From owner-acedb@net.bio.net Wed Dec 01 10:15:24 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.maxwell.syr.edu!logbridge.uoregon.edu!uwm.edu!biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Dec 1999 02:00:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199912011000.CAA11760@net.bio.net> NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software.acedb:363 (LAST REVISION: 14-AUG-99) 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. -------------------------------------------------------- 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 -------------------------------------------------------------------- the UK-HGMP-Resource Centre (known as hgmp.mrc.ac.uk): ----------------------------------------------------- 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@hgmp.mrc.ac.uk. 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 majordomo@hgmp.mrc.ac.uk. 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 Please ask for help at biosci@hgmp.mrc.ac.uk 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. 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. 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You may rcmove your name from our opt-in list by sending an e-mail to the address below with the word rcmove in the subj. ; From owner-acedb@net.bio.net Sat Dec 04 23:06:17 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!logbridge.uoregon.edu!newsfeed.stanford.edu!remarQ70!rQdQ!supernews.com!remarQ.com!remarQ69!WReNclone!WReNphoon3.POSTED!WReN!not-for-mail From: tacettin Subject: Submission Software Newsgroups: bionet.software.acedb Message-ID: <004aa0e3.bde18677@usw-ex0102-009.remarq.com> Lines: 19 Bytes: 741 X-Originating-Host: 152.163.207.191 Organization: http://www.remarq.com: The World's Usenet/Discussions Start Here X-Wren-Trace: eMLnz87XkNqRg9rew4vQ68PZ09XX1ZLdw8vfj8jZ1sKckdCNndSEgpyTkYmd24A= Date: Sat, 04 Dec 1999 14:58:44 -0800 NNTP-Posting-Host: 10.0.2.9 X-Complaints-To: wrenabuse@remarq.com X-Trace: WReNphoon3 944348525 10.0.2.9 (Sat, 04 Dec 1999 15:02:05 PST) NNTP-Posting-Date: Sat, 04 Dec 1999 15:02:05 PST Xref: hgmp.mrc.ac.uk bionet.software.acedb:367 Hi, If you are looking to find out how to submit your site to search engines? 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From owner-acedb@net.bio.net Mon Dec 06 07:45:12 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!biosci!rlamqpls.radioweb.de!cbsjhgfsjk From: cbsjhgfsjk@rlamqpls.radioweb.de Newsgroups: bionet.software.acedb Subject: Lose Weight For The Holidays and Eat What you want -dyopti Date: 5 Dec 1999 23:35:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software.acedb:369 YES! You can lose weight with FAT ABSORB! Over 1 Million bottles sold last year alone. You've probably seen this product on T.V. Fat absorb is a new concept in losing weight for both men and women. This new product actually traps the fats from foods you eat every day. 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To order call 24 hours a day 800-711-0145 From owner-acedb@net.bio.net Tue Dec 07 01:07:58 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!logbridge.uoregon.edu!uwm.edu!biosci!EARTHLINK.NET!kannh From: kannh@EARTHLINK.NET Newsgroups: bionet.software.acedb Subject: Happy Holidays Date: 6 Dec 1999 17:15:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 61 Sender: daemon@net.bio.net Distribution: world Message-ID: <199912070105.RAA20258@eagle.prod.itd.earthlink.net> Reply-To: kannh@earthlink.net NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software.acedb:372 Transfer or Register a .COM for yourself or your company. 19.95 a month. Call Now 407-622-1336 No banners or popup ads. This is your 50 megs of space. We get you online fast and easy with live help via our "1-800" toll free support line. We pride ourselves on customer service. We will walk you through every step. Everything (see below) is included. 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From owner-acedb@net.bio.net Tue Dec 07 12:15:09 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.maxwell.syr.edu!logbridge.uoregon.edu!uwm.edu!biosci!CS.HUJI.AC.IL!cheny From: cheny@CS.HUJI.AC.IL (Chen Yanover) Newsgroups: bionet.software.acedb Subject: Non coding regions. Date: 7 Dec 1999 04:13:49 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software.acedb:374 Hi, Is there any straightforward way to extract the non-coding regions out of the entire genome ? Thanks again, Chen. From owner-acedb@net.bio.net Tue Dec 07 12:15:09 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.maxwell.syr.edu!logbridge.uoregon.edu!uwm.edu!biosci!CS.HUJI.AC.IL!cheny From: cheny@CS.HUJI.AC.IL (Chen Yanover) Newsgroups: bionet.software.acedb Subject: ACeDb 4_8b compiler errors Date: 7 Dec 1999 04:00:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: hgmp.mrc.ac.uk bionet.software.acedb:373 Hi all, I am trying to compile ACeDB, version 4_8b sources (downloaded from ftp://ftp.sanger.ac.uk/pub/acedb/ace.development/src.4_8b.tgz) on a linux machine and receive a lot of errors (specifically, when compiling graphcon_srk.c) - for example: graphcon_srk.c: In function `graphLoop': graphcon_srk.c:264: structure has no member named `hasLoop' graphcon_srk.c:266: structure has no member named `graphDevLoop' graphcon_srk.c:267: structure has no member named `graphDevLoop' etc. Does anybody know what I am missing ? Or - where can I find linux 4_8b executables ? Thanks in advance, Chen. From owner-acedb@net.bio.net Tue Dec 07 16:57:32 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!news.nott.ac.uk!news.nottingham.ac.uk!cress!keith From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Problem with upgrading AcePerl Date: Tue, 7 Dec 1999 16:52:21 +0000 Organization: ACS, The University of Nottingham Lines: 80 Message-ID: NNTP-Posting-Host: cress.life.nottingham.