From pan from cs.gsu.edu Tue Dec 4 11:34:53 2007 From: pan from cs.gsu.edu (Yi Pan) Date: Tue Dec 4 12:24:27 2007 Subject: [Computational-biology] Call for Bioinformatics Book Projetcts In-Reply-To: References: Message-ID: Dear Colleagues: I and Prof. Albert Zomaya have served as Editors-in-Chief for the Wiley Book Series on Bioinformatics for over one year. So far, the book series has been very successful. The first book was published a few months ago, and eight books are either in press or in the planning stage. Please take a look at book series web page for more information: http://www.cs.gsu.edu/~cscyip/WileyBook.htm If you are interested in editing or authoring a book related to bioinformatics, please contact us. Below is the detailed information on the book series. For more information, go to the home page at http://www.cs.gsu.edu/~cscyip/WileyBook.htm -------------------------------------------------------------------------- Dr. Yi Pan Chair and Professor Department of Computer Science Georgia State University 34 Peachtree Street, Suite 1450 Atlanta, GA 30302-4110, USA email: pan@cs.gsu.edu Phone: (404) 413-5719 Fax: (404) 413-5717 http://www.cs.gsu.edu/pan -------------------------------------------------------------------------- Wiley Book Series on Bioinformatics: Computational Techniques and Engineering http://www.cs.gsu.edu/pan/WileyBook.htm AIMS: Research and development in bioinformatics and computational biology require the cooperation of specialists from the fields of biology, computer science, mathematics, statistics, physics, and such related sciences. It is the comprehensive application of mathematics (e.g., probability and graph theory), statistics, science (e.g., biochemistry), and computer science (e.g., computer algorithms and machine learning) to the understanding of living systems. Bioinformatics is fast emerging as an important discipline for academic research and industrial application. The large size of biological data sets, inherent complexity of biological problems and the ability to deal with error-prone data all result in special requirements such as large memory space and huge computation time. These challenges require computer scientists to rethink our traditional methods and algorithms and to adapt to the new research area. The objective of this book series is therefore to provide timely treatments of the different aspects of bioinformatics spanning theory, new and established techniques, enabling technologies and tools, and application domains. SCOPE: This series emphasizes the algorithmic, mathematical, statistical and computational methods that are central in bioinformatics and computational biology. Although the possible set of book topics is large, the following areas are particularly suitable for our book series (but not exhaustive): Bioinformatic databases Biomedical image processing (segmentation, registration, fusion) Bio-ontology and data mining Computational genomics Computational intelligence in bioinformatics Data visualisation DNA assembly, clustering, and mapping Drug design Gene expression and microarrays Gene identification and annotation Machine learning methods in bioinformatics Molecular evolution and phylogeny Molecular modeling and simulation Protein, RNA and DNA sequence analysis Parallel computing in bioinformatics Phylogeny reconstruction algorithms Protein and RNA structure prediction Sequence assembly, sequence search and alignment System biology WILEY BOOK SERIES ON BIOINFORMATICS Series Editors: Yi Pan and Albert Y. Zomaya Current Volumes Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications (Tony Hu & Yi Pan) Future Volumes ? Grid Computing for Bioinformatics (Talbi & Zomaya) ? Biological Networks Analysis (Bj?rn H. Junker & Falk Schreiber) ? Bioinformatics Algorithms: Techniques and Applications (Alexander Zelikovsky and Ion Mandoiu) ? Machine Learning in Bioinformatics (Yanqing Zhang and Jagath Rajapakse) ? Computational Approaches for Protein Function Prediction (Gaurav Pandey, Vipin Kumar, and Michael Steinbach) ? Classification Analysis of DNA Microarray Data (Leif Peterson) ? Elements of Computational Systems Biology (Lodhi and Muggleton) ? Biomolecular Networks - Computational Methods and Applications in Bioinformatics and Systems Biology (Luonan Chen, Rui-Sheng Wang, Xiang-Sun Zhang) Formatting Instructions: Below is the link to the guidelines for preparing the LaTex style for the manuscript. The link also contains guidelines for various other aspects of submitting the final manuscript. http://www.wiley.com/WileyCDA/Section/id-862.html