From owner-genome-program@net.bio.net Sun Nov 03 22:00:00 1996 Path: biosci!biosci!not-for-mail From: marketing@wwwebmaster.com Newsgroups: bionet.molbio.genome-program Subject: Help?: 2 Genetics questions Date: 4 Nov 1996 13:08:40 -0800 Organization: Seanet Online Services, Seattle WA Lines: 21 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Thank you in advance for your time- Two Genetics questions: ONE: I am looking for references and information regarding the implementation of genetic testing in the Olympics. This relates to the extra sex chromosome (Y) that East German females were discovered to have that gave them an unfair advantage and, are now prohibited from competetion. TWO: Any research references relating to genetic traits and Criminal behavior THANK YOU Any references or information can be sent to: Kevin_Corbett@everett.wednet.edu From owner-genome-program@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!biosci!not-for-mail From: sigurd.orstavik@basalmed.uio.no (Sigurd rstavik) Newsgroups: bionet.molbio.genome-program Subject: EST Database Question Date: 8 Nov 1996 07:07:14 -0800 Organization: Universitet i Oslo Lines: 10 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <55uu7b$7q9@ratatosk.uio.no> NNTP-Posting-Host: net.bio.net Hi! I have a question concerning the EST database. Of the sequences submitted to the EST database, how large proportion of them would we expect to be expressed (not only transcribed, but encoding real proteins). I anyone could answear my question, I would appreciate it. Sigurd Orstavik From owner-genome-program@net.bio.net Sun Nov 10 22:00:00 1996 Path: biosci!biosci!not-for-mail From: "Patricia A. Foster" Newsgroups: bionet.molbio.genome-program Subject: RH Transcript Maps in GDB Date: 11 Nov 1996 13:48:31 -0800 Organization: Genome Database Lines: 13 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <5686vf$8mu@net.bio.net> NNTP-Posting-Host: net.bio.net 11-Nov-96 Whole Genome Transcript Maps from SCIENCE The whole genome transcript maps published in Science (Schuler et al., 1996) and displayed in GDB at the ASHG meeting in San Francisco,have now been loaded into the GDB production database (http://gdbwww.gdb.org/). These maps can be viewed using GDB's Mapview helper application. You can find the list of maps at http://gdbwww.gdb.org/gdb-bin/genera/genera/hgd/IntegratedMap?!action=query& displayName=RH* From owner-genome-program@net.bio.net Tue Nov 12 22:00:00 1996 Path: biosci!biosci!not-for-mail From: "E. Kolker" Newsgroups: bionet.molbio.genome-program Subject: Conf.on Mathematical and Computer Modelling and Scientific Computing Date: 13 Nov 1996 05:38:13 -0800 Organization: University of Washington Lines: 84 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: References: <199610242019.QAA03581@stc06.ctd.ornl.gov> NNTP-Posting-Host: net.bio.net ANNOUNCEMENT AND CALL FOR PAPERS Computational Biology Session: "Computing in the Genome Era" Eleventh International Conference on Mathematical and Computer Modelling and Scientific Computing March 31 - April 3, 1997 Georgetown University Conference Center Washington, DC, USA The Eleventh International Conference on Mathematical and Computer Modelling and Scientific Computing is scheduled to take place March 31 - April 3, 1997 at the Georgetown University Conference Center, Washington, DC, U.S.A. Plenary lectures by world-renowned scientists and sessions on many recent developments in engineering and sciences comprise a long-standing tradition at the ICMCM's. Mathematical and computer modelling and scientific computing have become powerful tools for solving complex problems and providing greater insights into the future. The objective of the conference is to bring together researchers from various disciplines including the traditional and emerging areas of engineering and sciences for cross-fertilization of ideas and exchange of information. The objective of the Computational Biology Session "Computing in the Genome Era" is to discuss the current state of computational biology, its approaches, methods, general problems, achievements, and future developments with emphasis on sequence research and analysis for the Genome Projects. Speakers of the session include: S. Altschul (NCBI, NIH, Bethesda), A. Bairoch (Geneva Univ., Switzerland), W. Gish (Wash. Univ., St. Louis), P. Green (Univ. of Wash., Seattle), S. Henikoff (FHCRC, HHMC, Seattle), L. Hood (Univ. of Wash., Seattle), E. Koonin (NCBI, NIH, Bethesda), D. Searls (SmithKline Beecham, King of Prussia), E. Trifonov (Weizmann Inst., Israel). Papers (Abstracts) are invited on all relevant aspects of computational biology for presentation at the session, to be selected on competitive basis by a steering committee. One-page abstracts (about 200 words) should clearly describe the work and its conclusions. Full length manuscripts (limited to six pages) of papers presented at the conference will be published in the Conference Proceedings, in a special issue of the journal MATHEMATICAL MODELLING AND SCIENTIFIC COMPUTING, Vol. 8, 1997 (ISSN 1067-0688). The manuscripts for the special issue are due June 15, 1997. The special