From owner-gene-linkage@net.bio.net Wed Oct 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!208.134.241.18!newsfeed.internetmci.com!205.217.206.132!ns2.borg.com!usenet From: Newsgroups: bionet.molbio.gene-linkage Subject: GUARANTEED 2-5 LBS WEIGHT LOSS PER WEEK Date: 2 Oct 1997 02:07:42 GMT Organization: Borg Lines: 9 Message-ID: <60uvle$i6i@ns2.borg.com> NNTP-Posting-Host: l194a.borg.com yes its true....this new all natural wieght loss product in which you will lose between 2 an 5lbs per week.....no exercise....no diet.....no nothing....sound to good to be true....i know i thought so to till i lost 30 lbs in one month..so i know it works.....for complete info please write to PO Box 4664 Utica, New York.....13501 You wont regret it.....you will be glad you did.....its simply amazing.....and its GUARANTEED...you have nothing to lose...but unwanted pounds.....feel good...look good....... From owner-gene-linkage@net.bio.net Thu Oct 02 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!cam-news-feed2.bbnplanet.com!news.bbnplanet.com!sol.caps.maine.edu!news.ycc.yale.edu!yale!usenet From: you@somehost.somedomain (a) Newsgroups: bionet.molbio.gene-linkage, Subject: best linkage and mapping program? Date: 3 Oct 1997 03:52:14 GMT Organization: Your Organization Lines: 10 Message-ID: <611q5e$kgl@babyblue.cs.yale.edu> NNTP-Posting-Host: s02p07.ppp.uconn.edu Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.5 Hello. I was wondering what opinions there were out there for the best mapping/linkage program. I'm currently using mapmaker3, and it's not bad but it's also not too user friendly. Any opinions? Sincerely, Gary Vanzin University of Connecticut Department of Molecular and cell Biology gfv94001@uconnvm.uconn.edu From owner-gene-linkage@net.bio.net Thu Oct 02 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!tin!pfoley From: "Mr. P.J. Foley" Newsgroups: bionet.molbio.gene-linkage Subject: family pedigree maps software?? Date: Fri, 3 Oct 1997 13:27:21 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 9 Message-ID: NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: pfoley@tin Hi- Does anyone know if there are any freeware/shareware programs for drawing maps of family pedigrees? Thanks in advance, Patrick Foley, National Heart and Lung Institute, London. From owner-gene-linkage@net.bio.net Thu Oct 02 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-feed1.tiac.net!news-master.tiac.net!news@tiac.net From: jamesl@healthtech.com (James W. Larkin) Newsgroups: bionet.molbio.gene-linkage Subject: Cambridge Healthtech Institute's Genome Tri-Conference Date: 3 Oct 1997 14:20:48 GMT Organization: Cambridge Healthtech Institute Lines: 457 Message-ID: <612v00$mal@news-central.tiac.net> NNTP-Posting-Host: 207.60.238.8 Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.9 Beta 1 (x86 32bit) Cambridge Healthtech Institute's Genome Tri-Conference The Fairmont Hotel —San Francisco, California February 9-15, 1998 The first two conferences highlight key technical progress and its application in the development of new therapeutic understanding and novel compounds. The third program showcases emerging genomics companies and is designed to facilitate evaluation and networking. Look closely at each meeting and decide to attend one, a pair, or all three. Our goal is to make the entire week work for you! Special Multi-Conference Rates Available Contact us directly, or visit the News/Features section of our website at http://www.healthtech.com/conferences/ for more information. Fifth Annual HUMAN GENOME PROJECT: Commercial Implications February 9-11, 1998 Corporate Support Provided by: PE Applied Biosystems As the Human Genome Project gears up into the sequencing phase, the expectations for translating such data into valuable information increase. While automated gel-based sequencing remains the workhorse of this effort, newer approaches have moved much closer to becoming practical. Much greater emphasis is also being placed on software for analyzing sequences and the creation of gene expression libraries and databases. Such databases, in combination with analysis of gene function, will play a key role in the identification of novel targets for diagnostic and therapeutic applications. The third day of this meeting will again feature case studies of genomic data-based drug development efforts. This meeting has become established as a key forum for academic and commercial researchers to discuss and find out about the latest technology and applied developments in the genomics field. Scientific Advisors Dr. Roger Brent, Massachusetts General Hospital and Harvard Medical School Dr. Carol A. Dahl, National Cancer Institute Dr. Mark Schena, Stanford University Medical Center Dr. Robert L. Strausberg, National Cancer Institute Overview Keynote Presentations A Toothpick-Wielding Microbial Geneticist Looks at the Future Dr. Ira Herskowitz, University of California, San Francisco Perspective on Where Genomics Is Heading Dr. Randy Scott, Incyte Pharmaceuticals The Hammer and the Handshake: Coordinate Approaches for Obtaining Meaningful Intellectual Property Protection and Operating in a Patent-Protected Environment in Genomics Dr. Kathleen Madden Williams, Banner & Witcoff Ltd. Panel on Prospects for Genomic Investments Dr. Brian Atwood, Brentwood Venture Capital Dr. Jean-François Formela, Atlas Venture Dr. Hugh Reinhoff, Abingworth Venture Management, Inc. Strategic Use of Genomic Information Identifying Genes and Other Important Sequence Elements Using ESTs and Comparative Sequencing Efforts Dr. Richard Wilson, Washington University Full-Length cDNA, an Entry to Function Determination Dr. C. Thomas Caskey, Merck Research Laboratories Cancer Genome Anatomy Project Dr. Robert L. Strausberg The Use of Information from Functional Genomics and Pharmacology in the Discovery of New Approaches to the Treatment of Human Disease Dr. Gordon Baxter, Pharmagene Laboratories Ltd. Pharmacogenomics and Drug Prescription Dr. Marta Blumenfeld, Genset Comprehensive Molecular Analysis Tools Keynote Presentation Assessing the Human Genome Project at the Halfway Point Dr. Francis S. Collins, National Human Genome Research Institute Moving Beyond the Sequence: Protein-Based Tools for Assigning Gene and Allele Function Dr. Roger Brent ARAKIS, a Powerful Technology for Genome Sequencing and Clinical Diagnostic Dr. Hartmut Voss, Lion Bioscience AG Automation for Cost Reduction in Large-Scale DNA Sequencing Dr. Andre Marziali, Stanford DNA Sequencing and Technology Development Center Integrating the Complementary Information from High-Throughput Sequencing and DNA Microarray Analysis Dr. David Barker, Molecular Dynamics SELDI: Connecting Gene Expression Monitoring with Protein Function and Drug Discovery Dr. William Hutchens, Ciphergen Biosystems Parallel Analysis with Biological Chips Accelerating Drug Discovery with Gene Expression Microarrays Dr. Dari Shalon, Synteni Inc. Chip-Based Expression Analysis: Linking Sequence and Function Dr. Mark Schena Genome Analysis Using SBH Tools Dr. Radoje Drmanac, Hyseq, Inc. cDNA Arrays for the Masses Dr. Paul Siebert, Clontech Inc. Integrated Microelectronic Systems for Genomic Research and Diagnostic Applications Dr. Michael J. Heller, Nanogen, Inc. Methods for Identification of Lead Genes The First Gene Targets from a Novel Academic-Industry Liaison Dr. Richard E. Kouri, VIMRX Genomics, Inc. Using Viral Signposts to Zoom In on Therapeutically Important Genes Dr. Subha Srinivasan, Immunex Corporation Leveraging Bioinformatics and a Gene Expression Technology Platform to Accelerate Lead Discovery Dr. Keith Elliston, Gene Logic, Inc. Applications of Genomics in Target Identification and Lead Development Dr. Douglas R. Smith, Genome Therapeutics Corporation Aptameric Antagonists as Target Validation Tools Dr. Barry Polisky, NeXstar Pharmaceuticals Genomic Drug Discovery Novel Approaches to Drug Discovery Research Dr. Lee E. Babiss, Glaxo Wellcome Research and Development New Approaches to Target Identification in Mouse and Man Dr. David Galas, Darwin Molecular Corporation Pyrrole-Imidazole Polyamides as Specific Inhibitors of Gene Transcription in Vitro and in Vivo Dr. Joel Gottesfeld, Scripps Research Institute DiscoverEase™ Program for Identifying Secreted Proteins Dr. Sharan Pagano, Genetics Institute Second Annual GENE FUNCTIONAL ANALYSIS February 12-13, 1998 As the complete genomes of the first model organisms become available, it is now possible to explore how well such data can be interpreted in terms of functional analysis. The sheer volume of genetic sequence is going to require a paradigm shift from laborious determination of function for one gene at a time to high-throughput approaches that can automatically assist in such efforts, via homolgy and cross-species comparisons. The use of libraries of mutants or knockouts also represents a key approach toward faster analysis. Efforts to determine function of gene sequences and relate them to genetic pathways and roles in disease will be key for exploiting genetic information for medicinal purposes. Scientific Advisors Dr. Doug Bassett, Fred Hutchinson Cancer Research Center Dr. Roger Brent, Massachusetts General Hospital and Harvard Medical School Dr. Edward M. Rubin, University of California, Berkeley Keynote Presentation Dr. Patrick O. Brown, Stanford University School of Medicine Functional Genomics Model Organisms and Human Disease Dr. Doug Bassett Genome Diversity and Functional Genomics Dr. Mark W. Bodmer, Hexagen Gene Function Analysis by the Integration of Phenotypic and Genotypic Databases Dr. Dirk Gewert, Gemini Biochemical Research Identification of Critical Genes in Disease Pathways Dr. Lynne Zydowsky, Exelixis Pharmaceuticals Large-Scale Functional Analysis of the S. Cerevisiae Genome Dr. Petra Ross-Macdonald, Yale University Gene Expression Using Protein Networks and Peptide Aptamers to Elucidate Pathways, Genes, and Alleles Dr. Roger Brent Functional Analysis in Silico Dr. Reinhard Schneider, Lion Bioscience AG CodeSig™ Technology for Discovery of Variation in Gene Expression Dr. Gualberto Ruano, Genaissance Pharmaceuticals Finding Genes Across Species Dr. Pavel Pevzner, University of Southern California Linking Genome to Metabolome by High-Throughput Mass Spectrometric Genetic Profiling: Novel Strategy to Unravel Gene Function Dr. Adelbert A. Roscher, GeneValid GmbH Genomic Analysis of C. Elegans Dr. Erik Sonnhammer, National Center for Biotechnology Information (invited) Genome Manipulation Radiation-Induced Deletions in Mice Using ES Cells Dr. John Schimenti, Jackson Laboratory Exploiting the Mouse to Sift Sequence for Function Dr. Edward M. Rubin OmniBank: An Engine of Drug Discovery Dr. Arthur T. Sands, Lexicon Genetics Streamlined Approaches to Targeted Loss- and Gain-of-Function Mouse Genetics Dr. George Gaitanaris, National Cancer Institute Chromophore-Assisted Laser Inactivation Dr. Daniel Jay, Harvard University From Database to Drug: Genomic Approaches to Therapeutic Discovery A Systematic Approach to the Identification of Surrogate Ligands for Orphan G Protein Coupled Receptors Dr. David R. Webb, Cadus Pharmaceuticals Ribozymes: A Key Tool for Target Validation Dr. Ralph E. Christoffersen, Ribozyme Pharmaceuticals A Targeted Genomics Approach to the Discovery of New Antifungal Agents Dr. Georges Natsoulis, Microcide Pharmaceuticals Use of Yeast Genome for Drug Discovery Dr. Matthew Ashby, Acacia Biosciences New Approaches for Screening and Validating Novel Targets Dr. Dana M. Fowlkes, Novalon Pharmaceutical Corp. GENOMIC OPPORTUNITIES: Emerging and Early Stage Partners February 14-15, 1998 The growing role of genomics in diagnostics and therapeutic development, along with dramatic advances in technology, is fueling the formation of new companies designed to exploit these opportunities. This program showcases several dozen impressive startup companies in a format suitable for comparison and networking. The presentations have been grouped by key topics, including sequencing and mutation detection, bioinformatics, gene expression monitoring, functional genomics, proteome and clinical genomics. Expert commentators will introduce and provide a perspective on each session. The intended audience include licensing, business development, and strategic planning personnel from pharmaceutical, biotechnology, and genomic companies, as well as equipment, software, or other vendors. The partnering possibilities that will be discussed may enhance the development efforts of these attendees. Investors and analysts will also find the program to be rich in potential for consideration. Sequencing and Mutation Detection BioSeq, Dr. James Laugharn Transgenomic, Mr. Brian Perry Sequenom, Mr. Toni Schuh Mosaic Technologies, Dr. Chris Adams (invited) Bioinformatics Lion Bioscience AG, Dr. Reinhard Schneider Genomica, Mr. Tom Marr CuraGen, Dr. Greg Went (space available for one more presentation) Gene Expression Monitoring Synteni, Inc., Dr. Dari Shalon Acacia Biosciences, Dr. Bruce Cohen Gene Logic, Inc., Dr. Keith Elliston Digital Gene Technologics PE GenScope, Mr. Mark Zabeau Hyseq, Inc., Dr. Radoje Drmanac (invited) (space available for one more presentation) Functional Genomics Pharmagene, Dr. Gordon Baxter Vyrex, Dr. Jon Jarvik Lexicon Genetics, Dr. Arthur Sands Hexagen, Dr. Mark Bodmer Eos Biotechnologies, Dr. David Martin GenQuest, Mr. David Fanning Exelixis Pharmaceuticals, Dr. Lynn Zydowski VIMRx Pharmaceuticals, Dr. Richard Kouri (tentative) geneNetworks, Dr. Jonathan Cool (tentative) Brax Genomics, Mr. Guenter Schmidt (invited) Proteome Ciphergen Biosystems, Inc., Dr. William Rich GeneValid GmbH, Dr. Adelbert Roscher