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News and Events
ViroLab MSc theses
Tuesday, 22 September 2009 08:36
Last Friday (18.09.2009) three new important Virolab MSc theses, supervised by Marian Bubak and Maciej Malawski have been successfully defended at AGH:
Bioinformatics Applications in the Virtual Laboratory, by Tomasz Jadczyk,
Environment for management of experiments on the grid, by Paweł Charkowski,
Security in Virtual Laboratory System, by Jan Meizner,
You will find them at:http://virolab.cyfronet.pl ---> go to "Master of Science Theses related to ViroLab"
The thesis by Tomasz Jadczyk is exceptional.
ViroLab demo at EGEE'09 conference
Tuesday, 22 September 2009 08:14
The Virtual Laboratory, which was successfully developed and deployed in the scope of ViroLab project, has its follow-up in the framework of PL-Grid project. You can see a demo which has been shown at EGEE'09 conference in Barcelona, an event of 21-25 September 2009, with a participation of more than 600 delegates(Youtube Link).
Virtual Laboratory to run on PL-Grid
Tuesday, 22 September 2009 08:07
Recently the steering body of the Polish E-Science infrastructure project PL-Grid (www.plgrid.pl) decided to choose GridSpace as one of the building blocks of the future computational infrastructure for science in Poland. PL-Grid tools are foreseen to be used by approximately seven hundreds of Polish scientists by the end of this three-year Project.
GridwiseTech released AdHoc Resource Management Toolkit
Monday, 31 August 2009 11:37
GridwiseTech released the first version of its new software toolkit named AdHoc - Resource Management which has been developed in the scope of the ViroLab project. Further information about the functionalities and application fields of AdHoc can be found at http://gridwisetech.com/adhoc.
Paper entitled "Your large data: query, process, share – in no time" has been presented on June 29 at 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB).More information on the ISMB conference:http://www.iscb.org/ismbeccb2009/
Press attention for the Computational HIV research results by Peter Sloot et al.
Paper on ViroLab Research in Philosophical Transactions of the Royal Society A
Tuesday, 02 June 2009 08:20
Paper on ViroLab research to appear in upcoming issue of Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Theme Issue ‘Crossing boundaries: computational science, e-Science and global e-Infrastructure II. Selected papers from the UK e-Science All Hands Meeting 2008’ compiled by P. V. Coveney and M. P. Atkinson: 13 July 2009; Vol. 367, No. 1898.
HIV decision support: from molecule to man P.M.A. Sloot, Peter V. Coveney, G. Ertaylan, V. Müller, C.A. Boucher, and M. Bubak Phil Trans R Soc A 2009;367 2691-2703.
We are pleased to announce that the FP7 VPH-NoE has secured an allocation of time on the DEISA infrastructure for use by VPH-I & ViroLab projects. Following on from an initial requirements gathering exercise conducted by NoE WP3 staff toward the end of 2008, an application to the DEISA (Distributed European Infrastructure for Supercomputing Applications) Virtual Communities Programme was made in February. The VPH Initiative has now been awarded an allocation of 2 million CPU hours for 2009, available for use by any VPH-I project and by ViroLab, to support research that requires access to high performance compute faculties. Continuing allocations should ensue for the lifetime of the VPH-I.
DEISA (http://www.desia.eu) operates a heterogeneous high performance computing (HPC) infrastructure currently formed by eleven European national supercomputing centres that are interconnected by a dedicated high performance network. The DEISA supercomputing resources incorporate several different platforms and operating systems: IBM AIX on Power5-6, IBM Linux on PowerPC, IBM BlueGene/P, SGI Linux on Itanium, Cray XT, and NEC vector systems. Since the inception of VPH- NoE, partners at UCL have been petitioning DEISA to establish a Virtual Communities Programme to underpin HPC requirements of long term (i.e. 3-5 year) EU funded projects, as previously DEISA project access and allocations had been decided in on national basis, with no reference to EU funded initiatives.