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 944585466 16486 128.243.116.120 (7 Dec 1999 16:51:06 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 7 Dec 1999 16:51:06 GMT X-Sender: keith@cress Xref: hgmp.mrc.ac.uk bionet.software.acedb:375 Hello, I've just started experiencing difficulties with our AceBrowser interface to our Arabidopsis database (AGR). The only thing I can imagine that this is related to is the upgraded version of AcePerl that I installed last week. I am new to Ace-related things and have been working through various help files all day to no avail. Can anyone help please? A brief outline of problem... When you use AceBrowser to try and retrieve a sequence object from AGR, the following message appears in the main part of the AceBrowswer display: " Software error: Can't locate auto/Ace/Object/cDNA.al in @INC (@INC contains: /usr/local/lib/perl5/sun4-solaris/5.00404 /usr/local/lib/perl5 /usr/local/lib/perl5/site_perl/sun4-solaris /usr/local/lib/perl5/site_perl . /crick/web/ /crick/web/lib/perl) at /crick/web/apache_perl/ace/AGR-sequence line 109 " This problem only occurs with AGR, other databases that we host (e.g. BrassicaDB) do not have this problem. I suspect that this is due to the fact that AGR is the only database we host which has it's display configured differently in SiteDefs.pm, e.g. %DATABASES = ( 'AGR' => { host => '128.243.116.29', ...snipped... url_mapper => \&agr_mapper, displays => \%agr_displays, }, ...snipped... %agr_displays = ( Sequence => [ { 'url' => 'AGR-sequence', 'label' => 'Sequence Report', 'icon' => '/icons/layout.gif' }, ], ); Other databases that we mirror just have 'undef' in their displays field. We had AcePerl 1.51 and I upgraded last week to 1.57. Nothing unusual happened during installation, and it was only today I noticed the problem with retrieving sequences. We currently have AceBrowser 2.02, Apache 1.33, and Perl 5.004_04 all running on Solaris 2.6. I've noticed that a lot of perl scripts that contain 'use Ace' often have a version number as well, e.g. 'use Ace 1.41' - should these always point to the latest version number? The file which the error message relates to (auto/Ace/Object/cDNA.al) does not seem to exist anywhere on our system, and I've still not been able to find any script that mentions this file. Any ideas??? To see this error in action, have a look at: http://synteny.nott.ac.uk/perl/ace/AGR-sequence/AGR?name=EMBL%3AA47152 Hope someone can help, Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@net.bio.net Thu Dec 09 15:05:17 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!news.nikoma.de!news0.de.colt.net!colt.net!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.bbsrc.ac.uk!not-for-mail From: Hamish McWilliam Newsgroups: bionet.software.acedb Subject: TableMaker query Date: Thu, 09 Dec 1999 14:50:17 +0000 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 30 Message-ID: <384FC1A9.14112FC0@bbsrc.ac.uk> NNTP-Posting-Host: pc7120.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en Xref: hgmp.mrc.ac.uk bionet.software.acedb:379 I'm trying to build a table of sequence blast results, with query map positions, and I have run into the following issues: Can TableMaker sort on more than one column of a table? I want to be able to sort by map name and map position with a map (I know I could do this with AQL, but I want to be able to store the definition in the database). Is any way of controling the level of recursion it performs? I really only want the first blast hit (satisfiing a set of criterea) instead of all of them. Any ideas? Hamish. -- ===================================================================== Hamish McWilliam Brassica and Oilseeds Research John Innes Center Norwich Research Park Colney Lane Norwich NR4 7UH Tel: +44(0)1603-452571 WWW: http://jiio10.jic.bbsrc.ac.uk/ --------------------------------------------------------------------- God invented Brownian motion to stir his coffee. ===================================================================== From owner-acedb@net.bio.net Thu Dec 09 16:40:02 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!do.de.uu.net!news-koe1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: Mark Wilkinson Newsgroups: bionet.software.acedb Subject: Sequences seem to be arbitrarily displayed or not found... Date: Thu, 09 Dec 1999 17:41:06 +0100 Organization: GWDG, Goettingen Lines: 31 Message-ID: <384FDBA2.8CB6180A@cheerful.com> NNTP-Posting-Host: pczs01.mpiz-koeln.mpg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: gwdu67.gwdg.de 944757590 43952 193.174.239.101 (9 Dec 1999 16:39:50 GMT) X-Complaints-To: news@gwdg.de NNTP-Posting-Date: 9 Dec 1999 16:39:50 