If you are interested in writing or editing a book, you are encouraged to submit a proposal (see a proposal template at http://www.cs.gsu.edu/pan/wiley-proposal.doc) to one of the following Series Editors: Series Editors: Professor Yi Pan Chair Department of Computer Science Georgia State University Atlanta, GA 30303, USA Phone: (404) 413-5719 Fax: (404) 413-5717, Email: pan@cs.gsu.edu http://www.cs.gsu.edu/pan Professor Albert Y. Zomaya CISCO Systems Chair Professor School of Information Technologies Madsen Building, F09 The University of Sydney Sydney, NSW 2006 AUSTRALIA Tel. +61 2 9351 6442 Fax +61 2 9351 3838 Email: zomaya@it.usyd.edu.au http://www.it.usyd.edu.au/~zomaya Publisher Paul Petralia Senior Editor Wiley Interscience 111 River Street Hoboken, NJ 07030-5774 201-748-8784 ppetrali@wiley.com http://www.wiley.com/WileyCDA/ -- From javeda from cs.rpi.edu Mon Dec 10 12:25:38 2007 From: javeda from cs.rpi.edu (javeda@cs.rpi.edu) Date: Mon Dec 10 13:23:08 2007 Subject: [Computational-biology] workshop on Data Mining for Biomedical Informatics at SDM08 Message-ID: <2204.72.230.6.173.1197307538.squirrel@webmail.cs.rpi.edu> Dear Colleague: We would like to bring to your attention a workshop on Data Mining for Biomedical Informatics at the SIAM International Conference on Data Mining (SDM08), in Atlanta, Georgia, April 24 - 26, 2008. This is the second workshop in the series of Data Mining for Biomedical Informatics workshops held in conjunction with SDM. The URL for the workshop is: http://www.cs.rpi.edu/DMBIO08/ This workshop intends to provide a venue to facilitate the exchange of ideas between scientists in computer science, biology, mathematics and clinical research by bringing together researchers to discuss and present sources of data, research topics that may be addressed by such data, and data mining algorithms that may be used to analyze them. We encourage the submission of papers that use techniques from disciplines such as statistics, linear algebra, functional analysis, and signal processing, applied in some biomedical domain, as well as papers exposing rich sources of publicly available biomedical data that are of interest to the data mining community. Important Dates =============== Papers due: January 11, 2008 Notification of acceptance: January 20, 2008 Final version: February 4, 2008 Workshop: April 26, 2008 We are looking forward to receiving your submission. With best regards, Asif Javed, Publicity Chair javeda@cs.rpi.edu On behalf of the organizers Petros Drineas drinep@cs.rpi.edu Michael W. Mahoney mahoney@yahoo-inc.com Rui Kuang kuang@cs.umn.edu From ELPWang from ntu.edu.sg Tue Dec 11 07:20:32 2007 From: ELPWang from ntu.edu.sg (Lipo WANG) Date: Tue Dec 11 13:38:46 2007 Subject: [Computational-biology] ICNC'08-FSKD'08 Call for Papers: Jinan, China Message-ID: ** Our apologies if you receive multiple copies of this announcement * ---------------------------------------------------------------------- The 4th International Conference on Natural Computation (ICNC'08) The 5th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD'08) ---------------------------------------------------------------------- 25-27 August 2008, Jinan, China *** Submission Deadline: 25 March 2008 *** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ http://www.icnc-fskd2008.sdu.edu.cn ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Call for Papers, Invited Sessions & Sponsorship The joint ICNC'08-FSKD'08 will be held in Jinan, China. Jinan is the capital of Shandong Province, which is known for the home of Confucius, the Taishan Mountain, and the Baotu Spring. ICNC'08-FSKD'08 aims to provide an international forum for scientists and researchers to present the state of the art of intelligent methods inspired from nature, including biological, ecological, and physical systems, with applications to data mining, manufacturing, design, and more. It is an exciting and emerging interdisciplinary area in which a wide range of techniques and methods are being studied for dealing with large, complex, and dynamic problems. Previously, the joint conferences in 2005, 2006 and 2007 each attracted over 3000 submissions from more than 30 countries. All accepted papers will appear in conference proceedings published by the IEEE and will be indexed by both EI (Compendex) and ISTP. Further- more, extended versions of selected papers will be published in a special issue of Soft Computing: An International Journal (SCI indexed). For more information, visit the conference web page or email the secretariat at nc2008@sdu.edu.cn Join