From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!kristoff From: kristoff@genbank.bio.net (David Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: Re: Genbank server Message-ID: Date: 2 May 91 06:38:30 GMT References: Organization: GenBank Online Service Lines: 6 Peter, The schema has also been available for anonymous ftp from genbank.bio.net in pub/doc/schema for quite some time. Dave From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!nccibm1.bitnet!VCD From: VCD@nccibm1.bitnet Newsgroups: bionet.molbio.bio-matrix Subject: Positions Available Message-ID: <9109232107.AA15618@genbank.bio.net> Date: 21 Sep 91 12:35:00 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 52 Numerous positions are waiting to be filled at CSC. If interested, read on and send a PRINTED copy of your resume and cover letter to the address at the end of the note. No EMAIL, please. Vince ======================================================================== Computer Sciences Corporation, one of the world's most diversified information services companies, employs more than 24,000 of the brightest people in the computer industry. Due to our phenomenal growth, the Applied Technology Division is seeking experienced computer and environmental professionals to join our technical team in Research Triangle Par, NC, supporting the Environmental Protection Agency. Opportunities exist for the following: SOFTWARE/DATABASE DEVELOPMENT SPECIALIST (MAINFRAME & PC PLATFORMS) ADABAS/NATURAL PROGRAMMERS UNIX/C PROGRAMMERS SAS GRAPHICS PROGRAMMERS ORACLE PROGRAMMERS VAX/VMS SYSTEMS MANAGER NETWORK/TELECOMMUNICATIONS MANAGER ENVIRONMENTAL ENGINEERS/SCIENTISTS SOFTWARE PROJECT MANAGER ATMOSPHERIC CHEMIST BIOSTATICIAN DOCUMENTATION SPECIALIST VISUALIZATION SPECIALIST HIGH PERFORMANCE COMPUTING SPECIALIST Most positions require a batchelor's degree (advanced degrees are highly desirable) and related work experience. If you would like to cultivate a career that is as challenging as it is rewarding and join some of the best minds in the information services industry, then come grow with us! For these and other positions, please submit a PRINTED copy of your resume and a cover letter to: Vincent C. DelGobbo Computer Sciences Corporation c/o US EPA, Mail Drop 43 Research Triangle Park, NC 27711 CSC is an equal opportunity employer. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!AI.SRI.COM!pkarp From: pkarp@AI.SRI.COM (Peter Karp) Newsgroups: bionet.molbio.bio-matrix Subject: Re: newsletter subscription Message-ID: Date: 21 Aug 91 22:39:29 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 4 I'd say it was an oversight -- I for one certainly want to see use of the newsgroup continue. Peter From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!spool.mu.edu!uunet!zephyr.ens.tek.com!uw-beaver!uw-june!june.cs.washington.edu!dhubbell From: dhubbell@june.cs.washington.edu (David Hubbell) Newsgroups: bionet.molbio.proteins,bionet.molbio.bio-matrix Subject: Wanted: simulator source Message-ID: <15354@june.cs.washington.edu> Date: 6 Mar 91 20:59:26 GMT Sender: dhubbell@cs.washington.edu Reply-To: dhubbell@june.cs.washington.edu (David Hubbell) Distribution: bionet Organization: U of Washington, Computer Science, Seattle Lines: 7 Xref: bionet bionet.molbio.proteins:80 bionet.molbio.bio-matrix:201 Posted: Wed Mar 6 14:59:26 1991 I'm looking for the source code to a molecular dynamical simulator that uses either the Beeman, Verlet, or SHAKE integration methods. The more recent, the better. I'm trying to get an idea of how simple one could make the processors in an array processor and still map one atom (or extended atom) per processor. Thanks in advance, Dave Hubbell From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: Re: newsletter subscription Message-ID: Date: 21 Aug 91 22:19:55 GMT Sender: kristoff@genbank.bio.net Distribution: bionet Lines: 14 > In response to one of David's questions, I believe the current > issue is Vol 2 because some of the traffic on this mailing list > had been printed and distributed as Vol 1 of this newsletter a year > or two ago. Peter, Dan, or Ginger, What about continued use of the newsgroup? With all of the e-mail addresses listed in the newsletter it was surprising not to see the newsgroup address. Is this just an oversight or has the Society intentionally given up on it? Dave From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!apple!julius.cs.uiuc.edu!wuarchive!uunet!shelby!rutgers!caip.rutgers.edu!aramis.rutgers.edu!paul.rutgers.edu!dcohen From: dcohen@paul.rutgers.edu (Dawn Myfanwy Cohen) Newsgroups: dcs.csgss,dcs.general,ru.classifieds,nj.general,nj.wanted,ny.general,ny.wanted,bionet.jobs,bionet.molbio.bio-matrix,misc.jobs.offered Subject: Job opening for database applications programmer Keywords: computational chemistry application Message-ID: Date: 7 Nov 90 21:23:49 GMT Followup-To: dcs.csgss Distribution: na Organization: Rutgers Univ., New Brunswick, N.J. Lines: 30 Xref: bionet bionet.jobs:252 bionet.molbio.bio-matrix:106 misc.jobs.offered:4106 Job Opening: Database Applications Programmer A position is available to implement a scientific DBMS to be used in the development of a database of nucleic acid structures. Responsibilities include training users and preparing documentation. A bachelors degree in computer science or related field plus extensive experience in database programming and development is required. Experience in computational chemistry preferred. Position offers competitive salary and benefits. Please send resume to Dr. Helen Berman Department of Chemistry Wright Labs Busch Campus Rutgers University Piscataway, NJ 08903 or via email to berman@dnarna.rutgers.edu -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Good Morning! --Dawn Send fan mail to: uucp: {ames,bosgd,harvard,moss}!rutgers!paul.rutgers.edu!dcohen arpa: dcohen@paul.rutgers.edu From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!news.cs.indiana.edu!sdd.hp.com!spool.mu.edu!munnari.oz.au!bruce!monu0.cc.monash.edu.au!news From: ins749r@monu3.cc.monash.edu.au (mr k.h. geppert) Newsgroups: bionet.molbio.bio-matrix Subject: Request for data/help Message-ID: <1991Oct22.151834.13098@monu0.cc.monash.edu.au> Date: 22 Oct 91 15:18:34 GMT Sender: news@monu0.cc.monash.edu.au (Usenet system) Organization: Monash University, Clayton, Vic 3168, Australia Lines: 52 A program that can simulate people has long been an interest of computer scientists. So far, an unfulfilled interest... However, there is a fairly small field in which a simulation is possible, and if not useful, or insightful then at least amusing. This is a simulation of the free associations produced by people. This is easier because there is less structure to be interpreted, and the raw content is more visible. I am trying to do the simulation by using a simple neural network based on some classical conditioning rules established by Grossberg in the late 60's and in his book "Studies of Mind and Brain", and updated by Klopf in a recent paper. It is a system for learning temporal sequences, where each node represents an item (or word, or concept), instead of a vector representing an item. I am presently attempting to get context to work, so that the next item to be output by the simulation will depend on what went before, and not just the immediate predecessor. Grossberg mentions the idea of context, but doesn't say much useful about it. I've found one article that does say something about it : "Neural networks that learn temporal sequences by selection", Stanislas Dehaene et. al., Proc. Nat. Acad. Sci. USA, Vol. 84, pp. 2727-2731, May 1987 If anyone is doing research in this area, please drop me a line: bren@bruce.cs.monash.edu.au If you are not, you might still like to contribute free-associations to help train the network. Here's a blurb: Free-associations are words that follow each other with no set relationship between them, apart from that a person has said them one after the other. An example is: fire truck car petrol middle east africa englad america macdonalds kentucky fried grease pizza late coke sleep It's good to visualize scenes as you go along, and it's also very relaxing. If you would like to contribute free-associations to help train this network, please post them to: bren@bruce.cs.monash.edu.au Thanks! From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!FCRFV1.NCIFCRF.GOV!gunnell From: gunnell@FCRFV1.NCIFCRF.GOV ("Gunnell, Mark") Newsgroups: bionet.molbio.bio-matrix Subject: (none) Message-ID: <9111221636.AA07863@genbank.bio.net> Date: 22 Nov 91 16:31:00 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 31 I'd like to invite all of you who may be attending the DECUS meeting in Anaheim, Dec. 7-13 to an informal Birds-of-a-Feather (BOF) meeting for VAX users or managers working in the field of Molecular Biology. In the past, this has been a time of getting acquainted, information exchange, airing complaints and helping one another with problems. At our last meeting in Atlanta (May '91), Joseph King, of GCG, was in attendance and gave us a preview of the GCG-Unix port. Overall, I have found the GCG-BOF meetings extremely rewarding for the small amount of time invested. Joseph King, his schedule permitting, has again indicated his intention to attend the BOF. This might be an opportune time to provide suggestions to GCG regarding additions, improvements, or problems with the GCG package. Compliments will also be allowed! I will attempt to schedule the BOF for Tuesday or Wednesday unless I hear a number of requests for alternate days. Watch the information monitors and/or Update.Daily for the exact date and time. I hope many of you can attend. ------------------------------------------------------------------------------- Mark A. Gunnell | Internet: gunnell@ncifcrf.gov Sci. Applications Analyst | Bitnet: gunnell%ncifcrf.gov@cunyvm.bitnet Advanced Scientific Computing Lab.| Phone: (301) 846-5779 PRI/DynCorp | NCI-FCRDC | PO Box B, Bldg 430 | Frederick, MD 21702-1201 USA | ------------------------------------------------------------------------------- From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!FINSUN.CSC.FI!harper From: harper@FINSUN.CSC.FI (Robert Harper) Newsgroups: bionet.molbio.bio-matrix Subject: Selling roadmaps for the soul... Message-ID: <9106171137.AA10299@finsun.csc.fi> Date: 17 Jun 91 11:37:44 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 103 Here is an interesting overview of the state of networking. Are biologists in the same boat... or are we swimming in the open sea? do you ever get the feeling that all this NREN stuff is going to build us a network that's extraordinarily fast but impossible to use? mitch kapor, in his "building the open road: policies for the national public network" [*], compares the existing mess in the current state of the art at cataloging and describing the services available on the net today as "like a giant library with no card catalog". who is going to provide the moral equivalent of the rand-mcnally road atlas, the texaco road maps, the aaa trip-tiks? what we have now is much more like the old Lincoln Highway, with painted markings on trees and oral tradition that helps you get through the rough spots on the road. efforts by existing commercial internet providers have been mediocre at best. none appear to be much interested in mapping out the network beyond the immediate needs of their customers. if you consider that one of the roles of a commercial internet provider is to provide access to software archives, and then you take a look at the state of the software archives on uunet.uu.net and uu.psi.com, you see enormous duplication, strange and hard to understand organizations of files, no aids in finding materials beyond a cryptic "ls-lR" file, and dozens if not hundreds of files which are stale and out of date compared with the One True Version maintained by the author of the documents. [&] Visiting these places is like reading magazines at a dentist's office, you know that what you're reading was new once a few weeks or months ago. efforts by nsf-funded network information centers have been similarly muddled and half-useful. if you read the Merit proposal to NSFnet closely, you saw plans for GRASP (Grand interface to SPIRES) which was