From owner-gdb@net.bio.net Tue Jan 07 22:00:00 1997 Path: biosci!HGSI.COM!John_Greene From: John_Greene@HGSI.COM ("John M. Greene, Ph.D") Newsgroups: bionet.molbio.gdb Subject: Bioinformatics Associate Director position Date: 8 Jan 1997 11:52:53 -0800 Organization: Human Genome Sciences, Inc./Bioinformatics Group Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: <32D3FB79.6CBE@hgsi.com> Reply-To: John_Greene@hgsi.com NNTP-Posting-Host: net.bio.net BIOINFORMATICS POSITION AVAILABLE As a result of expanded collaborations with Schering/Plough, Pharmacia and Upjohn, and others, Human Genome Sciences is expanding our Bioinformatics Group, under Mike Fannon, our Director. We have an immediate opening for an ASSOCIATE DIRECTOR - This person would essentially be "second in command" in our growing world-class Bioinformatics group. This position will be filled by someone with 3-5 years of experience in developing user interfaces and managing large quantities of biological data at a staff Bioinformatics Scientist level, preferably in the computer, biotechnology, or pharmaceutical industries. This person must be extremely comfortable in both the computer and biological spheres and has to have a substantial UNIX/Sybase background as well as extensive experience in sequence analysis and database design and manipulation. He or she would be involved in continuing to develop information management solutions to seek out novel genes of therapeutic value from our database of well over one million Expressed Sequence Tags. The ideal candidate must have top notch communication and managerial skills and would be capable of making presentations with and to senior management on short notice (to stock analysts, potential corporate partners, etc.). A Ph.D would be required in either biological or computer sciences. Please send a CV by FAX to 301-340-7159 or reply by E-mail as soon as possible. Human Genome Sciences, Inc. supports and is committed to the principle of equal employment opportunity. It is our policy to recruit, hire, train, and promote individuals, as well as to administer any and all personnel actions, without regard to race, color, national origin, sex, sexual orientation, religion, age, disability, or veteran status. In accord with the provisions of the Civil Rights Act of 1964, as amended. Executive Order No. 11246, as amended, and The Americans and Disabilities Act, this policy fully embraces equality of opportunity with respect to all employment matters, such as recruitment, hiring, compensation, benefits, transfer, promotion, demotion, discharge, layoff, training and development, educational assistance, and social and recreational programs. From owner-gdb@net.bio.net Sun Jan 12 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.gdb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 Jan 1997 02:00:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199701131000.CAA07219@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-gdb@net.bio.net Mon Jan 13 22:00:00 1997 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!math.ohio-state.edu!uwm.edu!newsfeeds.sol.net!news-xfer.netaxs.com!cs.utexas.edu!atlantis.utmb.edu!news From: bdodson@beowulf.utmb.edu (M. L. Dodson) Newsgroups: bionet.biophysics,bionet.jobs,bionet.molbio.gdb,bionet.molbio.genbank,bionet.molbio.methds-reagents,bionet.molbio.proteins,bionet.molec-model Subject: Postdoctoral positions in rapid kinetics Date: 14 Jan 1997 20:46:16 GMT Organization: The Sealy Center for Molecular Science Lines: 19 Distribution: world Message-ID: <5bgrap$cn4@atlantis.utmb.edu> Reply-To: bdodson@beowulf.utmb.edu NNTP-Posting-Host: beowulf.utmb.edu Keywords: kinetics,enzymology,DNA,repair,polymerase Xref: biosci bionet.biophysics:2555 bionet.molbio.gdb:563 bionet.molbio.genbank:2481 bionet.molbio.proteins:9728 bionet.molec-model:1321 Two postdoctoral positions are currently available to carry out rapid kinetic analyses of both DNA repair enzymes and DNA polymerases on defined substrates. Experience with fast kinetics is essential. Send CV to: R. Stephen Lloyd Center for Molecular Science Rt. 1071 University of Texas Medical Branch Galveston, TX 77555-1071 or reply by email: kinetics@scms.utmb.edu UTMB is an affirmative action employer M/F/D/V. From