From Johan.Suykens at esat.kuleuven.ac.be Thu Dec 5 05:32:31 2002 From: Johan.Suykens at esat.kuleuven.ac.be (Johan Suykens) Date: Thu, 05 Dec 2002 11:32:31 +0100 Subject: [BiO BB] [Fwd: LS-SVMs: book announcement and related LS-SVMlab software] Message-ID: <3DEF2B3F.9080803@esat.kuleuven.ac.be> We are glad to announce the publication of a new book ************************************************************************* J.A.K. Suykens, T. Van Gestel, J. De Brabanter, B. De Moor, J. Vandewalle, Least Squares Support Vector Machines, World Scientific Pub. Co., Singapore, 2002 http://www.esat.kuleuven.ac.be/sista/lssvmlab/book.html ************************************************************************* This book focuses on Least Squares Support Vector Machines (LS-SVMs) which are reformulations to standard SVMs. LS-SVMs are closely related to regularization networks and Gaussian processes but additionally emphasize and exploit primal-dual interpretations from optimization theory. The authors explain the natural links between LS-SVM classifiers and kernel Fisher discriminant analysis. Bayesian inference of LS-SVM models is discussed, together with methods for imposing sparseness and employing robust statistics. The framework is further extended towards unsupervised learning by considering PCA analysis and its kernel version as a one-class modelling problem. This leads to new primal-dual support vector machine formulations for kernel PCA and kernel CCA analysis. Furthermore, LS-SVM formulations are given for recurrent networks and control. In general, support vector machines may pose heavy computational challenges for large data sets. For this purpose, a method of fixed size LS-SVM is proposed where the estimation is done in the primal space in relation to a Nystr?m sampling with active selection of support vectors. The methods are illustrated with several examples. Contents: . Introduction . Support vector machines . Least squares support vector machines, links with Gaussian processes, regularization networks, and kernel FDA . Bayesian inference for LS-SVM models . Weighted versions and robust statistics . Large scale problems: Nystrom sampling, reduced set methods, basis formation and Fixed size LS-SVM . LS-SVM for unsupervised learning: support vector machines formulations for kernel PCA. Related methods of kernel CCA. . LS-SVM for recurrent networks and control . Illustrations and applications Readership: Graduate students and researchers in neural networks; machine learning; data-mining; signal processing; circuit, systems and control theory; pattern recognition; and statistics. Info: 308pp., Publication date: Nov. 2002, ISBN 981-238-151-1 Order information: World Scientific http://www.wspc.com/books/compsci/5089.html http://www.esat.kuleuven.ac.be/sista/lssvmlab/book.html ******************************************************** LS-SVMlab: Least Squares - Support Vector Machines Matlab/C Toolbox http://www.esat.kuleuven.ac.be/sista/lssvmlab/ ******************************************************** Toolbox: . Matlab LS-SVMlab1.4 - Linux and Windows Matlab/C code . Basic and advanced versions . Functional and object oriented interface Tutorial User's Guide (100pp.): . Examples and demos . Matlab functions with help Solving and handling: . Classification, Regression . Tuning, cross-validation, fast loo, receiver operating characteristic (ROC) curves . Small and unbalanced data sets . High dimensional input data . Bayesian framework with three levels of inference . Probabilistic interpretations, error bars . hyperparameter selection, automatic relevance determination (ARD) input selection, model comparison . Multi-class encoding/decoding . Sparseness . Robustness, robust weighting, robust cross-validation . Time series prediction . Fixed size LS-SVM, Nystrom method, kernel principal component analayis (kPCA), ridge regression . Unsupervised learning . Large scale problems Related links, publications, presentations and book: http://www.esat.kuleuven.ac.be/sista/lssvmlab/ Contact: LS-SVMlab at esat.kuleuven.ac.be GNU General Public License: The LS-SVMlab software is made available for research purposes only under the GNU General Public License. LS-SVMlab software may not be used for commercial purposes without explicit written permission after contacting LS-SVMlab at esat.kuleuven.ac.be . [we apologize for receiving multiple copies of this message] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From tmi0m0 at spi.power.uni-essen.de Thu Dec 5 08:45:40 2002 From: tmi0m0 at spi.power.uni-essen.de (=?iso-8859-1?Q?Johannes_H=FCsing?=) Date: Thu, 5 Dec 2002 14:45:40 +0100 Subject: [BiO BB] [Fwd: LS-SVMs: book announcement and related LS-SVMlab software] In-Reply-To: <3DEF2B3F.9080803@esat.kuleuven.ac.be>; from Johan Suykens on Thu, Dec 05, 2002 at 11:32:31AM +0100 References: <3DEF2B3F.9080803@esat.kuleuven.ac.be> Message-ID: <20021205144540.43563@spi.power.uni-essen.de> On Thu 2002-12-05 (11:32), Johan Suykens wrote: [...] > GNU General Public License: > The LS-SVMlab software is made available for research purposes only > under the GNU General Public License. LS-SVMlab software may not be > used for commercial purposes without explicit written permission after > contacting LS-SVMlab at esat.kuleuven.ac.be . In this case, it is not the GNU General Public License you are using for licensing this product. The GNU General Public License does not know restrictions on usage (freedom 0 of software). You can only restrict the redistribution of the software to be under the same license. See also http://www.gnu.org/licenses/gpl-faq.html Cheers Johannes From hjm at tacgi.com Fri Dec 6 13:44:10 2002 From: hjm at tacgi.com (Harry Mangalam) Date: Fri, 06 Dec 2002 10:44:10 -0800 Subject: [BiO BB] ANN: O'Reilly's 2003 Bioinformatics Technology Conference In-Reply-To: References: Message-ID: <3DF0EFFA.4020006@tacgi.com> Hi All, This is an announcement for: O'Reilly's 2003 Bioinformatics Technology Conference, taking place February 3 - 6, 2003, in San Diego, California More information at: http://www.oreillynet.com/biocon2002/ It's an unusual but compelling mix of information technology, bit twiddlers, academic researchers, industry types, headhunters, and standards setters (and wannabes), brought together in in one 3 ring circus by the O'Reilly organization, the people who document Open (and some closed) Source IT with their retro-animal covered screeds on Perl, Python, apache, etc. This year, the keynotes include emissions from the minds of: - Lincoln Stein - too-young godfather of Perl Bioinfo, CGI.pm, DAS, Moby, etc - Stephen Wolfram - ex-boy genius of Mathematica, author of 'A New Kind of Science' - Suzi Lewis - Godmother of the Gene Ontology project - Alvis Brazma - Lead cheerleader for the MGED, MIAME gene expression standards. - James Gosling - programming god/demon (Java, NeWS, EMACS), Sun Fellow, Canadian - Damian Conway - nonpareil Perl Edutainment speaker, Author, Australian, singer - James Kent - late-blooming/exploding bioinformatics genome gnome from UCSC. - Francis Ouellette - longtime NCBI vet, now escaped to UBC Bioinformatics Ctr - and others For a sense of what last year's conference was like, check out its coverage page: http://www.oreillynet.com/biocon2002/ Disclaimer: I don't work for O'Reilly, but I did attend the 2002 conference, liked most things, didn't like some things, then got hit up by the organizers, to assure more-of-the-former/less-of-the-latter and so have been volunteering some time to help them do an even better job this year. -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com <> From hjm at tacgi.com Fri Dec 6 15:14:33 2002 From: hjm at tacgi.com (Harry Mangalam) Date: Fri, 06 Dec 2002 12:14:33 -0800 Subject: [BiO BB] Re: ANN: O'Reilly's 2003 Bioinformatics Technology Conference