The DEISA VPH Virtual Community is being administered by VPH-NoE WP3 staff. The bulk of the allocation will be distributed amongst the VPH- I projects that previously responded to the NoE HPC requirements questionnaire, although there are many CPU hours still available for other projects in 2009. The NoE intends to manage the allocation through a system of 'community champions', designated individuals from each group of VPH/ViroLab DEISA users, who provide a central contact point between the NoE, DEISA and their respective projects. If you could make use of this allocation, we ask that you nominate an individual from your project to act as a DEISA contact point for the members of your project, and to work with DEISA staff to help deploy your simulation codes on their resources. The nominated individual should contact the NoE WP3 by emailing
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PhD Studentship at UCL: Development of molecular simulation methods for patient specific HIV drug treatment
Monday, 25 May 2009 11:54
The UCL Centre for Computational Science seeks to appoint a PhD student, funded by the UCLH/UCL Comprehensive Biomedical Research Centre (CBRC), to pursue an interdisciplinary, translational research project in the area of patient specific HIV drug treatment, using genotypic molecular simulation. The project will be supervised by Professor Peter Coveney (UCL Centre for Computational Science) and Professor Deenan Pillay (UCL Centre for Infection), and will involve:
Analysis/development of current and alternative methods for molecular binding affinity calculation, for HIV enzymes and their anti- retroviral ligands
Development of a HIV-1 integrase/inhibitor binding affinity calculation system
Establishment of links with experimentalists to facilitate validation of findings from simulations and provide information on novel mutations and anti-retroviral mutational pathways to be investigated
Incorporation of new/improved HIV drug/enzyme simulations into patient-specific a treatment evaluation and decision support pipeline.
The post requires a candidate with a strong ability in physical/ computational science, an affinity for and interest in biological sciences, and who is willing to integrate and progress their knowledge across these disciplines.
Students will register during the 2009/10 academic year for a three year full-time MPhil/PhD degree, with an expected commencement date of 1st October 2009. Funding includes UK/EU tuition fees and a tax-free stipend equivalent to the MRC rate of £15,100 (in 2008/9). The position is available to both UK and EU applicants who must have, or expect to obtain, a very good first degree in a relevant subject (Chemistry, Physics or Virology, Computer Science) as a minimum qualification.
To apply, please send a covering letter, application form and CV by email to Professor Peter Coveney (p.v.coveney(at)ucl.ac.uk), including the contact details of at least two academic referees. Application forms and details of the admissions process are available online at: http://www.ucl.ac.uk/prospective-students/graduate-study/applicationadmission/downloadable-applications.
Informal inquiries may be made to Professor Coveney (p.v.coveney(at)ucl.ac.uk).
Simplifying grid computing: Application Hosting Environment V2.0 released by partner UCL
Thursday, 30 April 2009 08:51
We are pleased to announce the release of AHE 2.0, a lightweight middleware tool designed to facilitate scientific investigations using grid resources. AHE provides scientists with application specific services to utilize grid resources in a quick, transparent manner with the scientific objective as the main driver of the activity.
Version 2.0 of the AHE brings us a step closer to making use of HPC grids fully transparent to the end user, by building upon the original AHE services and integrating them with other useful middleware tools, with the focus constantly on simplifying grid and HPC use. Support is included for creating and launching advanced co-reservations of time on machines using HARC, facilitating the launch of computational steering jobs using the RealityGrid steering library, and launching cross-site simulations using MPIg. AHE can launch applications on grid resources running a variety of back end middleware, including Globus GRAM 4 and GridSAM, as well as the Unicore 6 OGSA BES interface. This means that the AHE provides a single interface to a wide range of federated resources provided by different grid projects.
