From pankaj at nii.res.in Mon Aug 2 01:39:14 2004 From: pankaj at nii.res.in (Pankaj Kamra) Date: Mon, 02 Aug 2004 11:09:14 +0530 (IST) Subject: [BiO BB] refine models Message-ID: hi all, I have built a model of a protein with a single template using a standard modeller package (using script model-default.top). Now i want to refine my model so that it has minimum bumps and proper side chain orientations. how do i do that? thanking all in advance pankaj From pankaj at nii.res.in Mon Aug 2 07:30:09 2004 From: pankaj at nii.res.in (Pankaj) Date: Mon, 02 Aug 2004 17:00:09 +0530 (IST) Subject: [BiO BB] prosite pattern Message-ID: hi all, i m working on a protein family. however i do not know in total how many sequences of this protein family are available in public databases. i know the prosite motif of this family. using this can i find how many sequences in swiss-prot and ncbi belong to this family. pankaj From erick at amaze.ulb.ac.be Wed Aug 4 05:01:06 2004 From: erick at amaze.ulb.ac.be (erick antezana) Date: Wed, 4 Aug 2004 11:01:06 +0200 Subject: [BiO BB] Graph Formats Message-ID: Hello, does anyone know or use some XML-based exchange graph format for representing pathways/regulatory networks/etc ? GraphML (http://graphml.graphdrawing.org/index.html) seems to be a nice format as well as GINML (http://www.esil.univ-mrs.fr/~chaouiya/Recherche/GINML/index.html)... could someone advice me which one to use? Pros ans Cons? thanks in advance, erick From michael_jennings at mail.ru Mon Aug 2 10:10:11 2004 From: michael_jennings at mail.ru (Michael Jennings) Date: Mon, 02 Aug 2004 18:10:11 +0400 Subject: [BiO BB] photon activated enzymes Message-ID: Hello All! I'm currently looking for specific photo activated enzymes ... does anyone know anything? Specifically for the polymerisation of materails. Thanking you in advance. Mike Email:mike at physics.otago.ac.nz http://Mail.Ru - ?????? ????? ? ?????????????? ??????? ????????? ?????! From s0340567 at sms.ed.ac.uk Thu Aug 5 19:16:47 2004 From: s0340567 at sms.ed.ac.uk (FJPB Asselbergs) Date: Fri, 6 Aug 2004 00:16:47 +0100 Subject: [BiO BB] question on clustering Message-ID: <1091747807.4112bfdfb82f7@sms.ed.ac.uk> Hi all, I have a question that concerns my MSc project. I am trying to cluster 30 CCP-modules (Complement Receptor 1) after having used a novel approach that looks at the electrostatic surfaces. I have reached the stage where I have obtained a similarity matrix of 30 by 30 filled with positive scores. The higher a score the more similar two modules are. For example, if matrix entry (3,6) = 13 and entry (3,8) = 24 then module 3 is more similar to module 8 than to module 6 due to a higher score. My problem now is to cluster these 30 modules based on this one similarity matrix. I am not used to have to cluster small datasets or in this case a similarity matrix and not having training data. I have searched around a lot on Google for programs that could cluster my modules using the similarity matrix but so far I have not found anything very helpful. Does anyone know of a program (preferably free software) that could help me out here, or another way which I could easily implement myself in a script, that would be valid? I would really appreciate all replies to this message and thank you all already for looking at this and thinking about this. Thanks and regards, Floris From thompson at wadsworth.org Fri Aug 6 13:24:35 2004 From: thompson at wadsworth.org (William Thompson) Date: Fri, 6 Aug 2004 13:24:35 -0400 (EDT) Subject: [BiO BB] Re: question on clustering Message-ID: <200408061724.i76HOZp16027@csserv.wadsworth.org> You might want to look into R http://www.r-project.org/ R is a programming tool for statistics and data analysis. R has a fairly complete clustering package. It's free, robust and there are lots of web resources for it. Bill Bill Thompson, PhD Bioinformatics Center NYS Department of Health Center for Medical Science, rm 2006 150 New Scotland Avenue Albany, New York 12208 (518) 486-7882 > Hi all, > > I have a question that concerns my MSc project. I am trying to cluster 30 > CCP-modules (Complement Receptor 1) after having used a novel approach that > looks at the electrostatic surfaces. I have reached the stage where I have > obtained a similarity matrix of 30 by 30 filled with positive scores. The > higher a score the more similar two modules are. For example, if matrix entry > (3,6) = 13 and entry (3,8) = 24 then module 3 is more similar to module 8 than > to module 6 due to a higher score. My problem now is to cluster these 30 > modules based on this one similarity matrix. I am not used to have to cluster > small datasets or in this case a similarity matrix and not having training > data. I have searched around a lot on Google for programs that could cluster my > modules using the similarity matrix but so far I have not found anything very > helpful. Does anyone know of a program (preferably free software) that could > help me out here, or another way which I could easily implement myself in a > script, that would be valid? I would really appreciate all replies to this > message and thank you all already for looking at this and thinking about this. > > Thanks and regards, > Floris From dmb at mrc-dunn.cam.ac.uk Fri Aug 6 14:02:52 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 6 Aug 2004 19:02:52 +0100 (BST) Subject: [BiO BB] Re: question on clustering In-Reply-To: <200408061724.i76HOZp16027@csserv.wadsworth.org> Message-ID: I tried to get a 'community answer' page going at... http://en.wikipedia.org/wiki/Sequence_clustering but it dosen't explicitly deal with similarity matrix clustering techniques. Please feel free to contribute! Dan. On Fri, 6 Aug 2004, William Thompson wrote: >You might want to look into R http://www.r-project.org/ R is a programming tool >for statistics and data analysis. R has a fairly complete clustering package. >It's free, robust and there are lots of web resources for it. > >Bill > >Bill Thompson, PhD >Bioinformatics Center >NYS Department of Health >Center for Medical Science, rm 2006 >150 New Scotland Avenue >Albany, New York 12208 >(518) 486-7882 > > > >> Hi all, >> >> I have a question that concerns my MSc project. I am trying to cluster 30 >> CCP-modules (Complement Receptor 1) after having used a novel approach that >> looks at the electrostatic surfaces. I have reached the stage where I have >> obtained a similarity matrix of 30 by 30 filled with positive scores. The >> higher a score the more similar two modules are. For example, if matrix entry >> (3,6) = 13 and entry (3,8) = 24 then module 3 is more similar to module 8 than >> to module 6 due to a higher score. My problem now is to cluster these 30 >> modules based on this one similarity matrix. I am not used to have to cluster >> small datasets or in this case a similarity matrix and not having training >> data. I have searched around a lot on Google for programs that could cluster >my >> modules using the