Message-ID: <3DF10529.1020108@tacgi.com> Oops! 2003 conference URL should be: http://conferences.oreilly.com/bio2003/ Sorry.. -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com <> From jeff at bioinformatics.org Fri Dec 6 17:48:07 2002 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 06 Dec 2002 17:48:07 -0500 Subject: [BiO BB] Call for Papers: NAR Web Software Issue Message-ID: <3DF12927.57143F16@bioinformatics.org> Anyone with unpublished web software hosted at Bioinformatics.Org? >From NAR: ----------- Nucleic Acids Research is planning a special edition devoted to Web Software, which will be published in July 2003. This will be a companion to our Annual Database Issue. Manuscripts are sought that describe computer programs which are accessible through the web and perform interesting calculations or manipulations on DNA, RNA and protein sequences and/or three-dimensional structures submitted to them. Such programs are becoming invaluable resources in the biological sciences, but many are described only secondarily in other publications or have never been published and are found by word-of-mouth or chance. This special Web Software Issue of NAR will afford authors an opportunity to describe their programs in a fashion similar to that available to contributors to the Annual Database Issue. The Web Software Issue will provide a focal point for users interested in finding out what is available and links to each resource will be provided from the NAR web site. This Web Software Issue of NAR, like the Database Issue, will be freely available online. Potential authors should contact Dr R. J. Roberts (roberts at neb.com) as soon as possible to determine the relevancy of any proposed submission. The final deadline for receipt of manuscripts will be February 15, 2003, although earlier submission would be welcomed. Instructions for manuscript preparation can be found on the NAR web site (http://nar.oupjournals.org/). ----------- -- 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 harvey at biology.ucsc.edu Fri Dec 6 17:46:06 2002 From: harvey at biology.ucsc.edu (Julio.Harvey) Date: Fri, 6 Dec 2002 14:46:06 -0800 (PST) Subject: [BiO BB] Windows (XP) sequence analysis software Message-ID: Hi, Graduate student in evolutionary biology seeks software suggestions for analyzing thesis data (nucleotide sequences) using Windows or (Red Hat) Linux. After years of using Macintosh based software to analyze my data, I am frustrated in my search for PC based equivalents. My needs and the Mac programs I have been using to satisfy them are as follows: 1) Assembly and editing of contigs from electropherogram data (bi-directional sequencing of cloned genes) generated. Currently use: AutoAssembler (Mac). 2) Alignment of edited gene sequence data in preparation for entry into PAUP. Currently use: Sequence Navigator (Applied Biosystems) or ClustalX (both Mac). 3) Analysis of sequence similarity and subsequent production of gene phylogenies using recent versions of PAUP (Swofford). Currently using PAUP versions for Mac. I would very much appreciate any advice leading to the acquisition of Windows or even 'windows like' (ie Red Hat) based programs to accomplish the above. I have heard of and (briefly) used the package "GCG" in the past but do not currently have the means to purchase the same. Do other such softwares exist or must I learn Unix or Linux to accomplish my goals? Many Sincere Thanks, Julio Harvey _______________________________________________________ Julio Harvey Department of Ecology and Evolutionary Biology (EEB) A316 Earth and Marine Sciences University of California Santa Cruz, 95064 (831) 459-2832 (lab) (831) 459-4882 (fax) "The way to do is to be". -Lao-Tse _______________________________________________________ From johnjakson at yahoo.com Fri Dec 6 18:15:37 2002 From: johnjakson at yahoo.com (John Jakson) Date: Fri, 6 Dec 2002 15:15:37 -0800 (PST) Subject: [BiO BB] Windows (XP) sequence analysis software In-Reply-To: Message-ID: <20021206231537.11594.qmail@web13108.mail.yahoo.com> If Mac SW is 68K based and you need to run on Windows or Linux, you could install the free Basilisk2 (just google) emulator on Windows or Linux and run the Mac under emulation. 1G Athlon/P3 runs acceptably fast, atleast faster than any 68k Mac that ever existed. If it is PPC SW, there is no known emulator for that. --------------------------------- Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now -------------- next part -------------- An HTML attachment was scrubbed... URL: From A.Bossers at id.dlo.nl Mon Dec 9 04:28:27 2002 From: A.Bossers at id.dlo.nl (Bossers, A.) Date: Mon, 09 Dec 2002 10:28:27 +0100 Subject: [BiO BB] Windows (XP) sequence analysis software Message-ID: Hi, alternatively you might want to look at the FREE unix/linux software available at TIGR. It has tools for seq assembly etc etc etc. http://www.tigr.org/software/ Regards, Alex > -----Original Message----- > From: Julio.Harvey [mailto:harvey at biology.ucsc.edu] > Sent: Friday, December 06, 2002 11:46 PM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Windows (XP) sequence analysis software > > > Hi, > > Graduate student in evolutionary biology seeks software > suggestions for > analyzing thesis data (nucleotide sequences) using Windows or > (Red Hat) > Linux. > > After years of using Macintosh based software to analyze my data, I am > frustrated in my search for PC based equivalents. > > My needs and the Mac programs I have been using to satisfy them are as > follows: > > 1) Assembly and editing of contigs from electropherogram data > (bi-directional sequencing of cloned genes) generated. > > Currently use: AutoAssembler (Mac). > > 2) Alignment of edited gene sequence data in preparation > for entry > into PAUP. > > Currently use: Sequence Navigator (Applied > Biosystems) or ClustalX > (both Mac). > > 3) Analysis of sequence similarity and subsequent > production of gene > phylogenies using recent versions of PAUP (Swofford). > > Currently using PAUP versions for Mac. > > > > I would very much appreciate any advice leading to the acquisition of > Windows or even 'windows like' (ie Red Hat) based programs to > accomplish > the above. I have heard of and (briefly) used the package > "GCG" in the > past but do not currently have the means to purchase the same. > > Do other such softwares exist or must I learn Unix or Linux > to accomplish > my goals? > > Many Sincere Thanks, > > Julio Harvey > > > > > > _______________________________________________________ > Julio Harvey > Department of Ecology and Evolutionary Biology (EEB) > A316 Earth and Marine Sciences > University of California > Santa Cruz, 95064 > (831) 459-2832 (lab) > (831) 459-4882 (fax) > "The way to do is to be". -Lao-Tse > _______________________________________________________ > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From ramesh43212000 at yahoo.com Mon Dec 9 07:54:17 2002 From: ramesh43212000 at yahoo.com (ramesh kumar) Date: Mon, 9 Dec 2002 04:54:17 -0800 (PST) Subject: [BiO BB] Article -bioinformatics Message-ID: <20021209125417.10363.qmail@web14506.mail.yahoo.com> http://www.bioinformaticscentre.org/files/bioxml.html http://www.bioinformaticscentre.org/files/blast_protein_sequence.html --------------------------------- Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now -------------- next part -------------- An HTML attachment was scrubbed... URL: From rong at bu.edu Mon Dec 9 11:36:48 2002 From: rong at bu.edu (Rong Chen) Date: Mon, 9 Dec 2002 11:36:48 -0500 (EST) Subject: [BiO BB] A fast and reliable protein complex structure prediction software! In-Reply-To: Message-ID: Hi, A fast and reliable protein docking software ZDOCK is available at http://zlab.bu.edu/~rong/dock/software.shtml . Its performance has been proved by a large protein docking benchmark and