From owner-embldatabank@net.bio.net Fri Oct 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!sunic!uts!biobase!ali From: ali@biobase.aau.dk (Ali Karami) Newsgroups: bionet.molbio.embldatabank Subject: Re: Borrelia linear plasmid Message-ID: Date: 9 Oct 93 17:49:35 GMT References: ali Distribution: bionet Organization: The Danish BioBase Lines: 19 Dear neters I,m working on my Ph.D project for Molecular chracterisation ofv 25-27 Kb linear plasmid of Borrelia Burgdorferi , I want to know is there any body working on Linear plasmids of borrelia specially larg linear plasmid like mine. regards ali Copenhagen university From owner-embldatabank@net.bio.net Mon Oct 11 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.embldatabank Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9310120900.AA11808@net.bio.net> Date: 12 Oct 93 09:00:05 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 243 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.welch.jhu.edu and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-embldatabank@net.bio.net Mon Oct 11 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!dapsun.lif.icnet.uk!bison.lif.icnet.uk!alex From: alex@bison.lif.icnet.uk (Alex Whittaker - BIU) Newsgroups: bionet.molbio.embldatabank Subject: EMBL weekly update 931010.dat Keywords: EMBL weekly update Message-ID: <29bcrlINNn77@dapsun.lif.icnet.uk> Date: 11 Oct 93 10:34:29 GMT Organization: Imperial Cancer Research Fund Lines: 18 NNTP-Posting-Host: bison.lif.icnet.uk This morning, the automatic updating software I installed to pull weekly updates of EMBL failed. I wonder how many other updates failed allong with it. The cause is the double entry for Z25875, present in weekly update 931010.dat.Z consecutively with locus names SYHA12M and SYHA12MX. Is this an oversight at EMBL's end or have I just failed to read the rules of engaement correctly? -- Alex Whittaker ______ \||/_ | | oo \ "All I know Biomedical Informatics Unit | | L_ is that I know Imperial Cancer Research Fund |______| \/ nothing" London ________ | [========] / alex@bison.biu.icnet.uk ---OOO- |ooooooo| From owner-embldatabank@net.bio.net Tue Oct 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!tcsi.tcs.com!agate!msuinfo!netnews.upenn.edu!hmivax!bailey From: bailey@hmivax.humgen.upenn.edu (Charles Bailey) Newsgroups: bionet.molbio.embldatabank Subject: EMBL 'unique' entries available for ftp? Message-ID: <1993Oct13.111756.1@hmivax> Date: 13 Oct 93 15:17:56 GMT Sender: news@netnews.upenn.edu Organization: HHMI/Human Genetics, Univ of Pa. Lines: 28 Nntp-Posting-Host: hmivax.humgen.upenn.edu We use GenBank as our primary nucleic acid sequence database, but also maintain a local copy of those entries in EMBL whose primary accession numbers do not appear in GenBank. This was about 10000 entries as of EMBL release 34, and is, I gather, dropping as GenBank, EMBL, and DDBJ sort out the backlog. Nontheless, as long as there remain 'unique' EMBL entries, we would like to keep them available to local users. Until this summer, we were grateful users of Mike Cherry's ftp site in the US to obtain the 'unique' dataset, but that has been closed due to concerns about the network load generated by the transAtlantic transfers. I am coming, then, hat in hand, to ask whether anyone has this dataset available? I would be happy to mirror it for anonymous ftp here, and don't see any need for incremental updates, since I expect very few of these 'unique' entries are corrected or altered without a corresponding addition to GenBank. Since I'm using this via the GCG package, I can take the dataset as flatfile or in GCG format. Many thanks to all for their consideration and advice. Regards, Charles Bailey !------------------------------------------------------------------------------- ! Dept. of Genetics / Howard Hughes Medical Institute ! University of Pennsylvania School of Medicine Rm. 430 Clinical Research Bldg. ! 422 Curie Blvd. Philadelphia, PA 19104 USA Tel. (215) 898-1699 ! Internet: bailey@genetics.upenn.edu (IN 128.91.200.37) !