GMT X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en Xref: hgmp.mrc.ac.uk bionet.software.acedb:380 Hello all! I have been pounding away at this problem all day and finally decided to send it off to the group because I ran out of ideas: first let me give you the address of my site so that you can see the problem for yourself: http://www.antirrhinum.net/ace/simple/DragonDB okay, now do a search for Sequence objects with the prefix ZS* - there is quite a list of them! Now select ZS3H7 (for example) - no problem right? Now select ZS1, or ZS101... a never ending loop of 'Document contains no data'. But if you do a search for the DNA objects you will find that they *DO* exist! Moreover, using XAce directly reveals no problem at all - the sequences come up as called. Moreover, they all came from the same .ace read, of a single .ace file generated in one run from the same parsing program! I can't see the difference between the sequences which do 'exist' and those which don't... is it a GifAceServer problem? An AcePerl problem? Or a Mark_Is_Dumb problem??? Any help appreciated as my bench has a forehead-shaped dent in it by now... cheers all! Mark From owner-acedb@net.bio.net Mon Dec 13 05:25:05 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!daresbury!uninett.no!news.algonet.se!algonet!newsfeed.tli.de!newsfeed.gamma.ru!Gamma.RU!news.rt.ru!MTU.ru!mtu.ru!not-for-mail From: "Alexey Nazarov" Newsgroups: be.forsale.comp.software,bionet.software,bionet.software.acedb Subject: Create your professional slide shows with Photoslider 2.0 Date: Mon, 13 Dec 1999 08:09:09 +0300 Organization: MTU-Intel ISP Lines: 36 Message-ID: <831vgp$11mc$6@gavrilo.mtu.ru> NNTP-Posting-Host: dial53218.mtu-net.ru X-Trace: gavrilo.mtu.ru 945062233 34508 195.34.53.218 (13 Dec 1999 05:17:13 GMT) X-Complaints-To: usenet-abuse@mtu.ru NNTP-Posting-Date: 13 Dec 1999 05:17:13 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Xref: hgmp.mrc.ac.uk bionet.software:957 bionet.software.acedb:384 **************************************************************************** New release of popular program!!! Photoslider 2.0!!!! **************************************************************************** PhotoSlider harnesses the power of DirectX to let you easily create slide shows with impressive transition effects. Just point to the directory that holds your images and click the Show button. The program will automatically display the images one after another, with more than 140 transition effects at your disposal. Options let you accompany the show with music from a CD, .wav, or .mid file; specify the duration between images; change effects using different methods; and run the show full-screen in your choice of several screen modes. Command-line parameters and support for animated .gif files are included. There are 3 editions of Photoslider 2.0: Photoslider 2.0 Pro - for professional using. May be used as a viewer or autorun on CD. Photoslider 2.0 Lite - "lite" edition of the program. For your home slide shows creation. Photoslider 2.0 screen saver - provides you to create your oun screen savers. It's looks like a series of sliding photos with your company logo, products images e.t.c To find out more, please visit our website at www.photoslider.8m.com _____________________________________________________ Alexey Nazarov CD makeR studio From owner-acedb@net.bio.net Mon Dec 13 20:00:26 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!news-peer.gip.net!news.gsl.net!gip.net!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: schwartz@uclink4.berkeley.edu Newsgroups: bionet.software.acedb Subject: parser for BLAST2? Date: Mon, 13 Dec 1999 19:53:13 GMT Organization: Deja.com - Before you buy. Lines: 13 Message-ID: <833iqu$lus$1@nnrp1.deja.com> NNTP-Posting-Host: 131.243.57.13 X-Article-Creation-Date: Mon Dec 13 19:53:13 1999 GMT X-Http-User-Agent: Mozilla/4.5 [en] (X11; I; SunOS 5.7 sun4u) X-Http-Proxy: 1.0 x31.deja.com:80 (Squid/1.1.22) for client 131.243.57.13 X-MyDeja-Info: XMYDJUIDtheo5 Xref: hgmp.mrc.ac.uk bionet.software.acedb:385 Hi All, I was wondering if there is a parser for Blast2, gapped blast? I have been using ungapped blast and MSPCrunch to parse it into ACeDB format and was just wondering if there is a newer version? (I can't seem to find Eric Sonhammer's current ftp site.) Thank you. Jody Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@net.bio.net Tue Dec 14 10:12:03 1999 Path: hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!not-for-mail From: Tim Cutts Newsgroups: bionet.software.acedb Subject: Re: parser for BLAST2? Date: 14 Dec 1999 10:07:06 +0000 (GMT) Organization: Linux Unlimited Lines: 16 Message-ID: References: <833iqu$lus$1@nnrp1.deja.com> NNTP-Posting-Host: rrw1000.sel.cam.ac.uk X-Newsreader: trn 4.0-test70 (17 January 1999) Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) Xref: hgmp.mrc.ac.uk bionet.software.acedb:386 In article <833iqu$lus$1@nnrp1.deja.com>, wrote: >Hi All, > >I was wondering if there is a parser for Blast2, gapped blast? > I have been using ungapped blast and MSPCrunch to parse it into >ACeDB format and was just wondering if there is a newer version? >(I can't seem to find Eric Sonhammer's current ftp site.) The latyest version of MSPcrunch certainly supports BLAST 2. I was trying it out yesterday! You can download it from: ftp://ftp.cgr.ki.se/pub/prog/MSPcrunch+Blixem Tim. From owner-acedb@net.bio.net Tue Dec 14 10:34:27 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!server2.netnews.ja.net!news.nott.ac.uk!news.nottingham.ac.uk!thale!jamie From: Jamie Kincaid Newsgroups: bionet.software.acedb Subject: write access Date: Tue, 14 Dec 1999 10:18:52 +0000 Organization: ACS, The University of Nottingham Lines: 25 Message-ID: NNTP-Posting-Host: thale.life.nottingham.