going to be the ideal delivery mechanism for information about the NSFnet to users of the net. Promises promises. What you do have from nis.nsf.net is a stale collection of out of date maps [%], a bunch of traffic measurement aggregate numbers [#], and some newsletters[=]. the work at nnsc.nsf.net isn't all that much better. part of the problem is reliance on volunteered information -- the general approach to network information gathering appears to be not much more than send out a survey, wait, tabulate the responses. very little of this work is what you would call "pro-active", that's why chapter 3 (archives) lists just 26 of the over 1000 anonymous FTP sites and mail-based archive servers available on the net. [?] (Think of it as a road atlas that shows less than 1 road in 40 and you'll get the right idea.) that's not to say that there aren't skilled people out there, it's just that they're generally not supplied with resources adequate to the task they're facing. you aren't seeing organizations like ANS, which seems to be flush with cash and hiring skilled people left and right, hiring anyone with the archivist skills of a (say) Keith Peterson. you aren't seeing innovative applications like "archie", a union list catalog of FTP sites around the globe, funded as part and parcel of NSF infrastructure; it's being done in Canada, with no guarantee to continued existence if it starts to swamp their already soggy USA-Canada slow link or if they need the machine back. [+] you don't see nic.ddn.mil hosting the arpanet "list of lists" anymore, they didn't like the contents so it's gone. [@] the internet library guides are run as best they can by individuals, and they're in the form of long ascii lists of instructions on how to connect rather than an interactive front-end that would make the connections for you -- not that the technology isn't there, just that no one has a mission and the resources to provide them. [!] so what do we end up with? a very fast net (in spots) with a "savage user interface" [*]. multi-megabit file transfers, you can get anything you want in seconds, but no way to find it. regional networks spending large amounts of federal dollars on bandwidth but very little on ways to use it effectively. a vast, largely uncharted network, with isolated pockets of understanding here and there, and no one yet who has appeared with any of the proper incentives and resources to map it out. -- Edward Vielmetti, MSEN Inc. moderator, comp.archives emv@msen.com references for further study: [*] eff.org:/npn/. discussion in comp.org.eff.talk. [@] ftp.nisc.sri.com:/netinfo/interest-groups. see also dartcms1.dartmouth.edu:siglists and vm1.nodak.edu:listarch:new-list.* discussion in bit.listserv.new-list. [!] vaxb.acs.unt.edu:[.library], also nic.cerf.net:/cerfnet/cerfnet_info/internet-catalogs* discussion in comp.misc and bit.listserv.pacs-l. [+] see discussion in comp.archives.admin. archie information can be found in quiche.cs.mcgill.ca:/archie/doc/ [%] in nis.nsf.net:maps. note that several are as old as 1988. no readily apparent newsgroup for discussion. [#] in nis.nsf.net:stats. no readily apparent newsgroup for discussion. [=] in nis.nsf.net:linklttr. no convenient way to search through them short of downloading the whole set. [&] for instance, see uunet.uu.net:/sitelists/ (empty) uunet.uu.net:/citi-macip/ (CITI has withdrawn this code) uu.psi.com:/pub/named.ca (out of date named cache file still shows nic.ddn.mil as root nameserver) discussion in comp.archives.admin [?] nnsc.nsf.net:/resource-guide/chapter.3/. note that many entries have not been updated since 1989. discussion in comp.archives.admin. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UH.EDU!Davison From: Davison@UH.EDU (Dan Davison) Newsgroups: bionet.molbio.bio-matrix Subject: new version of Biomatrix bibliography now on UH gene-server Message-ID: <9105140339.AA13137@Menudo.UH.EDU> Date: 14 May 91 03:39:14 GMT Sender: daemon@genbank.bio.net Lines: 31 Peter Karp said: > Thanks to contributions from Jim Holloway, I have compiled an expanded > version of the bibliography related to Biomatrix topics. [...] > matrix-bib.bib Latex bibliography format > matrix-bib.txt Text format > matrix-bib.ps Postscript format > These files should also appear on the University of Houston server > shortly. These files are now on the UH Gene-Server. They can be retrieved by sending the lines send matrix matrix-bib.txt send matrix matrix-bib.bib send matrix matrix-bib.ps to gene-server@bchs.uh.edu on the Internet or gene-server%bchs.uh.edu@CUNYVM from BITNET/CREN dan -- dr. dan davison/dept. of biochemical and biophysical sciences/univ. of Houston/4800 Calhoun/Houston,TX 77054-5500/davison@uh.edu/DAVISON@UHOU Disclaimer: As always, I speak only for myself, and, usually, only to myself. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!nyspi.bitnet!XIE From: XIE@nyspi.bitnet (xiaoli) Newsgroups: bionet.molbio.bio-matrix Subject: help Message-ID: <9104052309.AA02191@genbank.bio.net> Date: 5 Apr 91 21:23:26 GMT Sender: daemon@genbank.bio.net Lines: 20 I am a user of OS2 and now I have following problems: 1. I installed OS2 on my PC and I want to use a serial port (COM2) to connect to a printer but when I want to print a file, the printer did not respose. I set COM2: speed 960; parity none;stop bit 1;length 8; hankshake none and connected COM2 to PRINTER1. Is there a trick to set a printer? I installed OS2 on others with paralell printer and it is fine. Please let me know if you know what the problem is? 2. I wrote a program using PROSPERO PASCAL to carry out linkage analysis. This program has to use the very big ARRAYs and RECORDs. I mean it needs a lot of space. So, when I compile I always get error message indicate that "SIZE EX- CEEDS 65520 BYTE". If I use large memory model, I can get rid of some of the errors but not all of them. Is there a way to solve this problem? If not, what is the advantage to use OS2? And are there some other computer languages can do so? (on PC) Thanks in advance Xiaoli Xie From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: Nice newsletter Message-ID: Date: 20 Aug 91 23:15:44 GMT Sender: kristoff@genbank.bio.net Distribution: bionet Lines: 17 I just received my Biomatrix Society newsletter yesterday and it looks nice. I noticed, however, that the number is vol. 2, no. 1. Did I miss some issues or is the number incorrect? On another note, it didn't escape my notice that the networking article made no mention of this forum (nor was it listed anywhere else in the newsletter). Traffic on BIO-MATRIX/bionet.molbio.bio-matrix has been virtually non-existant. Does the Society still want to maintain this forum or has it outlived its usefulness??? Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: P.S. Message-ID: Date: 20 Aug 91 23:20:18 GMT Sender: kristoff@genbank.bio.net Distribution: bionet Lines: 12 If the newsgroup is still of use, I would humbly suggest that instructions for subscribing and posting to it be included routinely in a small box in the newsletter. Many personal and server e-mail addresses were included in the letter but not the above. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: Changes coming to BIOSCI Message-ID: Date: 7 May 91 22:50:25 GMT Sender: kristoff@genbank.bio.net Lines: 36 Dear BIOSCI users, I apologize for sending a copy of this to each of the newsgroups, but I need to make sure that all of our e-mail subscribers are notified of an impending reorganization of BIOSCI. It appears that we will be doing some substantive reconfiguration work on BIOSCI in the very near future. I will provide details soon on the BIONEWS/bionet.general newsgroup (where this has previously been discussed), but I am sending this message out now as an alert for the following reasons: 1) if anyone finds that their BIOSCI subscriptions cease, please send a message to me at biosci@genbank.bio.net. It is possible that some addresses may cause problems and may have to be withheld from mailings until clarification is received. You can help us if you notice that you no longer are receiving postings by sending me mail from the address at which you wish to receive bulletins. In the event that you subscribe only to the less frequently used newsgroups, please let a week go by before you conclude that you have been dropped from the mailing list. 2) There is always the possibility when mailing lists are transferred that some problems with duplicates or lost messages may temporarily arise. I'd appreciate your indulgence during the reorganization. We have made substantial progress in the last few days but some details remain to be worked out. I will make further announcements on BIONEWS as developments warrant. Thanks for your cooperation. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UH.EDU!Davison From: Davison@UH.EDU (Dan Davison) Newsgroups: bionet.molbio.bio-matrix Subject: 1st Announcement - Congress on the Biocomputing and Human Genome (fwd) Message-ID: <9106131857.AA29911@Menudo.UH.EDU> Date: 13 Jun 91 18:57:27 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 202 This note just appeared on one of the other bionet newsgroups. dan > The Role of Biocomputing in the Characterization of > Human Genome Sequences > > October 13-14, 1991 > > Tecnopolis Novus Ortus > > Valenzano - Bari, Italy > > > 1st Announcement > > > > UNDER THE AUSPICES OF > CONSIGLIO NAZIONALE DELLE RICERCHE C.N.R. (ITALY): > - "Progetto Finalizzato Ingegneria Genetica Sottoprogetto Genoma Umano" > - "Progetto Strategico Biotecnologie e Biostrumentazione" > - "Progetto Speciale Bioinformatica" > TECNOPOLIS CSATA NOVUS ORTUS (ITALY) > > CONFERENCE ORGANIZATION > Honorary Committee > - Attilio Alto Rettore Universit< degli Studi di Bari (Italy) > - Gianfranco Dioguardi Presidente Tecnopolis CSATA, Bari (Italy) > - Luigi Rossi Bernardi Presidente C.N.R. (Italy) > > Scientific Committee > chairman > - Renato Dulbecco > President of the Salk Institute, San Diego, CA > - Martin Bishop > MRC Molecular Genetics Unit, Cambridge (U.K.) > - Cecilia Saccone > Dipartimento di Biochimica e Biologia Molecolare > Universita' degli Studi di Bari (Italy) > - Glauco Tocchini-Valentini > Istituto di Biologia Cellulare C.N.R.,Roma (Italy) > > > Organizing Committee > - Marcella Attimonelli > Dipartimento di Biochimica e Biologia Molecolare > Universit< degli Studi di Bari (Italy) > - Lorenzo Cellamare > Tecnopolis CSATA, Bari (Italy) > - Paolo Vezzoni ITBA C.N.R., Milano (Italy) > > Organizing Secretariat > - Centro Internazionale Congressi > Viale Papa Pio XII, 18 > 70124 Bari (Italy) > Tel. +39 - 80 - 517299 > Fax +39 - 80 - 514533 > > > With the collaboration of the Communication Department of Tecnopolis > Csata Novus Ortus > > OBJECTIVE > The Human Genome Project entails a worldwide activity aimed at studying > the human DNA, the location of all its genes and their nucleotide sequences. > Hence a massive quantity of data is being produced, whose reliable storage, > processing and classification require the usage of more and more sophisticated > bioinformatic tools. > This workshop will review the most recent advances in the field of > Bioinformatics regarding the analysis of biosequences. > It will also identify future developments in, and uses of, new bioinformatic > tools for fast characterization of raw sequence data with particular reference > to the Human Genome Project. > > INVITED SPEAKERS > A. Bairoch D.J. Lipman > D. Benson B. Keil > G. Bernardi N. Kolchanov > M. Bishop C. Matessi > G. Cameron H. W. Mewes > A. F. W. Coulson V. A. Ratner > R. Doolittle C. Sander > C. Frontali E. Trifonov > > PRELIMINARY PROGRAM > Sunday, October 13 > Introductory Remarks > - Morning session > Biocomputing and the Human Genome Project > - Afternoon session > Fast Characterization of Raw Sequence Data > > Monday, October 14 > - Morning session > Work Station Session (Network Connection) > Poster Presentation and Discussion > Short Talks by Representatives of the Various > > > Operative Units of the C.N.R. Special Project > > Bioinformatics > - Afternoon session > Molecular Evolution: a Tool for Understanding. > Open discussion > Concluding Remarks > > > > > > > > CALL FOR POSTER PRESENTATION > A poster presentation and discussion session will