------------------------------------------------------------------------------- From owner-embldatabank@net.bio.net Tue Oct 12 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Newsgroups: bionet.molbio.embldatabank Subject: Re: EMBL weekly update 931010.dat Message-ID: Date: 13 Oct 93 07:54:14 GMT References: <29bcrlINNn77@dapsun.lif.icnet.uk> Followup-To: bionet.molbio.embldatabank Organization: EMBL Data Library Lines: 26 Nntp-Posting-Host: rainer-mac.embl-heidelberg.de In article <29bcrlINNn77@dapsun.lif.icnet.uk>, alex@bison.lif.icnet.uk (Alex Whittaker - BIU) wrote: > This morning, the automatic updating software I installed to pull weekly > updates of EMBL failed. I wonder how many other updates failed allong with > it. The cause is the double entry for Z25875, present in weekly update > 931010.dat.Z consecutively with locus names SYHA12M and SYHA12MX. Is this an > oversight at EMBL's end or have I just failed to read the rules of engaement > correctly? What happened was that an EMBL entry was renamed for some reason, i.e., the entry name changed from SYHA12M to SYHA12MX. Unfortunately, the old entry was not removed from the file store which is used to build the weekly updates. We try to keep this sort of changes to a minimum. To be on the safe side you could instruct your software to check the DT lines if it comes across two entries with identical accession numbers, so that it can throw away the older version. -- Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-embldatabank@net.bio.net Tue Oct 12 23:00:00 1993 Path: biosci!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!pipex!sunic!uts!biobase!ali From: ali@biobase.aau.dk (Ali Karami) Newsgroups: bionet.molbio.embldatabank Subject: Re: Borrelia linear plasmid Message-ID: Date: 9 Oct 93 17:49:35 GMT References: ali Distribution: bionet Organization: The Danish BioBase Lines: 19 Dear neters I,m working on my Ph.D project for Molecular chracterisation ofv 25-27 Kb linear plasmid of Borrelia Burgdorferi , I want to know is there any body working on Linear plasmids of borrelia specially larg linear plasmid like mine. regards ali Copenhagen university From owner-embldatabank@net.bio.net Wed Oct 13 23:00:00 1993 Path: biosci!parc!decwrl!ames!agate!msuinfo!netnews.upenn.edu!hmivax!bailey From: bailey@hmivax.humgen.upenn.edu (Charles Bailey) Newsgroups: bionet.molbio.embldatabank Subject: EMBL 'unique' entries available for ftp? Message-ID: <1993Oct13.111756.1@hmivax> Date: 13 Oct 93 15:17:56 GMT Sender: news@netnews.upenn.edu Organization: HHMI/Human Genetics, Univ of Pa. Lines: 28 Nntp-Posting-Host: hmivax.humgen.upenn.edu We use GenBank as our primary nucleic acid sequence database, but also maintain a local copy of those entries in EMBL whose primary accession numbers do not appear in GenBank. This was about 10000 entries as of EMBL release 34, and is, I gather, dropping as GenBank, EMBL, and DDBJ sort out the backlog. Nontheless, as long as there remain 'unique' EMBL entries, we would like to keep them available to local users. Until this summer, we were grateful users of Mike Cherry's ftp site in the US to obtain the 'unique' dataset, but that has been closed due to concerns about the network load generated by the transAtlantic transfers. I am coming, then, hat in hand, to ask whether anyone has this dataset available? I would be happy to mirror it for anonymous ftp here, and don't see any need for incremental updates, since I expect very few of these 'unique' entries are corrected or altered without a corresponding addition to GenBank. Since I'm using this via the GCG package, I can take the dataset as flatfile or in GCG format. Many thanks to all for their consideration and advice. Regards, Charles Bailey !------------------------------------------------------------------------------- ! Dept. of Genetics / Howard Hughes Medical Institute ! University of Pennsylvania School of Medicine Rm. 430 Clinical Research Bldg. ! 422 Curie Blvd. Philadelphia, PA 19104 USA Tel. (215) 898-1699 ! Internet: bailey@genetics.upenn.edu (IN 128.91.200.37) !------------------------------------------------------------------------------- From owner-embldatabank@net.bio.net Wed Oct 13 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!usc!howland.reston.ans.net!agate!doc.ic.ac.uk!