AlphaGene, Inc., Dr. George Scheele Structural Bioinformatics, Inc., Dr. Susan Burgess Large Scale Biology Corp., Dr. N. Leigh Anderson (invited) Clinical Genomics Eurona Medica, Dr. Per Lindstrom Professional Genetics Laboratories, Dr. Jörgen Lönngren Gemini Research, Dr. Paul Kelly deCode Genetics, Dr. Kari Stefansson (tentative) Commentators Mr. Todd Morrill, Burrill & Co. Mr. Jeffrey Casdin, Hambrecht & Quist (invited) Dr. William Bains, Merlin Ventures (invited) Mr. Stephen Edgington, Nature Biotechnology HOTEL INFORMATION The Fairmont Hotel Atop Nob Hill San Francisco, CA 94108 T: 800-527-4727 415-772-5000 F: 415-772-5086 Cut-off Date: January 11, 1998 Main Bldg. Standard: $150 Tower City View: $195 Main Bldg. Deluxe: $170 Tower Bay View: $250 Reservations made after the cut-off date will be accepted on a space-and-rate-availability basis. Available rooms are limited, so please book early. Please identify yourself as a Cambridge Healthtech Institute conference attendee to receive the reduced room rate. TRAVEL INFORMATION TRAVELWORLD T: 717-288-9311 or 800-828-6033 601 Market Street F: 717-288-4693 Kingston, PA 18704 Exclusive airline discounts are available on American Airlines as well as other specific airlines when tickets are purchased through Travelworld at least 14 days prior to the meeting date. Some restrictions apply. CALL FOR POSTERS Cambridge Healthtech Institute encourages attendees to gain further exposure by presenting their work in the poster sessions. Please fill out the registration form, with the poster title and primary author. To ensure inclusion in the conference binder, a one-page summary must be submitted by January 9, 1998. CALL FOR EXHIBITORS Companies interested in reaching this targeted audience of researchers and legal professionals should consider exhibiting at this meeting. Please contact Jim MacNeil at 617-630-1341 for more information. Each registration includes all conference sessions, posters and exhibits, continental breakfasts, three lunches, reception, all refreshment breaks, and a copy of the document binder. Handicapped Equal Access: In accordance with the ADA, Cambridge Healthtech Institute is pleased to arrange for special accommodations for attendees with special needs. All requests for such assistance must be submitted in writing to CHI at least 30 days prior to the start of the meeting. Substitution/Cancellation Policy In the event that you need to cancel a registration you may: Transfer your registration to a colleague within your organization. Credit your registration to another Cambridge Healthtech Institute program. Request a refund minus a $75 processing fee. Request a refund minus the cost ($195) of ordering a copy of the document binder. Cancellations will only be accepted up to one week prior to the conference. Program and speakers are subject to change. --------------------------Cut and Print Here------------------------ Yes! |__| Please register me for the TRI - GENOME CONFERENCE E-TRI Individual Conference Pricing |__| Human Genome Project Academic, Government, Hospital-Affiliated |__| $395 Early Registration (by Nov. 10, 1997) |__| $445 Advance Registration (by Dec. 29, 1997) |__| $495 Late/Onsite Registration Commercial |__| $795 Early Registration (by Nov. 10, 1997) |__| $945 Advance Registration (by Dec. 29, 1997) |__| $1095 Late/Onsite Registration |__| Gene Functional Analysis |__| Genomic Partnering Academic, Government, Hospital-Affiliated |__| $370 Early Registration (by Nov. 10, 1997) |__| $395 Advance Registration (by Dec. 29, 1997) |__| $445 Late/Onsite Registration Commercial |__| $745 Early Registration (by Nov. 10, 1997) |__| $845 Advance Registration (by Dec. 29, 1997) |__| $945 Late/Onsite Registration Multiple Conference Pricing |__| Human Genome Project/Gene Functional Analysis |__| Human Genome Project/Genomic Partnering Academic, Government, Hospital-Affiliated |__| $690 Early Registration (by Nov. 10, 1997) |__| $740 Advance Registration (by Dec. 29, 1997) |__| $790 Late/Onsite Registration Commercial |__| $1390 Early Registration (by Nov. 10, 1997) |__| $1490 Advance Registration (by Dec. 29, 1997) |__| $1590 Late/Onsite Registration |__| Gene Functional Analysis/Genomic Partnering Academic, Government, Hospital-Affiliated |__| $545 Early Registration (by Nov. 10, 1997) |__| $595 Advance Registration (by Dec. 29, 1997) |__| $645 Late/Onsite Registration Commercial |__| $1190 Early Registration (by Nov. 10, 1997) |__| $1290 Advance Registration (by Dec. 29, 1997) |__| $1390 Late/Onsite Registration Full Tri-Genome Conference Package |__| Human Genome Project/Gene Functional Analysis/Genomic Partnering Academic, Government, Hospital-Affiliated |__| $925 Early Registration (by Nov. 10, 1997) |__| $1035 Advance Registration (by Dec. 29, 1997) |__| $1145 Late/Onsite Registration Commercial |__| $1995 Early Registration (by Nov. 10, 1997) |__| $2225 Advance Registration (by Dec. 29, 1997) |__| $2445 Late/Onsite Registration FIRST NAME:______________________________________________________ LAST NAME:_______________________________________________________ TITLE:___________________________________________________________ DIV./DEPT.:______________________________________________________ COMPANY:_________________________________________________________ ADDRESS:_________________________________________________________ City/State/ZIP:__________________________________________________ COUNTRY:_________________________________________________________ TELEPHONE:____________________________ Fax:______________________ E-MAIL:__________________________________________________________ |__| Please send information on exhibiting and opportunities to present workshops. |__| Enclosed is a check or money order payable to Cambridge Healthtech Institute, drawn on a U.S. bank, in U.S. currency. |__| Please charge: |__| AMEX (15 digits) |__| Visa (13 to 16 digits) |__| MasterCard (16 digits) Card #:___________________________________________________________ Exp. Date:________________________________________________________ Cardholder's Name:________________________________________________ Signature:________________________________________________________ Cardholder's Address (if different from above):___________________ __________________________________________________________________ |__| Reserve with credit card information listed above and invoice me. (Invoices must be paid in full by the deadline to retain registration discount. Invoices unpaid one week prior to conference will be billed to credit card at full registration rate.) If you plan to register on site, please check with CHI beforehand for space availability. |__| I am interested in presenting a poster at the Tri-Genome Conference and will provide an abstract by January 9, 1998. Poster title:________________________________________________ __________________________________________________________________ FAX or MAIL your reservation/registration to: Cambridge Healthtech Institute tel: 617-630-1300 1037 Chestnut Street fax: 617-630-1325 Newton Upper Falls, MA 02164 e-mail: chi@healthtech.com http:www.healthtech.com/conferences/ From owner-gene-linkage@net.bio.net Sun Oct 05 23:00:00 1997 Path: biosci!IASI.RM.CNR.IT!rafanelli From: rafanelli@IASI.RM.CNR.IT (Maurizio Rafanelli) Newsgroups: bionet.molbio.gene-linkage Subject: Call for Papers 10th SSDBM Date: 6 Oct 1997 13:29:33 -0700 Organization: I.A.S.I. - C.N.R. Lines: 143 Sender: daemon@net.bio.net Distribution: world Message-ID: <34391D81.3AD6@iasi.rm.cnr.it> Reply-To: rafanelli@IASI.RM.CNR.IT NNTP-Posting-Host: net.bio.net CALL FOR PAPERS of the 10th International Conference on SCIENTIFIC and STATISTICAL DATABASE MANAGEMENT (10th SSDBM) (See also http://www.iasi.rm.cnr.it/conferences/SSDBM98/ ) Capri, Italy - July 1-3, 1998 Organizer: Istituto di Analisi dei Sistemi ed Informatica Italian National Research Council The 10th International SSDBM Conference will take place in Capri, in July 1-3, 1998. This International Conference will bring together database researchers, practitioners, and developers, as well as domain scientists from multiple scientific disciplines, for the presentation and exchange of current research and on concepts, tools, and techniques for scientific and statistical database applications. The 10th SSDBM will provide a forum for original research contributions and practical system design, implementation, and evaluation. The conference will also feature keynote talks, panel sessions, and demonstrations of research prototypes and industrial systems. It will continue the tradition of past SSDBM meetings in providing a stimulating environment to encourage discussion and the exchange of ideas in the drawing-room of the world: Capri. Topics of Interest Topics of interest include but are not limited to the following: System Architectures, Modeling and Semantics, Process Models, Query Languages and User Interfaces, Data Visualization, Metadata Management, Physical Organization, Data Compression, Knowledge Discovery and Data Mining, Uncertainty Management, Data Integration, Multi-media Data, Probabilistic DB, Privacy/Security, Distributed SDB, Data Warehouse,Temporal Data, Spatial Data, Collaborative Work, Experiment Management, Tertiary Storage. Of particular interest are results that address issues arising in providing DB support to specific statistical applications or scientific disciplines, such as the following: Biological Sciences, Biostatistics, Census DBs, Chemistry, Decision Support, Earth and Space Sciences, Economics and Finance, Engineering, Enterprice Analysis, Environmental Risks, Geography, Medicine, On-Line Analytical Processing, Physics, Pollution, Social Sciences. The 10th SSDBM invites two separate types of papers: 1. Research Papers. They will describe the most recent and important advances in Scientific and Statistical DBs. Theoretical papers should include a solid motivation for why the specific results are important to domain scientists and how they are going to influence the development of scientific or statistical database systems. System papers should describe either complete working systems which are being tested by domain scientists or specialized techniques which can significantly increase the power of actual scientific and statistical database systems. 2. Experience/Challenge Papers. They will describe actual prototype implementations, pose problems which current technology cannot handle well, or identify important industrial trends which could affect the future research directions. They should be based on real-life experiences and should clearly place their contribution in the context of the current state of the art and relevant literature. Submitted papers should be clearly marked at the top of the first page by the appropriate category for which they are intended. The Program Committee will decide , at its discretion, the class (full or short paper) in which to put the accepted research papers, as well as to switch papers that are deemed more appropriate for the other category (Research to Experience/Challenge or vice versa). In addition, the 10th SSDBM invites proposals for panels, as well as prototypes for demonstration at the Conference. SUBMISSION GUIDELINES PAPERS should be up 20 pages long, 2-spaced, in font size at least 10 (8,000 words) and submitted in five copies. PANEL PROPOSALS should be at most 2 pages long and should at least include a tentative list of panellists. DEMONSTRATION PROPOSALS should be at most 2 pages long and should specify the kind of hardware required. All papers and proposals should be sent electronically or in hard-copies to the Program Chairman. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ IMPORTANT DATES DATE MILESTONE January 12, 1998 Deadline for submission of papers March 31, 1998 Notification of acceptance/rejection May 1, 1998 Deadline for having final papers at the publisher ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ORGANIZATION Steering Committee: Arie Shoshani (USA, Chair) Hans Hinterberger (Switzerland) James C. French (USA) Per Svensson (Sweden) Yannis Ioannidis (Greece) General Chairman Maurizio Rafanelli IASI - CNR viale Manzoni 30, 00185 Roma, Italy Phone: +39.6.77161 - Fax: +39.6.771 6461 e-mail: rafanelli@iasi.rm.cnr.it Program Chairman Matthias Jarke Informatik V, RWTH Aachen 52056 Aachen, Germany Phone: +49.241.802 1500 - Fax: +49.241.888 8321 e-mail: jarke@informatik.RWTH-Aachen.DE Organization Secretariat / Technical Support Mary Carbone, Armanda Filacchioni Antonia Bezenchek, Angelo Maliziola, Sergio Medici Local Arrangment P. De Gennaro Hotel La Residenza, Capri Phone:+39.81.8370833 - Fax:+39.6.8377564 - Telex: 720075 SADHOTEL e-mail: Laresidenza@capri.it Internet: http://caprionline.com/laresidenza From owner-gene-linkage@net.bio.net Sun Oct 05 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!ulcc.ac.uk!usenet From: dcurtis@hgmp.mrc.ac.uk (Dave Curtis) Newsgroups: bionet.molbio.gene-linkage Subject: Re: family pedigree maps software?? Date: Mon, 06 Oct 1997 21:56:12 GMT Organization: University of London Computer Centre Lines: 14 Message-ID: <34395dda.7395450@usenet-news.ulcc.ac.uk> References: Reply-To: dcurtis@hgmp.mrc.ac.uk NNTP-Posting-Host: a014.ds.ulcc.ac.uk X-Newsreader: Forte Free Agent 1.1/16.230 On Fri, 3 Oct 1997 13:27:21 +0100, "Mr. P.J. Foley" wrote: >Hi- >Does anyone know if there are any freeware/shareware programs for drawing >maps of family pedigrees? You can look at my pedraw program, at http://www.gene.ucl.ac.uk/public-files/packages/dcurtis/ wpdraw10.zip is the Windows version, and pedraw16.zip is the older DOS version Dave Curtis http://www.gene.ucl.ac.uk/~dcurtis/ From owner-gene-linkage@net.bio.net Mon Oct 06 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!ais.