software and it has an excellent oligo synthesis section for PCR and sequencing primers. It also does a lot of other manipulations, especially finding good sites for subcloning. Demos are available and the academic price is $400. ================================================================ Gary Rudnick |voice (203) 785-4548 Department of Pharmacology |fax (203) 785-7670 Yale University School of Medicine |bitnet RUDNICK@YALEMED 333 Cedar Street, P.O. Box 208066 |internet: New Haven, CT 06520-8066 |RUDNICK@BIOMED.MED.YALE.EDU ---------------------------------------------------------------- What separates the men from the boys is the price of their toys. From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!spool.mu.edu!torn!news.unb.ca!nbt.nbnet.nb.ca!CommSet From: holmesd@MailServ.nbnet.nb.ca Newsgroups: bionet.software Subject: Adobe Illustrator for Windows Date: Fri, 03 Jun 1994 15:37:17 Organization: NB*Net Lines: 4 Message-ID: <940603153717.211A@News.nbnet.nb.ca> NNTP-Posting-Host: holmesd.nbnet.nb.ca X-Newsreader: CommSet NewsReader Ver: 01 Rev: 0030 I am using Adobe Illustrator for Windows ver. 4.0. Is there a newer version?? tks Dave Holmes holmesd@nbnet.nb.ca From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uknet!liv!pmiller From: pmiller@liverpool.ac.uk (Dr. P.G.G. Miller) Subject: Re: Education Software Message-ID: Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: fir-13.liv.ac.uk Organization: The University of Liverpool X-Newsreader: TIN [version 1.2 PL2] References: <2sm2k0$c1v@styx.uwa.edu.au> Date: Fri, 3 Jun 1994 17:43:14 GMT Lines: 42 Andrew Hobbs (andrewh@uniwa.uwa.edu.au) wrote: : Hi, : Some time ago (last year) I saw reference to a gopher site which : contained a database of educational software; reviews, publishers etc. : I did log onto it and did some preliminary browsing but it was badly : out of date. It had the promise that it was being rewritten. In the : meantime I have lost the address, the original message and my backup, : and I can't find any indication of its existence using gopher. I think : it was in the UK somewhere. I would appreciate it if someone could help : me by giving me some directions. : Thanks in advance for any help : ********************************************************* : * * : * Andrew Hobbs * * You may have been looking at the CTI Centre for Biology's gopher on gopher.csc.liv.ac.uk, port 70. As you say, much of the info is circa 1991 though it will be updated shortly when we get some staff (we have about 0.75 of a person at present). The gopher itself is located on a machine in our local computer science dept and was not accessible 5 mins ago -- I don't know why. We (or more correctly 0.25 of I) also have a nascent W3 service which tells you a bit about what's going on in computers and education in the UK. The URL is:- http://fs2.liv.ac.uk/ctibiol.html As of a month or so hence we should have a person working full-time in this area (albeit only for a year). Regards Peter Miller CTI Centre for Biology University of Liverpool From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!columba.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.software Subject: Re: software information Date: 3 Jun 1994 17:07:51 GMT Organization: Uppsala University Lines: 12 Distribution: world Message-ID: <2sno17$mhr@columba.udac.uu.se> References: <1994Jun3.094637.1@clstac> NNTP-Posting-Host: rigel.bmc.uu.se Keywords: software information In article <1994Jun3.094637.1@clstac>, hdnguyen@csupomona.edu (HIEN NGUYEN) writes: |> can someone out there give me a list of some of the software used. The most |> popular one only please. |> |> thank you |> hien My "list" of the "most popular one": (1) MacWrite II --Gerard From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!olivea!uunet!news.claremont.edu!nntp-server.caltech.edu!fennel.bio.caltech.edu!user From: schwarze@starbase1.caltech.edu (Erich Schwarz) Newsgroups: bionet.software Subject: Re: ANNOUNCEMENT : TREECON 3.0 for comfortable phylogeny ! Followup-To: bionet.software Date: 3 Jun 1994 01:28:08 GMT Organization: Div. of Biology, Caltech Lines: 31 Distribution: world Message-ID: References: <2pl73q$j09@sun2.ruf.uni-freiburg.de> <1994Jun2.183857.16852@midway.uchicago.edu> NNTP-Posting-Host: fennel.bio.caltech.edu In article <1994Jun2.183857.16852@midway.uchicago.edu>, ecec@quads.uchicago.edu (Eric Cabot) wrote: > In article schwarze@starbase1.caltech.edu (Erich Schwarz) writes: > >In article <2pl73q$j09@sun2.ruf.uni-freiburg.de>, > >rensing@sun1.ruf.uni-freiburg.de (Stefan Rensing) wrote: > >> > >> A disadvantage is that no parsimony or maximum likelihood methods are > > ^^ ^^^^^^^^^ > >> to be run with TREECON. > > > > Boooo! ;^) > > > >--Erich Schwarz > > Geez! Smiley or not, you've got a heck of a lot of nerve to criticize > a software tool that someone has graciously made available to the scientific > community at large. Why don't you just write your own gosh-darn > parsimony program l'user? I was JOKING, dammit! JOKING! Yeesh, wotta humor-challenged newsgroup, feh. :^/ --Erich Schwarz (who actually finds Felsenstein's arguments in favor of statistical phylogenies way more convincing than "Hennig-style" single-tree analyses) From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!usenet From: clewley@wi.mit.edu (Suzanne Clewley) Newsgroups: bionet.software Subject: Re: GNU and GCC Date: 3 Jun 1994 17:00:05 GMT Organization: Massachvsetts Institvte of Technology Lines: 26 Sender: -Not-Authenticated-[5871] Distribution: world Message-ID: <2snnil$kj1@senator-bedfellow.MIT.EDU> References: <09BCB7DA02BF20293A@vxircm.IRCM.UMontreal.CA> NNTP-Posting-Host: clewley.wi.mit.edu X-Posted-From: InterNews 1.0.1@clewley.wi.mit.edu Xdisclaimer: No attempt was made to authenticate the sender's name. In article <09BCB7DA02BF20293A@vxircm.IRCM.UMontreal.CA> JOHANNE@IRCM.UMontreal.CA writes: > We are a VMS site and want to go on Unix. Many program that I want to > migrate talk about GCC and GNU for compiling. What exactly is that? Is there > any knowned user group for this kind of question. Hi. Yes you are, and in spades. VMS and Unix bear about as much resemblance as English and Chinese: they're both operating systems, but their underlying premises are completely different. GCC is the most commonly used C compiler for Unix; GNU is the source of GCC and EMACS, most peoples "favorite" Unix text editor. There are quite a few news groups for C and Unix. You might start with comp.lang.c, comp.unix.admin, comp.unix.misc (or any other comp.unix...). Since the dialects of Unix for different machines are different, you may want to check out the news group(s) associated with the type of hardware you're moving to, comp.unix.osf or comp.unix.aux, for example. I hope this helps. Suzanne Clewley clewley@wi.mit.edu From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!usc!nic-nac.CSU.net!clstac!hdnguyen From: hdnguyen@csupomona.edu (HIEN NGUYEN) Newsgroups: bionet.software Subject: software information Date: 3 Jun 94 09:46:37 PST Organization: California State Polytechnic University, Pomona Lines: 5 Distribution: world Message-ID: <1994Jun3.094637.1@clstac> NNTP-Posting-Host: vmsa.is.csupomona.edu Summary: software information Keywords: software information can someone out there give me a list of some of the software used. The most popular one only please. thank you hien From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!agate!library.ucla.edu!psgrain!ticsa.com!ucthpx!pc8.mmi.uct.ac.za!bbabb From: bbabb@medmicro.uct.ac.za Newsgroups: bionet.software Subject: Looking for MS-Windows sequence entering program Date: Fri, 3 Jun 1994 11:06:46 Organization: University of Cape Town Lines: 8 Message-ID: NNTP-Posting-Host: 137.158.128.186 X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] I am looking for a sequence entering program for Windows that has a) re-definable keys b) check mode If there are any programs available please let me know Thank you Brendan From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!wupost!medicine.wustl.edu!medicine.wustl.edu!usenet From: HAVILAND@KIDS.WUSTL.EDU (David L. Haviland, Ph.D.) Newsgroups: bionet.software,bionet.molbio.methds-reagnts Subject: Re: Looking for OSP - a primer application Date: 3 Jun 1994 15:25:35 GMT Organization: Washington University School of Med. Lines: 45 Distribution: world Message-ID: <2sni1fINNk76@medicine.wustl.edu> References: <199406031154.EAA12702@net.bio.net> NNTP-Posting-Host: kids2.wustl.edu X-News-Reader: VMS NEWS v1.25 In-Reply-To: mike@BISON.LIF.ICNET.UK's message of 3 Jun 1994 04:54:46 -0700 Xref: biosci bionet.software:8381 bionet.molbio.methds-reagnts:14898 In <199406031154.EAA12702@net.bio.net> mike@BISON.LIF.ICNET.UK writes: > I would greatly appreciae any information on an application called OSP > that chooses PCR and sequencing primers. > > Thanx in advance for your help. > > ************************************************************************** > *Michael Mitchell * "Smoke me a kipper, I'll be back for * > *User Support * breakfast!" * > *Molecular Biology Software * * > *Imperial Cancer Research Fund * Ace Rimmer, Test Pilot Extrordinaire * > *+44 (0)71 269 3115 * Red Dwarf V, BBC TV * > ************************************************************************** Mike: Try this: To one and all - here is the FAX number and address by which to obtain the OSP oligo software. (E-mail request won't do it!) In your request you *MUST* state what format you need (PC,VMS, maybe MAC and unix), you will not distribute to 3rd parties, sell for profit and the usual freeware/shareware obligations. A description of the program appears in PCR Methods and Applications 1:124-128 (1991). Hope this helps. David haviland@kids.wustl.edu --------------- Addresses: FAX: 314-286-1810 Snail mail: LaDeana Hillier Genome Sequencing Center Washington University School of Medicine 4444 Forest Park Avenue St. Louis, MO 63108 USA ---------- From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!menzies.su.edu.au!garry From: garry@menzies.su.edu.au (Garry Myers) Newsgroups: bionet.software Subject: Re: Looking for OSP - a primer application Date: 3 Jun 1994 06:09:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net In article mike@bison.lif.icnet.uk (Mike Mitchell) writes: >I would greatly appreciae any information on an application called OSP >that chooses PCR and sequencing primers. >Thanx in advance for your help. Hi Mike, OSP is the Oligo Selection Program by LaDeana Hillier and P. Green of Washington Uni. St Louis. It's free but you have to sign a licence agreement beforehand. LaDeana's email address is - lfw@elegans.wustl.edu. or by regular mail - Washington University