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Newsgroups: bionet.molbio.embldatabank Subject: Re: EMBL weekly update 931010.dat Message-ID: Date: 13 Oct 93 07:54:14 GMT References: <29bcrlINNn77@dapsun.lif.icnet.uk> Followup-To: bionet.molbio.embldatabank Organization: EMBL Data Library Lines: 26 Nntp-Posting-Host: rainer-mac.embl-heidelberg.de In article <29bcrlINNn77@dapsun.lif.icnet.uk>, alex@bison.lif.icnet.uk (Alex Whittaker - BIU) wrote: > This morning, the automatic updating software I installed to pull weekly > updates of EMBL failed. I wonder how many other updates failed allong with > it. The cause is the double entry for Z25875, present in weekly update > 931010.dat.Z consecutively with locus names SYHA12M and SYHA12MX. Is this an > oversight at EMBL's end or have I just failed to read the rules of engaement > correctly? What happened was that an EMBL entry was renamed for some reason, i.e., the entry name changed from SYHA12M to SYHA12MX. Unfortunately, the old entry was not removed from the file store which is used to build the weekly updates. We try to keep this sort of changes to a minimum. To be on the safe side you could instruct your software to check the DT lines if it comes across two entries with identical accession numbers, so that it can throw away the older version. -- Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-embldatabank@net.bio.net Fri Oct 15 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!howland.reston.ans.net!pipex!sunic!uts!biobase!ali From: ali@biobase.aau.dk (Ali Karami) Newsgroups: bionet.molbio.embldatabank Subject: Re: Borrelia linear plasmid Message-ID: Date: 9 Oct 93 17:49:35 GMT References: ali Distribution: bionet Organization: The Danish BioBase Lines: 19 Dear neters I,m working on my Ph.D project for Molecular chracterisation ofv 25-27 Kb linear plasmid of Borrelia Burgdorferi , I want to know is there any body working on Linear plasmids of borrelia specially larg linear plasmid like mine. regards ali Copenhagen university From owner-embldatabank@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.embldatabank Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9310120900.AA11808@net.bio.net> Date: 12 Oct 93 09:00:05 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 243 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.welch.jhu.edu and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-embldatabank@net.bio.net Sat Oct 16 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!yeshua.marcam.com!news.kei.com!sol.ctr.columbia.edu!math.ohio-state.edu!howland.reston.ans.net!agate!doc.ic.ac.uk!dapsun.lif.icnet.uk!bison.lif.icnet.uk!alex From: alex@bison.lif.icnet.uk (Alex Whittaker - BIU) Newsgroups: bionet.molbio.embldatabank Subject: EMBL weekly update 931010.dat Keywords: EMBL weekly update Message-ID: <29bcrlINNn77@dapsun.lif.icnet.uk> Date: 11 Oct 93 10:34:29 GMT Organization: Imperial Cancer Research Fund Lines: 18 NNTP-Posting-Host: bison.lif.icnet.uk This morning, the automatic updating software I installed to pull weekly updates of EMBL failed. I wonder how many other updates failed allong with it. The cause is the double entry for Z25875, present in weekly update 931010.dat.Z consecutively with locus names SYHA12M and SYHA12MX. Is this an oversight at EMBL's end or have I just failed to read the rules of engaement correctly? -- Alex Whittaker ______ \||/_ | | oo \ "All I know Biomedical Informatics Unit | | L_ is that I know Imperial Cancer Research Fund |______| \/ nothing" London ________ | [========] / alex@bison.biu.icnet.uk ---OOO- |ooooooo| From owner-embldatabank@net.bio.net Sun Oct 17 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!nctuccca.edu.tw!TWNMOE10.Edu.TW!GOVE350 From: GOVE350@TWNMOE10.Edu.TW (Chiu) Newsgroups: bionet.molbio.embldatabank Subject: Spatial Autocorrelation Keywords: Spatial Heterogeneity Message-ID: <16C6BDD94S85.GOVE350@TWNMOE10.Edu.TW> Date: 18 Oct 93 20:45:24 GMT Organization: MOECC Computer Center, Taiwan Lines: 8 NNTP-Posting-Host: twnmoe10.edu.tw It is just a note to informpeople who are interested in or bothered by spatial autocorrelation in their study that there are good articles in this issue of "Ecolgoy"(a journal printed every two months). I hope that this information is of some help. From owner-embldatabank@net.bio.net Sat Oct 23 23:00:00 1993 Path: biosci!parc!decwrl!ames!agate!doc.ic.ac.uk!