From dmb at mrc-dunn.cam.ac.uk Thu Apr 1 03:57:55 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 1 Apr 2004 09:57:55 +0100 (BST) Subject: [BiO BB] Distributed System and Bioinformatic In-Reply-To: Message-ID: On Wed, 31 Mar 2004, Boris Steipe wrote: > Google for "mygrid". And "biogrid" ;) > > > best, > > > Boris > > On Wednesday, Mar 31, 2004, at 12:50 Canada/Eastern, Ulisses wrote: > > > I'm graduating in computer science and I'm writing a paper about > > distributed > > system, but I would like to join with some concepts of bioinformatic. > > So, > > I'd like to receive some links about any works in this area. > > > > Grato pela aten??o. > > Ulisses Dias > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From pooja at igc.gulbenkian.pt Thu Apr 1 04:44:25 2004 From: pooja at igc.gulbenkian.pt (Pooja Jain) Date: Thu, 1 Apr 2004 10:44:25 +0100 (WEST) Subject: [BiO BB] DNA Strider In-Reply-To: <8D9C0586-825B-11D8-AF58-000393CAA04A@poulet.org> References: <8D9C0586-825B-11D8-AF58-000393CAA04A@poulet.org> Message-ID: <46924.194.117.22.137.1080812665.squirrel@webmail.igc.gulbenkian.pt> Hi Yannick, Have you ever had a look at SimVector. Its a standalone tool and works very well on windows and Mac OS X. http://www.premierbiosoft.com/plasmid_maps/index.html Its one of the most powerful vector map drawing tool, with great graphic support. It is quite fast in opening any sequence from GenBank and to present the sequence features in graphic format. Moreover you can export the plasmid/sequence map to EPS, SVG and gif, jpeg and various other formats. You can also use the customizable graphic designing options that it provides. Apart from all these it has various other features but are limited to cloning, vector designing and generating restriction maps, you might want to explore. For me it was most useful in constructing the restriction maps of my cloning vector and resultant recombinant, before I actually performed the experiment in my lab and to put the plasmid maps in my presentation. Its not that expensive also ! I hope this helps. -Pooja > Hi, > I'm a student in Bioinformatics and Modeling at a French engineering > school in Lyon, France (http://biosciences.insa-lyon.fr). Currently in > my last year, I'm currently doing a six month internship in a C. > elegans lab at McGill University in Montreal. > The lab's computer are Macs, and besides standard browsing, word > processing and image processing, lab members also use them to aid them > in their molecular biology work. > One of the programs they use is called DNA Strider. This piece of > software has not been updated in a long time (probably since Apple's > System 6.x - window sizes are fixed to the small old mac screen size!) > and could require a face-lift. > > In the lab, it is mainly used for managing and manipulating sequences > of genes, primers and constructs. The main features of interest here > are: > - Sequence management > - Graphical (circular or linear) restriction maps of a given > sequence (or part of it), showing restriction site data concerning the > part or whole sequence (for each enzyme, you get the number of > restriction sites, and the obtained fragement sizes) > - Reverse complementary sequence > - Quick and simple alignment between two sequences > > I've searched the web and could not find an all-in-one package that > seemed as user friendly and coherent as DNA Strider. Individual web > sites and software tools do offer these features, but > - the internet is slow (you click and need to wait before getting your > result) > - having everything in one place is nice > > Sequence Analysis (for Mac OS X) http://informagen.com/SA/ seems to be > aiming to do what DNA Strider does, but is still very young (and > closed-source, but thats a different debate). > > http://www.mekentosj.com/ has some very nice tools as well, but they're > very problem-specific. > > Have I missed something? Is there a really cool java app or web > software (that I could install locally for speed) that would replace > DNA Strider? What does your molecular biology lab use in for it's day > to day work? > Oh and buying something expensive is not a solution. > > Thanks for any leads, > > Yannick. > > \\\\\\\\\\\\\\\\\\\ > \\ http://yannick.poulet.org icq: 22044361 > \\ idh at poulet.org tel: ++33.6.16.41.71.92 > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From pmr at ebi.ac.uk Thu Apr 1 05:46:55 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 01 Apr 2004 11:46:55 +0100 Subject: [BiO BB] DNA Strider and EMBOSS In-Reply-To: <0034D92B-82AD-11D8-AF58-000393CAA04A@poulet.org> References: <0034D92B-82AD-11D8-AF58-000393CAA04A@poulet.org> Message-ID: <406BF31F.6050000@ebi.ac.uk> Yannick Wurm wrote: > I have checked out both sms2 and emboss, and both seem very powerfull. > From what I gather though, both only seem to output text! EMBOSS text output can be formatted - especially by the time EMBOSS 3.0.0 appears. Are there any formats that would be useful for visualisation of (for example) restriction sites or other sequence features? In particular, any preferred XML formats? regards, Peter Rice From dmb at mrc-dunn.cam.ac.uk Thu Apr 1 11:10:15 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 1 Apr 2004 17:10:15 +0100 (BST) Subject: [BiO BB] SCOL Message-ID: SCOL: The Structural Classification of Ligands No work and all play... http://bioinformatics.org/scol/links.html From steletch at biomedicale.univ-paris5.fr Thu Apr 1 12:14:34 2004 From: steletch at biomedicale.univ-paris5.fr (=?ISO-8859-1?Q?Teletch=E9a_St=E9phane?=) Date: Thu, 01 Apr 2004 19:14:34 +0200 Subject: [BiO BB] SCOL In-Reply-To: References: Message-ID: <1080839638.3672.24.camel@localhost.localdomain> Le jeu 01/04/2004 ? 18:10, Dan Bolser a ?crit : > SCOL: The Structural Classification of Ligands > > No work and all play... > > http://bioinformatics.org/scol/links.html > > VMD is missing, it is quite powerful and used ... http://www.ks.uiuc.edu/Research/vmd/ Stef -- http://www.steletch.org Fingerprint: 1E83 26EE A2F1 87E5 5865 4DBF F2B4 9083 F44C AE88 GPG key @ http://www.steletch.org/article.php3?id_article=13 GNU/Linux Mandrake 9.2 (http://www.linux-mandrake.com) 19:12:29 up 2:44, 1 user, load average: 0.27, 0.11, 0.04 From dmb at mrc-dunn.cam.ac.uk Thu Apr 1 17:11:37 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 1 Apr 2004 23:11:37 +0100 (BST) Subject: [BiO BB] SCOL In-Reply-To: Message-ID: Sorry the link should be... http://bioinformatics.org/scol/ And I think I ment all play and no work... On Thu, 1 Apr 2004, Dan Bolser wrote: > > SCOL: The Structural Classification of Ligands > > No work and all play... > > http://bioinformatics.org/scol/links.html > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From moyc at mail.med.upenn.edu Fri Apr 2 11:58:49 2004 From: moyc at mail.med.upenn.edu (Chris Moy) Date: Fri, 2 Apr 2004 11:58:49 -0500 Subject: [BiO BB] Forums for Molecular Biologist In-Reply-To: <20040331170141.C52F9D1F30@www.bioinformatics.org> References: <20040331170141.C52F9D1F30@www.bioinformatics.org> Message-ID: <031528FA-84C7-11D8-86E6-000A9599E70C@mail.med.upenn.edu> Hello, Does anyone know of similar forums/newsgroups like this one that is more catered to molecular biologist and techniques used in the lab? CM From gary at www.bioinformatics.org Fri Apr 2 14:48:39 2004 From: gary at www.bioinformatics.org (Gary Van Domselaar) Date: Fri, 2 Apr 2004 14:48:39 -0500 (EST) Subject: [BiO BB] Forums for Molecular Biologist In-Reply-To: <031528FA-84C7-11D8-86E6-000A9599E70C@mail.med.upenn.edu> Message-ID: HI Chris, Try the abrf: http://abrf.org/ Regards, g. On Fri, 2 Apr 2004, Chris Moy wrote: > Hello, > > Does anyone know of similar forums/newsgroups like this one that is > more catered to molecular biologist and techniques used in the lab? > > CM > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From shenhav at wicc.weizmann.ac.il Fri Apr 2 13:24:42 2004 From: shenhav at wicc.weizmann.ac.il (Barak Shenhav) Date: Fri, 2 Apr 2004 20:24:42 +0200 Subject: [BiO BB] Distributed System and Bioinformatic Message-ID: <406C58A5@wiccweb> I would be happy to get a copy of the paper >===== Original Message From bio_bulletin_board at bioinformatics.org ===== >I'm graduating in computer science and I'm writing a paper about distributed >system, but I would like to join with some concepts of bioinformatic. So, >I'd like to receive some links about any works in this area. > >Grato pela aten??o. > Ulisses Dias ==================================== Barak Shenhav Department of Molecular Genetics Weizmann Institute of Science +972 8 9343098 (office) +972 8 9344487 (fax) +972 5 2955550 (cellular) From paolo at ist.unige.it Mon Apr 5 09:57:08 2004 From: paolo at ist.unige.it (Paolo Romano) Date: Mon, 5 Apr 2004 15:57:08 +0200 Subject: [BiO BB] Call for Papers - NETTAB 2004 Message-ID: <200404051357.PAA05584@ist.unige.it> Dear BioBB members, I'm glad to announce the launch of the Call for Papers for the NETTAB 2004 Workshop on "MODELS AND METAPHORS FROM BIOLOGY TO BIOINFORMATICS TOOLS". Hope to see many of you in Camerino on next September. Bye. Paolo Romano --- NETTAB 2004 Call for Papers NETWORK TOOLS AND APPLICATIONS IN BIOLOGY Fourth International NETTAB Workshop on MODELS AND METAPHORS FROM BIOLOGY TO BIOINFORMATICS TOOLS http://www.nettab.org/2004/ Universita' di Camerino, September 5-7, 2004, Camerino, Italy IMPORTANT DATES ---------------------- Paper submission (full paper): June 15, 2004. Notifications of acceptance to authors: July 15, 2004. Final version of accepted papers: August 1, 2004 Poster submission: June 31, 2004 Workshop: September 5-7, 2004 MOTIVATION AND SCOPE ---------------------- The post-genomic era can be seen as characterized by two different scenarios: on the one hand, the huge amount of available biological data sets all over the world requires suitable tools and methods both for modelling biological processes and analyzing biological sequences; on the other, many new computational models and paradigms inspired and developed as metaphors of biological systems are ready to be applied in the context of computer science. It may now be a good time to: (i) report on the results achieved in these two areas, (ii) present