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References
Westerhoff, H. V. and Palsson, B. O. (2004) The evolution of molecular biology into systems biology. Nat. Biotechnol., 22, 1249–1252
Liao, W.-L. and Tsai, F.-J. (2013) Personalized medicine: A paradigm shift in healthcare. Biomedicine, 3, 66–72
Kolodkin, A., Boogerd, F. C., Plant, N., Bruggeman, F. J., Goncharuk, V., Lunshof, J., Moreno-Sanchez, R., Yilmaz, N., Bakker, B. M., Snoep, J. L., et al. (2012) Emergence of the silicon human and network targeting drugs. Eur. J. Pharm. Sci., 46, 190–197
Lawford, P. V., Narracott, A. V., McCormack, K., Bisbal, J., Martin, C., Brook, B., Zachariou, M., Kohl, P., Fletcher, K., Diaz-Zuccarini, V. (1921) Virtual physiological human: training challenges. Philoso. T. Roy. Soc., 2010, 368
Viceconti, M., Clapworthy, G. and Jan, S.V.S. (2008) The Virtual Physiological Human — A European Initiative for in silico Human Modelling —. J. Physiol., 58, 441–446
Olivier, B. G. and Snoep, J. L. (2004) Web-based kinetic modelling using JWS Online. Bioinformatics, 20, 2143–2144
Stoica, I., Sadiq, S.K. and Coveney, P.V. (2008) Rapid and accurate prediction of binding free energies for Saquinavir-Bound HIV-1 proteases. J. Am. Chem. Soc., 130 2639–2648
Hou, T., Wang, J., Li, Y. and Wang, W. (2011) Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J. Chem. Inf. Model., 51, 69–82
Mazzeo, M. D. and Coveney, P. V. (2008) HemeLB: A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries. Comput. Phys. Commun., 178, 894–914
Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P. and Kummer, U. (2006) COPASI—a COmplex PAthway SImulator. Bioinformatics, 22, 3067–3074
Cazzaniga, P., Damiani, C., Besozzi, D., Colombo, R., Nobile, M.S., Gaglio, D., Pescini, D., Molinari, S., Mauri, G., Alberghina L., et al. (2014) Computational strategies for a system-level understanding of metabolism. Metabolites, 4, 1034–1087
Karp, P. D., Paley, S. and Romero, P. (2002) The pathway tools software. Bioinformatics, 18,Suppl. 1, S225–S232
Pinney, J. W., Shirley, M. W., McConkey, G. A. and Westhead, D. R. (2005) metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res., 33, 1399–1409
Büchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., Mittag, F., Schubert, M., Glont, M., Golebiewski, M., et al. (2013) Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol., 7, 116
Fisher, C. P., Plant, N. J., Moore, J. B. and Kierzek, A. M. (2013) QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. Bioinformatics, 29, 3181–3190
Wu, C., Schwartz, J.-M. and Nenadic, G. (2013) PathNER: a tool for systematic identification of biological pathway mentions in the literature. BMC Syst. Biol., 7,Suppl. 3, S2
Chetty M., Rose, R.H., Abduljalil, K., Patel, N., Lu, G., Cain, T., Jamei, M. and Rostami-Hodjegan, A. (2014) Applications of linking PBPK and PD models to predict the impact of genotypic variability, formulation differences, differences in target binding capacity and target site drug concentrations on drug responses and variability. Front. Pharmacol., 5, 258
Valerio, L. G. Jr. (2011) In silico toxicology models and databases as FDA Critical Path Initiative toolkits. Hum. Genomics, 5, 200–207
Dobson, P. D. and Kell, D. B. (2008) Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule? Nat. Rev. Drug Discov., 7, 205–220
Kell, D. B., Dobson, P. D., Bilsland, E. and Oliver, S. G. (2013) The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so. Drug Discov. Today, 18, 218–239
Lanthaler, K., Bilsland, E., Dobson, P. D., Moss, H. J., Pir, P., Kell, D.B. and Oliver, S.G. (2011) Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast. BMC Biol., 9, 70
Yang, X., Liao, X., Xu, W., Song, J., Hu, Q., Su, J., Xiao, L., Lu, K., Dou, Q., Jiang, J., et al. (2010) TH-1: China’s first petaflop supercomputer. Front. Comput. Sci. China, 4, 445–455
Yang, X., Liao, X.-K., Lu, K., Hu, Q.-F., Song, J.-Q. and Su, J.-S. (2011) The TianHe-1. A supercomputer: Its hardware and software. J. Comput. Sci. Technol., 26, 344–351
Tianhe-2 (MilkyWay-2) Supercomputer. Available from: http://www.nscc-gz.cn/
Luo, R. B., Liu, B.H., Xie, Y. L., Li, Z.Y., Huang, W.H., Yuan, J.Y., He, G. Z., Chen, Y. X., Pan, Q., Liu, Y. J. et al. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience, 1, 18.
Luo, R., Wong, T., Zhu, J., Liu, C. M., Zhu, X., Wu, E., Lee, L. K., Lin, H., Zhu, W., Cheung, D.W., et al. (2013) SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner. PLoS One, 8, e65632
Jia, W., Qiu, K., He, M., Song, P., Zhou, Q., Zhou, F., Yu, Y., Zhu, D., Nickerson, M. L., Wan, S., et al. (2013) SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biol., 14, R12
Cui, Y., Liao, X.-K., Zhu, X. Q. and Wang, B. Q. (2014) mBWA: A massively parallel sequence reads aligner, in 8th international conference on practical applications of computational biology & bioinformatics (PACBB 2014). Springer International Publishing, 113–120
Guan, N.Y., Tao, D. C., Luo, Z. G. and Yuan, B. (2012) NeNMF: An optimal gradient method for Nonnegative Matrix Factorization. IEEE Trans. Signal Process., 60, 2882–2898
Murabito, E., Smallbone, K., Swinton, J., Westerhoff, H. V. and Steuer, R. (2011) A probabilistic approach to identify putative drug targets in biochemical networks. J. R. Soc. Interface, 8, 880–895
Murabito, E., (2013) Targeting breast cancer metabolism: A metabolic control analysis approach. Curr. Synthetic Sys. Biol., 1, 104
Murabito, E., Verma, M., Bekker, M., Bellomo, D., Westerhoff, H. V., Teusink, B. and Steuer, R. (2014) Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation. PLoS One, 9, e106453
Thiele, I., Swainston, N., Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) A community-driven global reconstruction of human metabolism. Nat. Biotechnol., 31, 419–425
Kent, E., Hoops, S. and Mendes, P. (2012) Condor-COPASI: high-throughput computing for biochemical networks. BMC Syst. Biol., 6, 91
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Murabito, E., Colombo, R., Wu, C. et al. SupraBiology 2014: Promoting UK-China collaboration on Systems Biology and High Performance Computing. Quant Biol 3, 46–53 (2015). https://doi.org/10.1007/s40484-015-0039-9
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DOI: https://doi.org/10.1007/s40484-015-0039-9