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!News1.Ottawa.iSTAR.net!news.istar.net!nr1.ottawa.istar.net!not-for-mail From: newaccounts@stopat.com Newsgroups: bionet.molbio.gene-linkage Subject: Free FrontPage Web Site Date: Mon, 06 Oct 1997 21:26:01 PDT Organization: Email PLATINUM Lines: 19 Message-ID: <34399095.1@199.166.219.107> NNTP-Posting-Host: news2.connectmmic.net At StopAt you get your Web Page for Free. You also get an e-mail address and Web site hosting for a month. You may also update your page whenever and however you wish with Microsoft® FrontPage. 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From owner-gene-linkage@net.bio.net Mon Oct 06 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!csulb.edu!logbridge.uoregon.edu!su-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!prodigy.com!prodigy.com!not-for-mail From: wila57@rocketmail.com Newsgroups: bionet.molbio.gene-linkage Subject: all==writers/876== Date: Mon, 6 Oct 1997 20:15:33 Organization: Prodigy Services Corp Lines: 26 Message-ID: <61bvgl$1k0k$11@newssvr09-int.news.prodigy.com> NNTP-Posting-Host: port66.myer.prodigy.net Our main office is in New York. We also have two branch offices. This agency is always looking for gifted writers, both new and previously published. For submission: Fiction: send a brief synopsis, first chapter, and a self addressed, stamped envelope (SASE). Nonfiction: brief synopsis, first chapter, SASE. For Short Stories: brief synopsis, 3 pages, SASE. For Poetry: send 3 poems, SASE. Do not submit entire manuscript unless invited. Please note that this agency strongly believes in providing a legitimate opportunity for writers in all newsgroups. Send to: New York Agency 1190-N. Collier Blvd. City of Marco Island, FL -34145 From owner-gene-linkage@net.bio.net Wed Oct 08 23:00:00 1997 Path: biosci!CS.PITT.EDU!chang From: chang@CS.PITT.EDU ("S. K. Chang") Newsgroups: bionet.molbio.gene-linkage Subject: (none) Date: 9 Oct 1997 07:30:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <199710091430.KAA28115@speedy.cs.pitt.edu> NNTP-Posting-Host: net.bio.net PLEASE DISTRIBUTE AND POST. OUR APOLOGIES IF YOU RECEIVE MULTIPLE MESSAGES. -----o-----o-----o-----o-----o-----o-----o-----o-----o-----o-----o-----o----- University of Pittsburgh Department of Computer Science The Department of Computer Science at the University of Pittsburgh invites applications for a tenure-track position at the rank of Assistant Professor, beginning with the 1998-1999 academic year. Outstanding candidates are sought in multimedia and related areas, in particular, with research interests in computer graphics, in the supporting technologies of computer networking, multimedia data management and distributed multimedia systems, in design and analysis of multimedia systems, and in intelligent multimedia systems. Responsibilities include research, supervision of graduate student research (PhD and MS), and graduate and undergraduate teaching. Candidates should have a PhD in Computer Science and demonstrate exceptional research potential and teaching ability. The Department currently has 22 full-time faculty members and provides a stimulating environment for research and teaching that results in strong graduate and undergraduate programs. Departmental resources include extensive computing facilities of over 300 workstations and personal computers with multimedia capabilities and specialized networks and devices. Each faculty member also has network access to additional high performance computing platforms provided by the general computing facilities of the University as well as by the Pittsburgh Supercomputer Center (of which the University of Pittsburgh is a founding member). For further information about the Department please see http://www.cs.pitt.edu. Applications should include a curriculum vitae, statement of research interests and names and addresses of at least three references and should be sent to: Prof. S. K. Chang, Chair of Faculty Search, Department of Computer Science, University of Pittsburgh, Pittsburgh, PA 15260. To ensure full consideration, applications must be received by January 16, 1998. The University of Pittsburgh is an equal opportunity/affirmative action employer and especially encourages women and ethnic minorities to apply. From owner-gene-linkage@net.bio.net Tue Oct 14 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!jobone!lynx.unm.edu!newshub.tc.umn.edu!newsstand.tc.umn.edu!lenti From: dean@lenti.med.umn.edu (Dean Flanders) Newsgroups: bionet.molbio.gene-linkage Subject: BIONET.MOLBIO.GENE-LINKAGE.FAQ Date: 15 Oct 1997 05:00:18 GMT Organization: University of MN, Medical School Lines: 987 Message-ID: <621il2$qtr@epx.cis.umn.edu> NNTP-Posting-Host: lenti.med.umn.edu Originator: dean@lenti.med.umn.edu BIONET.MOLBIO.GENE-LINKAGE FREQUENTLY ASKED QUESTIONS (FAQ) AS OF 1996/04/29 1.0) FAQ ADMINISTRATIVE INFORMATION [1995/05/18] 1.1) Where can I obtain and/or access the bionet.molbio.gene-linkage FAQ? [1995/03/01] 1.2) Who created the bionet.molbio.gene-linkage FAQ? [1995/03/01] 1.3) How can I help improve this FAQ? [1995/03/01] 1.4) Contributors to this FAQ. [1995/09/09] 1.5) When was the FAQ last updated? [1996/04/28] 2.0) INFORMATION RESOURCES 2.1) What anonymous FTP sites have programs/utilities useful for linkage analysis? [1995/03/01] 2.2) What books are helpful when learning about linkage analysis? [1995/03/01] 2.3) What WWW sites have useful linkage information? [1996/01/02] 2.4) What gopher sites have useful linkage information? [1995/03/01] 2.5) What "linkage centers" make information and assistance available to researchers? [1995/12/11] 2.6) What journals are useful for linkage analysis? [1995/06/02] 2.7) What courses are offered in linkage analysis? [1995/09/09] 3.0) GENE-LINKAGE SOFTWARE OVERVIEW 3.1) What database management programs do people use for linkage data? [1995/05/31] 3.2) What programs are available for pedigree drawing? [1995/04/01] 3.3) What linkage analysis helper programs are available? [1996/04/29] 3.4) Why are some programs used primarily for chromosome mapping, while others are used for disease mapping? [1995/03/01] 3.5) What programs are used for physical mapping? [1995/11/30] 3.6) What programs are used for disease gene mapping? [1995/09/07] 3.7) What programs are available for running genetic simulations? [1995/11/30] 3.8) What programs are available to help detect errors in linkage data? [1995/11/30] 3.9) What programs help me recode genetic markers? [1995/03/01] 4.0) LINKAGE PACKAGE SPECIFIC INFORMATION 4.1) How do I get my CEPH data into CRI-MAP format? [1995/03/01] 4.2) How do you calculate MAXHAP? [1995/09/09] 4.3) When should you use binary coding instead of numeric allele coding? [1995/03/01] 4.4) What do you do when allele frequencies do not add up to 1; for example, when alleles are not present in a pedigree under study? [1995/03/01] 4.5) I use LINKAGE and/or FASTLINK. Which references should I include in my papers? [1995/03/01] 4.6) What is recoding of alleles all about anyway? [1995/03/01] 4.7) What do you do when you get thetas greater than 0.5 when using linkage? [1996/22/01] 5.0) COMPUTER ADMINISTRATION AND OPTIMIZATION 5.1) How w can I increase the speed of the LINKAGE/FASTLINK package on my workstation? [1995/05/18] 6.0) MOLECULAR BIOLOGY ISSUES IN LINKAGE ANALYSIS 6.1) What screening sets are available for linkage analysis? [1995/09/14] 1.0) FAQ ADMINISTRATIVE INFORMATION 1.1) Where can I obtain the bionet.gene-linkage FAQ? [1995/03/01] It is available by anonymous FTP from lenti.med.umn.edu in /pub/linkage. The best way to view the FAQ is via the WWW, from http://lenti.med.umn.edu/linkage/linkage.html. The FAQ is also available via gopher at lenti.med.umn.edu in /Biologically Related Information/Linkage Analysis. The FAQ will also be posted in the USENET groups bionet.molbio.gene-linkage and news.answers the 1st and 15th of each month. 1.2) Who created the bionet.molbio.gene-linkage FAQ? [1995/03/01] Darrell Root (rootd@ohsu.edu) originally started the bionet.molbio.gene-linkage FAQ in May of 1994 in an attempt to share information and experiences that may be of use to other people involved in linkage analysis. I am Dean Flanders (dean@lenti.med.umn.edu), the current maintainer of the FAQ, and began my tenure in December of 1994. The FAQ will never serve as a short course in linkage analysis, but instead it will ideally be a place to help beginners get started in the area and to help experts not make the same mistakes as others. All of the information in this FAQ by no means comes completely from Darrell or me, but from a large number of people that work in the area of linkage analysis. Their names are listed at the end of this section of the FAQ. 1.3) How can I help improve this FAQ? [1995/03/01] Feel free to send any information that you think would be beneficial for other people who are just beginning in linkage or have been doing linkage for years to linkage@lenti.med.umn.edu. Also, if there is information you would like to see or errors in this FAQ please let us know by sending email to linkage@lenti.med.umn.edu. If you would like to see something changed or added to the FAQ please to send it in a format that can be quickly incorporated into the FAQ, such as correcting the errors in the section of the FAQ and emailing it back to the FAQ maintainer. 1.4) Contributors to this FAQ. [1995/09/09] David Adler, John Attwood, Michael Boehnke, Marcia Brott, Don Bowden, Michael Braverman, Lucien Bachner, Young B Choi, Kevin Crawford, Dave Curtis, Peter Doris, Bennett Dyke, David Featherstone, Dean Flanders, Jonathan Haines, Rob Harper, Pierre Janssens, David Kikuchi, Wentian Li, Tim Little, Tara Matise, Eli Meir, Mike Miller, Jurg Ott, Darrell Root, Alex Schaffer, Robert Stodola, Frank Visser, Dan Weeks, Ellen Wijsman, Scott Wildenberg, Matthias Wjst, and Kim Worley. 1.5) When was the FAQ last updated?[1996/04/29] The last update of the FAQ was on 1996/04/29. All sections should indicate what month and year they were last updated. In addition one can go to the list of updates that are maintained at http://lenti.med.umn.edu/linkage/gefaqup.html. This is a list in chronological order of updates with direct links to the updates in the FAQ. 2.0) INFORMATION RESOURCES 2.1) What anonymous-FTP sites have programs/utilities useful for linkage analysis? [1995/03/01] At present there is no one site that serves as a repository for all linkage software. So the best way of finding FTP site information is to read the software package information below, which should provide all of the necessary FTP information. 2.2) What books are helpful when learning about linkage analysis? [1995/03/01] Bishop, M. J. "Guide to Human Genome Computing." Academic Press, 1994. Davies, K. E. "Human Genetic Diseases - A Practical Approach." IRL Press, Oxford England and Washington, D.C., 1986. Dracopoli, N. C., Haines, J. L., Korf, B. R., Moir, D.T., Morton, C. C., Seidman, C. E., Seidman, J. G., Smith, D. R. "Current Protocols in Human Genetics." John Wiley and Sons, Inc., USA, 1994. Khoury, M. J., Beaty, T. H., and Cohen, B. H. "Fundamentals of Genetic Epidemiology." Oxford University Press, 1993. Ott, J. "Analysis of Human Genetic Linkage." Johns Hopkins University Press, 1991. Terwilliger, J. D. and Ott, J. "Handbook of Human Genetic Linkage," Johns Hopkins University Press, 1994. Thompson, E. A. "Pedigree Analysis in Human Genetics." Johns Hopkins University Press, Baltimore and London, 1986. 2.3) What WWW sites have useful linkage information? [1996/01/02] This is in no way an attempt to list the explosion of WWW sites of biological interest on the Internet, but it is a listing of some of the major ones and ones of particular interest in linkage analysis. http://www.yahoo.com/Science/Biology/Genetics/, this is a list of sites related to genetics that is kept very up to date. http://www.gdb.org/Dan/DOE/intro.html, this is a short course of sorts that gives some very basic information on how to go about gene mapping. http://lenti.med.umn.edu/linkage/linkage.html, which is serving as linkage analysis home page, will have links to all of the WWW sites listed as well as gopher servers and a hypertext version of the FAQ. http://www.genethon.fr, the Genethon Center, Genethon's home page. http://www.chlc.org, the Cooperative Human Linkage Center, CHLC's home page. http://gdbwww.gdb.org has a version of GDB available and access to OMIM. http://www.pathology.washington.edu has human and mouse standard idiograms. The idiograms are useful for making illustrations for gene mapping and for constructing abnormal chromosomes. The PostScript idiograms can be manipulated band by band with illustration software such as Adobe Illustrator, Aldus FreeHand, Canvas, and Altsys Virtuoso. http://www.gene.ucl.ac.uk/~john/programs.html contains software by John Attwood. http://www.gene.ucl.ac.uk/packages/dcurtis/ contains software by Dave Curtis. http://linkage.cpmc.columbia.edu has a lot of useful information on linkage analysis; in particular it offers information on software, the course offered by J. Ott, and the Linkage Newsletter. 2.4) What gopher sites have useful linkage information? [1995/03/01] There is one that will be maintained with links to other gophers of interest in linkage analysis, as well as links to other gopher servers of biologically related information. It is at lenti.med.umn.edu, and the path to it is Biologically Related Information/Genetic Linkage Analysis. 