From jprudhomme from healthtech.com Thu Oct 1 14:41:03 2009 From: jprudhomme from healthtech.com (JPrudhomme) Date: Thu Oct 1 15:06:35 2009 Subject: [Bio-software] Adopting R&D Informatics Systems Message-ID: Hello, For those who may be interested in the above topic, my company, Cambridge Healthtech Institute, has organized a 3-day conference that will be held on February 3-5, 2009 in San Francisco, CA. For details and to register, go to http://www.tri-conference.com/ird.asp Please contact me with any questions. Best regards, James Prudhomme Cambridge Healthtech Institute Tel: 781-972-5486 jprudhomme@healthtech.com From bent from cbs.dtu.dk Wed Oct 7 14:41:53 2009 From: bent from cbs.dtu.dk (Bent Petersen) Date: Wed Oct 7 15:44:38 2009 Subject: [Bio-software] Secondary Structure and Surface Accessibility predictions easily made Message-ID: Hi Everyone, I have seen that many people are interested in Secondary Structure predictions, and also interested in the surface of proteins. I therefore want to bring your attention to a paper I have recently published, which has the title: A generic method for assignment of reliability scores applied to solvent accessibility predictions., which is freely available here: http://www.biomedcentral.com/1472-6807/9/51 It describes a new method, which is implemented in our freely available method: NetSurfP: http://www.cbs.dtu.dk/services/NetSurfP/ Basically it predicts the secondary structure of a protein, its surface accessibility and also the reliability of surface accessibility prediction in form of a z-score :-) I hope you will find it useful in your research :-) Best Regards, Bent Petersen, Ph.D Student, M.Sc. Center for Biological Sequence Analysis - CBS Department of Systems Biology, Technical University of Denmark. Bld. 208, DK-2800 Lyngby, Denmark From cmc2010cfp from szu.edu.cn Wed Oct 21 13:56:17 2009 From: cmc2010cfp from szu.edu.cn (CMC 2010) Date: Wed Oct 21 14:01:03 2009 Subject: [Bio-software] CMC 2010 Shenzhen China: Extended Deadline 15 November Message-ID: 2nd International Conference on Communications and Mobile Computing (CMC 2010) April 12-14, 2010 Shenzhen, China http://world-research-institutes.org/conferences/CMC/2010 http://world-research-institute.org/conferences/CMC/2010 Call for Papers & Expo CMC 2010 intends to be a global forum for researchers and engineers to present and discuss recent advances and new techniques in communications and mobile computing. We invite you to submit your original papers on the most recent results and technology trends to one of the 5 symposiums. Due to numerous requests, the submission deadline is extended to 15 November 2009. CMC 2010 conference proceedings will be published by the IEEE Computer Society's Conference Publishing Services (CPS) which will include the conference proceedings in the IEEE Xplore and submit to Ei Compendex and ISTP for indexing (CMC 2009 proceedings were already indexed in Ei). CMC 2010 is organized by the College of Information Engineering, Shenzhen University, China. In addition to research papers, CMC 2010 also seeks exhibitions of modern products and equipment for communications and mobile computing. Shenzhen, situated just across the border from Hong Kong, is a beautiful coastal city in southern China. It is a showcase of China¡¯s reforms and opening up to the rest of the world. In 27 years, Shenzhen has developed from a small fishing village into a modern city with a population of 12 million and a gross domestic product (GDP) ranking among the highest in China. Famous tourist attractions include Dapeng Fortress, Lotus Hill, Shennan Thoroughfare, and Yangtai Mountain. If you have any questions, please email us at cmc2010 szu.edu.cn or call +86 755 2653 6198 or +86 755 2653 5259. Important Dates: Paper Submission Deadline: 15 November 2009 Review Notification: 10 December 2009 Final Papers and Author Registration Deadline: 30 December 2009 *** Please forward to those who may be interested. *** (To unsubscribe, please reply with the email subject being "Unsubscribe bio-soft@iubio.bio.indiana.edu".) (Thanks and apologies) From bigr from live.nl Fri Oct 23 04:26:00 2009 From: bigr from live.nl (BIGR) Date: Fri Oct 23 10:19:24 2009 Subject: [Bio-software] Last Call for Papers: 2010 IEEE International Symposium on Biomedical Imaging (ISBI) Message-ID: <289aa454-1708-4bd2-b7e7-64a58bb8b5fb@e34g2000vbm.googlegroups.com> ************************** CALL FOR PAPERS ************************** 2010 IEEE International Symposium on Biomedical Imaging (ISBI) To be held 14-17 April 2010, Rotterdam, The Netherlands Four-page paper submission deadline: 2 November 2009 !!! NEW: Best Student Paper Awards (see below) See http://www.biomedicalimaging.org/ for details The IEEE International Symposium on Biomedical Imaging (ISBI) is the premier forum for the presentation of technological advances in theoretical and applied biomedical imaging. ISBI 2010 will be the seventh meeting in this series. The previous meetings have played a leading role in facilitating interaction between researchers in medical and biological imaging. The 2010 meeting will continue this tradition of fostering crossfertilization among different imaging communities and contributing to an integrative approach to biomedical imaging across all scales of observation. ISBI is a joint initiative of the IEEE Engineering in Medicine and Biology Society (EMBS) and the IEEE Signal Processing Society (SPS). The 2010 