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.embldatabank,embnet.general Subject: Re: EMBL 'unique' entries available for ftp? Message-ID: <1993Oct24.130801.24171@comp.bioz.unibas.ch> Date: 24 Oct 93 13:08:01 GMT References: <1993Oct13.111756.1@hmivax> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 88 Xref: biosci bionet.molbio.embldatabank:253 Nntp-Posting-Host: biox.embnet.unibas.ch Charles Bailey wrote some time ago; >We use GenBank as our primary nucleic acid sequence database, but also maintain >a local copy of those entries in EMBL whose primary accession numbers do not >appear in GenBank. This was about 10000 entries as of EMBL release 34, and is, >I gather, dropping as GenBank, EMBL, and DDBJ sort out the backlog. Nontheless, >as long as there remain 'unique' EMBL entries, we would like to keep them The 'backlog' is rather a negotiation between database providers. The most recent EMBL data library has a list of entries called "BBMATCH". These entries from the NCBI backbone database are expected to be duplicates of already exis- ting data, and are not included in the EMBL data library. This implies that searches for an accession number in the EMBL data library will need to search this file as well in order to locate the correct data from the backbone en- tries. As established software is currently not prepared to go that way, it is required to keep these 'additions' if the users want to retrieve entries by accession numbers. >available to local users. Until this summer, we were grateful users of Mike >Cherry's ftp site in the US to obtain the 'unique' dataset, but that has been >closed due to concerns about the network load generated by the transAtlantic >transfers. I must admit that I was the origin of the primary data, and Mike Cherry mirrored these via ftp script in order to compute the exclusion set of these the data. As we (Biocomputing Basel) were requested to reduce network traffic as much traffic as possible, we cancelled this mirror. This measure was essential in order to avoid that we needed to shut down the entire services. My apologies for any inconvenience caused by this. Thus, EMBL has a FTP ser- ver (ftp.embl-heidelberg.de) with primary data in case of real need. >I am coming, then, hat in hand, to ask whether anyone has this dataset >available? I would be happy to mirror it for anonymous ftp here, and don't see >any need for incremental updates, since I expect very few of these 'unique' >entries are corrected or altered without a corresponding addition to GenBank. >Since I'm using this via the GCG package, I can take the dataset as flatfile or >in GCG format. I mailed Charles privately with respect to options. Let me raise a rather general point here. The EMBL data library, as other data libraries, is public domain. They get resources paid as part of their contract to make the data available. The way of accessing these data is via CD-ROM subscription. Updates via elec- tronic networks are extremely expensive if run as full-file FTP copy via transatlantic links. In particular, this affects sites which are _not_ paid for the data distribution activities as part of their business. These costs are the costs to run the network, as well as keeping the data sets stable. Therefore, for us (Biocomputing Basel) there is - staff cost to maintain and monitor the preparation of updates - disk and other hardware cost to prepare datasets and backups - network cost to be paid to the network provider. Making data available for 'free' therefore means that the cost as listed above needs to be covered. Funding agencies which fund EMBnet Switzerland are interested to fund access for local or national sources, and do not desire to spend money in this kind of global service provision. Notabene: _Collaborations_, i.e. a bilateral exchange, is fine, but we had in the end several Gigabytes per month downloads towards transatlantic destinations. My point is that public domain data are free, but providing access to these data cost