Both client and server can be obtained from the AHE download page. The server is supplied as a preconfigured VirtualBox virtual machine image. For more information and to download the software, visit: http://www.realitygrid.org/AHE
The key aspect of AHE V2.0 is the adoption of a novel approach to simplifying the use of grid computing: grid application virtualisation. The motivation behind this approach is to simplify grid use: a layer of user friendly Web services have been placed between the user and the grid, which hides much of its complexity and provides a virtual, ‘abstracted’ interface for any given scientific application in deployment. In practical terms this means that AHE services take care of the actual process of launching an application, manages the staging of input and output files associated with a simulation, sends files needed to run a simulation to their required destination, and retrieves simulation output to locations easily accessible by the user, for further interpretation.
AHE allows for scientific applications to be easily exposed as Web services, and run on a variety of different resources, from high performance grid machines in different continents, to local clusters and even desktop workstations hosted within a single administrative domain. The AHE does not mandate any required features for the applications it hosts, meaning that legacy community applications, often with many years of development investment, can be easily deployed on a grid and hosted in AHE without further modification.
ViroLab chapter in Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare
Wednesday, 25 March 2009 16:29
A chapter of the ViroLab Virtual Laboratory is included in the Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare. This book has recently entered its production stage and a release date is foreseen in May, 2009. For more information please visit http://www.igi-global.com/reference/details.asp?id=34292
ViroLab research presentation at the HealthGrid 2009 conference
Wednesday, 25 March 2009 03:32
Paper entitled "A Collaborative Environment Allowing Clinical Investigations on Integrated Biomedical Databases" has been accepted for presentation and publication at the HealthGrid 2009 conference held on June, 27 - July, 1 in Berlin, Germany. More information on the HealthGrid 2009 conference:http://berlin2009.healthgrid.org/
ViroLab news item in the eHealth Monthly Focus of the European Commission
ViroLab will be present at SC08 conference Nov.15-21,2008,Austin,Texas,USA
Wednesday, 12 November 2008 14:56
Between 18 and 20.11.2008 our partner GridwiseTech will be an exhibitor at SC08 in Austin, Texas, which is USA’s leading event for High Performance Computing. Virolab demo, including Virtual Organizations Management GUI Community Technology Preview, will be one of showcased products and services.
More information on the SC08 conference:http://sc08.supercomputing.org/
SKG 2008 conference - Dec. 4-6, 2008, Beijing, China
Tuesday, 04 November 2008 14:43
Research paper entitled "An Ontology Model for Execution Records of Grid Scientific Applications" has been accepted for presentation at the SKG 2008 conference held on next December(3-5) in Beijing, China.
More information on the SKG 2008 conference: http://www.culturegrid.net/SKG2008/
ViroLab presence at ICT-BIO 2008
Thursday, 30 October 2008 14:16
Members of the ViroLab team attended the ICT-BIO 2008 conference in Brussels last week (23-24 October), which provided an insight into existing and future prospects on integrative research for complex human diseases at European and international levels.
A presentation and a demonstration were given by ViroLab during the event to show features of the Virtual Laboratory. The presentation and demo movies are now available online.
You may also find more demo movies on the dedicated Virtual Laboratory Website.
Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases - Peter Coveney
Tuesday, 14 October 2008 07:55
S. Kashif Sadiq, David Wright, Simon J. Watson, Stefan J. Zasada, Ileana Stoica, and Peter V. Coveney. Centre for Computational Science, Department of Chemistry, University College London,London, WC1H 0AJ, U.K. Received March 14, 2008
The DEISA consortium has awarded the ViroLab project as a European life science project 1.5 mio cpu-core-hours to be consumed for challenging projects in 2008.
DEISA2 and ViroLab agree to closely collaborate for the advancement of science through high performance computing. The specific aim is to strengthen the European Life Science Community engaged in the ViroLab project through support of its HPC needs. The agreement is part of the DEISA mission for global virtual community support in an upcoming European HPC ecosystem.
