From chitsukha1 from yahoo.com Mon Sep 14 17:35:37 2009 From: chitsukha1 from yahoo.com (Testing) Date: Tue Sep 15 09:51:05 2009 Subject: [Bio-software] Handling NA's in REST 2008 software Message-ID: <411476.86363.qm@web83001.mail.mud.yahoo.com> Hello, ? Can any PCR data analysis experts in the forum please answer this question ? ? How does one handle NA's (unknown data items) while analysing PCR data using REST 2008 software ? ? NA are not accepted by the program. While zeros are accepted, I suspect, the results are not correct if zeros are used instead of NAs. ? Thanks Suki From faizabg from gmail.com Tue Sep 15 21:28:09 2009 From: faizabg from gmail.com (FAIZ-UL HASSAN) Date: Wed Sep 16 07:10:41 2009 Subject: [Bio-software] Scoring of AFLP bands Message-ID: Hi I want to know about analysis of AFLP gels using some statistical software. Can any body guide me about co-dominant scoring of AFLP bands. Many thanks in advance. Regards Faiz FAIZ-UL-HASSAN Lecturer Department of Animal Breeding and Genetics University of Agriculture, Faisalabad, Pakistan Phone 00 92 41 9200161-70 Ext. 3202 Cell 00 92 333 8317328 From Vince.Mulholland from sasa.gsi.gov.uk Thu Sep 17 04:13:07 2009 From: Vince.Mulholland from sasa.gsi.gov.uk (Vince Mulholland) Date: Thu Sep 17 10:04:50 2009 Subject: [Bio-software] Software to display genetic and geographical relationships - any suggestions? Message-ID: Hi, I have some viral sequences from around the world. When I construct dendrograms they suggest a geographical relationship in the clustering of the sequences. Is there any software I can use which could simultaneously analyse genetic distances AND geographical distances to represent the clustering I can see. I had thought of principal co-ordinate analysis (PCA), but if there is something out there designed to do this sort of thing that would be better. Any suggestions (including how I could do a PCA on these data) would be gratefully received. Vince Vincent Mulholland Science and Advice for Scottish Agriculture (SASA) SASA is a Division of the Scottish Government Rural Payments and Inspections Directorate Correspondents should note that all communications to or from SASA (Science and Advice for Scottish Agriculture – a Division of the Rural Payments and Inspections Directorate of the Scottish Government) may be automatically logged, monitored and/or recorded for lawful purposes. The original of this email was scanned for viruses by the Government Secure Intranet (GSi) virus scanning service. On leaving the GSi this email was certified virus-free. From Heather.Vincent from manchester.ac.uk Mon Sep 21 01:30:42 2009 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Mon Sep 21 10:02:33 2009 Subject: [Bio-software] Professional development through distance learning Message-ID: <4AB71D92.2010906@manchester.ac.uk> At the University of Manchester, UK, we have over 10 years experience in providing advanced, multidisciplinary, training to participants from a range of backgrounds, including Biology, Healthcare, Medicine and Computer Science. These courses are designed to enable biologists and computer scientists to update their skills while remaining in the workplace. Our distance courses are also very suitable for home study, helping you to keep in touch with a research environment while taking a career break. The courses beginning on 5 October 2009 include: - Introduction to Bioinformatics - Bioinformatics for Systems Biology - Introduction to software development in Java - Theory and Applications in Bioinformatics You will find further information, including fees and a link to the online application form, here: http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any questions, or need advice on the module options, please contact Heather.Vincent@manchester.ac.uk From conf from topaz.gatech.edu Fri Sep 25 18:17:18 2009 From: conf from topaz.gatech.edu (Georgia Tech Conference Announcement) Date: Fri Sep 25 19:20:52 2009 Subject: [Bio-software] 7th Georgia Tech - ORNL Conference on Bioinformatics Message-ID: <20090925231718.CE68E7D4864@topaz.gatech.edu> The 7th Georgia Tech - ORNL Conference on Bioinformatics - In silico Biology: Genome Biology and Bioinformatics will be held in Atlanta, Georgia, November 12-14, 2009 http://www2.isye.gatech.edu/binf2009/ Georgia Tech continues the tradition of organizing bi-annual International Conference on