biomedical sciences research institute - Research - University of Ulster

Silva CG, Brito J, Swain M, Dubitzky W and Brito RMM; P-found GRID: A distributed repository for protein folding andunfolding simulations; The Protein Folding and Unfolding Simulation Repository, IBERGRID, May 12-14, Porto, 2008Stankovski V, Swain M, Kravtsov V, Niessen T, Wegener D, Röhm M, Trnkoczy J, May M, Franke J, Schuster A & DubitzkyW; Digging Deep into the Data Mine with DataMiningGrid; IEEE Internet Computing, 12: 69-76, 2008Stankovski V, Swain M, Kravtsov V, Niessen T, Wegener D, Kindermann J & Dubitzky W; Grid-enabling data miningapplications with DataMiningGrid: An architectural perspective; Future Generation Computer Systems, 24: 259–279,2008Swain M, Mandel JJ and Dubitzky W; Comparing Grid Computing Solutions for Reverse-Engineering Gene RegulatoryNetworks, in Proceedings of the International Conference on Computational Science (ICCS 2008), Poland, 106-115, 2008Swain M, Ostropytskyy V, Silva CG, Stahl F, Riche O, Brito RMM, Dubitzky W; Grid Computing Solutions for DistributedRepositories of Protein Folding and Unfolding Simulations; Proceedings of the International Conference on ComputationalScience (ICCS 2008), Krakow, Poland, 70-79, 2008Swain M and Chue Hong N P; Data pre-processing using OGSA-DAI; Book chapter in Data Mining Techniques in GridComputing Environments, Wiley, 2008Vitaliy OstropytskyyResearch AssociateVitaliy Ostropytskyy has been mostly focussed on the European FP6 Chemomentum project during this period.Chemomentum is aimed at developing new ICT in the context of in the context of the European regulatory initiative“Registration and Evaluation of Chemicals” (REACH), promoting the REACH initiative aimed at reducing animaltesting, by developing in silico, grid-based tools. His activities included ongoing development on distributed datamanagement and ontology management of the Chemomentum system. He has been developing software usingJava and Maven tool; and also performing system administration tasks, integrating dedicated server to the sharedChemomentum project’s test-bed.Some of Vitaliy’s work focussed on the Protein Folding and Unfolding Data repository; the system facilitates thesharing of simulation data created by molecular dynamics protein unfolding simulations. The early prototype of thesystem has been updated based on the feedback from the corresponding research community. The repository ispopulated with protein folding and unfolding simulations in order to perform data mining procedures.Some highlights of his work in the reporting period include:• Presenting a talk on “Chemomentum Project - Data Management” at the “European Software, Services and GridTechnology Days”, September 2007, Brussels.• Attending European FP6 Chemomentum project meetings in Juelich (Germany), Milan (Italy), Tartu (Estonia),Dresden (Germany): presented results from our Working Package research and participating in discussionsrelated to project development.• Visiting the Technical University of Dresden (Germany) for 1 week to collaborate on the Chemomentumproject.Vitaliy is Member of the Technical Group 5 of Grid related IST projects, created at the European Grid TechnologyDays 2007.Publications:Swain M, Ostropytskyy V, Silva CG, Stahl F, Riche O, Brito RMM, Dubitzky W; Grid Computing Solutions for DistributedRepositories of Protein Folding and Unfolding Simulations; Proceedings of the International Conference on ComputationalScience (ICCS 2008), Krakow, Poland, 70-79, 2008105