us at this major event in historic Jinan !!! ----- Lipo WANG School of Electrical and Electronic Engineering Nanyang Technological University Block S1, 50 Nanyang Avenue, Singapore 639798 http://www.ntu.edu.sg/home/elpwang Phone: +65 6790 6372? Fax +65 6793 3318 elpwang@ntu.edu.sg ? ? From prash from ruc.dk Tue Dec 11 12:06:29 2007 From: prash from ruc.dk (Prash) Date: Tue Dec 11 13:38:51 2007 Subject: [Computational-biology] NYC meeting: Travel fellowships! Message-ID: <1197392789.475ec395d4458@webmail.ruc.dk> NYC Computational Biology Student Meeting 2008 In collaboration with the Institute for Computational Biomedicine at Weill Cornell (ICB) and the Computational Biology Center at MSKCC (cBio) * Key dates: Tuesday 15th January 2008 -- Application submission deadline Friday 15th February 2008 -- Notification of acceptance Thursday 24 to Saturday 26 July -- The event starts * A Student Council-led meeting is organized from * Thursday 24 July to Saturday 26 July*, directly after the Toronto meeting (one whole day and two part days). The event will take place at the Institute for Computational Biomedicine at Weill Cornell (ICB). *The Aim* of this get together is to show students the variety of research possible in computational biology, the very broad opportunities that there are in academia and to serve as an introduction to some of the people leading this research. *The Speakers* in this meeting come mainly from two institutes: the Institute for Computational Biomedicine at Weill Cornell (ICB) and the Computational Biology Center at MSKCC (cBio) . The faculty have very wide and varied interests, ranging from retinal neuroscience to natural language parsing to cardiac electrophysiological dynamics, and from modelling of biological networks to investigating the robustness of the immune system, to transcriptional gene regulation. *The Schedule* of events will consist of a session of short (~20-30 mins) * presentations* by a number of the faculty, to highlight the types of research the faculty are involved in, followed by short presentations by the students themselves on their projects or interests (*the afternoon poster session*), and then a general gathering where the students can mix with the faculty, be shown around their labs, and be shown some of the fun facilities available, such the *immersive visualization environment*. *Funding and Eligibility:* Funding is available to support the travelling of students. This funding will be distributed to two classes: 1. *Travel stipend* of $1020 to attend ISMB Toronto and the NYC Student Meeting. Here only low and lower-middle income countries (according to World Bank statistics) are invited to apply. In addition to this, we will also fund a one way flight from Toronto to NYC or return Amtrak ticket, and accomodation and meals in NYC ($460). 2. *Funding to cover the attendance to the NYC Student Meeting 2008 *only**. This includes accomodation and meals ($260). All nationalities are encouraged to apply. 3. *Students with their own funding* are also encouraged to apply. *Note that the registration fee including meals and accomodation costs $260. * The student must attend ISMB-2008 at Toronto. The student must be an ISCB and Student Council memberin good standing. The ISCB membership requirement may be waived for students from low or lower middle countries if they show proof of belonging or having actively contributed to the development of a Regional Student Group. *Selection process:* - The number of places is limited to 20 students. - Write a paragraph about what lab you come from. - Write a paragraph about how/why you think you would benefit from being selected? - Send your application by email to no later than *15 January 2008*. - The Student Council Leadership will shortlist the best candidates and the final decision for approval will be decided by the Institute for Computational Biomedicine at Weill Medical College of Cornell University. - If by *15 February 2008* you do not hear from us you should assume your application was unsuccessful. - We would be most grateful if you would book your flight as soon as you are notified in the near future. Courtesy: Dr. Manuel Corpas Prashanth Suravajhala PhD Fellow http://ruc.dk/~prash/ 'Stop AIDS. Keep the Promise ? Leadership? ..AIDS awareness, theme for the year 2007 From hra from pixel.cviog.uga.edu Mon Dec 17 13:51:43 2007 From: hra from pixel.cviog.uga.edu (Hamid R. Arabnia) Date: Mon Dec 17 14:35:30 2007 Subject: [Computational-biology] Call For Papers: WORLDCOMP'08 - Computer Science and Engineering Conferences, USA, July 