similarity matrix but so far I have not found anything very >> helpful. Does anyone know of a program (preferably free software) that could >> help me out here, or another way which I could easily implement myself in a >> script, that would be valid? I would really appreciate all replies to this >> message and thank you all already for looking at this and thinking about this. >> >> Thanks and regards, >> Floris > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From dmb at mrc-dunn.cam.ac.uk Mon Aug 9 10:53:48 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 9 Aug 2004 15:53:48 +0100 (BST) Subject: [BiO BB] Structural genomics and PDB growth? Message-ID: Can anyone point me at definative literature for estimates of PDB growth and the impact of structural genomics? What evidence do we have that the PDB will keep growing? What is the best current estimate of that growth rate? Cheers, Dan. From rfsouza at citri.iq.usp.br Fri Aug 6 20:55:49 2004 From: rfsouza at citri.iq.usp.br (Robson Francisco de Souza {S}) Date: Fri, 6 Aug 2004 21:55:49 -0300 Subject: [BiO BB] question on clustering In-Reply-To: <20040806160105.32D39D1F07@www.bioinformatics.org> References: <20040806160105.32D39D1F07@www.bioinformatics.org> Message-ID: <20040807005549.GA24137@cecm.usp.br> Take a look at TribeMCL. This software can cluster sequences based on a similarity score matrix, thouch you will probably have to format your matrix in an appropriate text format. Robson > Hi all, > > I have a question that concerns my MSc project. I am trying to cluster 30 > CCP-modules (Complement Receptor 1) after having used a novel approach that > looks at the electrostatic surfaces. I have reached the stage where I have > obtained a similarity matrix of 30 by 30 filled with positive scores. The > higher a score the more similar two modules are. For example, if matrix entry > (3,6) = 13 and entry (3,8) = 24 then module 3 is more similar to module 8 than > to module 6 due to a higher score. My problem now is to cluster these 30 > modules based on this one similarity matrix. I am not used to have to cluster > small datasets or in this case a similarity matrix and not having training > data. I have searched around a lot on Google for programs that could cluster my > modules using the similarity matrix but so far I have not found anything very > helpful. Does anyone know of a program (preferably free software) that could > help me out here, or another way which I could easily implement myself in a > script, that would be valid? I would really appreciate all replies to this > message and thank you all already for looking at this and thinking about this. > > Thanks and regards, > Floris > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest > From H.Bhaskar at exeter.ac.uk Mon Aug 9 09:36:48 2004 From: H.Bhaskar at exeter.ac.uk (Harish Bhaskar) Date: Mon, 9 Aug 2004 14:36:48 +0100 Subject: [BiO BB] Summer School on Bioinformatics ! Message-ID: Dear Colleugue, This is to bring to your notice, the British Computer Society Summer School on Bioinformatics that is being organised at the University of Exeter (29,August - 3,September). This event is directed to PhD students, academics and industrial participants in the area of bioinformatics. The school involves lectures delivered by leading academics and practitioners in the UK. This is a fully residential summer school for one week and the registration cost covers accomodation, breakfast, tea/coffee and lunch. We would like to specially invite researchers and scientists from your group to attend this event. The registration forms are available at http://www.dcs.ex.ac.uk/bcs-par/bioinformatics04.html. To avail the early bird registration discount, fax us your registration forms to 01392-264067 before 13th August. Also, please circulate this email to interested colleagues in your organisation. There are several other benefits to registering before the 13th of August, 2004 as highlighted below: -- FREE IEEE Computer Society Membership for students for 2005 -- FREE IEEE Transactions on Computational Biology and Bioinformatics Subscription for 2005 -- FREE 20% discount on all Springer Books till October 2004 -- FREE British Computer Society PAR Specialist Group Membership for 2005 -- Best poster presentation prize of ?100 if your poster is judged best at the school -- Guaranteed accommodation on campus close to the venue -- Discounted fee, which increases after the 13th of August We look forward to seing you in the summer school. Harish Bhaskar (H.Bhaskar at ex.ac.uk) Secretary Summer School on Bioinformatics. From idoerg at yahoo.com Mon Aug 9 15:10:33 2004 From: idoerg at yahoo.com (Iddo Friedberg) Date: Mon, 9 Aug 2004 12:10:33 -0700 (PDT) Subject: [BiO BB] Structural genomics and PDB growth? In-Reply-To: Message-ID: <20040809191033.6779.qmail@web41606.mail.yahoo.com> Hi Dan, For your first question: We published something in PSB'04 http://helix-web.stanford.edu/psb04/bourne.pdf I don't know about definitive, but it is fairly exhaustive, based on data which was up-to-date for summer 2003. PDB will keep growing as long as crystallographers/NMR people have jobs and have families to feed. Future growth rate, as always, is estimated by extrapolation. However, come the technological breakthrough whcih will enable faster solutions for membrane proteins, the growth rate will probably increase :) Cheers, Iddo --- Dan Bolser wrote: > > Can anyone point me at definative literature for estimates of PDB > growth > and the impact of structural genomics? > > What evidence do we have that the PDB will keep growing? What is > the best > current estimate of that growth rate? > > Cheers, > Dan. > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ===== -- Iddo Friedberg The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA, 92037 USA T: (858) 646 3100 x3516 http://ffas.ljcrf.edu/~iddo __________________________________ Do you Yahoo!? Yahoo! Mail - 50x more storage than other providers! http://promotions.yahoo.com/new_mail From dmb at mrc-dunn.cam.ac.uk Tue Aug 10 19:46:53 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 11 Aug 2004 00:46:53 +0100 (BST) Subject: [BiO BB] Structural genomics and PDB growth? In-Reply-To: <20040809191033.6779.qmail@web41606.mail.yahoo.com> Message-ID: On Mon, 9 Aug 2004, Iddo Friedberg wrote: >Hi Dan, > >For your first question: > >We published something in PSB'04 > >http://helix-web.stanford.edu/psb04/bourne.pdf Cheers. > >I don't know about definitive, but it is fairly exhaustive, based on >data which was up-to-date for summer 2003. > >PDB will keep growing as long as crystallographers/NMR people have >jobs and have families to feed. Future growth rate, as always, is >estimated by extrapolation. However, come the technological >breakthrough whcih will enable faster solutions for membrane >proteins, the growth rate will probably increase :) That is the thing, but is the rate of increase increasing? >Cheers, > >Iddo > > > >--- Dan Bolser wrote: > >> >> Can anyone point me at definative literature for estimates of PDB >> growth >> and the impact of structural genomics? >> >> What evidence do we have that the PDB will keep growing? What is >> the best >> current estimate of that growth rate? >> >> Cheers, >> Dan. >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > >===== >-- >Iddo Friedberg >The Burnham Institute >10901 N. Torrey Pines Rd. >La Jolla, CA, 92037 >USA >T: (858) 646 3100 x3516 >http://ffas.ljcrf.edu/~iddo > > > >__________________________________ >Do you Yahoo!? >Yahoo! Mail - 50x more storage than other providers! >http://promotions.yahoo.com/new_mail >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From katia at cin.ufpe.br Wed Aug 11 11:47:28 2004 From: katia at cin.ufpe.br (Katia Silva Guimaraes) Date: Wed, 11 Aug 2004 12:47:28 -0300 (BRT) Subject: [BiO BB] CompBioNets 2004 - Poster submission open Message-ID: COMPBIONETS 2004 Algorithms and Computational Methods for Biochemical and Evolutionary Networks Recife, Brazil, December 15-18, 2004 CALL FOR POSTERS We invite the submission of posters to the Conference "Algorithms and Computational Methods for Biochemical and Evolutionary Networks" (CompBioNets'04) that is being organized in Recife, Brazil, December 15-18, 2004. The Conference topics will be computational biology in general, and more specifically, but not exclusively, genetic regulation, motifs, metabolism, protein-protein interaction, biochemical networks, protein function and structure, genome dynamics, genome rearrangements, comparative genomics. The best submitted posters will be invited for a short 10 minutes presentation, besides appearing in the local proceedings that will be available at the Conference. We strongly encourage contributions from all scientific communities involved in the topics of CompBioNets. We are particularly interested in contributions from the biological perspective. Visit our site (http://compbionets.cin.ufpe.br) to submit a poster. Deadline for poster submission: September 28, 2004. We are looking forward to receiving your contributions. Katia Guimar?es and Marie-France Sagot From james.fraser at mail.mcgill.ca Wed Aug 11 12:19:26 2004 From: james.fraser at mail.mcgill.ca (James Fraser) Date: Wed, 11 Aug 2004 12:19:26 -0400 Subject: [BiO BB] Help with standalone Blast Message-ID: <1092241166.411a470e91327@webmail.mcgill.ca> Hello, I have tried to resolve this problem on two copies of standalone blast (one on linux and one on windows). I have created a custom db of 65 sequences: formatdb -i ig.txt -n ig Then I ran an all against all blast blastall -p blastp -d ig -i ig.txt -o ig.out This worked fine. The problem is that when I change the e value cutoff (using -e ) i get odd results. For example: running blastall -p blastp -d ig -i ig.txt -o ig.out -e 1.0 yields: Score E Sequences producing significant alignments: (bits) Value 12764866 190 9e-53 129567005 33 2e-05 146402107 24 0.014 133620536 23 0.018 116798795 22 0.054 19626396 20 0.27 145686327 20 0.27 19630478 19 0.35 and running blastall -p blastp -d ig -i ig.txt -o ig.out -e 0.1 yields: Sequences producing significant alignments: (bits) Value 12764866 190 9e-53 133620536 23 0.018 My question is: Where did the hits for 129567005 and 146402107 go? The only thing I changed is the e value and I reiterate that I have tried this on two different machines running different OS. Thank you, James Fraser From landman at scalableinformatics.com Fri Aug 13 00:08:59 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Fri, 13 Aug 2004 00:08:59 -0400 Subject: [BiO BB] Bioinformatics Benchmark System version 3 released Message-ID: <411C3EDB.6040005@scalableinformatics.com> Version 3 of the Bioinformatics Benchmark System (BBS v3) has been released. Many new features, bug fixes, and suggested changes have been made. New benchmarks have been added and updated for mpiBLAST, HMMer, NCBI BLAST, and others in the baseline tests. The version 1 tests are still there if you wish to run them. The Bioinformatics Benchmark System is an attempt to build a flexible and power testing framework, and meaningful tests, to enable end users and vendors to probe the performance of their systems. As the most important benchmark is your benchmark, and not a pre-packaged benchmark, the system is specifically designed to allow you to easily modify or add new tests. Moreover, the source to these tests are available under GPL, and are hosted on Bioinformatics.org (http://bioinformatics.org/bbs) and Scalable Informatics (http://www.scalableinformatics.com/BBS). For those who wish to run their own tests by hand without any testing framework, the --dryrun switch will emit the final command line that would be run. Additional documentation on the XML input format is forthcoming. A submission system for results, and baseline curation and data set tagging will commence in short order. Better handling of errors is in place, as are better IPC methods. You can pull the binary tarball from http://downloads.scalableinformatics.com/downloads/bbs/bbsv3.tar.gz . Please note that this includes data for a rather large mpiBLAST job. If someone has a sizeable cluster they are willing to play with, mpiBLAST installed and some time, we would like to see the speedup curve for 16 - 256 nodes (or higher). We would be happy to help out with this. Joe -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 612 4615 From mgollery at unr.edu Fri Aug 13 16:52:33 2004 From: mgollery at unr.edu (Martin Gollery) Date: Fri, 13 Aug 2004 13:52:33 -0700 Subject: [BiO BB] Bioinformatics Benchmark System version 3 released In-Reply-To: <411C3EDB.6040005@scalableinformatics.com> References: <411C3EDB.6040005@scalableinformatics.com> Message-ID: <411D2A11.7050103@unr.edu> Thanks Joe. One addition that might be useful would be to have a space where people could post their results, with complete information about the system, of course. This would allow people to see how their system compares to any other. Marty Joe Landman wrote: > Version 3 of the Bioinformatics Benchmark System (BBS v3) has been > released. Many new features, bug fixes, and suggested changes have been > made. New benchmarks have been added and updated for mpiBLAST, HMMer, > NCBI BLAST, and others in the baseline tests. The version 1 tests are > still there if you wish to run them. > > The Bioinformatics Benchmark System is an attempt to build a flexible > and power testing framework, and meaningful tests, to enable end users > and vendors to probe the performance of their systems. As the most > important benchmark is your benchmark, and not a pre-packaged benchmark, > the system is specifically designed to allow you to easily modify or add > new tests. > > Moreover, the source to these tests are available under GPL, and are > hosted on Bioinformatics.org (http://bioinformatics.org/bbs) and > Scalable Informatics (http://www.scalableinformatics.com/BBS). > > For those who wish to run their own tests by hand