From johnv at silicocyte.com Tue Jun 3 05:39:11 2003 From: johnv at silicocyte.com (John) Date: Tue, 3 Jun 2003 15:09:11 +0530 Subject: [BiO BB] (no subject) Message-ID: <017401c329b4$008ae2e0$a801a8c0@sapna> Dear SIr/Madam, We wish to post the following attached message to the list members bio_bulletin_board. We are a bioinformatics company called Cytogenomic Inc, and are promoting our comprehensive end-to-end microarray analysis software, Silicocyte. The information regarding this would be beneficial to scientists conducting microarray analysis experimentation. This is a complete solution in itself, giving a single platform for operation of the entire microarray analysis, eliminating the need for scientists to employ different pieces of software for different funcitons in the microarray analysis. We request you to post this message to the list members of your mailing list as this would certainly be an important piece of information for them. Warm regards, Sapna Singh Marketing Executive Cytogenomic Inc sapna.s at silicocyte.com support at silicocyte.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bulkJunedrft.doc Type: application/msword Size: 22016 bytes Desc: not available URL: From bio_front at hotmail.com Tue Jun 3 07:14:17 2003 From: bio_front at hotmail.com (MyungHo Kim) Date: Tue, 3 Jun 2003 07:14:17 -0400 Subject: [BiO BB] 2D Electrophoresis Gel Image in Proteomics Message-ID: 2D Electrophoresis Gel Image and Diagnosis of a Disease The process of diagnosing a disease from the 2D gel electrophoresis image is a challenging problem. This is due to technical difficulties of generating reproducible images with a normalized form and the effect of negative stain. Here, we discuss a new concept of interpreting the 2D images and overcoming the aforementioned technical difficulties. This concept makes use of 2D gel images of proteins in serums and we explain a way of representing the images as vectors in order to apply machine-learning methods, such as the support vector machine, a decision tree, and neural network etc. (For details, see www.biofront.biz or http://arxiv.org/abs/cs.CC/0305048) 1. Representation I) Taking the whole image By enumerating the whole set of numbers (densities) corresponding to each pixel in a predetermined order, we will represent an image as a vector in a finite dimensional Euclidean space. II) Choosing spots Choose a finite number, K, of conspicuous spots representing proteins and their quantities, for example, we may take CA-1, BD-1 CA-2 and CA-3. Each of these chosen spots will have a corresponding number, which is the sum of the numbers assigned to each pixel consisting of the spot. Thus, the sum of each spot will represent the relative quantity of the protein corresponding to the spot relative to other spots. By enumerating the quantities of those four proteins, we have a vector in the four dimensional Euclidean space. Discussions: At a glance, in representing an electrophoresis image, the second method seems more natural than the first one. However, though considering the quantities of proteins looks intuitive and appealing to biological meaning, the procedure of measuring the relative quantities of chosen proteins may not be accurate for our purpose. On the contrary, accepting the whole image could contain more than we realize. We all know from a meticulous analysis that recognition of a person with a picture is due to the human brain??s ability of computing relative positions of specific objects such as nose, eye, mouth, ears, distance between eyes. Each pixel with its own density plays a role as a member of a whole image. Though each pixel does not give any clue by itself, all pixels together with others send us a concrete picture we conceive. Therefore, it is reasonable to say that the intrinsic invariants of an image are the relative position of a pixel with its density. The first method is about considering the whole package of all relative positions and their densities. 2. Problems in 2D gel image and its staining methods 2D gel electrophoresis is a method that separates proteins in a 2-dimensional plane by mass and pH of proteins. As is often the case in the most of experiments, there are two technical problems we have to compromise so that the process of numericalization is acceptable and tolerable. 1. When the amount of a certain protein reaches a ??threshold??, the silver stain density decreases. This phenomenon is known as the negative staining effect. 2. Even if the experiments are performed carefully, there always will be some variations of images. For example, in the image, the same protein will not be in the same position relative to other proteins. Discussions: Conceptually we need to find out a method of representation of each serum, which is reproducible with some tolerable variations. This attempt, as we did in the previous discussion, is feasible. Whatever qualities we observe, estimate or sample, there are variations in measurements or recording, since everything changes and it is impossible to produce the equivalent results every time. For example, our heights changes at morning and night, and blood pressures vary every hour. Likewise, there are variations in 2D gel images even under the assumption that all the experiments are perfectly accurate and executed the exactly same way. It could be caused by the status of a donor of serums or experimental setting. However, patterns of the variations seem quite consistent and, if we ponder our heights in micrometer, then it is even natural to accept an image as it is. From drjohn08318 at yahoo.com Tue Jun 3 14:21:04 2003 From: drjohn08318 at yahoo.com (John G. Hoey, Ph.D.) Date: Tue, 3 Jun 2003 11:21:04 -0700 (PDT) Subject: [BiO BB] 2D Electrophoresis Gel Image in Proteomics In-Reply-To: Message-ID: <20030603182104.4582.qmail@web14402.mail.yahoo.com> Check out 2D DIGE technology from Amersham! MyungHo Kim wrote: 2D Electrophoresis Gel Image and Diagnosis of a Disease The process of diagnosing a disease from the 2D gel electrophoresis image is a challenging problem. This is due to technical difficulties of generating reproducible images with a normalized form and the effect of negative stain. Here, we discuss a new concept of interpreting the 2D images and overcoming the aforementioned technical difficulties. This concept makes use of 2D gel images of proteins in serums and we explain a way of representing the images as vectors in order to apply machine-learning methods, such as the support vector machine, a decision tree, and neural network etc. (For details, see www.biofront.biz or http://arxiv.org/abs/cs.CC/0305048) 1. Representation I) Taking the whole image By enumerating the whole set of numbers (densities) corresponding to each pixel in a predetermined order, we will represent an image as a vector in a finite dimensional Euclidean space. II) Choosing spots Choose a finite number, K, of conspicuous spots representing proteins and their quantities, for example, we may take CA-1, BD-1 CA-2 and CA-3. Each of these chosen spots will have a corresponding number, which is the sum of the numbers assigned to each pixel consisting of the spot. Thus, the sum of each spot will represent the relative quantity of the protein corresponding to the spot relative to other spots. By enumerating the quantities of those four proteins, we have a vector in the four dimensional Euclidean space. Discussions: At a glance, in representing an electrophoresis image, the second method seems more natural than the first one. However, though considering the quantities of proteins looks intuitive and appealing to biological meaning, the procedure of measuring the relative quantities of chosen proteins may not be accurate for our purpose. On the contrary, accepting the whole image could contain more than we realize. We all know from a meticulous analysis that recognition of a person with a picture is due to the human brain??s ability of computing relative positions of specific objects such as nose, eye, mouth, ears, distance between eyes. Each pixel with its own density plays a role as a member of a whole image. Though each pixel does not give any clue by itself, all pixels together with others send us a concrete picture we conceive. Therefore, it is reasonable to say that the intrinsic invariants of an image are the relative position of a pixel with its density. The first method is about considering the whole package of all relative positions and their densities. 