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 945167247 5487 128.243.116.150 (14 Dec 1999 10:27:27 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 14 Dec 1999 10:27:27 GMT X-Sender: jamie@thale Xref: hgmp.mrc.ac.uk bionet.software.acedb:387 Hi all, The ACEDB documentation says that to specify other users with write access you put their name in the passwds.wrm file. Yet when I try this and the user runs xace I get the message 'unable to set readlock for session xxxx' and I have no option for getting write access, (the edit button is missing) What have I overlooked? Jamie _______________________________________________________________________________ Jamie Kincaid Nottingham Arabidopsis Stock Centre (NASC) School of Biological Sciences University of Nottingham, Nottingham, NG7 2RD Phone: 0115 951 3091 Fax: 0115 951 3297 NASC website: nasc.nott.ac.uk From owner-acedb@net.bio.net Tue Dec 14 13:11:31 1999 Path: hgmp.mrc.ac.uk!biosci From: edgrif@sanger.ac.uk (Ed Griffiths) Newsgroups: bionet.software.acedb Subject: Re: write access Date: 14 Dec 1999 13:11:30 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 51 Message-ID: References: NNTP-Posting-Host: mercury.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 945177091 8497 193.62.192.80 (14 Dec 1999 13:11:31 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 14 Dec 1999 13:11:31 GMT X-Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA16566 for ; Tue, 14 Dec 1999 13:11:27 GMT X-Received: from griffin.sanger.ac.uk (edgrif@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id NAA08367; Tue, 14 Dec 1999 13:11:26 GMT X-Received: from localhost (edgrif@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id NAA05983; Tue, 14 Dec 1999 13:11:25 GMT X-Authentication-Warning: griffin.sanger.ac.uk: edgrif owned process doing -bs X-To: Jamie Kincaid X-cc: acedb@hgmp.mrc.ac.uk X-In-Reply-To: Xref: hgmp.mrc.ac.uk bionet.software.acedb:389 Jamie, oopppss...sorry, just realised on rereading your mail that you were talking about xace, not the aceclient/server....sorry. The same comments almost apply however..... You need to set up the database directory following the instructions in the file wdoc/WRITE_ACCESS, note well the stuff about permissions for directories/files. If you have problems, send me a note. cheers Ed > > Hi all, > > The ACEDB documentation says that to specify other users with write access > you put their name in the passwds.wrm file. Yet when I try this and the > user runs xace I get the message > 'unable to set readlock for session xxxx' > and I have no option for getting write access, (the edit button is > missing) > > What have I overlooked? > > Jamie > _______________________________________________________________________________ > > Jamie Kincaid > Nottingham Arabidopsis Stock Centre (NASC) > School of Biological Sciences > University of Nottingham, Nottingham, NG7 2RD > > Phone: 0115 951 3091 > Fax: 0115 951 3297 > > NASC website: nasc.nott.ac.uk > ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ --- From owner-acedb@net.bio.net Wed Dec 15 20:00:22 1999 Path: hgmp.mrc.ac.uk!server1.netnews.ja.net!fu-berlin.de!feeder.qis.net!hermes.visi.com!news-out.visi.com!newsfeed.enteract.com!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail From: schwartz@uclink4.berkeley.edu Newsgroups: bionet.software.acedb Subject: efetch in acedb Date: Wed, 15 Dec 1999 19:50:28 GMT Organization: Deja.com - Before you buy. Lines: 21 Message-ID: <838re2$gbv$1@nnrp1.deja.com> NNTP-Posting-Host: 131.243.57.13 X-Article-Creation-Date: Wed Dec 15 19:50:28 1999 GMT X-Http-User-Agent: Mozilla/4.5 [en] (X11; I; SunOS 5.7 sun4u) X-Http-Proxy: 1.0 x43.deja.com:80 (Squid/1.1.22) for client 131.243.57.13 X-MyDeja-Info: XMYDJUIDtheo5 Xref: hgmp.mrc.ac.uk bionet.software.acedb:392 To all who have been answering my questions, I can't thank you enough. Another question. I am trying to use efetch for multiple databases within ACeDB. I am using several from Genbank, nr and an est database and Unigene. I formatted the indices with 'fastaentrynamelong.script db' and 'mkdiv -f db', and then moved the indices to the respective genbank database directory. I set the EFETCH_PREFIX to each of the directories. Efetch nr:giXXX works. But ACeDB doesn't have a clue about where to find the databases. It only looks for entrynam.idx (the index file) in $ACEDB/database. Which means I am limited to only one database. How do I get ACeDB to look at the envt. variable to find the others? Do I need to prefix each homology in ACeDB with the database prefix? It seems like I would have to do that, but I didn't see that said anywhere. Thanks again. Jody Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Fri Dec 17 05:18:11 