From jay at ccmb.res.in Thu Aug 1 06:54:30 2002 From: jay at ccmb.res.in (jayanti) Date: Thu, 1 Aug 2002 17:24:30 +0630 Subject: [BiO BB] ///Re:.......... no mssgs from 27th july......../ In-Reply-To: <20020730160104.99A6663A19@www.bioinformatics.org> Message-ID: Yup ......I started getting mails once again.......I guess the ccmb server was down..... tnx bill .....got all those messages of 30 th today only......including mine. jai. From colorbasepair at yahoo.com Fri Aug 2 00:59:15 2002 From: colorbasepair at yahoo.com (Color Basepair) Date: Thu, 1 Aug 2002 21:59:15 -0700 (PDT) Subject: [BiO BB] A New Bioinformatics Website Message-ID: <20020802045915.72638.qmail@web13103.mail.yahoo.com> A new bioinformatics website: http://www.colorbasepair.com/ -- Bioinformatics news -- Bioinformatics events -- Bioinformatics job and resume posting -- Bioinformatics discussion forum -- Bioinformatics links and other resources. __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From mllrdm at mail.rnu.tn Thu Aug 1 19:52:55 2002 From: mllrdm at mail.rnu.tn (mllrdm at mail.rnu.tn) Date: Thu, 1 Aug 2002 19:52:55 -0400 Subject: [BiO BB] Call for Papers/BIOKDD-CBGI'03 Message-ID: <265000-22002841235255981@M2W073.mail2web.com> CALL FOR PAPERS BIOKDD-CBGI'03 Biological Knowledge Discovery and Data Mining Session of Atlantic Symposium on Computational Biology and Genome Information Systems & Technology (CBGI'03) Cary, North Carolina, U.S.A. September 26-30, 2003 With the development of Molecular Biology during the last decades, we are witnessing an exponential growth of both the volume and the complexity of biological data. The Human Genome Project is providing the sequence of the 3 billion DNA bases that constitute the human genome. And, consequently, we are provided too with the sequences of about 100,000 proteins. Therefore, we are entering the post-genomic era : After having focused so much efforts on the accumulation of data, we have now to focus as much efforts, and even more, on the analysis of these data. This will enable us to learn more about gene expression, protein interactions and other biological mechanisms. Analyzing this huge volume of data is a challenging task because, not only, of its complexity and its multiple numerous correlated factors, but also, because of the continuous evolution of our understanding of the biological mechanisms. Classical approaches of biological data analysis are no longer efficient and produce only a very limited amount of information, compared to the numerous and complex biological mechanisms under study. Actually, these approaches use only a very limited number of parameters, to represent the so-many correlated factors involved in the biological mechanisms. From here comes the necessity to use computer tools and develop new in silico high performance approaches, to support us in the analysis of biological data. And, hence, to help us in our understanding of the correlations that exist between, on one hand, structures and functional patterns of biological sequences, i.e., DNA, RNA and proteins, and, on the other hand, genetic and biochemical mechanisms. Knowledge Discovery and Data mining (KDD) are a response to these new trends : Knowledge discovery is an emerging field where we combine techniques from Algorithmics, Artificial Intelligence, Mathematics and Statistics to deal with the theoretical and practical issues of extracting knowledge, i.e., new concepts or concept relationships, hidden in volumes of raw data. Knowledge discovery offers the capacity to automate complex search and data analysis tasks. We distinguish two types of knowledge discovery systems : verification systems and discovery ones. Verification systems are limited to verifying the users hypothesis, while, discovery ones autonomously predict and explain new knowledge. Biological knowledge discovery process should provide for the selection of the appropriate data mining approaches by taking into account both the characteristics of the biological data and the general requirements of knowledge discovery process. Data mining is one of the