2. Problems in 2D gel image and its staining methods 2D gel electrophoresis is a method that separates proteins in a 2-dimensional plane by mass and pH of proteins. As is often the case in the most of experiments, there are two technical problems we have to compromise so that the process of numericalization is acceptable and tolerable. 1. When the amount of a certain protein reaches a ??threshold??, the silver stain density decreases. This phenomenon is known as the negative staining effect. 2. Even if the experiments are performed carefully, there always will be some variations of images. For example, in the image, the same protein will not be in the same position relative to other proteins. Discussions: Conceptually we need to find out a method of representation of each serum, which is reproducible with some tolerable variations. This attempt, as we did in the previous discussion, is feasible. Whatever qualities we observe, estimate or sample, there are variations in measurements or recording, since everything changes and it is impossible to produce the equivalent results every time. For example, our heights changes at morning and night, and blood pressures vary every hour. Likewise, there are variations in 2D gel images even under the assumption that all the experiments are perfectly accurate and executed the exactly same way. It could be caused by the status of a donor of serums or experimental setting. However, patterns of the variations seem quite consistent and, if we ponder our heights in micrometer, then it is even natural to accept an image as it is. _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Do you Yahoo!? Free online calendar with sync to Outlook(TM). -------------- next part -------------- An HTML attachment was scrubbed... URL: From drjohn08318 at yahoo.com Tue Jun 3 14:21:00 2003 From: drjohn08318 at yahoo.com (John G. Hoey, Ph.D.) Date: Tue, 3 Jun 2003 11:21:00 -0700 (PDT) Subject: [BiO BB] 2D Electrophoresis Gel Image in Proteomics In-Reply-To: Message-ID: <20030603182100.4561.qmail@web14402.mail.yahoo.com> Check out 2D DIGE technology from Amersham! MyungHo Kim wrote:2D Electrophoresis Gel Image and Diagnosis of a Disease The process of diagnosing a disease from the 2D gel electrophoresis image is a challenging problem. This is due to technical difficulties of generating reproducible images with a normalized form and the effect of negative stain. Here, we discuss a new concept of interpreting the 2D images and overcoming the aforementioned technical difficulties. This concept makes use of 2D gel images of proteins in serums and we explain a way of representing the images as vectors in order to apply machine-learning methods, such as the support vector machine, a decision tree, and neural network etc. (For details, see www.biofront.biz or http://arxiv.org/abs/cs.CC/0305048) 1. Representation I) Taking the whole image By enumerating the whole set of numbers (densities) corresponding to each pixel in a predetermined order, we will represent an image as a vector in a finite dimensional Euclidean space. II) Choosing spots Choose a finite number, K, of conspicuous spots representing proteins and their quantities, for example, we may take CA-1, BD-1 CA-2 and CA-3. Each of these chosen spots will have a corresponding number, which is the sum of the numbers assigned to each pixel consisting of the spot. Thus, the sum of each spot will represent the relative quantity of the protein corresponding to the spot relative to other spots. By enumerating the quantities of those four proteins, we have a vector in the four dimensional Euclidean space. Discussions: At a glance, in representing an electrophoresis image, the second method seems more natural than the first one. However, though considering the quantities of proteins looks intuitive and appealing to biological meaning, the procedure of measuring the relative quantities of chosen proteins may not be accurate for our purpose. On the contrary, accepting the whole image could contain more than we realize. We all know from a meticulous analysis that recognition of a person with a picture is due to the human brain??s ability of computing relative positions of specific objects such as nose, eye, mouth, ears, distance between eyes. Each pixel with its own density plays a role as a member of a whole image. Though each pixel does not give any clue by itself, all pixels together with others send us a concrete picture we conceive. Therefore, it is reasonable to say that the intrinsic invariants of an image are the relative position of a pixel with its density. The first method is about considering the whole package of all relative positions and their densities. 2. Problems in 2D gel image and its staining methods 2D gel electrophoresis is a method that separates proteins in a 2-dimensional plane by mass and pH of proteins. As is often the case in the most of experiments, there are two technical problems we have to compromise so that the process of numericalization is acceptable and tolerable. 1. When the amount of a certain protein reaches a ??threshold??, the silver stain density decreases. This phenomenon is known as the negative staining effect. 2. Even if the experiments are performed carefully, there always will be some variations of images. For example, in the image, the same protein will not be in the same position relative to other proteins. Discussions: Conceptually we need to find out a method of representation of each serum, which is reproducible with some tolerable variations. This attempt, as we did in the previous discussion, is feasible. Whatever qualities we observe, estimate or sample, there are variations in measurements or recording, since everything changes and it is impossible to produce the equivalent results every time. For example, our heights changes at morning and night, and blood pressures vary every hour. Likewise, there are variations in 2D gel images even under the assumption that all the experiments are perfectly accurate and executed the exactly same way. It could be caused by the status of a donor of serums or experimental setting. However, patterns of the variations seem quite consistent and, if we ponder our heights in micrometer, then it is even natural to accept an image as it is. _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Do you Yahoo!? Free online calendar with sync to Outlook(TM). -------------- next part -------------- An HTML attachment was scrubbed... URL: From willy.valdivia at ndsu.nodak.edu Wed Jun 4 22:47:02 2003 From: willy.valdivia at ndsu.nodak.edu (willy.valdivia at ndsu.nodak.edu) Date: Wed, 4 Jun 2003 21:47:02 -0500 (CDT) Subject: [BiO BB] Third Virtual Conference on genomics and bioinformatics Message-ID: <3725.129.44.48.162.1054781222.squirrel@webmail.ndsu.NoDak.edu> Third Virtual Conference on Genomics and Bioinformatics http://www.ndsu.edu/virtual-genomics/conference_2003.htm