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6E7A217A97; Fri, 17 Dec 1999 05:18:11 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id FAA24137 for ; Fri, 17 Dec 1999 05:18:09 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA23942 for acedb-list@hgmp.mrc.ac.uk; Fri, 17 Dec 1999 05:18:08 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f Message-ID: <3859C6C8.AF00D001@pacbell.net> From: vonda X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 X-Newsgroups: bionet.software.acedb Subject: Project Manager Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Lines: 81 Date: Thu, 16 Dec 1999 21:14:48 -0800 X-Complaints-To: abuse@pacbell.net X-Trace: nnrp1-w.sbc.net 945407803 209.233.18.78 (Thu, 16 Dec 1999 21:16:43 PST) Organization: SBC Internet Services To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk BRIAN BROOKS Email: mort@mediaone.net OBJECTIVE: PROJECT MANAGER NETWORKS: NT 4.0 server, Novell 3.x, TCP/IP, Dial up Networking, Microsoft Lan Manager CLIENT SOFTWARE: NT 4.0 Workstation, Windows 3.1-98, Macintosh 7.x-8.1, Most Microsoft products, Visual Basic, Quark Xpress, PhotoShop 4-5, Illustrator 7-8, MediaBank, Intercept OPI, On-net 32, Soft PC, Xywrite, PageMaker, Adobe Acrobat, FlightCheck, Hijaak Pro, Debabelizer, Copyflow, NAPS H&J, Beyond press, type managers (ATM), Lotus Notes, Lotus Word Pro, MS TechNet, cc:Mail, cc:Mail/Remote, MS Mail, MS FrontPage, WinFax Pro 7.0, MS Outlook, MS Office 2000. HARDWARE: Setup installation and maintenance of standard PCs, Macs and Laptops, 10 baseT, 10 base2, Ethernet, cable installations, network hubs, network cards, PNP devices, modems, networked printers, scanners, Compaq servers. PROFESSIONAL EXPERIENCE PROJECT MANAGER Cahners Publishing Company December 96 to present ? Provide internal consulting and analysis for editorial departments and third level support. ? Managed and developed Y2k testing of Novell 3.20 based editorial workflow. ? Administered Y2k re-mediation of proprietary VB applications. ? Migrated publications from Mac to NT/Win95 platforms. ? Converted ad-layout artists to Win95 platform. ? Implementation of MediaBank/Intercept OPI digital asset management utility. Developed pre-flight workflow for Manufacturing Market Place®. ? Managed the upgrade for Quark users of 48 publications. ? Developed NT/win95 based scanning workstation configurations. ? Standardized editorial Mac's and PC's workstations. ? Configured and setup server for editorial test lab. ? Migrated Font Folio from 6 to 8. ? Training of cross-platform applications (Quark Xpress, PhotoShop, Illustrator, FlightCheck, MS Outlook, Adobe Type Manager Deluxe). ? Standardized editorial printers and drivers. ? Developed Postscript pre-press workflow. STRATEGIC SUPPORT MANAGER - Stream International February 93 to March 97 ? Managed a staff of 41 including three supervisors for 7x24 technical support center. ? Approved schedules for the 41 support representatives for the off-hours team. ? Evaluated call volume/service level reports. ? Wrote performance reviews and feed--back forms. ? Identified, proposed and implemented policies and procedures. TechNet, cc:Mail, cc:Mail/Remote and MS Mail. Helped maintain operations of the 138-person DTS (Desktop Operating Systems) team and promoted an "all hands on deck" attitude among the team. Developed incentive programs. The total call center stationed over 600 phone representatives. EDUCATION/CERTIFICATION/ASSOCIATIONS Phoenix Institute of Technology – ? AutoCad - Engineering and Architectural drafting (1990) ? Intro to project management ? Administrating NT Server #803 ? BU Workflow design ? Advanced Mac ? Intro to VBA for Access ? Intro to VB6.0 ? Train the trainer for MediaBank (from Bitstream and Inso) From owner-acedb@hgmp.mrc.ac.uk Fri Dec 17 10:02:06 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D25C217A81; Fri, 17 Dec 1999 10:02:05 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA16698 for ; Fri, 17 Dec 1999 10:02:03 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA27324 for acedb-list@hgmp.mrc.ac.uk; Fri, 17 Dec 1999 10:02:02 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Tim Cutts X-Newsgroups: bionet.software.acedb Subject: Re: efetch in acedb Date: 17 Dec 1999 09:57:15 +0000 (GMT) Organization: Linux Unlimited Lines: 8 Message-ID: References: <838re2$gbv$1@nnrp1.deja.com> X-Newsreader: trn 4.0-test70 (17 January 1999) Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk One thing you can do is replace efetch with a perl script that does the same thing. This can then retrieve data from a variety of sources by different methods. For example, our version of efetch gets sequence data from our in-house SRS server, in some cases, and from FASTA format files in others, and from BLAST 2 format in yet others. Tim. From owner-acedb@hgmp.mrc.ac.uk Fri Dec 17 14:55:57 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1AC3617AB0; Fri, 17 Dec 1999 14:55:55 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA12697 for ; Fri, 17 Dec 1999 14:55:53 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA01150 for acedb-list@hgmp.mrc.ac.uk; Fri, 17 Dec 1999 14:55:52 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: albert4@indiatimes.com X-Newsgroups: bionet.software.acedb