From BIOSCI-REQUEST Thu Jan 4 15:37:56 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id PAA04760; Thu, 4 Jan 1996 15:37:56 -0800 Received: from po8.andrew.cmu.edu (PO8.ANDREW.CMU.EDU [128.2.10.108]) by net.bio.net (8.6.12/8.6.6) with ESMTP id PAA04751 Received: (from postman@localhost) by po8.andrew.cmu.edu (8.7.1/8.7.1) id SAA13665; Thu, 4 Jan 1996 18:35:53 -0500 Received: via switchmail; Thu, 4 Jan 1996 18:35:50 -0500 (EST) Received: from unix21.andrew.cmu.edu via qmail ID ; Thu, 4 Jan 1996 18:35:06 -0500 (EST) Received: from unix21.andrew.cmu.edu via qmail ID ; Thu, 4 Jan 1996 18:35:02 -0500 (EST) Received: from mms.4.60.Jan.26.1995.18.43.47.sun4c.411.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix21.andrew.cmu.edu.sun4c.411 via MS.5.6.unix21.andrew.cmu.edu.sun4c_411; Thu, 4 Jan 1996 18:35:02 -0500 (EST) Message-ID: Date: Thu, 4 Jan 1996 18:35:02 -0500 (EST) From: Marcella Madrid To: Outbound News Subject: Biomedical Workshops Cc: Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , bruker-users-mail@bloch.cchem.berkeley.edu, ammrl-request@bloch.cchem.berkeley.edu, rna@net.bio.net, bphyssoc@net.bio.net, amber@cgl.ucsf.edu PITTSBURGH SUPERCOMPUTING CENTER Biomedical Workshops offered by the Pittsburgh Supercomputing Center typically consist of theoretical lectures taught by leaders in the respective scientific discipline, and extensive hands-on computer sessions. During the computer sessions, participants are able to work on the examples provided or on their own experimental data. Attendance is limited to 20 participants to allow one-on-one instruction and encourage scientific interactions and discussions. Application deadlines are six weeks prior to the workshop. Researchers nationwide are invited to apply. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu TO APPLY FOR A WORKSHOP, please fill out the application form. The following four workshops will be offered during 1996: SUPERCOMPUTING TECHNIQUES FOR BIOMEDICAL RESEARCHERS; May 5-9. The purpose of this workshop is to introduce attendees to the concepts of supercomputing. The main goal is to provide researchers with a firm basis from which to analyze their applications for implementation in a supercomputing environment. After a brief introduction to PSC's supercomputing environment, including the architectures of the CRAY C90 and T3E, various vector and massively parallel programming models, their differences and similarities, their strengths and weaknesses will be discussed. Message passing, performance monitoring, optimization techniques, and heterogeneous supercomputing will be introduced with emphasis on practical considerations. Specific real-world biomedical supercomputing applications will be presented to illustrate these concepts. Finally, a panel discussion will attempt to address researchers' individual application questions. NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS; June 9-14. Emphasis will be on alignment of and pattern extraction from multiple sequences. Topics to be discussed include Comparing and aligning sequences Identifying informative patterns in a set of sequences Using extracted informative patterns to identify related sequences. Leaders are Dr. Gary Churchill, Cornell University; Dr. Michael Gribskov, San Diego Supercomputing Center and Dr. Hugh B. Nicholas, Jr., Pittsburgh Supercomputing Center. METHODS AND APPLICATIONS OF MOLECULAR MECHANICS AND DYNAMICS TO MOLECULES OF BIOLOGICAL INTEREST; August 7-10. Instructors include Dr. David Case, the Scripps Research Institute, Thomas Cheatham, UCSF; Prof. Peter A. Kollman, UCSF, Dr. David A. Pearlman, Vertex Pharmaceuticals; and Bill Ross, UCSF. General aspects of molecular mechanics and dynamics theory and software will be discussed. The program AMBER will be utilized extensively in demonstrations. ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS; Dates TBA. Open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have appreciable experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for analyzing families and superfamilies of genes and proteins. Please fill out the following application form. APPLICATION FORM - Biomedical Workshop Application Deadline: six weeks prior to each workshop. PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE APPLICATION Workshop I am interested in attending:_____________________________________ Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: ___________________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials six weeks before the workshop you are applying for to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From BIOSCI-REQUEST Tue Jan 9 02:00:20 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id CAA01317; Tue, 9 Jan 1996 02:00:20 -0800 Received: (from biohelp@localhost) by net.bio.net (8.6.12/8.6.6) id CAA01301; Tue, 9 Jan 1996 02:00:11 -0800 Date: Tue, 9 Jan 1996 02:00:11 -0800 From: BIOSCI Administrator Message-Id: <199601091000.CAA01301@net.bio.net> To: rna@net.bio.net Subject: BIOSCI miniFAQ, ver. 14-DEC-95 (LAST REVISION: 14-DEC-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/. Contents: -------- 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. 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 in addition to the master index for the entire set. 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 BIOSCI-REQUEST Wed Jan 10 02:58:28 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id CAA26406; Wed, 10 Jan 1996 02:58:28 -0800 Received: from amcada.amc.uva.nl (amcada.amc.uva.nl [145.18.204.34]) by net.bio.net (8.6.12/8.6.6) with ESMTP id CAA26399; Wed, 10 Jan 1996 02:58:19 -0800 Received: from eland.amc.uva.nl by amc.uva.nl (PMDF V4.3-7 #2498) id <01HZUERGKM1S94E30H@amc.uva.nl>; Wed, 10 Jan 1996 11:56:09 +1 Received: by eland.amc.uva.nl (5.x/SMI-5.0) id AA28357; Wed, 10 Jan 1996 11:56:03 +0100 Date: Wed, 10 Jan 1996 11:56:02 +0100 (MET) From: "Paul Sloof (molbio)" Subject: EMBO workshop RNA Editing X-Sender: sloof@eland To: rna@net.bio.net Message-id: X-Envelope-to: rna@net.bio.net MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT EMBO workshop RNA EDITING september 5-8, 1996,Vaeshartelt Castle, Maastricht, The Netherlands organized by Rob Benne and Paul Sloof, Academic Medical Centre University of Amsterdam The scientific program will include: -Insertion/Deletion Editing [Kinetoplastids, Physarum, Paramyxoviruses] -Conversion/Substitution Editing [Plants, Mammals, Viruses] Among the speakers: A.Araya, B.Bass, A.Brennicke, N.Davidson, U.Goeringer, J.Gott, M.Gray, J.Grienenberger, S.Hajduk, T.Innerarity, W.Keller, D.Kolakofsky, H.Koessel, P.Maliga, L.Marechal-Drouard, S.Paabo, W.Schuster, J.Scott P.Seeburg, L.Simpson, B.Sollner-Webb, K.Stuart and J.Yang. Applications by April 15, 1996 with CV and brief summary of current research to: Paul Sloof/Rob Benne, Dept. of Biochemistry, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands. Tel: (3120) 5665159 Fax: (3120) 6915519 Email: p.sloof@amc.uva.nl attendance is limited to 80 participants. The registration fee is Fl.800,- covering full board and lodging. A limited number of fellowships is available. Applicants are asked to indicate whether they wish to present experimental data. They will be notified of their acceptance by May 15, 1996; abstracts for a (poster/oral) presentation are expected before June 28, 1996. From BIOSCI-REQUEST Wed Jan 24 22:33:15 1996 Return-Path: BIOSCI-REQUEST Received: (from daemon@localhost) by net.bio.net (8.6.12/8.6.6) id WAA04229; Wed, 24 Jan 1996 22:33:15 -0800 Received: from reflex.kaist.ac.kr (reflex.kaist.ac.kr [143.248.37.64]) by net.bio.net (8.6.12/8.6.6) with ESMTP id WAA04200; Wed, 24 Jan 1996 22:32:32 -0800 Received: by reflex.kaist.ac.kr (8.6.12H1/940406.SGI.AUTO) for rna@net.bio.net id GAA09329; Thu, 25 Jan 1996 06:29:23 GMT From: haekap@reflex.kaist.ac.kr (Cheong Hae Kap) Message-Id: <199601250629.GAA09329@reflex.kaist.ac.kr> Subject: How can I obtain RNA synthesis reagents? To: rna@net.bio.net Date: Thu, 25 Jan 1996 15:29:22 +0900 (KST) X-Mailer: ELM [version 2.4 PL21-h4] Content-Type: text Content-Length: 266 I am here in Korea. I want to synthesize RNA using ABI 391 DNA synthesizer for NMR study. I want RNA monomers and columns with 2'-OH protected by dimethy-tertbutyl-silyl group. Please let me know which company make these compounds and how can I contact them.