without any testing > framework, the --dryrun switch will emit the final command line that > would be run. > Additional documentation on the XML input format is forthcoming. A > submission system for results, and baseline curation and data set > tagging will commence in short order. Better handling of errors is in > place, as are better IPC methods. > > You can pull the binary tarball from > http://downloads.scalableinformatics.com/downloads/bbs/bbsv3.tar.gz . > Please note that this includes data for a rather large mpiBLAST job. If > someone has a sizeable cluster they are willing to play with, mpiBLAST > installed and some time, we would like to see the speedup curve for 16 - > 256 nodes (or higher). We would be happy to help out with this. > > Joe > -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- Marty's Law- the number of Bioinformatics acronyms will double every 18 months. From landman at scalableinformatics.com Fri Aug 13 17:13:24 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Fri, 13 Aug 2004 17:13:24 -0400 Subject: [BiO BB] Bioinformatics Benchmark System version 3 released In-Reply-To: <411D2A11.7050103@unr.edu> References: <411C3EDB.6040005@scalableinformatics.com> <411D2A11.7050103@unr.edu> Message-ID: <20040813211251.M55120@scalableinformatics.com> Hi Martin: This is definitely in the works. Should be ready shortly, and we will announce then. Thanks! Joe On Fri, 13 Aug 2004 13:52:33 -0700, Martin Gollery wrote > Thanks Joe. One addition that might be useful would be to have a space > where people could post their results, with complete information about > the system, of course. This would allow people to see how their system > compares to any other. > > Marty > > Joe Landman wrote: > > > Version 3 of the Bioinformatics Benchmark System (BBS v3) has been > > released. Many new features, bug fixes, and suggested changes have been > > made. New benchmarks have been added and updated for mpiBLAST, HMMer, > > NCBI BLAST, and others in the baseline tests. The version 1 tests are > > still there if you wish to run them. > > > > The Bioinformatics Benchmark System is an attempt to build a flexible > > and power testing framework, and meaningful tests, to enable end users > > and vendors to probe the performance of their systems. As the most > > important benchmark is your benchmark, and not a pre-packaged benchmark, > > the system is specifically designed to allow you to easily modify or add > > new tests. > > > > Moreover, the source to these tests are available under GPL, and are > > hosted on Bioinformatics.org (http://bioinformatics.org/bbs) and > > Scalable Informatics (http://www.scalableinformatics.com/BBS). > > > > For those who wish to run their own tests by hand without any testing > > framework, the --dryrun switch will emit the final command line that > > would be run. > > Additional documentation on the XML input format is forthcoming. A > > submission system for results, and baseline curation and data set > > tagging will commence in short order. Better handling of errors is in > > place, as are better IPC methods. > > > > You can pull the binary tarball from > > http://downloads.scalableinformatics.com/downloads/bbs/bbsv3.tar.gz . > > Please note that this includes data for a rather large mpiBLAST job. If > > someone has a sizeable cluster they are willing to play with, mpiBLAST > > installed and some time, we would like to see the speedup curve for 16 - > > 256 nodes (or higher). We would be happy to help out with this. > > > > Joe > > > > -- > Martin Gollery > Associate Director > Center For Bioinformatics > University of Nevada at Reno > Dept. of Biochemistry / MS330 > 775-784-7042 > ----------- > Marty's Law- the number of Bioinformatics acronyms will double every > 18 months. _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From information at virtualgenomics.org Mon Aug 16 18:33:23 2004 From: information at virtualgenomics.org (information at virtualgenomics.org) Date: Mon, 16 Aug 2004 15:33:23 -0700 Subject: [BiO BB] Fourth Virtual Conference on Genomics and Bioinformatics Message-ID: <20040816223323.29995.qmail@webmail-2-5.mesa1.secureserver.net> *********************************************************************** Fourth Virtual Conference on Genomics and Bioinformatics September 21-24, 2004 www.VirtualGenomics.Org *********************************************************************** Location: Virtual Locations Worldwide (List available at www.VirtualGenomics.Org) Registration fees: None The Virtual Conference on Genomics and Bioinformatics is an advanced collaborative environment featuring high profile researchers involved in the development and use of cutting edge technologies and approaches which allow a better understanding of the molecular structure and dynamics of biological systems. The objectives of the conference are: * Transcend geographical and economical barriers for the exchange of ideas that facilitates the interaction and collaboration among scientists and educators around the world. * Address the benefits and limitations of the newest developments in post-genomic technologies. * Explore the social and ethical implications of genomic and bioinformatic research. * Establish new ways to introduce the high school community to today's multidisciplinary science. Speakers: Uri Alon, Weizmann Institute of Science. Israel Wanda Andreoni, IBM Z?rich Research Laboratory, Switzerland Kim Baldridge, Universit?t Z?rich. Switzerland Patsy Babbitt. University of California, San Francisco. USA Irene Bosch, University of Massachusetts Medical School. USA Carlos Camacho, University of Pittsburgh, USA Colin C. Collins, Medicine and Cancer Research Institute, UCSF. USA Charles DeLisi, Boston University. USA Martin Gollery, University of Nevada at Reno. USA Fern Hunt, National Institute of Standards and Technology. USA S.S. Iyengar, Louisiana State University. USA Maricel Kann, National Institutes of Health. NCBI. USA Eugene Koonin, National Institutes of Health. USA Luis Rocha, Los Alamos National Laboratory. USA John B. Shabb, University of North Dakota. USA Wibke Sudholt, Universit?t Z?rich. Switzerland Christoph W. Sensen, University of Calgary. Canada Richard Simon, National Institutes of Health. NCI. USA Jason Suen, California Institute of Technology, USA Sarah B. Tegen, National Academy of Sciences, USA William Perrizo, North Dakota State University. USA Willy Valdivia-Granda. Orion Integrated Biosciences. USA Yuzhen Ye, The Burnham Institute. USA Roie Yerushalmi, Weizmann Institute of Science. Israel For more information visit www.VirtualGenomics.Org From dmb at mrc-dunn.cam.ac.uk Wed Aug 18 07:29:23 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 18 Aug 2004 12:29:23 +0100 (BST) Subject: [BiO BB] Bioinformatics (potential) needs assessment form? Message-ID: Hi, Has anyone ever done a survey of bioinformatics needs for an experimentalist (molecular biology) community? I need to survey the (potential) bioinformatics