Bioinformatics, bringing together leading researchers in genomics, bioinformatics and genome biology to present recent advances in the field and to discuss open problems. Important Dates Deadline for early registration: October 15, 2009 Deadline for poster abstract subsmission: October 1, 2009 Notification of acceptance of abstracts: October 11, 2009 We invite papers submissions in the following areas * genomics * transcriptomics * proteomics * reconstruction and modeling of gene networks * evolutionary biology SPEAKERS Margaret O. Dayhoff lecture: David Lipman , NCBI/NIH, Bethesda, MD, USA Plenary Speakers: Vineet Bafna, University of California at San Diego, USA Gill Bejerano, Stanford University, Stanford, CA, USA Jeffrey Bennetzen, University of Georgia, Athens, GA, USA Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA Nick Grishin, University of Texas, Dallas, TX, USA Curtis Huttenhower, Harvard University, Boston, MA, USA King Jordan, Georgia Tech, Atlanta, GA, USA Igor Jouline (Zhulin), University of Tennessee - ORNL, Oak Ridge, TN, USA Eugene Koonin, NCBI/NIH, Bethesda, MD, USA Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA Boris Lenhard, University of Bergen, Norway Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA Yael Mandel-Gutfreund, Technion, Israel Insitute of Technology, Haifa, Israel Joanna Masel, University of Arizona, Tucson, AZ, USA Andrey Mironov, Moscow State University, Russia Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA Natasa Przulj, University of California at Irvine, CA, USA John Reinitz, State Uiversity of New York at Stony Brook, NY, USA Pierre Rouze, Gent University, Gent, Belgium CONFERENCE CHAIRS Mark Borodovsky, Georgia Tech and Emory University Eva K. Lee, Georgia Tech and Emory University PROGRAM COMMITTEE Nicholas Bergman, Georgia Tech Dmitrij Frishman, Technische Universitaet Muenchen, Germany Andrey Gorin, Oak Ridge National Laboratory Andrzej M. Kierzek, University of Surrey, UK. Eileen Kraemer, University of Georgia Jun Liu, Harvard University Hannah Margalit, Hebrew University Andrey Rzhetsky, University of Chicago Andre Rogatko, Samuel Oschin Comprehensive Cancer Institute Gary Stormo, Washington University Lance Waller, Emory University Ying Xu, University of Georgia and Oak Ridge National Laboratory Soojin Yi, Georgia Tech Igor Zhulin, Oak Ridge National Laboratory and University of Tennessee ADMINISTRATION Harry Sharp, Georgia Tech CONFERENCE LOCATION The Georgia Tech Ferst Center for the Arts. The Georgia Tech campus is located in Midtown Atlanta near the center of the 1996 Olympic development, close to the Fox Theatre and Margaret Mitchell house. From rapacki from cbs.dtu.dk Mon Sep 28 22:52:42 2009 From: rapacki from cbs.dtu.dk (Kristoffer Rapacki) Date: Tue Sep 29 01:48:40 2009 Subject: [Bio-software] Perl-SQL-WebServices workshop at CBS-DTU Message-ID: EMBRACE Workshop on Perl, SQL and Web Services, CBS, November 16-20, 2009 The workshop will be held at the Center for Biological Sequence Analysis (CBS), Technical University of Denmark. The workshop is intended to give the participant an introduction to a set of skills needed to perform basic bioinformatics work without the assistance of professional programmers. It will cover a general-purpose scripting language (Perl), database manipulation (SQL) and programmatic access to remote resources (Web Services). Brief introductory lectures will be followed by extensive hands-on exercises aiming at the ability to develop clean, efficient Perl scripts accessing relational databases and remote resources. There will be template scripts to take home and develop further in the context of the participant's own work. The workshop is open to everybody, free of charge. PhD students can receive credits for participation (for details please consult Dorthe Kjaersgaard at dorthek@cbs.dtu.dk). For registration and more information please see the workshop page: http://www.cbs.dtu.dk/courses/embrace/2009-11-16/ Registration deadline is on September 30, 2009. Kristoffer Rapacki ------------------------------------------------------------------------ Kristoffer Rapacki Center for Biological Sequence Analysis phone: +45 4525 2483 Department of Systems Biology fax: +45 4593 1585 Technical University of Denmark Building 208 e-mail: rapacki@cbs.dtu.dk DK-2800 Lyngby Denmark ------------------------------------------------------------------------