Medical School Department of Genetics Box 8232 4566 Scott St Louis, MO 63110 USA I've used it and am quite satisfied with the results; I think it is heavily used for selection of sequencing primers for the nematode sequencing project and selection of PCR primers for YAC/STS human genome project so its credentials are quite good :) Hope this helps. Cheers Garry. From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!IRCM.UMontreal.CA!JOHANNE From: JOHANNE@IRCM.UMontreal.CA Newsgroups: bionet.software Subject: GNU and GCC Date: 3 Jun 1994 05:34:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <09BCB7DA02BF20293A@vxircm.IRCM.UMontreal.CA> NNTP-Posting-Host: net.bio.net Good morning This might the be the right user group but may be someone can give me a hit where to get the information. We are a VMS site and want to go on Unix. Many program that I want to migrate talk about GCC and GNU for compiling. What exactly is that? Is there any knowned user group for this kind of question. Thank you ___________________________________________________________________________ Johanne Duhaime tel (514)987-5556 Institut de recherches cliniques de Montreal fax (514)987-5644 Johanne@ircm.umontreal.ca ___________________________________________________________________________ From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!BISON.LIF.ICNET.UK!mike From: mike@BISON.LIF.ICNET.UK (Mike Mitchell) Newsgroups: bionet.software Subject: Looking for OSP - a primer application Date: 3 Jun 1994 04:54:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406031154.EAA12702@net.bio.net> NNTP-Posting-Host: net.bio.net I would greatly appreciae any information on an application called OSP that chooses PCR and sequencing primers. Thanx in advance for your help. ************************************************************************** *Michael Mitchell * "Smoke me a kipper, I'll be back for * *User Support * breakfast!" * *Molecular Biology Software * * *Imperial Cancer Research Fund * Ace Rimmer, Test Pilot Extrordinaire * *+44 (0)71 269 3115 * Red Dwarf V, BBC TV * ************************************************************************** From owner-software@net.bio.net Thu Jun 02 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!spool.mu.edu!agate!violet.berkeley.edu!xtang2 From: xtang2@violet.berkeley.edu (Comrade Richard) Newsgroups: bionet.software Subject: LOD score calc Date: 3 Jun 1994 17:01:21 GMT Organization: University of California, Berkeley Lines: 6 Message-ID: <2snnl1$2bo@agate.berkeley.edu> NNTP-Posting-Host: violet.berkeley.edu Hi, Does anybody have a short program in C or C++ to calculate LOD score? Thanks. -Richard From owner-software@net.bio.net Fri Jun 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!doc.ic.ac.uk!lyra.csx.cam.ac.uk!pipex!uknet!gdt!aber!gepasi.dbs.aber.ac.uk!prm From: prm@aber.ac.uk (Pedro Mendes) Subject: Re: bioinformatics definition Message-ID: Lines: 23 Sender: news@aber.ac.uk (USENET news service) Nntp-Posting-Host: pcfchb.dbs.aber.ac.uk Organization: The University of Wales Aberystwyth X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] References: <4085@CAMVAX.CINECA.IT> <594133437wnr@gardner.demon.co.uk> Date: Fri, 3 Jun 1994 10:14:23 GMT steve@gardner.demon.co.uk (Steve & Rowan Gardner) writes: >For what its worth, the best I could come up with for my thesis was.... >Bioinformatics is the field that marries computational information >management techniques with an understanding and appreciation >of the significance of biological data. Bioinformatic databases store, >retrieve, manipulate and correlate biological data from diverse >sources, providing efficient and flexible scanning tools to identify >biologically significant similarities. Why is it that most people relate computers in biology to database management and sequence analysis? There is a lot more being done with computers in biological sciences. I spend my time modelling steady-state and dynamic behaviour of biochemical systems. This equates to a lot of processor time solving differential equations and then using the computer to analyse the simulated data (plotting, etc.). Very similar applications (also modelling and solving diff. equations) are made by ecologists, population biologists and others (yes, _even_ some molecular biologists think quantitatively, although a small minority). Pedro Mendes prm@aber.ac.uk From owner-software@net.bio.net Fri Jun 03 23:00:00 1994 Path: biosci!agate!library.ucla.edu!csulb.edu!paris.ics.uci.edu!news.claremont.edu!nntp-server.caltech.edu!fennel.bio.caltech.edu!user From: schwarze@starbase1.caltech.edu (Erich Schwarz) Newsgroups: bionet.software Subject: Re: ANNOUNCEMENT : TREECON 3.0 for comfortable phylogeny ! Followup-To: bionet.software Date: 4 Jun 1994 02:48:35 GMT Organization: Div. of Biology, Caltech Lines: 23 Distribution: world Message-ID: References: <1994Jun2.183857.16852@midway.uchicago.edu> NNTP-Posting-Host: fennel.bio.caltech.edu In article , mes@zoo.toronto.edu (Mark Siddall) wrote: > We call it cladistics or phylogentic systematics, and I don't > know where you came up with the single-tree thing. Ever heard of > multiple equally parsimonious trees? Yes. I was thinking of situations where there is in fact one single most parsimonious tree. As I understand the debate, one either can consider that tree to have a probability of effectively 100% (which I think is the cladistics position) or try to assign it some other probability (which I understand to be Dr. Felsenstein's position.) Of course I may have gotten it wrong -- in fact cladistics may assign a less-than-100% value to the probability of the most parsimonious tree, or to the sum of probabilities of the equally most parsimonious trees... Or the entire debate may be about something else altogether. --Erich Schwarz From owner-software@net.bio.net Fri Jun 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!library.ucla.edu!csulb.edu!csus.edu!netcom.com!delgene From: delgene@netcom.com (Angelo Delegeane) Subject: Re: bioinformatics? Message-ID: Organization: NETCOM On-line Communication Services (408 261-4700 guest) X-Newsreader: TIN [version 1.2 PL1] Date: Sat, 4 Jun 1994 05:06:58 GMT Lines: 28 In article <2rqmhp$a9@mserv1.dl.ac.uk> Guy Tremblay wrote: : Hi net fans! : I would like to have some hints on the future of computing : related to biology. I am an undergraduate student at UQAM and I am : strongly interested in computer applications, but I am not sure of the : market's practical needs. Do you think that IBM PCs will overwhelm UNIX : hold on scientific applications? Where could I find some documentation? : Information on biocomputing graduate studies? : Thanks in advance... : Being involved in Bioinformatics, I can tell you that if you are going to depend on an IBM PC to help you, you'll find that the bioinformatics world is going to pass you by in a flash. With the improvements being made in chip technology today and in the near future and with the incredible amount of information that is being derived and managed, UNIX operating systems are the only ones that will be able to handle the incredible load. Sure, Apple has been working on scripting languages but they don't compare to the power of the shell scripts that can be written and are still to slow. You might write to the DOE and the Human Genome Project to learn of the current advances that are being made in bioinformatics and sequencing technology. Good luck!! Angelo Delegeane Incyte Pharmaceuticals, Inc. From owner-software@net.bio.net Fri Jun 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!spool.mu.edu!torn!utnut!utzoo!mes From: mes@zoo.toronto.edu (Mark Siddall) Subject: Re: ANNOUNCEMENT : TREECON 3.0 for comfortable phylogeny ! Message-ID: Date: Sat, 4 Jun 1994 05:08:21 GMT References: Organization: U of Toronto Zoology Lines: 46 In article schwarze@starbase1.caltech.edu (Erich Schwarz) writes: > > I was thinking of situations where there is in fact one single most >parsimonious tree. As I understand the debate, one either can consider >that tree to have a probability of effectively 100% (which I think is the >cladistics position) or try to assign it some other probability (which I >understand to be Dr. Felsenstein's position.) > > Of course I may have gotten it wrong -- in fact cladistics may assign a >less-than-100% value to the probability of the most parsimonious tree, or >to the sum of probabilities of the equally most parsimonious trees... > > Or the entire debate may be about something else altogether. > > >--Erich Schwarz This is likely no longer the correct forum for this so I'll be mercifully short... Cladists do not assign probabilities to their most parsimonious tree(s) except that they contend that by being most parsimonious, they are more likely than those that are less parsimonious. The most ardent of us would suggest that ALL equally parsimonious tree are equally well supported. We start getting into grey area here when one considers the criterion of choice by cladists to be more like goodness of fit, and, unless I am mistaken, the criterion of maxlik (Felsenstein) to be based more on confidence than g-o-f. I have yet to hear a compelling argument for something with a worse fit to the data having a better p-value than something with a better fit but then I don't claim to fully (or perhaps even partially) understand maximum liklihood. That wasn't at all short.. sorry. Wanna move this to sci.bio.evolution or bionet.molbio.evolution??? Or maybe just drop it? Mark -- Mark E. Siddall "I don't mind a parasite... mes@vims.edu I object to a cut-rate one" Virginia Inst. Marine Sci. - Rick Gloucester Point, VA, 23062 From owner-software@net.bio.net Fri Jun 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!uunet!nwnexus!krel.iea.com!comtch!wayneb From: wayneb@comtch.iea.com (Wayne Barnhart) Newsgroups: bionet.software Subject: cdroms Date: 4 Jun 1994 02:47:42 GMT Organization: CompuTech, Spokane WA Lines: 4 Message-ID: <2soq0e$a42@krel.iea.com> NNTP-Posting-Host: comtch.iea.com X-Newsreader: TIN [version 1.2 PL1] Is there a listing or catalog of cdrom disks for biology available? Thought by now there would be plant/animal keys, journels and such. Thanks. From owner-software@net.bio.net Fri Jun 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!fauern!