needs of a group of experimentalists with a wide range of bioinformatics knowledge (from 'some in-depth specialist' through 'general' to 'none'). Ideally I would like to capture both what is currently being used, and what would be really useful if it were being used. The problem is in the last case people may not know what could potentially be helpful. i.e. they need training and/or the form needs to be educational (gulp). I would be very grateful if someone could point me at a stock form, and I would be more than willing to help try to create such a stock form from the condensed knowledge of this community. Thanks very much for any assistance, Dan. From sourangshu at csa.iisc.ernet.in Wed Aug 18 07:45:35 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Wed, 18 Aug 2004 17:15:35 +0530 (IST) Subject: [BiO BB] Bioinformatics (potential) needs assessment form? In-Reply-To: References: Message-ID: Hi, I agree with Dan. It will be very helpful to know the needs of an experimentalist. Can there be an online survey of some kind on the bioinformatics.org website ? Thank you, Sourangshu. On Wed, 18 Aug 2004, Dan Bolser wrote: > > Hi, > > Has anyone ever done a survey of bioinformatics needs for an > experimentalist (molecular biology) community? > > I need to survey the (potential) bioinformatics needs of a group of > experimentalists with a wide range of bioinformatics knowledge (from 'some > in-depth specialist' through 'general' to 'none'). > > Ideally I would like to capture both what is currently being used, and > what would be really useful if it were being used. > > The problem is in the last case people may not know what could potentially > be helpful. i.e. they need training and/or the form needs to be > educational (gulp). > > I would be very grateful if someone could point me at a stock form, and I > would be more than willing to help try to create such a stock form from > the condensed knowledge of this community. > > Thanks very much for any assistance, > > Dan. > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From landman at scalableinformatics.com Wed Aug 18 08:24:10 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 18 Aug 2004 08:24:10 -0400 Subject: [BiO BB] Bioinformatics (potential) needs assessment form? In-Reply-To: References: Message-ID: <41234A6A.9080903@scalableinformatics.com> Hi Dan: A real needs assessment tends to be an interview. You might be able to do a set of interviews to get a better understanding of what questions to put into your poll. The needs assessments vary depending upon the target group and their problems. A single poll might not capture the necessary details. Needs assessments are critical to my companies business, as we need to understand our customers computational problems. I would think that a similar approach might work here, though it is usually hard to condense everything into a single document before the interview. You might try several sample interviews, see where they take you, and then refine it. Iterate until you are satisfied. Joe Dan Bolser wrote: >Hi, > >Has anyone ever done a survey of bioinformatics needs for an >experimentalist (molecular biology) community? > >I need to survey the (potential) bioinformatics needs of a group of >experimentalists with a wide range of bioinformatics knowledge (from 'some >in-depth specialist' through 'general' to 'none'). > >Ideally I would like to capture both what is currently being used, and >what would be really useful if it were being used. > >The problem is in the last case people may not know what could potentially >be helpful. i.e. they need training and/or the form needs to be >educational (gulp). > >I would be very grateful if someone could point me at a stock form, and I >would be more than willing to help try to create such a stock form from >the condensed knowledge of this community. > >Thanks very much for any assistance, > >Dan. > > > > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 612 4615 From dmb at mrc-dunn.cam.ac.uk Wed Aug 18 08:39:26 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 18 Aug 2004 13:39:26 +0100 (BST) Subject: [BiO BB] Bioinformatics (potential) needs assessment form? In-Reply-To: <41234A6A.9080903@scalableinformatics.com> Message-ID: Thanks very much for this information. I agree that interviews are the best way to serve an actual group of users (instead of a generic hypothetical group). However, I was looking for a generic form that I could taylor given my specific knowlage (based on beging around these guys for the last 2 years). A generic form could have several 'modules' to cover different lines of experimantal research, and could be used as a template to get things off the ground quickly. For example, one section (or 'module') could specifically address the need for further discussion and interviews. That way you could target your interviews to those people who are most likely to benifit from them. Perhaps... I definatly agree with what you have put below, but I am lazy (this isn't really my job anyway), and I would find a form or questionnaire much more appealing (in the short term). I know this isn't a good advert for good practice, but I do think that a well structured form could go a long way to quickly gathering good (but not the best) information in a fraction of the time and with a fraction of the effort. What do you think? Thanks again, Dan. On Wed, 18 Aug 2004, Joe Landman wrote: >Hi Dan: > > A real needs assessment tends to be an interview. You might be able >to do a set of interviews to get a better understanding of what >questions to put into your poll. > > The needs assessments vary depending upon the target group and their >problems. A single poll might not capture the necessary details. > > Needs assessments are critical to my companies business, as we need to >understand our customers computational problems. I would think that a >similar approach might work here, though it is usually hard to condense >everything into a single document before the interview. You might try >several sample interviews, see where they take you, and then refine it. >Iterate until you are satisfied. > >Joe > >Dan Bolser wrote: > >>Hi, >> >>Has anyone ever done a survey of bioinformatics needs for an >>experimentalist (molecular biology) community? >> >>I need to survey the (potential) bioinformatics needs of a group of >>experimentalists with a wide range of bioinformatics knowledge (from 'some >>in-depth specialist' through 'general' to 'none'). >> >>Ideally I would like to capture both what is currently being used, and >>what would be really useful if it were being used. >> >>The problem is in the last case people may not know what could potentially >>be helpful. i.e. they need training and/or the form needs to be >>educational (gulp). >> >>I would be very grateful if someone could point me at a stock form, and I >>would be more than willing to help try to create such a stock form from >>the condensed knowledge of this community. >> >>Thanks very much for any assistance, >> >>Dan. >> >> >> >> >> >>_______________________________________________ >>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > > > From jeff at bioinformatics.org Wed Aug 18 11:11:29 2004 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 18 Aug 2004 11:11:29 -0400 Subject: [BiO BB] Re: Bioinformatics (potential) needs assessment form? In-Reply-To: References: Message-ID: <412371A1.8090003@bioinformatics.org> Sourangshu Bhattacharya wrote: > Can there be an online survey of some kind on the bioinformatics.org > website ? As Joe indicated, the survey would need to be more detailed than the average poll placed on our main page. If someone wants to create a form that uses MySQL or Postgres on the backend, we'd be happy to host it here :-) Cheers. Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From mgollery at unr.edu Wed Aug 18 11:42:07 2004 From: mgollery at unr.edu (Martin Gollery) Date: Wed, 18 Aug 2004 08:42:07 -0700 Subject: [BiO BB] Bioinformatics (potential) needs assessment form? In-Reply-To: References: Message-ID: <1092843727.412378cf43351@webmail.unr.edu> I have a form that I have used with some success. I will send it to you, Dan, when I get back to work- I am at a conference at Stanford right now. Marty Quoting Dan Bolser : > > Thanks very much for this information. I agree that interviews are the > best way to serve an actual group of users (instead of a generic > hypothetical group). However, I was looking for a generic form that I > could taylor given my specific knowlage (based on beging around these guys > for the last 2 years). > > A generic form could have several 'modules' to cover different lines of > experimantal research, and could be used as a template to get things off > the ground quickly. > > For example, one section (or 'module') could specifically address the need > for further discussion and interviews. That way you could target your > interviews to those people who are most likely to benifit from > them. Perhaps... > > I definatly agree with what you have put below, but I am lazy (this isn't > really my job anyway), and I would find a form or questionnaire much more > appealing (in the short term). > > I know this isn't a good advert for good practice, but I do think that a > well structured form could go a long way to quickly gathering good (but > not the best) information in a fraction of the time and with a > fraction of the effort. > > What do you think? > > Thanks again, > Dan. > > On Wed, 18 Aug 2004, Joe Landman wrote: > > >Hi Dan: > > > > A real needs assessment tends to be an interview. You might be able > >to do a set of interviews to get a better understanding of what > >questions to put into your poll. > > > > The needs assessments vary depending upon the target group and their > >problems. A single poll might not capture the necessary details. > > > > Needs assessments are critical to my companies business, as we need to > >understand our customers computational problems. I would think that a > >similar approach might work here, though it is usually hard to condense > >everything into a single document before the interview. You might try > >several sample interviews, see where they take you, and then refine it. > >Iterate until you are satisfied. > > > >Joe > > > >Dan Bolser wrote: > > > >>Hi, > >> > >>Has anyone ever done a survey of bioinformatics needs for an > >>experimentalist (molecular biology) community? > >> > >>I need to survey the (potential) bioinformatics needs of a group of > >>experimentalists with a wide range of bioinformatics knowledge (from > 'some > >>in-depth specialist' through 'general' to 'none'). > >> > >>Ideally I would like to capture both what is currently being used, and > >>what would be really useful if it were being used. > >> > >>The problem is in the last case people may not know what could > potentially > >>be helpful. i.e. they need training and/or the form needs to be > >>educational (gulp). > >> > >>I would be very grateful if someone could point me at a stock form, and I > >>would be more than willing to help try to create such a stock form from > >>the condensed knowledge of this community. > >> > >>Thanks very much for any assistance, > >> > >>Dan. > >> > >> > >> > >> > >> > >>_______________________________________________ > >>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 > Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From letondal at pasteur.fr Wed Aug 18 12:21:42 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Wed, 18 Aug 2004 18:21:42 +0200 Subject: [BiO BB] Re: [Bioclusters] Bioinformatics (potential) needs assessment form? In-Reply-To: Your message of "Wed, 18 Aug 2004 12:29:23 BST." Message-ID: <200408181621.i7IGLgU5504033@electre.pasteur.fr> Dan Bolser wrote: > > Hi, > > Has anyone ever done a survey of bioinformatics needs for an > experimentalist (molecular biology) community? > > I need to survey the (potential) bioinformatics needs of a group of > experimentalists with a wide range of bioinformatics knowledge (from 'some > in-depth specialist' through 'general' to 'none'). > > Ideally I would like to capture both what is currently being used, and > what would be really useful if it were being used. > > The problem is in the last case people may not know what could potentially > be helpful. i.e. they need training and/or the form needs to be > educational (gulp). > > I would be very grateful if someone could point me at a stock form, and I > would be more than willing to help try to create such a stock form from > the condensed knowledge of this community. > > Thanks very much for any assistance, > > Dan. > Hi, I'm not sure I understand what "stock form" means :-) but since we actually run a lot of users studies (survey, interviews, workshops, ...) in our lab, I can tell a little bit about it. We have in fact made a survey about the use of informatics in our institute (600 answers), but to be honest, it is a lot of work and it is the worst way of getting information from users I have ever experienced. The problem is that "bioinformatics needs", even for a restricted domain of biology, are (at least in my experience), a quite rich issue. Every single biologist works differently and has different needs. In fact, the risk, by doing a survey, is that the information that will be gathered by this mean is something that you already know, not more. So, how to get more useful information with less work? Interviews are a great way of getting data. An useful idea for efficient interviews is to ask the user about an actual situation (critical incident technique for instance). Avoid generalities. Although apparently too specific, it's a good way to really understand what people need since they sometimes don't know how to describe it. And you can generalize after. Running 20 interviews provides a rich set of data, but running only 3 to 5 is very useful as well. I also do interviews with biologists