a worldwide blind test competition CAPRI. Rong Chen Ph.D. Candidate Bioinformatics Program Boston University Boston, MA 02148 Tel: (617)358-1552 Fax: (617)358-1067 E-mail: rong at bu.edu http://zlab.bu.edu/~rong From webmaster at syndetics.net Mon Dec 9 17:01:39 2002 From: webmaster at syndetics.net (Nick Semenkovich) Date: Mon, 9 Dec 2002 16:01:39 -0600 Subject: [BiO BB] Distributed Computing Message-ID: <001801c29fce$8cad1d30$0401a8c0@na> Is there any software on bioinformatics.org that needs distributed computing members? I'm looking for something like folding at home or genome at home... - Nick Semenkovich -------------- next part -------------- An HTML attachment was scrubbed... URL: From boris.steipe at utoronto.ca Mon Dec 9 17:54:33 2002 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Mon, 09 Dec 2002 17:54:33 -0500 Subject: [BiO BB] Distributed Computing References: <001801c29fce$8cad1d30$0401a8c0@na> Message-ID: <3DF51F2A.FAE67164@utoronto.ca> > Nick Semenkovich wrote: > > Is there any software on bioinformatics.org that needs distributed computing > members? > I'm looking for something like folding at home or genome at home... > > - Nick Semenkovich See , for example. Best regards, Boris --- Boris Steipe University of Toronto Program in Proteomics & Bioinformatics Departments of Biochemistry & Molecular and Medical Genetics http://biochemistry.utoronto.ca/steipe From sanges at iigb.na.cnr.it Tue Dec 10 04:34:35 2002 From: sanges at iigb.na.cnr.it (Remo Sanges) Date: Tue, 10 Dec 2002 10:34:35 +0100 Subject: [BiO BB] RE: Windows (XP) sequence analysis software (Bossers, A.) References: <20021209170104.C44E563B5F@www.bioinformatics.org> Message-ID: <003101c2a02f$5a331740$7a3ca48c@Remo> I thing you should use Linux you can try the Staden Package http://www.mrc-lmb.cam.ac.uk/pubseq/staden_home.html or can use Phred for base-calling and quality Phrap for assembling of genomic sequence or Cap3 for EST Consed to visualize and editing contigs http://www.phrap.org http://genome.cs.mtu.edu/sas.html I thing clustal is good for phylogenesis and the clone open source and better of GCG is at the moment the EMBOSS package http://www.emboss.org Bye __________________________________ Remo Sanges BioGeM Gene Expression Core Lab Via Pietro Castellino 111 80131 Naples Italy +39 081 6132303 sanges at biogem.it sanges at iigb.na.cnr.it __________________________________ From mgollery at unr.edu Tue Dec 10 13:07:57 2002 From: mgollery at unr.edu (Martin Gollery) Date: Tue, 10 Dec 2002 10:07:57 -0800 Subject: [BiO BB] Windows (XP) sequence analysis software In-Reply-To: References: Message-ID: <1039543677.3df62d7dcb2cd@webmail.unr.edu> I have used PHRAP, ClustalW, ClustalX, BLAST, Hmmer, seqweb, The Vector NTI suite, Jellyfish, DNAstar, DeCypher, and HMMpro on windows, as well as many others that I have probably forgotten. Marty Quoting "Julio.Harvey" : > Hi, > > Graduate student in evolutionary biology seeks software suggestions for > analyzing thesis data (nucleotide sequences) using Windows or (Red Hat) > Linux. > > After years of using Macintosh based software to analyze my data, I am > frustrated in my search for PC based equivalents. > > My needs and the Mac programs I have been using to satisfy them are as > follows: > > 1) Assembly and editing of contigs from electropherogram data > (bi-directional sequencing of cloned genes) generated. > > Currently use: AutoAssembler (Mac). > > 2) Alignment of edited gene sequence data in preparation for entry > into PAUP. > > Currently use: Sequence Navigator (Applied Biosystems) or ClustalX > (both Mac). > > 3) Analysis of sequence similarity and subsequent production of gene > phylogenies using recent versions of PAUP (Swofford). > > Currently using PAUP versions for Mac. > > > > I would very much appreciate any advice leading to the acquisition of > Windows or even 'windows like' (ie Red Hat) based programs to accomplish > the above. I have heard of and (briefly) used the package "GCG" in the > past but do not currently have the means to purchase the same. > > Do other such softwares exist or must I learn Unix or Linux to accomplish > my goals? > > Many Sincere Thanks, > > Julio Harvey > > > > > > _______________________________________________________ > Julio Harvey > Department of Ecology and Evolutionary Biology (EEB) > A316 Earth and Marine Sciences > University of California > Santa Cruz, 95064 > (831) 459-2832 (lab) > (831) 459-4882 (fax) > "The way to do is to be". -Lao-Tse > _______________________________________________________ > > > > _______________________________________________ > 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 concini at brenta.dit.unitn.it Wed Dec 11 06:54:53 2002 From: concini at brenta.dit.unitn.it (Michela de Concini) Date: Wed, 11 Dec 2002 12:54:53 +0100 Subject: [BiO BB] call for partecipation Message-ID: Dear all, I apologies if you receive multiple copies. To participate to the Workshop on Computational Methods in Systems Biology to be held in Rovereto - Italy next february, please check the URL http://www.unitn.it/convegni/cmsb.htm Please note that reservation of hotels and inscription at a reduced fare is only possible until the end of this year! The programme of the workshop and the list of accepted papers will be available by the end of the month. Recall that the deadline for hotel reservation for the review and CMSB meeting is 31st of december Best wishes, Michela de Concini Organizing Committee CMSB -- From Ingrid.Marchal at univ-lille1.fr Wed Dec 11 12:38:21 2002 From: Ingrid.Marchal at univ-lille1.fr (Ingrid Marchal) Date: Wed, 11 Dec 2002 18:38:21 +0100 Subject: [BiO BB] Re: Windows (XP) sequence analysis software In-Reply-To: <20021211170108.B62E963B70@www.bioinformatics.org> Message-ID: <5.2.0.9.0.20021211183020.00ab5778@pop.univ-lille1.fr> You can also try EMBOSS. It's an open source client-server package. It is free and includes many valuable programs. I think it is mainly intended for a text based usage but there are graphical interfaces like jemboss, a java based interface. http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ cheers, Ingrid At 18:01 11/12/2002, you wrote: >Message: 1 >Date: Tue, 10 Dec 2002 10:07:57 -0800 >From: Martin Gollery >To: bio_bulletin_board at bioinformatics.org, > "Julio.Harvey" >Subject: Re: [BiO BB] Windows (XP) sequence analysis software >Reply-To: bio_bulletin_board at bioinformatics.org > >I have used PHRAP, ClustalW, ClustalX, BLAST, Hmmer, seqweb, The Vector NTI >suite, Jellyfish, DNAstar, DeCypher, and HMMpro on windows, as well as many >others that I have probably forgotten. >Marty >Quoting "Julio.Harvey" : > > > Hi, > > > > Graduate student in evolutionary biology seeks software suggestions for > > analyzing thesis data (nucleotide sequences) using Windows or (Red Hat) > > Linux. > > > > After years of using Macintosh based software to analyze my data, I am > > frustrated in my search for PC based equivalents. > > > > My needs and the Mac programs I have been using to satisfy them are as > > follows: > > > > 1) Assembly and editing of contigs from electropherogram data > > (bi-directional sequencing of cloned genes) generated. > > > > Currently use: AutoAssembler (Mac). > > > > 2) Alignment of edited gene sequence data in preparation for entry > > into PAUP. > > > > Currently use: Sequence Navigator (Applied Biosystems) or ClustalX > > (both Mac). > > > > 3) Analysis of sequence similarity and subsequent production of gene > > phylogenies using recent versions of PAUP (Swofford). > > > > Currently using PAUP versions for Mac. > > > > > > > > I would very much appreciate any advice leading to the acquisition of > > Windows or even 'windows like' (ie Red Hat) based programs to accomplish > > the above. I have heard of and (briefly) used the package "GCG" in the > > past but