pre-processing steps in the knowledge discovery process. It consists in extracting nuggets of information, i.e., pertinent patterns, pattern correlations, estimations or rules, hidden in bodies of data. The extracted information will be used in the verification of hypothesis or the prediction and explanation of knowledge. Biological data mining aims at extracting motifs, functional sites or clustering/classification rules from biological sequences. Numerous techniques suitable for data mining in Molecular Biology are available, however, the selection of ad hoc ones is non-trivial. In our session, we are interested in papers that deal with issues of biological KDD. INSTRUCTIONS TO AUTHORS You are invited to submit a hardcopy or a pdf version of a draft paper, about 4 to 5 pages including figures and references, before May 1, 2003 to the Session Chair: Dr. Mourad Elloumi, Mailing Address: Cite Intilak bloc 6, app. 7, El Menzah 6, 2091 Tunis, Tunisia. Phone : +216 71 233 253 Fax : +216 71 712 093 E.Mail: Mourad.Elloumi at fsegt.rnu.tn BIG : www.groups.yahoo.com/group/bioinformaticsgroup URL : www.MouradElloumi.homestead.com/home.html IMPORTANT DATES May 1, 2003 : Draft papers (about 4 to 5 pages) due June 1, 2003 : Notification of acceptance July 1, 2003 : Camera-Ready papers & Prereg. due September 26 - 30, 2003: CBGI'03 Conference -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . -------------- next part -------------- A non-text attachment was scrubbed... Name: Cbgi03.doc Type: application/octet-stream Size: 30208 bytes Desc: Cbgi03.doc URL: From wstepnio at yahoo.com Tue Aug 6 15:59:22 2002 From: wstepnio at yahoo.com (wstepnio at yahoo.com) Date: Tue, 6 Aug 2002 12:59:22 -0700 (PDT) Subject: [BiO BB] Bioinformatics, Linux, and learning. Message-ID: <20020806195922.36435.qmail@web14810.mail.yahoo.com> Hello all members, I am a recent graduate with a Masters degree in Biology. I have recently become very interested in using computers (embedded and distributed uses of Linux as a tool) to solve biological problems involving the scientific application of food and supplement nutrition for disease prevention, and health and longevity promotion. Considering I have never used Linux not any type of Bioinformatics software, could you offer any suggestion regarding what kind of computer console and Linux I would need to get started. Also, I would like to know what software you would recommend I start with and which literature books I should obtain. Since most of the positions in Bioinfotmatics I have been applying for will not hire me because I lack experience, I feel this would be the best way to get some knowledge to offer to them! Thank you! __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From jacobsen at contentsoft.de Mon Aug 12 05:03:22 2002 From: jacobsen at contentsoft.de (jacobsen) Date: Mon, 12 Aug 2002 11:03:22 +0200 Subject: [BiO BB] GeneViz 2.0 released References: <001f01c223fb$b6e91fd0$6508a8c0@winyobbo> Message-ID: <056501c241df$450df410$6508a8c0@winyobbo> GeneViz 2.0 released http://www.contentsoft.de/download.php Free software is available for qualifying non-commercial research institutions. This microarray data analysis tool features now the following techniques: - Double Conjugated Clustering (unsupervised and supervised) - Singular Value Decomposition sorting - Principal Component Analysis with 3D visualization From jeff at bioinformatics.org Mon Aug 12 13:30:16 2002 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 12 Aug 2002 13:30:16 -0400 Subject: [BiO BB] Now Accepting Nominations for the 2003 Benjamin Franklin Award Message-ID: <3D57F0A8.A1C5B87E@bioinformatics.org> Benjamin Franklin (1706 - 1790) was one of the most remarkable men of his time. Scientist, inventor, statesman, Franklin freely and openly shared his ideas and refused to patent his inventions. It is the opinion of the founders of Bioinformatics.Org that he embodied the best traits of a scientist, and we seek to honor those who share these virtues. The Benjamin Franklin Award is presented annually by Bioinformatics.Org to an individual who has in his or her practice promoted freedom and openness in the field of bioinformatics. We are now accepting nominations for the 2003 Benjamin Franklin Award from the members of Bioinformatics.Org. They may be submitted using this form: https://bioinformatics.org/franklin/nominate/ NOTE: You must be a member and logged in to submit a nomination. Please also note the following criteria for nominees: 1. There must ultimately be at least two (2) nominations submitted per nominee. 