Advances in sequence analysis, transcriptional profiling, protein structural elucidation and other genomic techniques are producing an overwhelming accumulation of data and the shift in the way biological research is conducted. As new disciplines are integrated, the "Virtual Conferences on Genomics and Bioinformatics" provides an advanced collaborative environment for the exchange and discussion of information related to innovations of the post-genomic era. Since 2001 the Virtual Conferences are featuring high profile researchers working actively in the development of new applications to understand complex biological systems. Without registration fees, and using the Access Grid technology and live video streaming the 2002 Virtual Conference was broadcast simultaneously to more 2000 researchers in 40 countries. The Goals of the Virtual Conferences on Genomics and Bioinformatics are: Transcend geographical and economical barriers for the exchange of ideas that facilitates the interaction and collaboration among scientists and educators around the world. Address the benefits and limitations of the newest developments in post-genomic technologies. Explore the social and ethical implications of genomic and bioinformatic research. Establish new ways to introduce the high school community to today's multidisciplinary science. 2003 VCGB Topics and Speakers Computational Chemistry and Structural Genomics. Track Organizer: Kim Baldrigde, San Diego Supercomputer Center. USA Kim Baldrigde, San Diego Supercomputer Center. USA Nathan Baker, Washington University in St. Louis School of Medicine. USA Jim Briggs, University of Houston. USA Jan Jensen, University of Iowa. USA Julie Mitchell, University of Wisconsin, Madison. USA Complex Biological Systems: Deanne Taylor. Track Organizer: Serono Reproductive Biology. USA George M. Church, Harvard Medical School & MIT Health Sciences & Technology. USA Toni Kazic, University of Missouri Columbia. USA Eberhard Voit, Medical University of South Carolina. USA Deanne Taylor. Serono Reproductive Biology. USA Andreas Wagner, University of New Mexico. USA Yaneer Bar-Yam, New England Complex Systems Institute. USA RNA-interference: Michael T. McManus, Center for Cancer Research. Massachusetts Institute of Technology, USA Genomics of Infectious Diseases: Larry Simpson Howard Hughes Medical Institute/UCLA. USA Jose Stoute, US Army Medical Research Command. USA John H Adams, Center for Tropical Disease Research & Training. University of Notre Dame, USA Bioinformatics Douglas L. Brutlag, Stanford University. USA Carole Goble, University of Manchester. United Kingdom Elia Stupka, Temasek Life Sciences Laboratory. Singapore Akihiko Konagaya, RIKEN Genomic Sciences Center, Japan David Sankoff, Department of Mathematics and Statistics. University of Ottawa. Canada Mark Wilkinson, Illuminae Media, Canada Transcriptional Analysis: Bruce Aronow, Cincinnati Childrens Hospital Medical Center. USA Kristy Meyers, Spotfire Bioethics and Intellectual Property Rights Protection: Dennis Fernandez, Fernandez and Associates LLP. USA From mjmccorm at mtu.edu Thu Jun 5 19:27:39 2003 From: mjmccorm at mtu.edu (mjmccorm at mtu.edu) Date: Thu, 05 Jun 2003 19:27:39 EDT Subject: [BiO BB] prokaryotic RT-PCR Message-ID: <200306052327.h55NRd325162@node5.> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From adarshramakumar at yahoo.co.uk Fri Jun 6 04:48:27 2003 From: adarshramakumar at yahoo.co.uk (=?iso-8859-1?q?Adarsh=20Ramakumar?=) Date: Fri, 6 Jun 2003 09:48:27 +0100 (BST) Subject: [BiO BB] prokaryotic RT-PCR In-Reply-To: <200306052327.h55NRd325162@node5.> Message-ID: <20030606084827.95079.qmail@web41407.mail.yahoo.com> Hi, There are quite a lot of kits out there but none like out of tehbox and use kind, that I know off...however different tailor made possibilities are there for it depending on the specific issues.... If more specific with ur prob then help can be offerred to cater the problem! --- mjmccorm at mtu.edu wrote: > Hi, > I am new to this board. My question is : Does anyone > know of any > commerical kits for RT-PCR that will work for > prokaryotes? I am having > trouble overcoming the polyadenylation issues. > Thank you. > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== Mr. Adarsh Ramakumar, BioInformatics, University of Bremen. http://www.biox.uni-bremen.de Tel (W) +49-421-2182911 Mobile +49-1747273680. __________________________________________________ Yahoo! Plus - For a better Internet experience http://uk.promotions.yahoo.com/yplus/yoffer.html From adarshramakumar at yahoo.co.uk Fri Jun 6 04:57:09 2003 From: adarshramakumar at yahoo.co.uk (=?iso-8859-1?q?Adarsh=20Ramakumar?=) Date: Fri, 6 Jun 2003 09:57:09 +0100 (BST) Subject: [BiO BB] Some info needed on Geneprediction Message-ID: <20030606085709.46512.qmail@web41403.mail.yahoo.com> Hi, Is anyone out there who uses the Geneplot, of DNASTAR, Inc for gene prediction....? How does it work for you? Any newer versions available for it which works well and can be ported? Thank you! ===== Mr. Adarsh Ramakumar, BioInformatics, University of Bremen. http://www.biox.uni-bremen.de Tel (W) +49-421-2182911 Mobile +49-1747273680. __________________________________________________ Yahoo! Plus - For a better Internet experience http://uk.promotions.yahoo.com/yplus/yoffer.html From mgollery at unr.edu Fri Jun 6 12:06:29 2003 From: mgollery at unr.edu (Martin Gollery) Date: Fri, 6 Jun 2003 09:06:29 -0700 Subject: [BiO BB] Some info needed on Geneprediction In-Reply-To: <20030606085709.46512.qmail@web41403.mail.yahoo.com> References: <20030606085709.46512.qmail@web41403.mail.yahoo.com> Message-ID: <1054915589.3ee0bc05717ac@webmail.unr.edu> Hi Adarsh, I haven't looked at Geneplot. I did an informal survey two years ago about gene finders, and discovered that most people that I asked used GeneScan. That method has now been extended by the original authors into Genomescan, and by another group into a program called Twinscan. Marty Quoting Adarsh Ramakumar : > Hi, > Is anyone out there who uses the Geneplot, of DNASTAR, > Inc > for gene prediction....? > How does it work for you? > Any newer versions available for it which works well > and can be ported? > Thank you! > > ===== > Mr. Adarsh Ramakumar, > BioInformatics, > University of Bremen. > http://www.biox.uni-bremen.de > Tel (W) +49-421-2182911 > Mobile +49-1747273680. > > __________________________________________________ > Yahoo! Plus - For a better Internet experience > http://uk.promotions.yahoo.com/yplus/yoffer.html > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Martin Gollery Associate Director of Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS200 (775)784-6048 ------------------------------------------------- This mail sent through https://webmail.unr.edu From a.bashir at bioc.cam.ac.uk Fri Jun 6 16:33:09 2003 From: a.bashir at bioc.cam.ac.uk (Asam Bashir) Date: Fri, 6 Jun 2003 23:33:09 +0300 Subject: [BiO BB] New Masters Programme in Bioinformatics, Athens In-Reply-To: References: Message-ID: If anyone Greek (or anyone that wants to learn Greek) is out there, I would like to direct them to a new postgraduate programme in Bioinformatics at the University of Athens, Greece. http://bioinformatics.biol.uoa.gr/msc/ There may be the possibility to study the course in English, without taking formal exams from the University of Athens. Anyone keen is asked to keep checking the web pages and I will try to get the English version of the site as soon as I get the translated material. Informal enquires can be sent to me or mailto:shamodr at cc.uoa.gr Regards, Asam... From whotdr at icgeb.res.in Sat Jun 7 05:32:52 2003 From: whotdr at icgeb.res.in (whotdr) Date: Sat, 07 Jun 2003 15:02:52 +0530 Subject: [BiO BB] Announcement for "South East Asian Training Course on Bioinformatics Applied to Tropical Diseases" Message-ID: <3EE1B144.5070200@icgeb.res.in> Hi group, We are happy to inform that the WHO sponsored bioinformatics training programme for the year 2003 is scheduled to begin by *22nd September*. Applications are invited for the same. The selected participants will get full support for travel and participation in the programme. For details please visit our web site http://www.icgeb.res.in/~whotdr . Thanks, Duraisamy Sekhar, International Centre for Genetic Enginnering and Biotechnology(ICGEB), New Delhi, India. From pfern at igc.gulbenkian.pt Mon Jun 9 14:09:34 2003 From: pfern at igc.gulbenkian.pt (pfern at igc.gulbenkian.pt) Date: Mon, 9 Jun 2003 19:09:34 +0100 (WEST) Subject: [BiO BB] (no subject) Message-ID: <1554.193.126.12.87.1055182174.squirrel@webmail.igc.gulbenkian.pt> Reminder: FCUL-IGC Post Graduate programme in Bioinformatics, 2003-2004 edition Application deadline June 15th 2003 for details http://bioinformatics.fc.ul.pt Pedro Fernandes From cchao at rcsb.rutgers.edu Mon Jun 9 14:43:06 2003 From: cchao at rcsb.rutgers.edu (Jimmy Chao) Date: Mon, 9 Jun 2003 14:43:06 -0400 Subject: [BiO BB] Any bioinformatics database? Message-ID: <002001c32eb6$f811fd80$65b20680@VMwin2k> Hi, I have created a universal database interface for any relational database through JDBC. And eventually would focus on database integration. For this connection to work, I'll need the database name, user name, password, host name, port #, and the type of database (Oracle, db2, mysql, sybase, etc). If you happen to know any bioinformatics database that open for public access with above mentioned information, please let me know. If you are a DBA or have the access to the database, but rather keep the database private, you can give me those information or I'll show you how to register through the web. The user name and password would be encoded so no one will know how to access your database. Thanks, ========================== Chi-Ming Jimmy Chao Phone: (732) 397-8840 Fax: (732) 445-4320 ========================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From priami at dit.unitn.it Thu Jun 12 06:04:32 2003 From: priami at dit.unitn.it (Corrado Priami) Date: Thu, 12 Jun 2003 12:04:32 +0200 Subject: [BiO BB] SYSTEOMATICS - Call for papers Message-ID: I apologise for multiple copies.. ===== Systeomatics - Dynamic biological systems informatics http://www.unitn.it/events/systeomatics.htm held in connection with WISICT04 (http://www.wisict.org) Hyatt Regency Cancun, Mexico January 5-8th, 2004 The aim of the workshop is to bring together researchers from the bio side and the computer science side (both academic and industrial) to make emerge the new bioinformatics aspects connnected with the emerging paradigm of systems biology. The main topics of the workshop will be modelling, simulation and analysis of the dynamic behaviour of complex biological sysems such as protein interaction, cell differentiation, pathway simulation. We accept four different kind of papers - Research paper (up to 15 A4 pages) describing results of original research results; - Survey/tutorial papers (up to 20 A4 pages) that describe in detail subfield of the main topics of the workshop or promote interdisciplinary training between biologists and computer scientists; - Experience paper (up to 10 A4 pages) which describes successful case studies and cross-fertilization of the bio and computer field; - Position/vision paper that illustrates the potential impact and futere development arising from the marriage of systems biology and computer science. Submission will be available through the web page of the workshop. submission deadline: 1st july 2003 notification of acceptance: 20 july 2003 camera ready deadline: 20 august 2003 All workshops will be published together in the hardcopy proceedings with ISBN of Computer Science Press, Trinity College Dublin. In order for a paper to be published in the proceedings, at least one author MUST REGISTER for the Workshop by 1 SEPTEMBER 2003. Programme Committee Charles Auffray - Genexpress CNRS Vincent Danos - CNRS Monika Heiner - University of Cottbus Satoru Miyano - University of Tokyo Magali Roux-Rouquie' - Institut Pasteur Paris Gordon Plotkin - University of Edinburgh Corrado Priami - University of Trento (CHAIR) Aviv Regev - Harward University MG Sriram - National Space Biomedical Research Institute, NASA Adelinde Uhrmacher - University of Rostock -- ============================================================= Prof. Corrado Priami Tel. 0461 882085 Dipartimento di Informatica e Telecomunicazioni Mob Universita' di Trento Fax 0461 88 2093 Via Sommarive, 14 http://www.science.unitn.it/~priami 38050 Povo (TN) - Italia priami at dit.unitn.it ============================================================= From mourad12345678 at yahoo.com Thu Jun 12 14:10:45 2003 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Thu, 12 Jun 2003 11:10:45 -0700 (PDT) Subject: [BiO BB] Call for Papers : Congrès Annuel de la Société Française de Biochimie et Biologie Moléculaire Message-ID: <20030612181045.88152.qmail@web12308.mail.yahoo.com> Congr?s Annuel de la Soci?t? Fran?aise de Biochimie et Biologie Mol?culaire POSTGENOMIQUE : De la prot?ine aux mol?cules bioactives 4 - 5 Novembre 2003, Lyon-Gerland. Deuxi?me annonce Appel ? communications Ce congr?s, co-organis? par deux groupes th?matiques : le GGMM (Groupe de Graphisme et de Mod?lisation Mol?culaire) et le GRIP (Groupe de Recherche et d'Ing?nierie des Prot?ines) a pour th?matique g?n?rale la Postg?nomique. Il s'agit de montrer comment, gr?ce aux approches exp?rimentales (prot?omique structurales, criblage ? haut d?bit, phage display ...) et in silico (mod?lisation mol?culaire, drug design, exploitation des g?nomes, bioinformatique), il est possible d'identifier des cibles potentielles et de nouvelles mol?cules bioactives. Tous les renseignements se trouvent sur le site www.ibcp.fr/SFBBM Avant le 30 mai 2003, les projets de communications peuvent ?tre soumis, sous forme de fichier Word ou ?quivalent soit via le site Internet, soit par courrier ?lectronique ? l'adresse Email : c.geourjon at ibcp.fr. Les inscriptions peuvent se faire en ligne, soit sur le site Web www.ibcp.fr/SFBBM, soit par courrier ? l'adresse ci-dessous : Congr?s Annuel de la SFBBM - Maria Foka Centre Universitaire des Saints-P?res 45, rue des Saints-P?res 75270 Paris cedex 06 Email : sfbbm at cep.u-psud.fr Pour le Comit? d'organisation : Michel Desmadril Christophe Geourjon Institut de Biochimie et de Biophysique Institut de Biologie et Chimie Mol?culaire et Cellulaire (Orsay) des Prot?ines (Lyon) Pr?sident du GRIP Pr?sident du GGMM Email : Michel.Desmadril at mip.u-psud.fr Email : c.geourjon at ibcp.fr ***************************************** Dr. Michel Desmadril Directeur Adjoint de l'Institut de Biochimie UMR CNRS 8619 Laboratoire MIP B?t 430 Universit? de Paris-Sud F-91405 ORSAY CEDEX Tel : (+33) 1 69 15 79 75 Portable : 06 30 55 49 55 Fax : (+33) 1 69 85 37 15 e mail: michel.desmadril at mip.u-psud.fr http://www.u-psud.fr/b-430/ibbmc.nsf/ ****************************************** __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com From jasoncting at hotmail.com Thu Jun 12 16:51:03 2003 From: jasoncting at hotmail.com (Jason Ting) Date: Thu, 12 Jun 2003 20:51:03 +0000 Subject: [BiO BB] Any suggestions for a plant repetitive sequences database? Message-ID: Greetings, We are working on a repetitive sequences database and annotation system for plant genomes. To make it more useful to the bioinformatics