money. Furthermore, the collection and synchronisation of updates involves resources and therefore generates added-value data. The fu- ture development will hopefully allow us to provide data to the community, within reasonable limits, for free, but we can neither promise nor make sure that network costs will always be covered by general infrastructure rather than by the institutions causing the traffic. Not to mention staff and main- tenance cost for the hardware... This discussion is not only valid for 'unique' data from EMBL in Genbank but certainly also applies to the other way round. Regards Reinhard Doelz EMBnet Switzerland -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-embldatabank@net.bio.net Sun Oct 24 22:00:00 1993 Path: biosci!HAMLET.UCDAVIS.EDU!fzbritt From: fzbritt@HAMLET.UCDAVIS.EDU Newsgroups: bionet.molbio.embldatabank Subject: sequence submission Message-ID: <9310252205.AA01099@hamlet.ucdavis.edu> Date: 25 Oct 93 22:05:14 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 I would like to enter the sequence for an Arabidopsis cDNA encoding a 3-methyladenine glycosylase. Could you send me instructions on how this is done? Also, there's a sequence in the bank already which is described, incorrectly, as a 3-methyladenine glycosylase. Thsi is the tag gene of Vibrio cholerae. I thi nk the tag stands for T Antigen Gene, or something like that. It does not stand for Threemethyl Adenine Glycosylase. Thanks, Anne B. Britt Section of Plant Biology U. C. Davis Davis, CA 95616 fzbritt@hamlet.ucdavis.edu From owner-embldatabank@net.bio.net Mon Oct 25 22:00:00 1993 Path: biosci!lhc!ray!dab From: dab@ray.nlm.nih.gov (Dennis Benson) Newsgroups: bionet.molbio.embldatabank Subject: Re: sequence submission Message-ID: <1993Oct26.160214.13352@nlm.nih.gov> Date: 26 Oct 93 16:02:14 GMT References: <9310252205.AA01099@hamlet.ucdavis.edu> Sender: news@nlm.nih.gov Distribution: bionet Organization: National Library of Medicine Lines: 94 X-Newsreader: Tin 1.1 PL4 fzbritt@HAMLET.UCDAVIS.EDU writes: : I would like to enter the sequence for an Arabidopsis cDNA encoding a 3-methyladenine glycosylase. Could you send me instructions on how this is done? : Also, there's a sequence in the bank already which is described, incorrectly, as a 3-methyladenine glycosylase. Thsi is the tag gene of Vibrio cholerae. I thi : nk the tag stands for T Antigen Gene, or something like that. It does not stand for Threemethyl Adenine Glycosylase. : Thanks, : Anne B. Britt : Section of Plant Biology : U. C. Davis : Davis, CA 95616 : fzbritt@hamlet.ucdavis.edu Anne -- Below is a summary of sequence submission instructions. As for the sequence with the incorrect description, you are probably referring to M60658 and you are correct. The 'tag' gene in this sequence from Vibrio cholerae refers to the 'ToxR activated gene', and not the '3-methyladenine DNA glycosylase' gene. The keywords and product name have been corrected and the revised record will be available from GenBank within 48 hours. Dennis Benson GenBank -------------------------------------------------------------------------- Sequence Data Submissions to GenBank, EMBL, and DDBJ -------------------------------------------------------------------------- The sequence databases depend on scientists to contribute sequences and associated biological annotation in electronic form. The three databases in the U.S., Europe, and Japan collaborate in collecting and distributing all sequence information received and consequently make available comprehensive collections of DNA and RNA sequence data in the GenBank, EMBL, and DDBJ databases. Researchers are encouraged to submit data to whichever of the three databases is most convenient. The receiving database will transmit the data to the other two. Collectively, the databases will make the sequence information available to scientists throughout the world through computer networks, magnetic tapes, and CD-ROMs. Many editorial policies require submission of sequence data and the issuance of an accession number by the databases as a condition of publication. (At the authors' option, sequence data may be kept confidential until publication.) But even when