From owner-software@net.bio.net Sun Nov 01 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!swrinde!sdd.hp.com!usc!snorkelwacker.mit.edu!bloom-picayune.mit.edu!wccf.mit.edu!karuzis From: karuzis@wccf.mit.edu (GLENN HOLM) Newsgroups: bionet.software Subject: Re: NeXT and biology, anyone? Message-ID: <1NOV199218384640@wccf.mit.edu> Date: 1 Nov 92 23:38:00 GMT References: <921031131619.2380ba74@CCSUA.CTSTATEU.EDU> Sender: news@athena.mit.edu (News system) Distribution: bionet Organization: MIT - Whitaker College Lines: 122 News-Software: VAX/VMS VNEWS 1.41 Nntp-Posting-Host: wccf.mit.edu In article <921031131619.2380ba74@CCSUA.CTSTATEU.EDU>, LETTIERE_DAJ@CCSUA.CTSTATEU.EDU writes... >Hello, > > I am wondering if there is any biology software in existance for the >NeXT computer. I would prefer to see public domain (e.g. free) software but >would be interested in commercial packages as well. In addition, are there any >ftp sites with biology software for the Sun? > > > Thanks in advance > > Dan Lettiere > >******************************************************************************** >E-Mail: lettiere_daj@ccsu.ctstateu.edu > >Snail Mail: Central Connecticut State University > Dept. of Biological Sciences, Copernicus Hall > 1615 Stanley Street > New Britain, CT 06050 >******************************************************************************** >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > The following just appeared in comp.sys.next.misc: Path: bloom-picayune.mit.edu!enterpoop.mit.edu!snorkelwacker.mit.edu!tamsun.tamu.edu!cs.utexas.edu!zaphod.mps.ohio-state.edu!caen!uunet!rosie!NeXT.com From: Conrad_Geiger@NeXT.com (Conrad Geiger - Manager, International NeXT User Groups) Newsgroups: comp.sys.next.misc Subject: NeXT Education Software Sampler: CD-ROM Software Compendium Message-ID: <5686@rosie.NeXT.COM> Date: 31 Oct 92 00:10:24 GMT Sender: news@NeXT.COM Reply-To: user_groups@next.com Lines: 79 News FOR IMMEDIATE RELEASE Contact: Angela Grady Allison Thomas Associates (415) 780-3786 Announcing: NeXT(tm) Education Software Sampler: CD-ROM Software Compendium BALTIMORE, October 28, 1992 -- At the EDUCOM'92 conference today, NeXT Computer, Inc. announced the availability of the first NeXT Education Software Sampler, a CD-ROM containing a wide assortment of public domain shareware education software for NeXTSTEP(tm) computers. "Our goal with the NeXT Education Software Sampler is to provide users with useful, easily accessible software as well as to stimulate users' imaginations by providing ideas for further development with NeXTSTEP," said David Spitzler, higher education marketing manager for NeXT. "Because all the software on the disc was submitted to NeXT specifically for redistribution, we encourage users to share anything on the Software Sampler with others who may be interested in educational NeXTSTEP software." Most of the software on the CD-ROM is ready to run and can be used free of charge. The software was submitted by faculty, researchers and students as well as representatives from various industries. The disc also contains demonstration versions of a variety of commercially available applications, submitted by the third-party developers themselves. In addition, NeXT has also included the source code of its modifications to the Free Software Foundation's GNU-based development tools, including the compilers, debugger and the emacs editor. Examples of education software on the disc include FlyLab, an application written for an introductory genetics course at the California State University at Los Angeles. Fly Lab teaches the principles of genetic inheritance by simulating a genetics laboratory of the common fruit fly. Students can design flies that carry various combinations of mutations, then "mate" the flies to study the inheritance of genetic traits in the offspring. Other examples include Geo4 and Geo5, software for teaching and learning historical geography, written at St. Mary's College of Maryland, and a demonstration of Tarski's World, an application for learning first-order logic written at Stanford University. Organized into sections by subject, the CD-ROM contains more than 500 megabytes (MB) of applications, utilities, documents and much more. For instance, the disc includes nearly 15 MB of music software, more than 70 MB of mathematics software and almost 80 MB of programming examples and source code from full-functioning applications. Each submission includes a README file with minimum standard information about the application and who to contact for more information. Price and Availability The NeXT Education Software Sampler is available now directly from NeXT for $25.00. Interested parties can call 1-800-879-NeXT to order. About NeXT Computer, Inc. NeXT Computer, Inc. designs and markets the industry-acclaimed NeXTSTEP object-oriented operating system, and designs, manufactures and markets UNIX-based workstations that run NeXTSTEP. NeXTSTEP and NeXT workstations are used by medium and large organizations to develop and deploy mission-critical applications, using both custom and shrink-wrapped software. NeXT is headquartered at 900 Chesapeake Drive, Redwood City, Calif., 94063. -30- NeXT, the NeXT logo and NeXTSTEP are trademarks of NeXT Computer, Inc. All other trademarks mentioned belong to their respective owners. ------------------------------------------------------------------ |Glenn Holm Internet:karuzis@wccf.mit.edu| |M.I.T Dept. of Brain + Cog. Sci. This VAX doesn't do NeXTmail | |Cambridge, MA 02139 "Real Neuroscientists don't do gels!" | ------------------------------------------------------------------ From owner-software@net.bio.net Sun Nov 01 22:00:00 1992 Path: biosci!uwm.edu!cs.utexas.edu!uunet!munnari.oz.au!ariel.ucs.unimelb.EDU.AU!ucsvc.ucs.unimelb.edu.au!lugb!lure.latrobe.edu.au!extim From: extim@lure.latrobe.edu.au Newsgroups: bionet.software Subject: Info on Waters Millenium HPLC software? Message-ID: <1992Nov2.173418.1@lure.latrobe.edu.au> Date: 2 Nov 92 07:34:18 GMT Sender: news@lugb.latrobe.edu.au (USENET News System) Organization: VAX Cluster, Computer Centre, La Trobe University Lines: 75 Dear HPLC specialists, We are considering the purchase of the Waters Millenium software (2010 Multisystem with Bus LAC/E card) and our own computer system consisting of a clone 486DX/33, 16 Meg memory, 200 Meg HD, SVGA. This system will be used for the control of two simple gradient systems. What follows is a request for information about the performance of this equipment. We have had experience in running gradient systems with WISP by Maxima for multiple sample analysis. One system will be formed of a simple Waters UV detector (481) Waters 710 WISP and will be used for analysis of samples for ivermectin either by an isocratic or simple gradient protocol. For this we need the ability to reliably perform and store overnight runs and the ability to re-integrate unsatisfactory runs. The software will also be used to control a gradient system for research uses based around a standard injector and a Waters 996 photodiode array. At present, none of the equipment has instrumentation interfaces so one of the decisions we have to make is what method to connect to Millenium, through either IEEE or SIM. To build this system within budget (actually trying to keep the overbudget to within $10,000) we are trying to keep everthing to a minimum. To try and find out what is possible we have limited sources of information. First the Waters reps out here seem to be on a significant learning curve (or have some commercial interests to push) and a limited number of users. We have been getting conflicting info so I would be gratefull if anyone out there who is using Millenium could perhaps clarify some matters. Will Millenium control either IEEE or SIM interfaces or both? (The Millenium manuals seem to suggest that SIM control is not possible, but people are using it with SIMs) Is the IEEE route significantly faster or has other major benefits worth $2,000 extra? How stable have you found the system? (Our contacts report system lockups with version 1.0) Is the overall performance sufficient to allow the control of two gradient systems? (We are told that the system is highly dependent on the absolute maximum performance of the computer system else long waits even with ordinary gradients) Are these performance problems going to be much worse if significant use is made of the PDA? Is it possible to manually integrate? (One group reports that Waters reps were unable to get that section of the program to manually integrate runs) There is some confusion as to the initial flow rates that are allowed. Either zero flow rates are not allowed as the first commands in programmes, or that the software will not start a pump from zero flow? A lot of questions! Some of these we are hoping to get sorted out by more detailed questioning here. However we need to make some decisions soon and some other imputs will be valuable. Thanks for any assistance. Ian McCauley Department of Biochemistry Victorian Institute of Animal Science Melbourne, Australia AARNET ... extim@lure.latrobe.edu.au.oz or ....... mccauleyi@agvic.gov.au.oz (much less reliable at present) From owner-software@net.bio.net Sun Nov 01 22:00:00 1992 Path: biosci!agate!ames!think.com!hsdndev!nmr-z!OPAL.MGH.HARVARD.EDU!CHERRY From: cherry@OPAL.MGH.HARVARD.EDU Newsgroups: bionet.software Subject: Re: Sequence databases on the network Message-ID: <1992Nov2.040633.14679@nmr-z.mgh.harvard.edu> Date: 2 Nov 92 04:06:33 GMT References: <9210281920.AA24061@phage.cshl.org>,<1992Oct31.153502.15279@comp.bioz.unibas.ch> Sender: usenet@nmr-z.mgh.harvard.edu (User for USENET news postings) Reply-To: cherry@OPAL.MGH.HARVARD.EDU Distribution: bionet Organization: Molecular Biology - Mass Gen Hospital Lines: 35 Nntp-Posting-Host: opal.mgh.harvard.edu >In article <1992Oct31.153502.15279@comp.bioz.unibas.ch>, doelz@comp.bioz.unibas.ch (Reinhard Doelz) writes: >>There are a variety of sources which can be used to download sequence >>databases (full releases) via FTP. I find this procedure tolerable on >>local or may be national networks, but it is definitively overkill >>on international lines. I am currently providing Swissprot and EMBL in generic, >>as well all other databases in GCG/PIR format. If the usage of FTP'ing >>these databases outside of Switzerland continues as it did in the past >>(e.g., EMBL was downloaded by more than 18 sites, five of them being >>information providers, which is okay, but the rest were sites who wanted >>to "save money", or didn't know about a resource on their national net), >>we will be forced to close down this way of access for international networks. An alternative location to obtain the least EMBL database and updates via anonymous ftp is amber.mgh.harvard.edu [IP 132.183.191.26]. This archive is open to all and is encouraged for sites outside of Switzerland. Amber is a VMS system so the compressed EMBL flat files are in the form: "xxx.dat_z". If you are running Unix you might need to rename the files to the form: "xxx.dat.Z". Weekly updates of EMBL are of available in two compressed flat files: xembl.flat_z additions to EMBL since the last release xxembl.flat_z modifications of sequences in the release All of the above files are obtained direct from the Swiss EMBnet node and are provided thanks to Reinhard Doelz. Remember that compressed files should be transferred as binary. Also available on Amber are VMS savesets of the EMBL database minus those sequences already in GenBank. These are produced using the latest GenBank database from ncbi.nlm.nih.gov plus daily updates and the GCG EMBLtoGCG/EXCLUDE command. Mike Cherry cherry@frodo.mgh.harvard.edu From owner-software@net.bio.net Sun Nov 01 22:00:00 1992 Path: biosci!CU.NIH.GOV!CZJ From: CZJ@CU.NIH.GOV Newsgroups: bionet.software Subject: Re: Looking for hydrophob. plot & helical wheel soft Message-ID: <9211020347.AA06036@net.bio.net> Date: 2 Nov 92 02:10:51 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 29 > In kh@litsun17.epfl.ch (Mark S.) writes: > > >Hello All, > > >this might very well be a FAQ, ... > > >but I am looking for software to do helical wheel plots and hydrophobicity plots. Does anyone have an idea where to grab this kind of soft? > >Or is there someone who has tried a package? > > GCG should be able to do this (if you have access to it). I just mention > this because I assume that anybody working in the molbiol/biochemistry > sector might have access to it. If you want to run the program(s) on a > personal computer instead, it would be a great help for others if you'd > specify the type of computer you're working with (and in some special > cases -- such as IBM compatibles running UNIX -- the operation system > as well). > -- > /* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen */ > /* email: krasel@studserv.zdv.uni-tuebingen.de (Internet) HAS CHANGED!! */ > /* krasel@student.uni-tuebingen.dbp.de (WIN/X400) HAS CHANGED!! */ > /* "People are DNA's way of making more DNA." (anonymous) */ > > Prograph does all of this. Prograph is available from the embl file server and other FTP sites. Prograph runs on DOS machines. Jim Cassatt From owner-software@net.bio.net Mon Nov 02 22:00:00 1992 Path: biosci!news.cs.indiana.edu!usenet.ucs.indiana.edu!sol.ctr.columbia.edu!caen!batcomputer!genie!olivea!sgigate!rutgers!utcsri!torn!news.ccs.queensu.ca!!BACKD@QUCDN.QueensU.CA From: BACKD@QUCDN.QueensU.CA@ Newsgroups: bionet.software Subject: Re: full sequence of pCR II from Invitrogen ? Message-ID: Date: 3 Nov 92 01:41:24 GMT References: <1cqqcdINN87r@uniwa.uwa.edu.au> Sender: news@knot.ccs.queensu.ca (Netnews control) Organization: Queen's University, Kingston Lines: 16 In article <1cqqcdINN87r@uniwa.uwa.edu.au> robert@arbo.microbiol.uwa.oz.au (Robert Coelen) writes: >Hi, >could anyone out there, who is in possession of the full sequence of >pCR II from InVitrogen email it to me ? >Thanks >Robert Coelen >Dept of Microbiology INVITROGEN has placed all of their sequences on a bulletin board. You can down load from (619) 597-6230 8-1-n Good luck From owner-software@net.bio.net Mon Nov 02 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!wupost!sdd.hp.com!nigel.msen.com!caen!saimiri.primate.wisc.edu!ames!agate!doc.ic.ac.uk!uknet!