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: GNU and GCC Date: 4 Jun 1994 15:55:28 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 30 Message-ID: <2sq85gINN1c35@sat.ipp-garching.mpg.de> References: NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] Benoit_Hebert@IAF.UQUEBEC.CA wrote: : JOHANNE@IRCM.UMontreal.CA wrote: : > This might the be the right user group but may be someone can give me a hit : > where to get the information. : > We are a VMS site and want to go on Unix. Many program that I want to : > migrate talk about GCC and GNU for compiling. What exactly is that? Is there : > any knowned user group for this kind of question. : the requirements for GCG under UNIX are available from the company. I have : lent a copy of the document to a colleague (Francois Shareck). The GCG suite : can be recompiled under UNIX without any problem. Give me a call if you have a : minute. Seems something is mixed up here. Johanne writes about GCC and GNU. GNU is a (recursive) acronym for "GNU's Not Unix" :-). This acronym is, as far as I understand it, kind of a "trademark" for the Free Software Foundation (FSF) which provides software with source code, often for free, always under a certain kind of license (the GPL = Gnu Public License). GCC is the GNU C compiler. It is available for a lot of platforms (even VMS, I think :-). Benoit talks about GCG. GCG is a software package for analyzing sequence data and has nothing to do with GNU or GCC (GCG is an acronym for "Genetics Computer Group"). --Cornelius (not a computer scientist or involved in computer maintenance). -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3795 */ /* "People are DNA's way of making more DNA." (Edward O. Wilson, 1975) */ From owner-software@net.bio.net Fri Jun 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: Kurt Schaudt Newsgroups: bionet.software Subject: Re: Reference Manager for Patents Date: 4 Jun 1994 11:37:42 +0100 Lines: 28 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2splhm$3vq@mserv1.dl.ac.uk> Original-To: biosoftware@dl.ac.uk On 3 Jun 1994, Diego M.Burrieza LU 674/90 wrote: > Dear netters, > I am posting this in behalf of my father. He works with > polymers for biomedical applications and he has lots of copies of > patents all around the office and the lab. He asked me about a way to > organize all the patents and I suggested him a Reference Manager with > an editor to edit notes. I look in my diskettes and I found a shareware > program for this (Papers, by DBF Systems). He asked me about an specific > program (DOS or Windows) to manage his patents. Have you heard about this > kind of software ? > Thanks for your time. And thanks for your help. > > > Diego M. Burrieza > Analytical Chemistry Dept. > Faculty of Exact and Natural Sciences > University of Buenos Aires > ARGENTINA > InterNet: bd4a@zorzal.dc.uba> > > "Papyrus" is capable in doing that. Kurt Schaudt From owner-software@net.bio.net Fri Jun 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!rutgers!mbcl!babcock From: babcock@mbcl.rutgers.edu Newsgroups: bionet.software,bionet.xtallography Subject: Nucleic Acid Structure Analysis Software Release Message-ID: <3478.2deb7975@mbcl.rutgers.edu> Date: 31 May 94 21:52:53 GMT Lines: 94 Xref: biosci bionet.software:8395 bionet.xtallography:952 Please: if you know someone who can use the program, forward a copy of this message to them. ANNOUNCING THE RELEASE OF A PROGRAM WHICH ANALYSES NUCLEIC ACID CRYSTALLOGRAPHIC COORDINATE DATA ACCORDINATE TO THE EMBO GUIDELINES OF 1988. Several years ago, the European Molecular Biology Organization published guidelines defining how nucleic acid duplex structures can be examined. The guidelines defined three rotational and three translational parameters between the bases comprising a base pair as well as from one base pair to the next. There are five programs readily distributed in order to perform the calculations. We are releasing a sixth which was created to be able to handle not only the calculations of normal duplexes, but also comparably examine mispaired bases, hoogstein base pairs, looped out bases, a single base adjacent to a base pair, intercalated drugs for which a coordinate frame has been defined, etc. The nucleic acid structure analysis program is written in Fortran and runs in a UNIX or VMS environment (please specify preference). The program calculates all of the rotational and translational parameters for complementary base pairs, neighboring base pairs in Cartesian and helical coordinate frames, and base to base Cartesian and helical parameters along each strand. A simple interactive user interface allows for one to specify what file is examined and which parameters to calculate. The program was designed so that the user needs to spend a minimal time reading the documentation in order for the program to run. Full disclosure of the mathematics has been made and published so that the user can readily understand what their parameters mean. The mathematics are unique for this type of calculation and aviod many of the problems previously encountered. In particular, the calculations are performed by a single rotation not sequential rotations avoiding the use of a midway coordinate frame for rotational parameter calculations. This ensures that the magnitude of the rotational parameters is strand free and direction free. Because a single rotation is used, the equations for each rotational parameter are equivalent, therefore, a 5 degree rotation about the X axis is equivalent to a 5 degree rotation about either the Y or the Z axis. This is not always true of other mathematical formulations presently being used. The mathematics used for calculating the complementary base parameters is identical to the math used to calculate the neighboring base/base pair parameters except that different axes are involved. This is not generally the case of the other available programs. In addition, since the calculations are bases upon local considerations, the value of the parameter depends on only the bases involved and are independent of adjacent bases. This allows for more accurate comparison of parameters from one structure to another. Copies of the code can be acquired by e-mailing me at: Marla@Rutchm.Rutgers.edu. Dr. Marla Babcock Dept of Chemistry Rutgers University P.O. Box 939 Piscataway, N.J. U.S.A 08855 Useful References: A users guide to the programs is provided in the paper: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: A Users Guide to a Collection of New Analysis Programs," Journal of Biomolecular Structure and Dynamics, Vol. 11, No. 3, pp 597-628, 1993. The issues surrounding the definition of nucleic acid structure parameters and how we address these issues are discussed in: Babcock, M.S., and Olson, W.K., "A New Program for the Analysis of Nucleic Acid Structure Interpretation," in Computation of Biomolecular Structures: Achievements, Problems, and Perspectives, Soumpasis, D.M., and Jovin, T.M., Eds., Springer-Verlag, Heidelberg, pp 65-85, 1993. The mathematical definitions of the nucleic acid structure parameters and the methods used to calculate them are presented in: Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid Structure Analysis: Mathematics for Local Cartesian and Helical Structure Parameters That are Truly Comparable Between Structures," Journal of Molecular Biology, Vol. 237, pp 125-156, 1994. In order to take into account base-stacking effects and other physical constraints, the mathematical definitions we have developed contain parameters called "pivot points", which are the points about which the bases in a structure buckle, propeller twist, and open. The statistical analyses that were performed to determine the optimum positions of the pivot points are presented in: Babcock, M.S., and Olson, W.K., "The Effect of Mathematics and Coordinate System on Comparability and 'Dependencies' of Nucleic Acid Structure Parameters," Journal of Molecular Biology, Vol. 237, pp 98-125, 1994. From owner-software@net.bio.net Sat Jun 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!doc.ic.ac.uk!uknet!EU.net!uunet!newsflash.concordia.ca!CC.UMontreal.CA!cumin.telecom.uqam.ca!UQuebec.CA!Benoit_Hebert From: Benoit_Hebert@IAF.UQUEBEC.CA () Subject: Re: GNU and GCC Sender: news@UQuebec.CA (news) Message-ID: Date: Sun, 5 Jun 1994 03:44:15 GMT References: <2sq85gINN1c35@sat.ipp-garching.mpg.de> Nntp-Posting-Host: panoramix.uqss.uquebec.ca Organization: Universite du Quebec X-Newsreader: TIN [version 1.2 PL2] Lines: 14 Cornelius Krasel (krasel@alf.biochem.mpg.de) wrote: > Benoit_Hebert@IAF.UQUEBEC.CA wrote: > : JOHANNE@IRCM.UMontreal.CA wrote: > Seems something is mixed up here. Johanne writes about GCC and GNU. GNU is > a (recursive) acronym for "GNU's Not Unix" :-). > Benoit talks about GCG. GCG is a software package for analyzing sequence > data and has nothing to do with GNU or GCC (GCG is an acronym for "Genetics > Computer Group"). kind of obvious... I'll increase the contrast on my laptop screen and will try to stop reading while drinking coffee. That should do it (!). Benoit From owner-software@net.bio.net Sat Jun 04 23:00:00 1994 Newsgroups: bionet.software From: steve@gardner.demon.co.uk (Steve & Rowan Gardner) Path: biosci!agate!usenet.ins.cwru.edu!gatech!swrinde!pipex!uknet!demon!gardner.demon.co.uk!steve Subject: Re: bioinformatics definition References: <4085@CAMVAX.CINECA.IT> <594133437wnr@gardner.demon.co.uk> Distribution: world Organization: Myorganisation Reply-To: steve@gardner.demon.co.uk X-Newsreader: Newswin Alpha 0.4 Lines: 25 Date: Sun, 5 Jun 1994 22:19:17 +0000 Message-ID: <90400476wnr@gardner.demon.co.uk> Sender: usenet@demon.co.uk In article: prm@aber.ac.uk (Pedro Mendes) writes: > > > Why ic it that most people relate computers in biology to database management > and sequence analysis? There is a lot more being done with computers in > biological sciences. I spend my time modelling steady-state and > dynamic behaviour of biochemical systems. This equates to a lot of processor > time solving differential equations and then using the computer to analyse the > simulated data (plotting, etc.). > > Very similar applications (also modelling and solving diff. equations) are > made by ecologists, population biologists and others (yes, _even_ > some molecular biologists think quantitatively, although a small minority). > > Pedro Mendes > prm@aber.ac.uk > > Sure there's lots that you, I and the rest of the world do with computers in biology, but the original question asked for a definition of bioinformatics, not computational biology ! Steve Gardner From owner-software@net.bio.net Sat Jun 04 23:00:00 1994 Path: biosci!agate!ames!lll-winken.llnl.gov!fastrac.llnl.gov!osi-east2.es.net!pnl-oracle!netnews.nwnet.net!news.u.washington.edu!evolution!joe From: joe@evolution.u.