From rabidstrikes at googlemail.com Sun Jan 6 09:57:00 2008 From: rabidstrikes at googlemail.com (Donnie Darko) Date: Sun, 6 Jan 2008 14:57:00 +0000 Subject: [BiO BB] Newbie question. Message-ID: Hi folks, Suppose I have a novel gene whose product is a DNA binding protein, how would I go about locating potential binding sites where this protein could bind? I'm only interested in finding sites for this specific protein and not a general scan of tfbs. I've extracted upstream sequences of genes that I'm interested in but I can't think of a way forward. Cheers and belated happy new year :-P From drjohn08318 at yahoo.com Sun Jan 6 19:20:30 2008 From: drjohn08318 at yahoo.com (drjohn08318 at yahoo.com) Date: Mon, 7 Jan 2008 00:20:30 +0000 Subject: [BiO BB] Newbie question. In-Reply-To: References: Message-ID: <1491812459-1199665228-cardhu_decombobulator_blackberry.rim.net-1034717091-@bxe134.bisx.prod.on.blackberry> Hi: Why not express the protein in E. coli, then carry out EMSA usong the recombinant protein to locate the binding sites on the DNA. John Sent via BlackBerry by AT&T -----Original Message----- From: "Donnie Darko" Date: Sun, 6 Jan 2008 14:57:00 To:bbb at bioinformatics.org Subject: [BiO BB] Newbie question. Hi folks, Suppose I have a novel gene whose product is a DNA binding protein, how would I go about locating potential binding sites where this protein could bind? I'm only interested in finding sites for this specific protein and not a general scan of tfbs. I've extracted upstream sequences of genes that I'm interested in but I can't think of a way forward. Cheers and belated happy new year :-P _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From drjohn08318 at yahoo.com Sun Jan 6 19:23:47 2008 From: drjohn08318 at yahoo.com (drjohn08318 at yahoo.com) Date: Mon, 7 Jan 2008 00:23:47 +0000 Subject: [BiO BB] Newbie question. In-Reply-To: <1491812459-1199665228-cardhu_blackberry.rim.net-copy_sent_folder-1288694011-@bxe134.bisx.prod.on.blackberry> References: <1491812459-1199665228-cardhu_blackberry.rim.net-copy_sent_folder-1288694011-@bxe134.bisx.prod.on.blackberry> Message-ID: <51335958-1199665423-cardhu_decombobulator_blackberry.rim.net-1916778053-@bxe134.bisx.prod.on.blackberry> Use the upstream seq. You've isolated along with the rec. protein with EMSA. Sent via BlackBerry by AT&T -----Original Message----- From: drjohn08318 at yahoo.com Date: Mon, 7 Jan 2008 00:20:30 To:"General Forum at Bioinformatics.Org" Subject: Re: [BiO BB] Newbie question. Hi: Why not express the protein in E. coli, then carry out EMSA usong the recombinant protein to locate the binding sites on the DNA. John Sent via BlackBerry by AT&T -----Original Message----- From: "Donnie Darko" Date: Sun, 6 Jan 2008 14:57:00 To:bbb at bioinformatics.org Subject: [BiO BB] Newbie question. Hi folks, Suppose I have a novel gene whose product is a DNA binding protein, how would I go about locating potential binding sites where this protein could bind? I'm only interested in finding sites for this specific protein and not a general scan of tfbs. I've extracted upstream sequences of genes that I'm interested in but I can't think of a way forward. Cheers and belated happy new year :-P _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From Lambert at Chatham.edu Sun Jan 6 19:55:33 2008 From: Lambert at Chatham.edu (Lambert, Lisa) Date: Sun, 6 Jan 2008 19:55:33 -0500 Subject: [BiO BB] Newbie question.[Scanned] References: Message-ID: <1C517CE6F2943C4EBD7A12FF4994274144E880@hickory.chatham.local> I haven't tested the procedure myself, but a paper in 2006 in BMC Bioinformatics described a "machine learning approach." See Yan et al. 7:262. Good luck! -----Original Message----- From: bbb-bounces at bioinformatics.org on behalf of Donnie Darko Sent: Sun 1/6/2008 9:57 AM To: bbb at bioinformatics.org Cc: Subject: [BiO BB] Newbie question.[Scanned] Hi folks, Suppose I have a novel gene whose product is a DNA binding protein, how would I go about locating potential binding sites where this protein could bind? I'm only interested in finding sites for this specific protein and not a general scan of tfbs. I've extracted upstream sequences of genes that I'm interested in but I can't think of a way forward. Cheers and belated happy new year :-P _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From wongls at comp.nus.edu.sg Sun Jan 6 23:39:40 2008 From: wongls at comp.nus.edu.sg (Limsoon Wong) Date: Mon, 7 Jan 2008 12:39:40 +0800 Subject: [BiO BB] RECOMB2008 - first call for participation Message-ID: <00f501c850e7$50f6fb10$76b81aac@comp.nus.edu.sg> FIRST CALL FOR PARTICIPATION: RECOMB 2008 30 MARCH - 2 APRIL 2008, SINGAPORE Dear Colleagues and Friends: We are hosting RECOMB2008 (12th International Conference on Research in Computational Molecular Biology) during 30 March - 2 April 2008 in Singapore. RECOMB is one of the best scientific forums on advances in computational biology and their applications in molecular biology and medicine. This year, the technical programme is expected to comprise (a) 7 keynote lectures from Edison Liu (Genome Institute of Singapore), Sang Yup Lee (KAIST), Andrei Lupas (Max Planck Institute for Developmental