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!seb1005 From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.software Subject: Looking for Protein Threading & Design Software, EMBL Documents Message-ID: <1992Nov3.000919.24583@infodev.cam.ac.uk> Date: 3 Nov 92 00:09:19 GMT Sender: news@infodev.cam.ac.uk (USENET news) Organization: U. of Cambridge, England Lines: 49 Nntp-Posting-Host: mbfs.bio.cam.ac.uk I would appreciate if if anyone could tell me where I could find any of the following programs, or if they tell me how to contact the authors by electronic mail. predipep described in Goraj et al, Protein Engineering 3:4 259-266 (1990) Universite de Liege, Insitut de Chimie (Belgium) structure alignment program described in Orengo et al, Proteins 14 139-167 (1992) National Institute for Medial Research, London (now at University College, London) threading program described in Jones et al, Nature v358 p86 (1992) University College, London 3D-1D (threading-type) program described in James Bowie et al, Science 253 p164-170 (1992) UCLA STAMP described in Russel & Barton, Proteins v14 309-323 (1992) Oxford Patchcharge described in Karpeisky & Illyin, J Mol Bio 224 629-638 (1992) USSR Academy of Sciences Also, does anyone know where the EMBL BIOcomputing Technical Documents can be found? The libraries here at Cambridge have never heard of them. Finally (as long as I'm posting) does anyone know the email or letter-mail address for Chris Sander, Marc Eberhard, Arne Elofsson, Tim JP Hubbard, & Lynne Regan? They are 5 of some two dozen authors of a paper which doesn't list individual addresses Thanks in advance for your collective help! Steven Brenner seb1005@mbfs.bio.cam.ac.uk Department of Biochemistry University of Cambridge From owner-software@net.bio.net Mon Nov 02 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!swrinde!zaphod.mps.ohio-state.edu!sol.ctr.columbia.edu!spool.mu.edu!hri.com!noc.near.net!news.bbn.com!hsdndev!golgi.harvard.edu!ribo!rindone From: rindone@ribo.harvard.edu (Wayne Rindone) Newsgroups: bionet.software Subject: Re: Protein Structure: Internal coords --> PDB Keywords: Protein, Conversion, Coordinates, PDB, Dihedral_angles Message-ID: Date: 2 Nov 92 20:51:08 GMT References: Sender: news@golgi.harvard.edu Distribution: bionet Organization: Harvard Genome Laboratory Lines: 46 Nntp-Posting-Host: ribo v071rw4p@UBVMSB.CC.BUFFALO.EDU (EMIL MARCUS) writes: > I would be most grateful if you could help me locate a program that >converts protein internal (dihedral angles: phi, psi, omega, chi's...) >coordinate files into cartesian - PDB (Protein Data Bank) type files ! > The program that does the reverse transformation is available from >The Protein Data Bank... >Thank you, >Emil >-------- > Emil Marcus V071RW4P@ubvms.cc.buffalo.edu MARCUS@acsu.buffalo.edu One software package that might be useful in this regard is the NIH-sponsored Prophet system for a variety of Unix workstations. Prophet includes an interactive procedure called makepolypeptide that constructs a three dimensional structure from a series of amino acid names, phi angles, and psi angles. It does not explicitly offer prepackaged control over the omega and chi angles (all the omegas are set to 180 degrees, chi angles are whatever was found in the template residues). However, what is created is a Prophet molecule, for which there are a variety of techniques, including interactive pointing as well as procedure calls, for modifying torsion angles and other geometric parameters. Prophet does know how to create a PDB-formatted file for any Prophet molecule. More information about Prophet can be obtained by sending email to prophet-info@bbn.com ************************************************************************** Wayne Rindone FlyBase Department of Cellular and Developmental Biology Harvard University rindone@nucleus.harvard.edu ************************************************************************** -- ************************************************************************** Wayne Rindone FlyBase Department of Cellular and Developmental Biology From owner-software@net.bio.net Mon Nov 02 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!swrinde!zaphod.mps.ohio-state.edu!sol.ctr.columbia.edu!spool.mu.edu!hri.com!noc.near.net!news.bbn.com!hsdndev!golgi.harvard.edu!ribo!rindone From: rindone@ribo.harvard.edu (Wayne Rindone) Newsgroups: bionet.software Subject: Re: Protein Structure: Internal coords --> PDB Keywords: Protein, Conversion, Coordinates, PDB, Dihedral_angles Message-ID: Date: 2 Nov 92 20:30:44 GMT References: Sender: news@golgi.harvard.edu Distribution: bionet Organization: Harvard Genome Laboratory Lines: 44 Nntp-Posting-Host: ribo v071rw4p@UBVMSB.CC.BUFFALO.EDU (EMIL MARCUS) writes: > I would be most grateful if you could help me locate a program that >converts protein internal (dihedral angles: phi, psi, omega, chi's...) >coordinate files into cartesian - PDB (Protein Data Bank) type files ! > The program that does the reverse transformation is available from >The Protein Data Bank... >Thank you, >Emil >-------- > Emil Marcus V071RW4P@ubvms.cc.buffalo.edu MARCUS@acsu.buffalo.edu One software package that might be useful in this regard is the NIH-sponsored Prophet system for a variety of Unix workstations. Prophet includes an interactive procedure called makepolypeptide that constructs a three dimensional structure from a series of amino acid names, phi angles, and psi angles. It does not explicitly offer prepackaged control over the omega and chi angles (all the omegas are set to 180 degrees, chi angles are whatever was found in the template residues). However, what is created is a Prophet molecule, for which there are a variety of techniques, including interactive pointing as well as procedure calls, for modifying torsion angles and other geometric parameters. Prophet does know how to create a PDB-formatted file for any Prophet molecule. More information about Prophet can be obtained by sending email to prophet-info@bbn.com ************************************************************************** Wayne Rindone FlyBase Department of Cellular and Developmental Biology Harvard University rindone@nucleus.harvard.edu ************************************************************************** -- ************************************************************************** Wayne Rindone FlyBase Department of Cellular and Developmental Biology From owner-software@net.bio.net Tue Nov 03 22:00:00 1992 Path: biosci!daresbury!news From: Fergus_Doherty@vme.nott.ac.uk Newsgroups: bionet.software Subject: GCG X-windows version Message-ID: <1992Nov4.132019.1590@gserv1.dl.ac.uk> Date: 4 Nov 92 13:20:21 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 3 Original-To: bio-soft@uk.ac.daresbury Hello, does nyone have any experience with the X-windows version of the GCG package. Is it much easier to use than then[D standard version? Fergus Doherty, Biochemistry, Nottingham University. From owner-software@net.bio.net Tue Nov 03 22:00:00 1992 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: IUBio Archive biology data searches via WAIS and Gopher Message-ID: Date: 4 Nov 92 21:03:33 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 168 Nntp-Posting-Host: sunflower.bio.indiana.edu This is a summary of new biology data searching and retrieval offerings at the IUBio Archive (Internet host ftp.bio.indiana.edu). These data are now available via a Wide Area Information Server, WAIS, as well as via Internet Gopher. General WAIS source to IUBio Archive of Biology software and data ------------------------------------------ (:source :version 3 :ip-address "129.79.224.25" :ip-name "ftp.bio.indiana.edu" :tcp-port 210 :database-name "INFO" :cost 0.00 :cost-unit :free :maintainer "archive@bio.indiana.edu" :description " This WAIS service includes several indexed Biology information sources, including Genbank nucleic acid gene sequence databank, Drosophila genetics BioSci/Bionet network news, and others. = = = = = = = = = = = = = = = = = = = = = = = = This WAIS service sports several zippy modifications. These include boolean operators 'and' and 'not', partial word matches, literal phrase matches, and extended number of results. Boolean searches: The terms 'and' and 'not' are effective in modifying the query. For example, Query: red and green not blue Result: just those records with both the words 'red' and 'green', excluding all records with the word 'blue'. Partial words: The asterisk (*) applied at the end of a partial word will match all documents with words that start with the partial word. For example, Query: hum* Result: all records with 'hum', 'hummingbird', 'human', 'humbug', etc. Literal phrases: If quotes (') or double quotes (\") surrounding a phrase, it will match that phrase exactly. For example, Query: 'red rooster-39' Result: only those records with the the full string 'red rooster-39' will be matched. These features can generally be mixed in a query, for example: Query: 'Df(32)-[34]red' and hum* not Brown Results limit (Gopher only): The maximum number of results that are returned for a query is by default up to 100. But you may set a higher, or lower, maximum by appending the greater than (>) symbol immediately followed by the number you wish at the end of your query. For example, Query: brown and cow* or "red rooster" >300 Result: up to 300 matches will be returned. The program source to these modifications will be available via Internet Gopher or anonymous ftp to ftp.bio.indiana.edu, in folder IUBio Software+Data/util/wais/ as iubio-wais-8b5.tar.Z (full source) or iubio-wais-8b5.tar.patches for a difference or patch file. (This is not ready as of 4Nov92). " ) Short list of current IUBio Archive WAIS sources ------------------------------------------------ (Note: These searches are also available via Internet Gopher to ftp.bio.indiana.edu) :database-name "arcdocs" :description " This is an index of abstracts, readme, help and related information on the IUBio Archive of Biology Software and Data. It is updated approximately monthly. Files described in these documents are generally available via ftp or gopher to ftp.bio.indiana.edu. :database-name "fly-address" :description " This is an index of the addresses for Drosophila researchers :database-name "fly-amero" :description " Cytological features database. This is a database of polytene chromosome sites that have been found to bind antibodies to particular Drosophila proteins. :database-name "fly-clones" :description " This is an index of UCLA DROSOPHILA GENMAPS DATABASE :database-name "fly-din" :description " This is an index of the electronic Drosophila Information Newsletter. :database-name "flybase" :description " This is an index of the Drosophila database, FlyBase, as maintained by Micheal Ashburner. :database-name "flystock-bg" :description " This is an index of the Drosophila fruitfly stocks maintained by the stock center at Bowling Green USA. :database-name "flystock-bl" :description " This is an index of the Drosophila fruitfly stocks maintained by the stock center at Bloomington USA. :database-name "flystock-um" :description " This is an index of the Drosophila fruitfly stocks maintained by the stock center at Umea Sweden. :database-name "genbank" :description " This is an index of the Genbank databank of gene sequences: Genetic Sequence Data Bank, NCBI-GenBank Flat File Release 73.1 86626 loci, 110208764 bases, from 86626 reported sequences :database-name "gbnew" :description " This is an index of updates sinces the latest full release of Genbank, the databank of all known gene sequences. It is updated weekly from the update files maintained by NCBI at ncbi.nlm.nih.gov. :database-name "journals" :description " This is an index of the table of contents of several biology journals. :database-name "methods" :description " This is an index of a collection of materials and methods recipes for molecular biologists. :database-name "netnews" :description " This is an index of news articles from the BioSci/Bionet newsgroups, as well as the Sci.Bio Usenet group and the bitnet.listserv.info-gcg group. :database-name "prosite" :description " This is an index of the PROSITE dictionary of protein sites and patterns, as produced by Amos Bairoch. :database-name "redbook" :cost 0.00 :cost-unit :free :maintainer "archive@bio.indiana.edu" :description " This is an index of the book 'The Genome of Drosophila melanogaster' by Dan Lindsley and Georgina Zimm. -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Tue Nov 03 22:00:00 1992 Path: biosci!SALK-SC2.SDSC.EDU!mangalam From: mangalam@SALK-SC2.SDSC.EDU Newsgroups: bionet.software Subject: Re: IUBio Archive biology data searches via WAIS and Gopher Message-ID: <9211042322.AA11207@net.bio.net> Date: 4 Nov 92 23:22:50 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 34 Don Gilbert modestly writes (on bio-soft): >This is a summary of new biology data searching and retrieval offerings >at the IUBio Archive (Internet host ftp.bio.indiana.edu). These >data are now available via a Wide Area Information Server, WAIS, as >well as via Internet Gopher. (much text deleted - read [and save!] his previous posting for the full report - basically announces the availability of boolean searches of genbank entries by gopher) Caramba! The biological community now has a virtual replacement for the IRX system! And one person wrote much of both ends of it - everyone owes DG a noisy round of cheers and hurrahs! Throw out your Genbank CDs, archive your databases, unsubscribe from the various proprietary databases. Don just saved an awful lot of people viewing this message a lot of money and disk space. Incidentally, we are examining the possibility of setting up a similar gopher hole on the west coast. What are your favorite databases? What kind of access would you like? Gopher? FTP? WAIS? All of the above? Let me know so we can get an idea of what kind of resources will have to be dedicated to it. Cheers, Harry Harry Mangalam Vox:(619) 453-4100, x250 Dept of Biocomputing Fax:(619) 552-1546 The Salk Institute mangalam@salk-sc2.sdsc.edu 10010 N Torrey Pines Rd mangalam@salk-sgi.sdsc.edu La Jolla CA 92037 mangalam@salk.bitnet From owner-software@net.bio.net Tue Nov 03 22:00:00 1992 Path: biosci!daresbury!news From: angelos@igmors.ups.circe.fr (Angelos Kalogeropoulos) Newsgroups: bionet.software Subject: GCG-X-Windows Message-ID: <1992Nov4.134218.2539@gserv1.dl.ac.uk> Date: 4 Nov 92 14:43:38 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 17 Original-To: bio-software@uk.ac.daresbury Original-Sender: angelos In addition to Fergus Doherty question: >Hello, does nyone have any experience with the X-windows version of the >GCG package. Is it much easier to use than then standard version? I ask if a X-windows version exists. Many thanks ****************************************** * Angelos KALOGEROPOULOS * * Institut de Genetique et Microbiologie * * Batiment 400 * * Centre Universitaire d'Orsay * * 91405 Orsay Cedex, France * * Angelos@igmors.ups.circe.fr * ****************************************** From owner-software@net.bio.net Wed Nov 04 22:00:00 1992 Path: biosci!LILLY.COM!SMITH_DENNIS_P From: SMITH_DENNIS_P@LILLY.COM ("DENNIS P. SMITH") Newsgroups: bionet.software Subject: Graphing Program Message-ID: <01GQRLSU3G6Q8WW08H@INET.D48.LILLY.COM> Date: 5 Nov 92 01:34:35 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 I looking for a MACINTOSH graphing program to plot receptor binding data. I have tried DeltaGraph Pro but it cannot graph the x-axis (peptide concentration) as 10 to the negative power. How do people plot the graphs pictured in published journals? Thanks DPSMITH INTERNET:smith_dennis_p@lilly.com From: SMITH DENNIS P (MCVAX0::BOOKS) To: VMS MAIL ADDRESSEE (INT::"bio-soft@genbank.bio.net") From owner-software@net.bio.net Wed Nov 04 22:00:00 1992 Path: biosci!