some open problems in computational biology, (iii) advertise novel computational tools successfully applied to biological issues, (iv) spread the knowledge on computational models inspired by biological processes, and (v) foster the application of computational models to govern real biological systems. The workshop intends to bring together bioscientists and computer scientists and to compare their approaches and their ideas for solving computational biology open problems. In particular, we expect the participation of those who are developing novel bioinformatics tools and those who are working towards the vision of biological systems as a model for designing new tools. The workshop will also aim to inspire future collaboration between the different communities, to strengthen the relationships within the bioinformatics community, to activate a cooperation between bioscientists and computer scientists, to collect the latest ideas, achievements and proposals in computational models and metaphors from biology. TOPICS OF INTEREST ---------------------- Topics to be covered will include, but not limited to, the following list: >From Biologists - Open problems in: - Molecular evolution and theoretical biology - Gene regulation and expression - Functional genomics - Comparative genomics - Protein structure and interaction - Gene and enzyme networks - Metabolic pathways and responses - Genetic and ecological systems - Pharmacogenomics and Toxicogenomics >From Bioinformaticians - Novel techniques and computational tools in: - Bio-information processing systems - Data Integration - Ontologies and knowledge management - Protein interaction pathways and responses - Protein structure and modelling - Gene networks - Genomics and comparative genomics - Functional genomics - Microarrays and gene expression patterns - Sequence analysis - Motif finding >From Computer Scientists - Promising models and metaphors in: - Bioware languages and models - Data management methods and systems - Biologically inspired systems - Evolutionary algorithms - Machine learning - Genetic computation - DNA computing - Computation in neural systems - Neural hardware - Autonomous and evolutionary robotic - Cellular automata - Self-organizing, self-repairing and self- replicating systems - Data mining in bioscience literature - Concurrent languages for biology - New technologies and methods SUBMISSION ---------------------- NETTAB04 welcomes original contributions, containing new and unpublished results, on both theoretical and practical issues of computational paradigms and novel tools inspired or applied particularly to biological systems. Submitted papers should normally have at most 12 pages using the Springer LNCS style. Templates (llncs.cls, llncs.sty, or sv-lncs.dot) are available under the "Downloads" heading at: http://www.springeronline.com/sgw/cda/frontpage/0,10735,5-164-2-72376-0,00.html Posters sessions will be organized as opportunity to exhibit late-breaking results and to discuss these results with conference participants in an informal setting. Abstracts for posters should consist of a 1-2 page summary of the work to be presented. PROCEEDINGS AND POST-PROCEEDINGS ---------------------- All accepted papers will be published in the conference proceedings. Furthermore, the best papers will be published in a special issue of Springer-Verlag "Transaction on Computational Systems Biology" http://www.springeronline.com/sgw/cda/frontpage/0,10735,5-164-2-109319-0,00.html WORKSHOP CHAIRS ---------------------- Emanuela Merelli, DMI, Universita' di Camerino, Italy (Emanuela.merelli at unicam.it) Pablo Gonzalez, DEIS, Universita' di Bologna a Cesena, Italy (pgonzalez at ingce.unibo.it) Andrea Omicini, DEIS Universita' di Bologna a Cesena, Italy (andrea.omicini at unibo.it) ADVISORY BOARD ---------------------- Paolo Romano, National Cancer Research Institute, Genova, Italy Luca Toldo, Merck KGaA, Germany Emanuela Merelli, Universita' di Camerino, Italy Luciano Milanesi, CNR Milano, Italy Angelo Facchiano, CNR Avellino, Italy Peter McBurney, University of Liverpool, UK PROGRAMME COMMITTEE ---------------------- Russ Altman, Stanford University Medical Center, USA Jeffrey Bradshaw, Human and Machine Cognition in Pensacola, USA Luca Cardelli, Microsoft Research, Cambridge,UK Pierpaolo Degano, Universita' di Pisa, Italy Marco Dorigo, Universita' Libre de Bruxelles, Belgium David Gilbert, City University, UK Carole Goble, University of Manchester, UK Pablo Gonzalez, DEIS, Universita' di Bologna a Cesena, Italy Anna Ingolfsdottir, University of Aalborg, Denmark Michael Luck, University of Southsampton, UK Peter McBurney, University of Liverpool, UK Emanuela Merelli, Universita' di Camerino, Italy Andrea Omicini, DEIS Universita' di Bologna a Cesena, Italy Corrado Priami, Universita' di Trento, Italy Aviv Regev, Harvard University, USA Giorgio Valle, Universita' di Padova, Italy Franco Zambonelli, Universita' di Modena e Reggio Emilia, Italy LOCAL ORGANIZERS ---------------------- Mauro Angeletti, Roberto Ciccocioppo, Emanuela Merelli, Cristina Miceli, Universita' di Camerino IMPORTANT DATES ---------------------- Paper submission (full paper): June 15, 2004. Notifications of acceptance to authors: July 15, 2004. Final version of accepted papers: August 1, 2004 Poster submission: June 31, 2004 Workshop: September 5-7, 2004 ABOUT CAMERINO ---------------------- Although not very famous, Camerino is indeed one of the most beautiful little towns of Central Italy, being its medieval historical center one of the oldest in Region Marche. Camerino hosts one of the most ancient university in Italy. Placed on a spur on the Appennini Mountains at 670 meters high on the sea-level, Camerino achieves its period of greatest splendour under the rule of the Da Varano family. From the top of its rock it dominates the large valleys of the rivers Chienti and Potenza underneath, occupied by towers and fortresses. But if the town might look austere, the countryside, instead, is colourful and offers a lot of farms holidays where to spend a weekend ---- Paolo Romano (paolo.romano at istge.it) National Cancer Research Institute Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From mourad12345678 at yahoo.com Thu Apr 1 17:48:19 2004 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Thu, 1 Apr 2004 14:48:19 -0800 (PST) Subject: [BiO BB] CfP : ALBIO'04/Extended Deadline Message-ID: <20040401224819.63301.qmail@web12307.mail.yahoo.com> CALL FOR PAPERS ALBIO'04 Algorithms in Molecular Biology Session of 6th Int. Conf. on Algorithms, Scientific Computing, Modelling and Simulation (ASCOMS'04) Cancun, Mexico, Mexique May 12-15, 2004 http://www.worldses.org/conferences/2004/mexico/ascoms/index.html Computational Molecular Biology, has emerged from the Human Genome Project as an important discipline for academic research and industrial application. The growing size of biological databases, the complexity of biological problems and the necessity to deal with errors in biological sequences all result in large run time and memory requirements. Biological sequence databases are growing at an exponential rate. All of these factors will make the development of fast, low memory requirements and high-performances algorithms increasingly important in Computational Molecular Biology. In our session, we are interested in papers that deal with all aspects of algorithms in Molecular Biology. We are, particularly, interested in algorithms that address fundamental and/or applied problems in Molecular Biology, that are computationally efficient, that have been implemented and experimented on simulated and/or on real biological sequences and that provide interesting new results. The submitted papers should present recent research results and identify and explore directions for future research. Topics include, but not limited to: (i) strings processing, (ii) biological sequences comparison, (iii) structures prediction, (iv) phylogeny reconstruction, (v) DNA sequences assembly, clustering, and mapping, (vi) molecular evolution, (vii) genes prediction/recognition, (viii) genes expression INSTRUCTIONS TO AUTHORS You are invited to submit a hardcopy or a pdf version of a draft paper, about 4 to 5 pages including figures and references, before April 15, 2004 to the Session Chair : Dr. Mourad Elloumi : Mailing Address : Cit? Intilak bloc 6, app. 7, El Menzah 6, 2091 Tunis, Tunisia. Mobile: +216 98 468 859 Phone : +216 71 233 253 E.Mail: Mourad.Elloumi at fsegt.rnu.tn IMPORTANT DATES Papers due: April 15, 2004 Author notification: April 22, 2004 Conference date: May 12, 2004 __________________________________ Do you Yahoo!? Yahoo! Small Business $15K Web Design Giveaway http://promotions.yahoo.com/design_giveaway/ From ruth.gull at continuing-education.oxford.ac.uk Fri Apr 2 04:45:02 2004 From: ruth.gull at continuing-education.oxford.ac.uk (Gull, Ruth) Date: Fri, 2 Apr 2004 10:45:02 +0100 Subject: [BiO BB] Virtual Open day for Oxford University Bioinformatics Message-ID: <250459F5945E84439644F58754F565A401535AAC@wildrice.conted.ox.ac.uk> To whom it may concern, I am the course Administrator for the part-time MSc in Bioinformatics offered jointly between the departments of Statistics and Continuing Education here at Oxford. We are very excited to be holding the first virtual open day that Oxford University has seen. We would like to give as many people as possible the chance to experience our course and therefore I wonder if you could include an item on you bulletin board about this. To attend the open day all you need to do it visit our website at www.conted.ox.ac.uk/bioinformatics and follow the open day link. If this is not the correct place to advertise this opportunity but you have another area of your site that you think would be more appropriate please let me know where to submit the information to. Many thanks, Ruth Miss Ruth Gull Bioscience Portfolio Administrator MSc in Bioinformatics Peter Medawar Building South Parks Road Oxford OX1 3SY Tel: 0044 (0) 1865 286946 Fax: 0044 (0) 1865 286934 Email: ruth.gull at conted.ox.ac.uk We would like to invite you to the MSc in Bioinformatics - VIRTUAL OPEN DAY 16th April www.conted.ox.ac.uk/bioinformatics -------------- next part -------------- An HTML attachment was scrubbed... URL: From anand.kumar at ifomis.uni-leipzig.de Mon Apr 5 15:26:41 2004 From: anand.kumar at ifomis.uni-leipzig.de (Anand Kumar) Date: Mon, 5 Apr 2004 21:26:41 +0200 (CEST) Subject: [BiO BB] Distributed System and Bioinformatic References: <406C58A5@wiccweb> Message-ID: <171631.1081193201841.SLOX.WebMail.wwwrun@hogwarts.imise.uni-leipzig.de> Me too. Anand. Am Fr 02.04.2004 20:24, Barak Shenhav schrieb: > I would be happy to get a copy of the paper > >===== Original Message From bio_bulletin_board at bioinformatics.org ===== > >I'm graduating in computer science and I'm writing a paper about distributed > >system, but I would like to join with some concepts of bioinformatic. So, > >I'd like to receive some links about any works in this area. > > > >Grato pela aten??o. > > Ulisses Dias > > ==================================== > Barak Shenhav > Department of Molecular Genetics > Weizmann Institute of Science > +972 8 9343098 (office) > +972 8 9344487 (fax) > +972 5 2955550 (cellular) > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Anand Kumar MBBS, PhD IFOMIS Faculty of Medicine University of Leipzig H?rtelstra?e 16-18 04107 Leipzig Germany http://www.uni-leipzig.de/~akumar/ From Joel.Dudley at asu.edu Mon Apr 5 16:56:19 2004 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Mon, 05 Apr 2004 13:56:19 -0700 Subject: [BiO BB] DNA Strider Message-ID: <9EAE2E44897BC749ACB3A62683B2C8D123F0FC@ex4.asurite.ad.asu.edu> Several such systems are already under development and released in the private sector. I know of a soon to be open-source project that has all of these features and is already quite mature. You should hear about it in a month or so. - Joel -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org on behalf of Marcos Oliveira de Carvalho Sent: Tue 3/30/2004 5:21 PM To: bio_bulletin_board at bioinformatics.org Cc: Subject: Re: [BiO BB] DNA Strider It would be nice to have a bioinformatics IDRE ( Integrated Development and Research Environment) with some basic features (sequence visualization, editing, annotation, data management, etc...) and a well designed plug-in API, for easy extension. An idea could be build it on top of the NetBeans platform , and with java we get platform-independent software. (with other languages too, but java do the job) One can suggest add bindings with python/perl/ruby/java and theirs Bio* libraries, interfaces to bioinformatics tools, including output capture (emboss, phred, phrap, BLAST, FASTA, Clustal,R/bioconductor, Mummer,...) . Also interfaces to webservices and data retrieving from major databases. Well, there are lots of possibilities. cheers Marcos On Tue, 30 Mar 2004 18:30:36 -0500, Ryan Golhar wrote: > You know, I'm constantly finding different programs to perform different > tasks. Either client applications, or web-based. Some run on Linux, > others Windows. > > I would like to see 1 application for multiple platforms to performs dna > sequence analysis. I started writing something in Java to do this but > haven't touched in awhile. > > I'm wondering how many people would be interested in helping to develop > a platform-independent application to perform all sorts of sequence > analysis - alignments, snp analysis, assembly, etc. Sort of like GCG, > but free and actually user-friendly and useful. If people are > interested, I think we should talk about a framework and start building > something as needed. > > Any comments? > > ----- > Ryan Golhar > Computational Biologist > The Informatics Institute at > The University of Medicine & Dentistry of NJ > > Phone: 973-972-5034 > Fax: 973-972-7412 > Email: golharam at umdnj.edu > > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of > Yannick Wurm > Sent: Tuesday, March 30, 2004 10:05 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] DNA Strider > > > Hi, > I'm a student in Bioinformatics and Modeling at a French engineering > school in Lyon, France (http://biosciences.insa-lyon.fr). Currently in > my last year, I'm currently doing a six month internship in a C. > elegans lab at McGill University in Montreal. > The lab's computer are Macs, and besides standard browsing, word > processing and image processing, lab members also use them to aid them > in their molecular biology work. > One of the programs they use is called DNA Strider. This piece of > software has not been updated in a long time (probably since Apple's > System 6.x - window sizes are fixed to the small old mac screen size!) > and could require a face-lift. > > In the lab, it is mainly used for managing and manipulating sequences > of genes, primers and constructs. The main features of interest here > are: > - Sequence management > - Graphical (circular or linear) restriction maps of a given > sequence (or part of it), showing restriction site data concerning the > part or whole sequence (for each enzyme, you get the number of > restriction sites, and the obtained fragement sizes) > - Reverse complementary sequence > - Quick and simple alignment between two sequences > > I've searched the web and could not find an all-in-one package that > seemed as user friendly and coherent as DNA Strider. Individual web > sites and software tools do offer these features, but > - the internet is slow (you click and need to wait before > getting your > result) > - having everything in one place is nice > > Sequence Analysis (for Mac OS X) http://informagen.com/SA/ seems to be > aiming to do what DNA Strider does, but is still very young (and > closed-source, but thats a different debate). > > http://www.mekentosj.com/ has some very nice tools as well, but they're > very problem-specific. > > Have I missed something? Is there a really cool java app or web > software (that I could install locally for speed) that would replace > DNA Strider? What does your molecular biology lab use in for it's day > to day work? > Oh and buying something expensive is not a solution. > > Thanks for any leads, > > Yannick. > > \\\\\\\\\\\\\\\\\\\ > \\ http://yannick.poulet.org icq: 22044361 > \\ idh at poulet.org tel: ++33.6.16.41.71.92 > > _______________________________________________ > 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 -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world. " Louis Pasteur _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 9598 bytes Desc: not available URL: From hchen at utmem.edu Mon Apr 5 18:08:22 2004 From: hchen at utmem.edu (hao chen) Date: Mon, 05 Apr 2004 17:08:22 -0500 Subject: [BiO BB] DNA Strider In-Reply-To: <9EAE2E44897BC749ACB3A62683B2C8D123F0FC@ex4.asurite.ad.asu.edu> References: <9EAE2E44897BC749ACB3A62683B2C8D123F0FC@ex4.asurite.ad.asu.edu> Message-ID: <4071D8D6.6050601@utmem.edu> Joel Dudley wrote: >Several such systems are already under development and released in the private sector. I know of a soon to be open-source project that has all of these features and is already quite mature. You should hear about it in a month or so. > >- Joel > > > Will you please put up a post on this list when that happens? Thanks. BTW, your names sounds familiar, did we met before? Oh, wait, you are my friend at one social network site :-) Hao Chen > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org on behalf of Marcos Oliveira de Carvalho > Sent: Tue 3/30/2004 5:21 PM > To: bio_bulletin_board at bioinformatics.org > Cc: > Subject: Re: [BiO BB] DNA Strider > > From ulimard at yahoo.com.br Tue Apr 6 07:38:02 2004 From: ulimard at yahoo.com.br (Ulisses) Date: Tue, 6 Apr 2004 08:38:02 -0300 Subject: [BiO BB] Distributed System and Bioinformatic References: <406C58A5@wiccweb> Message-ID: <006301c41bcb$9e67a480$8902100a@ULISSES> I live in Brasil and I'm writing the paper in portuguese, but if you want a copy I will send to you. Atenciosamente Ulisses Dias ----- Original Message ----- From: "Barak Shenhav" To: Sent: Friday, April 02, 2004 3:24 PM Subject: RE: [BiO BB] Distributed System and Bioinformatic I would be happy to get a copy of the paper >===== Original Message From bio_bulletin_board at bioinformatics.org ===== >I'm graduating in computer science and I'm writing a paper about distributed >system, but I would like to join with some concepts of bioinformatic. So, >I'd like to receive some links about any works in this area. > >Grato pela aten??o. > Ulisses Dias ==================================== Barak Shenhav Department of Molecular Genetics Weizmann Institute of Science +972 8 9343098 (office) +972 8 9344487 (fax) +972 5 2955550 (cellular) _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From SJaffe at The-Scientist.COM Tue Apr 6 09:09:00 2004 From: SJaffe at The-Scientist.COM (=?utf-8?B?U2FtIEphZmZl?=) Date: Tue, 6 Apr 2004 09:09:00 -0400 Subject: [BiO BB] =?utf-8?B?UkU6IFtCaU8gQkJdIEROQSBTdHJpZGVy?