2.5) What "linkage centers" make information and assistance available to researchers? [1995/11/11] One such center is the Cooperative Human Linkage Center (CHLC). The goal of this center is to generate a high resolution map of the human genome and rapidly distribute this information to the genome community. They are in the process of identifying more human markers and developing high resolution framework maps. One can obtain information about CHLC from via gopher from gopher.chlc.org , http://www.chlc.org , ftp://ftp.chlc.org , info-server@chlc.org, or help@chclc.org. Among other things, CHLC provides primer selection and linkage analysis via email. Information on those services can be found by sending email to: primer- server@chlc.org and linkage-server@chlc.org. David Featherston (davidf@caos.kun.nl) from the Dutch EMBnet Node is starting a linkage analysis service: software availability, support/advice initially, possibly training, and perhaps consultancy. At present they have MapMaker/EXP 3.0b, MapMaker/QTL 1.1, Lathrop and Lalouel's LINKAGE package, and Schaffer's FASTLINK package. This means that if users have Genomics Package accounts at the CAOS/CAMM Center, they can use these programs on their fast computers to analyze their data sets. Please contact David Featherston if you are interested in more information about such an account. A major European center is the Human Genome Mapping Project Resource Centre in Hinxton, England. It is funded by the Medical Research Council, and has a broad range of software and databases available, mainly focused on the Human Genome Project. In the area of Linkage analysis it has the following programs available: FASTLINK, CRIMAP, MAP MAPMAKER, HOMOZ, PEDPACK, APM, SIMLINK, FASTMAP, COMDS, DOLINK & QDB, HANDLINK, GAS and Jurg Ott's collection of programs. The aim is to have all major (Unix-based) gene linkage packages available for our users. The Center also gives courses on linkage analysis. More information about the Centre can be obtained from it's home- page: http://www.hgmp.mrc.ac.uk/. If you want to register as user, send e-mail to admin@hgmp.mrc.ac.uk for a registration form. For more information about the gene-linkage services you can contact Frank Visser (fvisser@hgmp.mrc.ac.uk). INFOBIOGEN: This is the French GDB node that offers also a linkage server and assistance in the process of linkage analysis. It uses LINKAGE, FASTLINK and other programs running on a Sparc Center 2000E with 1 giga RAM, 4 Gig of swap, and 6 CPU's. For furhter information contact Lucien Bachner at bachner@infobiogen.fr or look at the following web site http://www.infobiogen.fr/. 2.6) What journals are useful for linkage analysis? [1995/06/02] American Journal of Human Genetics, Annals of Human Genetics, Computer Applications in Biosciences (CABIOS), Genomics, Genetic Epidemiology, Human Genome News (available by gopher from gopher.gdb.org), Human Genome Project Journal, Human Heredity, Journal of Computational Biology, Nature Genetics. 2.7) What courses are offered on linkage analysis? [1995/09/09] There are three primary courses offered throughout the yeart on human linkage analysis. One is a four day course offered once per year by Drs. Margaret Pericak-Vance and Jonathan Haines. The next course will be offered in late April, 1996 in Boston. The focus of the course is on the overall design of a human disease gene mapping study, with particular emphasis on the problems of common/complex disorders. The course covers clinical classification, pedigree ascertainment, collection, and follow-up, basic linkage techniques, linkaghe and association analysis for complex disorders, laboratroy technqiues for genotyping, and gene characterization. The courseemphasizes the global decision-making process, rather than details of specific techniques. For more information write to Genetic Methods Course; c/o Dr. Margaret Pericak- Vance; Division of Neurology, Box 2900; Duke University Medical Center; Durham, NC 27710, or you can send e-mail to genclass@genemap.mc.duke.edu. The remaining two courses are both offered by Jurg Ott on the software used for human linkage. One is a beginner's course, and the other an advanced course for those familiar with the linkage analysis software. These courses are offered several times throughout the year and you can get more information by contacting Katherine Montague/Jurg Ott; Columbia University, Unit 58; 722 West 168th Street; New York, NY 10032. In addition you can fax to (212)568- 2750 or call (212)960 2507 or email km165@columbia.edu for more information. A new beginner's level linkage course will be offered in French October 24-25 1995 by INFOBIOGEN, in Villejuif south suburb of Paris. It's free for all academic institutions. For furhter information contact Lucien Bachner at bachner@infobiogen.fr or linkage@infobiogen.fr. 3.0) GENE-LINKAGE SOFTWARE OVERVIEW 3.1) What database management programs do people use for linkage data? [1995/05/31] One must be aware that some pedigree drawing software can also serve as databases for data as well as drawing pedigrees, see the next question in the FAQ for a description of those packages. CEPH DBMS: The CEPH DataBase Management System is specifically designed for chromosome mapping with CEPH style pedigrees. It can output data in ped.out format for the LINKAGE package. This program can now be picked up via anonymous FTP from ftp.cephb.fr in pub/ceph_genotype_db. DOLINK: This DOS custom database program by D. Curtis manages genetic data and sets up input files for linkage analysis. It is available from ftp.gene.ucl.ac.uk. The DOS and Windows versions of DOLINK program help manage genetic data and setup analysis. It is available with the C++ source allowing compilation on Unix host running X and possibly a Macintosh. File Express: This is a DOS shareware database which can be used to hold data for DOLINK (largely superseded by QDB). It is available as fe51-a/b/c.zip via FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. LABMAN and LINKMAN: These are linkage analysis databases for holding linkage data and exporting it in various formats for linkage analysis. They are available via anonymous FTP from lenti.med.umn.edu in /pub/linkage/labman. These databases were developed by P. Adams of Columbia University. LYNKSYS: This custom-made database program was written by J. Attwood and S. Bryant. Although they continue to use it, J. Attwood suggests using DOLINK instead. LINKSYS is not currently available at any FTP sites. Map Manager: It is a program for the Macintosh which helps analyze the results of genetic mapping experiments using backcrosses, intercrosses, or recombinant inbred strains. In addition it also has tools for statistical analysis of experiments. The program was created by K. F. Manly at the Roswell Cancer Institute and is available via FTP from mcbio.med.buffalo.edu in /pub/MapMgr. QDB: This is a database program available as DOS and Windows versions and with C++ source allowing compilation for X and possibly Macintosh. It is available as qdb16a.zip via FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. 3.2) What programs are available for pedigree drawing? [1995/04/01] One of the tricks of managing individuals in a mapping study is trying to get the database you are using to export your family data in a format acceptable for input into pedigree drawing programs. The marriage between these two can be of great assistance. However, some pedigree drawing programs have databases as a part of the package. CYRILLIC: This is a pedigree editor for Windows with facilities for including marker data which you can then have it output the input files for LINKAGE. It is Windows-based, so input of the pedigree is very efficient. You also have a data form associated with each individual where you can store names and other pertinent data. It also has the ability to interface with most standard PC databases. This program is not public domain and is available from Cherwell Scientific Publishing. If you would like more information send email to csp@sable.ox.ac.uk and they would be very happy to send you a demo of the program. Version 2 of Cyrillic should be coming out late summer of 1995. FTREE: This is a DOS pedigree program written by R. Go at the University of Alabama. GENETREE: GeneTree 1.0 is a DOS package which provides a convenient way to draw family tree diagrams suitable for genetics or genealogy. The package consists of the GeneTree program, which draws pedigree diagrams using a command language; and SC, using a menu driven program that facilitates creation of GeneTree commands. GeneTree and SC are made available with program manuals, examples of family tree diagrams, and a GeneTree Quick Reference Guide. GeneTree is written in C. Note that it is a DRAWING program and does not compute genetic parameters. The GeneTree program is available from wijsman@max.u.washington.edu at a price of $125 (because of licensing fees from a private company which wrote one of the drivers used in the program). KINDRED: This new DOS database program, distributed by Epicenter Software, is specifically designed for linkage analysis. A free demo is available by calling (818)-304-9487. In addition to database duties, this program will draw pedigrees, haplotype marker data, and can output data in LINKAGE format. PEDPAK: This package is designed to handle large datasets for animals. The package was written and distributed by Alan Thomas, who is in Bath, England. The software is not public domain and must be purchased. Pedigree/Draw: It is a Macintosh based program, written by B. Dyke, P. Mamelka, and J. MacCluer. It is available from bdyke@darwin.sfbr.org or Pedigree/Draw; Department of Genetics; Southwest Foundation for Biomedical Research; PO. Box 28147; San Antonio, TX 78228-0147. An upgrade from a previous version is $10, the current version is 4.4. Documentation costs $10 printed and the full package including documentation costs $45. There is a script which converts linkage format to Pedigree/Draw available via anonymous FTP at ftp.ee.pdx.edu in /pub/users/cat/rootd/convert.new. PEDRAW: This program is a pedigree drawing program written by D. Curtis for DOS and available via FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. The most current version is called pedraw16.zip. A companion program to PEDRAW is PEDHELP, it is a pop-up help for PEDRAW. PAP: The Pedigree Analysis Package (PAP) is a set of FORTRAN 77 programs for computing likelihoods and simulating phenotypes of genetic models on pedigrees. It is available via gopher from corona.med.utah.edu in Publicly Accessible Software, probes(sts), etc./software/pap. 3.3) What linkage analysis helper programs are available? [1996/04/29] CEPH2CRI: This program converts to output from the CEPH DBMS into the format useable in CRI- MAP. It can be found at ftp.gene.ucl.ac.uk in /pub/packages/linkage_utils. EASISTAT: This is a DOS statistics package, it contains EASIGRAF which draws graphs of lod scores from the output of FASTMAP. The lod scores first need to be run through the TABLE utility, which is included in the DOLINK and FASTMAP packages. It is available as estat21.zip via anonymous FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. FIRSTORD: A demonstration of a method for preliminary ordering of loci based on two-point lod scores. It is available as DOS executable and C source called first11.zip from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. LINKMEND: A program for converting LINKAGE-format files to MENDEL-format files. It is available by anonymous FTP from watson.hgen.pitt.edu as linkmend.tar.Z. MAP: A program to convert LINKMAP output into a table of multipoint lod scores. It is available by anonymous FTP from watson.hgen.pitt.edu as map.tar.Z. PEDPREP: A program for converting a MENDEL-format pedigree file ('pedm.dat') to a Pedigree/Draw file for graphical display on a Macintosh. It is available by anonymous FTP from watson.hgen.pitt.edu as pedprep.tar.Z. RECODE: A program for recoding character or sized-allele data into numbered-allele data. It is available by anonymous FTP from watson.hgen.pitt.edu as recode.tar.Z. 3.4) Why are some programs used primarily for human chromosome mapping, while others are used for human disease mapping? [1995/03/01] Any family can be used for chromosome mapping, so CEPH has picked a particular family "shape" and generated a large database with these families. Programs designed for chromosome mapping can be optimized for using these families, reducing the time needed for calculations. Only families afflicted with a disease can be used for disease gene mapping. As a result, programs designed for disease gene mapping need to be able to deal with arbitrary pedigrees. In addition, these programs need to be able to handle incomplete penetrance. 