2008. Message-ID: <20071217185143.E68B422468F3@pixel.cviog.uga.edu> Dear Colleagues: Please disseminate the following announcement to those who may be interested. I would be grateful. I hope you have a wonderful Christmas. Thank you, Hamid ----- CALL FOR PAPERS and Call For Workshop Proposals WORLDCOMP'08 The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing July 14-17, 2008, Las Vegas, USA (composed of 25 Joint Conferences) ACADEMIC SPONSORS: Research labs at Harvard University, UCLA, Georgia Institute of Technology, University of Texas at Austin, University of Iowa, and others (see below). You are invited to submit a paper (and/or a proposal to organize a session/workshop). All accepted papers will be published in the respective conference proceedings. The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'08) is composed of the following 25 conferences (all will be held simultaneously, same location and dates: July 14-17, 2008, USA): o BIOCOMP'08: The 2008 International Conference on Bioinformatics and Computational Biology o CDES'08: The 2008 International Conference on Computer Design o CGVR'08: The 2008 International Conference on Computer Graphics and Virtual Reality o CIC'08: The 2008 International Conference on Communications in Computing o CSC'08: The 2008 International Conference on Scientific Computing o DMIN'08: The 2008 International Conference on Data Mining o EEE'08: The 2008 International Conference on e-Learning, e-Business, Enterprise Information Systems, and e-Government o ERSA'08: The 2008 International Conference on Engineering of Reconfigurable Systems and Algorithms o ESA'08: The 2008 International Conference on Embedded Systems and Applications o FCS'08: The 2008 International Conference on Foundations of Computer Science o FECS'08: The 2008 International Conference on Frontiers in Education: Computer Science and Computer Engineering o GCA'08: The 2008 International Conference on Grid Computing and Applications o GEM'08: The 2008 International Conference on Genetic and Evolutionary Methods o ICAI'08: The 2008 International Conference on Artificial Intelligence o ICOMP'08: The 2008 International Conference on Internet Computing o ICWN'08: The 2008 International Conference on Wireless Networks o IKE'08: The 2008 International Conference on Information and Knowledge Engineering o IPCV'08: The 2008 International Conference on Image Processing, Computer Vision, and Pattern Recognition o ITSL'08: The 2008 International Conference on Information Theory and Statistical Learning o MLMTA'08: The 2008 International Conference on Machine Learning; Models, Technologies and Applications o MSV'08: The 2008 International Conference on Modeling, Simulation and Visualization Methods o PDPTA'08: The 2008 International Conference on Parallel and Distributed Processing Techniques and Applications o SAM'08: The 2008 International Conference on Security and Management o SERP'08: The 2008 International Conference on Software Engineering Research and Practice o SWWS'08: The 2008 International Conference on Semantic Web and Web Services (a link to each conference's URL can be found at http://www.world-academy-of-science.org) General Co-Chair and Coordinator: H. R. Arabnia, PhD Professor, Computer Science Editor-in-Chief, The Journal of Supercomputing (Springer) Vice President, Int'l Society of Intelligent Biological Medicine The University of Georgia Department of Computer Science 415 Graduate Studies Research Center Athens, Georgia 30602-7404, USA Tel: (706) 542-3480 Fax: (706) 542-2966 E-mail: hra@cs.uga.edu PURPOSE / HISTORY: This set of joint conferences is the largest annual gathering of researchers in computer science, computer engineering and applied computing. Many of the 25 joint conferences in WORLDCOMP are the premier conferences for presentation of advances in their respective fields. We anticipate to have 2,600 or more attendees from over 80 countries participating in the 2008 joint conferences. The motivation is to assemble a spectrum of affiliated research conferences into a coordinated research meeting held in a common place at a common time. The main goal is to provide a forum for exchange of ideas in a number of research areas that interact. The model used to form these annual conferences facilitates communication among researchers from all over the world in different fields of computer science, computer engineering and applied computing. Both inward research (core areas of computer science and engineering) and outward research (multi-disciplinary, inter-disciplinary, and applications) will