I have known for a long time: during the interview, we always focus on a specific topic/situation. Another wonderful communication tool is participatory design: you can do workshops where users brainstorm on some topic, or workshop to prototype some parts of the design. It's an invaluable tool to understand priorities of users regarding their bioinfomatics needs (something that you completely miss in a survey). (see http://www-ihm.lri.fr/~mackay/pdffiles/MasterClass2000.pdf for a tutorial) At first sight, this approach seems to focus on design more than one requirements specification, but it is in fact also a tool for it, because it lets users express their needs informally. If you really want to do a survey, it's easier to design your questionnaire after a few interviews, and after testing the questionnaire with 3-5 users. Some links: - A. Dalke presentation at BOSC (about usability) also tells about participatory methods (http://www.dalkescientific.com/bosc2002/usability/) - Papers and people from this workshop in Edinburgh could be of interest (R. Stevens from myGrid was there): Requirements Capture for Collaboration in eScience http://www.nesc.ac.uk/esi/events/320/ (I can send you our position paper describing user studies for a Web server in bioinformatics). - A very good paper illustrating user studies with molecular biologists: O'Day, V., A. Adler et al. (2001): When worlds collide: Molecular biology as interdisciplinary collaboration. In Proceedings of ECSCW'01. pp. 419-418. Hope this helps... -- Catherine Letondal http://www.pasteur.fr/~letondal From information at virtualgenomics.org Wed Aug 18 18:39:52 2004 From: information at virtualgenomics.org (information at virtualgenomics.org) Date: Wed, 18 Aug 2004 15:39:52 -0700 Subject: [BiO BB] Fourth Virtual Conference on Genomics and Bioinformatics Message-ID: <20040818223952.13442.qmail@webmail02.mesa1.secureserver.net> *********************************************************************** Fourth Virtual Conference on Genomics and Bioinformatics September 21-24, 2004 www.VirtualGenomics.Org *********************************************************************** Location: Virtual Locations Worldwide (List available at www.VirtualGenomics.Org) Registration fees: None The Virtual Conference on Genomics and Bioinformatics is an advanced collaborative environment featuring high profile researchers involved in the development and use of cutting edge technologies and approaches which allow a better understanding of the molecular structure and dynamics of biological systems. The objectives of the conference are: * Transcend geographical and economical barriers for the exchange of ideas that facilitates the interaction and collaboration among scientists and educators around the world. * Address the benefits and limitations of the newest developments in post-genomic technologies. * Explore the social and ethical implications of genomic and bioinformatic research. * Establish new ways to introduce the high school community to today's multidisciplinary science. Speakers: Uri Alon, Weizmann Institute of Science. Israel Wanda Andreoni, IBM Z?rich Research Laboratory, Switzerland Kim Baldridge, Universit?t Z?rich. Switzerland Patsy Babbitt. University of California, San Francisco. USA Irene Bosch, University of Massachusetts Medical School. USA Carlos Camacho, University of Pittsburgh, USA Colin C. Collins, Medicine and Cancer Research Institute, UCSF. USA Charles DeLisi, Boston University. USA Martin Gollery, University of Nevada at Reno. USA Fern Hunt, National Institute of Standards and Technology. USA S.S. Iyengar, Louisiana State University. USA Maricel Kann, National Institutes of Health. NCBI. USA Eugene Koonin, National Institutes of Health. USA Luis Rocha, Los Alamos National Laboratory. USA John B. Shabb, University of North Dakota. USA Wibke Sudholt, Universit?t Z?rich. Switzerland Christoph W. Sensen, University of Calgary. Canada Richard Simon, National Institutes of Health. NCI. USA Jason Suen, California Institute of Technology, USA Sarah B. Tegen, National Academy of Sciences, USA William Perrizo, North Dakota State University. USA Willy Valdivia-Granda. Orion Integrated Biosciences. USA Yuzhen Ye, The Burnham Institute. USA Roie Yerushalmi, Weizmann Institute of Science. Israel For more information visit www.VirtualGenomics.Org From merin at macfast.org Thu Aug 19 09:54:04 2004 From: merin at macfast.org (merin) Date: 19 Aug 2004 13:54:04 -0000 Subject: [BiO BB] Great idea Message-ID: <20040819135404.11634.qmail@macfast.org> Hi, It would be very interesting to work out this idea. I've worked as a survey officer,and I too feel interviewing is the best option.It'll be more useful & extensive.I don't think anyone has tried out a very extensive survey. Best of luck for your efforts. Merin From tibs at stat.Stanford.EDU Wed Aug 25 13:10:32 2004 From: tibs at stat.Stanford.EDU (Robert J. Tibshirani) Date: Wed, 25 Aug 2004 10:10:32 -0700 Subject: [BiO BB] data mining short course Message-ID: <200408251710.i7PHAWH9002272@miller.Stanford.EDU> Short course: Statistical Learning and Data Mining Trevor Hastie and Robert Tibshirani, Stanford University Georgetown University Conference Center Washington DC September 20-21, 2004 This two-day course gives a detailed overview of statistical models for data mining, inference and prediction. With the rapid developments in internet technology, genomics and other high-tech industries, we rely increasingly more on data analysis and statistical models to exploit the vast amounts of data at our fingertips. This sequel to our popular "Modern Regression and Classification" course covers many new areas of unsupervised learning and data mining, and gives an in-depth treatment of some of the hottest tools in supervised learning. The first course is not a prerequisite for this new course. Most of the techniques discussed in the course are implemented by the authors and others in the S language (S-plus or R), and all of the examples were developed in S. Day one focuses on state-of-art methods for supervised learning, including PRIM, boosting, support vector machines, and very recent work on least angle regression and the lasso. Day two covers unsupervised learning, including clustering, principal components, principal curves and self-organizing maps. Many applications will be discussed, including the analysis of DNA expression arrays - one of the hottest new areas in biology! ################################################### Much of the material is based on the book: Elements of Statistical Learning: data mining, inference and prediction Hastie, Tibshirani & Friedman, Springer-Verlag, 2001 http://www-stat.stanford.edu/ElemStatLearn/ A copy of this book will be given to all attendees. ################################################### For more information, and to register, visit the course homepage: http://www-stat.stanford.edu/~hastie/mrc.html From dmb at mrc-dunn.cam.ac.uk Wed