= Message-ID: <9320390441B9D211ACD6009027268297026207FD@odin.the-scientist.com> Joel, I write a short piece in every issue of The Scientist magazine called Software Watch that features an open source biology software program. I'm interested in hearing more about the system you mention as a possible item about which I could write. We have a lead time of as much as two months, so embargoing our coverage is no problem. Can you send me any information about the system? Sam Jaffe Associate Editor The Scientist Magazine (www.the-scientist.com) 3535 Market St. Second Floor Philadelphia, PA, 19104 215 386 9601 x.3015 sjaffe at the-scientist.com -----Original Message----- From: Joel Dudley [mailto:Joel.Dudley at asu.edu] Sent: Monday, April 05, 2004 4:56 PM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] DNA Strider Several such systems are already under development and released in the private sector. I know of a soon to be open-source project that has all of these features and is already quite mature. You should hear about it in a month or so. - Joel -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org on behalf of Marcos Oliveira de Carvalho Sent: Tue 3/30/2004 5:21 PM To: bio_bulletin_board at bioinformatics.org Cc: Subject: Re: [BiO BB] DNA Strider It would be nice to have a bioinformatics IDRE ( Integrated Development and Research Environment) with some basic features (sequence visualization, editing, annotation, data management, etc...) and a well designed plug-in API, for easy extension. An idea could be build it on top of the NetBeans platform , and with java we get platform-independent software. (with other languages too, but java do the job) One can suggest add bindings with python/perl/ruby/java and theirs Bio* libraries, interfaces to bioinformatics tools, including output capture (emboss, phred, phrap, BLAST, FASTA, Clustal,R/bioconductor, Mummer,...) . Also interfaces to webservices and data retrieving from major databases. Well, there are lots of possibilities. cheers Marcos On Tue, 30 Mar 2004 18:30:36 -0500, Ryan Golhar wrote: > You know, I'm constantly finding different programs to perform different > tasks. Either client applications, or web-based. Some run on Linux, > others Windows. > > I would like to see 1 application for multiple platforms to performs dna > sequence analysis. I started writing something in Java to do this but > haven't touched in awhile. > > I'm wondering how many people would be interested in helping to develop > a platform-independent application to perform all sorts of sequence > analysis - alignments, snp analysis, assembly, etc. Sort of like GCG, > but free and actually user-friendly and useful. If people are > interested, I think we should talk about a framework and start building > something as needed. > > Any comments? > > ----- > Ryan Golhar > Computational Biologist > The Informatics Institute at > The University of Medicine & Dentistry of NJ > > Phone: 973-972-5034 > Fax: 973-972-7412 > Email: golharam at umdnj.edu > > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [ mailto:bio_bulletin_board-admin at bioinformatics.org ] On Behalf Of > Yannick Wurm > Sent: Tuesday, March 30, 2004 10:05 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] DNA Strider > > > Hi, > I'm a student in Bioinformatics and Modeling at a French engineering > school in Lyon, France ( http://biosciences.insa-lyon.fr ). Currently in > my last year, I'm currently doing a six month internship in a C. > elegans lab at McGill University in Montreal. > The lab's computer are Macs, and besides standard browsing, word > processing and image processing, lab members also use them to aid them > in their molecular biology work. > One of the programs they use is called DNA Strider. This piece of > software has not been updated in a long time (probably since Apple's > System 6.x - window sizes are fixed to the small old mac screen size!) > and could require a face-lift. > > In the lab, it is mainly used for managing and manipulating sequences > of genes, primers and constructs. The main features of interest here > are: > - Sequence management > - Graphical (circular or linear) restriction maps of a given > sequence (or part of it), showing restriction site data concerning the > part or whole sequence (for each enzyme, you get the number of > restriction sites, and the obtained fragement sizes) > - Reverse complementary sequence > - Quick and simple alignment between two sequences > > I've searched the web and could not find an all-in-one package that > seemed as user friendly and coherent as DNA Strider. Individual web > sites and software tools do offer these features, but > - the internet is slow (you click and need to wait before > getting your > result) > - having everything in one place is nice > > Sequence Analysis (for Mac OS X) http://informagen.com/SA/ seems to be > aiming to do what DNA Strider does, but is still very young (and > closed-source, but thats a different debate). > > http://www.mekentosj.com/ has some very nice tools as well, but they're > very problem-specific. > > Have I missed something? Is there a really cool java app or web > software (that I could install locally for speed) that would replace > DNA Strider? What does your molecular biology lab use in for it's day > to day work? > Oh and buying something expensive is not a solution. > > Thanks for any leads, > > Yannick. > > \\\\\\\\\\\\\\\\\\\ > \\ http://yannick.poulet.org icq: 22044361 > \\ idh at poulet.org tel: ++33.6.16.41.71.92 > > _______________________________________________ > 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 -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world. " Louis Pasteur _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From jrambla at hotmail.com Tue Apr 6 12:16:01 2004 From: jrambla at hotmail.com (JRambla) Date: Tue, 6 Apr 2004 18:16:01 +0200 Subject: [BiO BB] DNA Analysis Open Platform (was: DNA Strider) In-Reply-To: Message-ID: Sorry for asking, What's the difference of this proposal with the JEMBOSS project? More depth in some areas? More features? Jordi Rambla Barcelona (Spain) -----Mensaje original----- De: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] En nombre de LJ Enviado el: mi?rcoles, 31 de marzo de 2004 23:23 Para: bio_bulletin_board at bioinformatics.org Asunto: RE: [BiO BB] DNA Strider i like this idea quite a bit. i know several programmers/bioinformaticists who might want to help out. they are really impressed with python these days lon james postgres, inc 1 fair oaks san francisco, ca 94110 415-573-9192 lon at efcodd.org -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Ryan Golhar Sent: Tuesday, March 30, 2004 3:31 PM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] DNA Strider You know, I'm constantly finding different programs to perform different tasks. Either client applications, or web-based. Some run on Linux, others Windows. I would like to see 1 application for multiple platforms to performs dna sequence analysis. I started writing something in Java to do this but haven't touched in awhile. I'm wondering how many people would be interested in helping to develop a platform-independent application to perform all sorts of sequence analysis - alignments, snp analysis, assembly, etc. Sort of like GCG, but free and actually user-friendly and useful. If people are interested, I think we should talk about a framework and start building something as needed. Any comments? ----- Ryan Golhar Computational Biologist The Informatics Institute at The University of Medicine & Dentistry of NJ Phone: 973-972-5034 Fax: 973-972-7412 Email: golharam at umdnj.edu -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Yannick Wurm Sent: Tuesday, March 30, 2004 10:05 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] DNA Strider Hi, I'm a student in Bioinformatics and Modeling at a French engineering school in Lyon, France (http://biosciences.insa-lyon.fr). Currently in my last year, I'm currently doing a six month internship in a C. elegans lab at McGill University in Montreal. The lab's computer are Macs, and besides standard browsing, word processing and image processing, lab members also use them to aid them in their molecular biology work. One of the programs they use is called DNA Strider. This piece of software has not been updated in a long time (probably since Apple's System 6.x - window sizes are fixed to the small old mac screen size!) and could require a face-lift. In the lab, it is mainly used for managing and manipulating sequences of genes, primers and constructs. The main features of interest here are: - Sequence management - Graphical (circular or linear) restriction maps of a given sequence (or part of it), showing restriction site data concerning the part or whole sequence (for each enzyme, you get the number of restriction sites, and the obtained fragement sizes) - Reverse complementary sequence - Quick and simple alignment between two sequences I've searched the web and could not find an all-in-one package that seemed as user friendly and coherent as DNA Strider. Individual web sites and software tools do offer these features, but - the internet is slow (you click and need to wait before getting your result) - having everything in one place is nice Sequence Analysis (for Mac OS X) http://informagen.com/SA/ seems to be aiming to do what DNA Strider does, but is still very young (and closed-source, but thats a different debate). http://www.mekentosj.com/ has some very nice tools as well, but they're very problem-specific. Have I missed something? Is there a really cool java app or web software (that I could install locally for speed) that would replace DNA Strider? What does your molecular biology lab use in for it's day to day work? Oh and buying something expensive is not a solution. Thanks for any leads, Yannick. \\\\\\\\\\\\\\\\\\\ \\ http://yannick.poulet.org icq: 22044361 \\ idh at poulet.org tel: ++33.6.16.41.71.92 _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From forward at hongyu.org Tue Apr 6 16:16:35 2004 From: forward at hongyu.org (Hongyu Zhang) Date: Tue, 6 Apr 2004 13:16:35 -0700 Subject: [BiO BB] Pfam list for Fe/Zn binding Message-ID: <1081282595.40731023754f4@hongyu.org> I am wondering whether anybody has a collection of all Pfam families that contains proteins binding to Fe or Zn. I have by myself compiled a list using key word search like "Fe", "Iron" etc., from the Pfam description and comments. However, it turned out that I missed those proteins like P450 which has heme cofactors but does not have specific "Fe" or "Iron" keyword in its Pfam description. Anyway, my original goal is to find all the proteins in a private protein database that bind to either Fe or Zn, so I tried Pfam first. Maybe I could also try GO annotation, but I would run into the similar problem. Can anyone here give me some advice how to accomplish that in a straightforward way? Thanks in advance. Hongyu Zhang From dmb at mrc-dunn.cam.ac.uk Tue Apr 6 17:33:00 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Tue, 6 Apr 2004 22:33:00 +0100 (BST) Subject: [BiO BB] Pfam list for Fe/Zn binding In-Reply-To: <1081282595.40731023754f4@hongyu.org> Message-ID: Try Prosite too On Tue, 6 Apr 2004, Hongyu Zhang wrote: > I am wondering whether anybody has a collection of all Pfam families that > contains proteins binding to Fe or Zn. I have by myself compiled a list using > key word search like "Fe", "Iron" etc., from the Pfam description and comments. > However, it turned out that I missed those proteins like P450 which has heme > cofactors but does not have specific "Fe" or "Iron" keyword in its Pfam > description. > > Anyway, my original goal is to find all the proteins in a private protein > database that bind to either Fe or Zn, so I tried Pfam first. Maybe I could > also try GO annotation, but I would run into the similar problem. > > Can anyone here give me some advice how to accomplish that in a straightforward > way? Thanks in advance. > > Hongyu Zhang > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From john.rowland at ncl.ac.uk Wed Apr 7 09:52:28 2004 From: john.rowland at ncl.ac.uk (John Rowland) Date: Wed, 7 Apr 2004 14:52:28 +0100 Subject: [BiO BB] Data-mining approaches for 2D Gel based proteomics Message-ID: <000001c41ca7$908332d0$3b60420a@campus.ncl.ac.uk> Hi, Could anyone tell me if there are software packages (windows or java only, I don't have access to nix boxes!) available FOR FREE that can mine data from 2D Gel based Proteomics experiments, and in particular the multiplexed 2D-DIGE proteomics platform. Specifically what I am looking for (at a minimum) is the ability to perform various cluster analyses (Heirarchical clustering, Principal Components Analysis etc) on matched spot data (intensities) and Gene Ontology classification (in a nice tree-like structured view) where spot identity is known. I have Googled for months for this sort of thing and can't find anything that suits. I realise that there are packages out there for this type of analysis using data from microarray experiments but I don't seem to be able to use them for my needs (the documentation is often rather poor!). Any help that could be offered would be gratefully received!! Regards, John From operon at www.ufsm.br Wed Apr 7 12:58:36 2004 From: operon at www.ufsm.br (Marcos Oliveira de Carvalho) Date: Wed, 07 Apr 2004 13:58:36 -0300 Subject: [BiO BB] Distributed System and Bioinformatic In-Reply-To: <006301c41bcb$9e67a480$8902100a@ULISSES> References: <406C58A5@wiccweb> <006301c41bcb$9e67a480$8902100a@ULISSES> Message-ID: Opa, eu quero uma c?pia, em portugu?s mesmo. :-) valeu Marcos On Tue, 6 Apr 2004 08:38:02 -0300, Ulisses wrote: > I live in Brasil and I'm writing the paper in portuguese, but if you > want a > copy I will send to you. > > Atenciosamente > Ulisses Dias > > > ----- Original Message ----- > From: "Barak Shenhav" > To: > Sent: Friday, April 02, 2004 3:24 PM > Subject: RE: [BiO BB] Distributed System and Bioinformatic > > > I would be happy to get a copy of the paper >> ===== Original Message From bio_bulletin_board at bioinformatics.org ===== >> I'm graduating in computer science and I'm writing a paper about > distributed >> system, but I would like to join with some concepts of bioinformatic. >> So, >> I'd like to receive some links about any works in this area. >> >> Grato pela aten??o. >> Ulisses Dias > > ==================================== > Barak Shenhav > Department of Molecular Genetics > Weizmann Institute of Science > +972 8 9343098 (office) > +972 8 9344487 (fax) > +972 5 2955550 (cellular) > > _______________________________________________ > 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 -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world. " Louis Pasteur From j.d.tucker at vla.defra.gsi.gov.uk Thu Apr 8 04:25:08 2004 From: j.d.tucker at vla.defra.gsi.gov.uk (Tucker, James) Date: Thu, 8 Apr 2004 09:25:08 +0100 Subject: [BiO BB] COGs Message-ID: <104FE795DA19D411A71A0008C733F76404A43C69@VLA6> Hi All, I'm looking in to regions of differences in 2 genomes. In order to help me simplify and understand the information I'm looking at the COG groups that they fall into. However one of the Genomes does not have COGs details on the NCBI site. Can anyone tell me of an alternative ? I've tried DDBJ but couldn't find any COG details. Thanks in advance for any help. Regards James James Tucker Brucella Research Group Department of Bacterial Diseases VLA Weybridge Woodham Lane New Haw Addlestone Surrey KT15 3NB Tel: ++44(0)1932 357227 / 359595 Fax: ++44(0)1932 357873 mailto:j.d.tucker at vla.defra.gsi.gov.uk Veterinary Laboratories Agency (VLA) This email and any attachments is intended for the named recipient only. Its unauthorised use, disclosure, storage or copying is not permitted. If you have received it in error, please destroy all copies and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within VLA systems we can accept no responsibility once it has left our systems. Communications on VLA's computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes. From mkgovindis at yahoo.com Thu Apr 8 05:44:59 2004 From: mkgovindis at yahoo.com (govind mk) Date: Thu, 8 Apr 2004 02:44:59 -0700 (PDT) Subject: [BiO BB] COGs In-Reply-To: <104FE795DA19D411A71A0008C733F76404A43C69@VLA6> Message-ID: <20040408094459.11262.qmail@web40112.mail.yahoo.com> Hi You could do a simple protein blast of COG regions -- > in genome 1 with the other genome. You could also subject both the genomes to domain analysis and identify /compare domains. Is there anything specific you are looking for ??? -Govind --- "Tucker, James" wrote: > Hi All, > I'm looking in to regions of differences in 2 > genomes. > In order to help me simplify and understand the > information I'm looking at > the COG groups that they fall into. > However one of the Genomes does not have COGs > details on the NCBI site. > Can anyone tell me of an alternative ? > I've tried DDBJ but couldn't find any COG details. > Thanks in advance for any help. > Regards > James > > James Tucker > Brucella Research Group > Department of Bacterial Diseases > VLA Weybridge > Woodham Lane > New Haw > Addlestone > Surrey > KT15 3NB > > Tel: ++44(0)1932 357227 / 359595 > Fax: ++44(0)1932 357873 > > mailto:j.d.tucker at vla.defra.gsi.gov.uk > > > > > > > > Veterinary Laboratories Agency (VLA) > > This email and any attachments is intended for the > named recipient only. Its > unauthorised use, disclosure, storage or copying is > not permitted. If you have > received it in error, please destroy all copies and > inform the sender. Whilst this > email and associated attachments will have been > checked for known viruses > whilst within VLA systems we can accept no > responsibility once it has left our > systems. Communications on VLA's computer systems > may be monitored > and/or recorded to secure the effective operation of > the system and for other > lawful purposes. > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________ Do you Yahoo!? Yahoo! Small Business $15K Web Design Giveaway http://promotions.yahoo.com/design_giveaway/ From boris.steipe at utoronto.ca Thu Apr 8 08:56:57 2004 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Thu, 8 Apr 2004 08:56:57 -0400 Subject: [BiO BB] COGs In-Reply-To: <20040408094459.11262.qmail@web40112.mail.yahoo.com> Message-ID: <37C02984-895C-11D8-AADC-000A9577512E@utoronto.ca> Hm. A simple BLAST will not necessarily find orthologues. Rememeber, COGs are not just functional annotations, they are Clusters of Orthologous Groups. Since COGs are produced by the NCBI you will not find them elsewhere, if they are not on the NCBI site. You can of course try to emulate their procedure of finding reciprocal best-matches. If you can define more precisely what you are trying to achieve, maybe there are alternative ways to do this. Boris > Hi > > You could do a simple protein blast of > COG regions -- > in genome 1 with the other genome. > You could also subject both the genomes to domain > analysis and identify /compare domains. > > Is there anything specific you are looking for ??? > > -Govind > --- "Tucker, James" > wrote: >> Hi All, >> I'm looking in to regions of differences in 2 >> genomes. >> In order to help me simplify and understand the >> information I'm looking at >> the COG groups that they fall into. >> However one of the Genomes does not have COGs >> details on the NCBI site. >> Can anyone tell me of an alternative ? >> I've tried DDBJ but couldn't find any COG details. >> Thanks in advance for any help. >> Regards >> James >> >> James Tucker >> Brucella Research Group >> Department of Bacterial Diseases >> VLA Weybridge >> Woodham Lane >> New Haw >> Addlestone >> Surrey >> KT15 3NB >> >> Tel: ++44(0)1932 357227 / 359595 >> Fax: ++44(0)1932 357873 >> >> mailto:j.d.tucker at vla.defra.gsi.gov.uk >> >> >> >> >> >> >> >> Veterinary Laboratories Agency (VLA) >> >> This email and any attachments is intended for the >> named recipient only. Its >> unauthorised use, disclosure, storage or copying is >> not permitted. If you have >> received it in error, please destroy all copies and >> inform the sender. Whilst this >> email and associated attachments will have been >> checked for known viruses >> whilst within VLA systems we can accept no >> responsibility once it has left our >> systems. Communications on VLA's computer systems >> may be monitored >> and/or recorded to secure the effective operation of >> the system and for other >> lawful purposes. >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - >> BiO_Bulletin_Board at bioinformatics.org >> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > __________________________________ > Do you Yahoo!? > Yahoo! Small Business $15K Web Design Giveaway > http://promotions.yahoo.com/design_giveaway/ > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > --- Boris Steipe University of Toronto Program in Proteomics & Bioinformatics Departments of Biochemistry & Molecular and Medical Genetics http://biochemistry.utoronto.ca/steipe/ From yzz100 at psu.edu Thu Apr 8 12:51:47 2004 From: yzz100 at psu.edu (Anne Y. Zhang) Date: Thu, 8 Apr 2004 12:51:47 -0400 Subject: [BiO BB] graph view of gene ontology Message-ID: <006501c41d89$c7d0ee20$6592cb82@ist.psu.edu> I meet a problem in annotating a cluster of genes. Given a set of gene names, is there any tool available that automatically retrieve gene annotation from Gene Ontology and generate a graph (network) represent for the set of genes? Thank you very much! Anne =================================================== Anne Ya Zhang Ph.D Candidate School of Information Sciences and Technology, Penn State University 313D Information Sciences and Technology Building University Park, PA 16802 =================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.fiedler at umiami.edu Thu Apr 8 14:41:33 2004 From: t.fiedler at umiami.edu (Tristan Fiedler) Date: Thu, 8 Apr 2004 14:41:33 -0400 Subject: [BiO BB] (no subject) In-Reply-To: <20040408160112.192DDD1F25@www.bioinformatics.org> References: <20040408160112.192DDD1F25@www.bioinformatics.org> Message-ID: <5B779AAF-898C-11D8-9DF1-000393C3A6B0@umiami.edu> >> Does anyone have experience or comments on the Mac bioinformatics cluster: >> http://www.apple.com/education/science/solutions/awcbio.html >> Cheers, Tristan ------------------------------- Tristan J. Fiedler, Ph.D. Postdoctoral Research Fellow - Walsh Laboratory NIEHS Marine & Freshwater Biomedical Sciences Center Rosenstiel School of Marine & Atmospheric Sciences University of Miami tfiedler at rsmas.miami.edu t.fiedler at umiami.edu (alias) 305 361 4626 From mgollery at unr.edu Thu Apr 8 15:00:49 2004 From: mgollery at unr.edu (Martin Gollery) Date: Thu, 08 Apr 2004 12:00:49 -0700 Subject: [BiO BB] (no subject) In-Reply-To: <5B779AAF-898C-11D8-9DF1-000393C3A6B0@umiami.edu> References: <20040408160112.192DDD1F25@www.bioinformatics.org> <5B779AAF-898C-11D8-9DF1-000393C3A6B0@umiami.edu> Message-ID: <4075A161.8080403@unr.edu> Tristan, No personal experience, as it is brand new, but I know a bit about it. This is a prebuilt G5 x cluster with the Inquiry tool from Bioteam preinstalled. If you want to get up and running quickly, without messing around with settings and installation scripts, this is an excellent way to go. They claim that you will have 200 apps running on the web 30 minutes after you open the box, and I believe it. If you have people that can set up EMBOSS, BLAST and HMMer with PISE on the web without a great amount of fuss, then it might save you some money to roll your own. And of course, religion may come into the decision as well, as it does any time that operating systems and CPU's are discussed... ;-) Tristan Fiedler wrote: >>> > > Does anyone have experience or comments on the Mac bioinformatics cluster: > >>> http://www.apple.com/education/science/solutions/awcbio.html >>> > Cheers, > > Tristan > > ------------------------------- > > Tristan J. Fiedler, Ph.D. > Postdoctoral Research Fellow - Walsh Laboratory > NIEHS Marine & Freshwater Biomedical Sciences Center > Rosenstiel School of Marine & Atmospheric Sciences > University of Miami > > tfiedler at rsmas.miami.edu > t.fiedler at umiami.edu (alias) > 305 361 4626 > > _______________________________________________ > 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 'Don't worry that the world will end today- it's already tomorrow in Australia...' -Charles Schulz From jeff at bioinformatics.org Mon Apr 12 19:36:02 2004 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 12 Apr 2004 19:36:02 -0400 Subject: [BiO BB] CFP: BOSC'2004 Message-ID: <407B27E2.9090503@bioinformatics.org> I'm posting this on behalf of Andrew Dalke: MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 5th annual Bioinformatics Open Source Conference (BOSC'2004) is organized by the not-for-profit Open Bioinformatics Foundation (not affiliated with Bioinformatics.Org). The meeting will take place July 29-30, 2004 in Glasgow, Scotland, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 12th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2004/ for more information. The focus of the meeting will be on current and emerging Open Source** informatics tools and toolkits. BOSC provides a forum for developers, project groups, users and interested parties to meet personally, exchange ideas and collaborate together. In addition, keynote speeches from well known Open Source Bioinformatics leaders are being planned. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2004/ * Email: bosc at open-bio.org * Online registration: https://www.cteusa.com/iscb3/ FEES * Corporate :GBP ?165.00 british pounds sterling * Academic : GBP ?120.00 british pounds sterling * Student : GBP ?90.00 british pounds sterling A 17.5% Valued Added Tax(VAT) will be added to all fees. Note: We have tried to set our fees as low as possible without risking the chance that the foundation will lose money on the event. We budget with the goal of breaking even on costs or realizing a small profit. REGISTER ONLINE FOR BOSC'2004 & ISMB AT: https://www.cteusa.com/iscb3/ SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2004. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstract for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2004, please send us by May 5th: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2004. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2004, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
SOFTWARE DEMONSTRATIONS WANTED! If you are involved in the development of Open Source Bioinformatics Software, you are invited to provide a short demonstration to attendees of BOSC 2004. If you are interested in giving a software demonstration at BOSC 2004, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * Internet connectivity requirements (e.g. website Application served on the world wide web, or web based client application). We will accept entries on-line until the BOSC starts, but space for demos and lightning talks is limited. ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy. See the following websites for further details: href="http://www.opensource.org/licenses/ href="http://www.opensource.org/docs/definition.php From kucej at fns.uniba.sk Thu Apr 8 05:56:04 2004 From: kucej at fns.uniba.sk (Martin Kucej) Date: Thu, 08 Apr 2004 11:56:04 +0200 Subject: [BiO BB] Librarian V1.3 released Message-ID: <40753DD4.3402.2828A735@localhost> Librarian, a program, which enables a group of researchers to create an annotated virtual library of articles in portable document format (PDF) is now available in version 1.3. This version comes with a couple of new features including improved download of data from PubMed and ability to add PDF articles to more categories. Also Librarian removes line breaks if you paste info into the upload form directly from PDF file. It is possible now to identify articles in PubMed according to PMIDs (you can enter more IDs separated by comma). The search than displays titles and first author. The next screen enables you to read over the article annotations and preselect most suitable categories. This selection is transferred into the final Upload form. The upload form contains multiple select field for categories. To select more categories you must Ctrl+Click or Command+Click on Mac. The older versions of Librarian (1.1, 1.1a, and 1.2) can be upgraded using 'Upgrade' release without reinstallation. http://bioinformatics.org/librarian/downloads.php This is probably the last release of the first generation of Librarian. A 2.0 series is planned for this summer and should include the abilities to add complete citation information, generate simple lists of citations in plain text, BibTex and maybe other formats, so that this lists can be imported into Citation Managers. Sincerely Yours, Martin Kucej Department of Biochemistry Comenius University Mlynska dolina CH-1 Bratislava 84215 Slovak Republic From maketo at sdf.lonestar.org Thu Apr 8 14:40:02 2004 From: maketo at sdf.lonestar.org (Ognen Duzlevski) Date: Thu, 8 Apr 2004 18:40:02 +0000 (UTC) Subject: [BiO BB] paup output parsing Message-ID: Hi all, I am trying to parse out paup output such as this one: tree PAUP_1 = [&U] (1:4,2:20,((3:14,5:200):17,4:13):24); What I want is to extract the length for each one. The number after : is the length For this case: Length of 1 will be 4 Length of 2 will be 20 Length of 3 will be 14+17+24=55 Length of 5 will be 200+17+24=241 Length of 4 will be 13+24=3 Naturally, the output gets pretty large and complicated and before I fire up my editor and start coding: are there any tools/scripts outhere that extract this information already and are available for download? Thanks, Ognen From pkerrwall at psu.edu Tue Apr 13 12:19:20 2004 From: pkerrwall at psu.edu (Kerr Wall) Date: Tue, 13 Apr 2004 12:19:20 -0400 Subject: [BiO BB] Re: paup output parsing In-Reply-To: <20040413160109.218DFD1F20@www.bioinformatics.org> Message-ID: On 4/13/04 12:01 PM, "Ognen Duzlevski" wrote: > Hi all, > > I am trying to parse out paup output such as this one: > tree PAUP_1 = [&U] (1:4,2:20,((3:14,5:200):17,4:13):24); > > What I want is to extract the length for each one. The number after : is > the length > > For this case: > Length of 1 will be 4 > Length of 2 will be 20 > Length of 3 will be 14+17+24=55 > Length of 5 will be 200+17+24=241 > Length of 4 will be 13+24=3 > > Naturally, the output gets pretty large and complicated and before I fire > up my editor and start coding: are there any tools/scripts outhere that > extract this information already and are available for download? > > Thanks, > Ognen Yes. Check out www.bioperl.org Specifically, Bio::Tree::TreeIO, Bio::Tree::TreeI, Bio::Tree::NodeI, etc. at http://doc.bioperl.org/releases/bioperl-1.4/ There's also a HOWTO on Phylogenetic Trees at http://bioperl.org/HOWTOs/html/Trees.html Kerr From murphy at genome.chop.edu Tue Apr 13 13:58:09 2004 From: murphy at genome.chop.edu (Kevin Murphy) Date: Tue, 13 Apr 2004 13:58:09 -0400 Subject: [BiO BB] Hosting a bioinformatics project In-Reply-To: Message-ID: <1F9853EA-8D74-11D8-A035-0003930D3626@genome.chop.edu> What are the pros and cons of hosting a project at bioinformatics.org as opposed to sourceforge? I have a project (http://genome.chop.edu/mePCR/) that I'd like to have hosted. Thanks, Kevin -- Kevin Murphy eGenome Administrator - http://genome.chop.edu/ 3535 Market St., Rm 1405 Children's Hospital of Philadelphia (215) 590-0471 murphy at genome.chop.edu From dave at unheardof.clara.co.uk Tue Apr 13 17:21:47 2004 From: dave at unheardof.clara.co.uk (Dave Richardson) Date: Tue, 13 Apr 2004 22:21:47 +0100 Subject: [BiO BB] Re: paup output parsing In-Reply-To: <20040413160106.A868ED1F1C@www.bioinformatics.org> References: <20040413160106.A868ED1F1C@www.bioinformatics.org> Message-ID: <407C59EB.90504@unheardof.clara.co.uk> Ognen wrote: >I am trying to parse out paup output such as this one: >tree PAUP_1 = [&U] (1:4,2:20,((3:14,5:200):17,4:13):24); > >What I want is to extract the length for each one. The number after : is >the length > >For this case: >Length of 1 will be 4 >Length of 2 will be 20 >Length of 3 will be 14+17+24=55 >Length of 5 will be 200+17+24=241 >Length of 4 will be 13+24=3 > >Naturally, the output gets pretty large and complicated and before I fire >up my editor and start coding: are there any tools/scripts outhere that >extract this information already and are available for download? > Hi, BioPerl has methods for dealing with trees, including getting the length between two nodes. You probably want to have a look at the Bio::TreeIO and Bio::Tree::TreeFunctionsI. TreeIO doesn't deal with paup/nexus format, but paup will use newick format if you ask nicely. Hope this helps, Dave Richardson From jeff at bioinformatics.org Tue Apr 13 18:19:52 2004 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 13 Apr 2004 18:19:52 -0400 Subject: [BiO BB] Hosting a bioinformatics project References: <1F9853EA-8D74-11D8-A035-0003930D3626@genome.chop.edu> Message-ID: <407C6788.5000608@bioinformatics.org> Hi Kevin. Bioinformatics.Org currently runs an earlier version of the SourceForge system. Other than specific differences in features, Bioinformatics.Org distinguishes itself in the following ways: 1. Our focus is on bioinformatics, with bioinformatic open labs (like foundries) coming. 