From owner-embldatabank@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!data-transport.com!scott_jokerst From: scott_jokerst@data-transport.com (R. Scott Jokerst) Newsgroups: bionet.molbio.embldatabank Subject: Bioinformatics resource upgrade. Date: 1 Oct 1996 17:47:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net I wanted to alert you (who were not already aware) to a significant upgrade to the Biological Data Transport bioinformatics resource. Among other things, the Query Depot was launched over a month ago. And it has been upgraded weekly based on your feedback. http://www.data-transport.com From this resource, several kinds of bioinformatics related searches can be executed - to GenBank, the MEDLINE molecular biology subset, OMIM, Entrez, the BCM Search Launcher, PDB, BLAST, GDB, etc. Direct searching of several life sciences vendor resources are available as well, all in one centralized location. We've simplified the UI to these free public resources significantly - you may find the Query Depot useful when you want to quickly scan for info at the start of your search for information on the Internet. Looking forward to your continued suggestions for additions and changes. Help us to continue making this resource a high value time saver for you, Scott R. Scott Jokerst (510-648-8229) scott_jokerst@data-transport.com Biological Data Transport http://www.data-transport.com Bringing FOCUS to life sciences informatics, product, & services resources From owner-embldatabank@net.bio.net Sat Oct 05 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.embldatabank Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 6 Oct 1996 02:01:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610060900.CAA21844@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-embldatabank@net.bio.net Mon Oct 07 23:00:00 1996 Path: biosci!agate!howland.erols.net!news.sgi.com!esiee.fr!jussieu.fr!oleane!in2p3.fr!swidir.switch.ch!01-newsfeed.univie.ac.at!news.cesnet.cz!rhino.cis.vutbr.cz!risc.upol.cz!decsys.vsb.cz!newsmast From: Respondby@Mail.com (LSAT Productions) Newsgroups: bionet.molbio.embldatabank Subject: !!!!!!!!!!! FREE INTERNET ACCESS !!!!!!!!!!! Date: Fri, 04 Oct 1996 08:23:50 GMT Organization: Home.com Lines: 74 Message-ID: <532hb6$73v@decsys.vsb.cz> Reply-To: Respondby@Mail.com NNTP-Posting-Host: cust104.max22.los-angeles.ca.ms.uu.net X-Newsreader: Forte Agent NS#8 1.0.82 !!!!!!!!!!! FREE INTERNET ACCESS !!!!!!!!!!! NEVER EVER pay for Internet Access AGAIN!!! E-V-E-R! 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Please make checks payable to -> LSAT From owner-embldatabank@net.bio.net Sun Oct 13 23:00:00 1996 Path: biosci!BRIC.POSTECH.AC.KR!mhlee From: mhlee@BRIC.POSTECH.AC.KR (mhlee) Newsgroups: bionet.molbio.embldatabank Subject: help; DNA sequence of Cotesia glomerata virus (Polydnavirus: Bracoviridae) Date: 13 Oct 1996 18:06:00 -0700 Organization: bric Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <326192A9.DB4@bric.postech.ac.kr> Reply-To: mhlee@bric.postech.ac.kr NNTP-Posting-Host: net.bio.net Hello! Is there anybody know the DNA sequence of Cotesia glomerata virus? Thanks in advance. Your Sincerely, Min-Ho Lee. Min-Ho Lee; mhlee@bric.postech.ac.kr Web for the Korean Entomologist(my home page); http://bric.postech.ac.kr/about/mhlee/ From owner-embldatabank@net.bio.net Tue Oct 22 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: scistra@cs.sandia.gov (Sorin C. Istrail) Newsgroups: bionet.molbio.embldatabank Subject: RECOMB 97: CALL FOR POSTERS; LIST OF ACCEPTED PAPERS Date: 23 Oct 1996 00:58:20 +0100 Lines: 233 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <54jn2s$8vj@mserv1.dl.ac.uk> Original-To: embl-db@dl.ac.uk RECOMB 97 NEWS ************** October 22, 1996 1. REMINDER: CALL FOR POSTERS (deadline Oct 25, 96) 2. List of accepted papers to RECOMB 97 ------------------------------------------------ FIRST ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 97) January 20-23, 1997 Eldorado Hotel Santa Fe, New Mexico Sponsored by ACM SIGACT with support from SLOAN Foundation US Department of Energy recomb97@hto.usc.edu http://www.cs.sandia.gov/recomb97 ------------------------------------------- 1. This is a reminder that the deadline for receiving a poster abstract for RECOMB 97 is OCTOBER 25, 1996. This call is for a one page abstract. The actual space for the poseter presentation will be a regular poster space accomodating about 15 pages. Call for RECOMB 97 Posters ************************** Please send a one-page abstract of your Poster including title, authors, affiliation and abstract-text *preferably* via email to recomb97@hto.usc.edu or hard copy to: Professor Michael Waterman RECOMB 97 Program Chair University of Southern California Department of Mathematics, DRB 155 Los Angeles, CA 90089-1113 Deadline for poster abstract submission: October 25, 1996 Notification of acceptance/rejection: November 15, 1996 --------------------------------------------- 2. The List of Accepted Papers for RECOMB 97: ****************************************** Name: Zheng Zhang, William R. Pearson, Webb Miller Title: Aligning a DNA Sequence with a Protein Sequence Name: Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller Title: Progressive Multiple Alignment wtih Constraints Name: Ken Dill, Andrew T. Phillips, J. Ben Rosen Title: Protein Structure