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: ANNOUNCEMENT : TREECON 3.0 for comfortable phylogeny ! Followup-To: bionet.molbio.evolution Date: 5 Jun 1994 03:58:35 GMT Organization: University of Washington, Seattle Lines: 10 Message-ID: <2srihb$ei1@news.u.washington.edu> References: NNTP-Posting-Host: evolution.genetics.washington.edu Summary: We're moving ... Keywords: parsimony, likelihood, cladistics, phylogenetic systematics In article mes@zoo.toronto.edu (Mark Siddall) writes: >In article schwarze@starbase1.caltech.edu (Erich Schwarz) writes: [deleted] I have written a fairly long reply to Mark's reply to Erich and put it on bionet.molbio.evolution. Let's move the discussion there. ----- Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195 Internet: joe@genetics.washington.edu (IP No. 128.95.12.41) From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!europa.eng.gtefsd.com!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!quartz.ucs.ualberta.ca!mac13.biochem.ualberta.ca!user From: keith@bones.biochem.ualberta.ca (Keith Robinson) Newsgroups: bionet.software Subject: Re: Mac C compiler software Followup-To: bionet.software Date: Mon, 06 Jun 1994 14:10:48 -0800 Organization: Dept. of Biochemistry, The U. of Alberta, Edmonton Ab Canada Lines: 54 Distribution: world Message-ID: References: <199406030958.CAA07833@net.bio.net> NNTP-Posting-Host: mac13.biochem.ualberta.ca In article <199406030958.CAA07833@net.bio.net>, A.Cox@rbgkew.org.uk (Tony Cox) wrote: > Can anyone recommend a good C compiler for the Mac. I've done a bit of stuff > on a PC + Windows but never on a Mac. Am I going to be in for a big surprise > in making the transition? Symantec's Think C compiler was my choice for a mac C compiler, mostly because it's inexpensive. It's great value for the money - a lot of people seem to do small and large programming projects with it. If you've used Borland's TurboC compilers on DOS, then you won't be on foreign territory with Think C. Apple also produces a C compiler for the mac (MPW), but it's cost was well above what I wanted to spend for learning programming on the mac. MetroWorks CodeWarrior is the newest kid on the compiler block. Lots of people on comp.sys.mac.programmer have good things to say about it, and pricing is competive with Symantec's. Try asking this question on comp.sys.mac.programmer and see what opinions you get. > Also, are there any good introductory books to Mac C programming? Yep. Have a look for "Macintosh C Programming Primer, Vol I, 2nd Edition" by Dave Mark and Cartwright Reed (Addison-Wesley, 1992) or "Macintosh Programming Techniques" by Dan Parks Sydow (M+T Books, 1994). I've got both, and either one would be a good place to start. The Mark and Reed book also has a sequel, aptly called "Macintosh C Programming Primer, Vol II" which covers more advanced topics in macintosh programming. You may also want to have browse through "How to Write Macintosh Software" by Scott Knaster (Addison-Wesley, 1992), though I think it's aimed at a more advanced level of programming. Both the Mark & Reed and the Sydow book are available with disks with all the code, but I find you learn more about the topic typing it all in yourself. You'll also need to pick up some of the volumes of Apple's programmer's reference "Inside Macintosh" - the volume "ToolBox Essentials" is a good starting point. If you've got a CD-ROM drive, a cheap way to get your hands on Inside Macintosh is to buy a back issue of 'develop' (Apple's developer magazine) from the Apple Professional Developer's Assn (APDA, email to apda@applelink.apple.com). Included with the magazine is the BookMark CD, which has formatted copies of the complete Inside Macintosh series, as well as lots of other useful stuff. Best $15 I've spent yet on programming tools. Keith -- Keith Robinson Dept. of Biochemistry keith@bones.biochem.ualberta.ca The University of Alberta Edmonton, Alberta Canada ........................................................ "The information highway is like teenagers and sex - all talk, but no action." From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!purdue!news.bu.edu!taco.cc.ncsu.edu!cc02du.unity.ncsu.edu!cjones From: cjones@unity.ncsu.edu (Chris Jones) Newsgroups: bionet.software Subject: Field/Lab Acquisition Software Date: 6 Jun 1994 21:23:50 GMT Organization: North Carolina State University Lines: 12 Message-ID: <2t0456$mnl@taco.cc.ncsu.edu> NNTP-Posting-Host: cc02du.unity.ncsu.edu X-Newsreader: TIN [version 1.2 PL2] I'm a grad student at N.C State University. Recently I've been involved in the development of Windows based standardized acquisition software for several environmental firms. This led me to wonder if there were similar products or needs for biologist in the field or the labs? What type of software is available to the scientific community? Is it Windows based? Is it user friendly and does it follow a Federal or State reporting standard? Any information regarding the types and avaiability of this type of software would be greatly appreciated. I'm particullarly interested in Federal Reporting requirements and standards. Thanks in advance, Chris From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Subject: Re: Mac C compiler software Message-ID: Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu Organization: Biology, Indiana University - Bloomington References: <199406060843.BAA11807@net.bio.net> Date: Mon, 6 Jun 1994 12:44:15 GMT Lines: 39 Symantec's "Think C" and C++ integrated development enviroment is the most commonly used Mac compiler. It is similar to Borland's MS Windows C/C++ i.d.e. I prefer the Mac/Symantec i.d.e. for my main work. Another Mac C/C++ i.d.e. to seriously consider is MetroWerk's CodeWarrior. They are new but have gotten lots of good comments (Symantec has a history of shipping somewhat buggy programs). CodeWarrior currently has versions for PowerPC as well as 68000 code while Symantec's doesn't yet support PowerPC (unless I missed an upgrade notice). CodeWarrior may be a bit faster also. The third commonly available Mac development environment is Apple's MPW workshop, which includes C, C++ and a few other options. Stay away from this one -- it when from being the best Mac dev. platform several years back to the worst currently (very slow, recent advancements are almost nil, although there is a PowerPC development kit for it). Sorry I don't have addresses for these products, but they are available thru usual Mac mailorder software companies like MacWarehouse & MacConnection (see ads in back of mac magazines). I don't have any suggestions for books. -- don Oh, here is part of a Metrowerk's info-ad. You can e-mail them at Ron Liechty mwron@aol.com Metrowerks Inc. For International orders, Educational discounts: BookMasters U.S./Canada: 1-800-247-6553 International: 1-419-281-1802 Fax No.: 1-419-281-6883 Educational pricing is: Gold $99.00 US, Silver $79.00, US Bronze $59.00 US (gold==powerpc & 68000 versions, silver==powerpc only,bronze==68K only) -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!phylo!scott From: scott@phylo.life.uiuc.edu (Scott Howard) Newsgroups: bionet.software Subject: Re: Mac C compiler software Date: 6 Jun 94 13:40:03 GMT Organization: University of Illinois at Urbana Lines: 16 Message-ID: References: <199406060843.BAA11807@net.bio.net> NNTP-Posting-Host: phylo.life.uiuc.edu Dave Mark has at least three books out on the subject. The material covered is adequate, but half of the book is filled with source code listings that you have to type in yourself. Worse yet, a good deal of the code has errors in it. You can send in for a code disk, but turnaround time for actually getting the disk is about three months, if the experiences of coworkers is any indication. There is a better book out by Thom Hogan covering the basics of C programming on the Mac. Source code disk included. Both books suffer from their dependence on THINK C/Symantec. CodeWarrior from Metrowerks is superior to Symantec's product(s) in terms of price, compilation speed, and speed & stability of code generated. However, there are no current editions of 'How to' books that utilize the CodeWarrior development system as of this writing. From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rhubner Newsgroups: bionet.software Subject: "PC-Rare" for PC and Mac//oligo optimization Message-ID: <1994Jun6.091649.1@molbiol.ox.ac.uk> From: rhubner@molbiol.ox.ac.uk Date: 6 Jun 94 09:16:49 GMT Organization: Oxford University Molecular Biology Data Centre Nntp-Posting-Host: oxpath Nntp-Posting-User: rhubner Lines: 8 hi there, anybody used "PC-Rare" for PCR optimization? It's quite recent (copyright 1993), but sounds excellent at least for diagnostic work ... uses octamer frequency disparity to select primers that are specific for target (only!)... 'host' genomes available are yeast, fly, rodent, man, E. coli (their sequence data is sufficiently well known for constructing the comparison table for octamers...) Greetings, Roland From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: kulmburg@sun1.ukl.uni-freiburg.de (Peter Kulmburg) Newsgroups: bionet.software Subject: Slide writer answers Date: 6 Jun 1994 10:25:36 +0100 Lines: 186 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2suq2g$2d6@mserv1.dl.ac.uk> X-Sender: kulmburg@skl1.ukl.uni-freiburg.de Original-To: bio-software@dl.ac.uk Dear netters, here are the answers I got from my call for help with Macs and slide writers. I am trying to get started soon, thank you all for your help. I hope it is not against the netticette to reposte answers to mail, if so, I apologize Peter From: epstein@gold.nlm.nih.gov (Jonathan Epstein) > I would be happy to get some direct answers, if not possible, please give > me the addresses of other newsgroups to whom I could ask my questions. Try mac.comp.scitech. Good luck! - Jonathan From: "Brian Halligan" We use a LaserGraphics Personal LFR system. It connects as a SCSI device and is a 'chooser' level printer, ie. choose the slide maker as the printer and print. It can be connected to both a PC and Mac simultaniously. Polaroid makes a similar system, but the resolution of the LaserGraphics unit is better. Brian D. Halligan halligan@post.its.mcw.edu Assistant Professor 414-257-8413 (voice) Department of Microbiology 414-257-8427 (FAX) Medical College of Wisconsin From: "Cliff Beall" Dear Peter, I saw a demo of a Polaroid system that had a "Chooser" printer driver so you could print from any program. I'm not sure about the networking abilities, but you could check with them. Yours, Cliff Beall Research Scientist Ohio State Biotechnology Center beall.3@osu.edu From: "thomas john ryan" Organization: University of Chicago I work for a company that does this sort of thing every day. They are a distributor for the software/hardware that you would need. I can forward a toll-free USA telephone number if you wish or could have a fax sent to you if you forward me