Details of the collaboration are
The provision of HPC resources by DEISA for challenging compute projects from ViroLab;
Feedback of ViroLab about experiences and scientific results obtained to allow DEISA to measure its impact;
Technical collaboration to facilitate usage of DEISA resources for Life Sciences;
DEISA and ViroLab plan to highlight the collaboration in presentations emphasizing the synergy between European research and infrastructure projects; for major scientific results obtained with the help of DEISA joint press releases are planned.
Enterprise Information Systems presentation
Thursday, 19 June 2008 06:48
The presentation given by Matthias Assel at the International Conference on Enterprise Information Systems (ICEIS 2008) last week is now available online.
Has HIV evolved to induce immune pathogenesis?
Tuesday, 27 May 2008 20:51
Upcoming publication:
Bartha, I., Simon, P. & V. Müller (2008) Has HIV evolved to induce immune pathogenesis? Trends in Immunology (in press)
10th International Conference on Enterprise Information Systems (ICEIS 2008)
Tuesday, 18 March 2008 21:25
Research paper entitled "Data Management and Integration within Collaborative Working Environments" has been accepted for presentation at the next June (13-16) in Barcelona, Spain.
The work will be presented by Matthias Assel (USTUTT-HLRS, Partner 3). The presentation will be posted on the website shortly after the conference.
More information on the ICEIS 2008 conference: http://www.iceis.org/index.htm
21th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2008)
Tuesday, 18 March 2008 21:23
A paper on the "ViroLab Virtual Laboratory" has been accepted for presentation at the CBMS 2008 meeting held on June 17-19, 2008 at University of Jyväskylä, Finland. More information on the CBMS 2008 conference: http://cbms2008.it.jyu.fi/
ViroLab Virtual Laboratory chapter in the Proceedings of CGW'07
Tuesday, 18 March 2008 20:56
The Cracow Grid Workshop is organized yearly to support the community of researchers, developers, practitioners as well as current and potential grid users who work in the fascinating field of grid technologies and their applications.
Virtual Laboratory will be presented at the KU KDM'08
Thursday, 28 February 2008 01:00
The KU KDM'08 (The Conference of the High Performance Computers' Users - http://www.cyfronet.pl/kdm08/program.html) will take place in Zakopane, Poland, on 6-7 March 2008. The Virtual Laboratory will be presented at this event in two ways: through poster titled "Virtual Laboratory for the Development and Execution of Collaborative Applications" and through brochure titled "ViroLab Virtual Laboratory". The brochure which will be distributed among the participants of the event.
Interaction and cooperation activities between EuResist and ViroLab projects in Bonn, January 29, 2008
Wednesday, 27 February 2008 16:49
We would like to draw your attention to a cooperative meeting between project members of the ViroLab and EuResist projects on "Interaction and cooperation activities between EuResist and ViroLab projects".
The meeting will be held at the Gustav Stresemann Institut in Bonn. Representatives from both E- Health projects will discuss potential collaborations and data sharing opportunties.
Virtual Human In HIV Drug Simulation - Peter Coveney
Wednesday, 27 February 2008 15:17
ScienceDaily (Feb. 2, 2008) — The combined supercomputing power of the UK and US ‘national grids’ has enabled UCL (University College London) scientists to simulate the efficacy of an HIV drug in blocking a key protein used by the lethal virus. The method – an early example of the Virtual Physiological Human in action – could one day be used to tailor personal drug treatments, for example for HIV patients developing resistance to their drugs.
The 21th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2008) will be held on June 17-19, 2008 at University of Jyväskylä, Finland. CBMS 2008 is held in cooperation with the Association for Computing Machinery (ACM) Special Interest Group on Applied Computing (SIGAPP), and is sponsored by the IEEE Computer Society (Technical Committee on Computational Medicine, TCCM) and the Department of Computer Science and Information Systems, University of Jyväskylä.
CBMS 2008 is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2008 will consist of invited keynote talks given by leading scientists in the field, and regular and special tracks sessions that cover a broad array of issues which relate computing to medicine.
A special track will be dedicated to Healthgrid Computing - Applications to Biomedical Research and Healthcare.
