From owner-bio-matrix@net.bio.net Mon Mar 07 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!news-feed-1.peachnet.edu!umn.edu!msus1.msus.edu!vax1.mankato.msus.edu!vengeance Newsgroups: bionet.molbio.bio-matrix Subject: Omaha Project Message-ID: <1994Mar8.084427.2358@vax1.mankato.msus.edu> From: vengeance@vax1.mankato.msus.edu Date: 8 Mar 94 08:44:27 -0500 Organization: Mankato State University Lines: 9 I am trying to build a list of names and E-Mail addresses of people in the Omaha Nebraska area for a school related project. If you live in Omaha or go to school there or know someone that does and will be around for three months or more, please reply via E-Mail to Vengeance@vax1.mankato.msus.edu. Thank you very much! Ryan Krueger From owner-bio-matrix@net.bio.net Wed Mar 09 22:00:00 1994 Path: biosci!CS.Arizona.EDU!math.arizona.edu!news.Arizona.EDU!hamblin.math.byu.edu!news.byu.edu!gatech!swrinde!sgiblab!rpal.rockwell.com!headwall.Stanford.EDU!nntp!brutlag From: brutlag@cmgm.stanford.edu (Doug Brutlag) Newsgroups: bionet.molbio.bio-matrix Subject: New Submission Deadline for ISMB '94 Conference Followup-To: bionet.molbio.bio-matrix Date: Thu, 10 Mar 94 13:33:58 GMT Organization: Stanford University Lines: 90 Message-ID: Reply-To: ismb@camis.stanford.edu NNTP-Posting-Host: biochem1-fp-dynamic.stanford.edu X-Newsreader: VersaTerm Link v1.1.1 *************** CHANGE IN SUBMISSION DEADLINE ***************** Due to late advertisement and numerous requests, we are changing the deadline for submission of papers to March 25, 1994. Papers must be received by March 25 to be considered. The Second International Conference on Intelligent Systems for Molecular Biology August 15-17, 1994 Stanford University Organizing Committee New Deadlines Russ Altman, Stanford U, Stanford Papers due: March 25, 1994 Doug Brutlag, Stanford U, Stanford Replies to authors: May 6, 1994 Peter Karp, SRI, Menlo Park Revised papers due: June 3, 1994 Richard Lathrop, MIT, Cambridge David Searls, U Penn, Philadelphia Program Committee K. Asai, ETL, Tsukuba A. Lapedes, LANL, Los Alamos D. Benson, NCBI, Bethesda M. Mavrovouniotis, Northwestern U, Evanston B. Buchanan, U of Pittsburgh G. Michaels, George Mason U, Fairfax C. Burks, LANL, Los Alamos G. Myers, U. Arizona, Tucson D. Clark, ICRF, London K. Nitta, ICOT, Tokyo F. Cohen, UCSF, San Francisco C. Rawlings, ICRF, London T. Dietterich, OSU, Corvallis J. Sallatin, LIRM, Montpellier S. Forrest, UNM, Albuquerque C. Sander, EMBL, Heidelberg J. Glasgow, Queen's U., Kingston J. Shavlik, U Wisconsin, Madison P. Green, Wash U, St. Louis D. States, Wash U, St. Louis M. Gribskov, SDSC, San Diego G. Stormo, U Colorado, Boulder D. Haussler, UCSC, Santa Cruz E. Uberbacher, ORNL, Oak Ridge S. Henikoff, FHRC, Seattle M. Walker, Stanford U, Stanford L. Hunter, NLM, Bethesda T. Webster, Stanford U, Stanford T. Klein, UCSF, San Francisco X. Zhang, TMC, Cambridge The Second International Conference on Intelligent Systems for Molecular Biology will take place at Stanford University in the San Francisco Bay Area, August 14-17, 1994. The ISMB conference, held for the first time last summer in Bethesda, MD, attracted an overflow crowd, yielded an excellent offering of papers, invited speakers, posters and tutorials, provided an exciting opportunity for researchers to meet and exchange ideas, and was an important forum for the developing field. We will continue the tradition of pre-published, rigorously refereed proceedings, and opportunities for fruitful personal interchange. The conference will bring together scientists who are applying the technologies of advanced data modeling, artificial intelligence, machine learning, probabilistic reasoning, massively parallel computing, robotics, and related computational methods to problems in molecular biology. We invite participation from both developers and users of any novel system, provided it supports a biological task that is cognitively challenging, involves a synthesis of information from multiple sources at multiple levels, or in some other way exhibits the abstraction and emergent properties of an "intelligent system." The four-day conference will feature introductory tutorials (August 14), presentations of original refereed papers and invited talks (August 