Biology), Howard Cedar (Hebrew University), Vivian Cheung (University of Pennsylvania), Temple F. Smith (Boston University), Suzanne Cory (Walter and Eliza Hall Institute of Medical Research); (b) 35 technical talks from accepted papers; and (c) 6 poster sessions. For further information about RECOMB2008: http://www.comp.nus.edu.sg/~recomb08 For registration information: http://www.comp.nus.edu.sg/~recomb08/registration.html The NUS School of Computing and the Office of Life Sciences are honoured to host RECOMB2008 at the NUS University Cultural Centre. We look forward to giving everyone a warm welcome to Singapore! Sincerely, Limsoon Wong National University of Singapore & Conference Chair, RECOMB2008 From maximilianh at gmail.com Tue Jan 8 05:50:52 2008 From: maximilianh at gmail.com (Maximilian Haeussler) Date: Tue, 8 Jan 2008 11:50:52 +0100 Subject: [BiO BB] Newbie question. In-Reply-To: References: Message-ID: <76f031ae0801080250j4ecc6a55hbc6b84925d448d52@mail.gmail.com> Do you know to which transcription factor class this proteins belongs to? They often bind to very similar / identical binding sites. If you scan for with Interpro and do some research on pubmed about this class (main classes: zinc finger, hemeobox, H2H, etc and their subclasses), while keeping an eye on Transfac and Jaspar, you should come up with an idea of the binding sites of your protein. You can still do EMSAs afterwards... But perhaps I've misunderstood the question... cheers, Max On 06/01/2008, Donnie Darko wrote: > > Hi folks, > > Suppose I have a novel gene whose product is a DNA binding protein, how > would I go about locating potential binding sites where this protein could > bind? I'm only interested in finding sites for this specific protein and > not > a general scan of tfbs. > > I've extracted upstream sequences of genes that I'm interested in but I > can't think of a way forward. > > Cheers and belated happy new year :-P > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Maximilian Haeussler, skype: maximilianhaeussler office: +33 1 69 82 41 29 From imitra at myezconnect.com Tue Jan 8 01:21:02 2008 From: imitra at myezconnect.com (Indranil Mitra) Date: Tue, 8 Jan 2008 11:51:02 +0530 Subject: [BiO BB] Newbie question.[Scanned] In-Reply-To: <1C517CE6F2943C4EBD7A12FF4994274144E880@hickory.chatham.local> References: <1C517CE6F2943C4EBD7A12FF4994274144E880@hickory.chatham.local> Message-ID: <013701c851be$a605e760$f211b620$@com> I am working on novel technologies of drug delivery and how we can simulate the same. If any body is working on the same or can give any more ideas I would be glad to discuss/collaborate. Thank u!!! Neil -----Original Message----- From: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] On Behalf Of Lambert, Lisa Sent: Monday, January 07, 2008 6:26 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Newbie question.[Scanned] I haven't tested the procedure myself, but a paper in 2006 in BMC Bioinformatics described a "machine learning approach." See Yan et al. 7:262. Good luck! -----Original Message----- From: bbb-bounces at bioinformatics.org on behalf of Donnie Darko Sent: Sun 1/6/2008 9:57 AM To: bbb at bioinformatics.org Cc: Subject: [BiO BB] Newbie question.[Scanned] Hi folks, Suppose I have a novel gene whose product is a DNA binding protein, how would I go about locating potential binding sites where this protein could bind? I'm only interested in finding sites for this specific protein and not a general scan of tfbs. I've extracted upstream sequences of genes that I'm interested in but I can't think of a way forward. Cheers and belated happy new year :-P _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From lichunjiang at sibs.ac.cn Tue Jan 8 01:40:14 2008 From: lichunjiang at sibs.ac.cn (lichunjiang) Date: Tue, 8 Jan 2008 14:40:14 +0800 (CST) Subject: [BiO BB] Newbie question.[Scanned] In-Reply-To: <1C517CE6F2943C4EBD7A12FF4994274144E880@hickory.chatham.local> References: <1C517CE6F2943C4EBD7A12FF4994274144E880@hickory.chatham.local> Message-ID: <1747.10.10.118.199.1199774414.squirrel@webmail.sibs.ac.cn> Hi, yeast one hybrid? will help in your case if you have no idea which gene will be the target gene. If you have some idea on the? target? gene,? Both? EMSA? John mentioned is a good choice. Good Luck! Lichun > I haven't tested the procedure myself, but a paper in 2006 in BMC > Bioinformatics described a "machine learning approach." See Yan et al. > 7:262. Good luck! > > -----Original Message----- > From: bbb-bounces at bioinformatics.org on behalf of Donnie Darko > Sent: Sun 1/6/2008 9:57 AM > To: bbb at bioinformatics.org > Cc: > Subject: [BiO BB] Newbie question.[Scanned] > > > > Hi folks, > > Suppose I have a novel gene whose product is a DNA binding protein, how > would I go about locating potential binding sites where this protein > could > bind? I'm only interested in finding sites for this specific protein and > not > a general scan of tfbs. > > I've extracted upstream sequences of genes that I'm interested in but I > can't think of a way forward. > > Cheers and belated happy new year :-P > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- lichunjiang at sibs.ac.cn Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences From drjohn08318 at yahoo.com Tue Jan 8 06:18:57 2008 From: drjohn08318 at yahoo.com (drjohn08318 at yahoo.com) Date: Tue, 8 Jan 2008 11:18:57 +0000 Subject: [BiO BB] Newbie question.