owner-gdb@net.bio.net Tue Jan 14 22:00:00 1997 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!newsfeeds.sol.net!uwm.edu!newsspool.doit.wisc.edu!night.primate.wisc.edu!ames!purdue!oitnews.harvard.edu!das-news2.harvard.edu!fas-news.harvard.edu!slippp2-20.fas.harvard.edu!user From: bttran@law.harvard.edu (tran) Newsgroups: bionet.molbio.genbank,bionet.molbio.gdb,bionet.molbio.genbank-updates Subject: gender behavioral differences and biology Date: Wed, 15 Jan 1997 08:54:00 -0500 Organization: Harvard University, Cambridge, Massachusetts Lines: 7 Message-ID: NNTP-Posting-Host: slippp2-20.fas.harvard.edu Xref: biosci bionet.molbio.genbank:2483 bionet.molbio.gdb:565 Hi. I'm taking a gender class at my law school. I would like to ask your opinion regarding the issue of whether or not some behavioral differences in males and femals are the product of biology and not mere socialization or culturalization. Please also give me any studies, statistics or articles which supports or refutes this view. I thank you in advance for your assistance. Please e-mail me with your information and thoughts. My e-mail address is bttran@law.harvard.edu. The class ends January 24. From owner-gdb@net.bio.net Thu Jan 16 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!hermod.uio.no!nntp.uio.no!usenet From: Ola Myklebost Newsgroups: bionet.molbio.gdb Subject: GDB clone search output Date: Fri, 17 Jan 1997 09:24:34 +0100 Organization: The Norwegian Radium Hospital Lines: 12 Message-ID: <32DF367B.2480@radium.uio.no> Reply-To: olam@radium.uio.no NNTP-Posting-Host: pcdnr05.uio.no Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) CC: aforus Dear GDB, when searching GDB for useful clones in a certain chromosomal segment (or by other criteria), one gets a list of clones. In most cases we would then want to contact the sources to receive those clones, and it would be most useful if the output also contained the contacts, as usually each contact has a number of clones from a region. Othervise one has to retrive each single clone to see who is the source. Anyway, thanks for the terrific GDB service!! Ola From owner-gdb@net.bio.net Mon Jan 20 22:00:00 1997 Path: biosci!HOLDEN.CHEM.YALE.EDU!djaustin From: djaustin@HOLDEN.CHEM.YALE.EDU ("David J. Austin") Newsgroups: bionet.molbio.gdb Subject: Restriction site frequency... Date: 20 Jan 1997 17:26:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Is it possible to determine the frequency of two restriction sites in human genes? I am interested in determining the frequency of BOTH an ApaL I (gtgcac) and a Sma I (cccggg) site within the same gene. I have searched the sequence gtgcac-cccggg, but only receive hits with contiguous sequence. I am afraid there are probably many more hits that are separated, but for some reason they are not meeting the search criteria. Any help would be appreciated. Thanks. -Dave David J. Austin, Ph.D. Department of Chemistry Assistant Professor Yale University djaustin@holden.chem.yale.edu 225 Prospect St. http://www.chem.yale.edu P.O. Box 208107 tel-(203)432-3962 New Haven, CT 06520-8107 fax-(203)432-6144 From owner-gdb@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!SCREAMS.GDB.ORG!avoltz From: avoltz@SCREAMS.GDB.ORG (Amy Voltz) Newsgroups: bionet.molbio.gdb Subject: Re: Restriction site frequency... Date: 21 Jan 1997 18:09:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net Dear David, I'm not sure what gene you have in mind for this restriction site information... As far as I know, a restriction map of the gene (as published in the literature) is still the best resource for this type of information. If you're interested in trying this by doing sequence searches using a restriction site sequence as you propose here, I would suggest contacting a sequence database such as GenBank. Sincerely, Amy ** Amy K. Voltz, Ph.D. Research Fellow Johns Hopkins University, Sch. of Medicine Division of Biomedical Information Sciences avoltz@gdb.org (410) 614-0440 On 20 Jan 1997, David J. Austin wrote: > > Is it possible to determine the frequency of two restriction sites in > human genes? I am interested in determining the frequency of BOTH an ApaL > I (gtgcac) and a Sma I (cccggg) site within the same gene. > > I have searched the sequence