From goodb at interchange.ubc.ca Sun Nov 2 14:52:42 2008 From: goodb at interchange.ubc.ca (Benjamin Good) Date: Sun, 02 Nov 2008 11:52:42 -0800 Subject: [MOBY-l] jamboree part one deadline approaching Message-ID: <0908A6DA-7ED5-4857-927D-074A6F7827E2@interchange.ubc.ca> Hi everyone, First, thanks to those of you who have contributed to the first phase of the jamboree! Things are going well so far, but we are still in need of a few more volunteers. The deadline for participating in phase one is now set for November 10, so there is still time. If you haven't done so already, please do go to http://www.entitydescriber.org/ed/mobyjamboreelogin.html and follow the instructions there to participate. Here are a few reasons why you might want to spend some time with this: 1) you can help improve the annotation and thus the utility of biomoby services 2) you can contribute data that will help to inform the design of future interfaces for annotating and interacting with semantic web services 3) you can earn yourself $20 in Amazon gift certificates (if you are among the first 10 to finish annotating your services). We have only had 4 people complete this phase so far, so there are still 6 remaining to give out. best regards -Ben p.s. Please use firefox and one of the openid providers suggested on the login page. It does work in other browsers and with other providers sometimes, but we can't guarantee it at this point (definitely does not work in IE or Chrome). Also, to claim your award when you finish, please send me an email (as we aren't collecting email addresses in the login process). From gordonp at ucalgary.ca Mon Nov 17 11:34:41 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 17 Nov 2008 09:34:41 -0700 Subject: [MOBY-l] (CFP) Workshop MODERN COMPUTER TOOLS FOR THE BIOSCIENCES - MBIO'09, Shanghai Message-ID: <49219D21.9020309@ucalgary.ca> Forwarding as potentially of interest... ##### MODERN COMPUTER TOOLS FOR THE BIOSCIENCES - MBIO'09 Second Edition of the Modern BIO Workshop Organized at the International Conference CCGrid 2009 May 2009, Shanghai, China http://gbio-pbil.ibcp.fr/modernbio INTEGRATING BIOLOGICAL DATA AND TOOLS The Workshop on 'Modern computer tools for the biosciences' is a one- day event focussing on topics including the added-value of the Grid for Bioinformaticians, Biologists and Medical scientists, and the readiness of the Grid for these end-users The grid concept has already produced a variety of middlewares, components and platforms that are available around the World. But are facilites ready to be exploited by the true end-user? There are several challenging points that are still under development in the biosciences domain. The workshop will focus on some of these critical areas, notably, sharing biological data within distributed filesystems and database management systems, providing developers with programmatic usage of independant remote components such as web services or standard grid APIs, providing end- users with uniform grid access including ergonomic and efficient portals, and creating workflow on distributed resources, ... TOPICS Topics of special interest, but not limited to, are the following. High-throughput and high-performance Bioinformatics - Genomics - Proteomics - Molecular structure prediction, modelling and dynamic - System biology - Tools for NextGen sequencing Biological data management - Data integration, semantic and ontologies - Grid distributed filesystems - Distributed database management systems Bioinformatics tools integration - Programmatic usage of independant remote components: Web services, grid APIs - Web Portals and remote interface - Workflow enactor and interface - Parallel and distributed applications KEYDATES - Submission Deadline: 15th December 2008 - Notification: 15th January 2009 - Camera Ready deadline: 15th February 2009 PROCEEDINGS Authors are invited to submit a full length 6-page "original" research paper of double column text using single spaced 10 pt size type on 8.5x11 paper, as per IEEE manuscript guidelines. Paper submission instructions will be placed on the conference web-page. The proceedings will be published by the IEEE Computer Society Press, USA, and will be made available online through the IEEE Digital Library.. Submission implies the willingness of at least one of the authors to register and present the paper. Authors must register and submit their paper through the online submission system. SCIENTIFIC COMMITTEE CHAIR Dr Christophe Blanchet Institute of Biology and Chemistry of Proteins Dr Erik Bongcam-Rudloff The Linnaeus Centre for Bioinformatics Dr Rodrigo Lopez European Bioinformatics Institute PROGRAM COMMITTEE - Sadaf Alam, Oak Ridge National Laboratory, Tennessee, USA - Christophe Caron,INRA MIG, Jouy-en-Josas, France - Frederic Desprez, INRIA LIP ENS Lyon, Lyon, France - Andreas Gisel, CNR-ITB, Bari, Italy - Paul Gordon, University of Calgary, Canada - Patricia Hernandez, SIB, Geneva, Switzerland - Ralf Herwig, MPI-MG, Berlin, Germany - Richard Lavery, CNRS IBCP, Lyon, France - Ignacio Llorente, UCM, Madrid, Spain - Luciano Milanesi, CNR-ITB, Milano, Italy - Omer Rana, Cardiff University, Cardiff, UK -- Dr Christophe BLANCHET CNRS, France Institut de Biologie et Chimie des Proteines IBCP Christophe.Blanchet at ibcp.fr http://gbio-pbil.ibcp.fr/cblanchet From groscurt at mpiz-koeln.mpg.de Wed Nov 26 06:19:00 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 26 Nov 2008 12:19:00 +0100 Subject: [MOBY-l] New Mobyclient Message-ID: <492D30A4.1030005@mpiz-koeln.mpg.de> HI all, I just checked in a new moby client called FeatureClient. For those of you who know my Jabba application (http://bioinfo.mpiz-koeln.mpg.de/jabba) - basically its the client i use there. Its a usual moby client with some features: - Calling services with the concrete objects (like AminoAcidSequence) instead of the internal Moby API structures. This helps to understand the input and output handling better and to work with full data structures. - Service discovery based on service name or input/output definition (like return all services which consume an AGI locus code and return PMIDs). This enables to automatically detect group of services which fulfill identical or nearly the same tasks. - Parallelization for multiple service calls. The client enables you to call multiple services at the same time. - Using a timeout if the service does not return in that time. Limit the time you want to wait for a service to return by providing a maximal time in which the service shall give back a result. - Calling a service once with possible different inputs. If you want to call one (or more) service(s) with several inputs the client does help you. if you update your moby you will find more information and how to build/use it in the html documentation files and in the README file in moby-live/Java/src/support/featureClient For any concerns,comments or bugs please contact me Cheers Andreas From groscurt at mpiz-koeln.mpg.de Fri Nov 28 07:08:41 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 28 Nov 2008 13:08:41 +0100 Subject: [MOBY-l] Secure (Java) Biomoby web services Message-ID: <492FDF49.6000702@mpiz-koeln.mpg.de> Hi, I have committed changes in the jMoby code to allow people to access secure BioMoby web services (this update does not inflict the existing code). I also set up a tutorial if someone is interested in creating and/or calling a BioMoby secure web service (http://www.eu-sol.net/science/bioinformatics/tutorials/secure-biomoby-web-services). Unfortunately the current tutorial / implementation is only valid for Java. It would be great if a Perl person could have a look at it and contact me so that we can also set up the system for Perl (the system follows basically a usal SSL & HTTP authentication principle). If you find any errors or have any comments, questions please contact me. Thanks and cheers Andreas -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/