do not currently have the means to purchase the same. > > > > Do other such softwares exist or must I learn Unix or Linux to accomplish > > my goals? > > > > Many Sincere Thanks, > > > > Julio Harvey From danag at bioinfo.weizmann.ac.il Wed Dec 18 21:55:34 2002 From: danag at bioinfo.weizmann.ac.il (Dana Reichmann) Date: Wed, 18 Dec 2002 18:55:34 -0800 Subject: [BiO BB] amino acid distribution in multiple alignment Message-ID: Hi all, I am looking for a program or script for calculation of amino acid distribution in specific column in ungaped multiple alignment. Most program I know calculates PSSM that includes weights calculation according to PAM or Blosum matrixes. I just need a simple representation of amino acid distribution in specific column in ungaped multiple alignment. Thanks a lot, Dana Reichmann -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From kenf at speakeasy.net Wed Dec 18 16:02:45 2002 From: kenf at speakeasy.net (Ken Firestone) Date: Wed, 18 Dec 2002 13:02:45 -0800 (PST) Subject: [BiO BB] Biochemistry book reccomendation needed In-Reply-To: Message-ID: Hi, I need a book recommendation. I am coming from a Computer Science background, and I would like a basic biochemistry text. I studied biochemistry many years ago, and I still have an ancient copy of Lehninger. So what should I get now. ============================================================================ Ken Firestone, W3CAT | For every problem there is one solution kenf at speakeasy.net | which is simple, neat, and wrong. ken at firestone.net | -- H. L. Mencken ============================================================================ From jeff at bioinformatics.org Wed Dec 18 16:36:24 2002 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 18 Dec 2002 16:36:24 -0500 Subject: [BiO BB] Biochemistry book reccomendation needed References: Message-ID: <3E00EA58.9456BE71@bioinformatics.org> Hi Ken. I've used both Stryer and Garrett & Grisham. They are comparable in size, covering enough material for several semesters of biochemistry. The latter is a bit easier to read, while the former is a bit more detailed. I think most biochemistry texts are overkill for those not choosing the field as a profession. One of my favorite texts, which is concise and nicely illustrated, is The Cell: A Molecular Approach, by G.M. Cooper. I would recommend it for those who don't intend to be biochemists but would like to know enough biochem and molecular biology to begin studying bioinformatics. Cheers. Jeff Ken Firestone wrote: > > I need a book recommendation. I am coming from a Computer Science > background, and I would like a basic biochemistry text. I studied > biochemistry many years ago, and I still have an ancient copy of > Lehninger. So what should I get now. -- 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 idoerg at burnham.org Wed Dec 18 12:22:19 2002 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 18 Dec 2002 09:22:19 -0800 Subject: [BiO BB] amino acid distribution in multiple alignment References: Message-ID: <3E00AECB.4020004@burnham.org> Hi Dana, I do not know of a complete application which does that. If you are inclined to write around existing modules, then: o Biopython has what you need in the Bio.Align.AlignInfo module. o AFAIK, Bioperl do not have a calculating script of the kind you are looking for, but you can write something around Bio::SimpleAlign. Hope this helped somewhat, Iddo Dana Reichmann wrote: > Hi all, > > I am looking for a program or script for calculation of amino acid > distribution in specific column in ungaped multiple alignment. Most program > I know calculates PSSM that includes weights calculation according to PAM or > Blosum matrixes. I just need a simple representation of amino acid > distribution in specific column in ungaped multiple alignment. > > > Thanks a lot, > Dana Reichmann -- Iddo Friedberg The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 From rong at bu.edu Wed Dec 18 16:40:38 2002 From: rong at bu.edu (Rong Chen) Date: Wed, 18 Dec 2002 16:40:38 -0500 (EST) Subject: [BiO BB] Biochemistry book reccomendation needed In-Reply-To: <3E00EA58.9456BE71@bioinformatics.org> Message-ID: The Cell: A Molecular Approach, by G.M. Cooper is really an excellent introductory book. I really like cooper's style. rong On Wed, 18 Dec 2002, J.W. Bizzaro wrote: > Hi Ken. > > I've used both Stryer and Garrett & Grisham. They are comparable in size, > covering enough material for several semesters of biochemistry. The latter is a > bit easier to read, while the former is a bit more detailed. > > I think most biochemistry texts are overkill for those not choosing the field as > a profession. One of my favorite texts, which is concise and nicely > illustrated, is The Cell: A Molecular Approach, by G.M. Cooper. I would > recommend it for those who don't intend to be biochemists but would like to know > enough biochem and molecular biology to begin studying bioinformatics. > > Cheers. > Jeff > > Ken Firestone wrote: > > > > I need a book recommendation. I am coming from a Computer Science > > background, and I would like a basic biochemistry text. I studied > > biochemistry many years ago, and I still have an ancient copy of > > Lehninger. So what should I get now. > > -- Rong Chen Ph.D. Candidate Bioinformatics Program Boston University Boston, MA 02148 Tel: (617)358-1552 Fax: (617)358-1067 E-mail: rong at bu.edu http://zlab.bu.edu/~rong From rhammer at mail.bio.tamu.edu Wed Dec 18 17:14:00 2002 From: rhammer at mail.bio.tamu.edu (Rick Hammer) Date: Wed, 18 Dec 2002 16:14:00 -0600 Subject: [BiO BB] Biochemistry book reccomendation needed Message-ID: I just finished a course using Fundamentals of Biochemistry, by Voet, Voet & Pratt, 1999. The Biochem department here at Texas A&M previously used Lehninger but moved to this text so as not to drown students in too much detail. I would say this is a good text for a bioinformatician wanting some basic concepts (like myself). Good luck, Rick <<< rong at bu.edu 12/18 3:42p >>> The Cell: A Molecular Approach, by G.M. Cooper is really an excellent introductory book. I really like cooper's style. rong On Wed, 18 Dec 2002, J.W. Bizzaro wrote: > Hi Ken. > > I've used both Stryer and Garrett & Grisham. They are comparable in size, > covering enough material for several semesters of biochemistry. The latter is a > bit easier to read, while the former is a bit more detailed. > > I think most biochemistry texts are overkill for those not choosing the field as > a profession. One of my favorite texts, which is concise and nicely > illustrated, is The Cell: A Molecular Approach, by G.M. Cooper. I would > recommend it for those who don't intend to be biochemists but would like to know > enough biochem and molecular biology to begin studying bioinformatics. > > Cheers. > Jeff > > Ken Firestone wrote: > > > > I need a book recommendation. I am coming from a Computer Science > > background, and I would like a basic biochemistry text. I studied > > biochemistry many years ago, and I still have an ancient copy of > > Lehninger. So what should I get now. > > -- Rong Chen Ph.D. Candidate Bioinformatics Program Boston University Boston, MA 02148 Tel: (617)358-1552 Fax: (617)358-1067 E-mail: rong at bu.edu http://zlab.bu.edu/~rong _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jmfreeman at attbi.com Wed Dec 18 23:52:16 2002 From: jmfreeman at attbi.com (James Freeman) Date: Wed, 18 Dec 2002 23:52:16 -0500 Subject: [BiO BB] Wolfram's Cellular Automata Message-ID: <3E015080.9000009@attbi.com> Hi Folks, If any of you have any spare time over the holidays and are interested in Cellular Automata as shown in Steven Wolfram's book: A New Kind of Science. I have made a Perl module which implements one dimensional non-totalistic cellular automata that can be found at: