From Bertram.Fronhoefer at inf.tu-dresden.de Sun Feb 7 14:48:22 2010 From: Bertram.Fronhoefer at inf.tu-dresden.de (Bertram =?iso-8859-1?Q?Fronh=C3=B6fer?=) Date: Sun, 7 Feb 2010 20:48:22 +0100 Subject: [Bioclusters] Announcement: ICCL Summer School 2010 Message-ID: <20100207194817.GA28778@janeway.inf.tu-dresden.de> Call for Participation ICCL Summer School 2010 COGNITIVE SCIENCE, COMPUTATIONAL LOGIC AND CONNECTIONISM Technische Universit?t Dresden August 29 -- September 11, 2010 http://www.computational-logic.org/iccl-ss-2010 TOPIC The summer school will focus on the relationship between modern formal logic (including its use for automated reasoning and computation) and, on the other hand, the rationality and common sense underlying human reasoning. Traditionally, a huge gap is perceived between the symbolic representation of knowledge used in modern logic and the sub-symbolic representation considered dominant in human reasoning. Psychological experiments of the past even suggested that people often don't reason logically and, in general, that logic seems to play only a minor role in human reasoning. However, recently, new ways of explaining human reasoning seem to revive its relatedness to logic. Connectionist models even show a closer relation between formal reasoning and brain activities. For these reasons this summer school attempts to bring together researchers from various sides for an exchange of views. REGISTRATION If you want to attend the summer school, we'd prefer that you register by April 1, 2010. (See the online registration on the web page mentioned above.) For all who want to apply for a grant, this deadline is obligatory. After April 1, 2010, registration will be possible as long as there are vacant places. (Since we intend to restrict participation to about 60 people, in case of excessive demand, we will have to close the registration to the summer school.) People applying until April 1, 2010, and applying for a grant will be informed about respective decisions on grants at latest by end of April 2010. FEES We ask for a participation fee of 200 EUR. GRANTS A limited number of grants may be available, please indicate in your application if the only possibility for you to participate is via a grant. Applications for grants must include an estimate of travel costs (to be filled in the respective part of the online registration form). INTEGRATED WORKSHOP It will be possible for some participants to present their research work during a small workshop integrated in the summer school. If you would like to do so, please register by means of the online workshop registration form on the web page mentioned above: (The title of your proposed talk, and, in addition, an extended abstract or a full paper of at most 10 pages in postscript or pdf format must be submit by April 1, 2010.) A program committee consisting of the summer school lecturers will select among the submissions. Notification of acceptance of a talk at the integrated workshop will be at latest by end of April 2010. Please note that participation at the summer school is a prerequisite for participation at the workshop. COURSE PROGRAM COGNITION, LANGUAGE, AND NEURAL COMPUTATION. Jerome Feldman (ICSI, Bekeley, USA) NEURO-SYMBOLIC COGNITIVE REASONING Artur d'Avila Garcez (City University London, UK) CONNECTIONIST MODEL GENERATION Steffen H?lldobler (Technische Universit?t Dresden) COMPLEX NETWORKS OF MINDFUL ENTITIES. Lu?s Moniz Pereira (Universidade Nova de Lisboa, Portugal) COGNITIVE COMPLEXITY IN DEDUCTIVE REASONING Marco Ragni (University of Freiburg) COMPUTING EVENT STRUCTURES WITH LOGIC PROGRAMS Fritz Hamm / Fabian Schlotterbeck (Universit?t T?bingen) PEOPLE INVOLVED Chair of the ICCL Summer School 2010 Steffen H?lldobler Organizing Committee Julia Koppenhagen Bertram Fronh?fer NOTE ON FUNDING This Summer School is funded by the German Academic Exchange Service (DAAD) with financial means from the German Federal Foreign Office From gianluigi.zanetti at crs4.it Thu Feb 11 16:35:00 2010 From: gianluigi.zanetti at crs4.it (Gianluigi Zanetti) Date: Thu, 11 Feb 2010 22:35:00 +0100 Subject: [Bioclusters] Call for papers: 5th Workshop on Virtualization in High-Performance Cloud