community, we are looking for suggestions on what usages such a database ought to have. If you could, please describe some details on the usage, like how will such usage be benefitial to it users. Regards, Jason Ting Bioinformatics Center Northern Illinois University jasoncting at hotmail.com _________________________________________________________________ MSN 8 helps eliminate e-mail viruses. Get 2 months FREE*. http://join.msn.com/?page=features/virus From cristiana at intelab.ufsc.br Fri Jun 13 06:55:49 2003 From: cristiana at intelab.ufsc.br (Cristiana) Date: Fri, 13 Jun 2003 10:55:49 -0000 Subject: [BiO BB] (no subject) Message-ID: <200306131355.h5DDtos2003629@citosina.intelab.ufsc.br> An HTML attachment was scrubbed... URL: From priyaa_b at yahoo.com Fri Jun 13 10:44:50 2003 From: priyaa_b at yahoo.com (padma priya) Date: Fri, 13 Jun 2003 07:44:50 -0700 (PDT) Subject: [BiO BB] (no subject) In-Reply-To: <200306131355.h5DDtos2003629@citosina.intelab.ufsc.br> Message-ID: <20030613144450.91904.qmail@web41210.mail.yahoo.com> hi cristina, THEATRE IS ONE TOOL WHICH GIVES THE COMPARITIVE TRANSCRIPTION FACTOR DISPLAY. PRIYA. --- Cristiana wrote: --------------------------------- I'm looking for a tool that seach Transcription Factor Binding Sites (TATAbox). Factor Binding Sites Search forTranscription --------------------------------------- M.Eng.Cristiana Gomesde Oliveira Grupo de Engenharia Gen?mica - UFSC fone: +55 48 331 9713(intelab) _____________________________________________ Mensagem Enviada Usando Intelab Webmail v.1.0 _______________________________________________BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.orghttps://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com From cristiana at intelab.ufsc.br Fri Jun 13 08:41:23 2003 From: cristiana at intelab.ufsc.br (Cristiana) Date: Fri, 13 Jun 2003 12:41:23 -0000 Subject: [BiO BB] TRANSCRIPTION FACTOR Message-ID: <200306131541.h5DFfNs2003944@citosina.intelab.ufsc.br> An HTML attachment was scrubbed... URL: From pajailwala at yahoo.com Fri Jun 13 11:48:42 2003 From: pajailwala at yahoo.com (Parthav Jailwala) Date: Fri, 13 Jun 2003 08:48:42 -0700 (PDT) Subject: [BiO BB] (no subject) In-Reply-To: <200306131355.h5DDtos2003629@citosina.intelab.ufsc.br> Message-ID: <20030613154842.93946.qmail@web12305.mail.yahoo.com> Try ProScan Dragon Promoter Search GenoMatix tools Do a search for these terms on google.com and you will hit the URL. Cristiana wrote: I'm looking for a tool that seach Transcription Factor Binding Sites (TATA box). Factor Binding Sites Search for Transcription --------------------------------------- M.Eng.Cristiana Gomes de Oliveira Grupo de Engenharia Gen?mica - UFSC fone: +55 48 331 9713 (intelab) _____________________________________________ Mensagem Enviada Usando Intelab Webmail v.1.0 _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Parthav Jailwala Analyst/Project Programmer Max McGee National Research Centre for Juvenile Diabetes Medical College of Wisconsin, Milwaukee, WI. Ph : 414-456-8269, Fax : 414-456-6663, E-mail : pajailwala at yahoo.com --------------------------------- Do you Yahoo!? Free online calendar with sync to Outlook(TM). -------------- next part -------------- An HTML attachment was scrubbed... URL: From johng at accelrys.com Tue Jun 17 11:54:51 2003 From: johng at accelrys.com (John M Garrison) Date: Tue, 17 Jun 2003 08:54:51 -0700 Subject: [BiO BB] DB2 and DiscoveryLink Message-ID: Hello, I work with Accelrys, a market-leading provider of software for the Life Science research marketplace. Accelrys is a strategic business partner of IBM and are in need of people who have experience creating Life Science databases in IBM's DB2. If you have such experience, I would very much like to speak with you concerning opportunites at Accelrys. Please reply by e-mail with information on your experience and how you may be reached. My e-mail is johng at accelrys.com. Best regards, John _____________________________ John M. Garrison Senior Director, Discovery Studio Accelrys 9685 Scranton Road San Diego, CA 92121 e-mail: johng at accelrys.com ____________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From SJaffe at The-Scientist.COM Tue Jun 17 17:08:54 2003 From: SJaffe at The-Scientist.COM (Sam Jaffe) Date: Tue, 17 Jun 2003 17:08:54 -0400 Subject: [BiO BB] SCO Lawsuit Message-ID: <9320390441B9D211ACD60090272682970199F373@ODIN> The SCO lawsuit has sent a chill through the corporate enterprise computing world, especially for anyone working with Linux or AIX. What about the bioinformatics community? Are you following the lawsuit with interest, or have you already dismissed it? Has your project formed a committee to deal with the potential implications? Have you started formulating plans for what to do if a judge issues an order to stop using Linux or AIX? I know that such a possibility is remote, but one never knows how the legal system will react to such lawsuits. Any replies would be appreciated. By the way, this is for a story I'm working on dealing with the subject. Thanks. Sam Jaffe Associate Editor The Scientist Magazine (www.the-scientist.com) 215 386 9601 x.3015 sjaffe at the-scientist.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From scott_baio at mymonkey.org Tue Jun 17 19:58:12 2003 From: scott_baio at mymonkey.org (scott_baio at mymonkey.org) Date: Tue, 17 Jun 2003 18:58:12 -0500 (CDT) Subject: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP Message-ID: <1055894292.3eefab14f05d4@webmail.mymonkey.org> I need a free multiple sequence alignment program for Windows XP- I would be very appreciative if anyone had suggestions. Clustal does not work in XP, and I will be doing work on a laptop that only has XP (I use the on-line sites now, but there will be times where that will not be available). Linux really isn't an option- I really don't want to install another OS and then have to boot between the two OSs just for one function when all my programs and work are already in the XP enviroment. If anyone knows of any program that will work, please let me know. I'm dealing with sequences that are on average 85-100% identical. Thanks! From ngadewal at yahoo.com Wed Jun 18 04:44:10 2003 From: ngadewal at yahoo.com (nikhil gadewal) Date: Wed, 18 Jun 2003 01:44:10 -0700 (PDT) Subject: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP In-Reply-To: <1055894292.3eefab14f05d4@webmail.mymonkey.org> Message-ID: <20030618084410.63436.qmail@web40904.mail.yahoo.com> Hi, Try BIOEDIT a freeware s/w. In that Clustal W is a one of the component. Nikhil --- scott_baio at mymonkey.org wrote: > > I need a free multiple sequence alignment program > for Windows XP- I would be > very appreciative if anyone had suggestions. > Clustal does not work in XP, and I > will be doing work on a laptop that only has XP (I > use the on-line sites now, > but there will be times where that will not be > available). Linux really isn't > an option- I really don't want to install another OS > and then have to boot > between the two OSs just for one function when all > my programs and work are > already in the XP enviroment. If anyone knows of > any program that will work, > please let me know. I'm dealing with sequences that > are on average 85-100% > identical. Thanks! > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== NIKHIL S. GADEWAL Bioinformatics center, ACTREC, Tata Memorial centre, Kharghar, Navi Mumbai E-mail: cri3 at soochak.ncst.ernet.in __________________________________ Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! http://sbc.yahoo.com From tfiedler at rsmas.miami.edu Wed Jun 18 11:04:35 2003 From: tfiedler at rsmas.miami.edu (Dr. Tristan J. Fiedler) Date: Wed, 