http://search.cpan.org/author/JMFREEMAN/Cellular-Automata-Wolfram-1.1/ This may seem off topic, but there are some interesting phenotypes which can be modeled with cellular automata, and it is a very interesting topic in its own right. See: http://www.wolframscience.com/ for more details. Warmest Regards, Jim -- Bioinformatics Consultant jmfreeman at attbi.com ?I am always doing that which I can not do, in order that I may learn how to do it.? - Pablo Picasso From landman at scalableinformatics.com Thu Dec 19 02:28:08 2002 From: landman at scalableinformatics.com (Joe Landman) Date: 19 Dec 2002 02:28:08 -0500 Subject: [BiO BB] beta available of ncbi2rpm Message-ID: <1040282887.2880.14.camel@squash.scalableinformatics.com> Hi Folks: I posted ncbi2rpm, which will take the ncbi.tar.gz tarball, build it, turn it into an RPM (sitting under /opt to make the LSB folk happy). It is semi-specific to x86 at this moment, as I dont have access to an OS-X machine to play with it under. The environment requires autospec (http://freshmeat.net/releases/98493/) and can be pulled from http://scalableinformatics.com/downloads/ncbi2rpm.tar.gz . This beta is primarily to get the environment out there for people to beat on, tell me what is wrong with it, what they would like to see, and so forth. I did build a rather large RPM of the 2.2.5 NCBI tools using the gcc 3.2.1 compiler with it, at http://scalableinformatics.com/downloads/ncbitools-gcc3.2.1-2.2.5-1.i686.rpm . Please be aware that this RPM is about 46MB in size, and the web site has a small uplink pipe. Eventually, this environment will be used to build other tools as well (it is generic for building codes). I wanted to get feedback from the RPM builders out there, as well as those who have non-RPM packaging requirements, please help me understand what format works, and where it is described. The final cleaned up bits of this may appear in the biopkg effort. Joe -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From pajailwala at yahoo.com Thu Dec 19 11:40:16 2002 From: pajailwala at yahoo.com (Parthav Jailwala) Date: Thu, 19 Dec 2002 08:40:16 -0800 (PST) Subject: [BiO BB] Wolfram's Cellular Automata In-Reply-To: <3E015080.9000009@attbi.com> Message-ID: <20021219164016.53187.qmail@web12306.mail.yahoo.com> Hi James, You are putting a great effort to program an automaton in perl. Keep it up. However, in his book, Wolfram claims (doesnt prove) that many biological mechanisms (including human disease manifestations) can be explained using automatons. How far do you agree or believe in this theory. I feel that biological processes and nature are not that simplistic and will still require classical newtonian physics/math/chemistry to explain its complexities. Any thought on this ? Any others wish to air their thoughts? Wolfram is making a remarkable (and startling) theory here, so it will help all of us to share our thoughts on it and satisfy our intellectual curiosities. thanks parthav jailwala James Freeman wrote:Hi Folks, If any of you have any spare time over the holidays and are interested in Cellular Automata as shown in Steven Wolfram's book: A New Kind of Science. I have made a Perl module which implements one dimensional non-totalistic cellular automata that can be found at: http://search.cpan.org/author/JMFREEMAN/Cellular-Automata-Wolfram-1.1/ This may seem off topic, but there are some interesting phenotypes which can be modeled with cellular automata, and it is a very interesting topic in its own right. See: http://www.wolframscience.com/ for more details. Warmest Regards, Jim -- Bioinformatics Consultant jmfreeman at attbi.com ?I am always doing that which I can not do, in order that I may learn how to do it.? - Pablo Picasso _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ---------------------------------------------------------------------------------------- If you would lift me up you must be on higher ground. Ralph Waldo Emerson 1803-1882, American Poet ---------------------------------------------------------------------------------------- Parthav Jailwala,Analyst/Project Programmer,Max McGee National Centre for Juvenile Diabetes,Pediatrics(Endocrinology), Medical College of Wisconsin, Milwaukee, WI. Ph : 414-456-8269,E-mail : pjailwal at mcw.edu, Alternate E-mail : pajailwala at yahoo.com --------------------------------- Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now -------------- next part -------------- An HTML attachment was scrubbed... URL: From wusu at ele.uri.edu Thu Dec 19 12:59:18 2002 From: wusu at ele.uri.edu (Su Wu) Date: Thu, 19 Dec 2002 12:59:18 -0500 Subject: [BiO BB] Biochemistry book reccomendation needed References: <3E00EA58.9456BE71@bioinformatics.org> Message-ID: <3E0208F6.90201@ele.uri.edu> Being an electrical engineer and computer scientist, I found Stryer's book very informative and enjoyable. But I will check out Cooper's and Garrett & Grisham's as well. Thanks for the recommendation! Su Wu J.W. Bizzaro wrote: > Hi Ken. > > I've used both Stryer and Garrett & Grisham. They are comparable in size, > covering enough material for several semesters of biochemistry. The latter is a > bit easier to read, while the former is a bit more detailed. > > I think most biochemistry texts are overkill for those not choosing the field as > a profession. One of my favorite texts, which is concise and nicely > illustrated, is The Cell: A Molecular Approach, by G.M. Cooper. I would > recommend it for those who don't intend to be biochemists but would like to know > enough biochem and molecular biology to begin studying bioinformatics. > > Cheers. > Jeff > > Ken Firestone wrote: > >>I need a book recommendation. I am coming from a Computer Science >>background, and I would like a basic biochemistry text. I studied >>biochemistry many years ago, and I still have an ancient copy of >>Lehninger. So what should I get now. >> > From John.Walley at BellSouth.com Thu Dec 19 09:15:12 2002 From: John.Walley at BellSouth.com (Walley, John ) Date: Thu, 19 Dec 2002 09:15:12 -0500 Subject: [BiO BB] Biochemistry book recommendation needed Message-ID: Ken, I am in the same situation as you transitioning from traditional IT to BioInformatics. I bought a BioChem study guide from my local bookstore which has most of the concepts in sufficient detail without it being too much detail. I also found these two course outlines on the web that were helpful to me as well. http://ull.chemistry.uakron.edu/biochem/ http://www.blc.arizona.edu/coursesF02.html Cheers John -----Original Message----- From: Ken Firestone [mailto:kenf at speakeasy.net] Sent: Wednesday, December 18, 2002 4:03 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Biochemistry book reccomendation needed Hi, I need a book recommendation. I am coming from a Computer Science background, and I would like a basic biochemistry text. I studied biochemistry many years ago, and I still have an ancient copy of Lehninger. So what should I get now. ============================================================================ Ken Firestone, W3CAT | For every problem there is one solution kenf at speakeasy.net | which is simple, neat, and wrong. ken at firestone.net | -- H. L. Mencken ============================================================================ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ***** "The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential, proprietary, and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from all computers." From jmfreeman at attbi.com Fri Dec 20 00:07:15 2002 From: jmfreeman at attbi.com (James Freeman) Date: Fri, 20 Dec 2002 00:07:15 -0500 Subject: [BiO BB] Wolfram's Cellular Automata References: <20021219164016.53187.qmail@web12306.mail.yahoo.com> Message-ID: <3E02A583.1090003@attbi.com> Hi Parthav, This might seem a little off topic, but what the