3.5) What programs are used for physical mapping? [1995/11/30] CLINKAGE: This is the special version of the LINKAGE programs for 3-generation CEPH pedigrees and codominant markers. The PC and VAX versions are available by FTP from linkage.cpmc.columbia.edu. The Unix version is available from corona.med.utah.edu. CHROMLOOK: This is a program for generating haplotypes of marker data in nuclear pedigrees with all individuals genotyped. It identified both the maternal and paternal recombination events, and provides the resulting haplotypes and recombinants in an easy-to-read format. It should be available via FTP server sometime this summer. It was written by Jonathan Haines and he can be contacted at haines@helix.mgh.harvard.edu. CINTMAX: This program is an extensively modified version of CILINK. It uses map functions to model the transmission of gametes from parent to child. Some of these map functions are multilocus feasible, and so can be used with more than 3 loci at a time. It is available by anonymous FTP from watson.hgen.pitt.edu as cintmax.tar.Z. CRI-MAP: This program has been used for chromosome mapping for years. It has options which can generate maps, calculate order probabilities, and printout recombination data. It works on .gen files with data from CEPH style families. It is written in K& R type C code, and the author Phil Green has successfully ran it on Unix, DOS, VMS, and Macintosh systems. It is not available via anonymous FTP. Phil Green distributes CRI-MAP freely ONLY to academics/academic institutions. Contact him at: Phil Green; Molecular Biotechnology Dept., FJ-20; Fluke Hall on Mason Rd.; Univ. of Washington; Seattle, WA 98195; USA; Phone (206) 685-4341; Fax (206) 685-7344; or email phg@u.washington.edu. FASTMAP: This program produces quick approximation to multipoint lod score, available as a DOS executable and C source as fstmap11.zip from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. MULTIMAP: This LISP based expert system uses an customized version of CRI-MAP to create a chromosome map. It is available via anonymous FTP from chimera.gene.cwru.edu. The authors T. Matise, M. Perlin, and A. Chakravarti continue to improve the code, add new functions, and provide excellent support. When used with the CRI-MAP chrompic option (to find double-recombinations to identify possible errors), it is incredibly useful. This is Unix-only (supported for DEC-Ultrix, HP9000, and Suns). The customized CRI-MAP version (called LISPCRI) is distributed at the FTP site, but was not meant to be used independently of MULTIMAP. MAPMAKER: Dr. Eric Lander; Whitehead Institute; 9 Cambridge Center; Cambridge, MA 02142; mapm%mitwibr@mitvma.mit.edu. MAPMAKER is available via FTP at genome.wi.mit.edu in /pub/mapmaker3. RHMAP: It is a set of three FORTRAN 77 programs that provide the means for a complete statistical analysis of RH mapping data. RH2PT is a program for data description and two-point analysis. It provides estimates of locus-specific retention probabilities and pairwise breakage probabilities, two-point lod scores for linkage of the various marker pairs, and linkage groups. RHMAP is now also available at the following URL http://www.sph.umich.edu/group/statgen/software. If you would like email notification of updates please send email to boehnke@umich.edu. 3.6) What programs are used for disease gene mapping? [1995/09/07] APM: The Affected Pedigree Member Method distribution contains the new APM programs, a new file conversion utility, and a histogram/statistics generator. To build the entire distribution, you need C, Pascal, and FORTRAN compilers, and a make utility is also helpful. The programs which are built include: APM, a program to calculate the single locus statistic over one or several marker loci; SIM, a program to simulate pedigrees and, using output files of APM, test for asymptotic normality of the null distribution; APMMULT, a program to generate the multilocus statistic; SIMMULT, a program like SIM but which simulates recombination and uses the output of APMMULT; CHAPM, a program to convert LINKAGE files to APM files, or APM files of one format to APM files of another format; and HIST, a program to compute various statistical figures, plot a histogram, and compute empirical p-values. The APMember package by D. Weeks is available via anonymous FTP from watson.hgen.pitt.edu. Additionally, there are pre-compiled executables of the APM programs for Sun-OS and Sun-Solaris available as newapm.sunos.tar.Z newapm.solaris.tar.Z. CLUMP: A Monte Carlo method for assessing significance of a case-control association study with a multi-allelic marker, available as DOS executable and C source. It is available as clump.zip via anonymous FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. ESPA: This is a program used for extended sib pair analysis. It comes in a DOS version and can only look at markers containing 5 alleles. It was written by Lodeijk Sandkuijl and can be obtained by writing to him at Voorstraat 27; Delft 2611 JK; THE NETHERLANDS. ERPA: A program for carrying out nonparametric linkage analysis, available as DOS executable and C source. It is called erpa12.zip via anonymous FTP at ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. FASTLINK: This is a much faster implementation of the main programs in LINKAGE (LODSCORE, ILINK, MLINK, LINKMAP) in C. The code is faster due to the use of new and better algorithms for the time intensive parts of the computation. FASTLINK is distributed by A. A. Schaffer from the FTP site softlib.cs.rice.edu (cd pub/fastlink). Version 1 of FASTLINK was instigated by R. W. Cottingham Jr. with implementation done by R. M. Idury and A. A. Schaffer. Version 2 of FASTLINK includes further improvements implemented by A. A. Schaffer, S. K. Gupta, and K. Shriram, with guidance from R. W. Cottingham Jr. Version 2 includes the capability to recover gracefully from a crash of the computer on which FASTLINK is running. FASTLINK was initially intended for UNIX machines, but the distribution now includes instructions for porting to VMS as well as a version for DOS. FASTLINK allows you to compile in "fast" or "slow" mode (the slow version of FASTLINK is still much faster than the old LINKAGE programs). The "fast" version uses lots of memory, but uses the extra memory to contain some of the intermediate results which are repetitively recalculated in the "slow" version (and the old linkage package). Best speed can be obtained by setting up 300 megs of virtual memory on a Unix workstation and using the "fast" version. Schaffer maintains a mailing list of fastlink users (fastlink-list@cs.rice.edu) to answer queries and keep users up to date. Schaffer, Gupta, and other colleagues at Rice University have implemented parallel versions of FASTLINK for either a shared-memory multiprocessor or a network of UNIX workstations. This version is now available as FASTLINK 2.3P at the above mentioned FTP site. Write to schaffer@cs.rice.edu for more information. GAS: It provides facilities for reading, writing, sectioning and performing statistical analyses on phenotypic and genotypic data and one of its features is sib pair analysis. It has been developed within the Department of Medicine at Oxford University and is available via FTP from well.ox.ac.uk in the directory pub/genetics/gas. GREGOR: It is a piece of DOS based software for producing simulated genetic data. It does not perform linkage analysis, but it may be useful for testing methods or assumptions about linkage analysis. GREGOR is operated by a series of hierarchical menus that permit the user to define hypothetical genetic scenarios (gene positions and effects) and produce simulated data-sets for a variety of population structures. GREGOR is available by FTP from the site sifon.cc.mcgill.ca in pub/McGill-Contrib. Questions should be directed to the authors tinker@agradm.lan.mcgill.ca or mather@agradm.lan.mcgill.ca. LINKAGE: This package of programs was developed by M. Lathrop with help from J. M. Lalouel, C. Jlier, and J. Ott. The LINKAGE package consists of several analysis and several utility programs. Versions are available for DOS, OS2, VAX, and Unix platforms. Here are some of the analysis programs: MLINK: 2-point lod-score calculations at fixed recombination distances; LINKMAP: multipoint lod score calculations at fixed distances; ILINK: calculates the recombination distance with the highest lod-score. Unix versions are available via gopher from corona.med.utah.edu in Publicly Accessible Software, probes(sts), etc./software/linkage, DOS and VMS versions are available from linkage.cpmc.columbia.edu, or on floppy disks, when you write to: Katherine Montague/Jurg Ott; Columbia University, Unit 58; 722 West 168th Street; New York, NY 10032. Send pre-formatted DOS disks if you request linkage by mail. You can send email to km165@columbia.edu if you need more information regarding mail requests for the LINKAGE package. LIPED: This DOS program written by J. Ott calculates probabilities for linkage between disease markers and genetic markers. Its input file differentiates between phenotypes and genotypes. As a result, this program is easiest to use when your data is from "old-style" genetic-markers (such as blood phenotype data). This was one of the first programs to do linkage analysis calculations, the LINKAGE package is more commonly used now. MIM: Multipoint IBD Method: mimintro.txt, mimsetup.txt, mim.txt, changes.txt, testa.dat, and testa.out. SAGE: Statistical Analysis Package for Genetic Epidemiology is composed of 18 programs: AGEON: Estimating the Distribution of Age-of-Onset, ASSOC: marker-trait Associations in Pedigree Data, BCROSS: Genetic Hypothesis for Quantitative Data on Inbred strains, their F1 and Backcross(es), CLUSTR: Power Transformation to Obtain Normality and Homoscedasticity from Clustered Data, FCOR: Family Correlations, FSP: Family Structure Program, LODLINK: Lod Score Linkage Analysis, MAPLOC: Mapping a Disease Related Trait Relative to a Set of Linked markers, MAXFUN: Function maximization Subroutine, REGC,REGD,REGTL,REGTN: Segregation Analysis Programs, RELATE: Relationship to Proband, SIBPAL: Sib-Pair Linkage Analysis, and DBSORT, RENUM, SPLIT: Toolkit Programs. Author Dr. R.C. Elston, address Department of Biometry and Genetics; Louisiana State University Medical Center; 1901 Perdido Street; New Orleans, Louisiana 70112, USA. The email contact address is sage@haldne.biogen.lsumc.edu. It is available for the following operating systems: VAX, SunOS 4.1.x, Apple Macintosh II, and DOS. This program is not shareware and must be bought. X-LINKED APM: X-linked version of the APM programs (single-marker), see APM above for more information on APM. It is available by anonymous FTP from watson.hgen.pitt.edu as xlinkapm.tar.Z. Also, xlinkapm.readm is available there, which is a readme about the X-linked version of the APM programs. 3.7) What programs are available for running linkage simulations? [1995/11/30] FASTSLINK: This is program is just like SLINK (see SLINK below), but it utilizes the enhancements incorporated into FASTLINK. It is available via anonymous FTP from watson.hgen.pitt.edu. SIMAPM: Is the SLINK based simulation program for the APM package. This represents a hacked together package which only runs under a Unix system. You will need FORTRAN, Pascal, and C compilers to use this package. It is available via anonymous FTP from watson.hgen.pitt.edu SIMLINK: This FORTRAN program developed by L. Ploughman and M. Boehnke simulates linkage analysis on a family, and gives you an estimate the probability, or power, of detecting linkage in a given family. It allows the researcher to determine whether a family has sufficient informativeness to detect linkage. SIMLINK requires large quantities of memory. It was written for DOS, but has been ported to many platforms. It is available from: Michael Boehnke; Department of Biostatistics; School of Public Health; University of Michigan; Ann Arbor, MI 48109-2029. No postage-money or blank disks are necessary to get SIMLINK sent to you. SIMLINK may be available via anonymous FTP soon. For further information send email to boehnke@umich.edu. SIMLINK is now also available at the following URL http://www.sph.umich.edu/group/statgen/software. If you would like email notification of updates please send email to boehnke@umich.edu. SLINK: It is a Pascal program developed by D. Weeks, M. Lathrop, and J. Ott. It is similar to SIMLINK. It is more general than SIMLINK in that it allows for partial marker typing at the locus to be generated, but it runs slower than SIMLINK. It is available from linkage.cpmc.columbia.edu and watson.hgen.pitt.edu or on floppies (use the same address as for LINKAGE). 3.8) What programs are available to help detect errors in linkage data? [1995/11/30] Typically the linkage packages in and of themselves will detect errors in linkage data that are obvious, such as impossible phenotypes and genotypes, and obvious errors in pedigrees. Typically the programs will just grind to halt and allow you to fix the error, and try again until you finally succeed. However, errors that "make sense" to linkage programs will not be detected. GENO: It is a genotype entry/edit tool that will allow you to easily enter and manipulate genotyping data. You can also check the quality of your data with the built-in Mendelian inheritance checker. The author the of program is Matt Stephenson and can be reaced at stephenm@bioimage.mfldclin.edu. The program is available via FTP from dgabby.mfldclin.edu in /pub/geno. GENOCHECK: It is an error checking program designed to identify individuals and loci that are likely to contain errors. the statistical method was designed to identify typing error, but is general enough to pinpoint any unlikely genotype still consistent with Mendelian inheritance. The author is Dr. Margaret Gelder Ehm the ftp site is at softlib.cs.rice.edu and it is in /pub/GenoCheck. It is written for Unix. 3.9) What programs help me recode genetic markers? [1995/03/01] DOLINK can downcode alleles automatically. However, the main use of DOLINK is to prepare files for LINKAGE from a database. In addition P. Adams package LABMAN and LINKMAN have features for the recoding of alleles. 