Subject: 3 Days - 2 Nights - Tickets for Two - FREE! Date: 17 Dec 1999 14:55:52 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 23 Message-ID: <199912171455.OAA12680@hgmp.mrc.ac.uk> X-Trace: niobium.hgmp.mrc.ac.uk 945442552 1148 193.62.192.80 (17 Dec 1999 14:55:52 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk X-Received: from mailserver.dstm.nl ([195.108.22.185]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA12680 for ; Fri, 17 Dec 1999 14:55:47 GMT X-Received: from 98CF6CFF.ipt.aol.com by mailserver.dstm.nl with SMTP (Microsoft Exchange Internet Mail Service Version 5.0.1460.8) id YDN02F79; Fri, 17 Dec 1999 15:44:41 +0100 X-To: freetravel@travelingfree.com To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk WEALTH IN THE NEW MILLENNIUM The Internet and new technology are creating more 7 Figure ($1,000,000) incomes than any time in history. If you feel you are not being paid what your worth, please visit our web site. The information is FREE. HUGE COMPENSATION AVAILABLE! 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Merry xmas & Happy Newyear --- From owner-acedb@hgmp.mrc.ac.uk Mon Dec 20 06:26:23 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3872417A94; Mon, 20 Dec 1999 06:26:23 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id GAA03942; Mon, 20 Dec 1999 06:26:12 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id GAA14608; Mon, 20 Dec 1999 06:26:11 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "oad" X-Newsgroups: bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software.srs,bionet.software.staden,bionet.software.x-plor,bnr.software-eng,chile.mercado.software,chinese.comp.software,comp.mail.list-admin.software,comp.os.ms-windows.nt.softwar Subject: Wordperfect invalid filename Date: Mon, 20 Dec 1999 14:16:48 +0800 Organization: IMS Netvigator Lines: 8 Message-ID: <83ki20$qem2@imsp212.netvigator.com> X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 To: acedb@hgmp.mrc.ac.uk, bio-software@hgmp.mrc.ac.uk, bio-srs@hgmp.mrc.ac.uk, info-gcg@hgmp.mrc.ac.uk, staden@hgmp.mrc.ac.uk, x-plor@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Why WordPerfect6.1 for windows will have a invalid filename of format @xxxx in the beginning characters? The software installed at LAN server running Netware. Workstations used OS2 Wrap 4. Users created documents and save at server will have the invalid filename problem if retrieved again. No problem if saved in local hard disk. From owner-acedb@hgmp.mrc.ac.uk Mon Dec 20 15:40:35 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 606D917AD9; Mon, 20 Dec 1999 15:40:33 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA11777 for ; Mon, 20 Dec 1999 15:40:29 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA21803 for acedb-list@hgmp.mrc.ac.uk; Mon, 20 Dec 1999 15:40:27 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Norman" X-Newsgroups: bionet.software.acedb Subject: HOT NEWS - NEW SOFTWAREZ ! Date: Mon, 20 Dec 1999 16:41:07 +0200 Organization: Omnitel, Lithuania Lines: 30 Message-ID: <83lm4o$ft6$80@trimpas.omnitel.net> Reply-To: "Norman" X-Trace: trimpas.omnitel.net 945707992 16294 195.22.176.145 (20 Dec 1999 16:39:52 GMT) X-Complaints-To: news@omnitel.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk HOT NEWS - 3D Studio Max 3.1 Artcam Pro 4 AUTOCAD LT 2000 (C) AUTODESK CATIA V5R2 SP4 CGTECH VERICUT V4.4 CIMATRON IT V10.6 FINAL ALREADY AVAILABLE ! Also a very big collection of newest engineering, CAD/CAM, multimedia, design and other softwarez. We can make custom CD's with your requested programs. It is available to visit our website. For more information, Please reply to: norm@urgentmail.com If you lost me please send a faxmessage to: Fax: +442076917580 (UK) Fax: +493069088166 (Germany) Fax: +18883572558 (USA) Fax: + 61294750241 (Sydney) Norman Tel: +370 8945459 ICQ: 51449232 From owner-acedb@hgmp.mrc.ac.uk Tue Dec 21 18:42:10 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5E3C817B61; Tue, 21 Dec 1999 18:42:08 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA29025 for ; Tue, 21 Dec 1999 18:41:58 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA20987 for acedb-list@hgmp.mrc.ac.uk; Tue, 21 Dec 1999 18:41:56 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Rizzo" X-Newsgroups: bionet.software.acedb Subject: II Free Strip Card Game II Date: Tue, 21 Dec 1999 13:20:52 -0600 Organization: www.lfplc.org Lines: 19 Message-ID: <83ohk9$210o$3@newssvr04-int.news.prodigy.com> Reply-To: "Rizzo" X-Trace: newssvr04-int.news.prodigy.com 945801673 2896869 209.156.182.185 (21 Dec 1999 18:41:13 GMT) X-Complaints-To: abuse@prodigy.net X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MSMail-Priority: Normal X-Priority: 3 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk II Strip Indian 2000 is here! -100% freeware -no registration or trial period -no adult check -various other games, utilities, and apps absolutely no catch just give us a look. www.lfplc.org LFPLC, the peoples freeware II From owner-acedb@hgmp.mrc.ac.uk Thu Dec 23 05:20:15 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0E10C17A6A; Thu, 23 Dec 1999 05:20:14 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id FAA03021 for ; Thu, 23 Dec 1999 05:20:13 