[Scanned] In-Reply-To: <1C517CE6F2943C4EBD7A12FF4994274144E880@hickory.chatham.local> References: <1C517CE6F2943C4EBD7A12FF4994274144E880@hickory.chatham.local> Message-ID: <169871911-1199791133-cardhu_decombobulator_blackberry.rim.net-1494535418-@bxe134.bisx.prod.on.blackberry> Why not just do the experiment? Sent via BlackBerry by AT&T -----Original Message----- From: "Lambert, Lisa" Date: Sun, 6 Jan 2008 19:55:33 To:General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Newbie question.[Scanned] I haven't tested the procedure myself, but a paper in 2006 in BMC Bioinformatics described a "machine learning approach." See Yan et al. 7:262. Good luck! -----Original Message----- From: bbb-bounces at bioinformatics.org on behalf of Donnie Darko Sent: Sun 1/6/2008 9:57 AM To: bbb at bioinformatics.org Cc: Subject: [BiO BB] Newbie question.[Scanned] Hi folks, Suppose I have a novel gene whose product is a DNA binding protein, how would I go about locating potential binding sites where this protein could bind? I'm only interested in finding sites for this specific protein and not a general scan of tfbs. I've extracted upstream sequences of genes that I'm interested in but I can't think of a way forward. Cheers and belated happy new year :-P _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From rabidphage at gmail.com Tue Jan 8 10:04:14 2008 From: rabidphage at gmail.com (darx) Date: Tue, 8 Jan 2008 15:04:14 +0000 Subject: [BiO BB] Newbie question. In-Reply-To: References: Message-ID: <87c8630a0801080704h4d1624fahe6dbc1b021104e03@mail.gmail.com> Any ideas for an insilico methodology? On 06/01/2008, Donnie Darko wrote: > > Hi folks, > > Suppose I have a novel gene whose product is a DNA binding protein, how > would I go about locating potential binding sites where this protein could > bind? I'm only interested in finding sites for this specific protein and > not > a general scan of tfbs. > > I've extracted upstream sequences of genes that I'm interested in but I > can't think of a way forward. > > Cheers and belated happy new year :-P > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From rabidphage at gmail.com Wed Jan 9 06:22:34 2008 From: rabidphage at gmail.com (darx) Date: Wed, 9 Jan 2008 11:22:34 +0000 Subject: [BiO BB] Newbie question. In-Reply-To: <76f031ae0801080250j4ecc6a55hbc6b84925d448d52@mail.gmail.com> References: <76f031ae0801080250j4ecc6a55hbc6b84925d448d52@mail.gmail.com> Message-ID: <87c8630a0801090322w2a149c1fl76a9c85219d07d66@mail.gmail.com> No, you are spot on. So you mean that at best, we can narrow down to potential sites? Cheers. On 08/01/2008, Maximilian Haeussler wrote: > > Do you know to which transcription factor class this proteins belongs to? > They often bind to very similar / identical binding sites. > If you scan for with Interpro and do some research on pubmed about this > class (main classes: zinc finger, hemeobox, H2H, etc and their > subclasses), > while keeping an eye on Transfac and Jaspar, you should come up with an > idea > of the binding sites of your protein. > You can still do EMSAs afterwards... > > But perhaps I've misunderstood the question... > > cheers, > Max > > On 06/01/2008, Donnie Darko wrote: > > > > Hi folks, > > > > Suppose I have a novel gene whose product is a DNA binding protein, how > > would I go about locating potential binding sites where this protein > could > > bind? I'm only interested in finding sites for this specific protein and > > not > > a general scan of tfbs. > > > > I've extracted upstream sequences of genes that I'm interested in but I > > can't think of a way forward. > > > > Cheers and belated happy new year :-P > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > Maximilian Haeussler, > skype: maximilianhaeussler > office: +33 1 69 82 41 29 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From maria.mirto at unile.it Tue Jan 8 17:59:44 2008 From: maria.mirto at unile.it (Maria Mirto) Date: Tue, 8 Jan 2008 23:59:44 +0100 (CET) Subject: [BiO BB] CFP: (IEEE CBMS2008) 4rd Special Track on Healthgrid Computing - Applications to Biomedical Research and Healthcare Message-ID: <49551.83.184.80.67.1199833184.squirrel@webmail.dii.unile.it> Dear all, Please find attached the Call For Papers for: 21th IEEE Symposium on Computer-Based Medical Systems (CBMS) - Track on Healthgrid Computing - Applications to Biomedical Research and Healthcare. Jyv?skyl?, Finland, June 17-19, 2008 http://sara.unile.it/cbms2008/cfp.htm http://cbms2008.it.jyu.fi/ sponsored by IEEE Computer Society and ACM The main goal of the Conference Track is to discuss well-known and emerging bio data-intensive systems in the context of Grids, and to analyse technologies and methodologies useful to develop such systems in these environments. IMPORTANT DATES January 28, 2008 Paper submission due February 28, 2008 Notification of acceptance March 28, 2008 Final camera-ready paper due March 28, 2008 Pre-registration deadline Best