2. All nominations must be submitted by current members of Bioinformatics.Org. 3. The nominee must be living. There will be no posthumous awards. 4. There must be evidence that the nominee has done something to promote freedom and openness in bioinformatics. The list of nominees will then be presented to the individual members of Bioinformatics.Org for a vote. The ceremony for the presentation of the Award is held at the Annual Meeting of Bioinformatics.Org. It involves a short introduction, the presentation of the certificate, and the laureate seminar. Award home page: http://bioinformatics.org/franklin/ Thanks. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, 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 martingoodson at hotmail.com Fri Aug 16 08:55:32 2002 From: martingoodson at hotmail.com (martin goodson) Date: Fri, 16 Aug 2002 12:55:32 +0000 Subject: [BiO BB] sequence editing software Message-ID: i am looking into sequence editing software for genome finishing and am trying to find something that can deal with very long sequences (1Mb) or something that can integrate really easily via java (either or both). thanks very much in advance martin _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.com From danag at bioinfo.weizmann.ac.il Fri Aug 16 09:47:31 2002 From: danag at bioinfo.weizmann.ac.il (danag) Date: Fri, 16 Aug 2002 16:47:31 +0300 Subject: [BiO BB] sequence editing software In-Reply-To: Message-ID: Hi, Try Artemis program. You can download it from Sanger site. http://www.sanger.ac.uk/Software/Artemis/ good luck, Dana on 8/16/02 3:55 PM, martin goodson at martingoodson at hotmail.com wrote: > i am looking into sequence editing software for genome finishing and am > trying to find something that can deal with very long sequences (1Mb) or > something that can integrate really easily via java (either or both). > > thanks very much in advance > martin > > > > > > > > > > > > > > > > _________________________________________________________________ > Send and receive Hotmail on your mobile device: http://mobile.msn.com > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From martingoodson at hotmail.com Fri Aug 16 10:37:37 2002 From: martingoodson at hotmail.com (martin goodson) Date: Fri, 16 Aug 2002 14:37:37 +0000 Subject: [BiO BB] sequence editing software Message-ID: thanks for the suggestion but I'm really looking for something that is more of an sequence editor than a viewer. its going to have to able to look at multiple aligments and edit them etc. thanks again martin >From: danag >Reply-To: bio_bulletin_board at bioinformatics.org >To: >Subject: Re: [BiO BB] sequence editing software >Date: Fri, 16 Aug 2002 16:47:31 +0300 > >Hi, > >Try Artemis program. You can download it from Sanger site. >http://www.sanger.ac.uk/Software/Artemis/ > >good luck, >Dana > > >on 8/16/02 3:55 PM, martin goodson at martingoodson at hotmail.com wrote: > > > i am looking into sequence editing software for genome finishing and am > > trying to find something that can deal with very long sequences (1Mb) or > > something that can integrate really easily via java (either or both). > > > > thanks very much in advance > > martin > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _________________________________________________________________ > > Send and receive Hotmail on your mobile device: http://mobile.msn.com > > > > _______________________________________________ > > 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 _________________________________________________________________ Join the world?s largest e-mail service with MSN