be held on Monday October 14. > Posters will be on exhibition for the two conference days. > Poster presentation specifications and abstract form will be sent only upon requ > est. > Poster presenters are envisaged to treat the following topics: > - Fast Characterization of Raw Sequence Data > - Molecular Evolution: a Tool for Understanding > - Specialized Data Bases: a Need for the Human Genome Project > > GENERAL INFORMATION > Conference location > The conference will be held at Tecnopolis Novus Ortus, Valenzano - Bari, Italy. > Tecnopolis Novus Ortus, the first Science Park in Italy, is an innovative > infrastructure to foster a technology based development of Southern regions. > It is focused on advanced industrial applications of the New Information > Technologies. > Since 1989 it has been experimenting the Tecnopolis Programme, financed by the > national Ministry for Special Intervention for Southern Italy. The Programme > aims at experimenting and assessing global policy of the Science Park as an > original model based on an organic combination of industrial, R&D, educational > activities and the promotion of the economic and cultural development. > In collaboration with the "CNR Bari Area di Ricerca", Tecnopolis represents > a national node of the European network EMBNET (European Molecular Biology > Network). > > Bari (450,000 inhabitants) is the capital of Apulia, one of the most active > regions in southern Italy. The presence of a large University with more than > 50.000 students makes Bari one of the most important reference point for the > cultural and scientific development. > > Conference Language > English is the official conference language. > > > Registration > All conference attendees are required to register in advance. > The registration form will be sent upon request along with next announcement. > A limited number of registrations will be accepted. > > Registration Fee > Lit. 180.000 VAT included (approximately $ 145) > The fee covers: > - The conference kit and the abstract volume > - Lunch on October 13 and 14 > - Gala dinner on October 13 > - Coffee breaks > - Shuttle bus service Tecnopolis-Hotels > > Hotel Accommodation > Blocks of rooms in various hotels in Bari have been reserved by the Organizing > Secretariat. > The hotel rates - breakfast included - are approximately the following: > Rate per Night > Hotel Category Single room Double room > 4 star hotel Lit. 170.000 Lit. 230.000 > 3 star hotel Lit. 100.000 Lit. 170.000 > 2 star hotel Lit. 70.000 Lit. 50.000 > Hotel accommodation forms will be enclosed with the next announcement > > Preliminary Application Form > If you wish to receive the next announcement and/or the poster specifications > and abstract form please fill in the enclosed preliminary application form > and send it to the Organizing Secretariat Centro Internazionale Congressi > by June, 30 1991. > For a first contact you may communicate by e-mail to the following address > ATTIMONELLI@mvx36.csata.it > > How to reach Bari > By air: Bari airoport has several daily flights to and from Rome, Milan, Turin. > Direct flights also operate three times a week to and from Paris > (Sun., Tue., Thu.) and Frankfurt (Mon., Wed., Sat.). > By train: Bari is connected by Intercitiy and TEE trains to all important cities > . > By car: Motorways A14 and A16 connect Bari to Rome (about 4 hours'drive) > and Nothern Italy. (Aggiungere piantina Italia e/o Puglia) > > -- dr. dan davison/dept. of biochemical and biophysical sciences/univ. of Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU Disclaimer: As always, I speak only for myself, and, usually, only to myself. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!ciunsa.edu.ar!deviana From: deviana@ciunsa.edu.ar ("M.Sc. Marta De Viana") Newsgroups: bionet.molbio.bio-matrix Subject: (none) Message-ID: <9103271636.AA02885@genbank.bio.net> Date: 27 Mar 91 16:36:17 GMT Sender: daemon@genbank.bio.net Lines: 15 I would like to contact researchers working on bats communities as well as on populations of DESMODUS ROTUNDUS. ----------------------------------------------- M.Sc. Marta De Viana email: UUCP: atina!ciunsa.edu.ar!deviana atina!unsa.edu.ar!deviana INTERNET: deviana%ciunsa.edu.ar@uunet.uu.net deviana%unsa.edu.ar@uunet.uu.net From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!AARDVARK.UCS.UOKNOR.EDU!JHANAS From: JHANAS@AARDVARK.UCS.UOKNOR.EDU Newsgroups: bionet.molbio.bio-matrix Subject: (none) Message-ID: <9109181409.AA04487@genbank.bio.net> Date: 18 Sep 91 14:09:00 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 1 SUBSCRIBE JHANAS From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!spool.mu.edu!uunet!mcsun!cernvax!chx400!chx400!bernina!neptune!inf.ethz.ch!reberhar From: reberhar@inf.ethz.ch (Rolf Georg Eberhardt) Newsgroups: bionet.molbio.bio-matrix,bionet.software,sci.bio,sci.bio.technology Subject: Computational Biochemistry at ETH Zuerich Message-ID: <27359@neptune.inf.ethz.ch> Date: 11 Mar 91 08:13:39 GMT Sender: news@neptune.inf.ethz.ch Reply-To: reberhar@inf.ethz.ch (Rolf Georg Eberhardt) Distribution: bionet Organization: ETH, Zurich Lines: 56 Xref: bionet bionet.molbio.bio-matrix:203 bionet.software:745 sci.bio:2283 sci.bio.technology:82 Posted: Mon Mar 11 02:13:39 1991 Computational Biochemistry Research at ETH Zuerich ================================================== The CBRG -------- The Computational Biochemistry Research Group (CBRG) is a research group at the Eidgenoessische Technische Hochschule Zuerich (ETH) in Switzerland, involving researchers from Organic Chemistry and Computer Science. Its main research goal is the derivation of biological/genetic information and theories through the analysis of genetic sequences. Current Interests ----------------- The CBRG is mainly interested in the following topics: - Cross-matching of an entire DNA-database against itself to record all significant homologies. - The computation of a theoretical measure of evolution either for homologous sequences, in which case we compute the distance from divergence, or for sets of sequences, in which case we compute phylogenetic (evolutionary) trees. In both cases we are interested in modelling and computing evolutionary distances between homologous sequences. - The effective visual representation of evolutionary information. - The search for genetic clocks, i.e. methods for estimating age of divergences based on sequence information. The goal of this research is to obtain timing information as reliable as possible. We have been studying methods based on non-coding DNA and methods based on the redundancy of the genetic code for this clock. - The reconstruction of ancestral sequences through probabilistic models. The main tool for our research is the DSF (DNA Searching Facility) system. DSF is interactive, has a set of powerful primitive operations. DSF currently runs on Sun-3, Sun-4/SPARC, DECstation 3100 and on MIPS machines. The CBRG will distribute binaries of DSF via ftp free of charge. If you are interested in our research we will gladly send you a hard-copy of our research paper describing CBRG and its activities. We can be reached through: e-mail: reberhar@inf.ethz.ch mail: ETH Zuerich Institut fuer wissenschaftliches Rechnen CRBG CH-8092 Zuerich ------------------------------------------------------------------------------- Rolf Eberhardt, Inst. fuer wissenschaftliches Rechnen, ETH Zuerich, Switzerland e-mail: reberhar@inf.ethz.ch From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!apple!olivea!uunet!mcsun!news.funet.fi!fuug!funic!finsun!harper From: harper@finsun.csc.fi (Robert Harper) Newsgroups: bionet.molbio.bio-matrix Subject: Re: Commercial Archives Keywords: software patents copyright MSEN SGML richtext richmail X11R5 emv filtering Message-ID: Date: 24 Jun 91 07:49:43 GMT References: Sender: usenet@nic.funet.fi Organization: Centre for Scientific Computing, Finland (CSC) Lines: 140 Nntp-Posting-Host: finsun.csc.fi Has anybody read the railway/highway model for networking? The railway model points out that the "west was won" when private commercial companies built the railroads that opened up the west. The highway model is where the government handles all of the communications infrastructure. Ask yourself if you are about to be railroaded? Check out COMP.ARCHIVES.ADMIN for some lively talk on the new information brokers... *************************** CLIP *********************************** In emv@msen.com (Ed Vielmetti) writes: > > The current comp.archives appears to be driven by "technology > push": you have the data available, so you're saving it. > Business doesn't work that way; it works by "pull." You > have to find customers who need a specific type of data, > then you let them pay for the archiving, indexing, and > knowledgeable data experts. > >There's something that you're missing here, I think. No doubt there's >some domain-specific knowledge involved in the production of >comp.archives; it's useful to have a feel for which of the 1000+ >archive sites in the world have the greatest likelihood of having >current stuff, which authors are most reliable, who is best organized. >But there's more to it than that. One of the fundamental technologies >involved is taking a piece of text and answering the question "Is this >interesting?", or more likely "Is this likely to be interesting to Ed >Vielmetti, or Chris Torek, or Mark Moraes, or Richard Stallman, or >Mitch Kapor?" That's not an easy question, but if you can solve it >(for free) for the person involved, then you can instantly market what >you have to everyone else in the world who respects these people's opinions. > > As an extreme case, you can imagine a host of consultants, > each with his or her own archive. Each consultant advertises > a specialty, collects related data, indexes it according to > personal needs, seeks out customers, prepares reports, and > occasionally even publishes a book. > >That's a good model to follow, and I would hope to start following it. >One of the things that's going to be part of the MSEN Archive >Service which is not in comp.archives now is a further breakdown >by subject classification; you'll be able to subscribe to >"msen.archives.tex" and get just the latest and greatest on TeX >software announcements and reviews, or "msen.archives.x" to track the >progress of X11 stuff. You'll particularly want the last one once >X11R5 rolls around. Each of these collections will have its own >archivist, who is responsible for quality control and additional >research. >I'm planning to apply the same technology to related fields as well, >subject to the availablility of some copyrighted information (and the >time and investment to pull it off). For instance, an MSEN Patent >Watch subscription would get you news of patent filings, >cross-license agreements, technical information (and raw speculation) >on the viability and challengability of software patents , >etc, culled from every available source and tagged (by experts) with >an assessment of quality and value. I'd bet that this on could even >make a go for itself on paper. > > Instead of following the consultant model, you seem to be > following the public library model. Why? There's no money > in it. > >One of the problems with the consultant model is that it doesn't scale >too well; you have to do all of the development yourself, and it's >hard to find like-minded people because you're hoarding all of your >efforts. By pursuing a strategy that includes some component of >public service / pro bono / for the good of the net, and by >aggressively tracking Internet standards (like the multipart, >multimedia "richmail" spec), it's possible to get a substantial amount >of goodwill, and perhaps enough visibility for people to take you >seriously. >After all, this sort of thing is very old, it's just a high tech >"clipping service". It's something that I would do just for >myself except that that hasn't been lucrative enough to buy the >necessary hardware and software I'd need to store all of the >interesting things I find, or to license the necessary rights to the >copyrighted newsfeeds (let alone have anything left over for me) . It >doesn't matter if there's "no money in it", so long as the venture is >self-supporting and sustainable. > >Edward