PharmML in Action: an Interoperable Language for Modeling and Simulation.
Ontology highlight
ABSTRACT:
SUBMITTER: Bizzotto R
PROVIDER: S-EPMC5658288 | biostudies-other | 2017 Oct
REPOSITORIES: biostudies-other
Publications
PharmML in Action: an Interoperable Language for Modeling and Simulation.
Bizzotto R R Comets E E Smith G G Yvon F F Kristensen N R NR Swat M J MJ
CPT: pharmacometrics & systems pharmacology 20170915 10
PharmML is an XML-based exchange format created with a focus on nonlinear mixed-effect (NLME) models used in pharmacometrics, but providing a very general framework that also allows describing mathematical and statistical models such as single-subject or nonlinear and multivariate regression models. This tutorial provides an overview of the structure of this language, brief suggestions on how to work with it, and use cases demonstrating its power and flexibility. ...[more]
Similar Datasets
Project description:The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems), an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE). BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language), a very common description language used in systems biology. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems) have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology).
| S-EPMC5546598 | biostudies-other
Project description:Memory is essential to many cognitive tasks including language. Apart from empirical studies of memory effects on language acquisition and use, there lack sufficient evolutionary explorations on whether a high level of memory capacity is prerequisite for language and whether language origin could influence memory capacity. In line with evolutionary theories that natural selection refined language-related cognitive abilities, we advocated a coevolution scenario between language and memory capacity, which incorporated the genetic transmission of individual memory capacity, cultural transmission of idiolects, and natural and cultural selections on individual reproduction and language teaching. To illustrate the coevolution dynamics, we adopted a multi-agent computational model simulating the emergence of lexical items and simple syntax through iterated communications. Simulations showed that: along with the origin of a communal language, an initially-low memory capacity for acquired linguistic knowledge was boosted; and such coherent increase in linguistic understandability and memory capacities reflected a language-memory coevolution; and such coevolution stopped till memory capacities became sufficient for language communications. Statistical analyses revealed that the coevolution was realized mainly by natural selection based on individual communicative success in cultural transmissions. This work elaborated the biology-culture parallelism of language evolution, demonstrated the driving force of culturally-constituted factors for natural selection of individual cognitive abilities, and suggested that the degree difference in language-related cognitive abilities between humans and nonhuman animals could result from a coevolution with language.
| S-EPMC4636343 | biostudies-literature
Project description:Theoretical and empirical accounts suggest that impairments in self-other discrimination processes are likely to promote the expression of hallucinations. Studies using a variety of paradigms involving self-performed actions argue in favor of perspective taking confusion in hallucination-prone subjects. However, our understanding of such processes during adolescence is still at an early stage. The present study thus aims (1) to delineate the neural correlates sustaining mental simulation of actions involving self-performed actions (first-person perspective; 1PP) and other-performed actions (third-person perspective; 3PP) during adolescence (2) to identify atypical activation patterns during 1PP/3PP mental simulation of actions in hallucination-prone adolescents (3) to examine whether differential risk for schizophrenia (clinical vs. genetic) is also associated with differential impairments in the 1PP/3PP mental simulation of actions during adolescence. Twenty-two typically developing controls (Control group; 6 females), 12 hallucination-prone adolescents [auditory hallucination (AH) group; 7 females] and 13 adolescents with 22q11.2 Deletion Syndrome (22q11.2DS group; 4 females) were included in the study. During the fMRI task, subjects were presented with a cue (self-other priming cues) indicating to perform the task using either a first person perspective ("you"-1PP) or a third person perspective ("best friend"-3PP) and then they were asked to mentally simulate actions based on the type of cue. Hallucination-proneness was assessed using a self-report questionnaire [Cardiff Anomalous Perception Scale (CAPS)]. Our results indicated that atypical patterns of cerebral activation, particularly in the key areas of self-other distinction, were found in both groups at risk for auditory hallucinations (AHs and 22q11.2DS). More precisely, adolescents in the AH group presented decreased activations in the right middle occipital gyrus BA19, left cingulate gyrus BA31, and right precuneus BA31 for the 3PP > 1PP contrast. Adolescents in the 22q11.2DS group presented decreased activations in the right superior occipital gyrus BA19, left caudate tail and left precuneus BA7 for the 3PP > 1PP contrast. In comparison to the Control group, only the 22q11.2DS adolescents showed a decreased activation for other-related cues (prime other > prime self contrast) in areas of visual imagery, episodic memory and social cognition. This study characterizes the neural correlates of mental imagery for actions during adolescence, and suggests that a differential risk for hallucination-proneness (clinical vs. genetic) is associated to similar patterns of atypical activations in key areas sustaining self-other discrimination processes. These observations may provide relevant information for future research and prevention strategies with regards to hallucination-proneness during adolescence.
| S-EPMC3701149 | biostudies-literature
Project description:This article describes an operational framework for implementing translational simulation in everyday practice. The framework, based on an input-process-output model, is developed from a critical review of the existing translational simulation literature and the collective experience of the authors' affiliated translational simulation services. The article describes how translational simulation may be used to explore work environments and/or people in them, improve quality through targeted interventions focused on clinical performance/patient outcomes, and be used to design and test planned infrastructure or interventions. Representative case vignettes are used to show how the framework can be applied to real world healthcare problems, including clinical space testing, process development, and culture. Finally, future directions for translational simulation are discussed. As such, the article provides a road map for practitioners who seek to address health service outcomes using translational simulation.