your fax number. Thanks Tom Ryan From: " (Brian Robertson)" There is a chooser level device such a s you describe - MacRascol - for use witht the LaserGraphics machine. The old LaserGraphics did not handle PostScript, but I believe the new one does, but I think it it is expensive. There is a dealer in Deutschland, VTE I think, but I suggest you contact Juergen Loeschinger at the Max-Planck in Tuebingen, Schwabenland, where I used to work. They have a LaserGraphics LFR and he should be able to tell more you more about how it works, as well as the details of the dealer. Wiederschauen! Brian >From derda@dogwood.botany.uga.edu Wed Jun 1 20:40:59 1994 Peter, We have a few slidemakers (Polaroid, LaserGraphics) here in the Department of Botany, University of Georgia (USA). Both brands come with Mac SCSI and PC connectors (Polaroid is LPT, other is dedicated card w/ cable for PC). Regardless of the platform, there is software with each that allows you to install drivers on other machines, then while on those machines (say a Mac), pick the driver from chooser, print to it from you application, and it will make PS files that you then take to the Mac with the slidemaker - at that Mac, you copy the files into a specified print queue folder, and tell it to print. The Polaroid model is the easiest to use. I think it cost about $8,000 US. Let me know if you need more info. Greg >From cummins@possum.murdoch.edu.au Thu Jun 2 02:22:18 1994 I've been making slides for some years using PowerPoint (now up to version 3.0). You can also use Aldus Persuasion. I don't know of any way to produce slides directly from the system-it would be nice. Even through PP one needs intermediate software to queue the images through a slide maker. Yours, virtually Jim Cummins From: "GEORGE HOLT, ICRF, LONDON, UK" tor which is not a postscript level programme. Using an intermediate piece of queueing software is common practice with film recorders, chooser level drivers as you seem to want are quite rare. I once had a Montage with a chooser driver but it never seemed to work. I can't speak from personal experience with the ImagePro but don't write off postscript until you've checked out third party software like Freedom of Press and Professional Output Manager which offer postscript and may well include drivers to support the ImagePro. Both packages come in various grades, 'lite' to high end film recorder, depending on the drivers you require. I would guess the ImagePro to be a low end film recorder, compared to the Solitare bureau film recorders, so you should be able to get away with a cheap version. Freedom of Press, I think, does postscript only but VBS Professional Output Manager handles PICT, Scrapbook, EPS and Postscript. Also have a look at the Lasergraphics range, the software that comes with them may have some ps support and a chooser driver is always worth asking about. We have a Management Graphics Sapphire film recorder and use the hideously expensive version of Professional Output Manager to drive it. The latest version has the ability to nominate an appleshare folder into which networked contributers may dump images for slidemaking. When you start POM it will look in this folder and automatically image anything it can in it. This is about as close as you come to networking the film recorder. With our setup images are generated all over the organisation, using Persuasion, Macdraw etc., and transferred to me either by sneakernet (floppy discs) by appleshare or occaisionally by ftp. I collate them onto queues and return the finished slides by post. These files can be pict, scrapbook, eps or postscript and come from macs, pcs and various flavours of unix machines. The system generally works well without the need for direct network access to the film recorder. From: "Howard Thistlewood, Agriculture Canada" Peter: If you have any helpful replies to your request please post a summary on the net or I would appreciate if copies were forwarded to me. We have a system linking VAX and IBM PCs through a file server and I would like to get Macs hooked up more directly or easily. Presently, on the Mac side we use PlotterGeist from Palomar software which can be used with any software package as it is reached through the print command as a chooser-selectable driver. PlotterGeist saves the output as an HPGL file, and it is then sent through our VAX/PC network to the film plane recorder, which accepts Laser Language and HPGL file formats. PlotterGeist Palomar Software Inc. 2964 Oceanside Blvd. Suite D Oceanside, California 92054 Palomar@applelink.apple.com From: "Robin Beech" I have recently bought the Colorfast II system which connects to the Mac via the SCSI interface and prints high quality colour slides at about one every 4 minutes. The computer sees it as a generic printer which understands postscript so any application can print directly. The system can be set up so that the Mac it is connected to talks to the others via a network and acts as a print server so every one can print. If you need the details of the system let me know. Peter KULMBURG (193.196.226.110 MacName: ktl110.ukl.uni-freiburg.de) home: Tel./Fax:+49 761 808439 work: Tel.:+49 761 270/7195 Fax:/7177 From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!rbgkew.org.uk!A.Cox From: A.Cox@rbgkew.org.uk (Tony Cox) Newsgroups: bionet.software Subject: Mac C compiler software Date: 6 Jun 1994 01:43:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406060843.BAA11807@net.bio.net> NNTP-Posting-Host: net.bio.net Can anyone recommend a good C compiler for the Mac. I've done a bit of stuff on a PC + Windows but never on a Mac. Am I going to be in for a big surprise in making the transition? Also, are there any good introductory books to Mac C programming? Thanks From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: bioinformatics definition Message-ID: <1994Jun6.180936.1805@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <4085@CAMVAX.CINECA.IT> <90400476wnr@gardner.demon.co.uk> <1994Jun6.183827.171275@eros.embl-heidelberg.de> Date: Mon, 6 Jun 1994 18:09:36 GMT Lines: 30 Christos Ouzounis (ouzounis@embl-heidelberg.de) wrote: : Sorry, but I would be very interested to know what's the difference between what you : call bioinformatics and computatinoal biology (!). ... confusion here... I call my unit 'biocomputing'. Is this a subset or a superset of both bioinformatics and computational biology ? :-) Seriously, the biggest problem is that there's no curriculum in either of them. What about confessing that there are computer people trying to learn biology and biology people trying to learn informatics. It might be difficult to apply Mendelian laws here - (a bioinformatics person is derived from informatics and a computational biologist is a person derived from the biology side, according to grammar books) but for me all the terms mean the same - an interdisciplinary approach to do research in a synergy of two established science branches. Not that serious, regards Reinhard -- +---------------------------+-------------------------------------------+ | Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 | | Biocomputing | electronic Mail doelz@urz.unibas.ch | |Biozentrum der Universitaet+-------------------------------------------+ From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!gatech!newsfeed.pitt.edu!uunet!news.delphi.com!usenet From: andreib@delphi.com Newsgroups: bionet.software Subject: File Manager StepUp v.2.0 for Win3.1 & WFWG3.11 uploaded Date: Mon, 6 Jun 94 14:16:31 -0500 Organization: Delphi (info@delphi.com email, 800-695-4005 voice) Lines: 399 Message-ID: NNTP-Posting-Host: bos1b.delphi.com Hello there, I've just uploaded the following program to various FTP sites: fmstep20.zip File Manager StepUp 2.0 for Win3.1 & WFWG3.11 File Manager StepUp v.2.0 for Windows 3.1 and Windows for Workgroups 3.11 - dramatically improves File Manager. Provides standard FM's dialog boxes with additional useful elements ('history' lists, 'verify' check boxes, etc.); shows the dialogs with 3D effects; brings customizable Quick Menu and Execute Menu; allows to easily view, edit, or print arbitrary files; contains useful utilities (calculating the size of dirs including their subdirs, etc.). FM StepUp makes the File Manager an actually user friendly application. Try it - and you won't believe you worked without FM StepUp before. The way software should be! Shareware. Currently it can be found in the following places: File: fmstep20.zip FTP site Uploaded into Will appear in ------------------- ---------------------- ------------------- ftp.uu.net /tmp (same) wuarchive.wustl.edu /pub/MSDOS_UPLOADS/win (same) archive.umich.edu /msdos/UPLOADS/ /msdos/windows/util ftp.sunet.se /pub/pc/uploads /pub/pc/windows/utils It will also appear in cica, garbo, and oakland, as well as in the group comp.binaries.ms-windows (in UUE format) shortly. Long description: ----------------- This is a MAJOR upgrade to the versions 1.x. If you tried any of the previous versions of the FM StepUp and did not like it by any reason, try this one - we hope you'll change your mind! SPECIAL NOTE for those who do not like registration reminders and love to evaluate shareware for long time: unlike many other shareware producers, we are using a passive reminder in this version -- you don't have to press any key or wait for some time to turn it off. SPECIAL NOTE for Windows for Workgroups users: if you tried and had given up the FM StepUp ver.1.x because of the conflict between FM StepUp and Toolbar, please take a look at the new version. That bug has been fixed and they (FM StepUp and Toolbar) enjoy each the other now. SPECIAL NOTE for network system administrators: now you can restrict File Manager in the same way as you do it for Program Manager - through [Restrictions] section in a file. SPECIAL NOTE for registered users: thanks to your support, we have found the possibility to make the UPGRADE FROM ANY PREVIOUS VERSION OF FM STEPUP to version 2.0 FREE! If you are a registered user of the FM StepUp 1.x, you will receive new disk from us shortly. ///////////////////////////////////////////////////////////////// // Welcome to File Manager StepUp! // // the File Manager Extender // for Microsoft(R) Windows(tm) 3.1, 3.11 // and Windows for Workgroups(tm) 3.11 // // Version 2.0 // Shareware edition // // Copyright (c) 1994, ChaoSoft. // All rights reserved. // ///////////////////////////////////////////////////////////////// TABLE OF CONTENTS ----------------- 1.1. About FM StepUp 1.2. What's new in version 2.0 1.3. Features of the FM StepUp 2.0 ///////////////////////////////////////////////////////////////// 1.1 About File Manager