Vielmetti, vice president for research, MSEN Inc. emv@msen.com >"MSEN Archive Service" and "MSEN Patent Watch" are trademarks of MSEN, Inc. > >On the Net, the Net-way is best. > It's just that we are trying to figure out what the Net-way is. > e. miya > > > >Markup information provided for use by news readers which implement >the experimental "Mechanisms for Specifying and Describing Internet >Message Bodies", available for anonymous ftp from > > thumper.bellcore.com > /pub/nsb > >This text has been marked up in the hopes that someone will be able to >print it out on paper and make it pretty! A five dollar reward goes >to the first nice paper copy. Send submissions to > > Edward Vielmetti > MSEN, Inc. > 317 S. Division, Suite 218 > Ann Arbor, MI 48104-2203 > USA > > > key words > emphasis > trademark > signature > paper mail ("snail mail") address > when in doubt, quote an RFC. > message id > from > > LAWS.91Jun22223423@sunset.ai.sri.com > laws@ai.sri.com (Kenneth I. Laws) > > > % Robert Harper % HARPER@FINFUN % HARPER@CSC.FI % % Finnish State Computer Centre % Bitnet % Internet % % Tietotie 6, 02101 Espoo Finland % Tel 358 0 4572076 % Fax 358 0 4572302 % From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!lhc!lhc!hunter From: hunter@work.nlm.nih.gov (Larry Hunter) Newsgroups: bionet.general,bionet.molbio.bio-matrix,comp.ai Subject: Version 1.6 of the AI and MolBio researchers database Message-ID: Date: 25 Oct 91 00:02:51 GMT Sender: usenet@nlm.nih.gov (usenet news poster) Organization: National Library of Medicine Lines: 37 Xref: bionet bionet.general:1675 bionet.molbio.bio-matrix:244 comp.ai:5710 Version 1.6 of the National Library of Medicine Database of Researchers in Artificial Intelligence and Molecular Biology is ready for downloading. The Lister Hill National Center for Biomedical Communications of the National Library of Medicine has compiled a database of scientists, graduate students, funding agents, and other researchers active in the field of artificial intelligence and molecular biology. This database contains the names, institutional affiiliations, addresses, telephone and fax numbers, email addresses, and research interests of more than 175 researchers. The purpose of the database is to facilitate scientific communication among this geographically and academically diverse group of researchers. The database will be made available by anonymous ftp from the internet, and by email upon request to researchers who do not have internet access. The internet host is lhc.nlm.nih.gov (130.14.1.128). The files are stored in the directory /pub/aimb-db. You can log in as user "anonymous" with your email address as your password. The README file contains all you need to know about the database and how to use it. The database will also be available via email request from the University of Houston biocomputing server. I hope this database is useful to the community. Please send any comments, corrections or questions to me at the address below. -- Lawrence Hunter, PhD. National Library of Medicine Bldg. 38A, MS-54 Bethesda. MD 20894 (301) 496-9300 (301) 496-0673 (fax) hunter@nlm.nih.gov (internet) From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!apple!usc!cs.utexas.edu!uunet!psinntp!sci.ccny.cuny.edu!cucrd0!cuccfa.columbia.edu!jovanovic From: jovanovic@cuccfa.columbia.edu Newsgroups: bionet.molbio.bio-matrix Subject: Re: P.S. Message-ID: <223@cucrd0.med.columbia.edu> Date: 30 Aug 91 20:52:05 GMT References: Sender: news@cucrd0.med.columbia.edu Distribution: usa Organization: Columbia University Lines: 18 In article kristoff@GENBANK.BIO.NET (Dave Kristofferson) writes: >If the newsgroup is still of use, I would humbly suggest that >instructions for subscribing and posting to it be included routinely >in a small box in the newsletter. Many personal and server e-mail >addresses were included in the letter but not the above. I'm actually interested in the group, even though it seems a bit inactive at the moment. It could use a regular posting explaining the purpose of the group (otherwise people might think it has something to do with columns ). I'll try getting in touch with some of the Bio-Matrix people, as if they don't have anyone that can regularly deal with the group, I wouldn't mind taking on the job. Oliver Jovanovic . . From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!snorkelwacker.mit.edu!apple!usc!cs.utexas.edu!uunet!mcsun!news.funet.fi!funic!finsun!harper From: harper@finsun.csc.fi (Robert Harper) Newsgroups: bionet.molbio.bio-matrix Subject: Re: BioComputing bibliographies Message-ID: Date: 23 Sep 91 07:27:46 GMT References: <9109222214.AA27429@starbase.mitre.org> Sender: usenet@nic.funet.fi Distribution: bionet Organization: Centre for Scientific Computing, Finland (CSC) Lines: 15 Nntp-Posting-Host: finsun.csc.fi In <9109222214.AA27429@starbase.mitre.org> amsler@STARBASE.MITRE.ORG (Robert A. Amsler) writes: >Electronic submissions may be sent to the GENTOOLS e-mail address >above. The GenTools project can handle electronic manuscripts in the >.TEX, .DVI, .PS and .ASCII format right now. We are trying to exend >our capability. The Sarah Barron literature database is available for on-line searching as a WAIS source called compalgo.src on the Finnish State Computer nic.funet.fi RGDS -=ROB=- % Robert Harper % HARPER@FINFUN % HARPER@CSC.FI % % Finnish State Computer Centre % Bitnet % Internet % % Tietotie 6, 02101 Espoo Finland % Tel 358 0 4572076 % Fax 358 0 4572302 % From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!AI.SRI.COM!pkarp From: pkarp@AI.SRI.COM (Peter Karp) Newsgroups: bionet.molbio.bio-matrix Subject: new version of Biomatrix bibliography Message-ID: Date: 13 May 91 22:51:59 GMT Sender: daemon@genbank.bio.net Lines: 16 Thanks to contributions from Jim Holloway, I have compiled an expanded version of the bibliography related to Biomatrix topics. Most of Holloway's additions are in the area of algorithms for sequence comparison. Further contributions are welcome. You can use anonymous FTP to obtain the following files from host ai.sri.com in directory pub/pkarp/biomatrix: matrix-bib.bib Latex bibliography format matrix-bib.txt Text format matrix-bib.ps Postscript format These files should also appear on the University of Houston server shortly. Peter From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!s.u-tokyo!ccut!sun-barr!lll-winken!uunet!mcsun!fuug!funic!harper From: harper@nic.funet.fi (Rob Harper) Newsgroups: bionet.general,bionet.molbio.bio-matrix,comp.ai,alt.wais Subject: Re: Version 1.6 of the AI and MolBio researchers database Message-ID: <1991Oct28.092718.9599@nic.funet.fi> Date: 28 Oct 91 09:27:18 GMT References: Organization: Finnish University and Research Network (FUNET) Lines: 25 Xref: bionet bionet.general:1683 bionet.molbio.bio-matrix:245 comp.ai:5740 alt.wais:146 In hunter@work.nlm.nih.gov (Larry Hunter) writes: *>Version 1.6 of the National Library of Medicine Database of *>Researchers in Artificial Intelligence and Molecular Biology is ready *>for downloading. The aimb database has now been made into a WAIS source and can be queried over the network. It has been added to the bioinfo.src so that it you can preview it from that source and save the aimb.src and its description to your MAC WAIStation or X-windows Xwais version. The original database can also be found in /pub/sci/molbio/databases/aimb on nic.funet.fi via anonymous ftp for Europeans. RGDS -=ROB=- -- Rob Harper / E-mail: Harper@convex.csc.fi Finnish State Computer Centre / Molbio/software: Harper@nic.funet.fi P.O. Box 40, SF-02101 Espoo / Telephone: +358 0 457 2076 Finland / Fax: +358 0 457 2302 From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!cu.warwick.ac.uk!lsrcj From: lsrcj@cu.warwick.ac.uk (M A McCrae) Newsgroups: bionet.molbio.bio-matrix Subject: (none) Message-ID: <24560.9105020847@clover.warwick.ac.uk> Date: 2 May 91 08:47:28 GMT Sender: daemon@genbank.bio.net Lines: 1 alwin From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!rutgers!tut.cis.ohio-state.edu!cis.ohio-state.edu From: moberg@cis.ohio-state.edu (Dale Moberg) Newsgroups: bionet.molbio.bio-matrix Subject: Mendelian Genetic Database Sought Message-ID: <111617@tut.cis.ohio-state.edu> Date: 23 Apr 91 16:42:46 GMT Sender: news@tut.cis.ohio-state.edu Organization: The Ohio State University, Department of Computer and Information Science Lines: 41 We need to locate a machine-readable, ftp-able database containing Mendelian genetic breeding data for some organism exhibiting the following combinations: 1. At least two genes (4 alleles), heterozygous, both incompletely dominant, linked. 2. At least two genes (4 alleles), heterozygous, both incompletely dominant, independent (in different linkage groups). Ideally the data would be raw numbers for the phenotypic characteristics and genes. We want data that has not been "cleaned up" into ratios, but is very close to lab notebook observations. (This is not usually found in textbooks or publications.) References to books or articles will also be appreciated, but a database would be ideal. The data is to be used by an AI theory generating program that starts with a simple Mendelian view of inheritance and progresses to Morgan's chromosomal theory. Thanks for any pointers. Lindley Darden ;; darden@cis.ohio-state.edu Dale Moberg;; moberg@cis.ohio-state.edu === Laboratory for Artificial Intelligence Research Department of Computer and Information Science The Ohio State University 228 Bolz Hall 2036 Neil Avenue Mall -- Dale Moberg, Assistant Director, moberg@cis.ohio-state.edu Laboratory for AI Research (LAIR), OSU, Caldwell 409, 614-292-8578 From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!news.cs.indiana.edu!samsung!spool.mu.edu!uunet!mcsun!hp4nl!dnlunx!pttrnl.nl!buys From: buys@pttrnl.nl Newsgroups: bionet.molbio.bio-matrix Subject: Help with Zoological database Message-ID: <1991Mar7.111149.65012@pttrnl.nl> Date: 7 Mar 91 10:11:49 GMT Lines: 13 At the moment I am studying the possibilities for a universal database structure for the Mollusca collection of the National Natural History Museum of the Leiden University in the Netherlands. Does anyone have experience with the design of databases for the registration of zoological data? Does anyone have a sample data-dictionary? All responses are most welcome. Regards, Jan-Paul Buys JP_Buys@pttrnl.nl From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!AI.SRI.COM!pkarp From: pkarp@AI.SRI.COM (Peter Karp) Newsgroups: bionet.molbio.bio-matrix Subject: newsletter subscription Message-ID: Date: 21 Aug 91 16:15:44 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 17 Generally, the newsletter is sent to members of the Biomatrix Society. Contact Ginger Richardson at the address below for information on joining the society, or to request a complimentary copy of the current issue: Ginger Richardson Santa Fe Institute 1660 Old Pecos Trail, Suite A Santa Fe, NM 87501 grr@sfi.santafe.edu In response to one of David's questions, I believe the current issue is Vol 2 because some of the traffic on this mailing list had been printed and distributed as Vol 1 of this newsletter a year or two ago. Peter From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111211257.AA16556@genbank.bio.net> Date: 21 Nov 91 12:53:31 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111211329.AA16952@genbank.bio.net> Date: 21 Nov 91 12:59:18 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111211244.AA16396@genbank.bio.net> Date: 21 Nov 91 12:36:32 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111211250.AA16460@genbank.bio.net> Date: 21 Nov 91 12:46:58 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: Problem on BIO-MATRIX should be fixed now Message-ID: Date: 21 Nov 91 20:55:31 GMT Sender: kristoff@genbank.bio.net Distribution: bionet Lines: 16 I have received word from the U.K. that the address causing the problem on the BIO-MATRIX list has been dealt with so I am turning our e-mail distribution at GenBank back on again. The UK Internet gateway continues to have major problems, however, so we will have to monitor things closely. Those who post to any BIOSCI newsgroup may get a note back to their personal mail file if mail can't get through to a UK address. We are taking steps to minimize these problems which I needn't bore you with here. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: (none) Message-ID: Date: 3 May 91 01:10:47 GMT Sender: kristoff@genbank.bio.net Lines: 15 > gb-schema > > This is the second message that I have seen today like this. The e-mail address for the server at LANL is bioserve@genome.lanl.gov. Please don't send these to the BIO-MATRIX newsgroup or to the genbank address here. Thanks. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!PUCC.PRINCETON.EDU!KONEIL%WHEATNMA From: KONEIL%WHEATNMA@PUCC.PRINCETON.EDU Newsgroups: bionet.molbio.bio-matrix Subject: Addresses of companies wanted Message-ID: <9104201440.AA00212@genbank.bio.net> Date: 20 Apr 91 00:10:00 GMT Sender: daemon@genbank.bio.net Lines: 13 I'm looking for the addresses of companies in the U.S., Australia, and France that are involved in biological processes as applied to industrial materials and processes concerning microorganisms. I'd appreciate any help I can get- I'm in desperate need of the information. My appologies if you receive multiple copies of this letter; I'm writing several lists. You're welcome to respond directly: koneil@wheatnma Thanks, Kathleen O'Neil. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UH.EDU!Davison From: Davison@UH.EDU (Dan Davison) Newsgroups: bionet.molbio.bio-matrix Subject: Help 'Save the Infosphere' (from EDTECH-fwd) Message-ID: <9106121446.AA02266@Menudo.UH.EDU> Date: 12 Jun 91 14:46:35 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 71 This is a repost from BIONEWS that will be of interest to Bio-Matrix'ers. dan Date: Mon, 10 Jun 91 00:26:48 EDT From: Sue Anderson Subject: Help "Save the Infosphere" ?? Sender: EDTECH - Educational Technology This summer and fall, the National Public Telecomputing Network (NPTN), a nonprofit public computer network headquartered in Cleveland, Ohio, will be working on it's first annual "Infosphere Report" -- a research project which will attempt to assess the nation's health with regard to information age issues. We are defining the infosphere as: the technical and organizational environment in which the general public can access computer-mediated communication and information resources. The central idea is to conduct an on-going study similar to those conducted in areas such as economics, population growth and the environment, with reports appearing every year. The data will be cumulative, comparative, and prescriptive. That is, it is expected that over-time a portrait will emerge which will describe this nation's progress as it enters an information age. It will show where we are doing well, where we are doing poorly, and where more emphasis is needed. One of the trickiest parts of doing a study like this is trying to figure out what the critical variables are when measuring something like the "infosphere." If you are measuring the health of the environment, you can measure the presence of various chemicals in the air, water, or soil. But how do you measure the health of our informational environment? We have some ideas about what information should be included. We might, for example, be interested in finding out how many homes, schools, and libraries have computers and modems; how many libraries allow modem and/or internet access to their computerized card catalogues; and how many government agencies allow modem and/or internet access to their informational resources. We want more ideas. So we are actively soliciting the computer networks and telecomputing community to be a part of this effort. If you have any thoughts on how the infosphere might best be assessed-- what kind of variables we should be looking at--we'd appreciate your input. All suggestion are valued. Suggestions which also tell us where we might go to actually FIND that information are cherished! Please send your suggestions to: Sue Anderson, M.Ed., NPTN - Infosphere Project aq941@cleveland.freenet.edu or Tom Grundner, Ed.D., NPTN - President aa001@cleveland.freenet.edu Please also feel free to re-post this message where ever you think appropriate. -- dr. dan davison/dept. of biochemical and biophysical sciences/univ. of Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU Disclaimer: As always, I speak only for myself, and, usually, only to myself. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!s.u-tokyo!ccut!sun-barr!lll-winken!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!magnus.acs.ohio-state.edu!usenet.ins.cwru.edu!ysub!psuvm!trearn!oprj10 From: OPRJ10@TREARN.BITNET Newsgroups: bionet.molbio.bio-matrix Subject: Growth Simulation of Saccharomyces cerevisiae Message-ID: <91221.153210OPRJ10@TREARN.BITNET> Date: 9 Aug 91 13:53:11 GMT Organization: Ege University - Computing Center Lines: 10 I am studying on writing a computer program which will simulate the growth of S. cerevisiae .The yeast is also known as Baker's yeast.To write this programme i will need some date about kinetics of S. cerevisiae , I also need relationships between some paremeters during growth (such as ph,tempera ture,dissolved oxygen , etc.) If anyone who dealt with this subject helps me , I will be very thankfull. Murat ILDIZ oprj10 at trearn From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111211108.AA15385@genbank.bio.net> Date: 20 Nov 91 23:14:34 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111211228.AA16136@genbank.bio.net> Date: 21 Nov 91 12:22:19 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111211220.AA16022@genbank.bio.net> Date: 21 Nov 91 12:15:38 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111211235.AA16281@genbank.bio.net> Date: 21 Nov 91 12:31:07 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!kristoff From: kristoff@genbank.bio.net (David Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: Re: Working to resolve list problem Message-ID: Date: 20 Nov 91 20:17:55 GMT References: Distribution: bionet Organization: GenBank Online Service Lines: 11 I am going to remove our e-mail subscribers from receiving further BIO-MATRIX postings until I receive confirmation that this problem is resolved. Because of the time zone difference it may take a while before things get corrected. Sorry once again for the problem. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111202212.AA22082@genbank.bio.net> Date: 20 Nov 91 21:08:21 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111202126.AA18982@genbank.bio.net> Date: 20 Nov 91 18:27:17 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: GenBank BIO-MATRIX list off-line Message-ID: Date: 20 Nov 91 23:06:54 GMT Sender: kristoff@genbank.bio.net Distribution: bionet Lines: 23 I have taken the BIO-MATRIX e-mail distribution at GenBank off-line since the "Authorization" bouncers are continuing to come through. Unfortunately those on the GenBank "send me all BIOSCI newsgroups" list will continue to get hit. Also unfortunately European subscribers will probably wake up to 20 or so copies of this message in their mailbox tomorrow. We sent warnings to the European BIOSCI sites when this was discovered but it was late in the day their time. Once again this problem is due to LISTSERV at IRLEARN snapping up an error message from the UK and reflecting it to the list. We have proposed solutions for this in the past, and I continue to hope that they will be implemented. Steps are in progress at other BIOSCI sites to prevent this kind of situation, and we have been more than patient to date. We can't afford to continue much longer and allow this kind of problem to irritate our users. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111201643.AA03272@genbank.bio.net> Date: 20 Nov 91 12:22:23 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111201750.AA05706@genbank.bio.net> Date: 20 Nov 91 14:22:26 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111201716.AA04609@genbank.bio.net> Date: 20 Nov 91 12:44:57 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!IRLEARN.UCD.IE!ADVISER From: ADVISER@IRLEARN.UCD.IE (Duty Adviser) Newsgroups: bionet.molbio.bio-matrix Subject: Proposal: BIONET.MOLBIO.HIV Message-ID: <9111201628.AA02362@genbank.bio.net> Date: 20 Nov 91 11:58:22 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 108 Dear Netters, Sorry for the crossposting, but as the voting period approaches its end i am reposting the proposal for the bionet.molbio.hiv newsgroup. Please activate all efforts to vote !! Mika Salminen ----------------------------------------------------------------------------- Proposal for the establishment of bionet.molbio.hiv :-) I would like to propose the establishment of a newsgroup under bionet.molbio for the discussion and information sharing of topics concerning the research on the Human Immunodeficiency Viruses, mainly dealing with concepts of molecular biology. Considering the enormous amount of research going on in this field i think that the newsgroup would be useful and receiwe many postings. I would like to point out that this newsgroup should really deal only with matters of molecular biology rather than clinical questions. There are other forums better suited for the exchange of clinical information, and i'm afraid that those questions would flood the group and blur the big picture. What i am really thinking of is a way of distributing information on questions such as different HIV-recombinant constructions, the availability of strains, info on PCR-primers and amplification procedures and so on. The group could also function as a discussion forum for theoretical questions dealing both with the function of the HIV virus and ideas on how it could be stopped. All HIV researchers are aware of the problems inwolved and would certainly appreciate comments from the rest of the molbio reseach community. Comments about this proposal and the organisation of bionet.molbio.hiv are appreciated and should be replied to the group where this posting appears NOT TO ME PERSONALLY!!! Yours, Mika Salminen, M.Sc. National Institute of Public Health HIV-laboratory msalminen@finnphi.bitnet msalminen@nphi.fi -------------------------- Advertize ------------------------------------- NEW USENET NEWSGROUP BIONET.MOLBIO.HIV Send email message: YES ON HIV (Empty subject line) Choose the adress below which is closest to you Adress: Loction Network _______ ------- ------- biovote@irlearn.ucd.ie Ireland EARN/BITNET biovote@uk.ac.daresbury U.K. JANET biovote@bmc.uu.se Sweden Internet biovote@genbank.bio.net U.S.A. Internet/BITNET NOTE! Voting period ends at 6 December 1991! The usenet newsgroups are international electronic discussion forums for day to day communication among computer users. The usenet lists are divided into interest groups of which one is the BIONET/BIOSCI utility. Bionet consists of many groups covering biologic subjects, mostly of a molecular biologic point of view. There are goups for employment exchange and laboratory cookbook topics etc. Bionet is a very fast and convenient way of exchanging information and get fast answears on everyday lab problems. BIONET is best reached by using NEWS-reading software that is distributed as shareware and awailabel for most computer platforms (UNIX, VMS, IBM etc.) There has been a proposal for the establishment of a new group on BIONET, bionet.molbio.hiv which is up for vote until 6 December 1991. The purpose of this group would be to provide a fast way for the large community of HIV researchers to exchange information. You can influence the establishment of the group by following the above voting procedure at your own computer, provided it is connected to international networks. If you dont have NEWS- reading software at your institute, consult your system manager to set it up. A plus: Most NEWS-readers are very easy to use! Know the latest tips: READ BIONET !!! Peter Coghlan Duty Adviser, UCD Computing Services. E-mail: ADVISER@IRLEARN.UCD.IE Phone: 353-1-706-8645 "If it's free, I'll have two." From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111201743.AA05301@genbank.bio.net> Date: 20 Nov 91 13:57:50 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: Working to resolve list problem Message-ID: Date: 20 Nov 91 17:59:13 GMT Sender: kristoff@genbank.bio.net Distribution: bionet Lines: 7 I have alerted the necessary people to kill the "authorisation" messages being sent to the BIO-MATRIX list. Sorry for the inconvenience. Dave Kristofferson From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111201837.AA07960@genbank.bio.net> Date: 20 Nov 91 15:25:40 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111201935.AA10924@genbank.bio.net> Date: 20 Nov 91 16:00:57 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111201718.AA04635@genbank.bio.net> Date: 20 Nov 91 13:27:38 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UGA.CC.UGA.EDU!authorisation%UK.AC.UKC From: authorisation%UK.AC.UKC@UGA.CC.UGA.EDU (Authorization Warning Daemon) Newsgroups: bionet.molbio.bio-matrix Subject: Authorization Warning Message-ID: <9111201809.AA06802@genbank.bio.net> Date: 20 Nov 91 14:38:03 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 39 Regarding your mail to: @uknet.ac.uk:g$pavulurir@snd02.pcr.co.uk On 1st October 1991 the UKnet Backbone at the University of Kent at Canterbury functionally separated from the rest of the University of Kent at Canterbury. Only mail that is destined for users actually at the University of Kent at Canterbury (lecturers, students, etc) should still be sent to: ukc.uucp / ukc.ac.uk / uk.ac.ukc All other mail should be sent to: uknet.uucp / uknet.ac.uk / uk.ac.uknet This message is being sent to you because either a) you have explicitly, or b) the machine you are using has by default, routed via: ukc.uucp / ukc.ac.uk / uk.ac.ukc instead of: uknet.uucp / uknet.ac.uk / uk.ac.uknet On this occasion your mail is being forwarded, but please switch to using the correct routing in the future. If you're a user and need advice talk to your local postmaster/administrator. If you're a postmaster/administrator and need advice, mail postmaster@uknet.uucp / postmaster@uknet.ac.uk / postmaster@uk.ac.uknet telephone +44 227 475497 if it's urgent. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!NOTE.NSF.GOV!rrobbins From: rrobbins@NOTE.NSF.GOV ("Robert J. Robbins") Newsgroups: bionet.molbio.bio-matrix Subject: electronic publishing Message-ID: <9008071208.aa22273@Note.NSF.GOV> Date: 7 Aug 90 16:08:48 GMT Sender: daemon@genbank.BIO.NET Lines: 101 A recent posting has raised some issues with regard to electronic publishing and has made particular reference the presentation by Patricia Morgan at the last BioMatrix meeting. The posting recalls two arguments against electronic publishing, half tones and cost to libraries, and notes that less than 5% of computer science journal articles contain photographs. The posting also notes that, 'when I mentioned the second argument to a friend they commented, "who needs libraries anyway?". That is, we could have direct distribution from publishers to readers.' In response to these comments, I offer some observations: - The posting is correct that the use of halftones is discipline dependent. Computer science, mathematics, logic, philosophy, and other abstract fields don't need them. Biology, especially molecular biology, does. Halftones are not the only problem, however. Other graphics make for difficulty, too. The argument, raised at the meeting, that PostScript can be used as the galactic standard for page layout just doesn't hold water. First, the standard isn't as standard as standards ought to be. I have had people send me PostScript reports via e-mail and when I print them out using a PostScript printer at NSF, occasionally a page comes out with a screwed up format. The source claims the file printed fine at home. This leads me to believe that not all PS files print identically on all PS printers. Second, not everyone has access to PS printers. Third, even when folks do have access to PS printers, they often would prefer to receive a printed article in the mail rather than fire up the printer and produce (at, say, 4 cents a page) a 100-page printout that then must be stapled or punched or whatever so that it can be carried around and read conveniently. - The doing-away-with-libraries notion sounds intriguing at first, but appears more naive and silly upon further thought. Libraries do not exist just to provide full employment opportunities for parasitic librarians. They provide real functions, such as allowing researchers access to many more journals than they could possibly afford individually. They also provide an archival function, which is essential in disciplines that are less ephemeral than computer science. Quick, give five computer-science citations that are over fifty years old that can still be read with profit. However, there are many biological manuscripts that are over a hundred years old that are still important and useful. Many of these involve detailed illustrations (engravings, usually) of anatomical studies that have not been redone, since the original 19th century work is considered definitive. Converting these to PostScript format would be costly and tedious, and would greatly reduce the value of the work. The archival problem is perhaps one of the more acute arguments against electronic publishing. Quick, give five examples of material written electronically over forty years ago that can still be read easily with current equipment. For electronic publishing to be considered even as a candidate for archival publishing, there will have to be some possibility that material published electronically will continue to be readable for decades, preferably centuries, without need for periodic copying onto new media in new formats. - The issue of cost is real, as well, and cannot be dismissed by doing away with libraries. Publishers publish to make a buck, not to provide a free service to the world. Serious electronic publishing involves user fees independently of whether the user is a library or an individual. Serious publishing also involves a concern for the rights, economic and otherwise, of the author and publisher. Sure, you can always make 50 xerox copies of the latest issue of Cell and distribute them to your friends, but that will involve a lot of work and expense and you are not likely to do it very often. Therefore, the publisher of Cell can set subscription fees on the assumption that most readers will be looking at a paid-for copy, not a xeroxed rip off. With an electronically delivered journal, say that arrives via email, you can, with a simple forward command, send 50 or 100 or 1000 copies off to many friends almost effortlessly. Therefore, a publisher working in this medium must assume that most of the readers will be using non-paid-for copies and the few fools (libraries?) who obtain their copies legitimately must be expected to carry the full cost for the subscription. I could add a few more observations, but I suspect my position is fairly clear. I believe that the idea that electronic publishing will replace print publishing is about as accurate and astute a prediction as the one made frequently in the fifties that private helicopters would replace private automobiles. Helicopters play many important roles in our society, but providing routine individual transportation is not one of them. Likewise, computers and electronic communication play important roles in our society, but replacing the printed word as the primary medium for scientific communication is not one of them. At the same time, there are certain kinds of scientific publishing that cry out for an electronic medium. Database materials are obviously one of these. How many people prefer to use GenBank in the hard-copy, multi-volume form? I think that those of us who believe that computers have an increasingly important role to play in the practice of biology should take care to avoid making exaggerated claims, either through naivete or excess enthusiasm. Nothing undercuts a good case more than a patently false assertion. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!NCBI.NLM.NIH.GOV!pkarp From: pkarp@NCBI.NLM.NIH.GOV (Peter Karp) Newsgroups: bionet.molbio.bio-matrix Subject: The Biomatrix Message-ID: Date: 2 Oct 90 20:47:48 GMT Sender: daemon@genbank.bio.net Lines: 49 I thought I would stimulate discussion on this list a bit by offering an alternative view to Dan Davison's regular postings that describe what the Biomatrix is. This message summarizes my own view. The Biomatrix is several things: The Biomatrix exists at this moment as the set of all data bases and knowledge bases that encode biological information, and as the collection of existing computer programs that manipulate this information. Databases such as MedLine, PIR, GENBANK, and SwissProt constitute the present-day Biomatrix. The Biomatrix embodies a vision of how biologists of the future will carry out their work. To a much larger degree than today, the biological knowledge and data of the future will reside in computer systems, and the biologist of the future will employ computer tools to access this information. All forms of biological information will be encoded electronically, including traditional forms such as laboratory data, reference works, journal publications, and texts. New forms of biological information will emerge in the future Biomatrix. The Biomatrix will constitute a substrate for electronic communication among scientists. Knowledge-based systems technology will encode biological knowledge, laws, and theories in more active forms that can be used for tasks such as simulation, experiment planning, teaching, and analogical reasoning. Information repositories will be linked together over high-speed networks so that although they will be distributed geographically, they will be instantly available to researchers around the globe. The effect of the future Biomatrix will be to increase the availability of biological information to people and machines. The biologist of the future will have access to information in greater quantities and at greater speeds than today. One result of this organization will be to facilitate reasoning by analogy, whereby a biologist will bring information about a distant biological system to bear on his or her problem of interest. A second result will be that as these electronic repositories grow in size, they will be more and more difficult for people to comprehend, so biologists will employ machine learning programs of various sorts as assistants that will aid biologists in discovering new regularities in the information stored in these repositories. Finally, the Biomatrix is a community of biologists and computer scientists who share this common goal. Many aspects of the Biomatrix of the future are unattainable without fundamental advances in computer science (such as networking, databases, knowledge representation, algorithms, machine learning, and neural networks) that will be achieved from collaborations between researchers in these fields. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!kristoff From: kristoff@genbank.bio.net (David Kristofferson) Newsgroups: bionet.molbio.bio-matrix Subject: Re: Oh foolish supporters of genome sequencing Message-ID: Date: 12 Feb 91 16:23:44 GMT References: <9102111908.AA07006@genbank.bio.net> <5695@husc6.harvard.edu> Organization: GenBank Online Service Lines: 14 > (1) The contention that scientists should somehow be fulfilled "not doing > real science," which seems like a self-contradictory sentence, ARGGHHH 8-)!!!! Perhaps my writing is extremely unclear, but, after a couple of attempts at clarification, this "paraphrase" still shows a misunderstanding of my position. I hope others who did not have a direct involvement in this exchange understood what I was trying to say. It was never my intention to try and "convert" Dr. Ellington, but only to speak to those scientists who were *already* tired of "real science" and let them know that, despite the trauma one can experience in deciding to leave research, there are other fulfilling career options out there. Enough said on this topic. Dave Kristofferson From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!FCRFV1.NCIFCRF.GOV!gribskov From: gribskov@FCRFV1.NCIFCRF.GOV ("Gribskov, Michael") Newsgroups: bionet.molbio.bio-matrix Subject: genome project Message-ID: <9102121616.AA03441@genbank.bio.net> Date: 12 Feb 91 16:11:00 GMT Sender: daemon@genbank.bio.net Lines: 98 I am glad to see that this discussion has, for the most part, returned to rational debate. Dr. Ellingtons's objections to the genome project seem to me to fall into 3 categories: financial, systematic, and scientific. 