heck. Reading the book A New Kind of Science will help following this thread. Parthav Jailwala wrote: > Hi James, > > You are putting a great effort to program an automaton in perl. Keep > it up. > Thanks, I hope that means you tried it and it worked :). > However, in his book, Wolfram claims (doesn't prove) that many > biological mechanisms (including human disease manifestations) can be > explained using automatons. How far do you agree or believe in this > theory. I feel that biological processes and nature are not that > simplistic and will still require classical newtonian > physics/math/chemistry to explain its complexities. > What I get out of the book is that there is random data or any complexity in a system that can come from two sources, randomness or complexity fed to a system, or randomness or complexity in the nature of the system itself. Randomness is defined as incompressibility or equivalently you have to run the system to know what will happen there is no predicting in advance. Systems which are not simply repeating or nested patterns are all of the same class and computationally equivalent, and probably able to support universal computation, given the right input. Simple rules can lead to extremely complicated outcomes, and what seems difficult (the patterns on the side of a seashell e.g.) can be generated by very simple automata. Automata can produce patterns complicated enough for any definition of complexity you might throw at it and Wolfram goes quite a ways in showing that. Can automata be made that model complex biological behavior? Lindenmayer's L systems are computationally equivalent to some automata and go quite a way in modeling plant growth and other biological systems. More is possible, I am sure, but I made this module for myself to learn and explore in my spare time and I hope it is some use to you and others. Warmest Regards, Jim > Any thought on this ? Any others wish to air their thoughts? Wolfram > is making a remarkable (and startling) theory here, so it will help > all of us to share our thoughts on it and satisfy our intellectual > curiosities. > > thanks > > parthav jailwala > > James Freeman wrote: > > Hi Folks, > > If any of you have any spare time over the holidays and are > interested > in Cellular Automata as shown in Steven Wolfram's book: A New Kind of > Science. > I have made a Perl module which implements one dimensional > non-totalistic cellular automata that can be found at: > > http://search.cpan.org/author/JMFREEMAN/Cellular-Automata-Wolfram-1.1/ > > This may seem off topic, but there are some interesting phenotypes > which > can be modeled with cellular automata, and it is a very interesting > topic in its own right. > > See: > > http://www.wolframscience.com/ > > for more details. > > Warmest Regards, > > Jim > > -- > Bioinformatics Consultant > jmfreeman at attbi.com > I am always doing that which I can not do, in order that I may > learn how to do it. > - Pablo Picasso > > > > _______________________________________________ > Bi O_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > ---------------------------------------------------------------------------------------- > > If you would lift me up you must be on higher ground. > Ralph Waldo Emerson 1803-1882, American Poet > ---------------------------------------------------------------------------------------- > > Parthav Jailwala,Analyst/Project Programmer,Max McGee National Centre > for Juvenile Diabetes,Pediatrics(Endocrinology), Medical College of > Wisconsin, Milwaukee, WI. Ph : 414-456-8269,E-mail : pjailwal at mcw.edu, > Alternate E-mail : pajailwala at yahoo.com > > > ------------------------------------------------------------------------ > Do you Yahoo!? > Yahoo! Mail Plus > - > Powerful. Affordable. Sign up now > -- Bioinformatics Consultant jmfreeman at attbi.com I am always doing that which I can not do, in order that I may learn how to do it. - Pablo Picasso From priami at dit.unitn.it Sat Dec 21 01:16:54 2002 From: priami at dit.unitn.it (Corrado Priami) Date: Sat, 21 Dec 2002 07:16:54 +0100 Subject: [BiO BB] CMSB03 - Call for participation Message-ID: Apologies for multiple copies =========================== Please note that the deadline for having special fare in hotels is the end of the year. After that date it could be difficult to find rooms in hotel due to high sky season in Rovereto. ============================ Computational Methods in Systems Biology (CMSB 2003) University of Trento 24-26 February, 2003 Rovereto, Italy http://www.unitn.it/convegni/cmsb.htm Molecular biology has until now mainly focussed on individual molecules, on their properties as isolated entities or as complexes in very simple model systems. However, biological molecules in living systems participate in very complex networks, including regulatory networks for gene expression, intracellular metabolic networks and both intra- and intercellular communication networks. Such networks are involved in the maintenance (homeostasis) as well as the differentiation of cellular systems of which we have a very incomplete understanding. Nevertheless, the progress of molecular biology has made possible the detailed description of the components that constitute living systems, notably genes and proteins. Large scale genome sequencing means that we can (at least in principle) delimneate all macromolecular components of a given cellular system, and microarray experiments as well as large scale proteomics will soon give us large amounts of experimental data on gene regulation, molecular interactions and cellular networks. The challenge of the 21st century will be to understand how these individual components integrate to complex systems and the function and evolution of these systems, thus scaling up from molecular biology to systems biology. By combining experimental data with advanced formal theories from computer science, "the formal language for biological systems" to specify dynamic models of interacting molecular entities would be essential for 1. understanding normal behaviour of cellular processes, and how changes may affect the processes and cause disease. It may be possible to correlate genetic properties and symptoms in new and more efficient ways, based on an actual understanding of how various processes interact. 2. Providing predictability and flexibility to academic, pharmaceutical, biotechnology and medical researchers studying gene or protein functions. In particular, it may save time by reducing the number of experiments needed, if inadequate hypotheses could be excluded by computer simulation. PARTICIPATION To participate please fill in the form at the URL http://www.unitn.it/convegni/cmsb_form.htm The inscription fee is 200EURO until the end of this year and 250EURO for later registrations. The fee cover a copy of the proceedinngs, coffee break and lunches, the social dinnner and the special event. Hotel reservation can be done at special fare by the end of the year according to the information that you find at the URL http://www.unitn.it/convegni/cmsb_hotels.htm The programme is available at the web page of the workshop. PROGRAMME COMMITTEE _ Charles Auffray, CNRS, Villejuif (F) _ Cosima Baldari, Universit? di Siena (I) _ Alexander Bockmayr, Universit? Henri Poincar?, Nancy (F) _ Luca Cardelli, Microsoft Research Cambridge (UK) _ Vincent Danos, Universit? Paris VII (F) _ Pierpaolo Degano, Universit? di Pisa (I) _ Fran?ois Fages, INRIA Rocquencourt (F) _ Drabl?s Finn, , Norwegian University of Science and Technology, Trondheim (N) _ Monika Heiner, Brandenburg University of Technology at Cottbus - (D) _ Ina Koch, University of Applied Sciences Berlin, (D). _ John E. Ladbury, University College London (UK) _ Patrick Lincoln, SRI (USA) _ Satoru Miyano, University of Tokyo (JP) _ Gordon Plotkin, University