StepUp ----------------------------- File Manager StepUp (or, briefly, FM StepUp) is a utility that dramatically improves File Manager. Instead of replacing File Manager, FM StepUp simply makes it better. When you install FM StepUp, additional commands are added to File Manager's menus, and existing commands are enhanced. FM StepUp makes the File Manager an actually user friendly application. With FM StepUp installed in your system you will perform various file management operations easier and faster. FM StepUp enhances standard dialog boxes of the File Manager, providing them with additional useful features (history lists, remembering you previous commands; 'verify' check boxes; 'browse' buttons; etc.). FM StepUp allows you to combine most frequently used commands of File Manager into Quick Menu, so that you can access them just pressing the right button of your mouse. FM StepUp makes your able to easily create, view, edit, or print arbitrary files, not necessarily associated with an application, and you can assign your favorite viewer or editor to do this. FM StepUp provides you with some unique or hard-to-find commands, allowing you, for example, to figure out the total size of a directory, including all its subdirectories; change date or time of the file; run the default screen saver whenever you want it to; etc. FM StepUp allows you to add your own commands to the File Manager and easily execute them. You may use this possibility to launch frequently used applications (such as Control Panel or Clipboard viewer) directly from File Manager menu, or to perform preprogrammed operations over files selected in a File Manager's window (UnZip or UnArj, for example). If you are a network administrator, FM StepUp can help you to restrict some of the File Manager's capabilities (in almost the same way as you do it for the Program Manager), allowing you to prevent your users from performing potentially dangerous or undesirable commands. After all, FM StepUp is highly customizable. You are in charge of almost every aspect of its functionality - from the size of the history lists to contents of the Quick Menu and Execute Menu. Try it - and you won't believe you worked without FM StepUp before. The way software should be! 1.2. What's new in the version 2.0 ---------------------------------- A LOT! New features (please see detailed list below), new documentation, new installation utility, new registration encouragement policy. No new bugs (hopefully!). The only old thing is the price. Yes, due to success of the FM StepUp ver.1.x and support of our registered users, we were able to significantly improve FM StepUp and keep the same low registration fee. 1.3. Features of the FM StepUp v.2.0 ------------------------------------ The following is the list of features the File Manager obtains after installing the FM StepUp. The signs 'NEW!' and 'UPDATED:' are used to mark new or updated features in comparison with previous versions of the FM StepUp. UPDATED: 1. 14 standard dialog boxes of the File Manager are now updated by the FM StepUp (and you are able to prevent any of them from updating, if you like!). Almost ALL the edit controls of the dialog boxes are provided with history lists keeping track of the text you typed into edit boxes. With FM StepUp you are able to recall any of them and edit it, if necessary, without typing all the text from scratch. (Before version 2.0 only a few specific dialog boxes were enhanced with the history lists). 2. The following dialog boxes: Move, Copy, and Copy Disk, are provided with the 'Verify' check boxes which enable you to easily set the verify mode on or off (with the same effect as entering command VERIFY ON/OFF at the DOS command prompt) before performing the operations. NEW! 3. The Run dialog box is supplied with two additional buttons, 'Command' and 'Argument', allowing you to browse your disks and choose a file to run or supply its filename as an argument for the command line. 4. The Move and Copy dialog boxes are provided with an additional button, 'Browse', in case you forgot the name of the directory to copy/move files in. 5. Print dialog is now provided with: 1) check box 'Copy to PRN' which makes you able to quickly print plain ASCII files, not necessarily associated with applications, or binary files obtained with using the 'Print to file' (or the like) option provided by many applications; NEW! 2) check box 'Eject', allowing you to specify whether to eject the last page or not, that is convenient for some printers; NEW! 3) edit box 'Copies', where you can specify the number of copies to make. The controls 2) and 3) above are activated and used only when using the 'Copy to PRN' mode. 6. The main menu of the File Manager is getting a new item, StepUp, containing a number of additional commands: New File - to instantaneously create a new file; View File - to view the contents of the file currently selected in the File Manager Directory Window using the Default Viewer; Edit File - to edit the contents of a selected file using the Default Editor. You are specifying the applications to be used as Default Editor and Viewer in the 'Preferences' dialog box of the FM StepUp; NEW! Execute - to perform a user-defined action on the currently selected file or to launch an application. By default it contains the following commands: Control Panel - to launch the Windows Control Panel from the File Manager; Clipboard - to run the Windows Clipboard viewer; DOS Prompt - to start the DOS session from the File Manager; PIF Editor - to run the PIF Editor; UnZip - to run the PKUNZIP utility for the currently selected file (assuming it's a ZIP archive); UnArj - to perform the 'ARJ x' command for the currently selected file (assuming it's an archive produced by the ARJ utility); You can change the commands of the 'Execute' menu, add new commands and otherwise customize it using the 'Preferences' dialog box of the FM StepUp. Special - to perform some useful operations: UPDATED: Total Size - to calculate the total length and space occupied for all the selected files and directories, including all the subdirectories; the directory to be analyzed can be selected in either Directory or Tree window of the File Manager; UPDATED: Change Date/Time - to change the date and/or time of all the selected files (not for just one file); NEW! Run Screen Saver - to launch the default Windows Screen Saver (usually specified with the Control Panel) any time you want to leave your machine (if you are using a screen saver with the password protection - you don't have to wait 5 min. to activate it!); Return to DOS, Restart Windows, Reboot System - name says it all; Preferences - to customize FM StepUp: UPDATED: - change the Default Viewer and/or Editor; you can now browse the directories to find the application you wish to use as the Default Viewer or Editor; NEW! - set up the desired way of dealing with the associated files; - specify the size of the 'history' lists; NEW! - choose the way of displaying new icon for the File Manager; UPDATED: - specify new name for the FM StepUp's menu item in the File Manager's main menu; NEW! - customize the Quick Menu; NEW! - customize the Execute Menu; UPDATED: - set up the desired appearance of the dialog boxes: (a) choose which standard dialog boxes of the File Manager (out of 14) you want to be updated by the FM StepUp (by maintaining history lists, verify check boxes, etc.); (b) specify the using the 3-D effects when displaying the controls; (c) specify the using the extended user interface when working with history lists; UPDATED:Help - to get detailed information on how to use the FM StepUp. About - to get information about the version of the FM UPDATED: StepUp and the person it's registered to (registered version only). 7. The right button of the mouse is now used to activate the Quick Menu - a set of frequently used commands, so that you don't have to spend time finding them in the File Manager's menu now. Starting from version 2.0, the Quick Menu consists of two portions: Top portion: the fixed set of the File Manager commands, collected in one place for your convenience. You UPDATED: can customize that part using the Preference dialog box. Any commands can be made easily accessible, even those created by you to be used in the 'Execute' menu; NEW! Bottom portion: the history list of the commands used. The most frequently used commands are accumulated here automatically and can be easily re-used. NEW! You can also specify the most convenient way of choosing commands from the Quick Menu - with the left or right button of mouse! UPDATED: 8. All the dialog boxes of the File Manager are now displayed with 3D effects (like that of Excel and some other applications). The bug which displayed improper 3D effects with some video drivers has been fixed. NEW! 9. FM StepUp comes with new cool icon for File Manager and you can specify its using with the Preferences dialog box; NEW! 10. For Network System Administrators: With the File Manager StepUp v.2.0 you can restrict the user's access to some of the features of the File Manager. (Microsoft has made it possible to restrict the Program Manager but somehow forgot to do it for the File Manager!) With the FM StepUp, you can place the file FMSTEPUP.SYS in the WINDOWS›SYSTEM directory, make the [Restriction] section in that file, and add the following boolean entries to it (standard rules for specifying boolean entries of the win.ini and system.ini files apply here; particularly, 1/ON/TRUE/YES can be used interchangeably to turn the mode on, 0/OFF/FALSE/NO - to turn it off): NoShowHiddenSysFiles - to disable the 'Show Hidden/System Files' check box of the 'By File Type' dialog box; NoChangeFileAttrib - to disable the 'Attributes' group of the 'Properties' dialog box (and prevent users from changing attributes of files) NoRun - to disable 'OK' button of the 'Run' dialog box and prevent users from running applications using it; NoSaveFMSettings - to prevent users from saving the current settings of the File Manager on exit; NoCloseFileManager - to prevent user from closing the File Manager (with some restrictions); NoChangeFileDateTime - to disable 'OK' button on the Change Date/Time dialog and prevent users from modifying these file attributes; NoUninstallStepUp - to prevent user from uninstalling the FM StepUp (with some restrictions); NoSaveStepUpSettings - to prevent users from saving the current settings of the FM StepUp on exit; NoCustomizeExecMenu - to prevent users from customizing the 'Execute' menu of the FM StepUp; NoCustomizeQuickMenu - to prevent users from customizing the Quick Menu of the FM StepUp; NoChangeViewerEditor - to prevent users