21 papers · ranked by Valyu relevance
Robert Marsland, Wenping Cui, Joshua Goldford, Pankaj Mehta
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating…
Vance Difan Gao, Sara Morley-Fletcher, Stefania Maccari, Martha Hotz Vitaterna + 1 more
Competition for resources often contributes strongly to defining an organism’s ecological niche. Biological rhythms are important adaptations to the temporal dimension of niches, but the role of other organisms in determining such temporal niches have not been much studied, and the role specifically of competition even…
Jeremy Foote, Nathan TeBlunthuis, Benjamin Mako Hill, Aaron Shaw
Why are online community sizes so extremely unequal? Most answers to this question have pointed to general mathematical processes drawn from physics like cumulative advantage. ese explanations provide lile insight into specic social dynamics or decisions that individuals make when joining and leaving communities. In…
Pablo Lechón, Tom Clegg, Jacob Cook, Thomas P. Smith + 1 more
New microbial communities often arise through the mixing of two or more separately assembled parent communities, a phenomenon that has been termed “community coalescence”. Understanding which features of complex parent communities determine the outcomes of any given coalescence event is an important challenge. While…
Barbara M. Walsh, Marc A. Auerbach, Marcie N. Gawel, Linda L. Brown + 2 more
'Bobbi J. Byrne' 'Aaron Calhoun' ''] Simulation-based methods are regularly used to train inter-professional groups of healthcare providers at academic medical centers (AMC). These techniques are used less frequently in community hospitals. Bringing in-situ simulation (ISS) from AMCs to community sites is an approach…
Burhanuddin Ali Akber, Mehak Ismail Rajani, Farah Khalid, Charles Docherty
'Charles Docherty'] Experiential learning through simulation can play a very significant role, not only in hospital settings but also in community contexts (Lubbers and Rossman, Nurse Educ. Today 48:140-144; Wheeler and McNelis, Nurs. Educ. Perspect 35:259-261). This paper discusses the concept of creating a novel…
Abbas Ganji, Negin Alimohammadi, Scott B. Miles
The importance of community resilience has become increasingly recognized in emergency management and post-disaster community well-being. To this end, three seismic resilience planning initiatives have been conducted in the U.S. in the last decade to envision the current state of community resilience. Experts who…
Benjamin Symon, Jesse Spurr, Victoria Brazil
Virtual Communities of Practice (vCoP) is a nascent approach to professional development for simulation educators (Thoma et al., Simul Healthc. 2018;13(2):124-30). vCoPs overcome geographic barriers to accessing expertise and professional networks and may promote ‘democratisation’ of voices in the simulation community.…
Li Xie, Wenying Shou
Microbial communities often perform important functions that arise from interactions among member species. Community functions can be improved via artificial selection: Many communities are repeatedly grown, mutations arise, and communities with the highest desired function are chosen to reproduce where each is…
Kyle Michael Schwing, Jonathan Pitt, Charles (Charlie) Jonathan Gomez
We propose a set of metrics, based upon the four flows theory of the communicative constitution of organizations, to evaluate the emergence of organization in a social network. Using an agent-based model (ABM), we validate that our metrics chart the evolution of partial organizations as the population progresses from…
Loes Crielaard, Andrew D Brown, Mary Nicolaou, Joshua Hayward + 2 more
'Karien Stronks' 'Steven Allender'] Abstract Objectives Systems approaches (SAs) seek to understand the dynamics behind system behaviour and formulate effective actions given these dynamics. In public health, SAs often rely on qualitative systems maps visualising factors and their interconnections, frequently developed…
Steven L. Peck, Andrew Heiss
Since the inception of the discipline, understanding causal complexity in ecological communities has been a challenge. Here we draw insights from recent work on constraint closure that suggests ways of grappling with ecological complexity that yield generalizable theoretical insights. Using a set of evolutionary…
David Carramiñana, Ana M. Bernardos, Juan A. Besada, José R. Casar
Providing a comprehensive view of the city operation and offering useful metrics for decisionmaking is a well-known challenge for urban risk-analysis systems. Existing systems are, in many cases, generalizations of previous domain specifc tools/methodologies that may not cover all urban interdependencies and makes it…
Jori Liesenborgs, Diana M Hendrickx, Elise Kuylen, David Niyukuri + 2 more
SimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible to the fast-growing community of R and Python users. Transmission, treatment and prevention of HIV…
Anna Matuszyńska, Oliver Ebenhöh, Matias D. Zurbriggen, Daniel C. Ducat + 1 more
Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a new era in which biology is being recreated in ways never before possible. It…
Daniel Silver, Ultan Byrne, Patrick Adler, Giorgio Fagiolo
This paper examines an important but underappreciated mechanism affecting urban segregation and integration: urban venues. The venue- an area where urbanites interact- is an essential aspect of city life that tends to influence residential location. We study the venue/segregation relationship by overlaying venues onto…
Petter Holme, Fredrik Liljeros
Quantitative social science is not only about regression analysis or, in general, data inference. Computer simulations of social mechanisms have an over 60 years long history. Tey have been used for many diferent purposes—to test scenarios, to test the consistency of descriptive theories (proof-of-concept models), to…
Yalin Li, John Trimmer, Steven Hand, Xinyi Zhang + 6 more
The pursuit of sustainability has catalyzed broad investment in the research, development, and deployment (RD&D) of innovative water, sanitation, and resource recovery technologies, yet the lack of transparent and agile methodologies to navigate the expansive landscape of technology development pathways remains a…
Weisi Guo, Guillem Mosquera Donate, Stephen Law, Samuel Johnson + 2 more
'Maria Liakata' 'Alan Wilson'] Abstract—In the past decade, cities have experienced rapid growth, expansion, and changes in their community structure. Many aspects of critical urban infrastructure are closely coupled with the human communities that they serve. Urban communities are composed of a multiplex of…
Christopher Woods, Lester Hedges, Adrian Mulholland, Maturos Malaisree + 10 more
Sire is a Python/C++ library that is used to both prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of…
Milosz Wieczor, Jacek Czub
Despite the increasing automation of workflows for the preparation of systems for molecular dynamics simulations, the custom editing of molecular topologies to accommodate non-standard modifications remains a daunting task even for experienced users. To alleviate this issue, we created Gromologist, a utility library…