Computing Message-ID: <1265924100.7719.91.camel@pflip> [Apology for cross postings!] ================================================================= CALL FOR PAPERS 5th Workshop on Virtualization in High-Performance Cloud Computing VHPC'10 as part of Euro-Par 2010, Ischia-Naples, Italy ================================================================= Date: August 31, 2010 Euro-Par 2010: http://www.europar2010.org/ Workshop URL: http://vhpc.org SUBMISSION DEADLINE: Abstracts: March 31, 2010 Full Paper: June 17, 2010 Scope: Virtualization has become a common abstraction layer in modern data centers, enabling resource owners to manage complex infrastructure independently of their applications. Conjointly virtualization is becoming a driving technology for a manifold of industry grade IT services. Piloted by the Amazon Elastic Computing Cloud services, the cloud concept includes the notion of a separation between resource owners and users, adding services such as hosted application frameworks and queuing. Utilizing the same infrastructure, clouds carry significant potential for use in high-performance scientific computing. The ability of clouds to provide for requests and releases of vast computing resource dynamically and close to the marginal cost of providing the services is unprecedented in the history of scientific and commercial computing. Distributed computing concepts that leverage federated resource access are popular within the grid community, but have not seen previously desired deployed levels so far. Also, many of the scientific datacenters have not adopted virtualization or cloud concepts yet. This workshop aims to bring together industrial providers with the scientific community in order to foster discussion, collaboration and mutual exchange of knowledge and experience. The workshop will be one day in length, composed of 20 min paper presentations, each followed by 10 min discussion sections. Presentations may be accompanied by interactive demonstrations. It concludes with a 30 min panel discussion by presenters. TOPICS Topics include, but are not limited to, the following subjects: 1/ Local and cloud resources - Virtualization in cloud, cluster and grid HPC environments - VM cloud, cluster load distribution algorithms - Cloud, cluster and grid filesystems - QoS and and service level guarantees - Cloud programming models, APIs and databases - Software as a service (SaaS) - Cloud provisioning 2/ HPC and Data intensive computing on virtual resources - Virtualized I/O - VMMs and storage virtualization - MPI, PVM on virtual machines - High-performance network virtualization - High-speed interconnects - Hypervisor extensions - Tools for cluster and grid computing - Xen/other VMM cloud/cluster/grid tools - Raw device access from VMs 3/ Efficiency and flexibility through virtualization - Cloud reliability, fault-tolerance, and security - Cloud load balancing - VMs - power efficiency - Network architectures for VM-based environments - VMMs/Hypervisors - Hardware support for virtualization - Fault tolerant VM environments 4/ The price to pay - Workload characterizations for VM-based environments - Bottleneck management - Metering - VM-based cloud performance modeling - Cloud security, access control and data integrity - Performance management and tuning hosts and guest VMs - VMM performance tuning on various load types - Management of VM environments and clouds - Deployment of VM-based environments 5/ Examples to follow - Research and education use cases - Cloud use cases PAPER SUBMISSION Papers submitted to the workshop will be reviewed by at least two members of the program committee and external reviewers. Submissions should include abstract, key words, the e-mail address of the corresponding author, and must not exceed 10 pages, including tables and figures at a main font size no smaller than 11 point. Submission of a paper should be regarded as a commitment that, should the paper be accepted, at least one of the authors will register and attend the conference to present the work. Accepted papers will be published in the Springer LNCS series - the format must be according to the Springer LNCS Style. Initial submissions are in PDF, accepted