of Edinburgh (UK) _ Simon Plyte, Pharmacia Corporation (I) _ Corrado Priami (CHAIR), Universit? di Trento (I) _ Aviv Regev, Weizmann Institute of Science (IL) _ Magali Roux-Rouqui?, BSMI Pasteur Institute (F) _ Vincent Schachter, Hybrigenics Paris (F) _ Masaru Tomita, Keio University (JP) _ Adelinde Uhrmacher, University of Rostock (D) _ Alfonso Valencia, CNB-CSIC Centro Nacional de Biotecnologia, Cantoblanco Madrid, (E) _ Olaf Wolkenhauer, UMIST, Manchester (UK) ORGANIZING COMMITTEE Linda Brodo, Michela de Concini, Corrado Priami, Debora Schuch da Rosa Machado Organizing Secretariat Universit? degli studi di Trento Ufficio Manifestazioni e Convegni c/o Molino Vittoria, Via Verdi, 6 I-38100 Trento - Italy Tel. (0039) 0461-883215-16-25 Fax (0039) 0461-883222 e-mail: ufficio.convegni at amm.unitn.it Proceedings The proceedings will be published in the Springer LNCS series and will be available at the workshop. HOW TO REACH ROVERETO Airports The closest international airport to Rovereto is VERONA Valerio Catullo (in Villafranca). Other Airports: MILAN Linate or Malpensa, VENICE Marco Polo (in Tessera) ROME Da Vinci (in Fiumicino) is about 8 hours train journey from Rovereto. Buses There is a regular coach shuttle service every 20 minutes from Malpensa and Linate airports to Milano Central Station Malpensa - Milano Central Station about 50 minutes. every 20 minutes from 04.15 - 00.15 (see timetable on website) Linate - Milano connections City bus n.73 >From the airport exit to town centre (piazza San Babila, Underground >station): about 25 mins, departure every 10 min. Tickets ( 0.77 >euro) on sale at news-stands. The 73 bus has special luggage racks. By coach from the Central railway station There is a coach service between the Air Terminal at the Central Station and Linate airport. Departures every 20 mins. The 20 min. ride costs 2.58 Euro. Coaches have large baggage-holds. Linate Malpensa - Linate A coach shuttle connects both airports in c.75 mins. Tickets cost 9.29 euro. >From Verona Valerio Catullo airport to Verona Porta Nuova central >train station about 15 minutes every 20 minutes from 6.10 - 23.30 Aereoporto Catullo: Connections Venice Marco Polo airport is about 30 minutes from Mestre train station by bus or you can take a vaporetto (taxi boat) to S. Lucia train station in Venice old city. Trains There is a bus shuttle service from all the airports to the nearest railway stations. You can check out the trains web site: www.trenitalia.com and click onto the British flag for train connections and times in English. Ask for "andata e ritorno" (return ticket) if you are going back to the same station, or "solo andata" (single). In big cities you will find someone who speaks English at the station but in small towns it is possible that they don't! Please note that trains marked ES (Euro Star), EC (Eurocity) or IC (Intercity) require a small supplement. The cheapest trains are Regionale (R) and Interregionale (IR). It is very important to remember to validate your ticket in one of the yellow machines on the platform before you get on the train. You will be fined if you forget! Taxi Taxis are available outside the railway station in Rovereto. Tel: 0464 421555/421 365 -- ============================================================= Prof. Corrado Priami Tel. 0461 882085 Dipartimento di Informatica e Telecomunicazioni Mob Universita' di Trento Fax 0461 88 1624 Via Sommarive, 14 http://www.science.unitn.it/~priami 38050 Povo (TN) - Italia priami at dit.unitn.it ============================================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: From vinod.bihal at inveniobio.com Sun Dec 22 23:56:52 2002 From: vinod.bihal at inveniobio.com (vinod) Date: Mon, 23 Dec 2002 10:26:52 +0530 Subject: [BiO BB] regariding list Message-ID: <001001c2aa3f$d2b14650$c801a8c0@oracleserver> Pls mail me the list. Thanks Vinod Bihal -------------- next part -------------- An HTML attachment was scrubbed... URL: From Neeraj_Tripathi at satyam.com Mon Dec 23 00:01:32 2002 From: Neeraj_Tripathi at satyam.com (Neeraj_Tripathi) Date: Mon, 23 Dec 2002 10:31:32 +0530 Subject: [BiO BB] FW: Help Pleezz !!! Message-ID: <877B003B6F03D511A22E00B0D078E7A80FCBDAED@hst.satyam.com> > ---------- > From: Christie Q.[SMTP:christie at webbench.com.au] > Reply To: Christie Q. > Sent: Saturday, December 21, 2002 2:36 PM > To: WebBench > Subject: Fw: Help Pleezz !!! > > Hi All, > > Just pass this on to as many people as may be possible. Its a matter of > somebody's life & death. > > Christie > > ========================================== > > Date: Thu, 5 Dec 2002 09:58:16 -0800 (PST) > > Dear Friends, > > Please help, if possible. This is important to me....so I am asking you > to please forward it. Please send this to all your contacts. If anyone > you know who has survived NON SMALL CELL LUNG CANCER, please inform me at > the address given below. My husband has it and I would like to know what > treatment was used. Please forward this to everyone on your contact list. > From the bottom of my heart I thank you. > > Thank you, > > Divya Singh > > > Inform here : > > SIEMENS, Siemens Information System Limited, > > #84, Keonics Electronics City, Hosur Road, Bangalore - 561 229. INDIA. > > Please keep forwarding this, even if you are unable to help. Somebody else > might be able to.... MAY GOD BE WITH U & BLESS U ALWAYS - Dinesh Narang, > E.I.T Simmons, Rockecharlie & Prince, Inc. > > > ========================================== > > > > ************************************************************************** This email (including any attachments) is intended for the sole use of the intended recipient/s and may contain material that is CONFIDENTIAL AND PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or distribution or forwarding of any or all of the contents in this message is STRICTLY PROHIBITED. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. ************************************************************************** From seabi at indiatimes.com Tue Dec 24 01:30:16 2002 From: seabi at indiatimes.com (seabi) Date: Tue, 24 Dec 2002 12:00:16 +0530 Subject: [BiO BB] (no subject) Message-ID: <200212240635.MAA13041@WS0005.indiatimes.com> Hello everybody, I wish u all a very happy and prosperous new year. I would request to kindly let me know the :: HOW TO CO-RELATE BIO WITH I.T AND THE SOFTWARES/LINKS WHICH CAN BE DOWNLOADED ON THE SYSTEM MAY PLEASE BE INFORMED. I HAVE SOME IDEA ABOUT RASMOL AND SWISSpdb. WILL U PLEASE EXPLAIN OTHER SIMILAR LINKS/SOFTWARES TO OPERATE AND WORK. THANKS Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy the best in Movies at http://www.videos.indiatimes.com Now bid just 7 Days in Advance and get Huge Discounts on Indian Airlines Flights. So log on to http://indianairlines.indiatimes.com and Bid Now ! -------------- next part -------------- An HTML attachment was scrubbed... URL: From kn_miura at ot.olympus.co.jp Fri Dec 27 02:53:25 2002 From: kn_miura at ot.olympus.co.jp (kn_miura at ot.olympus.co.jp) Date: Fri, 27 Dec 2002 16:53:25 +0900 Subject: [BiO BB] Question on the Journal Message-ID: Dear members; Does anybody know the publisher name or URL for the journal "Methods in Molecular Biology"? A fragment of information will be appreciated. Thank you in advance. Kunihiko F. Miura. Ph.D. From seabi at indiatimes.com Fri Dec 27 05:41:46 2002 From: seabi at indiatimes.com (seabi) Date: Fri, 27 Dec 2002 16:11:46 +0530 Subject: [BiO BB] Question on the Journal Message-ID: <200212271046.QAA03545@WS0005.indiatimes.com> Mr. kunihiko, please search the following links, may they be of any use to you : http://llama,med.harvard.edu/ www.genemed.com www3.oup.co.uk/nar http://bcmp.med.harvard.edu/ seabi bio_bulletin_board at bioinformatics.org wrote: Dear members; Does anybody know the publisher name or URL for the