be covered during the conferences. WORLCOMP'08 will be composed of research presentations, keynote lectures, invited presentations, tutorials, panel discussions, and poster presentations. In recent past, keynote and/or tutorial speakers included: Prof. Michael J. Flynn (Stanford U.); Prof. John H. Holland (U. of Michigan, Ann Arbor); Prof. H. J. Siegel (Colorado State U.); Prof. Barry Vercoe (MIT); Prof. Ruzena Bajcsy (U. of California, Berkeley); Prof. David Cheriton (Stanford U.), Prof. A. K. Dunker (Indiana U. and Purdue U.); Prof. Jun Liu (Harvard U.); Dr. Jim Gettys (developer of X Window, ...); Dr. Chris Rowen (President and CEO, Tensilica, Inc.); and many other distinguished speakers. SUBMISSION OF PAPERS: Prospective authors are invited to submit their draft paper (about 5 to 7 pages - single space, font size of 10 to 12) to H. R. Arabnia by Feb. 25, 2008. email submissions in MS document or PDF formats are preferable (Fax or postal submissions are also fine.) All reasonable typesetting formats are acceptable (later, the authors of accepted papers will be asked to follow a particular typesetting format to prepare their papers for publication.) The length of the Camera-Ready papers (if accepted) will be limited to 7 (IEEE style) pages. Papers must not have been previously published or currently submitted for publication elsewhere. The first page of the draft paper should include: title of the paper, name, affiliation, postal address, email address, and telephone number for each author. The first page should also identify the name of the Contact Author and a maximum of 5 topical keywords that would best represent the content of the paper. Finally, the name of the conference that the paper is being submitted to must be stated on the first page. Papers will be evaluated for originality, significance, clarity, impact, and soundness. Each paper will be refereed by two experts in the field who are independent of the conference program committee. The referees' evaluations will then be reviewed by two members of the program committee who will recommend a decision to the chair of the track that the paper has been submitted to. The chair will make the final decision. Lastly, the Camera-Ready papers will be reviewed by one member of the program committee. PROPOSAL FOR ORGANIZING SESSIONS/WORKSHOPS: Each session will have at least 6 paper presentations from different authors (12 papers in the case of workshops). The session chairs will be responsible for all aspects of their sessions; including, soliciting papers, reviewing, selecting, ... The names of session chairs will appear as Associate Editors in the conference proceedings and on the cover of the books. Proposals to organize sessions should include the following information: name and address (+ email) of proposer, title of session, a 100-word description of the topic of the session, the name of the conference the session is submitted for consideration, and a short description on how the session will be advertised (in most cases, session proposers solicit papers from colleagues and researchers whose work is known to the session proposer). email your proposal to H. R. Arabnia (address is given above). We would like to receive the proposals by January 16, 2008. IMPORTANT DATES: Jan. 16, 2008: Proposals for organizing/chairing sessions/workshops Feb. 25, 2008: Submission of papers (about 5 to 7 pages) March 25, 2008: Notification of acceptance April 25, 2008: Camera-Ready papers and Registration due July 14-17, 2008: The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing (WORLDCOMP'08 - 25 joint conferences) MEMBERS OF PROGRAM AND ORGANIZING COMMITTEES: The Program Committee includes members of chapters of World Academy of Science (chapters: supercomputing; scientific computing; AI; imaging science; databases; simulation; software engineering; embedded systems; internet and web technologies; communications; computer security; and bioinformatics.) The Program Committee for individual conferences is currently being formed. Those interested in joining the Program Committee should email H. R. Arabnia (hra@cs.uga.edu) the following information: Name, affiliation and position, complete mailing address, email address, a short biography together with research interests and the name of the conference offering to help with. Many who have already joined the committees of individual tracks are renowned leaders, scholars, researchers, scientists and practitioners of the highest ranks; many are directors of research laboratories, fellows of various societies, heads/chairs