2. We host web-based, server-side executables, including Perl, Python and CGI support. 3. We host web-based databases, including MySQL and Postgres support. 4. Project members have shell-level access to CVS, crontab and other resources. 5. Shell account use is not limited to software development. 6. Storage has no hard limit. 7. Users have IMAP4 access to e-mail (soon to be Web-based and POP3). 8. We can accommodate special needs, because we're smaller (150+ projects vs. 80,000 at SF) and can keep track of members more easily (has the president of VA Software ever contacted you personally? ;-)). 9. Bioinformatics.Org is non-profit, and even our resources are open source (vs. SF, which places commercial banners on project pages and has a commercial-only license for its current version). 10. Project members can give a presentation about their project at Organization meetings, and the presenter attends for free. Travel and other grants for project administrators are on the horizon. We're actually migrating to the GForge system, which is an open source fork of SF, by original SF developer Tim Perdue. It's very competitive with commercial SourceForge. Check out our system under development (sneak peek): http://groups.bioinformatics.org/ (caveat: under development!) We're currently running GForge 3.1 and will update to the latest (3.3+) before going live. This page has a good comparison of some of the hosts out there (not including us): http://www.ibiblio.org/fosphost/exhost.htm If you have any more questions, please ask. Cheers. Jeff Kevin Murphy wrote: > What are the pros and cons of hosting a project at bioinformatics.org as > opposed to sourceforge? I have a project > (http://genome.chop.edu/mePCR/) that I'd like to have hosted. > > Thanks, > Kevin > > -- 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 tmrhyne at ncsu.edu Wed Apr 14 14:08:20 2004 From: tmrhyne at ncsu.edu (Theresa-Marie Rhyne) Date: Wed, 14 Apr 2004 14:08:20 -0400 Subject: [BiO BB] CFP for Special issue on Bioinformatics Visualization: Jan 15, 2005 Message-ID: Hi Bioinformatics Colleagues: Chris North (at Virginia Tech) and I are guest editing a special issue of the Information Visualization journal (http://www.palgrave-journals.com/ivs/index.html) on Bioinformatics Visualization for the September 2005 issue of the journal. If you have work in this arena, we would like to encourage you to submit. Our submission deadline is January 15, 2005. See more details below. Smiles... Theresa-Marie ---------------------------------------------------------------- Call for Papers Bioinformatics Visualization Special Issue of Information Visualization Vol.4 No.3 Palgrave/Macmillan Guest Editors: Chris North & Theresa-Marie Rhyne Submissions due: 15 January 2005 Acceptance notices: 5 March 2005 Final revisions due: 15 April 2005 The theme for this special issue of Information Visualization (Palgrave/Macmillan) is Bioinformatics Visualization (Published 1st September 2005). Original papers are solicited in this area. In particular, we encourage innovative papers detailing the design, development, and evaluation of visualization methods for the bioinformatics domain. The mapping of the human, rice and other genomes has lead to rapid expansion of bioinformatics. High-throughput technology and other advances have resulted in the collection of massive quantities of data. These factors, combined with the complexity of the life sciences, set the standard for the future of information-intensive scientific investigation and create unique, difficult problems for information visualization. Exploratory visualization tools that enable visual investigation of computational biological data and bioinformatics databases are beginning to emerge. We seek original research and application papers that explore this important emerging arena of information visualization. Case studies and applications of bioinformatics topics are also welcome. Life scientists will be on the review board of this special issue. Example topics include, but are not limited to, the visualization of: ? Heterogeneous biological databases ? Sequence analysis, comparison, and alignment methods ? Molecular evolution ? Genomics, gene expression and gene regulatory networks ? Micro-Array Design and Analysis ? Proteomics ? Signalling pathways, biochemical networks ? Molecular docking and drug design ? Species taxonomies and functional ontologies ? Experiment data and process management ? Biochemical and cellular simulation and models Enquiries should be made to both guest editors. Authors should inform the guest editors of their intent to submit before submitting a manuscript. Electronic submissions of manuscripts in PDF or Word (97 or later) are recommended via email to Chris North [north at cs.vt.edu] and Theresa-Marie Rhyne [tmrhyne at ncsu.edu]. If manuscripts are submitted in printed form, please send four copies of full articles to either guest editor at: Chris North Theresa-Marie Rhyne 660 McBryde Hall Learning Technology Service/DELTA Dept of Computer Science NC State University Virginia Tech Campus Box 7113 Blacksburg, VA 24061-0106 Raleigh, NC 27695 email: north at cs.vt.edu email: tmrhyne at ncsu.edu ------------------------------------------------------------------------ -- Theresa-Marie Rhyne Coordinator of Special Technology Projects Learning Technology Service/DELTA NC State University Campus Box 7113 Venture III, Suite 267 Centennial Campus 900 Main Campus Drive Raleigh, North Carolina 27695 Phone: 919-513-4623 Fax: 919-513-4237 Email: tmrhyne at ncsu.edu ----------------------------------------- From rasmoo143a at yahoo.com Thu Apr 15 02:57:58 2004 From: rasmoo143a at yahoo.com (jain rashmi) Date: Wed, 14 Apr 2004 23:57:58 -0700 (PDT) Subject: [BiO BB] Hosting a bioinformatics project In-Reply-To: <407C6788.5000608@bioinformatics.org> Message-ID: <20040415065758.45748.qmail@web12008.mail.yahoo.com> Hello Sir I am a bioinformatics student, I have done P.G Diploma in bioinformatics after B.Sc with Biology. I have also done diploma in computer. After My diploma I have worked in Birla Institute of Scientific Research, Jaipur, for six month. My work was to create a database of medicinal and aromatic plants present on the deseart area and aravali hill of Rajasthan using PHP, MySQL on linux. I want to get involve in some bioinformatics project, It would be a great opportunity if you once give me chance to work on project. Thanking You Regards Rashmi Jain __________________________________ Do you Yahoo!? Yahoo! Tax Center - File online by April 15th http://taxes.yahoo.com/filing.html From dmb at mrc-dunn.cam.ac.uk Thu Apr 15 06:16:16 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 15 Apr 2004 11:16:16 +0100 (BST) Subject: [BiO BB] Hosting a bioinformatics project In-Reply-To: <20040415065758.45748.qmail@web12008.mail.yahoo.com> Message-ID: http://bioinformatics.org/scol/index.html *) On Wed, 14 Apr 2004, jain rashmi wrote: > > Hello Sir > > I am a bioinformatics student, I have done P.G Diploma > in bioinformatics after B.Sc with Biology. I have also > done diploma in computer. After My diploma I have > worked in Birla Institute of Scientific Research, > Jaipur, for six month. My work was to create a > database of medicinal and aromatic plants present on > the deseart area and aravali hill of Rajasthan using > PHP, MySQL on linux. > I want to get involve in some bioinformatics project, > It would be a great opportunity if you once give me > chance to work on project. > > Thanking You > Regards > > Rashmi Jain > > > > > __________________________________ > Do you Yahoo!? > Yahoo! Tax Center - File online by April 15th > http://taxes.yahoo.com/filing.html > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From landman at scalableinformatics.com Tue Apr 20 13:39:31 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Tue, 20 Apr 2004 13:39:31 -0400 Subject: [BiO BB] Two-day NCBI Course, May 26-27 2004] Message-ID: <1082482770.26068.45.camel@protein.scalableinformatics.com> -----Forwarded Message----- ================================================================= Enhanced Field Guide: Exploring sequences, genomes and structures ================================================================= For details and course registration see the course web page: http://www.ncbi.nlm.nih.gov/Class/FieldGuide/FGPlus Space is limited! Register early! Featuring: * Greater coverage of NCBI tools and databases * Longer and more detailed hands-on sessions * Web, standalone and client versions of BLAST * Disease genes mini-course * 3-D structures course Time and Place: Wednesday and Thursday, May 26 & 27, 2004 The National Library of Medicine on the NIH Campus Lister Hill Center Auditorium, Building 38A The National Center for Biotechnology Information presents an enhanced, two-day version of the popular Field Guide course. This expanded