Hotmail. http://www.hotmail.com From thomas at cbs.dtu.dk Fri Aug 16 10:56:43 2002 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: 16 Aug 2002 16:56:43 +0200 Subject: [BiO BB] sequence editing software In-Reply-To: References: Message-ID: "martin goodson" writes: > > > i am looking into sequence editing software for genome finishing and am > > > trying to find something that can deal with very long sequences (1Mb) or > > > something that can integrate really easily via java (either or both). > >Try Artemis program. You can download it from Sanger site. > >http://www.sanger.ac.uk/Software/Artemis/ > thanks for the suggestion but I'm really looking for something that is > more of an sequence editor than a viewer. its going to have to able to > look at multiple aligments and edit them etc. Do you really want to "edit" several Mb long multiple sequence alignments? If you are trying gap-closure and sequence finishing, look into Consed from the Phred/Phrap/Consed/Autofinish package. http://www.phrap.org/consed/consed.html cheers -thomas -- Sicheritz-Ponten Thomas, Ph.D, thomas at biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From btiwari at molbiol.ox.ac.uk Fri Aug 16 10:50:33 2002 From: btiwari at molbiol.ox.ac.uk (Bela Tiwari) Date: Fri, 16 Aug 2002 15:50:33 +0100 (BST) Subject: [BiO BB] sequence editing software In-Reply-To: Message-ID: >If you are trying gap-closure and sequence finishing, look into >Consed from the Phred/Phrap/Consed/Autofinish package. >http://www.phrap.org/consed/consed.html > Or the Staden package: http://www.mrc-lmb.cam.ac.uk/pubseq/ Bela .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. Dr. Bela Tiwari Acting Manager OU Bioinformatics Centre SWD School of Pathology South Parks Road Oxford OX1 3RE 01865 (2)75507 http://www.molbiol.ox.ac.uk .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. From martingoodson at hotmail.com Fri Aug 16 11:02:46 2002 From: martingoodson at hotmail.com (martin goodson) Date: Fri, 16 Aug 2002 15:02:46 +0000 Subject: [BiO BB] sequence editing software Message-ID: > >Do you really want to "edit" several Mb long multiple sequence alignments? > >If you are trying gap-closure and sequence finishing, look into >Consed from the Phred/Phrap/Consed/Autofinish package. >http://www.phrap.org/consed/consed.html you're right- it's for gap closure so only overlap alignments over short regions. thanks for the info martin > >cheers >-thomas > >-- >Sicheritz-Ponten Thomas, Ph.D, thomas at biopython.org ( >Center for Biological Sequence Analysis \ >BioCentrum-DTU, Technical University of Denmark ) >CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> >Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) > / > ... damn arrow eating trees ... ( _________________________________________________________________ Join the world?s largest e-mail service with MSN Hotmail. http://www.hotmail.com From landman at scalableinformatics.com Fri Aug 16 10:54:09 2002 From: landman at scalableinformatics.com (Joseph Landman) Date: 16 Aug 2002 10:54:09 -0400 Subject: [BiO BB] sequence editing software In-Reply-To: References: Message-ID: <1029509649.18880.29.camel@protein.scalableinformatics.com> It might be worth a pointer over to http://sal.kachinatech.com/Z/2/index.shtml (and generally http://sal.kachinatech.com). Even though sequence browsing wasn't indicated, one of the nicest protein structure viewers out there is built into VMD (http://www.ks.uiuc.edu). If you have a protein coordinate/sequence file (pdb, etc), you can view structure and sequence side by side and select based upon either set. Very nice system. Joe On Fri, 2002-08-16 at 10:37, martin goodson wrote: > thanks for the suggestion but I'm really looking for something that is more > of an sequence editor than a viewer. its going to have to able to look at > multiple aligments and edit them etc. > -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman at scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615 From biopolak at yahoo.co.uk Sun Aug 18 21:54:20 2002 From: biopolak at yahoo.co.uk (=?iso-8859-1?q?Peter=20oledzki?=) Date: Mon, 19 Aug 2002 02:54:20 +0100 (BST) Subject: [BiO BB] delta RMS Message-ID: <20020819015420.22993.qmail@web12202.mail.yahoo.com> Hello, I'm working on a project at the moment and I've come across something called delta root mean squared deviation....does anybody know what this is? Could they possily try and explain it to me.....? Any help would be much appreciated. Cheers Pete Oledzki =====

