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Pablo Granda Araujo, Anna Gras, Marta Ginovart
Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs) using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo...
2016: Computational and Structural Biotechnology Journal
Hugh Trenchard, Andrew Renfree, Derek M Peters
PURPOSE: Drafting in cycling influences collective behaviour of pelotons. Whilst evidence for collective behaviour in competitive running events exists, it is not clear if this results from energetic savings conferred by drafting. This study modelled the effects of drafting on behavior in elite 10,000 m runners. METHODS: Using performance data from a men's elite 10,000 m track running event, computer simulations were constructed using Netlogo 5.1 to test the effects of three different drafting quantities on collective behaviour: no drafting, drafting to 3m behind with up to ~8% energy savings (a realistic running draft); and drafting up to 3m behind with up to 38% energy savings (a realistic cycling draft)...
June 13, 2016: International Journal of Sports Physiology and Performance
Pablo Araujo Granda, Anna Gras, Marta Ginovart, Vincent Moulton
We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM, and is designed to simulate the bacterial cell population behavior and the product dynamics within the culture. The INDISIM-Paracoccus model assumes a culture medium containing succinate as a carbon source, ammonium as a nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitric oxide and nitrous oxide to simulate in continuous or batch culture the different nutrient-dependent cell growth kinetics of the bacterium Paracoccus denitrificans...
August 21, 2016: Journal of Theoretical Biology
Pere-Joan Cardona, Clara Prats
Infection with Mycobacterium tuberculosis (Mtb) can induce two kinds of lesions, namely proliferative and exudative. The former are based on the presence of macrophages with controlled induction of intragranulomatous necrosis, and are even able to stop its physical progression, thus avoiding the induction of active tuberculosis (TB). In contrast, the most significant characteristic of exudative lesions is their massive infiltration with polymorphonuclear neutrophils (PMNs), which favor enlargement of the lesions and extracellular growth of the bacilli...
2016: Frontiers in Microbiology
Susa H Stonedahl, Kevin R Roche, Forrest Stonedahl, Aaron I Packman
Advective exchange between the pore space of sediments and the overlying water column, called hyporheic exchange in fluvial environments, drives solute transport in rivers and many important biogeochemical processes. To improve understanding of these processes through visual demonstration, we created a hyporheic flow simulation in the multi-agent computer modeling platform NetLogo. The simulation shows virtual tracer flowing through a streambed covered with two-dimensional bedforms. Sediment, flow, and bedform characteristics are used as input variables for the model...
2015: Journal of Visualized Experiments: JoVE
Mário Veloso
A multiplicity of natural history studies of multiple sclerosis provides valuable knowledge of the disease progression but individualized prognosis remains elusive. A few decision support tools that assist the clinician in such task have emerged but have not received proper attention from clinicians and patients. The objective of the current work is to implement a web-based tool, conveying decision relevant prognostic scientific evidence, which will help clinicians discuss prognosis with individual patients...
September 2014: Multiple Sclerosis and related Disorders
Jagpreet Chhatwal, Tianhua He
Agent-based modelling (ABM) is a relatively new technique, which overcomes some of the limitations of other methods commonly used for economic evaluations. These limitations include linearity, homogeneity and stationarity. Agents in ABMs are autonomous entities, who interact with each other and with the environment. ABMs provide an inductive or 'bottom-up' approach, i.e. individual-level behaviours define system-level components. ABMs have a unique property to capture emergence phenomena that otherwise cannot be predicted by the combination of individual-level interactions...
May 2015: PharmacoEconomics
Richard R Chapleau, Peter J Robinson, John J Schlager, Jeffery M Gearhart
BACKGROUND: One of the leading causes of death and illness within the agriculture industry is through unintentionally ingesting or inhaling organophosphate pesticides. OP intoxication directly inhibits acetylcholinesterase, resulting in an excitatory signaling cascade leading to fasciculation, loss of control of bodily fluids, and seizures. METHODS: Our model was developed using a discrete, rules-based modeling approach in NetLogo. This model includes acetylcholinesterase, the nicotinic acetylcholine receptor responsible for signal transduction, a single release of acetylcholine, organophosphate inhibitors, and a theoretical novel medical countermeasure...
2014: Theoretical Biology & Medical Modelling
Ferdinando Chiacchio, Marzio Pennisi, Giulia Russo, Santo Motta, Francesco Pappalardo
Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents...
2014: BioMed Research International
Luis F Schettino
Young students struggle with concepts that involve the parallel activity of large numbers of similar entities, precisely the kind of concepts that abound in neuroscience. While a direct experience to laboratory work cannot be replaced, such activities include a steep learning curve and may be impractical in certain course settings. This article describes a set of computer simulations of a number of neural processes using NetLogo (Wilensky, 1999), a software environment for the design and implementation of multi-agent simulations that has an intuitive graphical interface and minimal learning curve...
2014: Journal of Undergraduate Neuroscience Education: JUNE: a Publication of FUN, Faculty for Undergraduate Neuroscience
Haiyan Liu, Xia Chen, Bo Zhang
In the social sciences, computer-based modeling has become an increasingly important tool receiving widespread attention. However, the derivation of the quantitative relationships linking individual moral behavior and social morality levels, so as to provide a useful basis for social policy-making, remains a challenge in the scholarly literature today. A quantitative measurement of morality from the perspective of complexity science constitutes an innovative attempt. Based on the NetLogo platform, this article examines the effect of various factors on social morality levels, using agents modeling moral behavior, immoral behavior, and a range of environmental social resources...