course provides more detailed coverage of NCBI molecular databases and tools, especially the Entrez system and NCBI BLAST (Web, standalone and client versions). Special emphases of the course are genomic information and molecular structures. The hands-on practical portion is more extensive and includes the "Exploring 3D Molecular Structures" and "Identification of Disease Genes" NCBI course materials. The course is free but registration is required. To register, and for more information, see the URL given above. This premier version of the course is limited to the first 40 applicants. Participants must provide their own network-ready laptop pre-configured or configurable for Dynamic Host Configuration Protocol (DHCP) and have a standard Web browser installed. NCBI software (Cn3D, BLAST and Netblast) and databases will be installed on the laptops during the course. Participants are responsible for their own accommodations. There are a number of hotels in Bethesda and Rockville that are convenient to the NIH campus. Questions to Peter Cooper (cooper at ncbi.nlm.nih.gov) -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From c.plessy at mangoosta.net Wed Apr 28 11:49:30 2004 From: c.plessy at mangoosta.net (c.plessy at mangoosta.net) Date: Wed, 28 Apr 2004 17:49:30 +0200 Subject: [BiO BB] display DNA multiple alignements with gray levels Message-ID: <20040428154930.GA27373@shadow.dunkklar.org> Hello, I am looking for a free program that would process DNA multiple alignments, so that that conserved nucleotides would be on a black background, moderately conserved on a grey background according to the frequency of the most frequent nucleotide, and non conserved nucleotides on a white background. Boxshade does that kind of thing, but uses gray for similarity, which is not useful for DNA multiple alignments. () Ideally, the output would be in eps, or something else importable in Illustrator. I would be mega happy If somebody knew such a tool. Have a nice day, Charles -- CHARLES PLESSY, mailto:charles.plessy at ulp.u-strasbg.fr \ IGBMC, B.P.10142, 67404 Illkirch Cedex, France }(?> Tel : (33) [0]388 65 33 38; Fax (33) [0]388 65 32 01 / http://zfin.org/cgi-bin/webdriver?MIval=aa-persview.apg&OID=ZDB-PERS-010827-9 From deletto at unisa.it Wed Apr 28 12:00:55 2004 From: deletto at unisa.it (deletto at unisa.it) Date: Wed, 28 Apr 2004 18:00:55 +0200 Subject: [BiO BB] dna strider for PC Message-ID: <1083168055.408fd5378dea7@webmail.unisa.it> Hi all, I am looking for a free program like gene jokey or DNA strider for a win platform. Can anyone of you be so kind to tell me where I can purchase it. tkanks in advance, best regards davide ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From combiofriends at yahoo.com Fri Apr 23 07:40:30 2004 From: combiofriends at yahoo.com (com bio) Date: Fri, 23 Apr 2004 04:40:30 -0700 (PDT) Subject: [BiO BB] G++ Tutorial; Message-ID: <20040423114030.44022.qmail@web61102.mail.yahoo.com> Urgent!!! G++ Tutorial needed!! Thanx ===== ------------------------------------------- center for biotechnology anna university chennai-25 india __________________________________ Do you Yahoo!? Yahoo! Photos: High-quality 4x6 digital prints for 25? http://photos.yahoo.com/ph/print_splash From operon at www.ufsm.br Wed Apr 28 12:05:30 2004 From: operon at www.ufsm.br (Marcos de Carvalho) Date: Wed, 28 Apr 2004 13:05:30 -0300 Subject: [BiO BB] display DNA multiple alignements with gray levels In-Reply-To: <20040428154930.GA27373@shadow.dunkklar.org> References: <20040428154930.GA27373@shadow.dunkklar.org> Message-ID: Try GeneDoc: http://www.psc.edu/biomed/genedoc/ It can export the alignment to bitmap, metafile and RTF. Cheers Marcos On Wed, 28 Apr 2004 17:49:30 +0200, wrote: > Hello, > > I am looking for a free program that would process DNA > multiple alignments, so that that conserved nucleotides would be on a > black background, moderately conserved on a grey background according > to the frequency of the most frequent nucleotide, and non conserved > nucleotides on a white background. > > Boxshade does that kind of thing, but uses gray for > similarity, which is not useful for DNA multiple alignments. > () > > Ideally, the output would be in eps, or something else > importable in Illustrator. > > I would be mega happy If somebody knew such a tool. > > Have a nice day, > > Charles > From joel.dudley at asu.edu Wed Apr 28 12:29:53 2004 From: joel.dudley at asu.edu (Joel Dudley) Date: Wed, 28 Apr 2004 09:29:53 -0700 Subject: [BiO BB] dna strider for PC In-Reply-To: <1083168055.408fd5378dea7@webmail.unisa.it> References: <1083168055.408fd5378dea7@webmail.unisa.it> Message-ID: <47753453-9931-11D8-991E-000A95A682D6@asu.edu> What features are most important to you? On Apr 28, 2004, at 9:00 AM, deletto at unisa.it wrote: > > > Hi all, > I am looking for a free program like gene jokey or DNA strider for a > win platform. > Can anyone of you be so kind to tell me where I can purchase it. > > tkanks in advance, > best regards > > davide > > ------------------------------------------------- > This mail sent through IMP: http://horde.org/imp/ > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From deletto at unisa.it Wed Apr 28 12:51:39 2004 From: deletto at unisa.it (deletto at unisa.it) Date: Wed, 28 Apr 2004 18:51:39 +0200 Subject: [BiO BB] dna strider for PC In-Reply-To: <47753453-9931-11D8-991E-000A95A682D6@asu.edu> References: <1083168055.408fd5378dea7@webmail.unisa.it> <47753453-9931-11D8-991E-000A95A682D6@asu.edu> Message-ID: <1083171099.408fe11b9d5b0@webmail.unisa.it> A program I would like to have got must have any useful tool needed for a cloning plan (full map restriction, translation in both direction, oligo design, ecc.). Scrive Joel Dudley : > What features are most important to you? > > On Apr 28, 2004, at 9:00 AM, deletto at unisa.it wrote: > > > > > > > Hi all, > > I am looking for a free program like gene jokey or DNA strider for a > > win platform. > > Can anyone of you be so kind to tell me where I can purchase it. > > > > tkanks in advance, > > best regards > > > > davide > > > > ------------------------------------------------- > > This mail sent through IMP: http://horde.org/imp/ > > _______________________________________________ > > 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 > ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From mgollery at unr.edu Wed Apr 28 13:02:35 2004 From: mgollery at unr.edu (Martin Gollery) Date: Wed, 28 Apr 2004 10:02:35 -0700 Subject: [BiO BB] display DNA multiple alignements with gray levels In-Reply-To: <20040428154930.GA27373@shadow.dunkklar.org> References: <20040428154930.GA27373@shadow.dunkklar.org> Message-ID: <408FE3AB.6080402@unr.edu> Jalview has many color choices, but I have not seen the particular one that you are asking for. Still, you might take a look to see if it meets your needs at http://www.ebi.ac.uk/~michele/jalview/ Marty c.plessy at mangoosta.net wrote: > Hello, > > I am looking for a free program that would process DNA > multiple alignments, so that that conserved nucleotides would be on a > black background, moderately conserved on a grey background according > to the frequency of the most frequent nucleotide, and non conserved > nucleotides on a white background. > > Boxshade does that kind of thing, but uses gray for > similarity, which is not useful for DNA multiple alignments. > () > > Ideally, the output would be in eps, or something else > importable in Illustrator. > > I would be mega happy If somebody knew such a tool. > > Have a nice day, > > Charles > -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 'Don't worry that the world will end today- it's already tomorrow in Australia...' -Charles Schulz From pooja at igc.gulbenkian.pt Thu Apr 29 08:13:25 2004 From: pooja at igc.gulbenkian.pt (Pooja Jain) Date: Thu, 29 Apr 2004 13:13:25 +0100 (WEST) Subject: [BiO BB] dna strider for PC In-Reply-To: <1083171099.408fe11b9d5b0@webmail.unisa.it> References: <1083168055.408fd5378dea7@webmail.unisa.it> <47753453-9931-11D8-991E-000A95A682D6@asu.edu> <1083171099.408fe11b9d5b0@webmail.unisa.it> Message-ID: <57231.194.117.22.137.1083240805.squirrel@webmail.igc.gulbenkian.pt> May be of some of your interest: http://www.premierbiosoft.com/plasmid_maps/index.html > A program I would like to have got must have any useful tool needed for a > cloning > plan (full map restriction, translation in both direction, oligo design, > ecc.). > > > Scrive Joel Dudley : > >> What features are most important to you? >> >> On Apr 28, 2004, at 9:00 AM, deletto at unisa.it wrote: >> >> > >> > >> > Hi all, >> > I am looking for a free program like gene jokey or DNA strider for a >> > win platform. >> > Can anyone of you be so kind to tell me where I can purchase it. >> > >> > tkanks in advance, >> > best regards >> > >> > davide >> > >> > ------------------------------------------------- >> > This mail sent through IMP: http://horde.org/imp/ >> > _______________________________________________ >> > 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 >> > > > > > ------------------------------------------------- > This mail sent through IMP: http://horde.org/imp/ > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From xj_cai at yahoo.com Thu Apr 29 12:51:35 2004 From: xj_cai at yahoo.com (Richard Cai) Date: Thu, 29 Apr 2004 09:51:35 -0700 (PDT) Subject: [BiO BB] A qestion about BLOSUM matrices in Genedoc Message-ID: <20040429165135.33036.qmail@web60708.mail.yahoo.com> Hi there, I recetly used Genedoc to align about 150 protein sequences, and I found that there were numbers/characters at the bottom of some of the conserved residues, for example, p, a, 1, 6 or 7. I chose the BLOSUM62 matirx. What are these symbols for? My understanding was that these positive numbers calculated by BLOSUM suggested better local similarity. But why no numbers were shown for other conserved residues? How about "p" and "a". Do they stand for amino acid "Pro" or "Ala"? Thanks a lot! -Richard- Richard Cai Dept. of Cardiovascular Sciences University of Calgary, Canada __________________________________ Do you Yahoo!? Win a $20,000 Career Makeover at Yahoo! HotJobs http://hotjobs.sweepstakes.yahoo.com/careermakeover