papers will be requested to provided source files. Format Guidelines: http://www.springer.de/comp/lncs/authors.html Submission Link: http://edas.info/newPaper.php?c=8553 IMPORTANT DATES March 31 - Abstract submission due May 17 - Full paper submission July 14 - Acceptance notification August 3 - Camera-ready version due August 31 - September 3 - conference CHAIR Michael Alexander (chair), scaledinfra technologies GmbH, Austria Gianluigi Zanetti (co-chair), CRS4, Italy PROGRAM COMMITTEE Padmashree Apparao, Intel Corp., USA Volker Buege, University of Karlsruhe, Germany Roberto Canonico, University of Napoli Federico II, Italy Tommaso Cucinotta, Scuola Superiore Sant'Anna, Italy Werner Fischer, Thomas Krenn AG, Germany William Gardner, University of Guelph, Canada Wolfgang Gentzsch, DEISA, Max Planck Gesellschaft, Germany Derek Groen, UVA, The Netherlands Marcus Hardt, Forschungszentrum Karlsruhe, Germany Sverre Jarp, CERN, Switzerland Shantenu Jha, Louisiana State University, USA Xuxian Jiang, NC State, USA Kenji Kaneda, Google, Japan Yves Kemp, DESY Hamburg, Germany Ignacio Llorente, Universidad Complutense de Madrid, Spain Naoya Maruyama, Tokyo Institute of Technology, Japan Jean-Marc Menaud, Ecole des Mines de Nantes, France Anastassios Nano, National Technical University of Athens, Greece Oliver Oberst, Karlsruhe Institute of Technology, Germany Jose Renato Santos, HP Labs, USA Borja Sotomayor, University of Chicago, USA Deepak Singh, Amazon Webservices, USA Yoshio Turner, HP Labs, USA Kurt Tuschku, University of Vienna, Austria Lizhe Wang, Indiana University, USA DURATION: Workshop Duration is one day. GENERAL INFORMATION The workshop will be held as part of Euro-Par 2010, Ischia-Naples, Italy. Euro-Par 2010: http://www.europar2010.org/ From masulli at disi.unige.it Fri Feb 12 09:16:32 2010 From: masulli at disi.unige.it (Francesco Masulli) Date: Fri, 12 Feb 2010 15:16:32 +0100 Subject: [Bioclusters] School on COMPUTATIONAL INTELLIGENCE METHODS FOR DATA ANALYSIS IN ONCOLOGY BIOINFORMATICS Message-ID: <201002121516.32938.masulli@disi.unige.it> *Our apologies if you receive multiple copies of this announcement* CALL FOR PARTICIPATION ===================================================================== International Course on COMPUTATIONAL INTELLIGENCE METHODS FOR DATA ANALYSIS IN ONCOLOGY BIOINFORMATICS Vietri sul Mare, Salerno (Italy) - May 24-29, 2010 School Website: http://ciob10.disi.unige.it/ Joint course of the International School on Neural Nets "E.R. Caianiello" and of the Italian Network for Oncology Bioinformatics ===================================================================== * Please pass this Call for Participation to interested Colleagues * PURPOSE OF THE COURSE The Twentieth century is often referred as the Century of Biology, as evidenced by the extraordinary development of this scientific area who concluded that century with the great success of the Human Genome Project and the subsequent complete sequencing of human DNA. Currently we are at the beginning of the so-called Post-Genomic Era, characterized on one hand by the availability of a huge amount of Bioinformatics data (often in the public domain), and on the other hand by the need for new and efficient mathematical methods and algorithms capable of distill the information contained in these data. As a matter of fact the emphasis of research in Bioinformatics is shifting from the development of efficient storing and handling data methods, to the one of methods able to extract useful information from data. Computational Intelligence methodologies (that is, neural networks, evolutionary algorithms and fuzzy logic), partly inspired by natural systems, are a family of powerful methods for data analysis, able to transform the available heterogeneous data into biological knowledge. In recent years, these algorithms have been successfully applied in Bioinformatics to the solution of complex problems concerning signal analysis, classification, clustering, feature selection, and data mining and visualization. Nowadays, their applications encompass almost all areas of Bioinformatics. The course covers the applications of Computational Intelligence methods to the analysis of