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA02299 for acedb-list@hgmp.mrc.ac.uk; Thu, 23 Dec 1999 05:20:11 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: schwartz@uclink4.berkeley.edu X-Newsgroups: bionet.software.acedb Subject: Re: efetch in acedb Date: Thu, 23 Dec 1999 05:07:59 GMT Organization: Deja.com - Before you buy. Lines: 27 Message-ID: <83sand$qnn$1@nnrp1.deja.com> References: <838re2$gbv$1@nnrp1.deja.com> X-Article-Creation-Date: Thu Dec 23 05:07:59 1999 GMT X-Http-User-Agent: Mozilla/4.5 [en] (X11; I; SunOS 5.7 sun4u) X-Http-Proxy: 1.0 x25.deja.com:80 (Squid/1.1.22) for client 131.243.57.3 X-MyDeja-Info: XMYDJUIDtheo5 To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk In article , Tim Cutts wrote: > One thing you can do is replace efetch with a perl script that does the > same thing. This can then retrieve data from a variety of sources by > different methods. For example, our version of efetch gets sequence > data from our in-house SRS server, in some cases, and from FASTA format > files in others, and from BLAST 2 format in yet others. > > Tim. > > Thanks Tim. I was hoping to do something easier than that though. It looks as if efetch is set up to deal with multiple databases; I should at least find out if I can get it to work as it should, or whether it is possible from within ACeDB, as it comes out of the box. Is your script public if I fail? Jody Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Thu Dec 23 05:50:18 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CA52617A59; Thu, 23 Dec 1999 05:50:17 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id FAA10259 for ; Thu, 23 Dec 1999 05:50:15 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA02645 for acedb-list@hgmp.mrc.ac.uk; Thu, 23 Dec 1999 05:50:14 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: schwartz@uclink4.berkeley.edu X-Newsgroups: bionet.software.acedb Subject: ACeDB bug in Solaris 7? Date: Thu, 23 Dec 1999 05:43:20 GMT Organization: Deja.com - Before you buy. Lines: 23 Message-ID: <83scpk$s6c$1@nnrp1.deja.com> X-Article-Creation-Date: Thu Dec 23 05:43:20 1999 GMT X-Http-User-Agent: Mozilla/4.5 [en] (X11; I; SunOS 5.7 sun4u) X-Http-Proxy: 1.0 x25.deja.com:80 (Squid/1.1.22) for client 131.243.57.3 X-MyDeja-Info: XMYDJUIDtheo5 To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi All, I've developed a horrible bug with ACeDB 4.7e. I have a new Ultra60 which got Solaris 7 (MU 4) installed on it. Something is now terribly wrong. When I try to do anything at all, the ready on the main menu starts to flicker, ACeDB takes over the entire window manager and freezes the screen. It has to be killed from another terminal. When you look at the processes running, dtwm and Xsun are taking up all the processor and ACeDB is gobbling up memory. I got the newest GCC compiler and recompiled ACeDB. Same problem. By the way, I had the same binary running on Solaris 7 on my old computer, where it was fine. Does anyone have the slightest idea what might be going on? If so, do you have any suggestions? Thank you and happy Holidays. Jody Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Thu Dec 23 08:53:11 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A55E717A43; Thu, 23 Dec 1999 08:53:10 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA15533 for ; Thu, 23 Dec 1999 08:53:08 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA04872 for acedb-list@hgmp.mrc.ac.uk; Thu, 23 Dec 1999 08:53:07 GMT From: edgrif@sanger.ac.uk (Ed Griffiths) X-Newsgroups: bionet.software.acedb Subject: Re: ACeDB bug in Solaris 7? Date: 23 Dec 1999 08:53:05 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 49 Message-ID: References: <83scpk$s6c$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 945939186 4869 193.62.192.80 (23 Dec 1999 08:53:06 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk X-Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA15525 for ; Thu, 23 Dec 1999 08:53:04 GMT X-Received: from griffin.sanger.ac.uk (edgrif@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id IAA29749; Thu, 23 Dec 1999 08:53:03 GMT X-Received: from localhost (edgrif@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id IAA10272; Thu, 23 Dec 1999 08:53:02 GMT X-Authentication-Warning: griffin.sanger.ac.uk: edgrif owned process doing -bs X-To: schwartz@uclink4.berkeley.edu X-cc: acedb@hgmp.mrc.ac.uk X-In-Reply-To: <83scpk$s6c$1@nnrp1.deja.com> To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Jody, > Hi All, > > I've developed a horrible bug with ACeDB 4.7e. I have a new Ultra60 > which got Solaris 7 (MU 4) installed on it. Something is now terribly > wrong. When I try to do anything at all, the ready on the main menu > starts to flicker, ACeDB takes over the entire window manager and > freezes the screen. It has to be killed from another terminal. When > you look at the processes running, dtwm and Xsun are taking up all the > processor and ACeDB is gobbling up memory. I got the newest GCC > compiler and recompiled ACeDB. Same problem. > I can answer this one, around this time someone inadvertantly intrduced a bug into the code that controls acedb's version of pop-up dialogs. Basically this bug tried to keep the dialog on top of all other windows on the screen by calling an X routine to raise the