1) Financial -- the genome project is cutting into NIH funding for other projects and molecular evolution projects are difficult to get funding for. While there is some truth to this, I think the bulk of the funding for the genome program is new money. NIH's funding problems can be traced to a number of sources, including the large increase in the number of continuing grants funded several years ago, and a substantial increase in the number of researchers competing for grants. It seems to me that it is very unlikely that cancellation of the genome program would result in the transfer of the allocated funds to NIH general program. Congress would probably see a "better" use for them (congressional salaries perhaps, certainly not deficit reduction). There are also a number of projects funded previously by the NIH which are now funded by genome project funding, thereby freeing up this money for non-genome projects. Or another way of looking at it: some of the genome project money way already being spent on the same projects even before the prject officially existed. 2) Systematic -- the information resulting form the genome project is available by other means and few if any new lines of research will be opened up. To apply this standard to the genome project seems unfair. Few if any grants describe a problem that can't be tackled by other means. Most merely continue an existing line of inquiry and do not open up new ones. 3) Scientific - too little is known about human genes; the genetic map is too poor to justify sequencing the genome, besides most of the DNA is "junk" anyway. Furthermore the project is anthropocentric, ignoring the genomes of species which are much better characterized genetically. Many, if not the majority, of genes can be identified and the identity of the protein product determined by comparison to known genes from other organisms. It is not unreasonable to expect that by the time actual genome sequence is available that most genes will be able to be identified in this way. My understanding of the current project is the large parts, if not all, of the sequences of the following model systems will be sequenced in the course of the genome project: E. coli, yeast, fly, nematode, and mouse. These include some of the most well characterized gneetic systems. Perhaps the project should have been called the "lots of genomes project", but this would have been difficult to sell to congress. Although we do not understand the function of much of the non-coding DNA, it is really premature to call it "junk". Only a few years ago, the self-splicing introns that Dr. Ellington find interesting would have also been characterized as junk. -------------------- As to whether the resulting information will be useful, I admit that we won't really know until we have a good piece of it. The project is speculative, as is a lot of good science. One of my main worries is that it is being heavily oversold to congress as a panacaea for human disease. This may ultimately result in a painful congressional backlash. The actual sequencing of genomes is still five years or more down the road and we will be in a much better position to judge the value of the project in a few years. In the meantime, the five year goals of the project appear to me to be very justifiable and of wide general use. My synopsis gleaned from the U.S. Human Genome Project: FY 1991-1995 (DOE/ER-0452P) report. 1) Complete a fully connected human genetic map with markers 2-5 centimorgans apart, each associated with an STS. 2) Assemble STS maps of all human chromosomes with markers at at 100kb intervals. Generate overlapping clones with continuity over 2mb. 3) improve sequencing technology to allow sequencing at a cost of $ 0.50/bp. 4) prepare a genetic map of the mouse genome based on DNA markers and physically map one or two chromosomes. 5) develop effective software and database designs to deal with mapping and sequence data. 6) support research training of up to 600 pre- and post-doctoral trainees. The technique of ridiculing a project (by comparison to phlogiston or N-Rays) would seem to indicate a lack of real arguments. Creationists often ridicule evolution with the same "ohmigosh, it's unimaginable" in the course of proving that evolution is impossible. I repeat -- many reputable scientists see some value in the genome project -- not all of them are fools. And no, I do not feel that I need to list them; Most of us know who they are, anyone can find out by reading a little. Michael Gribskov gribskov@ncifcrf.gov From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!AI.SRI.COM!pkarp From: pkarp@AI.SRI.COM (Peter Karp) Newsgroups: bionet.molbio.bio-matrix Subject: Metabolic Compound Database Message-ID: Date: 2 Oct 91 04:34:03 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 58 Announcing CompoundKB -- A Database of the Chemical Compounds of Intermediary Metabolism The CompoundKB database describes 981 chemical compounds of intermediary metabolism. For each compound the database lists: o Synonyms for the compound name o The systematic name of the compound o The CAS registry number o The chemical formula o The molecular weight o The chemical structure o Two-dimensional display coordinates for the structure The CompoundKB is available in three different database formats to facilitate access by end users: in a Knowledge Base form, as ASCII delimited tables that can easily be loaded into a relational database management system, and in the ASN.1 data-exchange standard format. Although no special-purpose software is provided for searching the CompoundKB, users can employ general software tools such as relational database management systems and ASN.1 software utilities for manipulating the database. The CompoundKB is available online via the Internet from the data repository at the National Center for Biotechnology Information. Use the Internet file transfer protocol (FTP) to connect to host ncbi.nlm.nih.gov using username "anonymous" and your name as password. Then connect to directory repository/metabolism/compounds/asn1 , and retrieve all of the files found there. This directory contains the ASN.1 representation of the dataset; to obtain the RDBMS or knowledge-base representation, substitute rdbms or kb for asn1 in the preceding directory name. The Lisp-language software that the author used to develop the KB is in directory lisp. The database has been reviewed for correctness by a number of scientists, and a manuscript (submitted to CABIOS) describing the CompoundKB documents its error rate, the methodology by which it was constructed, the semantics of the data, and the different database formats. The manuscript is available in subdirectory Doc of the compounds directory on the NCBI repository (in postscript and latex formats), and from the author. Please direct questions or error reports to the author at the following address: Peter D. Karp, PhD pkarp@ai.sri.com Artificial Intelligence Center SRI International, EJ229 office: 415-859-6375 333 Ravenswood Ave Menlo Park, CA 94025 fax: 415-859-3735 From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!PO.CWRU.EDU!rso2 From: rso2@PO.CWRU.EDU (Raymond S. Ochs) Newsgroups: bionet.molbio.bio-matrix Subject: Signon Message-ID: <9106031925.AA22099@cwns4.INS.CWRU.Edu> Date: 3 Jun 91 19:25:41 GMT Sender: daemon@genbank.bio.net Reply-To: rso2@po.cwru.edu Distribution: bionet Lines: 4 Please enter my subscription on line. My Address is rso2@po.cwru.edu Thanks From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!lhc!ncifcrf!fcs260c2!toms From: toms@fcs260c2.ncifcrf.gov (Tom Schneider) Newsgroups: bionet.molbio.bio-matrix Subject: Re: Roadmaps for the desert... the debeat goes on. Message-ID: <2241@fcs280s.ncifcrf.gov> Date: 19 Jun 91 20:42:47 GMT References: <9106180635.AA22188@finsun.csc.fi> Sender: news@ncifcrf.gov Distribution: bionet Organization: NCI Supercomputer Facility, Frederick, MD Lines: 31 In article <9106180635.AA22188@finsun.csc.fi> harper@FINSUN.CSC.FI (Robert Harper) writes: > All I know is that there are over 15,000 programs available publicly >in source code form in this great computer/software country of ours, and >I'm the only one that knows where. > >Gregory Aharonian >Source Translation & Optimization Seems to me that the recent NSF request for proposals on Research on Scientific Databases would perhaps be a haven for your work. Unfortunately the deadline was May 15,1991, but perhaps there will be another opportunity or they have extended the deadline. Here is the place to ask: Dr. Maria Zemankova Program Director, Database and Expert Systems IRIS -- Room 310 National Science Foundation 1800 G Street, N.W. Washington, D.C. 20550 Telephone: 202-357-9570 Fax: 202-357-0320 Email: mzemanko@note.nsf.gov Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!NOTE.NSF.GOV!rrobbins From: rrobbins@NOTE.NSF.GOV ("Robert J. Robbins") Newsgroups: bionet.molbio.bio-matrix Subject: FOR YOUR INFORMATION Message-ID: <9008240834.aa02576@Note.NSF.GOV> Date: 24 Aug 90 12:34:32 GMT Sender: daemon@genbank.BIO.NET Lines: 125 ------- Forwarded Message Date: Fri, 24 Aug 90 8:22:06 EDT Subject: Help for InfoServer Reply-To: info@note.nsf.gov From: NSF Info Server To: Robert J. Robbins Message-ID: <9008240822.ab01907@Note.NSF.GOV> "HELP" FOR "INFO" IN THE NSF INFO SERVER The NSF Info Server is a program that delivers information by electronic mail. If you are on the Internet, or can send mail to Internet sites, you access the Info Server by sending mail to: info@note.nsf.gov If you are on BITNET, you may address your requests to: INFO@NSF You do not need a subject field. The text of your message must be in a special format, such as: REQUEST: INFO TOPIC: HELP REQUEST: END This request asks for the document "HELP" from the "request" collection "INFO". Your message must have a "REQUEST" line, to specify the request collection, and one or more "TOPIC:" lines to specify documents from the collection. The optional statement "REQUEST: END" terminates your specification. Any subsequent text in the message is ignored by the Info Server. The document you are now reading can be requested by: REQUEST: INFO TOPIC: HELP It is also sent automatically if there are no "request:" lines in your message. At the end of this file you will find a list of the REQUEST collections currently available. For each REQUEST collection, topic "INDEX" contains a list of the available documents. You may specify a limit, in lines or bytes, to the maximum size of document that you wish to have sent in a single message. For example: LINE-LIMIT: 1000 or BYTE-LIMIT: 75K The Info Server will break the documents at exactly the specified number of lines, or at the line preceeding the specified number of bytes. The minimum limit is 2000 lines or 12000 bytes. You may use the form "75000" or "75K" in either limit, but NOT "75,000". The limit affects only lines up to the next REQUEST: line. You may combine different requests in the same message, and use any combination of upper- and lower-case letters in your text. You may also include or omit spaces and tabs, use any number of REQUEST and TOPIC lines, and omit "REQUEST: END". For example: REQUEST : info byte-limit: 22000 topic: help (Byte-limit in effect) Request : forms TOPIC : review (Byte-limit not in effect) If you include "REQUEST: END", the INFO SERVER will ignore whatever follows in your message. If you include "REQUEST: ATTENTION", the INFO SERVER will ignore whatever follows and deliver your entire message to "postmaster@note.nsf.gov". You are encouraged to suggest additional documents you would like to have available from the NSF Info Server. Mail suggestions to "postmaster@note.nsf.gov" (Internet sites), or "POSTMAST@NSF" (BITNET sites). NOTE to BITNET users: The info-server mails documents to the address it finds in the "From:" field of requests. If your system does not prepare the "From:" field in a format that the NSF computer recognizes, you may not be able to use the info-server. The following are valid BITNET formats that we accept: From: user@host From: user@host.BITNET If your system generates other types of addresses (e.g. "user AT host", or