Peter Oledzki

Bioinformatics Research Student

Department of Biochemistry and Molecular Biology

University of Leeds,UK

__________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From landman at scalableinformatics.com Sun Aug 18 22:08:34 2002 From: landman at scalableinformatics.com (Joseph Landman) Date: 18 Aug 2002 22:08:34 -0400 Subject: [BiO BB] delta RMS In-Reply-To: <20020819015420.22993.qmail@web12202.mail.yahoo.com> References: <20020819015420.22993.qmail@web12202.mail.yahoo.com> Message-ID: <1029722914.2393.99.camel@protein.scalableinformatics.com> Hi Pete: RMS deviation (also known as standard deviation) is generally well defined. Could what you have be delta (RMS deviation)[i,j] = SD(i) - SD(j) basically using the delta as a difference operator between two different SD's? This might be one of several possible "signatures" that an analysis would use to compare measurement distributions, or set thresholds for sub-sampling to help delineate clusters. On Sun, 2002-08-18 at 21:54, Peter oledzki wrote: > Hello, > > I'm working on a project at the moment and I've come > across something called delta root mean squared > deviation....does anybody know what this is? > > Could they possily try and explain it to me.....? > > Any help would be much appreciated. > > Cheers > > Pete Oledzki -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman at scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615 From biopolak at yahoo.co.uk Sun Aug 18 23:10:24 2002 From: biopolak at yahoo.co.uk (=?iso-8859-1?q?Peter=20oledzki?=) Date: Mon, 19 Aug 2002 04:10:24 +0100 (BST) Subject: [BiO BB] delta RMS In-Reply-To: <1029722914.2393.99.camel@protein.scalableinformatics.com> Message-ID: <20020819031024.72200.qmail@web12206.mail.yahoo.com> Thanks for that Joeseph, yes that does make sense. It did apply to measurement distributions as it is in the context of a geometric matching algorithm. Cheers for the help --- Joseph Landman wrote: > Hi Pete: > > RMS deviation (also known as standard deviation) > is generally well > defined. Could what you have be > > delta (RMS deviation)[i,j] = SD(i) - SD(j) > > basically using the delta as a difference operator > between two different > SD's? This might be one of several possible > "signatures" that an > analysis would use to compare measurement > distributions, or set > thresholds for sub-sampling to help delineate > clusters. > > > On Sun, 2002-08-18 at 21:54, Peter oledzki wrote: > > Hello, > > > > I'm working on a project at the moment and I've > come > > across something called delta root mean squared > > deviation....does anybody know what this is? > > > > Could they possily try and explain it to me.....? > > > > Any help would be much appreciated. > > > > Cheers > > > > Pete Oledzki > > -- > Joseph Landman, Ph.D > Scalable Informatics LLC > email: landman at scalableinformatics.com > web: http://scalableinformatics.com > phone: +1 734 612 4615 > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board =====

Peter Oledzki

Bioinformatics Research Student

Department of Biochemistry and Molecular Biology

University of Leeds,UK