of departments, deans and provosts. LOCATION OF CONFERENCES: The conferences will be held in the Monte Carlo hotel, Las Vegas, Nevada, USA (with any overflows at other near-by hotels). This is a mega hotel with excellent conference facilities and over 3,000 rooms. It is minutes from the airport with 24-hour shuttle service to and from the airport. This hotel has many recreational attractions, including: waterfalls, spa, pools, sunning decks, Easy River, wave pool, lighted tennis courts, health spa, nightly shows, a number of restaurants, ... The negotiated room rate for conference attendees is very reasonable. The hotel is within walking distance from most other attractions (recreational destinations, Golf courses, ...) SPONSORS: (this is a partial list) Academic Co-sponsors include: - Computational Biology and Functional Genomics Laboratory, Harvard University, Cambridge, Massachusetts, USA http://compbio.dfci.harvard.edu/ - Horvath Laboratory, University of California, Los Angeles (UCLA), USA http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/ - BioMedical Informatics & Bio-Imaging Laboratory, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA http://www.bio-miblab.org/ - Intelligent Data Exploration and Analysis Laboratory, University of Texas at Austin, Austin, Texas, USA http://www.ideal.ece.utexas.edu/ - Center for the Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, Georgia, USA http://opal.biology.gatech.edu/GeneMark/ - Hawkeye Radiology Informatics, Department of Radiology, College of Medicine, University of Iowa, Iowa, USA http://www.uiowa.edu/~hri/ - Medical Image HPC & Informatics Lab (MiHi Lab), University of Iowa, Iowa, USA http://www.uiowa.edu/mihpclab/ - The University of North Dakota, Grand Forks, North Dakota, USA http://www.und.edu - International Society of Intelligent Biological Medicine http://www.isibm.org/ - Institute for Informatics Problems of the Russian Academy of Sciences, Moscow, Russia. Other Co-sponsors: - NIIT Technologies http://www.niit-tech.com/ - High Performance Computing for Nanotechnology (HPCNano) http://www.hpcnano.org - International Technology Institute (ITI) http://www.itiworld.org/ - GridToday http://www.gridtoday.com/gridtoday.html - HPCwire http://www.hpcwire.com/ - Hodges' Health (H2CM), UK http://www.p-jones.demon.co.uk Future Announcements: If you do not wish to receive future announcements about this event, please send an email to hra@cs.uga.edu. From akhtung from gmail.com Mon Dec 17 20:56:49 2007 From: akhtung from gmail.com (akhtung@gmail.com) Date: Tue Dec 18 13:24:06 2007 Subject: [Computational-biology] Gemini: Free Software for Mining Gene Expression Data and Other High Dimensional Datasets Message-ID: <5aa058f6-6076-4cfa-8e68-e837e4410951@i12g2000prf.googlegroups.com> We are happy to announce the immediate availability of a set of gene expression mining tools that we have researched and developed over the past few years under the project "GEMINI: Gene Expression Mining". These tools include: CARPENTER: A closed pattern mining algorithm that is specially catered to mine tables with large number of columns (10,000-100,000) and small number of rows (200-1000) using a concept call row enumeration or samle enumeration under the gene expression context. TopkIRG: An efficient rule extraction and classifier construction algorithm that find top-k covering rules for each row/sample in the gene expression in order to construct a highly accurate rule-based classifier. RegMiner: A gene clustering algorithm that group coherent genes together even if they are shifted and scaled version of a common pattern. More details of GEMINI are available at http://nusdm.comp.nus.edu.sg/. To obtain the software, please click on "Resources" at the website. Anthony K. H. Tung School of Computing National University of Singapore(NUS) From margulis from gmail.com Sat Dec 22 11:56:34 2007 From: margulis from gmail.com (Michael Margulis) Date: Sat Dec 22 15:52:41 2007 Subject: [Computational-biology] Help needed in philogenetic tree alignment and sequences identification Message-ID: <7a2aa5bb0712220856v58578e7gf43b550363b8e590@mail.gmail.com> Hello! I need help in phylogenetic tree alignment: I've got many 16S rDNA sequences that were obtained from environmental samples. Sequences were aligned using ClustalW and phylogenetic tree was produced using neighbour joining method. The problem is that I don't know how to identify my sequences. Blast doesn't make very good method for identification and I don't know how to postion my tree and align it with the general philogenetic