not required, the inclusion of an accession number in a publication helps users efficiently retrieve the sequence from the databases. To facilitate the submission process, free software (Authorin) for PC and Macintosh computers is available. Contact NCBI for the software at the address below. For assistance with sequence submission, contact the most convenient database: GENBANK: National Center for Biotechnology Information National Library of Medicine Bldg. 38A, Rm. 8N-803 Bethesda, MD 20894 USA +1 (301) 496-2475 Submissions: gb-sub@ncbi.nlm.nih.gov Revisions: update@ncbi.nlm.nih.gov Information: info@ncbi.nlm.nih.gov EMBL Data Library EMBL Postfach 10.2209 Meyerhofstrasse 1 69012 Heidelberg Germany +49 (6221) 387258 Submissions: datasubs@embl-heidelberg.de Revisions: update@embl-heidelberg.de Information: datalib@embl-heidelberg.de DNA Databank of Japan DDBJ National Institute of Genetics Mishima Shizuoka 411 Japan +81 559 75 0771 Submissions: ddbjsub@ddbj.nig.ac.jp Revisions: ddbjupdt@ddbj.nig.ac.jp Information: ddbj@ddbj.nig.ac.jp From owner-embldatabank@net.bio.net Mon Oct 25 22:00:00 1993 Path: biosci!SELENE.CICHCU.UNAM.MX!enrique From: enrique@SELENE.CICHCU.UNAM.MX (Sec. Tec. Teleinformatica Enrique Barreto) Newsgroups: bionet.molbio.embldatabank Subject: help Message-ID: <9310261915.AA00215@selene.cichcu.unam.mx> Date: 26 Oct 93 19:15:18 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 HELP From owner-embldatabank@net.bio.net Thu Oct 28 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!caen!msuinfo!netnews.upenn.edu!hmivax!bailey From: bailey@hmivax.humgen.upenn.edu (Charles Bailey) Newsgroups: bionet.molbio.embldatabank Subject: Re: EMBL 'unique' entries available for ftp? Message-ID: <1993Oct29.165152.1@hmivax> Date: 29 Oct 93 20:51:52 GMT References: <1993Oct13.111756.1@hmivax> <1993Oct24.130801.24171@comp.bioz.unibas.ch> Sender: news@netnews.upenn.edu Organization: HHMI/Human Genetics, Univ of Pa. Lines: 107 Nntp-Posting-Host: hmivax.humgen.upenn.edu First off, I apologize to anyone confused by my long delay in following up this thread. I've received a few replies to my original post, which come to differnt conclusions about the size of the EMBL36-GenBank79 exclusions set, and I'm attempting to resolve this before I post a summary back to the net. More on this once I've sorted things out . . . In article <1993Oct24.130801.24171@comp.bioz.unibas.ch>, doelz@comp.bioz.unibas.ch (Reinhard Doelz) writes: > Charles Bailey wrote some time ago; > >>We use GenBank as our primary nucleic acid sequence database, but also maintain >>a local copy of those entries in EMBL whose primary accession numbers do not >>appear in GenBank. This was about 10000 entries as of EMBL release 34, and is, >>I gather, dropping as GenBank, EMBL, and DDBJ sort out the backlog. Nontheless, >>as long as there remain 'unique' EMBL entries, we would like to keep them > > The 'backlog' is rather a negotiation between database providers. The most > > [description of BBMATCH deleted] This kind of thing will be useful in the future, but, as you mention, for now one has to keep these entries around. This particular issue (scanned vs submitted entries) may take a while to solve, since, as I understand it, NCBI is finding that there are differences between some of the bb records and the 'equivalent' submitted records. I expect that thes represent changes to the data that the authors incorporated into their fiugres between submission of the original sequence and publication, but didn't pass on to the database maintainers. This highlights a problem: despite a strenuous effort by the database maintainers, the biologc community has not yet been convinved that sequences in the database must be viewed as 'live' data, and investigators should notify the databases of changes to the sequence as they are discovered. This will benefit everyone, as analysis of sequence data will be based on a better substrate, and investigators who want to use retrieved data for wet experiments won't have to rely on obsolete data or try to track down the original depositor. >>available to local users. Until this summer, we were grateful users of Mike >>Cherry's ftp