15-17). Paper submissions should be single-spaced, 12 point type, 12 pages maximum including title, abstract, figures, tables, and bibliography with titles. The first page should include the full postal address, electronic mailing address, telephone and FAX number of each author. Also, please list five to ten keywords describing the methods and concepts discussed in the paper. State whether you wish the paper to be considered for oral presentation only, poster presentation only or for either presentation format. Submit 6 copies to the address below. For more information, please contact ismb@camis.stanford.edu. Proposals for introductory tutorials must be well documented, including the purpose and intended audience of the tutorial as well as previous experience of the author in presenting such material. Those considering submitting tutorial proposals are strongly encouraged to submit a one-page outline, before the deadline, to enable early feed-back regarding topic and content suitability. The conference will pay an honorarium and support, in part, the travel expenses of tutorial speakers. Limited funds are available to support travel to ISMB-94 for those students, post-docs, minorities and women who would otherwise be unable to attend.. Please submit papers and tutorial proposals to: Intelligent Systems for Molecular Biology c/o Dr. Douglas L. Brutlag Beckman Center, B400 Department of Biochemistry Stanford University School of Medicine Stanford, California 94305-5307 From owner-bio-matrix@net.bio.net Sat Mar 12 22:00:00 1994 Newsgroups: bionet.molbio.bio-matrix Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!agate!library.ucla.edu!csulb.edu!csus.edu!netcom.com!rhaimann From: rhaimann@netcom.com (Richard Haimann) Subject: Ph.D. Research - fuzzy biotech Message-ID: Organization: NETCOM On-line Communication Services (408 241-9760 guest) X-Newsreader: TIN [version 1.2 PL1] Date: Sat, 12 Mar 1994 19:41:09 GMT Lines: 39 Hello netters, I'm interested in pursuing a Ph.D. in biotechnology/artificial intelligence and decision systems. I'm currently working an as an environmental engineering consultant. I'm interested in applying fuzzy logic to the monitoring, operation, predictive modeling, and design of engineered biological systems. Such systems include waste-water treatment systems, systems which biodegrade recalcitrant chemicals, agricultural production systems, food production systems such as fermentation and biosolids production systems, pharmaceutical production systems, biomedical engineering systems, air and water recycling systems for space exploration, and a myriad host of others. I've pretty good GRE scores and previous undergraduate and graduate grades plus some business skills learned in consulting (good for writing grants). My quandry is this: this Ph.D. research is multidepartmental in nature. Where are there schools which have significant expertise in both engineered biological systems and artificial intelligence/decision systems and where the political climate is conducive to interdepartmental research. Thanks in advance. Richard rhaimann@netcom.com -- |///////////////////////\\\\\\\\\\\\\\\\\\\\\\\\\\\| | Richard Haimann Reachable at: | |(home) rhaimann@netcom.com | |(work)___CH2MHILL!SCO!RHAIMANN@ch2m1.attmail.com__| From owner-bio-matrix@net.bio.net Tue Mar 15 22:00:00 1994 Newsgroups: bionet.molbio.bio-matrix Path: biosci!lhc!lhc!hunter From: hunter@work.nlm.nih.gov (Larry Hunter) Subject: Re: Ph.D. Research - fuzzy biotech In-Reply-To: rhaimann@netcom.com's message of Sat, 12 Mar 1994 19:41:09 GMT Message-ID: Sender: news@nlm.nih.gov Reply-To: Hunter@nlm.nih.gov Organization: National Library of Medicine References: Date: 16 Mar 1994 14:54:56 GMT Lines: 62 Richard Haimann asked about PhD programs in AI & Molecular Biology. Here is my list of schools offering computational biology programs. Most of these have strong AI components (except where noted). There are, of course, many schools with good programs in both molecular biology and AI, but that do not have explicit interdisciplinary degree programs (e.g. MIT). You may want to consider them as well. Good luck! Larry * University of Pittsburgh (in conjunction with Carnegie Mellon). A new program in computational biology, funded by the Keck