addresses with BITNET DOMAINS that are not registered with the Internet nameservers), or can't send mail at all (just files), the chances are that the info-server will not be able to respond to your requests. If you have the ability to send to the info-server's Internet address (info@note.nsf.gov) that may work. ==================================================================== REQUEST collections currently available: REQUEST: INFO Information on using the Info-Server. REQUEST: FORMS Templates and forms. REQUEST: GRAD-FEL Graduate Fellowship Program files. REQUEST: INT-SCIENG Reports on Foreign Science and Technology. Notice to INT-SCIENG Requestors ------------------------------- Thank you for your interest in "int-scieng," the National Science Foundation's on-line service for reports on foreign science and technology. At this time, the service--which is administered by NSF's Division of International Programs--is unavailable to outside users. It is being revamped for use in an upgraded system being developed specifically to provide outside users with direct access to these reports. This new system, which will incorporate many enhancements that we hope will be valuable to our future users, will begin operation later this year. Its availability will be widely announced in the U.S. scientific and engineering community. Thank you for your patience. ------- End of Forwarded Message From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!NOTE.NSF.GOV!rrobbins From: rrobbins@NOTE.NSF.GOV ("Robert J. Robbins") Newsgroups: bionet.molbio.bio-matrix Subject: REQUEST FOR INFORMATION Message-ID: <9008240827.aa02151@Note.NSF.GOV> Date: 24 Aug 90 12:27:31 GMT Sender: daemon@genbank.BIO.NET Lines: 19 A Dean at Minnesota recently asked me if I knew of any universities that had developed a database to track the research activities and professional expertise of its faculty. I did not, but I am familiar with the managerial practices of only a few institutions. Do any of you know of institutions with such a system in place? Any information, including rumors of possibilities, will be greatly appreciated. ====================================================================== Robert J. Robbins Program Director, Database Activities Phone: (202) 357-9880 Biological, Behavioral, and Social Sciences FAX: (202) 357-7745 National Science Foundation 1880 G Street, Room 312 InterNet: rrobbins@note.nsf.gov Washington, DC 20550 BitNet: rrobbins@nsf From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!zaphod.mps.ohio-state.edu!ub!uhura.cc.rochester.edu!troi.cc.rochester.edu!elmo From: elmo@troi.cc.rochester.edu (Eric Cabot) Newsgroups: bionet.molbio.bio-matrix Subject: Re: In defense of the Genome Boondoggle Message-ID: <12145@ur-cc.UUCP> Date: 11 Feb 91 22:31:23 GMT References: <9102111942.AA08834@genbank.bio.net> Sender: news@uhura.cc.rochester.edu Organization: University of Rochester, Rochester NY Lines: 25 In article <9102111942.AA08834@genbank.bio.net> gunnell@FCRFV1.NCIFCRF.GOV ("Gunnell, Mark") writes: >In article <9102111731.AA00773@genbank.bio.net> >Ellington@frodo.mgh.harvard.edu (Deaddog) writes: > >> >> Make me a list of similar worth that has to do with the Genome Boondoggle. > >Catalogue all human genes! Discover the functions of mapped genes; see how >genes evolve; evaluate molecular evolution theories and how species originate; >find amazing biological phenomena never before observed by human eyes. Yes, >all these and more can ... etc.,etc. 8-) You *must* be either kidding us or yourself! But seriously, item 1 is hardly possible, item 2 is probably not possible, and the remaining items are not even close to possible from a mere sequence determination of the (a?) human genome. -- =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Eric Cabot | elmo@uhura.cc.rochester.edu "insert your face here" | elmo@uordbv.bitnet =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!mshri.utoronto.ca!clark From: clark@mshri.utoronto.ca Newsgroups: bionet.molbio.bio-matrix Subject: Abstract from Fairfax meeting Message-ID: <9008071558.AA24220@lash.utcs.utoronto.ca> Date: 7 Aug 90 15:58:15 GMT Sender: daemon@genbank.BIO.NET Lines: 38 Here is the abstract for the poster that I presented at the Fairfax BioMatrix meeting last month: A SIMPLIFIED INTERFACE FOR DATABASE SEARCHING WITH THE GCG PROGRAMS Stephen Clark Samuel Lunenfeld Research Institute Mount Sinai Hospital, 600 University Avenue Toronto, Ontario, Canada M5G 1X5 clark@mshri.utoronto.ca (Internet) clark@utoroci (Netnorth/Bitnet) The Genetics Computer Group (GCG) package, running in the VAX/VMS environment, contains a number of programs to aid the molecular biologist in sequence entry and analysis. The user interface is designed to provide maximum flexibility through extensive use of command line switches. Unfortunately, inexperienced computer users find this reliance on command line switches very difficult to learn. The problem is compounded because most people use the programs only occasionally and forget how they are run between sessions. Especially problematic are the programs for searching the databases. They should be run in batch mode because of the extensive CPU times involved (often several hours), but there is no capability built into the GCG programs to do this automatically. To help overcome some of these problems, I have written DCL command procedure shells for CPU-intensive programs. These shells use a menu-driven interface to query the user about the available options and construct a command file that is automatically submitted to the batch queue, thus enabling people who are unfamiliar with command line options, text editors and batch processes to carry out a database search on their own. All user responses are checked for errors as rigorously as possible. Shells are available for Fasta, Tfasta, Wordsearch/Segments, Find and Strings. Other shells (Famail and Dbmail) construct and send messages to the GenBank Fasta and sequence retrieval email servers via Internet. Finally, there is a shell to facilitate multiple Compare/Dotplot analyses with various levels of stringency and window- or word-size. These command procedures are freely available to anyone who would like to use them. From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!snorkelwacker.mit.edu!hsdndev!husc6!Frodo.MGH.Harvard.EDU!Ellington From: Ellington@Frodo.MGH.Harvard.EDU (Deaddog) Newsgroups: bionet.molbio.bio-matrix Subject: Re: Oh foolish supporters of genome sequencing Message-ID: <5695@husc6.harvard.edu> Date: 11 Feb 91 21:11:58 GMT References: <9102111908.AA07006@genbank.bio.net> Sender: news@husc6.harvard.edu Organization: Molecular Biology, Mass. General Hospital Lines: 85 In article <9102111908.AA07006@genbank.bio.net> gribskov@FCRFV1.NCIFCRF.GOV ("Gribskov, Michael") writes: > Perhaps a more tightly reasoned argument would be more convincing? From my point of view, Michael, this is rather like trying to argue against N-rays or phlogiston: you point out that there is no evidence to support their existence, and that's about the end of it. I am sure that I will see justification for the project at some point, but so far none has appeared. I am truly mystified: given the ability to clone genes by a variety of methods (probing with oligos based on protein sequences, complementation, hybridization with homologous sequences, panning, subtraction cloning, etc.) I do not see a need to sequence the human genome. I do not see what information will be gained that cannot be garnered by other, more directed means. In terms of genetic disease, for example, the search for a given gene would still seem to be a directed search. You contend that sequencing genes at random and systematically sequencing a genome are opposites: I contend that they are both undirected searches and,in the current research climate, such undirected searches should not be funded to the detriment of research which has a higher probability of producing new insights into biology/chemistry/medicine. While there are genome mapping/sequencing projects whose goals I understand ("we want to know the sequences of all the genes in X, because we have a fantastic genetic map of organism X, we already know what many of the genes do, and we don't have to worry about the 95% of the genome that is essentially junk;therefore, the sequence of X's genome is just a way to get at a glut of information that we can immediately interpret"), these arguments do not seem to apply to humans. Even in this form, though, it is not sequencing "the genome" that is important, but sequencing "all the genes that we know are important." It seems as though anthrocentricity is driving this project, rather than a true quest for scientific knowledge. Consider: I remember when the sequence of all of SV40 was first determined; I also remember when the chloroplast genome was completed. What new lines of research have been opened up by this information? New lines mind you, that wouldn't have been available had not the sequence of the whole genome been available. For example, I am grateful for the sequences of additional Group I introns from the chloroplast genome, but a more diverse range of sequences has become available from directed searches of many different genomes. And if you defer to thinking about the sequence of the human genome as a tool, then it is a very, very expensive tool. And again I would suggest that finding the mechanism of one gene which causes MS is worth much more than knowing the sequences of all the genes together (when you don't know what the genes do and still have to go back and find out). > I would certainly > like to know the names of the ofFfFensive person or persons who "would > suggest I should just bag my ideals and go off to happily catalogue > genes at random. And I am outraged that *alternative service* in > science may come to mean just that." David Kristofferson (apologies for mis-spelling, if such is the case) makes the point that academics should consider industry as an option. A worthy point and one which I take to heart. However, he goes on to suggest that researchers should consider not doing 'real science,' and that a wealth of (not-'real-science'?) opportunities will be related (just how, we are not sure) to the Genome Project. Thus, my obviously fanciful statement is based on: (1) The contention that scientists should somehow be fulfilled "not doing real science," which seems like a self-contradictory sentence, and (2) The notion that the Genome Project will somehow provide opportunities in industry for real or unreal science. Again, I find this hard to imagine. IMO (obviously H would be a bit out of place here) the Human Genome Project does not have a direction or purpose that would make it more useful than a telephone book in a forgotten language. Non-woof (Look Ma, no flames! Yet.) (Michael, for someone who characterized my arguments as "he doesn't like it," you should do better than "9 out of 10 top docs support the Genome Initiative;" rather like a National Enquirer special report.) From owner-bio-matrix@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!UHNIX2.UH.EDU!davison From: davison@UHNIX2.UH.EDU (Dan Davison) Newsgroups: bionet.molbio.bio-matrix Subject: (none) Message-ID: Date: 25 Apr 90 22:03:33 GMT Sender: daemon@genbank.BIO.NET Lines: 141 >From ostell@object.nlm.nih.gov Wed Apr 25 14:02:22 1990 Received: from post-office.uh.edu by uhnix2.uh.edu (5.59/1.1) id AA11543; Wed, 25 Apr 90 14:02:22 CDT Received: from p.lanl.gov by post-office.uh.edu; Wed, 25 Apr 90 14:01 CDT Received: from beta.lanl.gov by p.lanl.gov (5.61/1.14) id AA04790; Wed, 25 Apr 90 13:01:44 -0600 Received: by beta.lanl.gov (5.57/Ultrix2.4-C) id AA08281; Wed, 25 Apr 90 12:59:38 MDT Received: from lhc.nlm.nih.gov by p.lanl.gov (5.61/1.14) id AA04777; Wed, 25 Apr 90 13:01:10 -0600 Received: from bio.nlm.nih.gov by lhc.nlm.nih.gov (4.0/SMI-4.0) id AA02936; Wed, 25 Apr 90 14:55:44 EDT Received: from object.nlm.nih.gov by bio.nlm.nih.gov (4.0/SMI-4.0) id AA02404; Wed, 25 Apr 90 14:52:11 EDT Received: by object.nlm.nih.gov (4.0/SMI-4.0) id AA02785; Wed, 25 Apr 90 14:55:33 EDT Date: Wed, 25 Apr 90 14:55:33 EDT From: ostell@object.nlm.nih.gov Subject: NCBI Software/Dbase Developers Meeting To: bits@object.nlm.nih.go