4.0) LINKAGE PACKAGE SPECIFIC INFORMATION 4.1) How do I get my CEPH data into CRI-MAP format? [1995/03/01] You can output the file in linkage format and use link2gen in CRI-MAP. The disadvantage here is that your marker names are separated from your data and it's easy to make a mistake and get them mixed up. You can output the file in ped.out format and use CEPH2CRI mentioned above in the FAQ to do the conversion as well. 4.2) How do you calculate MAXHAP? [1995/09/09] MAXHAP is the maximum possible number of haplotypes in your analysis. You multiply together the number of alleles at each locus used in a particular run; not all loci in your dataset, just the loci you are using in that particular calculation. Remember that the affection status counts as two alleles, regardless of the number of liability classes. For example, if a dataset has the following information: the liability classes, marker A has 3 alleles, marker B has 4 alleles, and marker C has 5 alleles and your run includes a LINKMAP run between affection status, marker A, and marker B, then your MAXHAP must be at least 2*3*4=24. FASTLINK 2.3P includes an auxiliary program called ofm (optimize for maxhap) which can be used to automatically recompile the desired program with the ideal value of maxhap under the following assumptions: using UNIX or VMS (not DOS), running ILINK or LINKMAP or MLINK (not LODSCORE), the main script is produced by the LINKAGE auxiliary program LCP), and the locus file is produced by the LINKAGE auxiliary program PREPLINK; see README.ofm in the FASTLINK distribution. 4.3) When should you use binary coding instead of numeric allele coding? [1995/03/01] Usually there is no advantage to coding disease loci as either binary or numeric using liability classes. Generally, binary coding is more complex in that we humans often have a hard time thinking that way. Some of the codominant phenotypes lend themselves to binary coding; for example, ABO blood types: A (101), B (011), O (001), AB (111), and unknown (000). Since you cannot distinguish AO from AA at the phenotype level you code both genotypes as (101), presence of A and O. In reality O represents absence of both A and B. However, do not code using (000), since it would be an unknown. Use of binary codes has decreased since DNA markers have come into use since they allow one to type an individual with respect to genotype. You can use binary codes if you have phenotypic data which does not allow for the discrimination of the underlying genotype exactly, and one can code it as the presence with 1 or absence with 0 of factors such as the A and B antigens. Binary codes allow the representing loci with codominant and dominant mode of inheritance, while allele number notation is good only for codominant loci. Few people use binary factor notation. They either use allele numbers for codominant loci, or affection status notation for dominant loci. The main reason why binary factor notation is still currently used is that CEPH's database is in that notation. 4.4) What do you do when allele frequencies not add up to 1, for example, when alleles are not present in a pedigree under study? [1995/03/01] The best approach is to specify n+1 alleles, where there are n alleles actually observed in the pedigree. Use the correct allele frequencies for the n alleles, and for the n+1 allele, use 1 minus the sum of the frequencies of the observed alleles. 4.5) I use LINKAGE and/or FASTLINK, what references should I cite in my papers? [1995/03/01] FASTLINK users should cite: Cottingham, R. W. Jr., Idury, R. M., and Schaffer, A. A. "Faster Sequential Linkage Computations." American Journal of Human Genetics. 53:252-263, 1993. Schaffer, A. A. , Gupta, S. K., Shriram, K., and Cottingham, R. W. Jr. "Avoiding Recomputation in Linkage Analysis". Human Heredity. 44(4):225-37, 1994 Jul-Aug. In addition, all FASTLINK and LINKAGE users should also cite the LINKAGE papers: Lathrop, G.M., Lalouel, J.M., Julier, C. , and Ott, J. "Strategies for Multilocus Analysis in Humans." PNAS. 81:3443-3446, 1984. Lathrop, G.M. and Lalouel, J.M., "Easy Calculations of LOD Scores and Genetic Risks on Small Computers." American Journal of Human Genetics. 36:460-465, 1984. Lathrop, G.M., Lalouel, J.M., and R. L. White. "Construction of Human Linkage Maps: Likelihood Calculations for Multilocus Analysis." Genetic Epidemiology. 3:39-52, 1986. 4.6) What is recoding of alleles all about anyway? [1995/03/01] One of the problems with highly polymorphic markers is that they can increase the computational requirements of the computers by several orders of magnitude due to the large number of alleles present. This can put the computation of some lod scores out of reach for DOS computers and take many days on higher end systems. So it is important to use methods that reduce the number of alleles, and recoding will reduce the number of alleles in your calculations. The method of recoding of alleles described by J. Ott in the Annals of Human Genetics, 42:255-257 (1978) works very well, but can only be done when the mode of inheritance of the disease is known. An article inspired by Ott's original work written M. Braverman in Computers and Biomedical Research, 18:24-36 (1985) extends the recoding of alleles in two ways: 1) it allows for pedigrees of arbitrary structure, and 2) it allows for missing/partially known marker phenotypes. It is usually possible to recode marker alleles to some extent even if the mode of inheritance of the disease is not known since what is still desired with respect to the marker is a labeling which preserves the available information about the source of each marker allele. It is important, however, where the full ancestry of alleles cannot be traced in a pedigree, that the recoded alleles maintain the allele frequencies appropriate to the original alleles. In a complex disorder, this may not be possible. Another method is if the marker in question has 14 alleles in the general population, but only 9 alleles in the study population, it is possible to collapse the functional number of alleles to 9 or 10. Usually, adjust the allele frequencies to sum to 1 by dividing each allele frequency by the sum of the (observed) allele frequencies. For the latter all the allele frequencies remain the same, but the unobserved ones are collapsed into a single allele (and frequency). If there are 9 observed alleles (but there are 14 in the population), then rescaling the frequencies of the observed 9 alleles will also not produce quite correct results. Consider the unlikely example of a huge pedigree with only the most recent generation observed in which the observed 9 alleles all have very low and equal frequency. If there are distantly separated relatives who are affected there is some reasonable support for linkage since the alleles are rare. But if we rescale frequencies to 1/9 per alleles, then sharing of alleles isn't so unlikely. Coding the marker with 10 alleles produces correct results as it will produce the same lod scores as would coding the marker with 14 alleles. 4.7) What do you do when you get thetas greater than 0.5 when using LINKAGE? [1996/22/01] This seems to occur when the GEMINI optimization procedure prefers to go for a local optimum of a theta greater than 0.5 as a result of the starting theta values being to high in a LINKAGE run using ILINK or LODSCORE. This can easily be fixed by modifying the starting theta direclty with LCP or editing the LCP generated script. One can also modify the starting value with PREPLINK or by editing the data file containing allele and disease frequencies. This can be an iterative process and one should change theta values by an order of magnitude until reasonable thetas are obtained. One must also be careful of having intial thetas too low, this can also cause problems in the form of erroneous values. One can also run MLINK to examine what is happening at different thetas to determine the best starting theta. 5.0) COMPUTER ADMINISTRATION AND OPTIMIZATION 5.1) How can I increase the speed of the LINKAGE/FASTLINK package on my workstation? [1995/05/18] 1. Use FASTLINK, which is the C version of the LINKAGE package with a few algorithmic improvements. It can increase the speed of your calculations by an order of magnitude. 2. Setting up lots of paging space, which uses the hard drive as virtual memory (300 megs is usually plenty). Note that paging space is the same as swap space. Then use the "fast" versions of FASTLINK. 3. Use GCC, which is the GNU/Free Software Foundation C compiler, to compile FASTLINK. GCC produces machine language that is about 10% faster than Sun's C compiler. 4. Install the generic small kernel instead of the generic kernel. The generic kernel has device files for almost everything, and can slow the system down. The generic small kernel is configured for a system without many devices and without many users. Installing a generic small kernel is an option during system installation on Sun workstations. 5. Reconfigure your kernel so it has only devices you need. This should give you a small improvement in overall system speed, but if you are already running the generic-small kernel, additional improvement may be so small that it's not worth the trouble. If the generic small kernel is insufficient for your system this step is a must. The generic kernel will slow down your workstation significantly and most of the device support is unnecessary. 6. Don't run your linkage analyses in the background, because running programs in the background gives them a lower priority. Either do the runs in the foreground or you can use the root password to nice the pedin process by -3 to compensate (negative nice values give a higher priority). If you need to log out, you can use the screen command and "detach" a session so you can log out without programs terminating. Later you can log back in and "reattach" the session, which continued to run while you were logged out. The screen command is available at prep.ai.mit.edu and is also on the O'Reilly Unix Power Tools CD- ROM. According to the Sun documentation, nicing below -10 can interfere with the operating system and actually reduce the process' speed. Running them at the standard default level of 0 is usually sufficient. Some people recommend to run a background job to using nice +19 (!). In this way, the job will not interfere with other normal processes like login. 7. Runs with 100% penetrance can run faster than runs with incomplete penetrance. Of course, if you have an unaffected obligate carrier, this won't work. In addition, incomplete penetrance runs may be necessary for your research to be "good". 8. Change the block size of your file system. One can increase performance of a file system by increasing the block size, thus decreasing the number of read-write operations. A block device, such as a hard disk, usually accesses a block of data simultaneously. Thus, if one is expecting to use large files, having large blocks will be an advantage. However, one usually trades the number of bytes lost to partial files since one has to increase the fragment size to a number larger than 1024, for example 2048. That is, each file or part of a file occupies 2048 bytes, a file of 100 bytes will still occupy 2048 bytes. Therefore, bigger blocks give faster bigger blocks with bigger fragments and more lost space. 9. It has been noted that you can increase the speed of programs which create/access large files in the /tmp directory by creating a tmpfs file system. 10. Of course, buying more RAM will increase your speed. It's been said that increasing RAM from 16 to 32 megs will result in a large increase in speed and increasing RAM from 32-64 megs will result in a significant increase. However, increasing beyond 64 megs is not particularly helpful. 6.0) MOLECULAR BIOLOGY ISSUES IN LINKAGE ANALYSIS 6.1) What screening sets are available for linkage analysis? [1995/09/14] For humans there are the Weber lab screening sets: 3, 3A, 4, 4A, 5, 5A, and 6 . Primers for the markers within these sets are available from Research Genetics, both in unlabeled and fluorescent dye-conjugated forms. The information on these screening sets can be downloaded via FTP from dgabby.mfldclin.edu, they are in /pub. EOF From owner-gene-linkage@net.bio.net Tue Oct 14 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: <79506204@prodigy.com> Newsgroups: bionet.molbio.gene-linkage Subject: (guest) TONER Date: 15 Oct 1997 04:51:04 +0100 Lines: 49 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <621ej8$9jv@mserv1.dl.ac.uk> Original-To: friend@piblic.com BENCHMARK PRINT SUPPLY 1091 Redstone Lane Atlanta GA 30338 (770)399-0953 ***NEW ANNOUNCEMENT**** ********OUR NEW, LASER/FAX TONER CARTRIDGE,PRICES******** NOW AS LOW AS $39 & UP WE CARRY MOST ALL LASER PRINTER CARTRIDGES, FAX SUPPLIES AND COPIER TONERS AT WAREHOUSE PRICES INCLUDING: HEWLETT PACKARD SERIES 2,3,4,5,2P,3P,4P,5P,4L,5L,3SI,4SI,5SI IBM/LEXMARK SERIES 4019,4029,4039,4049,OPTRA EPSON SERIES 1000,1100,1500,6000,7000,8000 NEC SERIES 95 CANON FAX/LASER CARTRIDGES INCLUDING 700/770/5000/7000 CANON COPIER PC SERIES INCLUDING 3,6RE,7,10 HP FAX SERIES INCLUDING FX1,FX2,FX3 PRICES CHANGE WEEKLY, PLEASE CALL TO GET MOST RECENT PRICING AND AVAILABILITY. 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TO BE REMOVED FROM OUR LIST CLICK ON BLUE BELOW AND IN THE HEADER TYPE "REMOVE". click here From owner-gene-linkage@net.bio.net Tue Oct 14 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.gene-linkage Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 15 Oct 1997 02:00:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199710150900.CAA12342@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. 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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. 