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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 microbial population dynamics in a reproducible, transparent and scalable way. The Community Simulator includes five major elements: tools for preparing the initial states and environmental conditions for a set of samples, automatic generation of dynamical equations based on a dictionary of modeling assumptions, random parameter sampling with tunable levels of metabolic and taxonomic structure, parallel integration of the dynamical equations, and support for metacommunity dynamics with migration between samples. To significantly speed up simulations using Community Simulator, our Python package implements a new Expectation-Maximization (EM) algorithm for finding equilibrium states of community dynamics that exploits a recently discovered duality between ecological dynamics and convex optimization. We present data showing that this EM algorithm improves performance by between one and two orders compared to direct numerical integration of the corresponding ordinary differential equations. We conclude by listing several recent applications of the Community Simulator to problems in microbial ecology, and discussing possible extensions of the package for directly analyzing microbiome compositional data.
This article was published in the following journal.
Name: PloS one
Single borehole dilution tests (SBDTs) are an inexpensive but effective technique for hydrogeological characterization of hard-rock aquifers. We present a freely available, easy-to-use, open-source Py...
PyIOmica is an open-source Python package focusing on integrating longitudinal multiple omics datasets, characterizing, and categorizing temporal trends. The package includes multiple bioinformatics t...
Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interac...
Quantifying the spatial pattern of landscapes has become a common task of many studies in landscape ecology. Most of the existing software to compute landscape metrics is not well suited to be used in...
Metabolic networks can model the behavior of metabolism in the cell. Since analyzing the whole metabolic networks is not easy, network modulation is an important issue to be investigated. Decomposing ...
The study will be a mixed methods, two-arm, cluster-randomized controlled trial. The primary aim of this evaluation is to measure the effectiveness of the Community-Based Nutrition Package...
This study evaluates the effectiveness of a wheelchair simulator in the training of power wheelchair driving skills. Practice with the simulator takes place at home.
Evaluation of a digital simulator to train diagnostic skills in Ophthalmology
A cluster randomised trial to determine the impact of an integrated community-based package of HIV services incorporating HIV testing, linkage to care and ongoing adherence support, combin...
Chronic non-healing wounds considerably impact quality of life in affected patients and are a substantial burden on the Canadian health care system. Microbes colonizing a chronic wound pla...
The collective designation of three organizations with common membership: the European Economic Community (Common Market), the European Coal and Steel Community, and the European Atomic Energy Community (Euratom). It was known as the European Community until 1994. It is primarily an economic union with the principal objectives of free movement of goods, capital, and labor. Professional services, social, medical and paramedical, are subsumed under labor. The constituent countries are Austria, Belgium, Denmark, Finland, France, Germany, Greece, Ireland, Italy, Luxembourg, Netherlands, Portugal, Spain, Sweden, and the United Kingdom. (The World Almanac and Book of Facts 1997, p842)
Enumeration by direct count of viable, isolated bacterial, archaeal, or fungal CELLS or SPORES capable of growth on solid CULTURE MEDIA. Each colony (i.e., microbial colony-forming unit) represents the progeny of a single cell in the original inoculum. The method is used routinely by environmental microbiologists for quantifying organisms in AIR; FOOD; and WATER; by clinicians for measuring patients' microbial load; and in antimicrobial drug testing.
A frequent complication of drug therapy for microbial infection. It may result from opportunistic colonization following immunosuppression by the primary pathogen and can be influenced by the time interval between infections, microbial physiology, or host resistance. Experimental challenge and in vitro models are sometimes used in virulence and infectivity studies.
The branch of science concerned with the interrelationship of organisms and their ENVIRONMENT, especially as manifested by natural cycles and rhythms, community development and structure, interactions between different kinds of organisms, geographic distributions, and population alterations. (Webster's, 3d ed)
Light absorbing proteins and protein prosthetic groups found in certain microorganisms. Some microbial photoreceptors initiate specific chemical reactions which signal a change in the environment, while others generate energy by pumping specific ions across a cellular membrane.