issue of the journal will be published by September 1997. All participants shall pay the registration fee (pre-registration before February 15, 1997: IAMCM or IMACS members - $330, non-members - $375, graduate students - $210, undergraduate students - $175). Abstracts may be submitted in hard copy or via fax or by e-mail (preferred!) under subject "Abstract". The abstracts must be formatted to fit on 8-1/2 x 11 inch (approximately 21.5 cm x 28 cm or European Standard A-4 size) paper, typed in single space. The title must be capitalized and centered followed by the author's name(s), institution, and full address, including fax and e-mail. Send two copies (ONE copy if sent by fax or e-mail) of the abstract to the session organizer BEFORE November 30, 1996: Eugene Kolker Dept of Molecular Biotechnology and Genome Center Box 357730, University of Washington Seattle, WA 98195-7730, USA Fax: +1-206-685-7301 E-mail: egn@u.washington.edu Important dates: Closing date for receiving abstracts: November 30, 1996 Notification of acceptance: December 27, 1996 The Computational Biology Session is sponsored by SILICON GRAPHICS. Companies are welcome to participate in the session, present their tools and products, and/or co-sponsor the session. The Web site for the session is under contruction and will include information on the session, a list of related sites, links to the sponsors etc. From owner-genome-program@net.bio.net Tue Nov 12 22:00:00 1996 Path: biosci!biosci!not-for-mail From: bkq@ornl.gov Newsgroups: bionet.molbio.genome-program Subject: New NIH NCHGR RFA Date: 13 Nov 1996 09:37:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 509 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <199611131535.KAA17256@stc06.ctd.ornl.gov> NNTP-Posting-Host: net.bio.net ================================================================= TECHNOLOGIES FOR GENOME ANALYSIS NIH GUIDE, Volume 25, Number 38, November 8, 1996 RFA: HG-97-001 P.T. 34; K.W. 1215018, 0755045 National Center for Human Genome Research Letter of Intent Receipt Date: February 27 1997 Application Receipt Date: March 27, 1997 PURPOSE The purpose of this Request for Applications (RFA) is to stimulate the development of genomic-scale technologies for the study of genome function and sequence variation. Within the next decade, it is anticipated that the complete DNA sequences of the human and numerous model organisms will be determined and available for comprehensive analysis. The next challenge lies in systematically decoding the genomic information, e.g., finding all the genes and understanding how their gene products function; defining common alleles and haplotypes, and associating them with phenotypes; and analyzing the conservation of genes and other features among species. Such analyses will facilitate the understanding of biological processes important in human health and disease, and the development of improved diagnoses, preventative strategies and therapies. The tools needed to analyze genomic DNA efficiently are just beginning to emerge and many more robust technologies are needed. The Human Genome Project has been successful in generating information and resources rapidly and economically, in part, by developing and applying high-throughput and efficient technologies. Therefore, the National Center for Human Genome Research (NCHGR) seeks the development of technologies that can be applied in similar ways to the rapid and efficient analysis of genome function and sequence variation. HEALTHY PEOPLE 2000 The Public Health Service (PHS) is committed to achieving the health promotion and disease prevention objectives of "Healthy People 2000," a PHS-led national activity for setting priority areas. This RFA, Technologies for Genome Analysis, is related to the priority areas of cancer, heart disease and stroke, diabetes and chronic disability conditions, and maternal and infant health. Potential applicants may obtain a copy of "Healthy People 2000" (Full Report: Stock No. 017-001-00474-0 or Summary Report: Stock No. 017-001-00473-1) through the Superintendent of Documents, Government Printing Office, Washington, DC 20402-9325 (telephone 202-512-1800). ELIGIBILITY REQUIREMENTS Applications may be submitted by domestic for-profit and non-profit organizations, public and private, such as universities, colleges, hospitals, laboratories, companies, units of State and local governments, and eligible agencies of the Federal government. Applications from social/ethnic minority individuals, women, and persons with disabilities are encouraged. Applications from foreign institutions will not be accepted. However, subcontracts to foreign institutions are allowable, with sufficient justification. MECHANISM OF SUPPORT This RFA will use the National Institutes of Health (NIH) individual research project grant (R01), program project grant (P01) and exploratory/developmental grant (R21) mechanisms. The total project period for an application submitted in response to this RFA may not exceed three years and the direct cost per year for research project (R01) or program project (P01) grants may not exceed $500,000. Exploratory/developmental (R21) grants will be limited to $100,000 direct costs per year for a maximum of two years. The R21 mechanism is used to support highly creative approaches for which substantial preliminary data are not yet available. Specific information about the R21 grant mechanism can be found in the NCHGR Program Announcement PAR-94-046, "Pilot Projects or Feasibility Studies for Genomic Analysis." The R21 grants are not renewable, but future project continuation is possible through other grant mechanisms such as the R01 or P01. Responsibility for the planning, direction, and execution of the proposed project will be solely that of the applicant. Awards will be administered under PHS grants policy as stated in the Public Health Service Grants Policy Statement. Future unsolicited competing continuation applications will compete with all investigator-initiated applications and will be reviewed according to the customary peer review procedures. The anticipated award date is September 30, 1997. FUNDS AVAILABLE It is anticipated that approximately $5 million (total costs) will be available for this initiative in fiscal year 1997. Awards pursuant to this RFA are contingent upon the availability of funds for this purpose. The amount of funding for these projects may be increased if a large number of highly meritorious applications are received and if funds are available. Only applications found to be of high scientific merit will be considered for funding and all of the funds will not be spent if there are not enough highly meritorious applications. Funding in future years will be subject to the availability of funds. Because the scope of the research proposed in response to this RFA encompasses the interest of several NIH Institutes and Centers, applications may receive dual assignments based on the established PHS referral guidelines. RESEARCH OBJECTIVES Background The entire DNA sequence of the genomes of several microorganisms, including prokaryotes (H. influenzae and M. genitalium), an archeon (M. jannaschii), and a eukaryote (S. cerevisiae) have recently been determined. Rapid progress has also been made in mapping and sequencing more complex genomes, leading to the expectation that, within the next two to nine years, the DNA sequence of the genomes of C. elegans, D. melanogaster, the human, and perhaps others will be finished. The availability of this information will usher in a new era in biomedical research. A complete genomic DNA sequence comprises the bounded set of genetic instructions of an organism. Once it has been determined, investigators will have access to every genetic element of that organism. This capability opens unparalleled opportunities to study both genomic function and sequence variation. Understanding both function and sequence variation is essential for a comprehensive understanding of the biology of an organism. The amount of information represented by genomic sequence and the underlying clone and map data is enormous, and investigators will need a wide variety of very robust techniques to make maximal use of these new resources. At present, however, the technology for making use of and interpreting the complete genetic "blueprints" is rather limited. Novel and improved technologies, developed to be cost-efficient and applicable at a large scale, have, in large measure, been responsible for the success of the Human Genome Project in producing detailed genomic maps and large amounts of DNA sequence. Analogous "genomic-scale" technologies will be required for the interpretation of the genomic sequence. Although several of these are beginning to emerge, they require further development; beyond them, many more novel approaches are needed. Objectives and Scope The purpose of this RFA is to stimulate the development of novel "genomic-scale" technologies for the study of genomic function and sequence variation. Through this solicitation, NCHGR intends to stimulate the development and implementation of innovative technologies that will facilitate, among other things, the elucidation of the biological roles of gene products and non-coding functional elements; the interactions among functional elements in the cell; the biological consequences of genome organization; the dynamics of polymorphisms in populations; and the functional significance of genomic variation. This RFA is intended to support the development of technologies that will take advantage of the genomic maps and DNA sequences for use in systematic and comprehensive approaches to the study of genomic function and sequence variation. The technologies needed for these analyses are those that are scaleable, rapid, efficient and take advantage of economies of scale. It is envisioned that when such technologies are applied to large-scale analyses, a genome will become annotated with biologic information that will, in turn, serve as a platform for more in-depth, detailed studies. The "process" of technology development can be considered to span a spectrum of stages. Initially, it involves the development of an entirely new methodology (or the significant improvement of an existing methodology) to the point