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From owner-gene-linkage@net.bio.net Sun Oct 19 23:00:00 1997 Path: biosci!ffp.csiro.au!Gavin.Moran From: Gavin.Moran@ffp.csiro.au (Gavin Moran) Newsgroups: bionet.molbio.gene-linkage Subject: postdoctoral position Date: 19 Oct 1997 18:08:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <2.2.32.19971020010623.0070733c@acacia> NNTP-Posting-Host: net.bio.net POSTDOCTORAL FELLOW AU$41K - AU$47K + Superannuation CSIRO Forestry and Forest Products and CRC for Sustainable Production Forestry Canberra, ACT, Australia The Division is seeking to appoint a molecular geneticist to work on the genetic basis of key quantitative traits for eucalypt breeding programs. The focus will be on wood and pulp traits in E. globulus. You will join a team which is carrying out research on molecular breeding of forest tree crops and assessment of genetic resources of native forests. The position will be funded by the CRC for Sustainable Production Forestry. The person we are seeking must have a PhD in genetics or a related field with experience in molecular techniques, including DNA marker technologies. Experience in genetic mapping and QTL analysis will be favourably received. You will need the ability to participate in collaborative studies and have excellent communication skills. The appointment will be for a period of three years. For further information contact Dr Gavin Moran on ph 612 62818208, fax 612 62818233, e-mail gavin.moran@ffp.csiro.au The duty statement and selection criteria for the position can be obtained from Kerrie Doutch Ph: 612 2818352, Fax: 612 62818312, e-mail: kerry.doutch@ffp.csiro.au Application must quote reference 97/0387 and include the names and addresses of two professional referees and can be forwarded to: The Personnel Manager CSIRO Forestry and Forest Products PO Box E4008 Kingston ACT 2604 Australia And should reach us by November 7 1997. Dr Gavin F. Moran Ph 616 2818208 Division of Forestry and Forest Products Fax 616 2818233 CSIRO Email gavin.moran@ffp.csiro.au PO Box E4008 Kingston ACT 2604 Australia From owner-gene-linkage@net.bio.net Wed Oct 22 23:00:00 1997 Path: biosci!BGSM.EDU!dbowden From: dbowden@BGSM.EDU (Don Bowden) Newsgroups: bionet.molbio.gene-linkage Subject: Installing GAS on IRX system Date: 23 Oct 1997 07:09:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <344F58F1.1840@bgsm.edu> NNTP-Posting-Host: net.bio.net We have been having trouble installing GAS on our IRX system. Apparently Alan Young is no longer at Oxford (??). Does anyone know where Alan can be reached, or who we can contact to get help in our installation. Thanks for your help. Don Bowden Wake Forest University Medical School From owner-gene-linkage@net.bio.net Mon Oct 27 22:00:00 1997 Path: biosci!MAIL.UWLAX.EDU!abler_ml From: abler_ml@MAIL.UWLAX.EDU (Mike Abler) Newsgroups: bionet.molbio.gene-linkage Subject: Genetics position Date: 27 Oct 1997 21:53:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.1.16.19971028005136.3ff70aae@mail.uwlax.edu> NNTP-Posting-Host: net.bio.net Assistant Professor - Genetics The University of Wisconsin- La Crosse invites applications for a tenure-track position in the Department of Biology/Microbiology. Applicants must have a Ph.D. in the field of genetics and a commitment to both teaching and research. The successful candidate will be expected to teach an introductory genetics course and an upper level undergraduate course in human/medical genetics. In addition, the successful candidate is expected to develop an externally funded research program for undergraduate and graduate (MS) students focusing on eukaryotic genetics, using an experimental system other than plants. Applicants should submit a letter of application, curriculum vitae, statements of teaching philosophy and research interests, graduate and undergraduate transcripts, and three letters of recommendation to: Dr. Thomas O. Claflin, Chair Department of Biology & Microbiology University of Wisconsin-La Crosse La Crosse, WI 54601 All application materials must be received no later than Dec. 1, 1997 UW-La Crosse is an Affirmative Action/Equal Opportunity Employer. Women, persons of color, and individuals with a disability are particularly encouraged to apply. From owner-gene-linkage@net.bio.net Thu Oct 30 22:00:00 1997 From: "PROMOTIONS" promotions@promotions-for-you6.com Newsgroups: bionet.molbio.gene-linkage Subject: >>> F R E E <<< Date: Wed, 22 Oct 1997 05:54:18 -0700 Organization: EFG1 Message-ID: <221097055418@promotions-for-you6.com> NNTP-Posting-Host: 206.139.152.37 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!out2.nntp.cais.net!in1.nntp.cais.net!newshub.sdsu.edu!newshub.csu.net!csulb.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!bullseye.news.demon.net!demon!gate.news.unisource.nl!amsterdam.news.unisource.nl!News.Amsterdam.UnisourceCS!newsfeed.mad.ibernet.es!uunet!in4.uu.net!news1.wt.net!news3.wt.net!206.139.152.37!promotions-for-you6.com Lines: 50 =================================== >>> F R E E V A C A T I O N S <<< =================================== *** FREE Akira 35mm Camera *** FREE 100 Rolls of Kodak/Fuji Film *** FREE $5.00 Prepaid Long Distance Calling Card *** Special Bonus Offer from CARNIVAL CRUISE LINES *** 3 DAY / 2 NIGHT STAY *** 105 LUXURIOUS RESORTS *** UP TO A FAMILY OF 5 *** SPECIAL PROMOTION *** LIMITED TIME OFFER !!! +++++++++++++++++++++++++++++ http://www.vacationpromotions.com +++++++++++++++++++++++++++++ =>><<<<=>=<>>=>><<>< From owner-gene-linkage@net.bio.net Fri Oct 31 22:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!gatech!141.211.144.13.MISMATCH!newsxfer3.itd.umich.edu!news-out.internetmci.com!newsfeed.internetmci.com!138.95.18.2!wilbur.sequent.com!newsfeed.orst.edu!128.101.135.70.MISMATCH!newshub.tc.umn.edu!newsstand.tc.umn.edu!lenti From: dean@lenti.med.umn.edu (Dean Flanders) Newsgroups: bionet.molbio.gene-linkage Subject: BIONET.MOLBIO.GENE-LINKAGE.FAQ Date: 1 Nov 1997 06:00:19 GMT Organization: University of MN, Medical School Lines: 1006 Message-ID: <63eghj$rh1@epx.cis.umn.edu> NNTP-Posting-Host: lenti.med.umn.edu Originator: dean@lenti.med.umn.edu BIONET.MOLBIO.GENE-LINKAGE FREQUENTLY ASKED QUESTIONS (FAQ) AS OF 1997/10/27 1.0) FAQ ADMINISTRATIVE INFORMATION [1995/05/18] 1.1) Where can I obtain and/or access the bionet.molbio.gene-linkage FAQ? [1995/03/01] 1.2) Who created the bionet.molbio.gene-linkage FAQ? [1995/03/01] 1.3) How can I help improve this FAQ? [1995/03/01] 1.4) Contributors to this FAQ. [1995/09/09] 1.5) When was the FAQ last updated? [1996/04/28] 2.0) INFORMATION RESOURCES 2.1) What anonymous FTP sites have programs/utilities useful for linkage analysis? [1995/03/01] 2.2) What books are helpful when learning about linkage analysis? [1995/03/01] 2.3) What WWW sites have useful linkage information? [1996/01/02] 2.4) What gopher sites have useful linkage information? [1995/03/01] 2.5) What "linkage centers" make information and assistance available to researchers? [1995/12/11] 2.6) What journals are useful for linkage analysis? [1995/06/02] 2.7) What courses are offered in linkage analysis? [1995/09/09] 3.0) GENE-LINKAGE SOFTWARE OVERVIEW 3.1) What database management programs do people use for linkage data? [1995/05/31] 3.2) What programs are available for pedigree drawing? [1995/04/01] 3.3) What linkage analysis helper programs are available? [1996/04/29] 3.4) Why are some programs used primarily for chromosome mapping, while others are used for disease mapping? [1995/03/01] 3.5) What programs are used for physical mapping? [1995/11/30] 3.6) What programs are used for disease gene mapping? [1995/09/07] 3.7) What programs are available for running genetic simulations? [1995/11/30] 3.8) What programs are available to help detect errors in linkage data? [1995/11/30] 3.9) What programs help me recode genetic markers? [1995/03/01] 4.0) LINKAGE PACKAGE SPECIFIC INFORMATION 4.1) How do I get my CEPH data into CRI-MAP format? [1995/03/01] 4.2) How do you calculate MAXHAP? [1995/09/09] 4.3) When should you use binary coding instead of numeric allele coding? [1995/03/01] 4.4) What do you do when allele frequencies do not add up to 1; for example, when alleles are not present in a pedigree under study? [1995/03/01] 4.5) I use LINKAGE and/or FASTLINK. Which references should I include in my papers? [1995/03/01] 4.6) What is recoding of alleles all about anyway? [1995/03/01] 4.7) What do you do when you get thetas greater than 0.5 when using linkage? [1996/22/01] 5.0) COMPUTER ADMINISTRATION AND OPTIMIZATION 5.1) How w can I increase the speed of the LINKAGE/FASTLINK package on my workstation? [1995/05/18] 6.0) MOLECULAR BIOLOGY ISSUES IN LINKAGE ANALYSIS 6.1) What screening sets are available for linkage analysis? [1995/09/14] 1.0) FAQ ADMINISTRATIVE INFORMATION 1.1) Where can I obtain the bionet.gene-linkage FAQ? [1995/03/01] It is available by anonymous FTP from lenti.med.umn.edu in /pub/linkage. The best way to view the FAQ is via the WWW, from http://lenti.med.umn.edu/linkage/linkage.html. The FAQ is also available via gopher at lenti.med.umn.edu in /Biologically Related Information/Linkage Analysis. The FAQ will also be posted in the USENET groups bionet.molbio.gene-linkage and news.answers the 1st and 15th of each month. 1.2) Who created the bionet.molbio.gene-linkage FAQ? [1995/03/01] Darrell Root (rootd@ohsu.edu) originally started the bionet.molbio.gene-linkage FAQ in May of 1994 in an attempt to share information and experiences that may be of use to other people involved in linkage analysis. I am Dean Flanders (dean@lenti.med.umn.edu), the current maintainer of the FAQ, and began my tenure in December of 1994. The FAQ will never serve as a short course in linkage analysis, but instead it will ideally be a place to help beginners get started in the area and to help experts not make the same mistakes as others. All of the information in this FAQ by no means comes completely from Darrell or me, but from a large number of people that work in the area of linkage analysis. Their names are listed at the end of this section of the FAQ. 1.3) How can I help improve this FAQ? [1995/03/01] Feel free to send any information that you think would be beneficial for other people who are just beginning in linkage or have been doing linkage for years to linkage@lenti.med.umn.edu. Also, if there is information you would like to see or errors in this FAQ please let us know by sending email to linkage@lenti.med.umn.edu. If you would like to see something changed or added to the FAQ please to send it in a format that can be quickly incorporated into the FAQ, such as correcting the errors in the section of the FAQ and emailing it back to the FAQ maintainer. 1.4) Contributors to this FAQ. [1995/09/09] David Adler, John Attwood, Michael Boehnke, Marcia Brott, Don Bowden, Michael Braverman, Lucien Bachner, Young B Choi, Kevin Crawford, Dave Curtis, Peter Doris, Bennett Dyke, David Featherstone, Dean Flanders, Jonathan Haines, Rob Harper, Pierre Janssens, David Kikuchi, Wentian Li, Tim Little, Tara Matise, Eli Meir, Mike Miller, Jurg Ott, Darrell Root, Alex Schaffer, Robert Stodola, Frank Visser, Dan Weeks, Ellen Wijsman, Scott Wildenberg, Matthias Wjst, and Kim Worley. 1.5) When was the FAQ last updated?[1996/04/29] The last update of the FAQ was on 1996/04/29. All sections should indicate what month and year they were last updated. In addition one can go to the list of updates that are maintained at http://lenti.med.umn.edu/linkage/gefaqup.html. This is a list in chronological order of updates with direct links to the updates in the FAQ. 2.0) INFORMATION RESOURCES 2.1) What anonymous-FTP sites have programs/utilities useful for linkage analysis? [1995/03/01] At present there is no one site that serves as a repository for all linkage software. So the best way of finding FTP site information is to read the software package information below, which should provide all of the necessary FTP information. 2.2) What books are helpful when learning about linkage analysis? [1995/03/01] Bishop, M. J. "Guide to Human Genome Computing." Academic Press, 1994. Davies, K. E. "Human Genetic Diseases - A Practical Approach." IRL Press, Oxford England and Washington, D.C., 1986. Dracopoli, N. C., Haines, J. L., Korf, B. R., Moir, D.T., Morton, C. C., Seidman, C. E., Seidman, J. G., Smith, D. R. "Current Protocols in Human Genetics." John Wiley and Sons, Inc., USA, 1994. Khoury, M. J., Beaty, T. H., and Cohen, B. H. "Fundamentals of Genetic Epidemiology." Oxford University Press, 1993. Ott, J. "Analysis of Human Genetic Linkage." Johns Hopkins University Press, 1991. Terwilliger, J. D. and Ott, J. "Handbook of Human Genetic Linkage," Johns Hopkins University Press, 1994. Thompson, E. A. "Pedigree Analysis in Human Genetics." Johns Hopkins University Press, Baltimore and London, 1986. 2.3) What WWW sites have useful linkage information? [1996/01/02] This is in no way an attempt to list the explosion of WWW sites of biological interest on the Internet, but it is a listing of some of the major ones and ones of particular interest in linkage analysis. http://www.yahoo.com/Science/Biology/Genetics/, this is a list of sites related to genetics that is kept very up to date. http://www.gdb.org/Dan/DOE/intro.html, this is a short course of sorts that gives some very basic information on how to go about gene mapping. http://lenti.med.umn.edu/linkage/linkage.html, which is serving as linkage analysis home page, will have links to all of the WWW sites listed as well as gopher servers and a hypertext version of the FAQ. http://www.genethon.fr, the Genethon Center, Genethon's home page. http://www.chlc.org, the Cooperative Human Linkage Center, CHLC's home page. http://gdbwww.gdb.org has a version of GDB available and access to OMIM. http://www.pathology.washington.edu has human and mouse standard idiograms. The idiograms are useful for making illustrations for gene mapping and for constructing abnormal chromosomes. The PostScript idiograms can be manipulated band by band with illustration software such as Adobe Illustrator, Aldus FreeHand, Canvas, and Altsys Virtuoso. http://www.gene.ucl.ac.uk/~john/programs.html contains software by John Attwood. http://www.gene.ucl.ac.uk/packages/dcurtis/ contains software by Dave Curtis. http://linkage.cpmc.columbia.edu has a lot of useful information on linkage analysis; in particular it offers information on software, the course offered by J. Ott, and the Linkage Newsletter. 