AB-QSSPN: Integration of Agent-Based Simulation of Cellular Populations with Quasi-Steady State Simulation of Genome Scale Intracellular Networks
We present a tool for simulation of populations of living cells interacting in spatial structures. Each cell is modelled with the Quasi-Steady Petri Net that integrates dynamic regulatory network expressed with a Petri Net (PN) and Genome Scale Metabolic Networks (GSMN) where linear programming is used to explore the steady-state metabolic flux distributions in the whole-cell model.
Similar simulations have already been conducted for single cells, but we present an architecture to simulate populations of millions of interacting cells organized in spatial structures which can be used to model tumour growth or formation of tuberculosis lesions. For that we use the Spark framework and organize the computation in an agent based “think like a vertex” fashion as in Pregel like systems. In the cluster we introduce a special kind of per node caching to speed up computation of the steady-state metabolic flux.
Our tool can be used to provide a mechanistic link between genotype and behaviour of multicellular system.
This research was sponsored by National Science Centre based on decision DEC-2012/07/D/ST6/02492.
- 1.Apache. Hadoop. http://hadoop.apache.org/
- 3.Dean, J., Ghemawat, S.: MapReduce: simplified data processing on large clusters. In: OSDI, pp. 137–150 (2004)Google Scholar
- 5.Gille, C., Bölling, C., Hoppe, A., Bulik, S., Hoffmann, S., Hübner, K., Karlstädt, A., Ganeshan, R., König, M., Rother, K., Weidlich, M., Behre, J., Holzhütter, H.-G.: HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol. Syst. Biol. 6(1), 411 (2010)CrossRefGoogle Scholar
- 6.Gonzalez, J.E., Xin, R.S., Dave, A., Crankshaw, D., Franklin, M.J., Stoica, I.: GraphX: graph processing in a distributed dataflow framework. In: Proceedings of the 11th USENIX Conference on Operating Systems Design and Implementation, OSDI 2014, pp. 599–613. USENIX Association, Berkeley, CA, USA (2014)Google Scholar
- 8.Li, T., Chiang, J.Y.L.: Bile acid signaling in liver metabolism and diseases. J. Lipids 2012 (2011)Google Scholar
- 9.Merkel, D.: Docker: lightweight linux containers for consistent development and deployment. Linux J. 2014(239), 2 (2014)Google Scholar
- 12.Zaharia, M., Chowdhury, M., Das, T., Dave, A., Ma, J., McCauley, M., Franklin, M.J., Shenker, S., Stoica, I.: Resilient distributed datasets: a fault-tolerant abstraction for in-memory cluster computing. In: Proceedings of the 9th USENIX Conference on Networked Systems Design and Implementation, NSDI 2012, p. 2. USENIX Association, Berkeley, CA, USA (2012)Google Scholar
Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 2.5 International License (http://creativecommons.org/licenses/by-nc/2.5/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.
The images or other third party material in this chapter are included in the chapter's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the chapter's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.