__________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From jeff at bioinformatics.org Mon Aug 19 22:45:03 2002 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 19 Aug 2002 22:45:03 -0400 Subject: [BiO BB] Re: delta RMS References: <20020820014949.42868.qmail@web20701.mail.yahoo.com> Message-ID: <3D61AD2F.19455749@bioinformatics.org> And, in the structural world, root mean square distance fluctuation is given by deltaRMSD = sqrt[(x2 - x1)^2 + (y2 - y1)^2 + (z2 - z1)^2] where x, y and z are 3-dimensional Cartesian coordinates, usually the position of an atom. This might be used to determine the difference between two protein structures, for example. Jeff Allen Henry wrote: > > I'm only a student in the BioInfo biz, but am very > good at math and come from an image processing > background where we called this the Root Mean Square > Error (RMSE). I recognized this right away because one > of my first 'bugs' that I fixed was in this very same > function. I found something on Google's groups with a > similar question as well as the equation: > > http://thesaurus.maths.org/dictionary/map/word/3701 > > I hope this of help > > :-) > > ======================================================= > > Hi all, > > Given a set of of tiepoints for images and/or maps, > how should one go about calculating the RMSE? This is > with respect to surface fitting models for image > registration > and rectification. Such methods include polynomials > and piecewise linear functions. No prior assumptions > 'bout anything. This, of course, rules out kriging > for rubber-sheeting... well, not exactly, but that's a > question for another day. > > So, given that this is a matter of developing a > deterministic model, would YOU account for degrees of > freedom? Two alternatives follow below for > polynomials. > > (1) > RMS for X = sqrt ( sum( (residual X)**2 ) / (N - K) > ) > RMS for Y = sqrt ( sum( (residual Y)**2 ) / (N - K) > ) > RMS Distance = sqrt ( (RMS for X)**2 + (RMS for Y)**2 > ) > > (2) > RMS for X = sqrt ( sum( (residual X)**2 ) / N ) > RMS for Y = sqrt ( sum( (residual Y)**2 ) / N) ) > RMS Distance = sqrt ( (RMS for X)**2 + (RMS for Y)**2 > ) > > where, > > N is the number of GCPs and K is the number of terms > for the specified order. > > Regards. > > -David > fogel at geog.ucsb.edu > > Hope this Helps > --- biodevelopers-request at bioinformatics.org wrote: > > Send Biodevelopers mailing list submissions to > > biodevelopers at bioinformatics.org > > > > To subscribe or unsubscribe via the World Wide Web, > > visit > > > > > http://bioinformatics.org/mailman/listinfo/biodevelopers > > or, via email, send a message with subject or body > > 'help' to > > biodevelopers-request at bioinformatics.org > > > > You can reach the person managing the list at > > biodevelopers-admin at bioinformatics.org > > > > When replying, please edit your Subject line so it > > is more specific > > than "Re: Contents of Biodevelopers digest..." > > > > > > Today's Topics: > > > > 1. Re: [BiO BB] delta RMS (Joseph Landman) > > > > --__--__-- > > > > Message: 1 > > From: Joseph Landman > > > > To: bio_bulletin_board at bioinformatics.org > > Cc: biodevelopers > > Date: 18 Aug 2002 22:08:34 -0400 > > Subject: [Biodevelopers] Re: [BiO BB] delta RMS > > Reply-To: biodevelopers at bioinformatics.org > > > > Hi Pete: > > > > RMS deviation (also known as standard deviation) > > is generally well > > defined. Could what you have be > > > > delta (RMS deviation)[i,j] = SD(i) - SD(j) > > > > basically using the delta as a difference operator > > between two different > > SD's? This might be one of several possible > > "signatures" that an > > analysis would use to compare measurement > > distributions, or set > > thresholds for sub-sampling to help delineate > > clusters. > > > > > > On Sun, 2002-08-18 at 21:54, Peter oledzki wrote: > > > Hello, > > > > > > I'm working on a project at the moment and I've > > come > > > across something called delta root mean squared > > > deviation....does anybody know what this is? > > > > > > Could they possily try and explain it to me.....? > > > > > > Any help would be much appreciated. -- J.W. Bizzaro jeff at bioinformatics.org Director, 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 drlivesay at csupomona.edu Mon Aug 26 20:06:09 2002 From: drlivesay at csupomona.edu (Dennis Livesay) Date: Mon, 26 Aug 2002 17:06:09 -0700 Subject: [BiO BB] Alignment of profiles Message-ID: <3D580B17@ganymede.as.csupomona.edu> Hi, I'm attempting to globally align two profiles. I need to determine a score for the overall similarity between the two profiles that won't be biased by the size of the initial