| S-EPMC7930894 | biostudies-literature
Project description:The notion of language comprehension as mental simulation has become popular in cognitive science. We revisit some of the original empirical evidence for this. Specifically, we attempted to replicate the findings from earlier studies that examined the mental simulation of object orientation, shape, and color, respectively, in sentence-picture verification. For each of these sets of findings, we conducted two web-based replication attempts using Amazon's Mechanical Turk. Our results are mixed. Participants responded faster to pictures that matched the orientation or shape implied by the sentence, replicating the original findings. The effect was larger and stronger for shape than orientation. Participants also responded faster to pictures that matched the color implied by the sentence, whereas the original studies obtained mismatch advantages. We argue that these results support mental simulation theory, show the importance of replication studies, and show the viability of web-based data collection.
| S-EPMC3530580 | biostudies-literature
Project description:A controversial question in cognitive neuroscience is whether comprehension of words and sentences engages brain mechanisms specific for decoding linguistic meaning or whether language comprehension occurs through more domain-general sensorimotor processes. Accumulating behavioral and neuroimaging evidence suggests a role for cortical motor and premotor areas in passive action-related language tasks, regions that are known to be involved in action execution and observation. To examine the involvement of these brain regions in language and nonlanguage tasks, we used functional magnetic resonance imaging (fMRI) on a group of 21 healthy adults. During the fMRI session, all participants 1) watched short object-related action movies, 2) looked at pictures of man-made objects, and 3) listened to and produced short sentences describing object-related actions and man-made objects. Our results are among the first to reveal, in the human brain, a functional specialization within the ventral premotor cortex (PMv) for observing actions and for observing objects, and a different organization for processing sentences describing actions and objects. These findings argue against the strongest version of the simulation theory for the processing of action-related language.
| S-EPMC3114551 | biostudies-literature
Project description:Experience alters behavior by producing enduring changes in the neural processes that support performance. For example, performing a specific action improves the execution of that action via changes in associated sensory and motor neural circuitry, and experience using language improves language comprehension by altering the anatomy and physiology of perisylvian neocortical brain regions. Here we provide evidence that specialized (sports) motor experience enhances action-related language understanding by recruitment of left dorsal lateral premotor cortex, a region normally devoted to higher-level action selection and implementation-even when there is no intention to perform a real action. Experience playing and watching sports has enduring effects on language understanding by changing the neural networks that subserve comprehension to incorporate areas active in performing sports skills. Without such experience, sport novices recruit lower-level sensory-motor regions, thought to support the instantiation of movement, during language processing, and activity in primary motor areas does not help comprehension. Thus, the language system is sufficiently plastic and dynamic to encompass expertise-related neural recruitment outside core language networks.
| S-EPMC2527992 | biostudies-literature
Project description:Count data, or number of events per time interval, are discrete data arising from repeated time to event observations. Their mean count, or piecewise constant event rate, can be evaluated by discrete probability distributions from the Poisson model family. Clinical trial data characterization often involves population count analysis. This tutorial presents the basics and diagnostics of count modeling and simulation in the context of pharmacometrics. Consideration is given to overdispersion, underdispersion, autocorrelation, and inhomogeneity.
| S-EPMC4150925 | biostudies-literature
Project description:It is generally difficult to define reasonable parameters and interpret their values in mathematical models of social phenomena. Rather than directly fitting abstract parameters against empirical data, we should define some concrete parameters to denote the sociocultural factors relevant for particular phenomena, and compute the values of these parameters based upon the corresponding empirical data. Taking the example of modeling studies of language competition, we propose a language diffusion principle and two language inheritance principles to compute two critical parameters, namely the impacts and inheritance rates of competing languages, in our language competition model derived from the Lotka-Volterra competition model in evolutionary biology. These principles assign explicit sociolinguistic meanings to those parameters and calculate their values from the relevant data of population censuses and language surveys. Using four examples of language competition, we illustrate that our language competition model with thus-estimated parameter values can reliably replicate and predict the dynamics of language competition, and it is especially useful in cases lacking direct competition data.
| S-EPMC3683775 | biostudies-literature
Project description:Complex networks can model a wide range of complex systems in nature and society, and many algorithms (network generators) capable of synthesizing networks with few and very specific structural characteristics (degree distribution, average path length, etc.) have been developed. However, there remains a significant lack of generators capable of synthesizing networks with strong resemblance to those observed in the real-world, which can subsequently be used as a null model, or to perform tasks such as extrapolation, compression and control. In this paper, a robust new approach we term Action-based Modeling is presented that creates a compact probabilistic model of a given target network, which can then be used to synthesize networks of arbitrary size. Statistical comparison to existing network generators is performed and results show that the performance of our approach is comparable to the current state-of-the-art methods on a variety of network measures, while also yielding easily interpretable generators. Additionally, the action-based approach described herein allows the user to consider an arbitrarily large set of structural characteristics during the generator design process.
| S-EPMC5532273 | biostudies-literature