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software,bionet.announce Subject: Drosophila database searches thru Gopher and WAIS Message-ID: Date: 4 Nov 92 15:44:15 GMT Sender: kristoff@net.bio.net Organization: Biology, Indiana University - Bloomington Lines: 148 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.software:3567 bionet.announce:242 New Drosophila data search and retrieval thru Internet network services are now available from the computer ftp.bio.indiana.edu. These services are found using Internet Gopher or Wide Area Information Service (WAIS). The Gopher services for Drosophila at ftp.bio.indiana.edu look like this: Root gopher server: ftp.bio.indiana.edu 1. About-IUBio-Gopher [21Jun92, 3kb]. 2. About-New-Features [ 1Nov92, 3kb]. --> 3. Drosophila/ 4. Genbank-Sequences/ 5. IUBio-Software+Data/ (more...) Drosophila --> 1. About Drosophila Gopher [23Feb92, 1kb]. 2. Clone database search 3. Cytological features search 4. Drosophila Archive/ 5. Drosophila Information Newsletter 6. Drosophila Stocks at Bloomington, USA 7. Drosophila Stocks at Bowling Green, USA 8. Drosophila Stocks at Umea, Sweden 9. Fly worker & GSA address search 10. Flybase/ 11. Flybase search 12. Redbook/ 13. Redbook search All of the services are WAIS/Gopher searches of fly data files that reside in the Drosophila Archive: Clone database search == search clonelist.txt Cytological features search == search Amero.txt Drosophila Information Newsletter == search newsletter issues Drosophila Stocks ... == search stock lists Fly worker address search == search Haynie & GSA address files Flybase search == search Ashburner flybase files Redbook search == search complete Lindsley & Zimm Genome book These search services are also available via WAIS client software. The relevant WAIS source for IUBio archive is: (:source :version 3 :ip-address "129.79.224.25" :ip-name "ftp.bio.indiana.edu" :tcp-port 210 :database-name "INFO" :cost 0.00 :cost-unit :free :maintainer "archive@bio.indiana.edu" :description " This WAIS service includes several indexed Biology information sources, including Genbank nucleic acid gene sequence databank, Drosophila genetics BioSci/Bionet network news, and others. ") And the fly wais databases are named: :database-name "fly-address" :database-name "fly-amero" :database-name "fly-clones" :database-name "fly-din" :database-name "flybase" :database-name "flystock-bg" :database-name "flystock-bl" :database-name "flystock-um" :database-name "redbook" As a reminder, client software for Macintosh, MS-Dos, Unix, VMS and other computer systems are available for Internet Gopher via anonymous ftp to boombox.micro.umn.edu, in /pub/gopher, and client software for WAIS is available via ftp to ftp.think.com. There are also some of these available via ftp to ftp.bio.indiana.edu, in /util/gopher and /util/wais directories. I've modified the WAIS indexing and searching software in several ways to make it more suitable for biology and genetic data searching. These modifications include a) use of symbols, so that queries like "In(4;5)red39" should work b) boolean 'and' and 'not' operators to limit a query results c) partial word searches, such as "hum*" matches human and hummingbird d) literal phrase searches, such finding "red rooster[45]" exactly e) output of data file headers (Gopher only so far). The use of symbols is still somewhat problematic, since WAIS is based on free text indexing, rather than on indexing of delimited fields in databases, it needs to use some characters and symbols to delimit words. I've tried to find a distinction between symbols needed for genetic "words" and symbols needed for distinguishing words (other than spaces), but there is some overlap. If you use the literal phrase search, by enclosing a phrase with symbols in quote (') or double quote (") marks, you may get better results. For instance, in some of the fly data files, esp. redbook, "(" and ")" are used both as genetic symbols and as word delimiters. Thus searching for Df(3)something will generally parse into searching for the three words "Df" "3" and "something", producing lots of matches. While using a literal search, 'Df(3)something' should limit the results to just that phrase. There are other ways to better index genetic symbols, but they involve more effort. I'd like to get some feedback first on the usefullness of this, from the general community of Internet-enabled fly researchers. The header file output adds a useful touch. Here is one result returned from a search of flybase for "ashburner": This section is from the document '//Drosophila/Drosophila Archive/flybase/ABREFS.TEXT'. gene-symbol first-author reference ------------ ---------------- ----------------------- Df(2L)ScoR+4 Ashburner, Genetics 126:679 McGill, Genetics 119:647 And a search for "red" produces this: This section is from the document '//Drosophila/Drosophila Archive/flybase/LOCI.TEXT'. gene-name-abbrev; full-gene-name gene-map-position cyto-map-position function nucleic-acid-databank-accession-number ditto-for-species-other-than-melanogaster protein-database-accession-number ditto-for-other-species ---------------------------------------------------------- red; red 3-53.6 88B1-88B2 -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Wed Nov 04 22:00:00 1992 Path: biosci!uwm.edu!spool.mu.edu!sgiblab!pacbell.com!well!well.sf.ca.us!dove From: dove@well.sf.ca.us (Rick Dove) Newsgroups: bionet.software Subject: Looking for movement tracking/analysis package Summary: Need to track lip movements as words are spoken, point-wise Message-ID: Date: 5 Nov 92 03:19:29 GMT Sender: news@well.sf.ca.us Organization: Whole Earth 'Lectronic Link Lines: 13 I need to analyze how lips move while speaking english words so I can use this mechanical movement info to drive animated lips. Actually, I will also be monitoring key muscle groups in the face as well probably. Is there any software available for the PC that will allow me to analyze video input and generate point displcaement over time? It would be ok to put "marks" on the human face before video input. I dont have access to any fancy pens or tablets - but it would be ok to "mark" a screen image with the mouse and have the software then track that point(s) as it moves through frames. Maybe you have another suggestion? Please forward any helpful suggestions to me at dove@well.sf.ca.us From owner-software@net.bio.net Wed Nov 04 22:00:00 1992 Path: biosci!daresbury!news From: robertson@mpib-tuebingen.mpg.dbp.de (BRAIN ROBERTSON) Newsgroups: bionet.software Subject: Mac front-end for VAX GCG Message-ID: <1992Nov5.153519.15673@gserv1.dl.ac.uk> Date: 5 Nov 92 15:34:33 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 30 Content-Identifier: 12 Original-To: bio-soft@uk.ac.daresbury Conversion: Prohibited Last week I posted a question concerning a Mac front end for the GCG programs running on a VAX that I has read about. Thanks to all those who troubled to reply. Here is a quick summary of the results: 1. Don Gilbert wrote a hypercard stack to acts as an interface, called HyperGCG.It is available by ftp from two places that I know of: ftp.bio.indiana.edu in molbio/mac hypergcg.hqx sunbcd.weizmann.ac.il in pub/software/mac/ However, Don Gilbert writes "I do not support this software.......nor do I recommend it except to those with some knowledge of hypercard programming and the time to mess with it." Well, I think that it plain enough! 2. Will Gilbert used MacWorkstation as a front end to VMS and GCG, and made a lot of progress, but abandoned it when good packages became available on the Mac, and because MWS became too expensive. None of what he wrote is available. Therefore it looks pretty bad if you are trying to introdue PC users to VMS and GCG. However, I have heard that a version of GCG running under Xwindows should be available sometime in 1993/94. This would allow users running MacX etc to access the system. Meantime hang on in there folks! Brian Robertson MPI fuer Biologie D74 Tuebingen Germany e-mail: robertson@mpib-tuebingen.mpg.dbp.de From owner-software@net.bio.net Wed Nov 04 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!ames!decwrl!concert!uvaarpa!gems.vcu.edu!agnew From: agnew@gems.vcu.edu Newsgroups: bionet.software Subject: Need help on analyzing ECG's Message-ID: <1992Nov5.150107.160@gems.vcu.edu> Date: 5 Nov 92 19:01:07 GMT Organization: Medical College of Virginia Lines: 12 Dear netpeople, I'm in search of software and or source code to analyze human ECG/EKG heart traces... Please reply to this net address. Many Thanks!!! Any leads at all will be much appreciated. Jim /^^^\ \ / Jim Agnew | AGNEW@RUBY.VCU.EDU (Internet) / > || Neurosurgery, | AGNEW@VCUVAX (Bitnet) /\_/ ' \ / MCV-VCU | This disc will self destruct in /________________> Richmond, VA, USA | five seconds. Good luck, Jim..." From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!agate!ames!saimiri.primate.wisc.edu!zaphod.mps.ohio-state.edu!sdd.hp.com!news.cs.indiana.edu!nstn.ns.ca!ac.dal.ca!isbruck From: isbruck@ac.dal.ca Newsgroups: bionet.software Subject: Data Entry into LIGAND Message-ID: <1992Nov5.214137.8652@ac.dal.ca> Date: 6 Nov 92 01:41:37 GMT Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 14 When using LIGAND, is it possible to bypass the SCAPRE program and use SCAFIT for data that is already in moles/L? How do I do this? Thanks, Richard Isbrucker ISBRUCK@AC.DAL.CA Dalhousie University Department of Pharmacology From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!swrinde!zaphod.mps.ohio-state.edu!news.acns.nwu.edu!network.ucsd.edu!sluggo!gribskov From: gribskov@sdsc.edu (Michael Gribskov) Newsgroups: bionet.software Subject: seqanalref->EndNote Message-ID: <1dbvd5INNtv@network.ucsd.edu> Date: 5 Nov 92 20:15:33 GMT Reply-To: gribskov@sdsc.edu Organization: San Diego Supercomputer Center @UCSD. Lines: 11 NNTP-Posting-Host: sluggo.sdsc.edu We have recently acquired the literature reference manager EndNote. I am interested in reading in some or all of the references in seqanalref, but need a filter to convert the format to something EndNote can read. If anyone has done this and can supply me with code for VMS,Unix,or Mac I would be very grateful. Alternatively, since EndNote is supposed to be able to read ProCite format, perhaps someone could provide me with seqanalref in ProCite format. Erik Sonnhammer at EMBL has apperently written a PC program to convert seqanalref to ProCite format. Unfort- unately, I do not have access to any kind of IBM type PC. Is anyone that has done this conversion willing to supply me with the converted file? Thanks for the help Michael Gribskov San Diego Supercomputer Center gribskov@sdsc.edu From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!swrinde!emory!wupost!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!ames!agate!doc.ic.ac.uk!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: Re: Mac front-end for VAX GCG Message-ID: <1992Nov6.063754.17892@comp.bioz.unibas.ch> Date: 6 Nov 92 06:37:54 GMT References: <1992Nov5.153519.15673@gserv1.dl.ac.uk> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Distribution: bionet Organization: EMBnet Switzerland [BASEL] Lines: 28 Nntp-Posting-Host: biox.embnet.unibas.ch In article <1992Nov5.153519.15673@gserv1.dl.ac.uk>, robertson@mpib-tuebingen.mpg.dbp.de (BRAIN ROBERTSON) writes: |> |> Therefore it looks pretty bad if you are trying to introdue PC users to VMS and |> GCG. However, I have heard that a version of GCG running under Xwindows should |> be available sometime in 1993/94. This would allow users running MacX etc to |> access the system. I (hopefully) will be able to get the QUERY system for public release quite soon. This is like the GCGNAV on UNIX but also runs on VMS. The pain with all these menu systems/front ends is that you need to maintain the menu definition langue to be quite simple. Thus, comfortable environments will cause a lot of overhead in maintenance (and , presumably, speed.). Second, who would like to start fasta with 20 clicks rather than type fasta and that's it? Last, don't overestimate the technology at the individual sites. Despite the growing 'high end' user basis, we still have the majority of our users on serial lines. I made some attempts to run SLIP along these lines. Not surprisingly, X performance is moderate at best. -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!SALK-SC2.SDSC.EDU!mangalam From: mangalam@SALK-SC2.SDSC.EDU Newsgroups: bionet.software Subject: Re: Message-ID: <9211061822.AA17484@net.bio.net> Date: 6 Nov 92 18:22:16 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 50 Jim Cassatt writes: >Got a couple of questions for those who run gopher. > >First - We are running tn3270 on a 3com network. The gopher >client cannot access the TCP stack even though the bat files have >been properly constructed. Our LAN manager says that the trouble >is the 3com network. Is this correct? Ack! Sorry, can't help you there - while you didn't want to hear this, this is one very real reason that Macs are much easier to interface with TCP/IP - one relatively solid, reliable interface (MacTCP). Drop the file into your system folder and everything (gopher, eudora, WAIStation, Fetch, Versaterm, etc) works 1st time every time (almost... 