regards, Maria Mirto. PhD Maria Mirto National Nanotechnology Laboratory (NNL/CNR-INFM) - www.nnl.it Euromediterranean Center for Climate Changes - https://www.cmcc.it SPACI Consortium - www.spaci.it Via per Monteroni - 73100 Lecce (Italy) email: maria.mirto at unile.it web: www.cact.unile.it/staff/mirto office: (+39) 0832.29.7304-8123 fax: (+39) 0832.29.8173 ******************************************************************************** We apologize if you received multiple copies of this Call for Papers. Please feel free to distribute it to those who might be interested. ******************************************************************************** -------------------------------------------------------------------------------- Special Track on Healthgrid Computing - Applications to Biomedical Research and Healthcare CBMS 2008: IEEE on Computer-Based Medical Systems (CBMS) Sponsored by the IEEE Computer Society June 17-19, 2008 Jyv?skyl?, Finland -------------------------------------------------------------------------------- CALL FOR PAPERS Bioinformatics, genomics, proteomics and medical image analysis are emerging methods in health care. Navigating between phenotype and genotype means that clinical data and genetic assessment are integrated in patient investigations. What is missing today is: ** full integration of these methods and technologies to enhance all phases of health care, including diagnosis, prognosis, etc.; **dissemination of such methods in clinical practice, whenever they are developed, deployed and maintained. Such a vision requires the design and implementation of computer tools, methods and platforms for seamless biomedical data and bioinformatics tools integration. Main issues to realize such a vision are: * Integration of multiple laboratories collecting genomics and post-genomics data, so that biology or bioinformatics research laboratories: o can continue to maintain their own biological, biomedical and computing resources autonomously; o can face effectively the growth of data they need to manage and process exploiting recent algorithms such as data mining taking into account that biomedical data are produced and stored continuously; * Provision of large computing power especially in areas such as: o The medical image processing community that is facing a growing need to analyse 2D, 3D, 4D images, to simulate medical treatments or surgeries (radiotherapy, plastic surgery, etc.), and to develop computer aided surgery; o Integration and access physicians to all of their patients medical data from their office. The Grid paradigm offers CPU and data handling capabilities, and allows users and laboratories to share their facilities (computing and data storage resources, instruments, software, knowledge, etc.) through high bandwidth networks between dynamically formed Virtual Organizations. Healthgrid computing can be a solution for the deployment of Grids in medical research centres, taking into account that it has been very limited, until now, for a number of reasons. Cost, both in terms of infrastructure and manpower, is a significant barrier. To face the complexity of novel, cooperative, distributed Health and Bioinformatics applications, new specialized Grid services have to be developed. Such services, integrated in a framework called Problem Solving Environment, allow deploying applications in a distributed way and carrying out complex ?in silico? simulations by composing single bio-applications into manageable workflows. In such a way Grids can be deployed to address the needs of the biomedical community. The main goal of the Conference Track is to discuss well-known and emerging bio data-intensive systems in the context of Grids, and to analyse technologies and methodologies useful to develop such systems in these environments. In particular, this Conference Track aims at offering a forum of discussion where young researchers and PhD students could present their research activities, either at an early or mature phase. TOPICS OF INTEREST include, but are not limited to: * Grid Infrastructures for Biomedical Data Analysis and Management * Problem Solving Environments for Biomedical and Bioinformatics Applications * Grid-based applications in the life sciences * Workflow application for complex analysis processes * High throughput for in-silico virtual screening * Grid Computing Infrastructures, Middleware and Tools for Healthcare * Grid Computing Biomedical Services * Collaboration Technologies * Databases and the Grid in the Biomedical Field * Extracting Knowledge from Biomedical Data Grids * Data Grids for Bioinformatics * Grid Architectures for Interactive Biomedical Applications * Grid Architectures and Solutions for Data-Intensive Biomedical Applications * Grid-based Biomedical Informatics Interoperability * Security in Biomedical Data Grids * Semantic Grids for Multimedia Biomedical Data * Ubiquitous Access to Grid-enabled Applications in Biomedicine * High-performance Computing for Data-Centric Biomedical Applications * Grid-based Visualization of Biomedical Data * Integration of Grid-enabled Applications into Clinical Practice IMPORTANT DATES January 28, 2008 Paper submission