site in the US to obtain the 'unique' dataset, but that has been >>closed due to concerns about the network load generated by the transAtlantic >>transfers. > > I must admit that I was the origin of the primary data, and Mike Cherry > mirrored these via ftp script in order to compute the exclusion set of these > the data. As we (Biocomputing Basel) were requested to reduce network traffic > as much traffic as possible, we cancelled this mirror. This measure was > essential in order to avoid that we needed to shut down the entire services. > My apologies for any inconvenience caused by this. Thus, EMBL has a FTP ser- > ver (ftp.embl-heidelberg.de) with primary data in case of real need. Please note that I wasn't casting aspersions on your decision to stop the mirror. In fact, it's for precisely the reason that bandwidth, especially across the Atlantic, is narrow and expensive, that I'd like to get and mirror an exclusion set - it minimizes the data which must be transferred, and it provides a site in NA to originate transfers to NA sites. > > [text deleted] > > My point is that public domain data are free, but providing access to > these data cost money. Furthermore, the collection and synchronisation of > updates involves resources and therefore generates added-value data. The fu- > ture development will hopefully allow us to provide data to the community, > within reasonable limits, for free, but we can neither promise nor make sure > that network costs will always be covered by general infrastructure rather > than by the institutions causing the traffic. Not to mention staff and main- > tenance cost for the hardware... This is a valid point. I agree that it's unreasonable to support routine access to full databases across transatlantic links. Ultimately, it may be necessary to require that this exchange of data occur offline via CD or tape. However, given that there seems to be bandwidth available within national networks for this kind of distribution, and given that it's arguably more efficient than getting every site static media containing the data, I'm hoping that a distribution scheme can be worked out. I'm willing to put the exclusion set I generate up for ftp for now; if I'm swamped beyond our local resources, I, too, may have to reconsider. In general, I'd advocate the following principles for data exchange: - we should try to provide sites with access to the available data in as efficient a manner as possible. Ultimately, this will be achieved when NCBI, EMBL, and DDBJ sort out the differences between their databases, and each database covers the content of the others. In the meantime, exclusion sets seem to me the best way to go, though figuring out precisely what should go into an exclusion set can be tricky. - we should try to provide this data in such a way as to minimize load on net bottlenecks. The Basel-Boston mirror was an example of this, but it fell victim to limitations on available resources, and to overuse of the Basel site by US sites which should have been using the mirror. - sites retrieving data should be careful to minimie net consumption. If you can get the data from a local site,do it in preference to a distant site. If you can use an exclusion set, use it instead of the whole database. Get daily incremental updates instead of retrieving the entire cumulative update every day. Cooperate with other nearby sites to exchange data and minimize the number of sites which have to go to the central source. Etc. I realize that this won't solve all usage problems, and in some ways assumes the presence of a backbone like NSFnet or EMBnet to make the intraregional transfers reasonable, but it's at least a start. Thanks for everyone's time and patience on this thread. Regards, Charles Bailey !------------------------------------------------------------------------------- ! Dept. of Genetics / Howard Hughes Medical Institute ! University of Pennsylvania School of Medicine Rm. 430 Clinical Research Bldg. ! 422 Curie Blvd. Philadelphia, PA 19104 USA Tel. (215) 898-1699 ! Internet: bailey@genetics.upenn.edu (IN 128.91.200.37) !-------------------------------------------------------------------------------