8-) > >Second - As an alternative I am using the gopher client that >resides on the NIH computer. Recently the PDB announced the >establishment of a gopher that I would like to access. Going >through the available menus it is not apparent to me how to >access a gopher hole that is not listed on the menus. Any >advice? Yes, just initaiate a new gopher wiith the following data: Type = 1 (so that the icon is a folder) Title = PDB/Brookhaven Data (or something more personal) Address = pdb.pdb.bnl.gov (domain name of the server) port = 70 (standard gopher port) This is done (if using Don Gilbert's Gopher App) by selecting the 'Internet | New Gopher Link' menu items and filling out the blanks appropriately. Or if using the PC version (PC Gopher II), you can use the Options | Configure menu selection and fill out the blanks as above. However, the "New Gopher" selection (Alt+G) does not work as appears to be advertised - all it does is bring up the initial screen again. A note to the authors is warranted. Cheers, Harry Harry Mangalam Vox:(619) 453-4100, x250 Dept of Biocomputing Fax:(619) 552-1546 The Salk Institute mangalam@salk-sc2.sdsc.edu 10010 N Torrey Pines Rd mangalam@salk-sgi.sdsc.edu La Jolla CA 92037 mangalam@salk.bitnet From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!CU.NIH.GOV!CZJ From: CZJ@CU.NIH.GOV Newsgroups: bionet.software Subject: (none) Message-ID: <9211061716.AA12536@net.bio.net> Date: 6 Nov 92 17:14:01 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 Got a couple of questions for those who run gopher. First - We are running tn3270 on a 3com network. The gopher client cannot access the TCP stack even though the bat files have been properly constructed. Our LAN manager says that the trouble is the 3com network. Is this correct? Second - As an alternative I am using the gopher client that resides on the NIH computer. Recently the PDB announced the establishment of a gopher that I would like to access. Going through the available menus it is not apparent to me how to access a gopher hole that is not listed on the menus. Any advice? Jim Cassatt From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!daresbury!news From: PARSONS_A@snd01.pcr.co.uk Newsgroups: bionet.software Subject: Weizmann Institute EMBNet node Message-ID: <1992Nov6.105425.4894@gserv1.dl.ac.uk> Date: 6 Nov 92 10:13:46 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 20 Original-To: BIO-SOFT Neteers, Am I right in thinking there is a sequence retrieval service in Israel that is available. I dont get a peep out of the NCBI and EMBL is a bit slow in turnaround. Any other pointers to other (faster but equally current) nodes would be much appreciated. Ta, Tony P. +----------------------------------------------------------------------------+ | Dr.Tony Parsons, VOX : + 44 304 616871 | | IT Department, FAX : + 44 304 616670 | | Pfizer Central Research, | | Ramsgate Road, +---------------------- e-mail ------------------------+ | Sandwich, |JANET : parsons_a@uk.co.pcr.snd01 | | KENT |Internet : parsons_a@snd01.pcr.co.uk | | CT13 9NJ UK |Compuserve : 100064,765 PSImail:234216700127.parsons_a | +-----------------+----------------------------------------------------------+ From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!daresbury!embnet.se!corax.udac.uu.se!sunic!lth.se!pollux.lu.se!nuntius From: Bo.Servenius@wblab.lu.se (Bo Servenius) Newsgroups: bionet.software Subject: GratefulMed over TCP/IP??? Message-ID: <1992Nov6.101626.5172@pollux.lu.se> Date: 6 Nov 92 10:16:26 GMT Sender: news@pollux.lu.se (Owner of news files) Organization: Lund University, SWEDEN Lines: 12 Nntp-Posting-Host: macservenius.wblab.lu.se X-Useragent: Nuntius v1.1 Dear Netters: Have started to look into GratefulMed for searching Medline. However I have a problem. The Swedish version of it can only handle communication over telephone modems. And that is costly and inconvinient as all my communications nowadays are over TCP/IP. Does anyone know if there is a version that is possible to run over TCP/IP???? yours BOSSE From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!daresbury!bioftp.unibas.ch!biox!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: Re: Weizmann Institute EMBNet node Message-ID: Date: 6 Nov 92 20:14:47 GMT References: <1992Nov6.105425.4894@gserv1.dl.ac.uk> Distribution: bionet Organization: EMBnet Switzerland [Basel] Lines: 20 PARSONS_A@snd01.pcr.co.uk writes: >Am I right in thinking there is a sequence retrieval service in Israel that >is available. I dont get a peep out of the NCBI and EMBL is a bit slow >in turnaround. Any other pointers to other (faster but equally current) nodes >would be much appreciated. If you mean internet-access GOPHER, there are gopher servers in Indiana, Houston and Basel serving you Genbank, PIR , EMBL and Swissprot respectively in a (crude) keyword search. Was that the meaning of "retrieval service"? Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!cs.utexas.edu!uunet!nih-csl.dcrt.nih.gov!donp From: donp@niaid.nih.gov (Don Preuss) Newsgroups: bionet.software Subject: Re: GratefulMed over TCP/IP??? Message-ID: <1992Nov6.192056.23513@alw.nih.gov> Date: 6 Nov 92 19:20:56 GMT References: <1992Nov6.101626.5172@pollux.lu.se> Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: National Institutes of Health Lines: 23 Bo.Servenius@wblab.lu.se (Bo Servenius) writes: Yes. Grateful Med 6.0 can work over tcpip. You can use either a version that works with Wollongong, or a version that works with a packet driver. (Uses ncsa for the engine.). I think it it somewhere around $25 to order it with hard copy, but it is all ftp'able from the National Library of Medicine. donp donp@niaid.nih.gov >Dear Netters: >Have started to look into GratefulMed for searching Medline. >However I have a problem. The Swedish version of it can only handle >communication over telephone modems. And that is costly and >inconvinient >as all my communications nowadays are over TCP/IP. Does anyone know >if there is a version that is possible to run over TCP/IP???? >yours >BOSSE From owner-software@net.bio.net Thu Nov 05 22:00:00 1992 Path: biosci!daresbury!bioftp.unibas.ch!biox!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: Re: (none) Message-ID: Date: 6 Nov 92 20:17:27 GMT References: <9211061716.AA12536@net.bio.net> Distribution: bionet Organization: EMBnet Switzerland [Basel] Lines: 26 CZJ@CU.NIH.GOV writes: >Second - As an alternative I am using the gopher client that >resides on the NIH computer. Recently the PDB announced the >establishment of a gopher that I would like to access. Going >through the available menus it is not apparent to me how to >access a gopher hole that is not listed on the menus. Any >advice? In the Bioftp gopher in Basel the PDB gopher has a link in EMBnet Resource Basel / Databases. It won't hel you much, though, if the client at NIH doesn't get you files saved or mailed to you. Very soon, Europe will have subject-oriented gopher trees so that there should be a central register for biology applications available. Maybe this helps Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | From owner-software@net.bio.net Fri Nov 06 22:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!decwrl!access.usask.ca!sklib.usask.ca!scott From: scott@sklib.usask.ca Newsgroups: bionet.software Subject: RE: (none) Message-ID: <7NOV92.15270067@sklib.usask.ca> Date: 7 Nov 92 15:27:00 GMT References: <9211061716.AA12536@net.bio.net> Sender: news@access.usask.ca (USENET News System) Organization: University of Saskatchewan Lines: 25 Nntp-Posting-Host: sklib.usask.ca In a previous article, CZJ@CU.NIH.GOV wrote: >Second - As an alternative I am using the gopher client that >resides on the NIH computer. Recently the PDB announced the >establishment of a gopher that I would like to access. Going >through the available menus it is not apparent to me how to >access a gopher hole that is not listed on the menus. Any >advice? One thing you can try is to connect to the main gopher at UMN via Telnet to consultant.micro.umn.edu, login gopher. Go to Other Gophers/North America/Brookhaven National Laboratory. Then pick the link to the NIH Gopher Site. This is defined as: Name=NIH Gopher site Type=1 Port=70 Path=1/ Host=helix.nih.gov Peter Scott - Manager, Small Systems, University of Saskatchewan Libraries From owner-software@net.bio.net Sat Nov 07 22:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!pipex!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!seb1005 From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.software Subject: Unix Bibliography Programs? Message-ID: <1992Nov8.002323.10817@infodev.cam.ac.uk> Date: 8 Nov 92 00:23:23 GMT Sender: news@infodev.cam.ac.uk (USENET news) Organization: U. of Cambridge, England Lines: 13 Nntp-Posting-Host: mbfs.bio.cam.ac.uk I'm looking to organize the articles I've read on the computer rather than keeping bits and pieces of references all over the place. I've seen in the bionet archives articles about bibliography managers for the Mac and PC, but haven't seen much discussion for Unix systems. Can people please suggest good bibliography/reference programs? I'll post a summary to to the net. Thanks very much Steven Brenner seb1005@mbfs.bio.cam.ac.uk From owner-software@net.bio.net Sun Nov 08 22:00:00 1992 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!zaphod.mps.ohio-state.edu!caen!uunet!mcsun!Germany.EU.net!uniol!Jens.Burkert From: Jens.Burkert@arbi.informatik.uni-oldenburg.de (Jens Burkert) Newsgroups: bionet.software Subject: wanted: neural spike trains Summary: wanted neural spike trains Keywords: neural spike Message-ID: <1992Nov9.133712.16135@arbi.Informatik.Uni-Oldenburg.DE> Date: 9 Nov 92 13:35:36 GMT Sender: news@arbi.Informatik.Uni-Oldenburg.DE Organization: University of Oldenburg, Germany Lines: 29 Hello! I'm looking for spike train data produced from real neurons. It is for the analyse of stochastic point processe described by Perkel, Gerstein and Moor (1967) and crosscorrellation analyse. Spike trains from two interacting (inhibitory or excitatory) pacemaker (or other) neurons would be very welcome. The organisation of the data should be in Intervals e.g. | | | | | <- neuronal spike train 10 10 15 10 ms or | | | | | 0 10 20 35 45 ms also floating point. Thank you Jens Burkert -- Jens Burkert (jens) * Abteilung Prozessinformatik Universitaet Oldenburg * DW-2900 Oldenburg (FRG) EARN: Jens.Burkert%arbi.informatik.uni-oldenburg.de@DOLUNI1 ISO: Jens.Burkert@arbi.informatik.uni-oldenburg.de From owner-software@net.bio.net Sun Nov 08 22:00:00 1992 Path: biosci!BRUFSC.bitnet!EEL3FPS From: EEL3FPS@BRUFSC.bitnet (Fernando Passold) Newsgroups: bionet.software Subject: Help Message-ID: <9211091929.AA08596@net.bio.net> Date: 9 Nov 92 19:29:45 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Universidade Federal de Santa Catarina/BRASIL Lines: 54 Dear Sir.: Fl 11/09/92 (List Moderator) I would like to know the intend of this list and if I could obtain some replies. I am a researcher tacking part of Biomedical Engineering Group Laboratory of Electrical Engineering Department at the Federal University of Santa Catarina. We develop little biomedical equipments and Expest Systems - such a Hospital Infection Control Aid and a Hybrid System (rule-based and neural network based) for Proposal and Evaluation of Anesthesian Plan. I am a master degree student, now, grapple in develop a Expert Network (also called, hybrid system: those whom combine neural networks with rule-based methods) for Planning and Evaluation of Plans of Anesthesia, continuing a PHD thesis, for Critical Patients (their who need critical cares) or Problem Patients (exceptional cases of patientes whom evaluate to critical patients). I have some troubles choosing the most suitable approach to develop this system. I do not know if neural networks could be the key to solve the main part of the problem, because we are dealing with exceptions that probably could best solved throught a rule-based method. At lately, there are a few shells systems applying object-orienthed technics with rule-based or frames methods such the new Kappa PC Application Development Systems for Windows environment, from IntellCorp. Inc.. So, I am interested in implementations of hybrid systems using object-oriented programming. Maybe, there will be a way to link neural networks simulators using object-oriented approach to another heuristical languages such as Turbo-Prolog object- oriented. I would be glad if someone could make a comment about it, as well as indicate if there exists a _similar research_. Please, reply directly to me as I am not subcribed to this list. Thanks a lot respect to this matter, best regards, Fernando Passold Biomedical Engineering Group Lab. UFSC/BRAZIL E-mail: ee3fps@brufsc.bitnet P.S.: I am interested in subcribing in your list if not a large amount of material is normaly posted to it. From owner-software@net.bio.net Sun Nov 08 22:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!mcsun!sunic!lth.se!pollux.lu.se!nuntius From: Bo.Servenius@wblab.lu.se (Bo Servenius) Newsgroups: bionet.software Subject: GratefulMed over tcp/ip???? for Mac!!! Message-ID: <1992Nov8.225129.15997@pollux.lu.se> Date: 8 Nov 92 22:51:29 GMT Sender: news@pollux.lu.se (Owner of news files) Organization: Lund University, SWEDEN Lines: 13 Nntp-Posting-Host: macservenius.wblab.lu.se X-Useragent: Nuntius v1.1 Dear Netters: Thanks for your comments about gm6.0. But which is the tcp/ip adress where I can find it for free FTP???? BTW gm6.0 is for PC isn't it??? Is there a tcp/ip version for Macs as well?? yours BOSSE From owner-software@net.bio.net Sun Nov 08 22:00:00 1992 Path: biosci!bcm!lib!dfenyes From: dfenyes@thesis1.med.uth.tmc.edu (David Fenyes,ms89,,7901935) Newsgroups: bionet.software Subject: Looking for *nix protein/gene software Keywords: protein dna rna analysis software Message-ID: <7790@lib.tmc.edu> Date: 9 Nov 92 22:00:06 GMT Sender: usenet@lib.tmc.edu Organization: University of Texas Medical School at Houston Lines: 19 Nntp-Posting-Host: thesis1.med.uth.tmc.edu Hello *, I'm a grad student studying the Alzheimer's beta-amyloid precursor protein at U.T Houston, and am looking for a suite of DOS or unix-based protein/gene analysis tools, particularly one with the capability to read the formats used my major gene/protein databases. I'm aware of DOS-based suites such as PC-Gene (tm), but in general the astronomical pricing and awkward usage makes these less than ideal. I'd be happy to post any information I receive. Thanks for any info, David -- David Fenyes dfenyes@thesis1.med.uth.tmc.edu University of Texas Medical School Houston, Texas From owner-software@net.bio.net Mon Nov 09 22:00:00 1992 Path: biosci!daresbury!embnet.se!bio.embnet.se!sunic!lth.se!pollux.lu.se!nuntius From: Bo.Servenius@wblab.lu.se (Bo Servenius) Newsgroups: bionet.software Subject: The program Amplify for PCR design - where can I find it??? Message-ID: <1992Nov10.012249.1058@pollux.lu.se> Date: 10 Nov 92 01:22:49 GMT Sender: news@pollux.lu.se (Owner of news files) Organization: Lund University, SWEDEN Lines: 8 Nntp-Posting-Host: macservenius.wblab.lu.se X-Useragent: Nuntius v1.1 Dear Netters: Have heard about a program Amplify for designing of PCR primers. Is it a freeware/shareware and if so where can I find it for FTP??? yours BOSSE From owner-software@net.bio.net Mon Nov 09 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!caen!batcomputer!reed!bowman From: bowman@reed.edu (Eric Bowman (bobo)) Newsgroups: bionet.software Subject: InPlot for Mac? Message-ID: <1992Nov10.000502.20308@reed.edu> Date: 10 Nov 92 00:05:02 GMT Organization: Reed College, Portland, OR Lines: 12 My apologies if you see this twice, we're having news problems... We got an add for some PC software, InPlot, which looks like exactly what we want for Macs. Specifically, very general data plotting capabilities (scatter, line, bar, error bars, etc.), plus non-linear regression, plus Scatchard plots. Does such a product exist for Macintosh? Thanks, Eric Bowman bowman@reed.edu From owner-software@net.bio.net Mon Nov 09 22:00:00 1992 Path: biosci!uwm.edu!caen!sdd.hp.com!elroy.jpl.nasa.gov!swrinde!network.ucsd.edu!riscsm!collet From: collet@scripps.edu (Thomas Collet) Newsgroups: comp.sys.mac.wanted,bionet.software Subject: MolBio Software for sale in Germany Message-ID: <1992Nov9.223937.4699@riscsm.scripps.edu> Date: 9 Nov 92 22:39:37 GMT Sender: usenet@riscsm.scripps.edu Organization: The Scripps Research Institute, La Jolla, California, USA Lines: 8 Xref: biosci comp.sys.mac.wanted:1482 bionet.software:3587 For sale in Germany: Molecular Biology software for the Macintosh PlasmidArtist 1.2 newest version !!! Draw publication-quality plasmid maps and print them or export the to page layout programs. AssemblyLign: alignment of DNA sequences in conjuntion with or without MacVector. As I now live in Germany and have only sporadic email access, I would very much prefer a phone call to 0211 / 31 72 19. I will then call back serious candidates. From owner-software@net.bio.net Mon Nov 09 22:00:00 1992 Path: biosci!agate!spool.mu.edu!sdd.hp.com!ux1.cso.uiuc.edu!news.cso.uiuc.edu!phylo!scott From: scott@phylo.life.uiuc.edu (Snooky Fudge) Newsgroups: bionet.software Subject: Re: The program Amplify for PCR design - where can I find it??? Message-ID: Date: 10 Nov 92 03:26:30 GMT References: <1992Nov10.012249.1058@pollux.lu.se> Sender: usenet@news.cso.uiuc.edu (Net Noise owner) Organization: University of Illinois at Urbana Lines: 9 anonymous ftp to sumex-aim.stanford.edu, among billions of others. -- Coffee Facts from Dr. Science: 1) You can never brew coffee too strong. 