from changing the default viewer and editor in the Preferences dialog box; For more information please see on-line Help. Thank you for trying File Manager StepUp! Uploaded by the author. Andrei Belogortseff andreib@delphi.com From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!ouzounis From: ouzounis@embl-heidelberg.de (Christos Ouzounis) Newsgroups: bionet.software Subject: Re: bioinformatics definition Message-ID: <1994Jun6.183827.171275@eros.embl-heidelberg.de> Date: 6 Jun 94 18:38:27 +0100 References: <4085@CAMVAX.CINECA.IT> <90400476wnr@gardner.demon.co.uk> Distribution: world Organization: European Molecular Biology Laboratory Lines: 16 In article <90400476wnr@gardner.demon.co.uk>, steve@gardner.demon.co.uk (Steve & Rowan Gardner) writes: > > Sure there's lots that you, I and the rest of the world do with computers in biology, > but the original question asked for a definition of bioinformatics, not computational > biology ! > > Steve Gardner > Sorry, but I would be very interested to know what's the difference between what you call bioinformatics and computatinoal biology (!). C A Ouzounis EMBL Heidelberg From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!headwall.Stanford.EDU!lyapunov.stanford.edu!user From: aberno@genome.stanford.edu (Anthony Berno) Newsgroups: bionet.software Subject: Wanted: gel and sequence data Followup-To: bionet.software Date: Mon, 06 Jun 1994 09:41:17 -0800 Organization: Genetics Department Lines: 26 Message-ID: NNTP-Posting-Host: lyapunov.stanford.edu I'm currently developing and testing software for the automatic interpretation of electrophoresis gels from fixed-detector flourescent sequencers, and it would be nice to have a wider variety of data to work with than can be found in our lab. If you have any data that you are willing to let me look at, please let me know. The sort of data I am most interested in is: 1. The data is of good enough quality that lane tracking and/or basecalling is at least theoretically possible. 2. The actual DNA sequence is known and available so that the results can be evaluated quantitatively. 3. The software you are currently using does not correctly interpret the data. 4. The file format is available so that I can read it. I'm particularly interested in data from "unconventional" machines that might use less than 4 dyes, odd chemical procedures, different dyesets, etc. Sorry, but the software is not available for distribution yet. I'm hoping to release a beta version at the Hilton Head conference. -Anthony From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!daresbury!not-for-mail From: Duncan Rouch Newsgroups: bionet.software Subject: Public and Commercial Software Disasters Date: 6 Jun 1994 17:22:19 +0100 Lines: 31 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2svifr$smu@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk Hi Netters Out of interest, I comment on part of a UK TV program shown last night, "Computer Triangle" from "The Money Program" on BBC2, about public and commercial software disasters. Imagine you wrote a program and it was beta-tested without you knowing: not so bad. Now imagine your program was an application to despatch ambulances in a major capital city.... This took place for real in London UK, October 26 1992. The new 1.5 M pounds (US$2.3 M) computer system was made the only live support for ambulance despatch while still at beta-test level. As messages on the system built up, chaos resulted as the system slowed down, ambulances were sent to the wrong places, or several of them to the same incident. This and other examples shown in the program indicate that major computing disasters are regular happenings in both the public and commercial sectors. Losses were quoted in millions of pounds, with one at 48 M pounds (US$72 M). The examples were from the UK only, but the same kinds of things are likely to be going on in other countries. The prime cause is usually management ignorance combined with bad commercial consultants. So, it might be useful if some of the computer-science know-how at universities was used in consultancies to help stop wasting all that public money on modern dinosaurs, not to mention to help the police, firebrigade and ambulance services do better jobs. Duncan Rouch New Chemistry Lab, University of Oxford, UK. From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!convex!news.duke.edu!news-feed-1.peachnet.edu!gatech!howland.reston.ans.net!wupost!kuhub.cc.ukans.edu!kuhub.cc.ukans.edu!nntp Newsgroups: bionet.software Subject: Re: oligo optimization programs Message-ID: <1994Jun6.143010.65337@kuhub.cc.ukans.edu> From: peterg@rnaworld.bio.ukans.edu (Peter Gegenheimer) Date: 6 Jun 94 14:30:09 CDT Reply-To: pgegen@kuhub.cc.ukans.edu (Peter Gegenheimer) References: Organization: Dept. Biochemistry, Univ. Kansas-Lawrence KS Nntp-Posting-Host: rnaworld.bio.ukans.edu X-Newsreader: IBM NewsReader/2 v1.00 Lines: 30 In , rudnick@biomed.med.yale.edu (Gary Rudnick) writes: >In article k-tougu@mskcc.org (Killu Tougu) writes: > >>We are currently demo'ing a copy of a commercial primer optimization >>program by NBI called "Oligo 4.0" that finds optimal primer sites for PCR, >>sequencing, hybridizations etc. While this program seems to work pretty >>nicely, we're still interested in what else is out there (and if any such >>programs would actually be freebies, since cost is an issue). Also, we'd >>greatly appreciate any comments on the utility and/or weaknesses of this or >>other such programs. We'd appreciate your answers at the address >>ktougu@mskcc.org or in this list! > >Wejust purchased Gene Runner for Windows from Hastings Software and it has an >excellent oligo synthesis section for PCR and sequencing primers. It also >does a lot of other manipulations, especially finding good sites for >subcloning. Demos are available and the academic price is $400. My preferred software is PRIMER Designer from Scientific and Educational Software, P.O. Box 440, State Line PA 17263 (717) 597-5307. Avail for DOS or Windows; we've made scores of good primers with it. Call for a DEMO DISK. Also, get a demo of their Clone program (cloning simulation/DNA analysis). By far the best I've seen. o-------------------------------------------------------------------------------o | Peter Gegenheimer | pgegen@kuhub.cc.ukans.edu | | Departments of Biochemistry and of Botany | voice: 913-864-3939 | | University of Kansas | FAX : 913-864-5321 | | 2045 Haworth Hall | "The sleep of reason produces | | Lawrence KS 66045-2106 | monsters." Goya | o_____________________________________________|_________________________________o From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Newsgroups: bionet.software From: steve@gardner.demon.co.uk (Steve & Rowan Gardner) Path: biosci!daresbury!doc.ic.ac.uk!lyra.csx.cam.ac.uk!pipex!demon!gardner.demon.co.uk!steve Subject: Re: bioinformatics? References: Distribution: world Organization: Myorganisation Reply-To: steve@gardner.demon.co.uk X-Newsreader: Newswin Alpha 0.4 Lines: 34 Date: Mon, 6 Jun 1994 19:39:10 +0000 Message-ID: <890177696wnr@gardner.demon.co.uk> Sender: usenet@demon.co.uk > In article <2rqmhp$a9@mserv1.dl.ac.uk> Guy Tremblay wrote: > : Hi net fans! > > : I would like to have some hints on the future of computing > : related to biology. I am an undergraduate student at UQAM and I am > : strongly interested in computer applications, but I am not sure of the > : market's practical needs. Do you think that IBM PCs will overwhelm UNIX > : hold on scientific applications? Where could I find some documentation? > : Information on biocomputing graduate studies? > : Thanks in advance... > : Personally I think its getting hard to tell PC and Unix systems apart. The low-end Unix boxes look more and more like high end PCs and Macs, and I use both in my job at a computational biology software house. Once DOS bites the dust as a development platform, there is going to be very little distinction indeed between the platforms. The computational biology market has moved from an entrenched position where 'serious science' such as bioinformatics, molecular modelling, phylogenetic analysis etc... was done on Vax/VMS or Sun machines, through an expansion of the Mac/PC platforms and is now converging on the level of cheap RISC based systems. Whether that infers Silicon Graphics Indy to you or PowerPC/Mac, or whether you will hold out for the next Intel offering is, I suspect, largely a matter of personal prejudice and whether you can get the next latest and greatest application to run on it. Sorry I can't help with references - these are just my opinions, and apart from a report by the Aberdeen Group on computational chemistry I couldn't really justify them further. Steve Gardner *************************************************************************** Disclaimer: What's mine's mi own, and nobody elses ! From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!lyra.csx.cam.ac.uk!warwick!bham!med242.bham.ac.uk!user From: s.d.huen@bham.ac.uk (David Huen) Newsgroups: bionet.software Subject: Re: Public and Commercial Software Disasters Followup-To: bionet.software Date: 6 Jun 1994 22:11:05 GMT Organization: Institute of Cancer Studies Lines: 27 Distribution: bionet Message-ID: References: <2svifr$smu@mserv1.dl.ac.uk> NNTP-Posting-Host: med242.bham.ac.uk In article <2svifr$smu@mserv1.dl.ac.uk>, Duncan Rouch wrote: > The prime cause is usually management ignorance combined with bad commercial > consultants. So, it might be useful if some of the computer-science know-how > at universities was used in consultancies to help stop wasting all that > public money on modern dinosaurs, not to mention to help the police, > firebrigade and ambulance services do better jobs. > I doubt if many academics have ever implemented large systems, involving large development teams, with tight performance and downtime specs and deadlines that had to be used by relatively untrained users. If the average university computer centre represents the level of service an academic consultancy can yield you in a life-critical program, I'd invest in a decent ambulance-chasing legal practice.. :-). The skills and experience you'd want are at the top end of the commercial sector, in businesses and organisations which have better things to do than make large donations to a certain political party. > > Duncan Rouch > New Chemistry Lab, University of Oxford, UK. Hi Dunx, So that's where you are!!!! From owner-software@net.bio.net Sun Jun 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!EU.net!ub4b!