gtgcac-cccggg, but only receive hits with > contiguous sequence. I am afraid there are probably many more hits that > are separated, but for some reason they are not meeting the search > criteria. Any help would be appreciated. Thanks. > > -Dave > > > David J. Austin, Ph.D. Department of Chemistry > Assistant Professor Yale University > djaustin@holden.chem.yale.edu 225 Prospect St. > http://www.chem.yale.edu P.O. Box 208107 > tel-(203)432-3962 New Haven, CT 06520-8107 > fax-(203)432-6144 > > > From owner-gdb@net.bio.net Tue Jan 21 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news3.cac.psu.edu!news.cse.psu.edu!news.cc.swarthmore.edu!netnews.upenn.edu!vesicle.dental.upenn.edu!ellis From: ellis@vesicle.dental.upenn.edu (Ellis Golub) Newsgroups: bionet.molbio.gdb Subject: Re: Restriction site frequency... Date: 22 Jan 1997 16:27:09 GMT Organization: University of Pennsylvania Lines: 35 Distribution: world Message-ID: <5c5f4t$klg@netnews.upenn.edu> References: NNTP-Posting-Host: vesicle.dental.upenn.edu If you have access to the GCG (Wisconsin) package, the program Findpatterns should be able to do what you want. The IG suite had a database program which allowed regular expression searching, but I don't remember the name of the program. Ellis In article , djaustin@HOLDEN.CHEM.YALE.EDU ("David J. Austin") writes: |> |> Is it possible to determine the frequency of two restriction sites in |> human genes? I am interested in determining the frequency of BOTH an ApaL |> I (gtgcac) and a Sma I (cccggg) site within the same gene. |> |> I have searched the sequence gtgcac-cccggg, but only receive hits with |> contiguous sequence. I am afraid there are probably many more hits that |> are separated, but for some reason they are not meeting the search |> criteria. Any help would be appreciated. Thanks. |> |> -Dave |> |> |> David J. Austin, Ph.D. Department of Chemistry |> Assistant Professor Yale University |> djaustin@holden.chem.yale.edu 225 Prospect St. |> http://www.chem.yale.edu P.O. Box 208107 |> tel-(203)432-3962 New Haven, CT 06520-8107 |> fax-(203)432-6144 |> -- Ellis Golub Phone: (215) 898-4629 Biochemistry Department FAX: (215) 898-3695 University of Pennsylvania ellis@biochem.dental.upenn.edu School of Dental Medicine 4001 Spruce Street Philadelphia, PA 19104-6003 From owner-gdb@net.bio.net Tue Jan 28 22:00:00 1997 Path: biosci!bcm.tmc.edu!news From: Kim Worley Newsgroups: bionet.molbio.gdb Subject: Re: Restriction site frequency... Date: Wed, 29 Jan 1997 15:51:17 -0500 Organization: Baylor College of Medicine Lines: 37 Message-ID: <32EFB845.557A@bcm.tmc.edu> References: NNTP-Posting-Host: dot.imgen.bcm.tmc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) To: "David J. Austin" David J. Austin wrote: > > Is it possible to determine the frequency of two restriction sites in > human genes? I am interested in determining the frequency of BOTH an ApaL > I (gtgcac) and a Sma I (cccggg) site within the same gene. > > I have searched the sequence gtgcac-cccggg, but only receive hits with > contiguous sequence. I am afraid there are probably many more hits that > are separated, but for some reason they are not meeting the search > criteria. Any help would be appreciated. Thanks. > > -Dave > > David J. Austin, Ph.D. Department of Chemistry > Assistant Professor Yale University > djaustin@holden.chem.yale.edu 225 Prospect St. > http://www.chem.yale.edu P.O. Box 208107 > tel-(203)432-3962 New Haven, CT 06520-8107 > fax-(203)432-6144 Check out the WebCutter page on the web at http://www.medkem.gu.se/cutter/ You can query GenBank for the sequence, or paste it in directly, choose which enzymes to report, and choose how to report the matches. WebCutter searches reporting a map of all sites of 6bp or greater cutter enzymes are included on the BCM Search Launcher Sequence Utilities page which can be reached from the main page in my signature. Choosing the [O] link takes you to the WebCutter search page. Kim ---------------------------------------------------------------- Kim C. Worley, Ph.D. kworley@bcm.tmc.edu P 713-798-8292 Baylor College of Medicine, Houston, TX 77030 F 713-798-5386 http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html ----------------------------------------------------------------