2) You can never drink too much coffee. 3) Coffee does not make you nervous. Your own inadequacies do that. Coffee merely increases your perception of your own inadequacies. 4) Tea is to coffee as ginger ale is to Scotch. From owner-software@net.bio.net Mon Nov 09 22:00:00 1992 Path: biosci!CSC.FI!Rob.Harper From: Rob.Harper@CSC.FI (Rob Harper) Newsgroups: bionet.software Subject: Recent msdos uploads to SIMTEL20 (25-Oct - 9-Nov 1992) Message-ID: <199211101018.AA01290@csc.fi> Date: 10 Nov 92 10:18:36 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 379 The following files have been recently uploaded to WSMR-SIMTEL20.ARMY.MIL (between 25-Oct-92 and 9-Nov-92): NOTE: Type B is Binary; Type A is ASCII Filename Type Length Date Description ============================================== Directory PD1: 4D401D.ZIP B 29134 921031 4DOS/4OS2 patch files to update to revision d 4DATEF.ZIP B 2372 921026 .BTM functions: Day-of-Week, Number-of-Week 4DMAN10B.ZIP B 2915 921026 Unix-like MAN, searches docs for cmds, .BTM 4DOS401D.ZIP B 257581 921031 4DOS401B COMMAND.COM replacement, manual, 1/2 4DOS401P.ZIP B 288840 921031 4DOS401B COMMAND.COM replacement, exe/pgms,2/2 4DOS401U.ZIP B 247377 921031 4DOS401B update for registered 4DOS 4.0 users 4DOSNG.ZIP B 98951 921031 Norton Guides Database for 4-DOS Command.Com 4DPATH.ZIP B 1467 921026 Add/remove path(s) to/from %PATH (.BTM) 4ERROR.ZIP B 2511 921026 Show description for given DOS error, .BTM 4FC12.ZIP B 25198 921031 4Comment: Extracts file descriptions from 4DOS 4MENU10B.ZIP B 5374 921026 Desktop MENU interface for 4dos (.BMT) 4RANDOM.ZIP B 2626 921026 Pseudo-random generator for 4dos (.BTM) 4WHTS10B.ZIP B 1952 921026 WHATIS, 'what-this-cmd-stands-for'-cmd, .BTM EZ-BTM04.ZIP B 49792 921026 4DOS BTM files: loaders/regular/libraries/help MAV120.ZIP B 3763 921029 4DOS BTM file: Mally's Archive Viewer Directory PD1: AM83.ZIP B 218768 921108 ArcMaster front-end/convrt for ARC/ARJ/LZH/ZIP FV141.ZIP B 8859 921108 View dirs of ARC/DWC/LBR/LZH/PAK/ZIP/ZOO/SFXs SHEZ82.ZIP B 207888 921031 Shell for archive manipulation, w/virus check SHEZT.ZIP B 35928 921031 Online tutorial for first time SHEZ users Directory PD1: NUMCMD.ZIP B 86656 921027 Number-Pad based Interface for AutoCAD R12/386 Directory PD1: BASWIZ18.ZIP B 303084 921107 ASM/BASIC lib routines for QBasic/BASCOM/PDS BPP10.ZIP B 52729 921107 Preprocessor for QBASIC/QuickBasic/BASCOM/PDS BWB110E.ZIP B 81068 921029 Bywater BASIC Interpreter 1.10, EXE and doc BWB110S.ZIP B 116429 921029 Bywater BASIC Interpreter 1.10, C source code LIBWIZ13.ZIP B 82579 921107 Hanlin's Library Wizard BASIC library manager PBCLON20.ZIP B 399272 921107 PBClone: ASM/BASIC lib. Replaces ProBas/ADVBAS Directory PD1: TSBAT39.ZIP B 93500 921026 Collection of useful batch files by Timo Salmi Directory PD1: BDOC_256.ZIP B 112733 921026 Binkleyterm mail/term pgm docs v2.56 Beta BNKB256.ZIP B 181752 921026 Binkleyterm 2.56 Beta executables & update doc NLFE10.ZIP B 71453 921106 NLFE v1.0: Frontend PCBoard for Internet/UUCP Directory PD1: ASPBBS24.ZIP B 59127 921108 Listing of all ASP approved BBSs, as of Oct 92 BBS1092C.ZIP B 95990 921026 'THELIST' national BBS list for October 1992 Directory PD1: QUIKC21.ZIP B 77016 921026 Quick screen utilities v2.1 for Turbo C & MS C Directory PD1: UCALC12.ZIP B 53551 921027 Scientific expr. evaluator with many features Directory PD1: CDISK632.ZIP B 258866 921026 Disk catalog system also does ARC/PAK/ZIP/LBR Directory PD1: FE51-A.ZIP B 308483 921026 File Express v5.10 database system, 1 of 3 FE51-B.ZIP B 353036 921026 File Express v5.10 database system, 2 of 3 FE51-C.ZIP B 305862 921026 File Express v5.10 database system, 3 of 3 GC11.ZIP B 60464 921107 Graphical employee scheduling program INV10.ZIP B 179672 921027 Home inventory and moving management program MM-701.ZIP B 204416 921026 MealMaster database program for recipes, v7.01 Directory PD1: DVCPY200.ZIP B 113239 921026 DESQview-aware copy util, works in Win3.x too Directory PD1: CCD100.ZIP B 43406 921106 Quickly change directories (for NT and DOS) Directory PD1: AEASY101.ZIP B 72300 921102 ASYNC support for djgpp AECUR101.ZIP B 133335 921102 Curses for djgpp AETSK101.ZIP B 88004 921102 Full pseudo-tasking support for djgpp AEWIN101.ZIP B 114601 921102 Text windows for djgpp CBGRD102.ZIP B 303098 921102 GRX library, documentation CBGRF102.ZIP B 879369 921102 GRX library, fonts CBGRX102.ZIP B 842221 921102 GRX library, libs and includes DJBSN116.ZIP B 164589 921102 GNU bison-1.16 (djgpp) DJDEV109.ZIP B 796370 921102 Minimum development environment (djgpp) DJDOC109.ZIP B 103508 921102 All documentation for djgpp 1.09 DJEMU109.ZIP B 78798 921102 EMU387 sources and executable (djgpp) DJFLX237.ZIP B 110526 921102 GNU flex-2.3.7 (djgpp) DJG16222.ZIP B 96126 921102 Real-mode gcc.exe DJGAS138.ZIP B 70425 921102 GNU gas-1.38.1 (djgpp) DJGCC222.ZIP B 856115 921102 GNU gcc-2.2.2, no cc1plus or cc1obj DJGPO222.ZIP B 977668 921102 GNU gcc-2.2.2 cc1plus and cc1obj DJLGR109.ZIP B 84001 921102 256-color graphics library (djgpp) DJLSR109.ZIP B 499781 921102 Sources for all libraries (djgpp) DJPRF109.ZIP B 274976 921102 Libraries and executables to use profiling DJSRC109.ZIP B 137481 921102 Sources for go32-utils-GNU-gr-drivers DJSUP109.ZIP B 26271 921102 readme, merge, split, manifest, Index, (djgpp) QDDVX101.ZIP B 975455 921102 Quarterdeck DESQview/X libraries for djgpp SRBNU100.ZIP B 219844 921102 djgpp source for binutils SRBSN116.ZIP B 281449 921102 djgpp sources for bison SRDIF115.ZIP B 123659 921102 djgpp sources for diff SRFLX237.ZIP B 177739 921102 djgpp sources for flex SRGAS138.ZIP B 369716 921102 djgpp sources for gas Directory PD1: CNFMT108.ZIP B 44469 921026 Background floppy disk formatter by SYDEX DOG320.ZIP B 54611 921026 Disk OrGanizer: Disk defragmenter DOS5-compat. FFIT161.ZIP B 42287 921108 Copies files to disks optimally (knapsack) HDTS535A.ZIP B 139775 921026 Comprehensive HD test with support for DOS 5.0 Directory PD1: CEDIT30.ZIP B 427997 921105 Mouse-based Chinese word processor (EGA/VGA) TDE21.ZIP B 339356 921102 PD multi-window/file text editor w/C & asm src TRIVED07.ZIP B 11593 921106 FOSSIL/console vi-like editor for BBS use VDE164C.ZIP B 149888 921031 Meyer's small, fast, WordStar-like text editor VDE164CS.ZIP B 17430 921031 Screen writers macros for VDE text editor XVIDOC.ZIP B 73662 921106 Xvi text editor - Documentation, 1 of 3 XVIEXE.ZIP B 66835 921106 Xvi text editor - MS-DOS executable, 2 of 3 XVISRC.ZIP B 261228 921106 Xvi text editor - Source code, 3 of 3 Directory PD1: AALPHA.ZIP B 485008 921026 Animated Alphabet for pre-school to 1st grader AMATH1.ZIP B 364071 921026 Animated Math: counting/addition/subtraction AMEM10.ZIP B 254102 921026 Animated Memory Game: aids kids' memory skills ANIMSHAP.ZIP B 294552 921026 Animated Shapes: shape & color identification Directory PD1: MYZ80103.ZIP B 76581 921106 Simeon Cran's Z80 CP/M and Z-System emulator Directory PD1: SIM9210.IDX A 24657 921103 Comma-delimited list of October 1992 uploads SIMAIL50.ZIP B 9463 921103 Converts output of SIMTEL35 & SIMTEL22 to mail SIMIBM.ZIP B 275659 921110 Comma-delim list of all MSDOS files w/descrip. SIMLIST.ZIP B 269582 921110 Text format list of all MSDOS files w/descrip. UPLOADS.OCT A 23615 921103 List of uploads to SIMTEL20 for October 1992 Directory PD1: NCDC151.ZIP B 60928 921026 Fast XX/UU de/encoder for DOS/VAX/UNIX w/C src UNLZEXE8.ZIP B 15021 921025 Converts LZEXE compressed EXE to original EXE Directory PD1: CGZDC31A.ZIP B 196577 921108 Capital Gainz 3.1-portfolio mgr, docs, 4/6 CGZDM31A.ZIP B 174191 921108 Capital Gainz 3.1-portfolio mgr, tutorial, 6/6 CGZDT31A.ZIP B 9110 921108 Capital Gainz 3.1-portfolio mgr, data, 3/6 CGZEX31A.ZIP B 27933 921108 Capital Gainz 3.1-portfolio mgr. examples, 5/6 CGZLB31A.ZIP B 154138 921108 Capital Gainz 3.1-portfolio mgr, library, 2/6 CGZPR31A.ZIP B 299940 921108 Capital Gainz 3.1-portfolio mgr, program, 1/6 Directory PD1: ILMP1192.ZIP B 77166 921107 GEnieLamp IBM Online Magazine (Nov 1992) Directory PD1: GIFV28.ZIP B 177850 921106 Reads GIF/BMP, excellent slide show capability SGIF18.ZIP B 30441 921030 Slideshow viewer for Tseng, ATI, Paradise, 24X Directory PD1: ARTFORM.ZIP B 396814 921107 Artform 3D graphics animation generator FRCAL032.ZIP B 344071 921028 Fractal drawing program: 15 formulae available GRPHCA20.ZIP B 306743 921109 Interactive scientific plotting program, v2.0 IFSE099.ZIP B 118771 921029 ImgFun: Image viewer and JPEG compression IMPROC41.ZIP B 362211 921026 Improces graphics editor. Req VGA/SVGA & mouse PCXDMP71.ZIP B 266203 921028 TSR to dump EGA, (S)VGA screens to PCX-files VX38611.ZIP B 102373 921107 32bit DOS GIF/JPEG/TARGA viewer for SS24X Directory PD1: READIT28.ZIP B 105010 921103 Text file reader with bookmark, etc for speech SFTKBD10.ZIP B 29518 921102 Virtual on-screen keyboard that uses the mouse TBRL31.ZIP B 112940 921103 DEMO version of 'Turbo Braille' program ZENWORD.ZIP B 44969 921102 Speech friendly menu based word processor Directory PD1: HLPDK10.ZIP B 161832 921029 Hypertext Help development kit SUREFI-1.ZIP B 210989 921104 Create Smart Documents, build in dbase, 1 of 2 SUREFI-2.ZIP B 258355 921106 Docs & demo for award-winning SUREFIRE. 2 0f 2 Directory PD1: ASP5801.ZIP B 468198 921031 Association of Shareware Professionals catalog BBSTIP12.ZIP B 5971 921026 Effective Shareware distribution via the BBS HACK1092.ZIP B 36390 921026 The Hack Report - trojan/virus/hacked programs MSDOSANN.ZIP B 3357 921025 Info on MS-DOS uploads announce mailing list NEWSLST.ZIP B 21864 921031 List of active Usenet newsgroups Directory PD1: LSALV103.ZIP B 39240 921105 List all salvagable files on Netware 3.x drive NETBDAY5.ZIP B 20766 921104 Birthday reminder at login for Novell networks Directory PD1: DOSLOGO.ZIP B 208443 921107 LOGO Turtle Graphics for MS-DOS MSWLGO24.ZIP B 495971 921102 MswLogo x2.4: LOGO fo From owner-software@net.bio.net Mon Nov 09 22:00:00 1992 Path: biosci!agate!doc.ic.ac.uk!uknet!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!seb1005 From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.software Subject: 3D drawing software for the Macintosh Message-ID: <1992Nov10.165755.11837@infodev.cam.ac.uk> Date: 10 Nov 92 16:57:55 GMT Sender: news@infodev.cam.ac.uk (USENET news) Organization: U. of Cambridge, England Lines: 13 Nntp-Posting-Host: mbfs.bio.cam.ac.uk A member of my laboratory is interested in drawing some 3-D structures on his macintosh. The structures need not be "perfect," so he wants something simple -- like a 3D version of MacDraw. (Rather than, for example, a mac version of autocad, etc.) Can anyone offer any suggestions on if there is any such software available? Thanks very much Steven Brenner seb1005@mbfs.bio.cam.ac.uk From owner-software@net.bio.net Mon Nov 09 22:00:00 1992 Path: biosci!ASRR.ARSUSDA.GOV!jkirkbride From: jkirkbride@ASRR.ARSUSDA.GOV ("JOSEPH H. KIRKBRIDE") Newsgroups: bionet.software Subject: Latest version of DELTA software available Message-ID: <9211102034.AA02629@net.bio.net> Date: 10 Nov 92 19:34:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 36 The latest version of the DELTA software system from Michael J. Dallwitz, CSIRO Division of Entomology, GPO Box 1700, Canberra ACT 2601, Australia, telephone +61 6 246 4075, FAX +61 6 246 4000, Internet delta@ento.csiro.au, is now available as shareware via Internet FTP. To get the DELTA software and associated databases for flowering plants, connect via FTP to HUH.HARVARD.EDU using the id FTP and the password FTP. The DELTA software is now available for three different operating systems: /PUB/SOFTWARE/DELTA/MSDOS DELTA programs for MS-DOS operating system on IBM-compatible microcomputers. /PUB/SOFTWARE/DELTA/OS2 DELTA programs for OS2 operating system on IBM-compatible microcomputers. /PUB/SOFTWARE/DELTA/SUNOS DELTA programs for the SUN operating system. There are two databases available ready use with the DELTA software (INTKEY) for identification of organism or querying for information. /PUB/SOFTWARE/DELTA/ANGIO Families of flowering plants of th e world with emphasis on Australia. /PUB/SOFTWARE/DELTA/GRASS Genera of grasses of the world. In addition there are a number of shareware programs for MS-DOS stored in: /PUB/SOFTWARE/DELTA/GRAHICS These programs are very useful in preparing graphic images for use with the DELTA software. Joseph H. Kirkbride, Jr. USDA, Agricultural Research Service Systematic Botany and Mycology Laboratory Building 265, BARC-East Voice telephone: 301-504-9447 Beltsville, Maryl and 20705-2350 USA Internet: JKIRKBRIDE@ASRR.ARSUSDA.GOV From owner-software@net.bio.net Mon Nov 09 22:00:00 1992 Path: biosci!agate!spool.mu.edu!nigel.msen.com!emory!sol.ctr.columbia.edu!news.columbia.edu!cunixb.cc.columbia.edu!ksb3 From: ksb3@cunixb.cc.columbia.edu (Katrin S Barth) Newsgroups: bionet.software Subject: program to identify factors binding to palindromic sequence?? Message-ID: <1992Nov10.161219.1329@news.columbia.edu> Date: 10 Nov 92 16:12:19 GMT Sender: usenet@news.columbia.edu (The Network News) Organization: Columbia University Lines: 4 Nntp-Posting-Host: cunixb.cc.columbia.edu Does anybody know about a program that can identify factors that bind to a given sequence (like a palindromic sequence?) Anukampa Barth KSB3@cunixb.cc.columbia.edu From owner-software@net.bio.net Tue Nov 10 22:00:00 1992 Path: biosci!agate!netsys!decwrl!uunet!emba-news.uvm.edu!emba-news.uvm.edu!brianf From: brianf@dna.uvm.edu (Brain Foley) Newsgroups: bionet.software Subject: Re: Re: Graphing Program Message-ID: Date: 11 Nov 92 01:33:57 GMT References: <01GQRLSU3G6Q8WW08H@INET.D48.LILLY.COM> Sender: news@uvm.edu Distribution: bionet Organization: Division of EMBA, University of Vermont Lines: 14 In-Reply-To: SMITH_DENNIS_P@LILLY.COM's message of 5 Nov 92 01: 34:35 GMT I have had no trouble using DeltaGraph Pro to plot 10 to the negative power numbers. In default mode it prints these numbers as .0001 .0000001 etc., but I can change that by selecting those data (just click on any of these numbers and they should all get selected at once), then changing the format of them to Scientific. Write back if you can't figure this out. I'm not seated at my Mac now, so I can't give more specific instructions. -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * ******************************************************************** From owner-software@net.bio.net Tue Nov 10 22:00:00 1992 Path: biosci!agate!spool.mu.edu!nigel.msen.com!emory!swrinde!zaphod.mps.ohio-state.edu!rpi!utcsri!torn!csd.unb.ca!morgan.ucs.mun.ca!cs.mun.ca!odie.cs.mun.ca!harold From: harold@odie.cs.mun.ca (Harold Wareham(Todd)) Newsgroups: bionet.software Subject: HELP: .HQX Format for Macs Message-ID: <1992Nov9.190919.12960@cs.mun.ca> Date: 9 Nov 92 19:09:19 GMT Sender: usenet@cs.mun.ca (NNTP server account) Distribution: na Organization: CS Dept., Memorial University of Newfoundland Lines: 12 I recently obtainted a Macintosh file in .HQX format from the UIBio archives. I need a copy of BinHex 4.0 or Stuffit to uncompress and use the thing. Where can I obtain copies of either of these programs? Thanks, - Todd Todd Wareham harold@odie.cs.mun.ca |"Success in science depends not Department of Computer Science | only on rational argument but Memorial University of Newfoundland | on a mixture of subterfuge, St. John, NF, Canada A1C 5S7 | rhetoric, and propaganda" | - Feyerabend From owner-software@net.bio.net Tue Nov 10 22:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!utcsri!newsflash.concordia.ca!