Prediction and Potential Energy Landscape Analysis using Continuous Global Minimization Name: Alberto Caprara Title: Sorting by Reversals is Difficult Name: J. Richard Bradley, Steven Skiena Title: Fabricating Arrays of Strings Name: Simon Heath Title: The application of Markov Monte Carlo methods to radiation hybrid mapping Name: Tatsuya Akutsu, Satoru Miyano Title: On the Approximation of Protein Threading Name: Eric L. Anson, Gene Myers Title: ReAligner: A Program for Refining DNA Sequence Multi-Alignments Name: George A. Komatsoulis, Michael Waterman Title: Chimeric alignment by dynamic programing: Algorithm and biological uses Name: Gary A. Churchill Title: Monte Carlo Sequence Alignment Name: Benno Schwikoski, Martin Vingron Title: The Deferred Path Heuristic for the Generalized Tree Alignment Problem Name: Tao Jiang, Richard M. Karp Title: Mapping Clones with a Given Ordering or Interleaving Name: Jamie Cohen, Martin Farach Title: Numerical Taxonomy on Data: Experimental Results Name: Dan Fasulo, Tao Jiang, Richard M. Karp, R. Settergren, E. C. Thayer Title: An Algorithmic Approach to Multiple Complete Digest Mapping Name: Sing-Hoi Sze, Pavel Pevzner Title: Towards 100% Accurate Gene Recognition: Suboptimal and Error-Tolerant Spliced Alignment Name: Ralf Zimmer, Tom Lengauer Title: Fast and Numerically Stable Parametric Alignment of Biosequences Name: Tao Jiang, Lusheng Wang, Dan Gusfield Title: A More Efficient Approximation Scheme for Tree Alignment Name: Serafim Batzogloa, Scott E. Decatur Title: Constant Approximation Algorithm on the Triangular Lattice and Generalized Hydrophobicity for Protein Folding in the Hydrophobic-Polar Model Name: S. Muthukrishnan, Laxmi Parida Title: A highly effective simple combinatorial approach for constructing physical maps by optical mapping Name: Richa Agarwala, V. Dancik, S. Hannenhalli, M. Farach, S. Muthukrishnan, S. Skiena Title: Local Rules for Protein Folding on a Triangular Lattice Name: K. Reinert, Hans-Peter Lenhof, P. Mutzel, K. Mehlhorn, J. D. Kececioglu Title: A Branch-and-Cut Algorithm for Multiple Sequence Alignment Name: Hans-Peter Lenhof Title: New Contact Measures for the Protein Docking Problem Name: Haim Kaplan, Ron Shamir, Robert Tarjan Title: Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals Name: Ying Xu, Edward Uberbacher Title: Reference-based Gene Model Prediction on DNA Contigs Name: B. DasGupta, T. Jiang, S. Kannan, M. Li, Z. Sweekyk Title: On the Complexity and Approximation of Syntenic Distance Name: Mutida Jain, Gene Myers Title: Algorithm for Computing and Integrating Physical Maps Using Unique Probes Name: Gary Benson Title: Sequence Alignment with Tandem Duplication Name: Hiroshi Mamitsuka Title: Supervised Learning of Hidden Markov Models for Sequence Discrimination Name: William Hart Title: On the Computational Complexity of Sequence Design Problems Name: William Hart, Sorin Istrail Title: Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86\% of Optimal Name: David Greenberg, Cynthia Phillips, David Wilson Title: Beyond Islands: Ambiguity in Random Clone-Probe Matrices Name: David Sankoff, V. Ferretti, Joe Nadeau Title: Conserved segment identification Name: John Kececioglu, T. Christof, M. J\"unger, P. Mutzel, G. Reinelt Title: A branch-and-cut approach to physical mapping with end-probes Name: Donna Slonim, L. Kruglyak, L. Stein, Eric Lander Title: Building Human Genome Maps with Radiation Hybrids Name: Bonnie Berger, Mona Singh Title: An Iterative Method for Improved Protein Structural Motif Recognition Name: Fengzhu Sun, Gary Benson, Mike Waterman Title: Pooling Strategies for Establishing Physical Genome Maps Using FISH Name: M. Ogihara, A. Ray Title: Simulating Boolean circuits on a DNA computer Name: M. G. Reese, F. H. Eeckman, D. Kulp, D. Haussler Title: Improved Splice Site Detection in Genie Name: Amir Ben-Dor, Benny Chor Title: On Constructing Hybrid Maps Name: Shili Lin, Terence P. Speed Title: An Algorithm for Haplotype Analysis Name: Tetsuo Shibuya, Hiroshi Imai Title: New Flexible Approaches for Multiple Sequence Alignment Name: Erich Bornberg-Bauer Title: Chain Growth Algorithms for HP-Type Lattice Proteins Name: W Cai, Anne Condon, RM Corn, E Glasser, Z. Fei, T. Frutos, Z. Guo, MG Lagally, Q Lui, LM Smith, A Theil Title: The Power of Surfaced-based DNA Computation ----------------------------------------- See you in Santa Fe, Mike Waterman, Pavel Pevzner and Sorin Istrail From owner-embldatabank@net.bio.net Thu Oct 24 23:00:00 1996 Path: biosci!EXTRA.NCHGR.NIH.GOV!benton From: benton@EXTRA.NCHGR.NIH.GOV (David Benton) Newsgroups: bionet.molbio.embldatabank Subject: Bioinformatics in the news Date: 25 Oct 1996 06:48:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <9610251349.AA14971@extra.nchgr.nih.gov> NNTP-Posting-Host: net.bio.net (With the usual apologies for cross-posting) Colleagues: The Washington Post published a quite laudatory article about Mark Boguski on the first page of the business section today. Congratulations to Mark! -- a few journalistic over-simplifications, for which Mark, I'm sure, is *not* responsible, notwithstanding. The full text of the article can be found at: http://wp1.washingtonpost.com/wp-srv/WPlate/1996-10/25/099L-102596-idx.html Sincerely, David Benton Director, Genome Informatics Program National Center for Human Genome Research, NIH