During the last decade, CBMS symposiums were held in different countries and locations including Maribor, Slovenia (2007, 2002, and 1997), Salt Lake City, USA (2006), Dublin (2005), Bethesda MD, USA (2004 and 2001), New York City, USA (2003), Houston TX, USA (2000), Stamford CT, USA (1999), and Lubbock TX, USA (1998).
HIV Pathogenesis Keystone Meeting 27 March - 1 April, Banff, Canada
Wednesday, 23 January 2008 15:46
Elucidating the molecular mechanisms of HIV infection is essential for the design and development of an effective vaccine and the next generation of antiviral agents. This Keystone Symposia meeting will focus on (1) our understanding of HIV proteins and their functions, (2) host factors used to aid in viral replication, (3) viral genetic diversity and adaptation, and (4) the central role of the destruction of CD4+ T cells in lymphoid tissue to the pathogenesis. The pathogenic mechanisms of HIV infection from transmission through clinical latency, including the means used by the virus to establish infection and propagate in target cells and evade the innate and adaptive host defense mechanisms will be examined. Scientists from diverse disciplines will be brought together with the objective of devising vaccines and other biology-based ways to prevent transmission and progression to AIDS. The meeting will promote further insights into the dynamic interplay between the virus, the host, and its immune response.
6th European HIV Drug Resistance Workshop 26-28 March 2008, Budapest, Hungary
Tuesday, 22 January 2008 15:14
The European HIV Drug Resistance Workshops have proven to meet the need of European researchers and clinicians working in the field of HIV treatment. The workshop has become the place to be to keep abreast of the latest scientific developments in the field of HIV drug resistance and to translate the latest science to daily clinical practice.
It is of major importance to continue this educational programme. Therefore we are organising a 6th European HIV Drug Resistance Workshop, From basic science to clinical implications, that will be held in Budapest, Hungary, from 26 – 28 March 2008.
ICCS 2008 conference - 23-25 June 2008, Krakow, Poland.
Tuesday, 22 January 2008 15:08
ICCS 2008 is the eighth in the series of highly successful conferences.
This conference will be a unique event focusing on recent developments in novel methods and modelling of complex systems for diverse areas of science, scalable scientific algorithms, advanced software tools, computational grids, advanced numerical methods, and novel application areas where the above novel models, algorithms and tools can be efficiently applied such as physical systems, computational and systems biology, environmental systems, finance, and others.
Peter Sloot contributed a short article to iSGTW, the International Science Grid This Week newsletter, which is read by more than 15,000 people every week. With 3500 subscribers, iSGTW promotes grid computing around the world by sharing stories of grid-empowered science and scientific discoveries (see http://www.isgtw.org/?pid=1000653).
The iSGTW weekly e-newsletter is emailed free to subscribers and is also available via RSS.
ViroLab is now an officially registered partner project of the OGSA-DAI project
Wednesday, 24 October 2007 10:36
ViroLab is now an officially registered partner project of the OGSA-DAI project.
It is listed in the overview page containing all projects which are using or planning to use or have used OGSA-DAI (see http://www.ogsadai.org.uk/about/projects.php#virolab).
ViroLab to contribute to the HealthGrid Wiki
Wednesday, 24 October 2007 10:36
ViroLab will contribute to the HealthGrid Wiki regarding Security and Privacy issues covered by the project’s security infrastructure. More information either on the HealthGrid Wiki at http://wiki.healthgrid.org/index.php/SecurityAndPrivacy:Index (user account required) or within the ViroLab Wiki at https://wiki.hlrs.de/virolab/index.php/HealthGrid (only for ViroLab consortium members)
Next technical integration meeting
Wednesday, 24 October 2007 08:37
ViroLab Integration Meeting in Dagstuhl, Germany, 6-10 April 2008
The goal of this meeting is to integrate the software developed within the project, before the second-year review.
For more info, go to http://www.hlrs.de/people/krammer/virolab-april08/