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.software Subject: Re: The program Amplify for PCR design - where can I find it??? Message-ID: Date: 11 Nov 92 12:21:02 GMT References: <1992Nov10.012249.1058@pollux.lu.se> Sender: news@sifon.cc.mcgill.ca Organization: McGill University Lines: 72 Nntp-Posting-Host: monod.biol.mcgill.ca Bo.Servenius@wblab.lu.se (Bo Servenius) writes: >Have heard about a program Amplify for designing of PCR primers. >Is it a freeware/shareware and if so where can I find it for FTP??? Dear Bosse, from last week on bionet.molbio.methds-reagnts: ---------8<---cut here ----8<----------------------- ******************************************************************* * * * Frequently Asked Question (FAQ) list * * for bionet.molbio.methds-reagnts * * * * Last update was on 01 November 1992 * * * ******************************************************************* This FAQ list is available by anonymous ftp to ncifcrf.gov Simply get the file pub/methods/FAQlist [ lots of usefull stuff removed ] Paul N. Hengen National Cancer Institute Frederick Cancer Research and Development Center Frederick, Maryland 21702-1201 USA e-mail: pnh@ncifcrf.gov [ lots of usefull stuff removed ] [ from the oligo/primer/pcr section ... ] *********************** 4. Amplify - MAC only *********************** This software is for use in designing, analyzing, and simulating experiments involving the polymerase chain reaction (PCR). PCR is a technique used by molecular biologists to amplify highly selected segments of DNA. You can obtain a copy of Amplify from sumex-aim.stanford.edu via anonymous ftp. Look for the file: /info-mac/app/amplify-10.hqx The author, Bill Engels, can be reached at WREngels@wisc.macc.edu ---------8<---cut here ----8<----------------------- regards, francis -- | B.F. Francis Ouellette | manager, yeast chromosome I project | dept of biology, McGill university, Montreal, Qc, Canada | francis@monod.biol.mcgill.ca From owner-software@net.bio.net Tue Nov 10 22:00:00 1992 Path: biosci!agate!doc.ic.ac.uk!daresbury!news From: PARSONS_A@snd01.pcr.co.uk Newsgroups: bionet.software Subject: Sequence of vector Lambda gt22 anybody?? Message-ID: <1992Nov11.143016.29901@gserv1.dl.ac.uk> Date: 11 Nov 92 14:28:42 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 23 Original-To: BIO-SOFT Netfolk, I am not sure this hit the bulletin board on my last mail so here goes again... Does anybody have or know where I can get the sequence of Lambda gt22 vector. The reference is Jang H. Han and William J. Rutter (1987) NAR vol 15 no. 15 "Lambda gt22 an improved lamda vector for the directional cloning of full-length cDNA" Any of the other lamda variants would also be a bonus (eg gt11, gt18 etc.) Many thanks, Tony Parsons +----------------------------------------------------------------------------+ | Dr.Tony Parsons, VOX : + 44 304 616871 | | IT Department, FAX : + 44 304 616670 | | Pfizer Central Research, | | Ramsgate Road, +---------------------- e-mail ------------------------+ | Sandwich, |JANET : parsons_a@uk.co.pcr.snd01 | | KENT |Internet : parsons_a@snd01.pcr.co.uk | | CT13 9NJ UK |Compuserve : 100064,765 PSImail:234216700127.parsons_a | +-----------------+----------------------------------------------------------+ From owner-software@net.bio.net Tue Nov 10 22:00:00 1992 Path: biosci!uwm.edu!cs.utexas.edu!usc!sol.ctr.columbia.edu!destroyer!uunet!munnari.oz.au!uniwa!uniwa!usenet From: robert@arbo.microbiol.uwa.oz.au (Robert Coelen) Newsgroups: bionet.software Subject: Re: GratefulMed over TCP/IP??? Message-ID: <1dqh8rINNcjs@uniwa.uwa.edu.au> Date: 11 Nov 92 08:46:19 GMT Organization: University of Western Australia Lines: 21 NNTP-Posting-Host: mve.microbiol.uwa.edu.au In article <1992Nov6.192056.23513@alw.nih.gov> donp@niaid.nih.gov (Don Preuss) writes: >Bo.Servenius@wblab.lu.se (Bo Servenius) writes: > > >Yes. Grateful Med 6.0 can work over tcpip. You can use either a version >that works with Wollongong, or a version that works with a packet >driver. (Uses ncsa for the engine.). I think it it somewhere around >$25 to order it with hard copy, but it is all ftp'able from the National ^^^^^^^^^ >Library of Medicine. > >donp >donp@niaid.nih.gov Can you give us any pointers (address & directory) Don ? Robert Coelen Dept of Microbiology University of Western Australia from the Land Down Under ! From owner-software@net.bio.net Tue Nov 10 22:00:00 1992 Path: biosci!uwm.edu!cs.utexas.edu!usc!sol.ctr.columbia.edu!destroyer!uunet!munnari.oz.au!uniwa!andrew.chi.uwa.edu.au!mike From: mike@chi.uwa.edu.au (Mike Schon-Hegrad) Newsgroups: bionet.software Subject: Re: GratefulMed over tcp/ip???? for Mac!!! -Ditto Message-ID: <1dqiqtINNef9@uniwa.uwa.edu.au> Date: 11 Nov 92 09:13:01 GMT References: <1992Nov8.225129.15997@pollux.lu.se> Organization: Western Australian Research Institute for Child Health Lines: 25 NNTP-Posting-Host: andrew.chi.uwa.edu.au X-UserAgent: Nuntius v1.1.1d12 X-XXMessage-ID: X-XXDate: Wed, 11 Nov 92 09:13:03 GMT In article <1992Nov8.225129.15997@pollux.lu.se> Bo Servenius, Bo.Servenius@wblab.lu.se writes: >Thanks for your comments about gm6.0. But which is the tcp/ip adress >where I can find it for free FTP???? > >BTW gm6.0 is for PC isn't it??? Is there a tcp/ip version for Macs >as well?? I would like to know this too. Many thanks Mike _________________________________________________ Mike Schon-Hegrad Research Officer Western Australian Research Institute for Child Health Roberts Road, SUBIACO Western Australia 6008 Phone (09) 340 8388 Fax (09) 388 3414 email mike@chi.uwa.edu.au __________________________________________________ From owner-software@net.bio.net Wed Nov 11 22:00:00 1992 Path: biosci!MED.PITT.EDU!bsh From: bsh@MED.PITT.EDU (Basavaraju Shankarappa) Newsgroups: bionet.software Subject: pub domain software for rearranging frag disk Message-ID: <9211121822.AA13955@miranda.med.pitt.edu> Date: 12 Nov 92 18:22:05 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Hello netters: Can any one tell me whether and where I can get a public domain software for correcting the fragmented disk space. I was told that some of the programs that can do the job are COMPRESS, SPIN-WRITE DISK OPTIMIZER etc., I am looking for a public domain software that can do the job above programs can do. Thank you for considering the request. Raj Shankarappa Univ of Pittsburgh bsh@med.pitt.edu From owner-software@net.bio.net Wed Nov 11 22:00:00 1992 Path: biosci!SALK-SC2.SDSC.EDU!mangalam From: mangalam@SALK-SC2.SDSC.EDU Newsgroups: bionet.software Subject: Mac Primer executable Message-ID: <9211121902.AA12502@net.bio.net> Date: 12 Nov 92 19:02:04 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 47 Hi, Since the Primer gang has still not put the Mac exe up on their FTP server, and I've received a couple of requests for it, I've bundled the distribution, with a ThinkC project, and the executable as a binhexed, self-extracting archive and put it up on our server (salk-sc2.sdsc.edu) in: [anonymous.mac] (it's a VAX). Feel free to distribute it, but only as a complete set (to adhere to the original distribution policy). Beware, macaholics, it is the same text-window interface that pops up on a VAX or PC, but it is certainly handy if you need it. The ThinkC project comes to you by the good graces of Richard Cooke of Universite de Perpignan (COOKE@FRPERP51.bitnet). For your info: Primer benchmarks Sample.seq Sample2.seq Sample3.seq SGI Crimson R4000/4010:50MHz 6s instantly 25s 16kB(1')/1MB(2') Cache, 64 MB Main Standard MIPS compiler PC Clone 386DX/387:25MHz 64 kB Cache, 8MB Main 30s 1s 75s (but only 640kB accessible) MS QuickC for Windows -> DOS exe MacIIci 68030/68881:25MHz 42s 3s 183s Std Cache card, 8MB Main Think C 5.0 Cheers Harry Harry Mangalam Vox:(619) 453-4100, x250 Dept of Biocomputing Fax:(619) 552-1546 The Salk Institute mangalam@salk-sc2.sdsc.edu 10010 N Torrey Pines Rd mangalam@salk-sgi.sdsc.edu La Jolla CA 92037 mangalam@salk.bitnet From owner-software@net.bio.net Wed Nov 11 22:00:00 1992 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!news.cso.uiuc.edu!uxa.cso.uiuc.edu!sepg1545 From: sepg1545@uxa.cso.uiuc.edu (Scott Eric Peterson) Newsgroups: bionet.software Subject: Mac tutorials/reviews - Help Summary: Looking for Mac tutorials/reviews Keywords: software Message-ID: Date: 11 Nov 92 05:52:51 GMT Sender: usenet@news.cso.uiuc.edu (Net Noise owner) Organization: University of Illinois at Urbana Lines: 7 Hello, I'm new to this group and couldn't find a FAQ, so I don't know just how dumb this question is- but here it is. I'm am looking for mac-software that may be useful for 2nd year medical students- reviewing for boards etc. I'm am aware of some shareware hypercard stacks that are pretty useful and was just wondering what was available. If anyone has any that is ftp-able or on a server somewhere I would appreciate any mail telling me about it. Thanks in advance. From owner-software@net.bio.net Wed Nov 11 22:00:00 1992 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: SeqApp sliding-base bug fix (Macintosh) Message-ID: Date: 12 Nov 92 14:59:47 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 38 Nntp-Posting-Host: sunflower.bio.indiana.edu 12 Nov 92, version 1.8a154 -- interim bug fix release. Cures problem introduced in version 1.8a153: sequence data was lost when the "sliding bases" feature of adding gaps was used, then the document was saved. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - SeqApp is a biological sequence editor and analysis program for Macintosh computers. It includes links to network services and external analysis programs. Features include multiple sequence alignment editor single sequence editor window read and write several sequence file formats easy hand alignment features including colored bases and sliding automatic multiple sequence alignment thru Clustal external app automatic gel fragment alignment to contigs thru exernal app consensus,reverse,complement,degap operations restriction maps dot plots translate dna to/from protein using various codon tables automatic preference saving internet send mail, read mail internet gopher, information retreival including genbank. internet sequence analysis services user-definable links to external analysis programs and more You can obtain updates of this program thru anonymous ftp to ftp.bio.indiana.edu, in folder /molbio/seqapp, as seqapp.hqx. You may also obtain updates directly thru an internet-connected Mac with SeqApp, using Gopher to the IUBio archive. Look for a folder called "IUBio Software+Data/SeqApp, Mac sequence editor". -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-software@net.bio.net Wed Nov 11 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!sol.ctr.columbia.edu!ira.uka.de!news.belwue.de!news.uni-tuebingen.de!studserv!zxmkr08 From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: GratefulMed over tcp/ip???? for Mac!!! Message-ID: Date: 11 Nov 92 19:39:58 GMT References: <1992Nov8.225129.15997@pollux.lu.se> Sender: news@softserv.zdv.uni-tuebingen.de (News Operator) Organization: Comp. Center (ZDV) U of Tuebingen, FRG Lines: 19 In <1992Nov8.225129.15997@pollux.lu.se> Bo Servenius writes: >BTW gm6.0 is for PC isn't it??? Is there a tcp/ip version for Macs >as well?? The TCP/IP software for Macs is MacTCP. The actual version is 1.1 (as far as I know). I have installed it under System 7 and it works like a dream (not like these darned IBM PCs... I always have troubles to find drivers for our 3C507 ethernet card, e.g. to get it to work with NCSA Telnet 2.3). To my knowledge, MacTCP is NOT in the public domain. You can ftp it nevertheless; if you get an Eudora Package somewhere, it is included. There is also some documentation somewhere in ftp-land about how to configure MacTCP, but I am not sure where I picked it up ... it is accessible via Archie, though (that was the way I found it). -- /* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen */ /* email: krasel@studserv.zdv.uni-tuebingen.de (Internet) HAS CHANGED!! */ /* NO WIN/X400 MAIL POSSIBLE AT THE MOMENT! */ /* "People are DNA's way of making more DNA." (anonymous) */ From owner-software@net.bio.net Wed Nov 11 22:00:00 1992 Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!zaphod.mps.ohio-state.edu!cs.utexas.edu!uunet!seas.gwu.edu!merlot.gwu.edu!danj From: danj@merlot.gwu.edu (Dan Jacobson ) Newsgroups: bionet.software Subject: Re: HELP: .HQX Format for Macs Message-ID: <1992Nov11.182552.13771@seas.gwu.edu> Date: 11 Nov 92 18:25:52 GMT References: <1992Nov9.190919.12960@cs.mun.ca> Sender: news@seas.gwu.edu Distribution: na Organization: George Washington University, Washington, D.C. Lines: 17 In article <1992Nov9.190919.12960@cs.mun.ca> harold@odie.cs.mun.ca (Harold Wareham(Todd)) writes: >I recently obtainted a Macintosh file in .HQX format from the UIBio >archives. I need a copy of BinHex 4.0 or Stuffit to uncompress and >use the thing. Where can I obtain copies of either of these >programs? Thanks, > >- Todd You can find Stuffit (among other places) in the util/mac directory at IUBIO (ftp.bio.indiana.edu). Cheers, Dan Jacobson danj@chablis.gwu.edu From owner-software@net.bio.net Wed Nov 11 22:00:00 1992 Path: biosci!ASRR.ARSUSDA.GOV!jkirkbride From: jkirkbride@ASRR.ARSUSDA.GOV ("JOSEPH H. KIRKBRIDE") Newsgroups: bionet.software Subject: Latest version of DELTA software available on Internet via FTP Message-ID: <9211121307.AA27578@net.bio.net> Date: 12 Nov 92 12:02:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 33 The latest version of the DELTA software system from Michael J. Dallwitz, CSIRO Division of Entomology, GPO Box 1700, Canberra ACT 2601, Australia, telephone +61 6 246 4075, FAX +61 6 246 4000, Internet delta@ento.csiro.au, is now available as shareware via Internet FTP. To get the DELTA software and associated databases for flowering plants, connect via FTP to HUH.HARVARD.EDU using the id FTP and the password FTP. The DELTA software is now available for three different operating systems: /PUB/SOFTWARE/DELTA/MSDOS