Bioinformatics data, with particular focus on applications in oncology. It is addressed to PhD students and researchers in Bioinformatics, Computer Science, Mathematics and Engineering, and includes: - theoretical lectures introducing the main aspects of Bioinformatics and Computational Intelligence methodologies; - lectures aimed to analyze some significant case studies of data analysis in oncology bioinformatics; - practical classes showing some relevant applications of Computational Intelligence methods to Bioinformatics data. LIST OF LECTURERS * Pierre Baldi, University of California, Irvine, CA, USA * Michele Ceccarelli, University of Sannio, Benevento, Italy * Raffaele Giancarlo, University of Palermo, Italy * Antonio Giordano, University of Siena, Italy and Director Sbarro Institute for Cancer research & Molecular Medicine, Philadelphia PA, USA * Paulo Lisboa, Liverpool John Moores University, Liverpool, UK * Francesco Masulli, University of Genoa, Italy & Temple University, PA, USA * Alfredo Petrosino, University Parthenope, Naples, Italy * Stefano Rovetta, University of Genoa, Italy * Giuseppe Russo, Temple University, Philadelphia, PA, USA * Roberto Tagliaferri, University of Salerno, Italy * Giorgio Valentini, University of Milan, Italy THE COURSE IS JOINTLY ORGANIZED BY International Institute for Advanced Scientific Studies (IIASS) Ettore Majorana Foundation and Center for Scientific Culture (EMFCSC) Italian Network for Oncology Bioinformatics (RNBIO) THE COURSE IS SPONSORED BY GNCS, Gruppo Nazionale per il Calcolo Scientifico INNS, International Neural Network Society S.I.G. on Bioinformatics SIREN, Italian Neural Networks Society DISI - University of Genoa, Italy University of Salerno, Italy APPLICATION Deadline: March 30-th 2010 (forms will be soon available at http://ciob10.disi.unige.it/application.html) The course is open to all motivated students and research scientists, of any nationality. Applicants with few experience should include a recommendation letter of their supervisor. Places are limited to a maximum of 60 participants in addition to the lecturers. These will be allocated on a first come, first served basis. FOR ANY FURTHER INFORMATION please visit the website http://ciob10.disi.unige.it ------------------------------------------------------- -- <--------------------------------------------------------------------> Dr. Francesco Masulli Associate Professor of Computer Science DISI - Dept. Computer and Information Sciences University of Genova - Via Dodecaneso 35, 16146 Genoa - ITALY tel. +39 010 353 6604 fax. +39 010 353 6699 and Adjunct Associate Professor Center for Biotechnology - College of Science and Technology -Temple University - Philadelphia - PA, USA. email: masulli at disi.unige.it skype id: masulli url: http://www.disi.unige.it/person/MasulliF <--------------------------------------------------------------------> From jpowell at takedacam.com Sun Feb 14 15:17:04 2010 From: jpowell at takedacam.com (Justin Powell) Date: Sun, 14 Feb 2010 20:17:04 +0000 Subject: [Bioclusters] BLAST speed mystery Message-ID: <9B26BA7041B65942A44DDC319519B6F4958B5BE921@cam-exch-01.takedacam.com> I have a couple of new fast servers with 24GB Ram and raid 0 15K SAS hard drives (2 in each server). I've run some tests using BLASTN on the est_mouse database which is 1.7GB. As one would expect the results when repeating identical BLASTS are fairly impressive as the database becomes effectively cached in RAM. However I have also been doing some timings of the first BLAST when no cached data is available. I've found that if I have the database on the local 15K drives the first blast takes about 45 seconds with my particular query sequence. However doing the identical BLAST but instead NFS mounting the databases off an old Apple G4 Xserver attached to an old Apple XRaid (which has 8 parallel ATA disks) the first blast runs in 30 seconds. (I ensure that there is no cached data in the NFS server too). Measuring straight throughput off disk using dd shows that the 15K disks can deliver 300MB/sec, whereas the NFS mounted Xserve/Xraid combination only delivers 70MB/second. So its not a problem with streaming throughput. Possibly its something