Aug 25 14:57:19 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 25 Aug 2004 19:57:19 +0100 (BST) Subject: [BiO BB] Cool! In-Reply-To: <3F1C6D78.60805@bioinformatics.org> Message-ID: Thanks for the news item! :) That made me feel much happier! I hope people join... Thanks, Dan. From dmb at mrc-dunn.cam.ac.uk Wed Aug 25 15:49:07 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 25 Aug 2004 20:49:07 +0100 (BST) Subject: [BiO BB] Re: Cool! - oops... In-Reply-To: Message-ID: Never mind. ;) Dan. On Wed, 25 Aug 2004, Dan Bolser wrote: > >Thanks for the news item! > >:) > >That made me feel much happier! > >I hope people join... > >Thanks, >Dan. > > From seasea at hotmail.com Wed Aug 25 23:43:19 2004 From: seasea at hotmail.com (Hai Zhang) Date: Thu, 26 Aug 2004 11:43:19 +0800 Subject: [BiO BB] data mining short course References: <200408251710.i7PHAWH9002272@miller.Stanford.EDU> Message-ID: Dear Dr. Tibshirani, I really love to attend this course. Because I am not sure about the status of my visa to United States. Would you have other suggestions for the application? Thanks a lot. With best regards, Hai ----- Original Message ----- From: "Robert J. Tibshirani" To: Sent: Thursday, August 26, 2004 1:10 AM Subject: [BiO BB] data mining short course > > Short course: Statistical Learning and Data Mining > > Trevor Hastie and Robert Tibshirani, Stanford University > > Georgetown University Conference Center > Washington DC > September 20-21, 2004 > > This two-day course gives a detailed overview of statistical models > for data mining, inference and prediction. With the rapid > developments in internet technology, genomics and other high-tech > industries, we rely increasingly more on data analysis and statistical > models to exploit the vast amounts of data at our fingertips. > > This sequel to our popular "Modern Regression and Classification" > course covers many new areas of unsupervised learning and data mining, > and gives an in-depth treatment of some of the hottest tools in > supervised learning. > > The first course is not a prerequisite for this new course. > Most of the techniques discussed in the course are implemented by the > authors and others in the S language (S-plus or R), and all of the > examples were developed in S. > > Day one focuses on state-of-art methods for supervised > learning, including PRIM, boosting, support vector machines, > and very recent work on least angle regression and the lasso. > > Day two covers unsupervised learning, including clustering, principal > components, principal curves and self-organizing maps. Many > applications will be discussed, including the analysis of DNA > expression arrays - one of the hottest new areas in biology! > > ################################################### > Much of the material is based on the book: > > Elements of Statistical Learning: data mining, inference and prediction > > Hastie, Tibshirani & Friedman, Springer-Verlag, 2001 > > http://www-stat.stanford.edu/ElemStatLearn/ > > A copy of this book will be given to all attendees. > > ################################################### > > For more information, and to register, visit the course homepage: > > http://www-stat.stanford.edu/~hastie/mrc.html > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From lxyiwc at yahoo.com Thu Aug 26 18:46:12 2004 From: lxyiwc at yahoo.com (l x yi) Date: Thu, 26 Aug 2004 15:46:12 -0700 (PDT) Subject: [BiO BB] MLE Message-ID: <20040826224612.32115.qmail@web52010.mail.yahoo.com> I was reading the paper "Maximum Likelihood Estimation of the Statistical distribution of Smith-Waterman Local Sequence Similarity Scores", published in Bulletin of Mathematical Biology Vol54, No1, p59-75 by R. Mott, and the paper "Sequence Comparison Significance and Poisson Approximation" published in Statistical Science vol9, 1994, 367-381,by M.S. Waterman et al. These articles discuss the ML method for estimating parameters for distributions obtained by searching a random sequence with a databank.It can be assumed that the sequences in the databank are independent sequences, but if we are using the same sequence as query each time,wouldn't the scores obtained be dependent? then the likelihood needs to be modified to account for this dependency? both of these papers used the likelihood assuming all the scores obtained are independent. Am I missing something here? Could someone please help me understand? Thanks very much. Lily __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - Send 10MB messages! http://promotions.yahoo.com/new_mail From information at virtualgenomics.org Sat Aug 28 10:33:17 2004 From: information at virtualgenomics.org (information at virtualgenomics.org) Date: Sat, 28 Aug 2004 07:33:17 -0700 Subject: [BiO BB] Fourth Virtual Genomics and Bioinformatics Conference Message-ID: <20040828143317.26750.qmail@webmail-2-5.mesa1.secureserver.net> An HTML attachment was scrubbed... URL: From idoerg at yahoo.com Wed Aug 11 03:53:17 2004 From: idoerg at yahoo.com (Iddo Friedberg) Date: Wed, 11 Aug 2004 00:53:17 -0700 (PDT) Subject: [BiO BB] Structural genomics and PDB growth? In-Reply-To: Message-ID: <20040811075317.91221.qmail@web41605.mail.yahoo.com> --- Dan Bolser wrote: > On Mon, 9 Aug 2004, Iddo Friedberg wrote: > > >Hi Dan, > > > >For your first question: > > > >We published something in PSB'04 > > > >http://helix-web.stanford.edu/psb04/bourne.pdf > > Cheers. > > > > >I don't know about definitive, but it is fairly exhaustive, based > on > >data which was up-to-date for summer 2003. > > > >PDB will keep growing as long as crystallographers/NMR people have > >jobs and have families to feed. Future growth rate, as always, is > >estimated by extrapolation. However, come the technological > >breakthrough whcih will enable faster solutions for membrane > >proteins, the growth rate will probably increase :) > > That is the thing, but is the rate of increase increasing? I'm not sure by what you mean by "an increasing rate of increase". PDB growth is exponential. ./I > > >Cheers, > > > >Iddo > > > > > > > >--- Dan Bolser wrote: > > > >> > >> Can anyone point me at definative literature for estimates of > PDB > >> growth > >> and the impact of structural genomics? > >> > >> What evidence do we have that the PDB will keep growing? What is > >> the best > >> current estimate of that growth rate? > >> > >> Cheers, > >> Dan. > >> > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - > >> BiO_Bulletin_Board at bioinformatics.org > >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >> > > > > > >===== > >-- > >Iddo Friedberg > >The Burnham Institute > >10901 N. Torrey Pines Rd. > >La Jolla, CA, 92037 > >USA > >T: (858) 646 3100 x3516 > >http://ffas.ljcrf.edu/~iddo > > > > > > > >__________________________________ > ===== -- Iddo Friedberg The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA, 92037 USA T: (858) 646 3100 x3516 http://ffas.ljcrf.edu/~iddo __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail