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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).