window. Unfortunately the call to this routine was put inside the event dispatching loop for the pop-up. As the raise routine generates events the loop would execute which would do another 'raise window' which would generate more events which would cause the loop to execute again which would another 'raise window' etc. etc. This bug did not show up straight away because of a small difference in the way window managers behave: if a window manager detects that an action on a window (such as raising it) would have no effect it is allowed to dispense with actually doing the action. So some window managers do not get overwhelmed with a flood of 'raise windows' from acedb because they ignore them, other windows managers (notably mwm in later incarnations) do not ignore the events and hence quickly get overwhelmed (which is still a bug in the window manager in my opinion). Later versions of 4_7 (I think we are to 4_7l) do not have this problem, I know, I fixed it. I would suggest you get the latest 4_7 code and try it. If you still have a problem then come back to me. cheers/happy Christmas/new year, Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ --- From owner-acedb@hgmp.mrc.ac.uk Thu Dec 23 17:41:32 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 95EAF17AAD; Thu, 23 Dec 1999 17:41:31 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA20060 for ; Thu, 23 Dec 1999 17:41:30 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA14924 for acedb-list@hgmp.mrc.ac.uk; Thu, 23 Dec 1999 17:41:29 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: unknown X-Newsgroups: bionet.software.acedb Subject: How to combine GeneMap and dbEST data? Date: Thu, 23 Dec 1999 12:41:29 -0500 Organization: Ohio State University Lines: 19 Message-ID: <38625EC9.B980E99E@medctr.osu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: charm.magnus.acs.ohio-state.edu 945970989 26662 140.254.128.20 (23 Dec 1999 17:43:09 GMT) X-Complaints-To: abuse@osu.edu X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I've seen this done, but haven't a clue as to how to proceed. I thought it would be a fairly common application for gene mappers. A look at GeneMap 99 will show you that most of the genes mapped are undocumented ESTs. I need to correlate the tissue specificity data in dbEST to hundreds of these mapped ESTs. The GeneMap web interface lists their own ID for each EST, and only gives an accession number if you drill down through the link for each one. I've the idea that if I can get the EST data from GeneMap into a table I can sort that with the tissue specificity query results from dbEST using Access. Is there a way I can obtain a table of GeneMap EST data with accession numbers? Is there a better way of going about this? I would have thought that this task was fairly standard. Thanks, Mike Holloway holloway@concentric.net From owner-acedb@hgmp.mrc.ac.uk Thu Dec 23 22:15:42 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6ADF217A56; Thu, 23 Dec 1999 22:15:41 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA16128 for ; Thu, 23 Dec 1999 22:15:39 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA26434 for acedb-list@hgmp.mrc.ac.uk; Thu, 23 Dec 1999 22:15:38 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: unknown X-Newsgroups: bionet.software.acedb Subject: Re: How to combine GeneMap and dbEST data? Date: Thu, 23 Dec 1999 17:15:39 -0500 Organization: Ohio State University Lines: 5 Message-ID: <38629F0A.BCF20E03@medctr.osu.edu> References: <38625EC9.B980E99E@medctr.osu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: charm.magnus.acs.ohio-state.edu 945987438 2065 140.254.128.20 (23 Dec 1999 22:17:18 GMT) X-Complaints-To: abuse@osu.edu X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en To: acedb@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Alright. Got it. Finally figured out how to use the Unigene web interface. I can get the answers with the marker interval I'm interested in. From owner-acedb@hgmp.mrc.ac.uk Tue Dec 28 10:50:22 1999 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2E89D17A96; Tue, 28 Dec 1999 10:50:21 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA17731; Tue, 28 Dec 1999 10:49:52 GMT Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA18532; Tue, 28 Dec 1999 10:49:51 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "ws-5" X-Newsgroups: bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software.srs,bionet.software.staden,bionet.software.x-plor,bnr.software-eng,chile.mercado.software,chinese.comp.software,comp.mail.list-admin.software,comp.os.ms-windows.nt.softwar Subject: Re: Wordperfect invalid filename Date: Tue, 28 Dec 1999 12:48:43 +0200 Organization: Kharkiv Online Lines: 4 Message-ID: <84a4k5$1dnc$1@uran.kharkiv.net> References: <83ki20$qem2@imsp212.netvigator.com> X-Trace: uran.kharkiv.net 946378181 46828 212.111.194.254 (28 Dec 1999 10:49:41 GMT) X-Complaints-To: usenet@news.kharkiv.net X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 To: acedb@hgmp.mrc.ac.uk, bio-software@hgmp.mrc.ac.uk, bio-srs@hgmp.mrc.ac.uk, info-gcg@hgmp.mrc.ac.uk, staden@hgmp.mrc.ac.uk, x-plor@hgmp.mrc.ac.uk Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk ÒÁÄÁ Â?ÌÁ ÐÒÏÞÉÔÁÔØ ×ÁÓ. 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