of proof of principle. The method must then be reduced to practice. For such a new method to have a significant impact for genomic studies, it must also be shown that it can be used efficiently on a large-scale, or genomic basis, which requires another level of technology development. This RFA is intended to solicit applications that address any of these phases of technology development. The NCHGR will give priority to the development of technologies that will be used to study the human genome and/or the genomes of S. cerevisiae, C. elegans, D. melanogaster and M. musculus. Technology development projects that utilize other eukaryotic organisms will be considered, but direct applicability of these technologies to the analysis of the human genome must be evident. An important feature of any newly-developed technology will be the ease with which it can be exported into other laboratories, or in other ways made readily accessible to investigators. The development of computational methods for the study of genomic function and variation is encouraged under this solicitation. Local databases necessary to conduct research funded under this RFA will be supported. The development of public, national databases, however, will not be supported under this RFA. In addition, applications proposing to analyze a particular gene, gene product or non-coding functional element will not be considered under this RFA. This RFA seeks applications to develop efficient technologies (both experimental and computational) for, but not limited to, the following areas: o development of single nucleotide polymorphisms in human DNA for genome-wide mapping; o identification and analysis of sequence variations within and among species to study normal and disease states in humans, and evolution; o identification of all functional elements (both coding and non-coding) in the genome; o analysis of the biological role that non-coding functional elements play in the cell; o analysis of expression of gene products (RNA and/or proteins), e.g., measurement of steady-state levels of gene products in a given cell type, temporal or induced changes in patterns of gene product levels, or comparative levels of gene product in different cell types; o analysis of the biological role that gene products (RNA and/or proteins) play in the cell, e.g., analysis of cellular localization of proteins, protein-protein or protein-nucleic acid interactions or comparative analysis of protein sequences and/or structures; and o analysis of genome organization and its effect on cellular functions. These examples are illustrative and should not be viewed as limiting in any way. Novel and innovative technologies to all areas of genome analysis are sought. Applicants should address the following issues: o advantages of the proposed approach over existing approaches; o value of the technology in furthering the understanding of eukaryotic biology; and o plans for making data and resources broadly accessible. The sharing of materials and data in a timely manner has been an essential element in the rapid progress made in genome research. Public Health Service (PHS) policy requires that investigators make the results and accomplishments of funded activities publicly available. The advisors to the NIH and the DOE genome programs have developed a set of guidelines for making data and material resources available to the scientific community in a timely manner. The guidelines call for material and information from genome research to be made available within six months of the time the data or materials are generated; more rapid sharing is encouraged and has become the norm in the genome community. Applications submitted in response to this RFA should include detailed plans for sharing data and materials generated through the grant. Where appropriate, grantees may work with the private sector in making unique resources available to the larger biomedical research community at a reasonable cost. The plans proposed for sharing and data release will be reviewed for adequacy by NIH staff prior to award of the grant and the proposed sharing plan will be made a condition of the award. Applicants may request funds to defray the costs of sharing materials or submitting data. Such requests must be adequately justified. Recently, it has become evident that special human subjects issues are raised by the large-scale sequencing of human genomic DNA because large amounts of DNA sequence information from single individuals may be generated. The NCHGR and the DOE have recently issued a document, "Guidance on Human Subjects Issues in Large-Scale DNA Sequencing" to address these issues. This document can be found on the NCHGR Home Page (http://www.nchgr.nih.gov/Grant_info/Funding/Statements/large_scale.h tml). As a result of the research supported under this RFA, it is possible that an analogous situation might exist, i.e., that a large amount of information about a single individual's genome might be generated and be made publicly available. Applicants should address these special human subjects issues, if applicable. LETTER OF INTENT Because of the specialized