18 Jun 2003 11:04:35 -0400 (EDT) Subject: [BiO BB] BLAST on iBook G3 Message-ID: <49449.129.171.111.124.1055948675.squirrel@domino.rsmas.miami.edu> Could someone please let me know whether the correct BLAST for a G3 iBook is : blast.darwin.tar.gz or blast.hqx I believe the 'darwin' version is correct, but I'm not sure. Please send replies directly to me. Thank you!! -- Tristan J. Fiedler, Ph.D. Postdoctoral Research Fellow NIEHS Marine & Freshwater Biomedical Sciences Center Rosenstiel School of Marine & Atmospheric Sciences University of Miami tfiedler at rsmas.miami.edu 305-361-4626 From krishna.datta at atcbiotech.com Wed Jun 18 12:49:41 2003 From: krishna.datta at atcbiotech.com (Krishna Datta) Date: Wed, 18 Jun 2003 17:49:41 +0100 Subject: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP Message-ID: Hi, Yes use Bio-Edit, really a good s/w for window's also very user friendly. ________________________________________________________ Advanced Technologies (Cambridge) Ltd 210 Cambridge Science Park Cambridge CB4 0WA Tel: +44 (0)1223 420284 Fax: +44 (0)1223 423448 The Information contained in this message is likely to be confidential. It is intended only for the person named above. Any dissemination, distribution, copying, disclosure or use of this message or its content unless authorised by Advanced Technologies (Cambridge) Ltd is prohibited. Any views or opinions expressed within this E-Mail are those of the author and do not necessarily represent those of Advanced Technologies (Cambridge) Ltd. If you have received this E-Mail in error, please immediately notify us and delete it. Thank you. -----Original Message----- From: nikhil gadewal [mailto:ngadewal at yahoo.com] Sent: 18 June 2003 09:44 To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP Hi, Try BIOEDIT a freeware s/w. In that Clustal W is a one of the component. Nikhil --- scott_baio at mymonkey.org wrote: > > I need a free multiple sequence alignment program > for Windows XP- I would be > very appreciative if anyone had suggestions. > Clustal does not work in XP, and I > will be doing work on a laptop that only has XP (I > use the on-line sites now, > but there will be times where that will not be > available). Linux really isn't > an option- I really don't want to install another OS > and then have to boot > between the two OSs just for one function when all > my programs and work are > already in the XP enviroment. If anyone knows of > any program that will work, > please let me know. I'm dealing with sequences that > are on average 85-100% > identical. Thanks! > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== NIKHIL S. GADEWAL Bioinformatics center, ACTREC, Tata Memorial centre, Kharghar, Navi Mumbai E-mail: cri3 at soochak.ncst.ernet.in __________________________________ Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! http://sbc.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From virajj at lycos.com Wed Jun 18 13:20:38 2003 From: virajj at lycos.com (vijaya raj) Date: Wed, 18 Jun 2003 13:20:38 -0400 Subject: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP Message-ID: Hi Clustal X is working fine with XP. Did you try that? Is that not enough? regards vijay --------- Original Message --------- DATE: Wed, 18 Jun 2003 17:49:41 From: Krishna Datta To: "'bio_bulletin_board at bioinformatics.org'" Cc: Hi, Yes use Bio-Edit, really a good s/w for window's also very user friendly. ________________________________________________________ Advanced Technologies (Cambridge) Ltd 210 Cambridge Science Park Cambridge CB4 0WA Tel: +44 (0)1223 420284 Fax: +44 (0)1223 423448 The Information contained in this message is likely to be confidential. It is intended only for the person named above. Any dissemination, distribution, copying, disclosure or use of this message or its content unless authorised by Advanced Technologies (Cambridge) Ltd is prohibited. Any views or opinions expressed within this E-Mail are those of the author and do not necessarily represent those of Advanced Technologies (Cambridge) Ltd. If you have received this E-Mail in error, please immediately notify us and delete it. Thank you. -----Original Message----- From: nikhil gadewal [mailto:ngadewal at yahoo.com] Sent: 18 June 2003 09:44 To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP Hi, Try BIOEDIT a freeware s/w. In that Clustal W is a one of the component. Nikhil --- scott_baio at mymonkey.org wrote: > > I need a free multiple sequence alignment program > for Windows XP- I would be > very appreciative if anyone had suggestions. > Clustal does not work in XP, and I > will be doing work on a laptop that only has XP (I > use the on-line sites now, > but there will be times where that will not be > available). Linux really isn't > an option- I really don't want to install another OS > and then have to boot > between the two OSs just for one function when all > my programs and work are > already in the XP enviroment. If anyone knows of > any program that will work, > please let me know. I'm dealing with sequences that > are on average 85-100% > identical. Thanks! > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== NIKHIL S. GADEWAL Bioinformatics center, ACTREC, Tata Memorial centre, Kharghar, Navi Mumbai E-mail: cri3 at soochak.ncst.ernet.in __________________________________ Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! http://sbc.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ____________________________________________________________ Get advanced SPAM filtering on Webmail or POP Mail ... Get Lycos Mail! http://login.mail.lycos.com/r/referral?aid=27005 -------------- next part -------------- An HTML attachment was scrubbed... URL: From virajj at lycos.com Wed Jun 18 13:21:31 2003 From: virajj at lycos.com (vijaya raj) Date: Wed, 18 Jun 2003 13:21:31 -0400 Subject: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP Message-ID: HiClustal X is working fine with windows XP.Did you try that? Is that not enough?regardsvijay --------- Original Message --------- DATE: Wed, 18 Jun 2003 17:49:41 From: Krishna Datta To: "'bio_bulletin_board at bioinformatics.org'" Cc: Hi, Yes use Bio-Edit, really a good s/w for window's also very user friendly. ________________________________________________________ Advanced Technologies (Cambridge) Ltd 210 Cambridge Science Park Cambridge CB4 0WA Tel: +44 (0)1223 420284 Fax: +44 (0)1223 423448 The Information contained in this message is likely to be confidential. It is intended only for the person named above. Any dissemination, distribution, copying, disclosure or use of this message or its content unless authorised by Advanced Technologies (Cambridge) Ltd is prohibited. Any views or opinions expressed within this E-Mail are those of the author and do not necessarily represent those of Advanced Technologies (Cambridge) Ltd. If you have received this E-Mail in error, please immediately notify us and delete it. Thank you. -----Original Message----- From: nikhil gadewal [mailto:ngadewal at yahoo.com] Sent: 18 June 2003 09:44 To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP Hi, Try BIOEDIT a freeware s/w. In that Clustal W is a one of the component. Nikhil --- scott_baio at mymonkey.org wrote: > > I need a free multiple sequence alignment program > for Windows XP- I would be > very appreciative if anyone had suggestions. > Clustal does not work in XP, and I > will be doing work on a laptop that only has XP (I > use the on-line sites now, > but there will be times where that will not be > available). Linux really isn't > an option- I really don't want to install another OS > and then have to boot > between the two OSs just for one function when all > my programs and work are > already in the XP enviroment. If anyone knows of > any program that will work, > please let me know. I'm dealing with sequences that > are on average 85-100% > identical. Thanks! > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== NIKHIL S. GADEWAL Bioinformatics center, ACTREC, Tata Memorial centre, Kharghar, Navi Mumbai E-mail: cri3 at soochak.ncst.ernet.in __________________________________ Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! http://sbc.