to do with IOPS - I'm not sure what a decent benchmarking tool would be for that so I don't have figures currently - is BLAST particularly sensitive to this? Interestingly I have tried mounting the database via NFS from one of the new servers across to the other. When using an 8K block size (same as for the XServe NFS mount) I again get 45 seconds for the first BLAST iteration. Interestingly when I increase the block size to 32K the time for the first BLAST iteration drops down to 30 seconds, comparable to the Xserve case. I'm not sure what this means. Possibly the block size result implies some sort of read-ahead would improve things, but turning on read-ahead on the RAID controller did not improve the performance of the SAS disk based BLAST. Is the problem possibly IOPs limitation and solvable by putting more disks in the raid 0 array? The NFS block size results imply some sort of tuning should be possible even with the existing disks, but I'm not sure what to try. Anyone have any ideas? Justin From georgios at biotek.uio.no Sat Feb 20 15:12:47 2010 From: georgios at biotek.uio.no (Georgios Magklaras) Date: Sat, 20 Feb 2010 21:12:47 +0100 Subject: [Bioclusters] BLAST speed mystery In-Reply-To: <9B26BA7041B65942A44DDC319519B6F4958B5BE921@cam-exch-01.takedacam.com> References: <9B26BA7041B65942A44DDC319519B6F4958B5BE921@cam-exch-01.takedacam.com> Message-ID: <4B80423F.4030105@biotek.uio.no> In general, I tend to use iozone (http://www.iozone.org/) to measure IOPS before I put cluster nodes into production. I assume that your BLAST versions between the G4 and the new server (Linux?) environment are the same. Doing a vm_stat (on MACOSX) and vmstat (Linux) during the BLAST op (both precached and with est_mouse cached) can give you rough figures of disk throughput and buffer cache (yes, having more stripes is useful, but something else might be happening) However, it would be useful to give us software (OS/kernel version) and hardware (RAID controller) versions on your new servers. GM On 02/14/2010 09:17 PM, Justin Powell wrote: > I have a couple of new fast servers with 24GB Ram and raid 0 15K SAS hard drives (2 in each server). I've run some tests using BLASTN on the est_mouse database which is 1.7GB. As one would expect the results when repeating identical BLASTS are fairly impressive as the database becomes effectively cached in RAM. However I have also been doing some timings of the first BLAST when no cached data is available. I've found that if I have the database on the local 15K drives the first blast takes about 45 seconds with my particular query sequence. However doing the identical BLAST but instead NFS mounting the databases off an old Apple G4 Xserver attached to an old Apple XRaid (which has 8 parallel ATA disks) the first blast runs in 30 seconds. (I ensure that there is no cached data in the NFS server too). > > Measuring straight throughput off disk using dd shows that the 15K disks can deliver 300MB/sec, whereas the NFS mounted Xserve/Xraid combination only delivers 70MB/second. So its not a problem with streaming throughput. Possibly its something to do with IOPS - I'm not sure what a decent benchmarking tool would be for that so I don't have figures currently - is BLAST particularly sensitive to this? > > Interestingly I have tried mounting the database via NFS from one of the new servers across to the other. When using an 8K block size (same as for the XServe NFS mount) I again get 45 seconds for the first BLAST iteration. Interestingly when I increase the block size to 32K the time for the first BLAST iteration drops down to 30 seconds, comparable to the Xserve case. > > I'm not sure what this means. Possibly the block size result implies some sort of read-ahead would improve things, but turning on read-ahead on the RAID controller did not improve the performance of the SAS disk based BLAST. Is the problem possibly IOPs limitation and solvable by putting more disks in the raid 0 array? The NFS block size results imply some sort of tuning should be possible even with the existing disks, but I'm not sure what to try. > > Anyone have any ideas? > > Justin > > > > > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bioclusters > >