profiles. Meaning, simply adding up the column scores from the final MSA won't suffice because the larger of the two initial profiles would have a larger influence on the final score. Any help? Thanks, Dennis -------------------------------------------------------------------- Dr. Dennis Livesay Department of Chemistry Cal Poly, Pomona phone: 909-869-4409 email: drlivesay at csupomona.edu From seabi at indiatimes.com Wed Aug 28 05:10:44 2002 From: seabi at indiatimes.com (seabi) Date: Wed, 28 Aug 2002 14:40:44 +0530 Subject: [BiO BB] mailing e.mail list Message-ID: <200208280858.OAA31622@WS0005.indiatimes.com> seabi at indiatimes.com add to mailing list Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. -------------- next part -------------- An HTML attachment was scrubbed... URL: From vipul_bhakta at yahoo.co.uk Thu Aug 29 04:55:53 2002 From: vipul_bhakta at yahoo.co.uk (=?iso-8859-1?q?Vipul=20Bhakta?=) Date: Thu, 29 Aug 2002 09:55:53 +0100 (BST) Subject: [BiO BB] (no subject) Message-ID: <20020829085553.42266.qmail@web12808.mail.yahoo.com> Hi, Has anyone used the MessageAmp aRNA kit from Ambion? How did you get on....and what did you label the aRNA with for microarray?? __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From jeff at bioinformatics.org Thu Aug 29 12:28:05 2002 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 29 Aug 2002 12:28:05 -0400 Subject: [BiO BB] Now Accepting Nominations for the 2003 Benjamin Franklin Award References: <3D57F0A8.A1C5B87E@bioinformatics.org> Message-ID: <3D6E4B95.9092DA4B@bioinformatics.org> Greetings. These are the nominations we've received so far: Name No. Nominations ========================================== =============== James Kent, UC Santa Cruz 1 Michael Ashburner, Cambridge University 1 Stuart Newman, New York Medical College 1 Don Gilbert, Indiana Univ. 2 Eric Lander, MIT 1 Francis Collins, NIH 1 We do need to get **2** nominations per candidate, in order for them to appear on the ballot. You are welcome to second the nomination of any person listed above or to nominate someone else. https://bioinformatics.org/franklin/nominate/ (you must be a member and logged in) We would like to begin voting in a couple weeks. It will be the first membership vote at Bioinformatics.Org, and we will be testing our new voting system, being developed by Dmitry Mozzherin. Cheers. Jeff "J.W. Bizzaro" wrote: > > Benjamin Franklin (1706 - 1790) was one of the most remarkable men of his time. > Scientist, inventor, statesman, Franklin freely and openly shared his ideas and > refused to patent his inventions. It is the opinion of the founders of > Bioinformatics.Org that he embodied the best traits of a scientist, and we seek > to honor those who share these virtues. > > The Benjamin Franklin Award is presented annually by Bioinformatics.Org to an > individual who has in his or her practice promoted freedom and openness in the > field of bioinformatics. > > We are now accepting nominations for the 2003 Benjamin Franklin Award from the > members of Bioinformatics.Org. They may be submitted using this form: > > https://bioinformatics.org/franklin/nominate/ > > NOTE: You must be a member and logged in to submit a nomination. > > Please also note the following criteria for nominees: > > 1. There must ultimately be at least two (2) nominations submitted per nominee. > 2. All nominations must be submitted by current members of Bioinformatics.Org. > 3. The nominee must be living. There will be no posthumous awards. > 4. There must be evidence that the nominee has done something to promote freedom > and openness in bioinformatics. > > The list of nominees will then be presented to the individual members of > Bioinformatics.Org for a vote. > > The ceremony for the presentation of the Award is held at the Annual Meeting of > Bioinformatics.Org. It involves a short introduction, the presentation of the > certificate, and the laureate seminar. > > Award home page: > http://bioinformatics.org/franklin/ -- J.W. Bizzaro jeff at bioinformatics.org Director, 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 --