From owner-acedb@net.bio.net Wed Aug 07 23:00:00 1996 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in3.uu.net!ott.istar!istar.net!van.istar!west.istar!n1van.istar!van-bc!news.mindlink.net!news.atl.bellsouth.net!newsrelay.iastate.edu!news.iastate.edu!macgrant.agron.iastate.edu!user From: dgrant@iastate.edu (David Grant) Newsgroups: bionet.software.acedb Subject: MacACE Date: Thu, 08 Aug 1996 09:31:06 -0500 Organization: Iowa State University Lines: 5 Message-ID: NNTP-Posting-Host: macgrant.agron.iastate.edu Can anyone shed some light on the status of MacACE? Will there be an update to match the current 4.3 release? If not, will the major bugs in the current 4.0/4.1 version be fixed? David Grant dgrant@iastate.edu From owner-acedb@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Petar_Stojadinovic@sequana.com (Petar Stojadinovic) Newsgroups: bionet.biophysics,bionet.genome.chromosomes,bionet.neuroscience,bionet.protista,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software.srs,bionet.software.staden,bionet.software.x-plor,bionet.structural-nmr,bionet.toxicology,bionet.users.addresses,bionet.women-in-bio,bionet.xtallography Subject: Clinical Lab Automation & Development, Computational Biology,Biotech Engineering Date: 8 Aug 1996 22:36:25 -0700 Organization: Sequana Therapeutics, Inc. Lines: 13 Sender: biohelp@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:2205 bionet.genome.chromosomes:1303 bionet.neuroscience:15213 bionet.protista:584 bionet.software:16272 bionet.software.acedb:956 bionet.software.gcg:1948 bionet.software.srs:286 bionet.software.staden:221 bionet.software.x-plor:680 bionet.structural-nmr:1434 bionet.toxicology:849 bionet.users.addresses:3079 bionet.women-in-bio:5326 bionet.xtallography:2789 Wanted: Abstracts, Interested members to Join Engineers in Biotechnology Subchapter of Assoc. of Laboratory Automation (ALA) or ICAR in Europe. please send email to : petar@sequana.com PS: Do you know how I may enter a new newsgroup in alt as alt.biotech.engineers? Thank you. Petar Stojadinovic Sequana Therapeutics Inc. Engineering Dept. Phone: 619-6468263 email: petar@sequana.com From owner-acedb@net.bio.net Thu Aug 08 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: acedb 4.3 updates Date: 9 Aug 1996 10:40:10 +0100 Lines: 4 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4uf11q$q85@mserv1.dl.ac.uk> Original-To: rla@galactose.mc.duke.edu in fact 4-...13 became too big and convoluted so WS1 REPLACES the other serie so you should save your personal modif if any by dumping them out as an eca file then rm $ACEDB/database/ACEDB.wrm and rerun and read the new serie of files From owner-acedb@net.bio.net Mon Aug 12 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!ncar!imci4!newsfeed.internetmci.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!sprout.nal.usda.gov!usenet From: Doug Bigwood Newsgroups: bionet.software.acedb,misc.test Subject: JOBs: Java/Perl Programmer/Analysts (2) wanted for genome project Date: Tue, 13 Aug 1996 10:32:02 -0400 Organization: Genome Informatics Group, University of Maryland Lines: 80 Message-ID: <321091E2.2499@gig.usda.gov> NNTP-Posting-Host: locus.gig.usda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b6 (X11; I; SunOS 5.5 sun4m) Xref: biosci bionet.software.acedb:958 misc.test:126480 Two programmer/analyst positions are available immediately for the Agricultural Genome Information Service (AGIS) project. This project, an ongoing cooperative effort between the University of Maryland and the USDA, provides genome data to scientists and other users throughout the world. If hired, you will be working in a state-of-the-art environment developing the next generation of software for Internet access of our databases and other information. Most of the development will be in Java and Perl 5 (and perhaps C) on Sun/Solaris and DEC Alpha systems. Experience in these languages in a real-world situation is strongly preferred and Unix experience is essential. Also, experience with ACeDB or another object-oriented database package is a big plus. Knowledge of molecular biology/genetics or experience with scientific databases is desired as well. You must be able to work cooperatively with group members. Creativity is strongly encouraged. Excellent benefits. The formal announcement is below. ---------------------------------------------------------------- PROGRAMMER FOR AGRICULTURAL GENOME PROJECT TITLE: Computer Programmer/Analyst (2 positions) LOCATION: National Agricultural Library, Beltsville MD. CATEGORY: One year contract position with possible renewal. SALARY: $35,000 minimum. Actual salary commensurate with experience. (This position has a 40-hour work week.) RESPONSIBILITIES: Works under the supervision of the project manager at the University of Maryland at College Park (UMCP), to provide programming services in support of the Agricultural Genome Information Service, a cooperative effort between UMCP and the U.S. Dept. of Agriculture. This program is located at the National Agricultural Library (NAL). Works directly with the Manager of the Genome Informatics Group to develop software for the scientific community in USDA and cooperating institutions. This is a one-year, renewable contract position, under a cooperative agreement between the NAL and UMCP. QUALIFICATIONS: Required: Degree in information/computer science from an accredited institution, or its equivalent in experience. EXPERIENCE: Required: Excellent knowledge of the Unix operating system. Preferred: Extensive experience with Perl 5 (extensive experience in another object- oriented language will also be considered) and C; real-world experience with Java; knowledge of World Wide Web server operation and configuration, and CGI program scripting; background or college coursework in biology or chemistry; greater than 3 years working experience, but recent college graduate will be considered. BENEFITS: 22 working days annual leave; 11 paid holidays; 15 days sick leave; other benefits may be negotiable. POSITION AVAILABLE: Immediately. APPLICATIONS: For full consideration submit resume and names/addresses of 3 references to Dr. Paul Bottino, H.J. Patterson Hall, Dept. of Plant Biology, University of Maryland, College Park, MD 20742-7011. Applications will be accepted until September 11, 1996 or until the positions are filled. THE UNIVERSITY OF MARYLAND IS AN EQUAL OPPORTUNITY EMPLOYER. From owner-acedb@net.bio.net Wed Aug 21 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.ecn.bgu.