Foundation. For information on that program, contact Bruce Buchanan (buchanan@cs.pitt.edu). * George Mason University. A new program in Computational Science and Informatics. [I am currently teaching the bioinformatics course there.] For more information, contact Harold Morowitz (hmorowitz@gmuvax.gmu.edu) or John Evans (jevans@gmuvax2.gmu.edu). * Washington State University, Pullman. A program in computational science including biology that has been going for at least three years. For more information, contact Keith Dunker (dunker@bobcat.csc.wsu.edu). [not much AI] * W.M. Keck Center for Computational Biology, in Houston, TX. A collaborative effort between Rice University, Baylor College of Medicine, and the University of Houston, has been offering graduate studies in computational biology since 1990. For more information, contact George Phillip, Jr. (georgep@rice.edu) [not much AI] * Washington University, St. Louis. They have just instituted a new Institute for Biological Computing, which will begin admitting students next fall. For more information contact David States (states@wucs1.wustl.edu). * Stanford Medical School. One of the nation's best medical informatics programs, recently hired Russ Altman to teach computational biology. For information, contact Ted Shortliffe (shortliffe@sumex-aim.stanford.edu) * University of California, San Diego. Computational biology has been an active research area for several years in the departments of computer science and biology, and with the NSF San Diego Supercomputer Center. Graduate fellowships are available through an NIH Human Genome Training Grant. For more information, contact Doug Smith (dmsith@ucsd.edu). And there are many departments of computer science or biology which offer the possibility of pursuing studies in computational biology. This is certainly not an exhaustive list. My appologies to anyone I left out; I welcome updates and corrections! Larry -- Lawrence Hunter, PhD. National Library of Medicine Bldg. 38A, MS-54 Bethesda. MD 20894 USA tel: +1 (301) 496-9300 fax: +1 (301) 496-0673 internet: hunter@nlm.nih.gov encryption: public key via RIPEM server or "finger hunter@work.nlm.nih.gov" From owner-bio-matrix@net.bio.net Tue Mar 29 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!concert!hearst.acc.Virginia.EDU!portal.gmu.edu!csi.gmu.edu!mark From: mark@csi.gmu.edu (Mark) Newsgroups: bionet.molbio.bio-matrix Subject: Russian Biological Database Workshop Date: 29 Mar 1994 23:28:59 GMT Organization: George Mason University, Fairfax, Virginia, USA Lines: 152 Message-ID: <2nadjr$1oa@portal.gmu.edu> NNTP-Posting-Host: csi.gmu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: TIN [version 1.2 PL2] An Informal Workshop Biological Database Integration June 8 - June 10, 1994 Pushchino, Russia We invite friends and colleagues interested in the integration of biological databases to join us for an informal workshop in Pushchino, Russia, in late spring. There are substantial benefits be gained by successfully integrating existing biological databases. There are numerous Russian databases that need cross referencing with Western counter parts. Toward this end, we wish to foster an environment in which researchers exchange insights, data, and tools. This particular meeting will focus on topics relating to metabolism, since the new availability of DBEMP --- with its extensive encoding of the literature relating to metabolism --- will offer numerous categories of data that have not been available before. In addition, we will invite a number of representatives from the Russian scientific community to discuss their biological databases. It is, perhaps, worth noting that the Russian scientific community developed a major computational infrastructure similar to that which has developed in Europe, America and Japan. They created substantial collections of data ranging from small efforts done by single experts curating a limited class of data to huge collections on topics like metabolism, medicinal properties of compounds, 3D structural data, sequence data, culture collections, and genetic markers. We intend to provide a framework where the contents of these databases can be discussed examined, and compared with what is currently available in Europe and America. The