2013: PloS One
Rafael Bravo, David E Axelrod
BACKGROUND: Normal colon crypts consist of stem cells, proliferating cells, and differentiated cells. Abnormal rates of proliferation and differentiation can initiate colon cancer. We have measured the variation in the number of each of these cell types in multiple crypts in normal human biopsy specimens. This has provided the opportunity to produce a calibrated computational model that simulates cell dynamics in normal human crypts, and by changing model parameter values, to simulate the initiation and treatment of colon cancer...
2013: Theoretical Biology & Medical Modelling
Alexey Solovyev, Maxim Mikheev, Leming Zhou, Joyeeta Dutta-Moscato, Cordelia Ziraldo, Gary An, Yoram Vodovotz, Qi Mi
Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform for Agent-based Representation of Knowledge), a framework for agent-based modeling specifically designed for systems-level biomedical model development...
2010: International Journal of Agent Technologies and Systems
Matthew B Biggs, Jason A Papin
Multiscale modeling is used to represent biological systems with increasing frequency and success. Multiscale models are often hybrids of different modeling frameworks and programming languages. We present the MATLAB-NetLogo extension (MatNet) as a novel tool for multiscale modeling. We demonstrate the utility of the tool with a multiscale model of Pseudomonas aeruginosa biofilm formation that incorporates both an agent-based model (ABM) and constraint-based metabolic modeling. The hybrid model correctly recapitulates oxygen-limited biofilm metabolic activity and predicts increased growth rate via anaerobic respiration with the addition of nitrate to the growth media...
2013: PloS One
James W Reinhardt, Daniel A Krakauer, Keith J Gooch
Using a top-down approach, an agent-based model was developed within NetLogo where cells and extracellular matrix (ECM) fibers were composed of multiple agents to create deformable structures capable of exerting, reacting to, and transmitting mechanical force. At the beginning of the simulation, long fibers were randomly distributed and cross linked. Throughout the simulation, imposed rules allowed cells to exert traction forces by extending pseudopodia, binding to fibers and pulling them towards the cell. Simulated cells remodeled the fibrous matrix to change both the density and alignment of fibers and migrated within the matrix in ways that are consistent with previous experimental work...
July 1, 2013: Journal of Biomechanical Engineering
Kenneth H Schatten
This article focuses on mapping the Sun's large-scale magnetic fields. In particular, the model considers how photospheric fields evolve in time. Our solar field mapping method uses Netlogo's cellular automata software via algorithms to carry out the movement of magnetic field on the Sun via agents. This model's entities consist of two breeds: blue and red agents. The former carry a fixed amount of radially outward magnetic flux: 10(23) Mx, and the latter, the identical amount of inward directed flux. The individual agents are distinguished, for clarity, by various shades of blue and red arrows whose orientation indicates the direction the agents are moving, relative to the near-steady bulk fluid motions...
December 2013: SpringerPlus
Christian Tokarski, Sabine Hummert, Franziska Mech, Marc Thilo Figge, Sebastian Germerodt, Anja Schroeter, Stefan Schuster
Opportunistic human pathogenic fungi like the ubiquitous fungus Aspergillus fumigatus are a major threat to immunocompromised patients. An impaired immune system renders the body vulnerable to invasive mycoses that often lead to the death of the patient. While the number of immunocompromised patients is rising with medical progress, the process, and dynamics of defense against invaded and ready to germinate fungal conidia are still insufficiently understood. Besides macrophages, neutrophil granulocytes form an important line of defense in that they clear conidia...
2012: Frontiers in Microbiology
Wenan Chen, Kevin Ward, Qi Li, Vojislav Kecman, Kayvan Najarian, Nathan Menke
The coagulation and fibrinolytic systems are complex, inter-connected biological systems with major physiological roles. The complex, nonlinear multi-point relationships between the molecular and cellular constituents of two systems render a comprehensive and simultaneous study of the system at the microscopic and macroscopic level a significant challenge. We have created an Agent Based Modeling and Simulation (ABMS) approach for simulating these complex interactions. As the scale of agents increase, the time complexity and cost of the resulting simulations presents a significant challenge...
2011: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Abdelkader Fekir, Nacéra Benamrane
This paper presents an original approach for detecting and tracking of objects in medical image sequence. We propose a multi-agent system (MAS) based on NetLogo platform for implementing parametric contour active model or snake. In NetLogo, mobile agents (turtles) move over a grid of stationary agents (patches). In our proposed MAS, each mobile agent represents a point of snake (snaxel) and it minimizes, in parallel with other turtles, the energy functional attached to its snaxel. Then, these turtles move over the image represented by a grid of patches...
2011: Advances in Experimental Medicine and Biology
Jason D Bishai, William R Bishai, David M Bishai
BACKGROUND: Prior infection with one strain TB has been linked with diminished likelihood of re-infection by a new strain. This paper attempts to determine the role of declining prevalence of drug-susceptible TB in enabling future epidemics of MDR-TB. METHODS: A computer simulation of MDR-TB epidemics was developed using an agent-based model platform programmed in NetLogo (See Eighty-one scenarios were created, varying levels of treatment quality, diagnostic accuracy, microbial fitness cost, and the degree of immunogenicity elicited by drug-susceptible TB...
September 22, 2010: PloS One
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