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in3.uu.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!bhamcs!news.ox.ac.uk!is.bbsrc.ac.uk!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: acedb data updates for C.elegans Date: 22 Aug 1996 12:28:57 +0100 Lines: 113 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4vhg9p$uj@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. ACEDB data updates WG1.4-5 and WS1.4-13 to 4-16 for C. elegans ============================================================== You should be using these in conjunction with release 4_3 of the acedb software. Reminder: there are now two versions of the C.elegans database. The WS1 update series contains everything, whereas WG1 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. The additions since WG1.4-4 and WS1.4-12 are: for both types of update - a physical map update with a few changes (Aug 9th) - some cgc references have been added (2411 onwards) also more connections between references and Loci - CGC strains (July 18th) - worm meeting 1996 citations, abstracts and cross-references (ecwm for east coast, euwm for europe, mwwm for mid-west wcwm for west coast abstracts respectively) - some more Tc1 insertion site positions on sequenced cosmids and for just the complete database including sequences (WS1.4-16) Data fom St Louis and Sanger Sequence databases taken in mid-August: - There are now 1586 (1464 before) cosmids totalling 47,908,858 (44,150,616 before) bases. - We are switching from using the PIR protein database for homology searches to the TREMBL database, hence many PIR homologies are being deleted and TR ones added. - new worm sequences from EMBL release 47 (June 1996) The total database sizes after adding these updates are around 390Mb for the WS1 database (we said it would grow!) and around 65Mb for the WG1 database. It will take a long time to read in the WS1 updates, particularly 4-15. All four updates took us several hours. APOLOGIES ========= - a set of transgenic strains from David Baillie was added to the last set of updates but the http URL address has not become visible. We are trying to put this right. Meanwhile his address for those interested is http//:darwin.mbb.sfu.ca/imbb/dbaillie/cosmid.html . Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb ftp.sanger.ac.uk (193.60.84.11) in England, in pub/acedb lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password: your user id or email address cd repository/acedb # change to relevant directoy binary # IMPORTANT dir # display files in this directory get README get NOTES get INSTALL cd ace4 # change to ace4 directory get bin.sunos.4_3.tar.Z # get program cd ../celegans # change to worm data directory mget update.WS1.* # get all WS1 update files quit -------------------------------- Get any update files that you do not have already and read the file NOTES before proceeding further. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb"), click "Yes" to accept initialising the database if starting from scratch, then choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button. If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Comments about the data should be sent to the data curator, Sylvia Martinelli (sylvia@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- From owner-acedb@net.bio.net Wed Aug 28 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Macace versions of latest C.elegans acedb Date: 30 Aug 1996 00:36:21 +0100 Lines: 25 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5059hl$j78@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk Macintosh versions of the most recent C.elegans acedb release are now available as self-extracting archives from the following two locations: ftp://ftp.sanger.ac.uk/pub/acedb/macace ftp://ncbi.nih.gov/repository/acedb/macace These directories contain macace.WS1.4-16.sea.bin (the version with sequences) and macace.WG1.4-5.sea.bin (the version without). The WS1 version is now 136Mb compressed and 440Mb uncompressed, much bigger than before. The main reasons are that there is much more sequence annotation now, and it actually contains the sequence. The DNA sequence itself was ommitted accidentally from the 4-8 macace version! This explains the dashes seen when trying to look at sequence in macace.WS1.4-8. Many apologies. Please read the README files in the macace directories for further information on macace. Further information about the latest data release was in the release email message for the Unix version, available from the file acedb/celegans/letter.aug96 in the ftp directories. Richard Durbin From owner-acedb@net.bio.net Sat Aug 31 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Sep 1996 02:00:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609010900.CAA01378@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net