2.4) What gopher sites have useful linkage information? [1995/03/01] There is one that will be maintained with links to other gophers of interest in linkage analysis, as well as links to other gopher servers of biologically related information. It is at lenti.med.umn.edu, and the path to it is Biologically Related Information/Genetic Linkage Analysis. 2.5) What "linkage centers" make information and assistance available to researchers? [1995/11/11] One such center is the Cooperative Human Linkage Center (CHLC). The goal of this center is to generate a high resolution map of the human genome and rapidly distribute this information to the genome community. They are in the process of identifying more human markers and developing high resolution framework maps. One can obtain information about CHLC from via gopher from gopher.chlc.org , http://www.chlc.org , ftp://ftp.chlc.org , info-server@chlc.org, or help@chclc.org. Among other things, CHLC provides primer selection and linkage analysis via email. Information on those services can be found by sending email to: primer- server@chlc.org and linkage-server@chlc.org. David Featherston (davidf@caos.kun.nl) from the Dutch EMBnet Node is starting a linkage analysis service: software availability, support/advice initially, possibly training, and perhaps consultancy. At present they have MapMaker/EXP 3.0b, MapMaker/QTL 1.1, Lathrop and Lalouel's LINKAGE package, and Schaffer's FASTLINK package. This means that if users have Genomics Package accounts at the CAOS/CAMM Center, they can use these programs on their fast computers to analyze their data sets. Please contact David Featherston if you are interested in more information about such an account. A major European center is the Human Genome Mapping Project Resource Centre in Hinxton, England. It is funded by the Medical Research Council, and has a broad range of software and databases available, mainly focused on the Human Genome Project. In the area of Linkage analysis it has the following programs available: FASTLINK, CRIMAP, MAP MAPMAKER, HOMOZ, PEDPACK, APM, SIMLINK, FASTMAP, COMDS, DOLINK & QDB, HANDLINK, GAS and Jurg Ott's collection of programs. The aim is to have all major (Unix-based) gene linkage packages available for our users. The Center also gives courses on linkage analysis. More information about the Centre can be obtained from it's home- page: http://www.hgmp.mrc.ac.uk/. If you want to register as user, send e-mail to admin@hgmp.mrc.ac.uk for a registration form. For more information about the gene-linkage services you can contact Frank Visser (fvisser@hgmp.mrc.ac.uk). INFOBIOGEN: This is the French GDB node that offers also a linkage server and assistance in the process of linkage analysis. It uses LINKAGE, FASTLINK and other programs running on a Sparc Center 2000E with 1 giga RAM, 4 Gig of swap, and 6 CPU's. For furhter information contact Lucien Bachner at bachner@infobiogen.fr or look at the following web site http://www.infobiogen.fr/. 2.6) What journals are useful for linkage analysis? [1995/06/02] American Journal of Human Genetics, Annals of Human Genetics, Computer Applications in Biosciences (CABIOS), Genomics, Genetic Epidemiology, Human Genome News (available by gopher from gopher.gdb.org), Human Genome Project Journal, Human Heredity, Journal of Computational Biology, Nature Genetics. 2.7) What courses are offered on linkage analysis? [1995/09/09] There are three primary courses offered throughout the yeart on human linkage analysis. One is a four day course offered once per year by Drs. Margaret Pericak-Vance and Jonathan Haines. The next course will be offered in late April, 1996 in Boston. The focus of the course is on the overall design of a human disease gene mapping study, with particular emphasis on the problems of common/complex disorders. The course covers clinical classification, pedigree ascertainment, collection, and follow-up, basic linkage techniques, linkaghe and association analysis for complex disorders, laboratroy technqiues for genotyping, and gene characterization. The courseemphasizes the global decision-making process, rather than details of specific techniques. For more information write to Genetic Methods Course; c/o Dr. Margaret Pericak- Vance; Division of Neurology, Box 2900; Duke University Medical Center; Durham, NC 27710, or you can send e-mail to genclass@genemap.mc.duke.edu. The remaining two courses are both offered by Jurg Ott on the software used for human linkage. One is a beginner's course, and the other an advanced course for those familiar with the linkage analysis software. These courses are offered several times throughout the year and you can get more information by contacting Katherine Montague/Jurg Ott; Columbia University, Unit 58; 722 West 168th Street; New York, NY 10032. In addition you can fax to (212)568- 2750 or call (212)960 2507 or email km165@columbia.edu for more information. A new beginner's level linkage course will be offered in French October 24-25 1995 by INFOBIOGEN, in Villejuif south suburb of Paris. It's free for all academic institutions. For furhter information contact Lucien Bachner at bachner@infobiogen.fr or linkage@infobiogen.fr. 3.0) GENE-LINKAGE SOFTWARE OVERVIEW 3.1) What database management programs do people use for linkage data? [1995/05/31] One must be aware that some pedigree drawing software can also serve as databases for data as well as drawing pedigrees, see the next question in the FAQ for a description of those packages. CEPH DBMS: The CEPH DataBase Management System is specifically designed for chromosome mapping with CEPH style pedigrees. It can output data in ped.out format for the LINKAGE package. This program can now be picked up via anonymous FTP from ftp.cephb.fr in pub/ceph_genotype_db. DOLINK: This DOS custom database program by D. Curtis manages genetic data and sets up input files for linkage analysis. It is available from ftp.gene.ucl.ac.uk. The DOS and Windows versions of DOLINK program help manage genetic data and setup analysis. It is available with the C++ source allowing compilation on Unix host running X and possibly a Macintosh. File Express: This is a DOS shareware database which can be used to hold data for DOLINK (largely superseded by QDB). It is available as fe51-a/b/c.zip via FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. LABMAN and LINKMAN: These are linkage analysis databases for holding linkage data and exporting it in various formats for linkage analysis. They are available via anonymous FTP from lenti.med.umn.edu in /pub/linkage/labman. These databases were developed by P. Adams of Columbia University. LYNKSYS: This custom-made database program was written by J. Attwood and S. Bryant. Although they continue to use it, J. Attwood suggests using DOLINK instead. LINKSYS is not currently available at any FTP sites. Map Manager: It is a program for the Macintosh which helps analyze the results of genetic mapping experiments using backcrosses, intercrosses, or recombinant inbred strains. In addition it also has tools for statistical analysis of experiments. The program was created by K. F. Manly at the Roswell Cancer Institute and is available via FTP from mcbio.med.buffalo.edu in /pub/MapMgr. QDB: This is a database program available as DOS and Windows versions and with C++ source allowing compilation for X and possibly Macintosh. It is available as qdb16a.zip via FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. 3.2) What programs are available for pedigree drawing? [1997/10/27] One of the tricks of managing individuals in a mapping study is trying to get the database you are using to export your family data in a format acceptable for input into pedigree drawing programs. The marriage between these two can be of great assistance. However, some pedigree drawing programs have databases as a part of the package. CYRILLIC: This is a pedigree editor for Windows with facilities for including marker data which you can then have it output the input files for LINKAGE. It is Windows-based, so input of the pedigree is very efficient. You also have a data form associated with each individual where you can store names and other pertinent data. It also has the ability to interface with most standard PC databases. This program is not public domain and is available from Cherwell Scientific Publishing. If you would like more information send email to csp@sable.ox.ac.uk and they would be very happy to send you a demo of the program. Version 2 of Cyrillic should be coming out late summer of 1995. FTREE: This is a DOS pedigree program written by R. Go at the University of Alabama. GENETREE: GeneTree 1.0 is a DOS package which provides a convenient way to draw family tree diagrams suitable for genetics or genealogy. The package consists of the GeneTree program, which draws pedigree diagrams using a command language; and SC, using a menu driven program that facilitates creation of GeneTree commands. GeneTree and SC are made available with program manuals, examples of family tree diagrams, and a GeneTree Quick Reference Guide. GeneTree is written in C. Note that it is a DRAWING program and does not compute genetic parameters. The GeneTree program is available from wijsman@max.u.washington.edu at a price of $125 (because of licensing fees from a private company which wrote one of the drivers used in the program). KINDRED: This new DOS database program, distributed by Epicenter Software, is specifically designed for linkage analysis. A free demo is available by calling (818)-304-9487. In addition to database duties, this program will draw pedigrees, haplotype marker data, and can output data in LINKAGE format. PEDPAK: This package is designed to handle large datasets for animals. The package was written and distributed by Alan Thomas, who is in Bath, England. The software is not public domain and must be purchased. Pedigree/Draw: It is a Macintosh based program, written by B. Dyke, P. Mamelka, and J. MacCluer. It is available from bdyke@darwin.sfbr.org or Pedigree/Draw; Department of Genetics; Southwest Foundation for Biomedical Research; PO. Box 28147; San Antonio, TX 78228-0147. An upgrade from a previous version is $10, the current version is 4.4. Documentation costs $10 printed and the full package including documentation costs $45. There is a script which converts linkage format to Pedigree/Draw available via anonymous FTP at ftp.ee.pdx.edu in /pub/users/cat/rootd/convert.new. PEDRAW: This program is a pedigree drawing program written by D. Curtis for DOS and available via FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. The most current version is called pedraw16.zip. A companion program to PEDRAW is PEDHELP, it is a pop-up help for PEDRAW. PAP: The Pedigree Analysis Package (PAP) is a set of FORTRAN 77 programs for computing likelihoods and simulating phenotypes of genetic models on pedigrees. It is available via gopher from corona.med.utah.edu in Publicly Accessible Software, probes(sts), etc./software/pap. 3.3) What linkage analysis helper programs are available? [1996/04/29] CEPH2CRI: This program converts to output from the CEPH DBMS into the format useable in CRI- MAP. It can be found at ftp.gene.ucl.ac.uk in /pub/packages/linkage_utils. EASISTAT: This is a DOS statistics package, it contains EASIGRAF which draws graphs of lod scores from the output of FASTMAP. The lod scores first need to be run through the TABLE utility, which is included in the DOLINK and FASTMAP packages. It is available as estat21.zip via anonymous FTP from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. FIRSTORD: A demonstration of a method for preliminary ordering of loci based on two-point lod scores. It is available as DOS executable and C source called first11.zip from ftp.gene.ucl.ac.uk in /pub/packages/dcurtis. LINKMEND: A program for converting LINKAGE-format files to MENDEL-format files. It is available by anonymous FTP from watson.hgen.pitt.edu as linkmend.tar.Z. MAP: A program to convert LINKMAP output into a table of multipoint lod scores. It is available by anonymous FTP from watson.hgen.pitt.edu as map.tar.Z. PEDPREP: A program for converting a MENDEL-format pedigree file ('pedm.dat') to a Pedigree/Draw file for graphical display on a Macintosh. It is available by anonymous FTP from watson.hgen.pitt.edu as pedprep.tar.Z. RECODE: A program for recoding character or sized-allele data into numbered-allele data. It is available by anonymous FTP from watson.hgen.pitt.edu as recode.tar.Z. 3.4) Why are some programs used primarily for human chromosome mapping, while others are used for human disease mapping? [1995/03/01] Any family can be used for chromosome mapping, so CEPH has picked a particular family "shape" and generated a large database with these families. Programs designed for chromosome mapping can be optimized for using these families, reducing the time needed for calculations. Only families afflicted with a disease can be used for disease gene mapping. As a result, programs designed for disease gene mapping need to be able to deal with arbitrary pedigrees. In addition, these programs need to be able to handle incomplete penetrance. 3.5) What programs are used for physical mapping? [1995/11/30] CLINKAGE: This is the special version of