due February 28, 2008 Notification of acceptance March 28, 2008 Final camera-ready paper due March 28, 2008 Pre-registration deadline PAPER SUBMISSION AND PUBLICATION We invite original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Unlike workshops, where position papers and reports on initial and intended work are appropriate, papers selected for a Special Track should report on significant unpublished work suitable for publication as a conference paper. Each contribution must be prepared following the IEEE 2-column format and should not exceed the length of 6 (six) Letter-size pages and submitted electronically before the paper submission deadline. All submissions including special track papers will be done electronically via the CBMS web submission system, which will be open approximately one month before the deadline. Prospective authors should choose the ST5: Healthgrid Computing - Applications to Biomedical Research and Healthcare title when submitting a paper. All submissions will be peer-reviewed by at least three reviewers of the Special Track Program Committee. All accepted papers will be included in the conference proceedings published by IEEE CS Press. At least one author must pay the registration fee before March 28, 2008 for each accepted paper. Please consult http://cbms2008.it.jyu.fi for further information. TRACK CHAIRS - Giovanni Aloisio, Univ. of Salento, Lecce, Italy - Maria Mirto, Univ. of Salento, Lecce, Italy - Almerico Murli, Univ. of Naples, Italy - Tony Solomonides, University of the West of England, UK - Alfredo Tirado-Ramos Univ. Amsterdam, The Netherlands PROGRAM COMMITTEE (PROVISIONAL) - Dave S. Angulo, DePaul University, USA - Robert G. Belleman, University of Amsterdam, The Netherlands - Christian Barillot, Campus de Beaulieu, 35042 Rennes Cedex, France - Vincent Breton, CNRS/IN2P3, LPC Clermont-Ferrand, France - Marian Bubak, Institute of Computer Science, Poland - Mario Cannataro, University "Magna Gr?cia" of Catanzaro, Italy - Rita Casadio, Biocomputing Lab, University of Bologna, Italy - Sandro Fiore, CACT/NNL-INFM, University of Salento, Lecce, Italy - Andreas R. Formiconi, Dept. of Clinical Pathophysiology - University of Florence, Italy - Carole Goble, University of Manchester, UK - Concettina Guerra, University of Padova, Italy - Vicente Hernandez, Universidad Politecnica de Valencia - Dieter Kranzlmueller, Joh. Kepler University Linz, Austria - Giuliano Laccetti, University of Naples "Federico II", Italy - Yannick Legre, CNRS/IN2P3 France - Silvia D. Olabarriaga, University of Amsterdam, The Netherlands - Cecilia Saccone, ITB/CNR Institute of Biomedical Technologies of Bari, Italy - Fabrizio Silvestri, Information Science and Technology Institute (ISTI), CNR Pisa, Italy - Peter M.A. Sloot, University of Amsterdam, The Netherlands From nb at todublin.com Thu Jan 10 06:17:02 2008 From: nb at todublin.com (nb at todublin.com) Date: Thu, 10 Jan 2008 06:17:02 -0500 Subject: [BiO BB] Special Track on Bioinformatics and its Medical Applications - IEEE CBMS 2008 Message-ID: <380-22008141011172835@M2W006.mail2web.com> Special Track on Bioinformatics and its Medical Applications 21st IEEE International Symposium on COMPUTER-BASED MEDICAL SYSTEMS (IEEE CBMS 2008) Jyvaskyla, Finland June 17-19, 2008 CALL FOR PAPERS Major computational challenges have been raised in the post-genomic era. Novel computational methods and approaches are required to acquire, store, organize, archive, analyse and visualize the large amount of biological and biomedical data. The goal of the track is to share ideas related to bioinformatics challenge among biological, biomedical and computer scientists. Authors are invited to submit original papers addressing any computational biology issue. Papers are invited (but not limited) to the following key themes: * Biomedical Research * Functional Genomics * Evolution and Phylogenetics * Visualization * Data Mining in Bioinformatics * Protein Structure and Analysis * Microarray Analysis * Comparative Genomics * RNAi Analysis * Pattern Recognition * Sequence Alignment * Ontologies * Pathways, Networks, Systems Biology * Software Systems Unlike workshops, where position papers and reports on initial and intended work are appropriate, papers selected for a special track should report on significant unpublished work suitable for publication as a conference paper.More information about the symposium, registration fees, venue can be found here: http://cbms2008.it.jyu.fi IMPORTANT DATES January 28, 2008 - Submission of (6-page, maximum) paper March 1, 2008 - Notification of acceptance March 28, 2008 - Final camera-ready paper due March 28, 2008 - Pre-registration deadline June 17-19, 2008 - Symposium SUBMISSION PROCEDURES FOR PAPER No hardcopy submissions are being accepted. Electronic submissions of original technical research papers will only be accepted in PDF format. Use a maximum of six pages IEEE two-column format, including figures and references. All submissions will be done electronically via the CBMS 2008 web submission system. Select the track title " Bioinformatics and its Medical Applications", provide the information about the paper