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ____________________________________________________________ Get advanced SPAM filtering on Webmail or POP Mail ... Get Lycos Mail! http://login.mail.lycos.com/r/referral?aid=27005 -------------- next part -------------- An HTML attachment was scrubbed... URL: From virajj at lycos.com Wed Jun 18 13:21:46 2003 From: virajj at lycos.com (vijaya raj) Date: Wed, 18 Jun 2003 13:21:46 -0400 Subject: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP Message-ID: HiClustal X is working fine with windows XP.Did you try that? Is that not enough?regardsvijay --------- Original Message --------- DATE: Wed, 18 Jun 2003 17:49:41 From: Krishna Datta To: "'bio_bulletin_board at bioinformatics.org'" Cc: Hi, Yes use Bio-Edit, really a good s/w for window's also very user friendly. ________________________________________________________ Advanced Technologies (Cambridge) Ltd 210 Cambridge Science Park Cambridge CB4 0WA Tel: +44 (0)1223 420284 Fax: +44 (0)1223 423448 The Information contained in this message is likely to be confidential. It is intended only for the person named above. Any dissemination, distribution, copying, disclosure or use of this message or its content unless authorised by Advanced Technologies (Cambridge) Ltd is prohibited. Any views or opinions expressed within this E-Mail are those of the author and do not necessarily represent those of Advanced Technologies (Cambridge) Ltd. If you have received this E-Mail in error, please immediately notify us and delete it. Thank you. -----Original Message----- From: nikhil gadewal [mailto:ngadewal at yahoo.com] Sent: 18 June 2003 09:44 To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Need a freeware multiple sequence alignment program for Windows XP Hi, Try BIOEDIT a freeware s/w. In that Clustal W is a one of the component. Nikhil --- scott_baio at mymonkey.org wrote: > > I need a free multiple sequence alignment program > for Windows XP- I would be > very appreciative if anyone had suggestions. > Clustal does not work in XP, and I > will be doing work on a laptop that only has XP (I > use the on-line sites now, > but there will be times where that will not be > available). Linux really isn't > an option- I really don't want to install another OS > and then have to boot > between the two OSs just for one function when all > my programs and work are > already in the XP enviroment. If anyone knows of > any program that will work, > please let me know. I'm dealing with sequences that > are on average 85-100% > identical. Thanks! > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== NIKHIL S. GADEWAL Bioinformatics center, ACTREC, Tata Memorial centre, Kharghar, Navi Mumbai E-mail: cri3 at soochak.ncst.ernet.in __________________________________ Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! http://sbc.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ____________________________________________________________ Get advanced SPAM filtering on Webmail or POP Mail ... Get Lycos Mail! http://login.mail.lycos.com/r/referral?aid=27005 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Wed Jun 18 23:06:40 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 18 Jun 2003 23:06:40 -0400 Subject: [BiO BB] Re: SCO Lawsuit References: <9320390441B9D211ACD60090272682970199F373@ODIN> Message-ID: <3EF128C0.7020704@bioinformatics.org> There is now a poll on our main page (http://bioinformatics.org) about this. Cheers. Jeff Sam Jaffe wrote: > The SCO lawsuit has sent a chill through the corporate enterprise > computing world, especially for anyone working with Linux or AIX. What > about the bioinformatics community? Are you following the lawsuit with > interest, or have you already dismissed it? Has your project formed a > committee to deal with the potential implications? Have you started > formulating plans for what to do if a judge issues an order to stop > using Linux or AIX? I know that such a possibility is remote, but one > never knows how the legal system will react to such lawsuits. Any > replies would be appreciated. By the way, this is for a story I'm > working on dealing with the subject. Thanks. > > Sam Jaffe > Associate Editor > The Scientist Magazine (www.the-scientist.com) > 215 386 9601 x.3015 > sjaffe at the-scientist.com > -- J.W. Bizzaro jeff at bioinformatics.org President, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From amaldeep75 at hotmail.com Sun Jun 8 10:08:20 2003 From: amaldeep75 at hotmail.com (amaldep) Date: Sun, 8 Jun 2003 19:38:20 +0530 Subject: [BiO BB] Re: SCO Lawsuit References: <9320390441B9D211ACD60090272682970199F373@ODIN> <3EF128C0.7020704@bioinformatics.org> Message-ID: what is the SCO/IBM Lawsuit ? regards amaldeep ----- Original Message ----- From: "J.W. Bizzaro" To: ; Sent: Thursday, June 19, 2003 8:36 AM Subject: [BiO BB] Re: SCO Lawsuit > There is now a poll on our main page (http://bioinformatics.org) about this. > > Cheers. > Jeff > > Sam Jaffe wrote: > > The SCO lawsuit has sent a chill through the corporate enterprise > > computing world, especially for anyone working with Linux or AIX. What > > about the bioinformatics community? Are you following the lawsuit with > > interest, or have you already dismissed it? Has your project formed a > > committee to deal with the potential implications? Have you started > > formulating plans for what to do if a judge issues an order to stop > > using Linux or AIX? I know that such a possibility is remote, but one > > never knows how the legal system will react to such lawsuits. Any > > replies would be appreciated. By the way, this is for a story I'm > > working on dealing with the subject. Thanks. > > > > Sam Jaffe > > Associate Editor > > The Scientist Magazine (www.the-scientist.com) > > 215 386 9601 x.3015 > > sjaffe at the-scientist.com > > > > > -- > J.W. Bizzaro jeff at bioinformatics.org > President, Bioinformatics.Org http://bioinformatics.org/~jeff > "As we enjoy great advantages from the inventions of others, we > should be glad of an opportunity to serve others by any invention > of ours; and this we should do freely and generously." > -- Benjamin Franklin > -- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From gary.bader at utoronto.ca Thu Jun 19 10:25:07 2003 From: gary.bader at utoronto.ca (Gary Bader) Date: Thu, 19 Jun 2003 10:25:07 -0400 Subject: [BiO BB] Re: SCO Lawsuit In-Reply-To: Message-ID: <001501c3366e$958cc900$1149a8c0@cbio.mskcc.org> Here's a summary: (linked to from Slashdot this morning) http://www.forbes.com/2003/06/18/cz_dl_0618linux.html Cheers, Gary > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of amaldep > Sent: Sunday, June 08, 2003 10:08 AM > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Re: SCO Lawsuit > > what is the SCO/IBM Lawsuit ? > > regards > > amaldeep > ----- Original Message ----- > From: "J.W. Bizzaro" > To: ; > > Sent: Thursday, June 19, 2003 8:36 AM > Subject: [BiO BB] Re: SCO Lawsuit > > > > There is now a poll on our main page (http://bioinformatics.org) about > this. > > > > Cheers. > > Jeff > > > > Sam Jaffe wrote: > > > The SCO lawsuit has sent a chill through the corporate enterprise > > > computing world, especially for anyone