meeting will be hosted by Evgenii Selkov, the leader of the team that has developed DBEMP over the past decade (the team now includes 24 individuals). The registration fee ($550 US), will cover housing and meals, as well as transportation to and from the Moscow airport (Pushchino is about 100 kilometers or so south of Moscow). In addition, each participant will be given a coupon worth $400 towards a purchase of DBEMP (normally sold at $400 for individuals and $4000 for commercial users). The database includes a detailed encoding of all of the quantitative data in over 10,000 articles on metabolism and enzymes. Graphical representations of the pathways described in DBEMP will also be available. A Prolog version of the pathways will also be made available, and we should be able to recast it to any other desired format on machines that will be available at the workshop. This meeting will not feature scheduled talks; rather, instead we envision organizing impromptu discussions on topics of common interest relating to the goal of integrating Russian biological databases with other international databases. We anticipate a fair amount of discussion relating to metabolism and enzymes, but other topics such as availability and exchange of data relating to phylogeny, alignments, compounds, motifs, and maps will certainly come up. We expect to spend about half of the time discussing the contents, use and how to curate the DBEMP, with its encoding of 10,000 articles on metabolism and enzymes. Informal presentations on the contents of this database, on how it can be connected to existing databases, and how it can be used to address specific computational problems will be discussed. We plan on offering tables that interrelate records in the DBEMP with specific enzyme numbers, specific organisms, and specific metabolic pathways. The remainder of the meeting will include poster sessions and informal demos by representatives of other database efforts within the FSU. We hope to include a number of the larger efforts, including databases relating to sequence analysis, the study of proteins, human genetics, medicine, and pharmacology. If you are actively involved in either the generation or use of integrated biological data, we urge you to consider joining us. Workshop supporters: Chris Beecher Anthony Bonner Terry Gaasterland Pat Gillevet Nat Goodman Niels Larsen Natalia Maltsev George Michaels Harold Morowitz Ross Overbeek Evgenii Selkov Rick Stevens Alexander Zamyatnin Registration Information The workshop is limited to 125 participants. To register for this workshop, complete the registration form and mail with your check made payable to George Mason University, or credit card authorization to: Center for Professional Development Business Office, Mail Stop 3G3 George Mason University Fairfax, VA 22030-4444 To register by FAX, fill out the form below and send it via FAX to 703/993-2112. Follow up by mailing the original enrollment form with your payment. Registration fees must be received by May 30, 1994. For further registration information, please call the Center for Professional Development at (703)993-2090. Center for Professional Development Mail Stop 3G3 Fairfax, Virginia 22030-4444 Workshop Questions can be directed to either Ross Overbeek (overbeek@mcs.anl.gov) George Michaels (gmichael@mason1.gmu.edu) *********************************************************************** NOTE: If you would like to use Mosaic to register for this conference, the URL is: "http://csi.gmu.edu/gsm/ConferenceForm.html" *********************************************************************** Russian Metabolic Database Conference Registration first_name = last_name = e-mail = title = organization = address = city = state = zip = phone = fax = payment_method = CHECK, MASTERCARD, VISA payment_amount = $550 Credit Card Authorization Credit Card Number: Expiration Date: Cardholder Name: Date: Authorizing Signature: From owner-bio-matrix@net.bio.net Wed Mar 30 23:00:00 1994 Path: biosci!mii.lu.lv!mahinovs From: mahinovs@mii.lu.lv (Jurijs Mahinovs) Newsgroups: bionet.molbio.bio-matrix Subject: help Date: 31 Mar 1994 01:14:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199403310914.AA14171@circenis.mii.lu.lv> NNTP-Posting-Host: net.bio.net help