interest of this RFA, prospective applicants are strongly encouraged to discuss their research objectives and the appropriate grant mechanism with NIH staff. Prospective applicants are asked to submit, by February 27, 1997, a letter of intent that includes a descriptive title of the proposed research, the name, address, and telephone number of the principal investigator, and the identities of other key personnel and participating institutions. Although a letter of intent is not required, is not binding, and does not enter into the review of subsequent applications, the information that it contains allows NCHGR staff to estimate the potential review workload and to avoid conflict of interest in the review. The letter of intent is to be sent to: Elise Feingold, Ph.D. Division of Extramural Research National Center for Human Genome Research Building 38A, Room 614, MSC 6050 Bethesda, MD 20892-6050 Telephone: (301) 496-7531 FAX: (301) 480-2770 Email: Elise_Feingold@nih.gov APPLICATION PROCEDURES The research grant application form PHS 398 (rev. 5/95) is to be used in applying for these grants. Applications kits are available at most institutional offices of sponsored research and may be obtained from the Grants Information Office, Office of Extramural Outreach and Information Resources, National Institutes of Health, 6701 Rockledge Drive, MSC 7910, Bethesda, MD 20892-7910, telephone 301/435-0714, email: ASKNIH@odrockm1.od.nih.gov; and from the program director listed under INQUIRIES. The RFA label available in the PHS 398 (rev. 5/95) application form must be affixed to the bottom of the face page of the application. Failure to use this label could result in delayed processing of the application such that it may not reach the review committee in time for review. In addition, the RFA title and number must be typed on line 2 of the face page of the application form and the YES box must be marked. Submit a signed, typewritten original of the application and three signed photocopies, in one package to: Division of Research Grants National Institutes of Health 6701 Rockledge Drive, Room 1040 - MSC 7710 Bethesda, MD 20892-7710 Bethesda, MD 20817 (for express/courier service) At the time of submission, two additional copies of the application, including appendices, must also be sent to: Dr. Ken Nakamura Office of Scientific Review National Center for Human Genome Research Building 38A, Room 613, MSC 6050 38 Library Drive Bethesda, MD 20892-6050 Applications must be received by March 27, 1997. If an application is received after that date, it will be returned to the applicant without review. The Division of Research Grants (DRG) will not accept any application in response to this RFA that is essentially the same as one currently pending initial review, unless the applicant withdraws the pending application. The DRG will not accept any application that is essentially the same as one already reviewed. This does not preclude the submission of substantial revisions of applications already reviewed, but such applications must include an introduction addressing the previous critique. The applicants should also ensure that their revised applications respond to the review criteria by which the applications in response to this RFA will be evaluated. REVIEW CONSIDERATIONS Upon receipt, applications will be reviewed for completeness by DRG and for responsiveness to the RFA by NIH program staff. Incomplete applications will be returned to the applicant without further consideration. If the application is not responsive to the RFA, NIH staff will contact the applicant to determine whether to return the application to the applicant or submit it for review in competition with unsolicited applications at the next review cycle. Those applications that are complete and responsive will be evaluated for scientific/technical merit in accordance with the criteria stated below by an appropriate peer review group convened by the NCHGR. As part of the initial merit review, all applications will receive a written critique and may undergo a process in which only those applications deemed to have the highest scientific merit will be discussed and assigned a priority score. All applications will receive a second level of review by the National Advisory Council for Human Genome Research. Review criteria will include: o scientific and technical merit of the proposed research; o extent to which the experimental approach makes use of and/or adds value to the complete genomic sequence; o value of the forthcoming data and/or technology in furthering the understanding of eukaryotic biology; o value and exportability of the forthcoming methodologies and resources (for software tools, portability at the source code level); o likelihood that the technology will be able to scale to a genomic level efficiently and in a timely manner; o qualifications and research experience of the principal investigator and staff in the area of the proposed research; o availability of the resources necessary to perform the research; o appropriateness of the proposed budget and duration in relation to the proposed research; o adequacy of plans