tree... Any help will be appreciated... Thanks in advance. Michael. From prash from ruc.dk Mon Dec 24 12:43:38 2007 From: prash from ruc.dk (Prash) Date: Mon Dec 24 13:01:47 2007 Subject: [Computational-biology] Re: Comp-bio Digest, Vol 31, Issue 6 In-Reply-To: <200712241703.lBOH3bL17846@net.bio.net> References: <200712241703.lBOH3bL17846@net.bio.net> Message-ID: <1198518218.476fefca42aa5@webmail.ruc.dk> Dear Michael, I think you could probbably use Tree viewer instead. It would provide you the sequences which you render as input. Infact, it does everything: http://iubio.bio.indiana.edu/treeapp/treeprint-form.html Secondly, incase, if you are not happy with above, you could use DIALIGN and evolutionary relationship software at http://bibiserv.techfak.uni-bielefeld.de/dialign/ I hope this helps Prash Prashanth Suravajhala PhD Fellow http://ruc.dk/~prash/ 'Stand up for what is right!? ~~ Gift the under-privileged children in new year. Please visit http://www.cry.org Quoting comp-bio-request@oat.bio.indiana.edu: Send Comp-bio mailing list submissions to comp-bio@net.bio.net To subscribe or unsubscribe via the World Wide Web, visit http://www.bio.net/biomail/listinfo/comp-bio or, via email, send a message with subject or body 'help' to comp-bio-request@net.bio.net You can reach the person managing the list at comp-bio-owner@net.bio.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Comp-bio digest..." Today's Topics: 1. Help needed in philogenetic tree alignment and sequences identification (Michael Margulis) ---------------------------------------------------------------------- Message: 1 Date: Sat, 22 Dec 2007 18:56:34 +0200 From: "Michael Margulis" Subject: [Computational-biology] Help needed in philogenetic tree alignment and sequences identification To: comp-bio@magpie.bio.indiana.edu Message-ID: <7a2aa5bb0712220856v58578e7gf43b550363b8e590@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hello! I need help in phylogenetic tree alignment: I've got many 16S rDNA sequences that were obtained from environmental samples. Sequences were aligned using ClustalW and phylogenetic tree was produced using neighbour joining method. The problem is that I don't know how to identify my sequences. Blast doesn't make very good method for identification and I don't know how to postion my tree and align it with the general philogenetic tree... Any help will be appreciated... Thanks in advance. Michael. ------------------------------ _______________________________________________ Comp-bio mailing list Comp-bio@net.bio.net http://www.bio.net/biomail/listinfo/comp-bio End of Comp-bio Digest, Vol 31, Issue 6 *************************************** From javeda from cs.rpi.edu Fri Dec 28 18:16:02 2007 From: javeda from cs.rpi.edu (javeda@cs.rpi.edu) Date: Sat Dec 29 12:48:18 2007 Subject: [Computational-biology] workshop on Data Mining for Biomedical Informatics at SDM08 In-Reply-To: <2204.72.230.6.173.1197307563.squirrel@webmail.cs.rpi.edu> References: <2204.72.230.6.173.1197307563.squirrel@webmail.cs.rpi.edu> Message-ID: <2391.72.230.6.173.1198883762.squirrel@webmail.cs.rpi.edu> Dear Colleague: We would like to bring to your attention a workshop on Data Mining for Biomedical Informatics at the SIAM International Conference on Data Mining (SDM08), in Atlanta, Georgia, April 24 - 26, 2008. This is the second workshop in the series of Data Mining for Biomedical Informatics workshops held in conjunction with SDM. The URL for the workshop is: http://www.cs.rpi.edu/DMBIO08/ This workshop intends to provide a venue to facilitate the exchange of ideas between scientists in computer science, biology, mathematics and clinical research by bringing together researchers to discuss and present sources of data, research topics that may be addressed by such data, and data mining algorithms that may be used to analyze them. We encourage the submission of papers that use techniques from disciplines such as statistics, linear algebra, functional analysis, and signal processing, applied in some biomedical domain, as well as papers exposing rich sources of publicly available biomedical data that are of interest to the data mining community. Important Dates =============== Papers due: January 11, 2008 Notification of acceptance: January 20, 2008 Final version: February 4, 2008 Workshop: April 26, 2008 We are looking forward to receiving your submission. With best regards, Asif Javed, Publicity Chair javeda@cs.rpi.edu On behalf of the organizers Petros Drineas drinep@cs.rpi.edu Michael W. Mahoney mahoney@yahoo-inc.com Rui Kuang kuang@cs.umn.edu