DELTA programs for MS-DOS operating system on IBM-compatible microcomputers. /PUB/SOFTWARE/DELTA/OS2 DELTA programs for OS2 operating system on IBM-compatible microcomputers. /PUB/SOFTWARE/DELTA/SUNOS DELTA programs for the SUN operating system. There are two databases available ready to use with the DELTA software (INTKEY) for identification of organism or querying for information. /PUB/SOFTWARE/DELTA/ANGIO Families of flowering plants of the world with emphasis on Australia. /PUB/SOFTWARE/DELTA/GRASS Genera of grasses of the world. In addition there are a number of shareware programs for MS-DOS stored in: /PUB/SOFTWARE/DELTA/GRAHICS These programs are very useful in preparing graphic images for use with the DELTA software. Joseph H. Kirkbride, Jr. USDA, Agricultural Research Service Systematic Botany and Mycology Laboratory Building 265, BARC-East Voice telephone: 301-504-9447 Beltsville, Maryland 20705-2350 USA Internet: JKIRKBRIDE@ASRR.ARSUSDA.GOV From owner-software@net.bio.net Wed Nov 11 22:00:00 1992 Path: biosci!agate!ames!elroy.jpl.nasa.gov!sdd.hp.com!nigel.msen.com!emory!europa.asd.contel.com!darwin.sura.net!uvaarpa!murdoch!cyclops.micr.Virginia.EDU!wrp From: wrp@cyclops.micr.Virginia.EDU (Bill Pearson) Newsgroups: bionet.software,bionet.molbio.embl,bionet.molbio.genbank,bionet.molbio.pir Subject: FASTA16c22 available Message-ID: <1992Nov12.190941.21010@murdoch.acc.Virginia.EDU> Date: 12 Nov 92 19:09:41 GMT Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Lines: 33 Xref: biosci bionet.software:3607 bionet.molbio.genbank:1069 Originator: wrp@cyclops.micr.Virginia.EDU Recently, several bugs in the FASTA package have been fixed and a new version is avaiable via anonymous ftp from: uvaarpa.virginia.edu:/pub/fasta/fasta16c22.shar(.Z) (1) Code has been included to allow the EMBL and PIR CD-ROM's to be read on unix systems. Because these CD-ROM's include a character but unix expects a end of line, sequence annotations were sometimes garbled. Hopefully this has been fixed. (2) A bug in RDF2 has been fixed. When comparing DNA sequences, RDF2 used an incorrect scoring method for initial regions. RDF2 worked properly on protein sequences. RDF2 does work properly on DNA sequences if the "-k" option is used. This problem was discovered because the unshuffled scores for RDF2 were different from the FASTA scores for many DNA sequences. This should not happen; if you find examples with the new version of RDF2, please contact me. In addition, a bug in the Mac FASTA version 1.6c2 has been reported. Code that was included in the Mac 1.4x version to allow the EMBL CD-ROM to be read properly was omitted from the 1.6 version. As a result, MacFASTA does not read properly the sequence files (either EMBL or PIR format) from the EMBL CD-ROM. It will also not read other CD-ROM formats properly. I hope to send out corrected versions of MacFASTA 1.6c this weekend or early next week. The CD-ROM problem does not affect DOS versions; the RDF2 problem is present in DOS and Macintosh versions. The Macintosh and DOS versions are not available via anonymous FTP. Bill Pearson From owner-software@net.bio.net Thu Nov 12 22:00:00 1992 Path: biosci!lhc!darwin.sura.net!haven.umd.edu!umd5!williams.smcm.edu!bwilliam From: bwilliam@oyster.smcm.edu (Bill Williams) Newsgroups: bionet.software Subject: Re: InPlot for Mac? Message-ID: <16966@umd5.umd.edu> Date: 13 Nov 92 20:55:10 GMT References: <1992Nov10.000502.20308@reed.edu> Sender: news@umd5.umd.edu Organization: St. Mary's College of Maryland Lines: 18 X-UserAgent: Nuntius v1.1.1d10 X-XXMessage-ID: X-XXDate: Fri, 13 Nov 92 21:59:16 GMT In article <1992Nov10.000502.20308@reed.edu> Eric Bowman, bowman@reed.edu writes: >Does such a product exist for Macintosh? I use IGOR, and I recommend it with the qualification that it is not overly user-friendly. It is extremely capable and fast. It will do all the things you request: curve fitting to a myriad of possible functions (polynomial, Fourier, exponential, etc., etc.), it'll happily do error bars (it'll calculate them for you, but I find it easier to do the calculations in Excel), bar plots, scatter plots, you name it. IGOR is available from WvaeMetrics, PO Box 2088, Lake Osego, OR 97035. 503-620-3001. They are reachable at WaveMetrics@AppleLink.Apple.com ___________________________________ William E. Williams, bwilliam@oyster.smcm.edu Divison of Natural Sciences and Mathematics St. Mary's College of Maryland St. Mary's City, MD 20686 From owner-software@net.bio.net Thu Nov 12 22:00:00 1992 Path: biosci!agate!spool.mu.edu!caen!destroyer!lambda.msfc.nasa.gov!saimiri.primate.wisc.edu!usenet.coe.montana.edu!Msu.oscs.montana.edu!uvsmr From: uvsmr@Msu.oscs.montana.edu (Matt Rognlie) Newsgroups: bionet.software Subject: Software for PC scanners Message-ID: <00963814.A3D75CE0@Msu.oscs.montana.edu> Date: 12 Nov 92 20:13:00 GMT Sender: usenet@coe.montana.edu (USENET News System) Reply-To: uvsmr@Msu.oscs.montana.edu (Matt Rognlie) Organization: Montana State University Lines: 12 We would like to purchase a flatbed scanner (i.e. HP ScanJet) to use with a DEC 486. Is there software available which would allow us to use the scanner as a densitometer? We want to scan autoradiograms or gels, but be able to get density data so that bands can be compared. Any suggestions on the latest scanner technology would also be appreciated. Thanks for your help. Matthew Rognlie | Veterinary Molecular Biology | uvsmr@trex.oscs.montana.edu Marsh Lab | phone: 406-994-6379 Montana State University | FAX: 406-994-4303 Bozeman, MT 59717-0360 | From owner-software@net.bio.net Thu Nov 12 22:00:00 1992 Path: biosci!lhc!darwin.sura.net!haven.umd.edu!umd5!williams.smcm.edu!bwilliam From: bwilliam@oyster.smcm.edu (Bill Williams) Newsgroups: bionet.software Subject: Re: HELP: .HQX Format for Macs Message-ID: <16967@umd5.umd.edu> Date: 13 Nov 92 20:58:05 GMT References: <1992Nov9.190919.12960@cs.mun.ca> Sender: news@umd5.umd.edu Organization: St. Mary's College of Maryland Lines: 19 X-UserAgent: Nuntius v1.1.1d10 X-XXMessage-ID: X-XXDate: Fri, 13 Nov 92 22:02:11 GMT In article <1992Nov9.190919.12960@cs.mun.ca> Harold Wareham, harold@odie.cs.mun.ca writes: >I recently obtainted a Macintosh file in .HQX format from the UIBio >archives. I need a copy of BinHex 4.0 or Stuffit to uncompress and >use the thing. Where can I obtain copies of either of these >programs? For anyone with a Mac but unfamiliar with the downloading conventions for Macs, I highly recommending downloading a number of very informative files (in text format, hence not requiring any fancy programs) at sumex-aim.stanford.edu in the directory /info-mac/reports. I don't have the specific names of the files handy, but looks for things like FTP-site directories, FTP how-to, etc. As I recall the reports are well written and direct. ___________________________________ William E. Williams, bwilliam@oyster.smcm.edu Divison of Natural Sciences and Mathematics St. Mary's College of Maryland St. Mary's City, MD 20686 From owner-software@net.bio.net Thu Nov 12 22:00:00 1992 Path: biosci!uwm.edu!spool.mu.edu!yale.edu!ira.uka.de!ira.uka.de!gmd.de!Germany.EU.net!mcsun!news.funet.fi!funic!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.software Subject: Re: Software for PC scanners Message-ID: <1992Nov13.115311.16255@nic.funet.fi> Date: 13 Nov 92 11:53:11 GMT References: <00963814.A3D75CE0@Msu.oscs.montana.edu> Sender: usenet@nic.funet.fi Organization: Finnish Academic and Research Network Project - FUNET Lines: 46 Nntp-Posting-Host: convex.csc.fi In <00963814.A3D75CE0@Msu.oscs.montana.edu> uvsmr@Msu.oscs.montana.edu (Matt Rognlie) writes: >We would like to purchase a flatbed scanner (i.e. HP ScanJet) to use >with a DEC 486. Is there software available which would allow us to >use the scanner as a densitometer? We want to scan autoradiograms or >gels, but be able to get density data so that bands can be compared. >Any suggestions on the latest scanner technology would also be This question has come up alot and there has been many responses to it The biosci.src which is available at you local bio-gopher hole will give you three pages of information on scanners. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% CLIP %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% biosci.src: scanner 1. GERLACHJ@Q Re: Hand Scanner and Autorads. 2. GERLACHJ@Q Re: Hand Scanner and Autorads. 3. BACKD@QUCD Re: Re: Hand Scanner and Autorads. 4. BACKD@QUCD Re: Re: Hand Scanner and Autorads. 5. marder@agr Re: Recording scanner. 6. GERLACHJ@Q Re: Software for Densitometry from Scanner Images. 7. smith@phyl Re: Re: Hand Scanner and Autorads. 8. Frank Yue Re: Re: Hand Scanner and Autorads. 9. NXK104@psu Re: OCR Software & Scanner. 10. GERLACHJ@Q Re: Software for Densitometry from Scanner Images. 11. smith@phyl Re: Re: Hand Scanner and Autorads. 12. BACKD@QUCD Re: Re: Hand Scanner and Autorads. --> 13. djt2@po.CW Re: Scanners for autorads- responses. 14. extim@lure Re: Scanners for DNA gel densitometry analysis. 15. david@ASTR Re: to be posted. 16. morrow@mur Re: REA patterns. 17. broe@aardv Re: Re: Macintosh Sequence Aligner/Editor?. 18. BDODSON%VU Re: RE: IMAGE ANALYSIS OF BLOTS AND CAT ASSAYS. Press ? for Help, q to Quit, u to go up a menu Page: 1/3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I have used the mail option from within gopher and I have posted you the best bits. I hope you find them useful. Rob "at your service" Harper -- ~ Rob Harper ~ E-mail: harper@convex.csc.fi ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi ~ P.O. Box 40 ~ Telephone: +358 0 457 2076 ~ SF-02101 Espoo Finland ~ Fax: +358 0 457 2302 From owner-software@net.bio.net Fri Nov 13 22:00:00 1992 Path: biosci!lhc!host!gish From: gish@host.nlm.nih.gov (Warren Gish) Newsgroups: bionet.software Subject: NCBI Search CD-ROM File Format Message-ID: <1992Nov13.235359.24134@nlm.nih.gov> Date: 13 Nov 92 23:53:59 GMT Sender: news@nlm.nih.gov Organization: National Library of Medicine Lines: 330 The following announcment of the NCBI Search CD-ROM file format for sequence data is directed primarily to software developers. Users who wish to be notified when the Search CD-ROM is available for ordering should subscribe to "NCBI News". A free subscription to this newsletter can be obtained by sending your name and postal address to: info@ncbi.nlm.nih.gov Sample Search CD-ROM data files and reference source code is available now, via anonymous ftp, on ncbi.nlm.nih.gov (130.14.20.1) beneath the /pub/searchcd directory. Additional recommended software and documentation is posted on the same ftp server beneath the /toolbox/ncbi_tools_rel2.0 and /pub/gish directories. While the software beneath /pub/searchcd has been used locally to produce the sample Search files, it is posted only as a developer reference. The code does not compile and link into an executable application and it should not be considered a stable basis for development of application software. A limited quantity of a prototype Search CD-ROM will be available within 8 weeks. Developers interested in obtaining a copy should send their name and postal address before Friday, November 20 to: searchcd@ncbi.nlm.nih.gov or contact me by phone. Sincerely, Warren Gish NCBI/NLM Voice: 301-496-2475 FAX: 301-480-9241 NCBI Search CD-ROM File Format -- Sample Distribution INTRODUCTION The NCBI Search CD-ROM will be a vehicle for distributing molecular sequence data in a format that is efficient for sequence similarity searches using methods such as FASTA and BLAST. The Search format further supports multiple definitions linked to each sequence (as may be desired in a nonredundant collection) and facilitates the application of incremental updates such as might be obtained via a network. The NCBI intends to migrate much of its software over to using the "Search CD" format. The set of sequences distributed on the Entrez:Sequences CD-ROM will be distributed every two months on a Search CD-ROM, as well, in the format outlined below and detailed in the accompanying C language source files. As space permits, sequences from the NCBI's GenInfo(R) Integrated Database, which will be available within the next several months, will also be included on the Search CD-ROM in a separate directory. Prof. William Pearson (Univ. of Virginia) has generously offered to produce PC and Mac versions of FASTA to search files on the Search CD-ROM; these programs will be distributed on the Search CD-ROM itself, with software support handled by Dr. Pearson. As they become available, UNIX, Mac, and PC versions of BLAST software from the NCBI will be posted "as is" for anonymous ftp access on ncbi.nlm.nih.gov. Commercial providers of software and services which support the NCBI Search CD-ROM are encouraged to notify the NCBI of their product availability. Their names and addresses will be placed on file and will be made available to potential customers who inquire about support. Please send all such announcements to searchcd@ncbi.nlm.nih.gov SAMPLE FILES There are 5 subdirectories in this sample distribution: src -- C language source files describing the Search CD-ROM file formats. Additional supporting source code is posted on ncbi.nlm.nih.gov beneath the /toolbox/ncbi_tools_rel2.0 and /pub/gish directories. search -- a mock Search CD-ROM with some sample files search/entrez -- sample files in Search CD-ROM format using a very small subset of the Entrez:Sequences data search/giid -- sample List file describing the division of GenInfo(R) Integrated database data into separate files fasta -- the FASTA-format data used to generate the Search CD-ROM files in the "search/entrez" directory. FASTA files will not be distributed on the Search CD-ROM. The most important single file for understanding the internal structure of files on the Search CD-ROM is src/headers.h. It is recommended that src/headers.h be browsed prior to studying the remainder of this document. Individual C structure elements are specified in the same order in which the data are stored within the files. All "unsigned long" integers are stored in a 4-byte big-endian format. Byte alignment is not observed--all elements are close packed. FIVE DISTINCT FILE TYPES For sequence similarity searching, only two types of files are of primary concern: Sequence and Definition. Each record in a Sequence file includes the record length, a sequence identifier, an encoded and/or packed sequence, and the file offset into the Definitions file for a linked list of Definition records. Each Definition record contains zero or more sequence identifiers and associated human-readable definitions, plus a (possibly NULL) file offset to the next Definition record in the linked list. A third file type, Table, contains file offsets into matching Sequence and Definition files. One potential use for a Table file is in the assignment of sequence records to individual processors in a multiprocessing or multithreaded implementation of a search program. A Table file may also store offsets to only a subset of the records in the database. A more obscure use of a Table file would be to provide offsets to alternate or ancillary definitions from those pointed to within the Sequence file itself. The fourth file type, Index, is used to look up Sequence and Definition record offsets, given a sequence identifier. An Index file can contain offsets into either amino acid or nucleic acid sequence files. The fifth file type, List, is used to describe an entire collection of Search files, including their base filenames, residue type (aa or nt), and division (e.g., primates, plants, invertebrates, etc.) This is the only file type whose content is entirely human readable text. List files may be a focal point for customizing the installation of the other Search files. FILE SIZE RESTRICTIONS The Search CD-ROM will be produced in ISO 9660 format, so on some computing platforms each of the file names will have a ";1" suffix tacked on. The ISO 9660 format restricts files to being 64 MB or less in size, while MS-DOS further restricts files to being 32 MB or less. Consequently, it may be necessary to split some data sets or divisions into multiple sets of Sequence, Definition, and Table files in order to stay under the 32 MB limit. Software written to support Search files for other operating systems and media should not be so limited. Index files can support nearly 2 million records (identifiers) and still reside below the 32 MB limit, so it is not anticipated that Index files will need to be split for a considerable length of time. FILE NAMING CONVENTIONS Sequence, Definition, and Table files that work together will share a common base filename. Similarly, List and Index files that work together will share a common base filename. For Sequence, Definition and Table files, their filename extensions will depend on the type of sequence (aa or nt) to which the files refer: *.