for dissemination of software tools developed under grant support; o adequacy of plans to place data and/or material resources in the public domain in a timely manner; and o adequacy of plans to protect human subjects, if applicable. For R21 applications, preliminary data are not required. However, the applicant does have the responsibility for developing a sound research plan and for presenting any other information that can be considered as evidence of feasibility. AWARD CRITERIA The earliest anticipated date of award is September 30, 1997. Factors that will be used to make award decisions are: o quality of the proposed project as determined by peer review; o balance among the projects in addressing different experimental approaches and their complementarity to other ongoing efforts; o adequacy of data/material release plan; and o availability of funds. Post-award Management During the course of the grant period, technologies will improve and the rate of progress and focus of work supported by the grant(s) may change. It is expected that the principal investigator(s) will make any necessary adjustments in scientific direction to accommodate the changing environment. During the course of the award period, the principal investigator(s) may be invited to meet with NIH program staff in Bethesda, MD to review scientific progress. Other scientists external to and knowledgeable about these studies may also be invited to participate. INQUIRIES Written and telephone inquiries concerning this RFA are encouraged. The opportunity to clarify any issues or questions from potential applicants is welcome. Direct inquiries regarding programmatic issues to: For biological research projects on genome function: Elise Feingold, Ph.D. Division of Extramural Research National Center for Human Genome Research 38 Library Drive, Room 614 - MSC 6050 Bethesda, MD 20892-6050 Telephone: (301) 496-7531 FAX: (301) 480-2770 Email: Elise_Feingold@nih.gov For biological research projects on sequence variation: Bettie J. Graham, Ph.D. Division of Extramural Research National Center for Human Genome Research 38 Library Drive, Room 614 - MSC 6050 Bethesda, MD 20892-6050 Telephone: (301) 496-7531 FAX: (301) 480-2770 Email: Bettie_Graham@nih.gov For all computational research projects: David Benton, Ph.D. Genome Informatics Program National Center for Human Genome Research 38 Library Drive, Room 614 - MSC 6050 Bethesda, MD 20892-6050 Telephone: (301) 496-7531 FAX: (301) 480-2770 Email: David_Benton@nih.gov Direct inquiries regarding fiscal matters to: Ms. Jean Cahill Grants Management Office National Center for Human Genome Research Building 38A, Room 613, MSC 6050 Bethesda, MD 20892-6050 Telephone: (301) 402-0733 FAX: (301) 402-1951 Email: Jean_Cahill@nih.gov AUTHORITY AND REGULATIONS This program is described in the Catalog of Federal Domestic Assistance No. 93.172. Awards are made under authorization of the Public Health Service Act, Title IV, Part A (Public Law 78-410, as amended by Public Law 99-158, 42 USC 241 and 285) and administered under PHS grants policies and Federal Regulations 42 CFR 52 and 45 CFR Part 74. This program is not subject to the intergovernmental review requirements of Executive Order 12372 or Health Systems Agency review. The PHS strongly encourages all grant and contract recipients to provide a smoke-free workplace and promote the non-use of all tobacco products. In addition, Public Law 103-227, the Pro-Children Act of 1994, prohibits smoking in certain facilities (or in some cases, any portion of a facility) in which regular or routine education, library, day care, health care or early childhood development services are provided to children. This is consistent with the PHS mission to protect and advance the physical and mental health of the American people. From owner-genome-program@net.bio.net Mon Nov 18 22:00:00 1996 Path: biosci!biosci!not-for-mail From: BIOSCI Administrator Newsgroups: bionet.molbio.genome-program Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Nov 1996 06:47:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 240 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <199611191000.CAA16159@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-genome-program@net.bio.net Thu Nov 21 22:00:00 1996 Path: biosci!biosci!not-for-mail From: David Gilbert Newsgroups: bionet.molbio.genome-program Subject: Research positions offered in Biotechnology/BioInformatics [corrected Date: 22 Nov 1996 06:54:17 -0800 Organization: School of Informatics, City University, London Lines: 82 Sender: daemon@net.bio.net Approved: k76@ornl.gov Distribution: world Message-ID: <574eqp$eqv@net.bio.net> NNTP-Posting-Host: net.bio.net Research positions offered in Biotechnology: Marie Curie Grants, Training and Mobility of Researchers, Framework 4 Department of Computer Science School of Informatics City University London, UK Applications are invited for research positions at both post-doctorate and also post-graduate level in the field of computational biotechnology at the department of Computer Science, City University. Areas of particular research interest within this field include -- Genome analysis -- Structural biology -- Bioinformatics and specifically -- the application of computational logic and constraint technology to bioinformatics in general and genome analysis in particular -- evolutionary development of structures Individuals would be funded by the European Community under Marie Curie Fellowships provided by the Training and Mobility of Researchers (TMR) scheme of the Framework 4 programme for a maximum of 36 months (post-grad) or 24 months (post-doc). Instructions for obtaining details of this scheme are appended below. Applicants should contact Dr David Gilbert at the address below as soon as possible, enclosing a CV (see guidelines below), a list of research interests and if possible an indication of the intended research area. NOTE: ----- Applicants must be nationals of the European Union (except the UK), or an associated state (Iceland, Israel, Lichtenstein, Norway, Switzerland), normally not older than 35. ------------------------------------------------------------------------------- Dr David Gilbert tel: +44-171-477-8444 (direct/answerphone) Department of Computer Science fax: +44-171-477-8587 School of Informatics City University email: drg@cs.city.ac.uk Northampton Square uucp : drg@citycs.uucp London EC1V 0HB UK http://www.cs.city.ac.uk/finger/drg ------------------------------------------------------------------------------ Guidelines for CV ----------------- detailed information (date & places) of the following where appropriate 1. University studies and diplomas obtained 2. Dissertations / Thesis [subjects and names of supervisors] 3. Professional experience 4. Relevant scientific techniques and skills acquired 5. List of publications and patents Obtaining the application forms ------------------------------- Further information about the TMR programme can be obtained from http://www.cordis.lu/tmr/home.html and specifically about the TRAINING THROUGH RESEARCH Marie Curie Fellowships from http://www.cordis.lu/tmr/src/howtoapp.htm which has a pointer to the application forms. These forms can also be obtained by anonymous ftp from ftp.cordis.lu by downloading the file /pub/EDOCDEL/tmr/tmr_annexes/B0299ENW.DOC The next deadline for applications to reach the European Union is 16 December 1996 From owner-genome-program@net.bio.net Wed Nov 27 22:00:00 1996 Path: biosci!biosci!not-for-mail From: "Joe Miano" Newsgroups: bionet.molbio.genome-program Subject: Functional Genomics Date: 28 Nov 1996 08:10:08 -0800 Organization: MCW-Physiology Lines: 17 Sender: daemon@net.bio.net Approved: biosci-help@net.bio.net Distribution: world Message-ID: <01bbdb0c$28419de0$21746a8d@meb_493a.cvrc.mcw.edu> NNTP-Posting-Host: net.bio.net In 7-8 years, all 100,000-odd genes will be identified and their position in the human and rodent genomes known. The next phase of science will be to understand what the gene products do during development and disease. Thus, a buzz phrase for the next century will be "(dys)functional genomics." We are considering offering a hands on mini course that will prepare investigators to take genomic sequences and ascertain functionality. The big question, of course, is whether there is an interest in this area of scientific inquiry. Please email me with your thoughts and comments Thanks in advance, -- The Love you take is equal to the Love you make--P. McCartney From owner-genome-program@net.bio.net Wed Nov 27 22:00:00 1996 Path: biosci!biosci!not-for-mail From: Pavel Pevzner Newsgroups: bionet.molbio.genome-program Subject: PROCRUSTES: New Gene Recognition Software Date: 28 Nov 1996 08:10:36 -0800 Organization: University of Southern California Lines: 34 Sender: daemon@net.bio.net Approved: biosci-help@net.bio.net Distribution: world Message-ID: <57kdhs$igd@net.bio.net> NNTP-Posting-Host: net.bio.net Announcement: New version of Procrustes gene recognition software now available. Version 3.01 beta of Procrustes is available as a WWW server: http://www-hto.usc.edu/software/procrustes/ or as an MS Windows application for the IBM PC. Procrustes uses previously-sequenced genes to recognize new ones as described in Gelfand, M.S., Mironov, A.A.,Pevzner, P.A. "Gene recognition via spliced sequence alignment", Proc. Natl. Acad. Sci. USA (1996), 93, 9061-9066 The distinctive features of Procrustes are: - high reliability of predictions (up to 99%) in the presence of related proteins as compared to 70-80% for most gene recognition programs; - the possibility to analyze extremely long (up to 150,000 bp) sequences with many (up to 20-30) exons; - insensitivity to statistical inhomogeneity of genomes; - the possibility to recognize very short exons; - insensitivity to the presence of several genes in one sequence. Version 3.01 beta of the WWW server includes: - graphical output for exon-intron maps and alignment profiles; - gene recognition by spliced alignment to several related proteins. The next release will include: - gene recognition in various species; - error-tolerant gene recognition; - assignment of confidence levels to recognition results; - using EST sequences for gene recognition; - gene recognition in incomplete sequences.