By Bin Ma (auth.), Zhipeng Cai, Oliver Eulenstein, Daniel Janies, Daniel Schwartz (eds.)
This booklet constitutes the refereed court cases of the ninth overseas Symposium on Bioinformatics examine and purposes, ISBRA 2013, held in Charlotte, NC, united states, in may possibly 2013. The 25 revised complete papers offered including four invited talks have been rigorously reviewed and chosen from forty six submissions. The papers hide quite a lot of biomedical databases and information integration, high-performance bio-computing, biomolecular imaging, high-throughput sequencing facts research, bio-ontologies, molecular evolution, comparative genomics and phylogenomics, molecular modeling and simulation, trend discovery and category, computational proteomics, inhabitants genetics, info mining and visualization, software program instruments and applications.
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Although some synchronisation primitives are available on GPUs, their usage totally contradicts the programming model of these devices and tends to ruin dramatically the raw computing performance they are capable of. Consequently, we prefer saving this technology for synchronous simulations of physical phenomena which could however interact with our particle-based asynchronous simulations. 2 L. Cr´epin et al. Perspectives and Future Work Due to the fact that we chose the microscopic scale, our diﬀusion algorithm requires a very short time step in order not to miss collisions (approximately 10 nanoseconds).
Keywords: Particle-based system, parallel computing, biochemical kinetics, microscopic scale simulation. 1 Introduction A common way to improve the understanding of complex biological systems is to run experiments on models in order to test hypotheses. The results are then extrapolated from the models to the real systems they represent. One usually distinguishes in vivo experimentation, taking place in a living organism, from in vitro experimentation, run in test tubes. One challenge for the upcoming years would be to save the various expenses of some of these experiments by running reliable computer simulations of predictive numerical models.
A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141(4), 1641–1650 (1995) 13. : Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of molecular evolution 17(6), 368–376 (1981) 14. : RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21), 2688–2690 (2006) 15. com/stamatak/standard-RAxML 16. : Improving genome rearrangement phylogeny using sequencestyle parsimony. In: Fifth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2005, pp.
Bioinformatics Research and Applications: 9th International Symposium, ISBRA 2013, Charlotte, NC, USA, May 20-22, 2013. Proceedings by Bin Ma (auth.), Zhipeng Cai, Oliver Eulenstein, Daniel Janies, Daniel Schwartz (eds.)