42,756 research outputs found
Measurement in biological systems from the self-organisation point of view
Measurement in biological systems became a subject of concern as a
consequence of numerous reports on limited reproducibility of experimental
results. To reveal origins of this inconsistency, we have examined general
features of biological systems as dynamical systems far from not only their
chemical equilibrium, but, in most cases, also of their Lyapunov stable states.
Thus, in biological experiments, we do not observe states, but distinct
trajectories followed by the examined organism. If one of the possible
sequences is selected, a minute sub-section of the whole problem is obtained,
sometimes in a seemingly highly reproducible manner. But the state of the
organism is known only if a complete set of possible trajectories is known. And
this is often practically impossible. Therefore, we propose a different
framework for reporting and analysis of biological experiments, respecting the
view of non-linear mathematics. This view should be used to avoid
overoptimistic results, which have to be consequently retracted or largely
complemented. An increase of specification of experimental procedures is the
way for better understanding of the scope of paths, which the biological system
may be evolving. And it is hidden in the evolution of experimental protocols.Comment: 13 pages, 5 figure
Multi-level agent-based modeling - A literature survey
During last decade, multi-level agent-based modeling has received significant
and dramatically increasing interest. In this article we present a
comprehensive and structured review of literature on the subject. We present
the main theoretical contributions and application domains of this concept,
with an emphasis on social, flow, biological and biomedical models.Comment: v2. Ref 102 added. v3-4 Many refs and text added v5-6 bibliographic
statistics updated. v7 Change of the name of the paper to reflect what it
became, many refs and text added, bibliographic statistics update
The Repast Simulation/Modelling System for Geospatial Simulation
The use of simulation/modelling systems can simplify the implementation of agent-based models. Repast is one of the few simulation/modelling software systems that supports the integration of geospatial data especially that of vector-based geometries. This paper provides details about Repast specifically an overview, including its different development languages available to develop agent-based models. Before describing Repast’s core functionality and how models can be developed within it, specific emphasis will be placed on its ability to represent dynamics and incorporate geographical information. Once these elements of the system have been covered, a diverse list of Agent-Based Modelling (ABM) applications using Repast will be presented with particular emphasis on spatial applications utilizing Repast, in particular, those that utilize geospatial data
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