title, authors, keywords, and corresponding author's information (telephone, fax, mailing address, e-mail address). Please note that author names should not appear on the paper. Submit your manuscript no later than January 28, 2008. Authors will be notified of acceptance by March 1, 2008 after a review process by three independent experts. Each accepted paper to the Special Track on Bioinformatics and its Medical Applications will be published in the conference proceedings by IEEE CS Press, conditional upon the author's advance registration. Papers that were not accepted by the Program Committee of the track can be considered for publication as regular submissions by the General Program Committee of IEEE CBMS 2008. Please note that the format of IEEE CBMS 2008 proceedings will be the IEEE Computer Science Press 8.5x11-inch Two-Column Format. Submission is encouraged in this format. For more details please see the website of IEEE CBMS 2008: (http://cbms2008.it.jyu.fi/). TRACK CHAIR Nadia Bolshakova - Trinity College Dublin, Ireland TRACK PROGRAM COMMITTEE Nadia Bolshakova - Trinity College Dublin, Ireland Aedin Culhane - Dana-Farber Cancer Institute, USA Fernando Martin-Sanchez - Institute of Health "Carlos III", Spain Heather Ruskin - Dublin City University, Ireland Anton Zamolotskikh - Trinity College Dublin, Ireland Huiru Zheng - University of Ulster, Northern Ireland For further questions, please contact Nadia.Bolshakova at tcd.ie -------------------------------------------------------------------- mail2web.com ? Enhanced email for the mobile individual based on Microsoft? Exchange - http://link.mail2web.com/Personal/EnhancedEmail From narengr at gmail.com Thu Jan 10 06:31:17 2008 From: narengr at gmail.com (Narendran GR) Date: Thu, 10 Jan 2008 17:01:17 +0530 Subject: [BiO BB] LINES SINES MICROSATELLITES and TFOs In-Reply-To: References: Message-ID: Hi friends.... > I want to collect information on LINES SINES MICROSATELLITES and TFOs in > Human genome... > > Where can i find the information??? > Is there any information about them in NCBI??? Please help me with the same.... > -- Regards Narendran G R From oceanhu at 126.com Sat Jan 12 10:17:01 2008 From: oceanhu at 126.com (ocean) Date: Sat, 12 Jan 2008 23:17:01 +0800 (CST) Subject: [BiO BB] LINES SINES MICROSATELLITES and TFOs In-Reply-To: References: Message-ID: <16381612.686151200151021279.JavaMail.coremail@bj126app66.126.com> i think you can try ucsc, use the repeatmasker information of human the following is RepeatMasker (rmsk) Track Description Short interspersed nuclear elements (SINE), which include ALUs Long interspersed nuclear elements (LINE) Long terminal repeat elements (LTR), which include retroposons DNA repeat elements (DNA) Simple repeats (micro-satellites) Low complexity repeats Satellite repeats RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA) Other repeats, which includes class RC (Rolling Circle) Unknown ?2008-01-10?"Narendran GR" ??? Hi friends.... > I want to collect information on LINES SINES MICROSATELLITES and TFOs in > Human genome... > > Where can i find the information??? > Is there any information about them in NCBI??? Please help me with the same.... > -- Regards Narendran G R _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From sankar.achuth at gmail.com Sat Jan 12 02:39:00 2008 From: sankar.achuth at gmail.com (Dr. Achuthsankar S. Nair) Date: Sat, 12 Jan 2008 13:09:00 +0530 Subject: [BiO BB] Bioinformatica Indica 08 Message-ID: <2b168b460801112339q2f1cd784pd5d7f4605228a461@mail.gmail.com> *Dear fellow academic,* First of all, I apologize for any cross-postings. May I invite you to the inaugural ceremony of Bioinformatica Indica 08, An international Symposium on Computational Biology, Bioinformatics and Synthetic Biology. This is being organised under the auspices of the DBT Sponsored Bioinformatics Facility at the Centre for Bioinformatics, University of Kerala in collaboration with Sooryakiran Bioinformatics Pvt Ltd. Dr T Madhan Mohan, Advisor, DBT, Govt of India will inaugurate the event at 11AM on *17.1.2008* at the Centre for Bioinformatics, University of Kerala, and Key-note address will be delivered by Dr Todd Taylor, Riken Research Institute, Tokyo. On 18.1.2008, Dr Krishna Kant, Director, MIT, Govt of India will release the proceedings. I request your presence, support and good wishes for the event. Please find attached the schedule. Regards -- Dr Achuthsankar S Nair (Organising Secretary, Bioinformatica India 08) Hon. Director, Centre for Bioinformatics University of Kerala, Trivandrum 695581, INDIA Tel (O) 471-2412759 (R) 471-2542220 www.achu.keralauniversity.edu From jeff at bioinformatics.org Tue Jan 15 16:20:48 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 15 Jan 2008 16:20:48 -0500 Subject: [BiO BB] Perl & R courses for the first quarter of 2008 Message-ID: <478D23B0.7000400@bioinformatics.org> Greetings, Our latest course offerings are outlined below. They are being offered from January 21 through February 15. Perl for Biologists, Level 1; Jan 21-25 (http://wiki.bioinformatics.org/CS101A_Perl_for_Biologists,_Level_1) R for Biologists, Level 1; Jan 28-Feb 1 (http://wiki.bioinformatics.org/CS101B_R_for_Biologists,_Level_1) Perl for Biologists, Level 2; Feb 4-8 (http://wiki.bioinformatics.org/CS102A_Perl_for_Biologists,_Level_2) R for Biologists, Level 2; Feb 11-15 (http://wiki.bioinformatics.org/CS102B_R_for_Biologists,_Level_2) These online courses offer several advantages to scientists over books and self-paced learning: - In-depth courses with innovative, easy-to-understand materials (slides, scripts and datasets) - Live instruction is done online via streaming multimedia with shorter, distributed sessions and plenty of time for assignments. - Opportunities to ask questions and seek clarification - Recorded videos of lectures and materials, which are available indefinitely for attendees - Discussion forums for students and instructors to share expertise and information Discounts are available for those in non-profit organizations and those who are unemployed. Please check the description pages for details. Thank you, and please forward this information to others who may find this useful. Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From slathe at openhelix.com Tue Jan 15 17:22:42 2008 From: slathe at openhelix.com (Scott Lathe) Date: Tue, 15 Jan 2008 14:22:42 -0800 Subject: [BiO BB] Bioinformatics and Genomics Blog Message-ID: <10f601c857c5$26607a90$0301a8c0@openhelia1076a> OpenHelix announced a new blog (www.openhelix.com/blog) exclusively focused on genomics and bioinformatics resources. The blog will be an instrumental, interactive forum for researchers to learn more about the rapidly changing and growing genomics databases and resources. The blog, authored by OpenHelix scientists with extensive experience with genomics and biology and industry expertise in databases and resources, will have daily postings about genomics resources, genomics news and research, and training tips on how to effectively find and use bioinformatics resources. In addition to daily posts on relevant topics, the OpenHelix Blog on Genomics and Bioinformatics will include: "Tip of the Week": A short video outlining a tip on how to use a database to find something you need, some feature that you might not have noticed before, or introducing a new resource. "What's Your Problem?": An "open office hours" open thread post every Thursday where you can ask questions about what database might have the data you need, how to find specific types of information from a resource, and more. With nearly immediate answers to your questions, you'll have a virtual help desk on genomics and bioinformatics resources. "Guest Post": A periodic guest post from a scientist on an issue or topic that they feel is important to the community. Our guest posters will be people directly involved in developing and maintaining resources or genomics research. "Free Tutorials": You'll find links to extensive tutorial suites on a number of genomics and bioinformatics resources. The suites include 40-60 minute narrated self-run tutorials, slide sets, hand-outs and exercises. Visit the OpenHelix Blog at (www.openhelix.com/blog). Scott Lathe Chief Executive Officer OpenHelix, LLC www.openhelix.com 12600 SE 38th Street, Suite 230 Bellevue, WA 98006 (425) 401-1400 From a.menze at kws.com Wed Jan 16 04:29:13 2008 From: a.menze at kws.com (a.menze at kws.com) Date: Wed, 16 Jan 2008 10:29:13 +0100 Subject: [BiO BB] Antwort: Perl & R courses for the first quarter of 2008 In-Reply-To: <478D23B0.7000400@bioinformatics.org> Message-ID: Dear Jeff, I am very interested in the course 'Perl for Biologists Lev. 1". Unfortunately I have not time for the whole next week. Would you recommend to do the course anyhow, because I can follow it a bit later? Or would you recommend to do the course later (if there will be one this year?)? I'm working for KWS SAAT AG, a breeding and biotechnology company in germany. best regards so far. Andreas - Dr. Andreas Menze - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - F&E Informationsmanagement KWS SAAT AG, Grimsehlstra?e 31, 37555 Einbeck Tel. +49 (0) 5561/311-564 Fax +49 (0) 5561/311-744 E-Mail: a.menze at kws.com http://www.kws.com - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - "J.W. Bizzaro" An Gesendet von: BBB bbb-bounces at bioin Kopie formatics.org Thema [BiO BB] Perl & R courses for the 15.01.2008 22:59 first quarter of 2008 Bitte antworten an "General Forum at Bioinformatics.Or g" Greetings, Our latest course offerings are outlined below. They are being offered from January 21 through February 15. Perl for Biologists, Level 1; Jan 21-25 ( http://wiki.bioinformatics.org/CS101A_Perl_for_Biologists,_Level_1) R for Biologists, Level 1; Jan 28-Feb 1 ( http://wiki.bioinformatics.org/CS101B_R_for_Biologists,_Level_1) Perl for Biologists, Level 2; Feb 4-8 ( http://wiki.bioinformatics.org/CS102A_Perl_for_Biologists,_Level_2) R for Biologists, Level 2; Feb 11-15 ( http://wiki.bioinformatics.org/CS102B_R_for_Biologists,_Level_2) These online courses offer several advantages to scientists over books and self-paced learning: - In-depth courses with innovative, easy-to-understand materials (slides, scripts and datasets) - Live instruction is done online via streaming multimedia with shorter, distributed sessions and plenty of time for assignments. - Opportunities to ask questions and seek clarification - Recorded videos of lectures and materials, which are available indefinitely for attendees - Discussion forums for students and instructors to share expertise and information Discounts are available for those in non-profit organizations and those who are unemployed. Please check the description pages for details. Thank you, and please forward this information to others who may find this useful. Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From jeff at bioinformatics.org Wed Jan 16 16:44:37 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 16 Jan 2008 16:44:37 -0500 Subject: [BiO BB] Antwort: Perl & R courses for the first quarter of 2008 In-Reply-To: References: Message-ID: <478E7AC5.3010402@bioinformatics.org> For the list: Yes, it is possible to register for the Perl and R courses and then follow the recordings (of the live lectures) at a later time. And a number of people have done that. Jeff a.menze at kws.com wrote: > Dear Jeff, > > I am very interested in the course 'Perl for Biologists Lev. 1". > Unfortunately I have not time for the whole next week. Would you recommend > to do the course anyhow, because I can follow it a bit later? Or would you > recommend to do the course later (if there will be one this year?)? > > I'm working for KWS SAAT AG, a breeding and biotechnology company in > germany. > > best regards so far. > > Andreas -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From jeff at bioinformatics.org Sun Jan 27 19:46:32 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sun, 27 Jan 2008 19:46:32 -0500 Subject: [BiO BB] Bioinformatics.Org monthly newsletter Message-ID: <479D25E8.7090603@bioinformatics.org> Greetings, We're happy to announce our new monthly newsletter. In this publication, we will include the best of our various online forums and detail some of our internal (and external) activities. From time-to-time we?ll even include a featured article by a guest contributor. In this month's issue: - Editorial "Big plans for '08" - Project spotlight: Genezilla - Book review: Bioinformatics: Methods Express - Franklin Award Nominees - Job search highlight - Upcoming events Download as a PDF: http://www.bioinformatics.org/newsletter/v01-n01.pdf Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From dan.bolser at gmail.com Wed Jan 30 09:52:21 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 30 Jan 2008 15:52:21 +0100 Subject: [BiO BB] Bioinformatics and Genomics Blog In-Reply-To: <10f601c857c5$26607a90$0301a8c0@openhelia1076a> References: <10f601c857c5$26607a90$0301a8c0@openhelia1076a> Message-ID: <2c8757af0801300652x814edco13c2e5940148067e@mail.gmail.com> Sorry for the blatant spam but; I put a link to the 'OpenHelix' blog here; http://biodatabase.org/index.php/List_of_blogs_for_biologists If anyone else has a BioBlog to share, please feel free to add it to the list on http://BioDatabase.Org Cheers, Dan. P.S. Join the fun at irc://irc.freenode.net/#Bioinformatics (or via a web portal here; http://www.acm.jhu.edu/cgi-irc/irc.cgi?chan=%23bioinformatics). On 15/01/2008, Scott Lathe wrote: > OpenHelix announced a new blog (www.openhelix.com/blog) exclusively focused > on genomics and bioinformatics resources. The blog will be an instrumental, > interactive forum for researchers to learn more about the rapidly changing > and growing genomics databases and resources. > > The blog, authored by OpenHelix scientists with extensive experience with > genomics and biology and industry expertise in databases and resources, will > have daily postings about genomics resources, genomics news and research, > and training tips on how to effectively find and use bioinformatics > resources. > > In addition to daily posts on relevant topics, the OpenHelix Blog on > Genomics and Bioinformatics will include: > > "Tip of the Week": A short video outlining a tip on how to use a database > to find something you need, some feature that you might not have noticed > before, or introducing a new resource. > > "What's Your Problem?": An "open office hours" open thread post every > Thursday where you can ask questions about what database might have the data > you need, how to find specific types of information from a resource, and > more. With nearly immediate answers to your questions, you'll have a > virtual help desk on genomics and bioinformatics resources. > > "Guest Post": A periodic guest post from a scientist on an issue or topic > that they feel is important to the community. Our guest posters will be > people directly involved in developing and maintaining resources or genomics > research. > > "Free Tutorials": You'll find links to extensive tutorial suites on a number > of genomics and bioinformatics resources. The suites include 40-60 minute > narrated self-run tutorials, slide sets, hand-outs and exercises. > > Visit the OpenHelix Blog at (www.openhelix.com/blog). > > > > > > Scott Lathe > > Chief Executive Officer > > OpenHelix, LLC > > www.openhelix.com > > 12600 SE 38th Street, Suite 230 > > Bellevue, WA 98006 > > (425) 401-1400 > > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- hello