journal "Methods in Molecular Biology"? A fragment of information will be appreciated. Thank you in advance. Kunihiko F. Miura. Ph.D. _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy the best in Movies at http://www.videos.indiatimes.com Now bid just 7 Days in Advance and get Huge Discounts on Indian Airlines Flights. So log on to http://indianairlines.indiatimes.com and Bid Now ! -------------- next part -------------- An HTML attachment was scrubbed... URL: From priyaa_b at yahoo.com Sat Dec 28 01:06:47 2002 From: priyaa_b at yahoo.com (padma priya) Date: Fri, 27 Dec 2002 22:06:47 -0800 (PST) Subject: [BiO BB] (no subject) Message-ID: <20021228060647.81992.qmail@web41214.mail.yahoo.com> hello members, i have modeled the enzyme nitrogenase using comparitive modeling procedures. i know the active site of my model now. can anybody tell me what else i can do? thank you priya. __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From lf at mrc-dunn.cam.ac.uk Sun Dec 29 17:45:29 2002 From: lf at mrc-dunn.cam.ac.uk (lf at mrc-dunn.cam.ac.uk) Date: Sun, 29 Dec 2002 22:45:29 -0000 (GMT) Subject: [BiO BB] use of comparative models Message-ID: <1409.192.76.27.83.1041201929.squirrel@www.mrc-dunn.cam.ac.uk> Hi Priya, I found the following very useful to answer this question in a thorough way: Peitsch, M.C., (2002). About the use of protein models. Bioinformatics, 18(7): 934-938. Lucy Forrest > hello members, > i have modeled the enzyme nitrogenase > using comparitive modeling procedures. i know the > active site of my model now. can anybody tell me what > else i can do? > thank you > priya. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From karen at scientecpersonnel.com Sun Dec 29 16:36:21 2002 From: karen at scientecpersonnel.com (karen at scientecpersonnel.com) Date: Sun, 29 Dec 2002 16:36:21 -0500 (EST) Subject: [BiO BB] Out of office notice Message-ID: <104119742201@202.157.164.2> Hi, thank you for your email. I will be away from 29 Dec to 2nd Jan. Please contact Wendy at 62253272 if you have urgent matters. I will not have internet access while I am away. Regards, Karen From ETIKYALA at aol.com Sat Dec 28 10:51:11 2002 From: ETIKYALA at aol.com (ETIKYALA at aol.com) Date: Sat, 28 Dec 2002 10:51:11 -0500 Subject: [BiO BB] Parnerships and collaborative ventures in Bioinformatics/Molecular biology Message-ID: <0100BA0F.798A8F84.006AADD8@aol.com> Attn: Graduate School advice Dear Joel, I have gone through the website and I have all the infrastructure (in NY) and experience to run the bioinformatics/computational biology programs. I am interested and enthusiastic to work with you and actively seeks partnerships and collaborative ventures in molecular and biodiversity informatics. Would you please let me know if I could work with the university or getting the approval of university in running the programs? Thanks Ashok From agabindia at hotmail.com Sat Dec 28 16:43:36 2002 From: agabindia at hotmail.com (Mukesh Sharma) Date: Sun, 29 Dec 2002 03:13:36 +0530 Subject: [BiO BB] Distance Education Program in Bioinformatics Message-ID: Admission Notice- Academy of Genomics & Applied Biology The new emerging field Bioinformatics is an integration of mathematical, statistical and computer methods to analyze biological, biochemical and biophysical data. Than Bioinformatics required a best knowledge not only in biology but in mathematics too. At that time many private institution in india providing bioinformatics education but offered courses are totaly dedicated to biological stream students, so this is necessary to know to actual requirments of bioinformatics field. AGAB understand all the requirment of the real bioinformatics world and designed two bioinformatics course based on the international standards and market requirments. Course offered by AGAB have the best mixture of biology & mathamatics to get best growth in the market. AGAB is trying to get best industrial interaction to provide best bioinformatics potential in India as well as in international market too. \"Academy of Genomics & Applied Biology\" is the non-profit making institute conducting the distance learning program in Bioinformatics for promoting high-end quality education in the field of Bioinformatics through its two program: 1) Advance Diploma in Bioinformatics (Hons.) Duration : 18 months Fee : 4500/- (4000/- for SC/ST/Govt./Defence prof) For Foreign Students: US$ 350 Elig. : Graduation in Science Stream with min 50% marks 2) Diploma in Bioinformatics Duration : 12 months Fee : 3500/- (3000/- for SC/ST/Govt./Defence prof) For Foreign Students: US$ 250 Elig. : 10+2 in Science Stream with min 50% marks The aim of these programs is to provide bioinformatics professionals for difference pharmacuticals/IT sectors/R&D Dept./Govt. & Non Govt. Organisations. Course commencing from 31st of Jan. 2003 How to apply Application form and Brochure: The online application form-course details can be obtain through the e-mail. (For hardcopy send e-mail with your postal address) Soon we are going to provide online registration facility through our website. For more information & any query write us: agabindia at hotmail.com Thanx, Vineet Massey Manager-Academics _________________________________________________________________ MSN 8: advanced junk mail protection and 3 months FREE*. http://join.msn.com/?page=features/junkmail&xAPID=42&PS=47575&PI=7324&DI=7474&SU= http://www.hotmail.msn.com/cgi-bin/getmsg&HL=1216hotmailtaglines_advancedjmf_3mf From karen at scientecpersonnel.com Sun Dec 29 23:00:23 2002 From: karen at scientecpersonnel.com (karen at scientecpersonnel.com) Date: Sun, 29 Dec 2002 23:00:23 -0500 (EST) Subject: [BiO BB] Out of office notice Message-ID: <104122046701@202.157.164.2> Hi, thank you for your email. I will be away from 29 Dec to 2nd Jan. Please contact Wendy at 62253272 if you have urgent matters. I will not have internet access while I am away. Regards, Karen From karen at scientecpersonnel.com Sun Dec 29 23:00:46 2002 From: karen at scientecpersonnel.com (karen at scientecpersonnel.com) Date: Sun, 29 Dec 2002 23:00:46 -0500 (EST) Subject: [BiO BB] Out of office notice Message-ID: <104122049101@202.157.164.2> Hi, thank you for your email. I will be away from 29 Dec to 2nd Jan. Please contact Wendy at 62253272 if you have urgent matters. I will not have internet access while I am away. Regards, Karen From priyaa_b at yahoo.com Mon Dec 30 01:32:32 2002 From: priyaa_b at yahoo.com (padma priya) Date: Sun, 29 Dec 2002 22:32:32 -0800 (PST) Subject: [BiO BB] use of comparative models In-Reply-To: <1409.192.76.27.83.1041201929.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <20021230063232.60447.qmail@web41206.mail.yahoo.com> hi lucy, thanx a lot! i definetly refer it. priya. --- lf at mrc-dunn.cam.ac.uk wrote: > Hi Priya, > I found the following very useful to answer this > question in a thorough way: > > Peitsch, M.C., (2002). About the use of protein > models. Bioinformatics, > 18(7): 934-938. > > Lucy Forrest > > > hello members, > > i have modeled the enzyme > nitrogenase > > using comparitive modeling procedures. i know the > > active site of my model now. can anybody tell me > what > > else i can do? > > thank you > > priya. > > > > _______________________________________________ > > 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 __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From karen at scientecpersonnel.com Mon Dec 30 01:32:30 2002 From: karen at scientecpersonnel.com (karen at scientecpersonnel.com) Date: Mon, 30 Dec 2002 01:32:30 -0500 (EST) Subject: [BiO BB] Out of office notice Message-ID: <104122959301@202.157.164.2> Hi, thank you for your email. I will be away from 29 Dec to 2nd Jan. Please contact Wendy at 62253272 if you have urgent matters. I will not have internet access while I am away. Regards, Karen