@article {Topa-et-al-2017,
	title = {Modelling ecology and evolution of Foraminifera in the agent-oriented distributed platform},
	journal = {Journal of Computational Science},
	volume = {18},
	year = {2017},
	pages = {69{\textendash}84},
	abstract = {We present a new software platform called eVolutus for simulating evolution of living organisms. We choose Foraminifera as model organisms that represent a group of single-cellular, mainly marine, organisms that construct well fossilisable protective shells. They have lived on Earth for more than 540 million years and have left an extraordinary fossil record that is excellent for testing palaeoecological and evolutionary hypotheses. We use the AgE platform, which is a lightweight agent-oriented platform supporting distributed computation. The paper presents the general architecture of this modelling environment as well as more detailed descriptions of the implemented rules and applied solutions. The utility of this software is demonstrated by presenting the configuration and results of sample experiments.},
	issn = {1877-7503},
	doi = {10.1016/j.jocs.2016.07.009},
	url = {https://doi.org/10.1016/j.jocs.2016.07.009},
	author = {Pawe{\l} Topa and {\L}ukasz Faber and Jaros{\l}aw Tyszka and Maciej Komosinski}
}
@article {Komosinski-et-al-2016,
	title = {Multi-agent simulation of benthic foraminifera response to annual variability of feeding fluxes},
	journal = {Journal of Computational Science},
	volume = {21},
	year = {2017},
	pages = {419{\textendash}431},
	abstract = {In this work we describe a novel simulation model of foraminifera and their microhabitat. The simulations reported here are focused on the response of foraminiferal populations to environmental feeding fluxes. The experiments allowed to calibrate the model and to simulate realistic population patterns known from culture experiments, as well as from oceanographic and paleoecologic studies. Variability of annual food flux has a direct impact on productivity of foraminifera: population sizes closely follow the intensity of constant and seasonal food fluxes in both scenarios. This correlation between the food influx and population size is interpreted as the consequence of changing the carrying capacity of the system. Seasonal pulses of particulate organic matter enhance the population size which is represented by a higher number of fossilized shells. Our model offers a flexible experimental design to run sophisticated in silico experiments. This approach reveals a novel methodology for testing sensitivity of fossil and recent foraminiferal assemblages to environmental changes. Furthermore, it facilitates predictive applications for monitoring studies based on simulation of various scenarios.},
	issn = {1877-7503},
	doi = {10.1016/j.jocs.2016.09.009},
	url = {http://www.framsticks.com/files/common/SimulationForaminiferaFeedingFluxes.pdf},
	author = {Maciej Komosinski and Agnieszka Mensfelt and Jaros{\l}aw Tyszka and Jan Gole{\'n}}
}
@inbook {Komosinski-et-al-2015,
	title = {Application of a morphological similarity measure to the analysis of shell morphogenesis in Foraminifera},
	booktitle = {Man{\textendash}Machine Interactions 4},
	series = {Advances in Intelligent Systems and Computing},
	volume = {391},
	year = {2016},
	pages = {215{\textendash}224},
	publisher = {Springer},
	organization = {Springer},
	abstract = {This work evaluates the genotype-to-phenotype mapping defined by one of the models of growth of foraminifera. Foraminifera are simple unicellular organisms with very diverse morphologies. To analyze the mapping, a morphological similarity measure is needed that compares 3D structures. One of the key components of the similarity estimation algorithm is Singular Value Decomposition (SVD). Since this algorithm is heavily used and its performance is important, four SVD implementations have been compared in this work. Distance matrices of the phenotypes obtained for equally distant genotypes were computed using the similarity measure. For the visualization of the phenotype space, multidimensional scaling techniques were used. Visual comparison of the genotype and the phenotype spaces revealed characteristics and potential weaknesses of the analyzed model of foraminifera growth, and demonstrated usefulness of the proposed approach.},
	isbn = {978-3-319-23436-6},
	doi = {10.1007/978-3-319-23437-3_18},
	url = {http://www.framsticks.com/files/common/ForaminiferaGenotypePhenotypeMapping.pdf},
	author = {Maciej Komosinski and Agnieszka Mensfelt and Pawe{\l} Topa and Jaros{\l}aw Tyszka},
	editor = {Gruca, Aleksandra and Brachman, Agnieszka and Kozielski, Stanis{\l}aw and Czach{\'o}rski, Tadeusz}
}
@inbook {107,
	title = {eVolutus: a configurable platform designed for ecological and evolutionary experiments tested on Foraminifera},
	booktitle = {Man{\textendash}Machine Interactions 4},
	series = {Advances in Intelligent Systems and Computing},
	volume = {391},
	year = {2016},
	pages = {269{\textendash}278},
	publisher = {Springer},
	organization = {Springer},
	isbn = {978-3-319-23436-6},
	doi = {10.1007/978-3-319-23437-3_23},
	url = {http://dx.doi.org/10.1007/978-3-319-23437-3_23},
	author = {Pawe{\l} Topa and Maciej Komosinski and Maciej Bassara and Jaros{\l}aw Tyszka},
	editor = {Gruca, Aleksandra and Brachman, Agnieszka and Kozielski, Stanis{\l}aw and Czach{\'o}rski, Tadeusz}
}
@inbook {108,
	title = {eVolutus: A New Platform for Evolutionary Experiments},
	booktitle = {Parallel Processing and Applied Mathematics: 11th International Conference, PPAM 2015, Krakow, Poland, September 6{\textendash}9, 2015. Revised Selected Papers, Part II},
	year = {2016},
	pages = {570{\textendash}580},
	publisher = {Springer},
	organization = {Springer},
	isbn = {978-3-319-32152-3},
	doi = {10.1007/978-3-319-32152-3_53},
	url = {http://dx.doi.org/10.1007/978-3-319-32152-3_53},
	author = {Topa, Pawe{\l} and Komosinski, Maciej and Tyszka, Jaros{\l}aw and Mensfelt, Agnieszka and Rokitta, Sebastian and Byrski, Aleksander and Bassara, Maciej},
	editor = {Wyrzykowski, Roman and Deelman, Ewa and Dongarra, Jack and Karczewski, Konrad and Kitowski, Jacek and Wiatr, Kazimierz}
}