[an]sq *.[an]df *.[an]tb. List and Index files can refer to both types of files. The filename extension for a List file is .fls. The filename extension for an Index file is .idx. Sequence, Definition, Table, and Index files each begin with a header structure described in headers.h. The four header types begin with a structure of common or standard elements (ScdStdHdr). Following the standard header elements and the file type-specific elements which complete each header, there will be zero or more records in a format specific to the particular file type. SEQUENCE IDENTIFIERS Sequence identifiers are unsigned integers. The identifiers are drawn from the same name space used for sequence identifiers on release 1.0 of the Entrez:Sequences CD-ROM. At present, these are "import identifiers" or "giim" identifiers, but will ultimately be "GenInfo Integrated Database" or "giid" identifiers. By using the same identifiers as the Entrez:Sequences CD-ROM, it is possible to use the identifiers obtained by a similarity search to directly look-up records on the Entrez:Sequences CD-ROM. REDUNDANCY OF SEQUENCE INFORMATION When practical, Search CD-ROM database files will be "nonredundant"--100% identical sequences will be merged into a single sequence-definition record pair. For instance, when two or more sequences are absolutely identical at the sequence level, only one of their identifiers will be stored in the Sequence record, but all of their identifiers will be available in the corresponding Definition record. The 'def_off' element in the Sequence record points to the head of the relevant linked list of Definition record(s) in the Definition file. DIVISIONAL CLUSTERING OF SEQUENCES Protein sequences are likely to be distributed in a single "All" division, which may need to be split into multiple sets of Sequence-Definition-Table files in order to avoid breaking the aforementioned 32 MB file size barrier. Nucleotide sequences will be distributed in the familiar GenBank(R) divisions, except Organelle which will disappear, plus a new EST division. The contents of the List format file giid/giid.fls provides a better outline than does the entrez/entrez.fls file of the divisions that are planned. For instance, in the sample Entrez files, NLM Backbone sequences appear in a separate division which will not be present in future releases. Again, it may be necessary to split divisions into multiple sets of Search files to avoid the file size barrier. "DV" records in .fls files indicate the particular division to which each set of files belongs. DEFINITIONS & ACCESSION NUMBERS As stored in a Definition record, Definition strings consist of a 4-byte length field followed by a NON-null-terminated, printable ASCII string of the specified length. In Search CD-ROM files, the binary encoded 'seqid' elements will NOT be repeated in printable ASCII form within the human readable definition strings. The definition strings may, however, contain identifiers from other name spaces. Definition strings in the sample files begin with an acronym representing the database from which the definition was obtained, followed by a colon (:), the accession number in the specified database, and finally the definition. The database acronyms used are: GB=GenBank(R), PIR=the NBRF PIR(R), SP=SWISS-PROT. Other acronyms that From owner-software@net.bio.net Fri Nov 13 22:00:00 1992 Path: biosci!agate!spool.mu.edu!yale.edu!news.yale.edu!YaleVM.YCC.Yale.Edu!LILMARA From: LILMARA@YaleVM.YCC.Yale.Edu (Martin Lilly) Newsgroups: bionet.software,bionet.molbio.embl,bionet.molbio.genbank,bionet.molbio.pir Subject: Re: FASTA16c22 available Message-ID: <1689E12475.LILMARA@YaleVM.YCC.Yale.Edu> Date: 14 Nov 92 01:47:39 GMT References: <1992Nov12.190941.21010@murdoch.acc.Virginia.EDU> Sender: news@news.yale.edu (USENET News System) Organization: Yale University Lines: 14 Xref: biosci bionet.software:3613 bionet.molbio.genbank:1070 Nntp-Posting-Host: yalevm.ycc.yale.edu In article <1992Nov12.190941.21010@murdoch.acc.Virginia.EDU> wrp@cyclops.micr.Virginia.EDU (Bill Pearson) writes: > > Recently, several bugs in the FASTA package have been fixed >and a new version is avaiable via anonymous ftp from: (TEXT DELETED) >The Macintosh and DOS versions are not available via anonymous FTP. > >Bill Pearson How can we get Macintosh/DOS versions? Thanks, LILMARA@YaleVM.YCC.YALE.EDU From owner-software@net.bio.net Sat Nov 14 22:00:00 1992 Path: biosci!uwm.edu!point.cs.uwm.edu!stonger From: stonger@point.cs.uwm.edu (Kelly Stonger) Newsgroups: bionet.software Subject: Thesis topic Message-ID: <1e644kINNc9d@uwm.edu> Date: 15 Nov 92 18:15:48 GMT Distribution: usa Organization: University of Wisconsin, Milwaukee Lines: 16 NNTP-Posting-Host: 129.89.2.5 Hi, I am a graduate student in computer science and I am looking for a masters thesis topic. Since I also have a masters in microbiology, I would like to work on a topic that relates to both computer science and biology (such as RNA folding or DNA sequencing). Can you recommend any research topics in this (or any other) area that I can use as a basis for a thesis. Any help would be greatly appreciated. K. Stonger From owner-software@net.bio.net Sat Nov 14 22:00:00 1992 Path: biosci!MED.PITT.EDU!bsh From: bsh@MED.PITT.EDU (Basavaraju Shankarappa) Newsgroups: bionet.software Subject: public domain software Message-ID: <9211151751.AA21920@miranda.med.pitt.edu> Date: 15 Nov 92 17:51:12 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Hi netters: Sometime back I had posted a request on info about the availabilit of public domain software for de-fragmenting the disk. I thank everyone who made suggestions to me on this behalf. Many of you also indicated that I will be better off buying this kind of software as it is worth the small amount of money it costs. In this regard I would like to explain the reason for my preference to public domain software. To make one thing clear, I am not opposed to paying money for a product/idea which someone has worked hard at. In my case, the reason for my request was to see that I can get the program in as short a time as possible. If I have to go through the University bureacracy, I will have to wait for atleast 15-20 days. I hope I have been able to make my position more clear. Thanks for putting up with me. ' Raj Shankarappa Univ of Pittsburgh bsh@med.pitt.edu From owner-software@net.bio.net Sat Nov 14 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!wupost!waikato.ac.nz!aukuni.ac.nz!nholford From: nholford@ccu1.aukuni.ac.nz (Nick Holford) Newsgroups: bionet.software Subject: Paperchase? How can I access it? (Boston/Beth Israel) Message-ID: <1992Nov15.201701.7068@ccu1.aukuni.ac.nz> Date: 15 Nov 92 20:17:01 GMT Organization: University of Auckland, New Zealand. Lines: 9 I have heard that there is a database of clinical trials under the name Paperchase. It originates from Beth Israel Hospital clinical computing I think. Can anyone tell me more about it and how I can access it? -- Nick Holford, Dept Pharmacology & Clinical Pharmacology University of Auckland, Auckland, New Zealand INTERNET: n.holford@aukuni.ac.nz From owner-software@net.bio.net Sat Nov 14 22:00:00 1992 Path: biosci!agate!usenet.ins.cwru.edu!po.CWRU.Edu!ccy From: ccy@po.CWRU.Edu (Cheung C. Yue) Newsgroups: bionet.software Subject: Re: HELP: .HQX Format for Macs Message-ID: <1e5r6pINN126@usenet.INS.CWRU.Edu> Date: 15 Nov 92 15:43:21 GMT References: <16967@umd5.umd.edu> <1992Nov9.190919.12960@cs.mun.ca> Reply-To: ccy@po.CWRU.Edu (Cheung C. Yue) Organization: Case Western Reserve University, Cleveland, OH (USA) Lines: 32 NNTP-Posting-Host: slc5.ins.cwru.edu In a previous article, bwilliam@oyster.smcm.edu (Bill Williams) says: >In article <1992Nov9.190919.12960@cs.mun.ca> Harold Wareham, >harold@odie.cs.mun.ca writes: >>I recently obtainted a Macintosh file in .HQX format from the UIBio >>archives. I need a copy of BinHex 4.0 or Stuffit to uncompress and >>use the thing. Where can I obtain copies of either of these >>programs? > >For anyone with a Mac but unfamiliar with the downloading conventions >for Macs, I highly recommending downloading a number of very >informative files (in text format, hence not requiring any fancy >programs) at sumex-aim.stanford.edu in the directory /info-mac/reports. > I don't have the specific names of the files handy, but looks for >things like FTP-site directories, FTP how-to, etc. As I recall the >reports are well written and direct. I confronted my own problems with Binhex some time ago by finding a friend with a copy of Stuffit Deluxe who could then unbinhex binhex40.hqx for me, and so on. Although sumex-aim.stanford.edu has a binary version of binhex (binhex.bin), I was unable to transfer it to my mac in Macbinary transfer. Perhaps you may have better luck with your own transfer. If that fails, you may have to resort to finding a friend locally who could unbinhex that first file for you (first file being binhex40.hqx). The above recommendation is an excellent suggestion, although I believe the files are in info-mac/help. Good luck. ccy@po.cwru.edu -- From owner-software@net.bio.net Sun Nov 15 22:00:00 1992 Path: biosci!XIBALBA.CSHL.ORG!mzhang From: mzhang@XIBALBA.CSHL.ORG (Michael Zhang) Newsgroups: bionet.software Subject: public domain games? Message-ID: <9211161336.AA00427@xibalba.cshl.org> Date: 16 Nov 92 13:36:57 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 4 Hi netters: Are there any public domain games or children educational softwares? M.Zhang mzhang@cshl.org From owner-software@net.bio.net Sun Nov 15 22:00:00 1992 Path: biosci!agate!ames!haven.umd.edu!umd5!williams.smcm.edu!bwilliam From: bwilliam@oyster.smcm.edu (Bill Williams) Newsgroups: bionet.software Subject: Re: HELP: .HQX Format for Macs Message-ID: <17011@umd5.umd.edu> Date: 16 Nov 92 16:33:39 GMT References: <1992Nov9.190919.12960@cs.mun.ca> <1e5r6pINN126@usenet.INS.CWRU.Edu> Sender: news@umd5.umd.edu Organization: St. Mary's College of Maryland Lines: 22 X-UserAgent: Nuntius v1.1.1d10 X-XXMessage-ID: X-XXDate: Mon, 16 Nov 92 17:37:52 GMT In article <1e5r6pINN126@usenet.INS.CWRU.Edu> Cheung C. Yue, ccy@po.CWRU.Edu writes: >The above recommendation >is an excellent suggestion, although I believe the files are in info-mac/help. Well, OK, I guess I'd better check... They are in info-mac/reports. I recommend the following reports: comp-sys-mac-comm-faq.txt ftp-primer.txt ftp-sites.txt I agree that you may have a bootstrap problem; I did all this so long ago that I've frankly forgotten how to get the first program. ___________________________________ William E. Williams, bwilliam@oyster.smcm.edu Divison of Natural Sciences and Mathematics St. Mary's College of Maryland St. Mary's City, MD 20686 From owner-software@net.bio.net Sun Nov 15 22:00:00 1992 Path: biosci!daresbury!mrccrc!warwick!uknet!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!seb1005 From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.software Subject: Biblography Programs: Summary of Responses Message-ID: <1992Nov16.013301.28748@infodev.cam.ac.uk> Date: 16 Nov 92 01:33:01 GMT Sender: news@infodev.cam.ac.uk (USENET news) Organization: U. of Cambridge, England Lines: 179 Nntp-Posting-Host: mbfs.bio.cam.ac.uk I recently posted asking about bibliography programs for unix. Here are the responses I received. Many thanks to all those who replied! I should note that the addbib/refer package seems to be standard on most unix systems (Sun has it as an option, BSD has it, AIX has it, IRIX doesn't have it on the machines I use) Cheers, Steven Brenner --- From: davis@nod.bms.com (Malcolm Davis) Subject: Unix Bibliography Programs? Hi, I use LaTeX to write my documents and so use the BibTeX bibliography database. There are a few programs around for working with this format. I just use the emacs bibtex-mode and a couple of Perl scripts I have written, but I have heard good things about the bibcard program. I also make big use of Current Contents on Disk and so have writtin a Perl script which will take CCOD's output and convert to BibTeX format along with my personal scheme for generating key names. Malcolm Davis / davis@nod.bms.com / BMSPRI Princeton, NJ --- From: dws@forager.unl.edu (David Stephens) There are two that I know of. The first, and I think the most widely used, is bibtex. It's designed to be used with LaTeX, and it's very programmable, but you have to be quite a nerd to program it. It's public domain, and maintained by the TeX group in stanford. There's lots of support for it in various forms, pre-programmed styles for various journals. Emacs modes for editing the database, and an openlook frontend called bibcard. There's also tib, I don't use this, but I understand it's more flexible. It can be used with non-TeX text processing systems (i.e. scribe). I don't know of any commerical packages. dave stephens ---- From: rodgers@maxwell.mmwb.ucsf.edu (R. P. C. Rodgers, M.D.) Steven, One system you will want to know about is bibIX. Although the current production release is tied to troff, we have a formatter-independent version in the works, and a prototyupe is working with Frame, for example. Cheerio, Rick Rodgers ******************************************************************************** * * ANNOUNCEMENT * * PROGRAM PACKAGE: BibIX Bibliographic Database and Text Format