meeting will feature an opening morning of tutorials, followed by a scientific program of plenary talks, special sessions, and oral and poster presentations of peer-reviewed contributed papers. Confirmed plenaries: New clinical imaging technologies (Richard Ehman); Challenges in bioimage informatics (Jason Swedlow); Molecular imaging and applications (Clemens Lowik); Challenges in biomedical image analysis (Milan Sonka). Special Sessions: fMRI & DTI (Carl- Fredrik Westin); High-field clinical MRI (Andrew Webb); Fluorescence guided surgery (Vasilis Ntziachristos); Whole-body imaging and analysis (Faiza Admiraal); Histological and intravital microscopy (Tom Vercauteren); Ultrasound imaging and analysis (Hans Bosch); Multi- parameter biomedical optical imaging and analysis (Atam Dhawan and Metin Gurcan); Computer aided diagnosis (Nico Karssemeijer). Tutorials: Biomedical image registration (Gustavo Rohde and Graeme Penney); Optical microscopy and deconvolution (Hans van der Voort and Erik Manders); Ultrasound imaging and therapeutics (Elisa Konofagou and Constantin Coussios); Machine learning for biomedical image analysis (Marco Loog and David Tax). Contributed Program: High-quality papers are solicited describing original contributions to the mathematical, algorithmic, and computational aspects of biomedical imaging, from nano- to macro-scale. Topics of interest include image formation and reconstruction, computational and statistical image processing and analysis, dynamic imaging, visualization, image quality assessment, and physical, biological, and statistical modeling. Papers on molecular, cellular, anatomical, and functional imaging modalities and applications are welcomed. All accepted papers will be published in the proceedings of the symposium and will be available online through the IEEE Xplore database. Best Student Paper Awards: ISBI 2010 awards a prize for best student paper, as judged by a special award committee. At most three papers will be awarded a prize of 500 euro each. A paper is eligible if the primary author is a student at the time of paper submission and this person will indeed present the paper at the symposium if it is accepted. Important Dates: Deadline for submission of 4-page paper: November 2, 2009 Notification of acceptance/rejection: January 15, 2010 Submission of final accepted 4-page paper: February 15, 2010 Deadline for author registration: February 15, 2010 Deadline for early registration: March 1, 2010 ********************************************************************* From richard from flymine.org Fri Oct 23 09:01:53 2009 From: richard from flymine.org (Richard Smith) Date: Fri Oct 23 10:19:35 2009 Subject: [Bio-software] InterMine workshop, Cambridge UK Message-ID: <4AE1B751.8000805@flymine.org> Dear all, We still have some places available on an InterMine workshop we are running in Cambridge, UK on November 16th-17th. InterMine is a free, open source system for integrating biological data and querying it via a powerful webapp and query API. http://www.intermine.org InterMine is used to build FlyMine (http://www.flymine.org) and is now being deployed at the yeast, rat and zebrafish model organism databases. The course is intended for software developers and will give a complete introduction to setting up an InterMine system. It is free to attend, more details and sign up information are available here: http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html Please get in touch if you have any questions. Regards, Richard. From mehdi.mpour from gmail.com Fri Oct 23 13:56:48 2009 From: mehdi.mpour from gmail.com (MehdiM) Date: Fri Oct 23 14:14:31 2009 Subject: [Bio-software] GeneJockey Message-ID: Hi, Our group has used the GeneJockey for sequence analysis in the past. Now that the program is no longer supported, we need to be able to use the files generated by GeneJockey in other programs. How do I do that? I have copied the files to another computer and tried to change the file format by changing the extension (suffix) to others and tried to open with CLC workbench, but it failed. Converting to .txt generated strange figures and letters. Are we doomed to keep the old Mac with the old program for ever? Thanks for all the help!!! From pDOTpagel from wzw.tum.de Sat Oct 24 09:12:04 2009 From: pDOTpagel from wzw.tum.de (Philipp Pagel) Date: Sat Oct 24 10:57:57 2009 Subject: [Bio-software] Re: GeneJockey References: Message-ID: MehdiM wrote: > Hi, > Our group has used the GeneJockey for sequence analysis in the past. > Now that the program is no longer supported, we need to be able to use > the files generated by GeneJockey in other programs. How do I do that? > I have copied the files to another computer and tried to change the > file format by changing the extension (suffix) to others and tried to > open with CLC workbench, but it failed. Converting to .txt generated > strange figures and letters. Are we doomed to keep the old Mac with > the old program for ever? Well, changing the extension of a file does not magically convert it to another format. If you cannot find a programm that understands the files created by your old software you will have to open them with the old program and export to a more generally understood format (assuming that GeneJockey is able to export to other formats). cu Philipp -- Dr. Philipp Pagel Lehrstuhl f. Genomorientierte Bioinformatik Technische Universit?t M?nchen http://webclu.bio.wzw.tum.de/~pagel/