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!krols From: krols@reks.uia.ac.be (Luc.Krols) Subject: Re: LOD score calc Message-ID: <1994Jun6.122823.17851@reks.uia.ac.be> Organization: U.I.A. X-Newsreader: Tin 1.1 PL5 References: <2snnl1$2bo@agate.berkeley.edu> Date: Mon, 6 Jun 1994 12:28:23 GMT Lines: 52 Hello, There is a complete C version of the LINKAGE programs available. Here are the instructions for retrieving the code: ftp softlib.cs.rice.edu Login as anonymous and leave your full e-mail address as password. cd pub/fastlink In that directory you will find various files. You can get everything at once by retrieving the file: fastlink.tar.Z The work has been done by R. Cottingham and A. Schaffer and is published: A. A. Schaffer, S. K. Gupta, K. Shriram, and R. W. Cottingham Jr. Avoiding Recomputation in Genetic Linkage Analysis, Human Heredity, to appear. R. W. Cottingham Jr., R. M. Idury, A. A. Schaffer. Faster Sequential Genetic Linkage Computations, American Journal of Human Genetics 53(1993), pp. 252-263. There is a really good Makefile available that makes compiling simple. Succes! Luc Krols ============================================================================== Luc Krols Neurogenetics Lab. Born - Bunge Foundation Dept. of Biochemistry University of Antwerp Universiteitsplein, 1 B-2610 Antwerpen (Wilrijk) Belgium E-mail: krols@reks.uia.ac.be Tel.: + 32 3 820 26 31 fax.: + 32 3 820 25 41 ============================================================================== From owner-software@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!swrinde!ihnp4.ucsd.edu!munnari.oz.au!ariel.ucs.unimelb.EDU.AU!ucsvc.ucs.unimelb.edu.au!wehi.edu.au!wehi.edu.au!vladimir Newsgroups: bionet.software Subject: Q: Artificial neural network in immunology? Message-ID: <1994Jun7.112940.1@wehi.edu.au> From: vladimir@wehi.edu.au Date: 7 Jun 94 11:29:40 +1000 Organization: Walter & Eliza Hall Institute NNTP-Posting-Host: wehit.wehi.edu.au Lines: 6 Hi bio-netters, does anyone know of some ANN (artificial neural networks) application in immunology? Vladimir From owner-software@net.bio.net Mon Jun 06 23:00:00 1994 Newsgroups: bionet.software,bionet.general Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!newsserver.jvnc.net!phinet!phm771.sb.com!user From: boones1@sb.com (Scott Boone) Subject: Lab Data collection Message-ID: Followup-To: bionet.software,bionet.general Sender: news@netnews.smithkline.com (USENET News System) Organization: SmithKline Beecham Date: Tue, 7 Jun 1994 01:36:29 GMT Lines: 21 Xref: biosci bionet.software:8439 bionet.general:9726 At SmithKline Beecham, we are looking into moving from a VAX-based data collection system to a more Client/Server based system. Most of the instruments we are trying to control are RS-232 based. What we would like to do is continue with either a VAX or Windows NT server with client software running on a PC and Macintosh. We have seen a couple products --Labstation from Fisons and Labware-- but weren't really happy with them. Is anyone aware of software that will do this sort of data collection? We would like to stay away from completely custom environments and would definitely like to move the interface off the VAX and onto the user's desktop. Right now were are using an inhouse, VAXbased system called RIGEL. Thanks for your help... Scott Boone ----------------------------------------------------------------- Lab Automation Email- boones1@sb.com SmithKline Beecham Phone- (215) 270-6312 From owner-software@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!usenet.ufl.edu!usenet.cis.ufl.edu!anshar.shadow.net!usenet From: gitter@shadow.net (David L. Gitter, CNE) Newsgroups: bionet.software Subject: imaging software - cosmetic surgery Date: 7 Jun 1994 05:12:02 GMT Organization: Gitter, Orlowsky & Associates Lines: 12 Message-ID: <2t0vj2$43i@anshar.shadow.net> NNTP-Posting-Host: ppp-10.shadow.net X-Newsreader: WinVN version 0.82 Does anyone know of any image manipulation systems that are designed for Cosmetic Surgery?? What I am looking for is the ability to take a digitized image of the patient and be able to manipulate the image (via morphing etc) to show them what they would look like with altered features (ie: noses, ears, hairlines etc.) Any assistance would be most appreciated. Dave Gitter [gitter@shadow.net] From owner-software@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!VMD.CSO.UIUC.EDU!tino From: tino@VMD.CSO.UIUC.EDU ("Constantin A. Rebeiz") Newsgroups: bionet.software Subject: RE: Beta Testers Wanted: CS Chem3D for Microsoft Windows Date: 7 Jun 1994 11:35:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 62 Sender: daemon@net.bio.net Distribution: world Message-ID: <2088.tino@vmd.cso.uiuc.edu> NNTP-Posting-Host: net.bio.net In message 7 Jun 1994 10:42:45 -0400, brecher@terminator.rs.itd.umich.edu (Jonathan Brecher) writes: > > Cambridge Scientific Computing, Inc., is preparing to enter the beta test > period for the Microsoft Windows version of CS Chem3D. CS Chem3D is a > molecular modeling and visualization application that supports MM2 energy > minimization and molecular mechanics calculations. It can readily > communicate not only with our own CS ChemDraw but with other programs > such as MOPAC, SYBYL, or any program that supports the Protein Data Bank > format. > We have some positions available for qualified beta testers of CS Chem3D. > If you are interested in participating in this beta, please fill out the > following form and return it to jsb@camsci.com (or just Reply to this > message). > Thanks a lot. > > Jonathan Brecher > Cambridge Scientific Computing, Inc. > jsb@camsci.com > > > > Your Name: Constantin A. Rebeiz > Company: University of Illinois, Urbana > Mailing Address: 240 A, PABL, 1201 West Dorner, University of Illinois, Uraban, IL. 61801 > > > > Shipping Address (if different): > > > > Phone Number: (217)-333-4726 > Fax Number: (217)-244-5625 > Electronic Address(es):Tino@VMD.CSO.UIUC.EDU > Do you have ftp capabilities: Yes > Do you currently have any versions of our software? (Please list): No > CSC software which you are willing to test: > CSC ChemDraw/Plus: yes > CSC Chem3D/Plus: yes > CSC ChemFinder/Plus: yes > Testing platforms with which you are willing to work: > Macintosh > Windows 3.1 (Please specify operating system): Dos 6.2. > Windows NT > UNIX > Please describe the computer system(s) on which you would be performing > the testing. (include computer type, operating system, printer type, > etc.): IBM model 80 with 16MB of RAM and a read-wtite optical drive, dos 6.2, IBM laser printer model 4019. > > Please tell us anything else you think might be relevent: I am an experienced user of Chemical Design ChemX, of Mopac (VMS platform and a DEC 3520 Workststion), of Molecular design Chembase and Isis draw. Constantin A. Rebeiz Laboratory of Plant Pigment Biochemistry and Photobiology 240 A PABL, 1201 West Gregory University of Illinois Urbana IL. 61801 From owner-software@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!dog.ee.lbl.gov!ihnp4.ucsd.edu!usc!howland.reston.ans.net!vixen.cso.uiuc.edu!news.cso.uiuc.edu!lwalsh From: lwalsh@nemo.life.uiuc.edu (Laura L. Walsh) Newsgroups: bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.software Subject: Annotated PDB Listing Date: 7 Jun 94 18:54:03 GMT Organization: University of Illinois at Urbana Lines: 62 Message-ID: NNTP-Posting-Host: nemo.life.uiuc.edu Xref: biosci bionet.molbio.embldatabank:338 bionet.molbio.genbank:1643 bionet.software:8438 Once again, I am making my "Annotated Guide to the Brookhaven Protein Data Bank" available. This file includes listings for all of the files in the January, 1994 release. The main additions this year are a complete listing of all of the lysozyme files, a better organization of the DNA files, and, most importantly, structure classifications for all of the protein chains in the data bank. There is also a companion file which lists all of the sequence relations among the individual protein chains. This file is called the "Sequence Relations" file. Most importantly, if there are errors, which there probably are, given that we are dealing with 2327 files, I would appreciate being informed of such. Please cite the work as suggested in the files if you use it in your own work. A write up of the work has been submitted for publication and may appear later this year. If so, the suggested citation will change. Laura Lynn Walsh ------------------- the retrieval instructions follow ------- e-mail) send a message: select chemistry cd documents/PDB/PDB_file_list limit 500kB size 70kB get pdb_annot_jan94.txt get pdb_annot_jan94 get pdb_seq_rel_jan94 quit to MAILSERV@osc.edu ftp) ftp infomeister.osc.edu (or ftp 128.146.36.5) Name: anonymous Passwd: YOUR_e-mail_address ftp> cd /pub/chemistry/documents/PDB/PDB_file_list ftp> get pdb_annot_jan94.txt ftp> get pdb_annot_jan94 ftp> get pdb_seq_rel_jan94 ftp> quit gopher) gopher infomeister.osc.edu 73 documents PDB PDB_file_list pdb_annot_jan94 pdb_annot_jan94.txt pdb_seq_rel_jan94 WWW) http://www.osc.edu/~ccl/documents.html Protein Data Bank PDB_file_list ------------------- end retrieval instructions -------------- Laura Walsh, Beckman Institute, University of Illinois 405 N. Mathews Ave., Urbana, IL 61801 (217) 244-2894 lwalsh@silibio.ncsa.uiuc.edu From owner-software@net.bio.net Mon Jun 06 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!overload.lbl.gov!dog.ee.lbl.gov!ihnp4.ucsd.edu!swrinde!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!umn.edu!x141-93.open.umn.edu!user From: herro001@staff.tc.umn.edu (Mike Herron) Subject: Mac ligand binding software? Message-ID: Followup-To: bionet.software Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: x141-93.open.umn.edu Organization: U of MN, Dermatology Date: Tue, 7 Jun 1994 18:34:51 GMT Lines: 9 I am looking for Mac software that will allow me to ananlyse competitive binding data. I have used Biosoft's Enzfitter and found it lacking. Can anyone rec. another program? Thanks! -- Mike Herron herro001@staff.tc.umn.edu From owner-software@net.bio.net Mon Jun 06 23:00:00 1994 Path: biosci!U.WASHINGTON.EDU!pr From: pr@U.WASHINGTON.EDU (Peter Ratiu) Newsgroups: bionet.software Subject: Re: imaging software - cosmetic surgery Date: 7 Jun 1994 10:07:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <2t0vj2$43i@anshar.shadow.net> NNTP-Posting-Host: net.bio.net Disclaimer: IAM IN NO WAY ASSOCIATED, ETC... Mirror Image of Lynnwood WA has a very nifty application for this purpose. Contact: Ray Linford Mirror Image Technology (206) 775-5077 (206) 775-7049 (FAX) 800 841-5678 It will most likely meet all the prectical needs of precticing plastic surgeons. -------------------------------------------------------------------------------- Peter Ratiu, MD email: pr@u.washington.edu University