working with Linux or AIX. What > > > about the bioinformatics community? Are you following the lawsuit > with > > > interest, or have you already dismissed it? Has your project formed a > > > committee to deal with the potential implications? Have you started > > > formulating plans for what to do if a judge issues an order to stop > > > using Linux or AIX? I know that such a possibility is remote, but one > > > never knows how the legal system will react to such lawsuits. Any > > > replies would be appreciated. By the way, this is for a story I'm > > > working on dealing with the subject. Thanks. > > > > > > Sam Jaffe > > > Associate Editor > > > The Scientist Magazine (www.the-scientist.com) > > > 215 386 9601 x.3015 > > > sjaffe at the-scientist.com > > > > > > > > > -- > > J.W. Bizzaro jeff at bioinformatics.org > > President, Bioinformatics.Org http://bioinformatics.org/~jeff > > "As we enjoy great advantages from the inventions of others, we > > should be glad of an opportunity to serve others by any invention > > of ours; and this we should do freely and generously." > > -- Benjamin Franklin > > -- > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From hugh at neoclassicists.net Thu Jun 19 11:04:39 2003 From: hugh at neoclassicists.net (Hugh DeLatham) Date: Thu, 19 Jun 2003 11:04:39 -0400 Subject: [BiO BB] Re: SCO Lawsuit References: <001501c3366e$958cc900$1149a8c0@cbio.mskcc.org> Message-ID: <000b01c33674$1c89b940$02010101@duncan> Anybody who believes they should be concerned about this lawsuit while IBM itself apparently is not may, among other things, consider FreeBSD, which is another UNIX-type open source OS capable of doing anything Linux can do. http://www.freebsd.org/ Duncan C. Kinder duncan at neoclassicists.net ----- Original Message ----- From: "Gary Bader" To: Sent: Thursday, June 19, 2003 10:25 AM Subject: RE: [BiO BB] Re: SCO Lawsuit Here's a summary: (linked to from Slashdot this morning) http://www.forbes.com/2003/06/18/cz_dl_0618linux.html Cheers, Gary > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of amaldep > Sent: Sunday, June 08, 2003 10:08 AM > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Re: SCO Lawsuit > > what is the SCO/IBM Lawsuit ? > > regards > > amaldeep > ----- Original Message ----- > From: "J.W. Bizzaro" > To: ; > > Sent: Thursday, June 19, 2003 8:36 AM > Subject: [BiO BB] Re: SCO Lawsuit > > > > There is now a poll on our main page (http://bioinformatics.org) about > this. > > > > Cheers. > > Jeff > > > > Sam Jaffe wrote: > > > The SCO lawsuit has sent a chill through the corporate enterprise > > > computing world, especially for anyone working with Linux or AIX. What > > > about the bioinformatics community? Are you following the lawsuit > with > > > interest, or have you already dismissed it? Has your project formed a > > > committee to deal with the potential implications? Have you started > > > formulating plans for what to do if a judge issues an order to stop > > > using Linux or AIX? I know that such a possibility is remote, but one > > > never knows how the legal system will react to such lawsuits. Any > > > replies would be appreciated. By the way, this is for a story I'm > > > working on dealing with the subject. Thanks. > > > > > > Sam Jaffe > > > Associate Editor > > > The Scientist Magazine (www.the-scientist.com) > > > 215 386 9601 x.3015 > > > sjaffe at the-scientist.com > > > > > > > > > -- > > J.W. Bizzaro jeff at bioinformatics.org > > President, Bioinformatics.Org http://bioinformatics.org/~jeff > > "As we enjoy great advantages from the inventions of others, we > > should be glad of an opportunity to serve others by any invention > > of ours; and this we should do freely and generously." > > -- Benjamin Franklin > > -- > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From mgollery at unr.edu Thu Jun 19 13:34:56 2003 From: mgollery at unr.edu (Martin Gollery) Date: Thu, 19 Jun 2003 10:34:56 -0700 Subject: [BiO BB] SCO Lawsuit In-Reply-To: <9320390441B9D211ACD60090272682970199F373@ODIN> References: <9320390441B9D211ACD60090272682970199F373@ODIN> Message-ID: <1056044096.3ef1f4408156d@webmail.unr.edu> AIX is rarely used in the life sciences, so this would not affect very many labs. Linux is another story in terms of use, of course, but is this a real danger? I have not heard anyone other than the media talking about a 'chill'. How long will this take, after all? The SCO lawsuit against CA is still going on after two years. How long would it take for someone to write around the ancient code? A lot less, I imagine. You should tell people to sell any SCO stock that they have. Nobody will buy their software now. Marty Quoting Sam Jaffe : > The SCO lawsuit has sent a chill through the corporate enterprise computing > world, especially for anyone working with Linux or AIX. What about the > bioinformatics community? Are you following the lawsuit with interest, or > have you already dismissed it? Has your project formed a committee to deal > with the potential implications? Have you started formulating plans for > what > to do if a judge issues an order to stop using Linux or AIX? I know that > such a possibility is remote, but one never knows how the legal system will > react to such lawsuits. Any replies would be appreciated. By the way, this > is for a story I'm working on dealing with the subject. Thanks. > > Sam Jaffe > Associate Editor > The Scientist Magazine (www.the-scientist.com) > 215 386 9601 x.3015 > sjaffe at the-scientist.com > > Martin Gollery Associate Director of Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS200 (775)784-6048 ------------------------------------------------- This mail sent through https://webmail.unr.edu From OGD at Stowers-Institute.org Thu Jun 19 13:42:40 2003 From: OGD at Stowers-Institute.org (Duzlevski, Ognen) Date: Thu, 19 Jun 2003 12:42:40 -0500 Subject: [BiO BB] SCO Lawsuit Message-ID: >-----Original Message----- >From: Martin Gollery [mailto:mgollery at unr.edu] >Sent: Thursday, June 19, 2003 12:35 PM >To: bio_bulletin_board at bioinformatics.org >Subject: Re: [BiO BB] SCO Lawsuit > [snipped] > >You should tell people to sell any SCO stock that they have. >Nobody will buy their software now. Are you trying to tell us someone actually bought it before? :) Ognen From yunlee at bme.jhu.edu Thu Jun 19 17:41:39 2003 From: yunlee at bme.jhu.edu (Yun Lee) Date: Thu, 19 Jun 2003 17:41:39 -0400 (EDT) Subject: [BiO BB] Base Trimming by PHRED Message-ID: <4643.128.220.136.228.1056058899.squirrel@webmail.bme.jhu.edu> I have been calling bases from ABI files using the following command. phred -trim_alt "" -trim_fasta -id -sd -qd This way, phred trims off low quality parts of the sequence. If I were to omit the first two flags, then I get a longer sequence containing the low quality parts of the sequence. After trimming, phred adds the trim information to the header line. For example, >CF-500-2-A04-T7.ab1 1015 0 1015 ABI trimmed According to the phred documentation, the first number(1015) is the number of bases called by phred, the second number(0) is the number of bases trimmed, and the third number(1015) is the number of bases remaining after trimming. My problem is that although trimming is occuring, the numbers on the header line are not appearing properly. I always get them in the form some_number 0 some_number Thus, it always seems like no bases were trimmed. However, I know they were trimmed since I get a longer sequence when I call bases on the same sequence file without the trimming options. Does anybody know what is going on? I am running phred version 0.020425.c on AIX 5.1 on an IBM p690 machine. Any advice would be greatly appreciated. Thank You!