Minimum Information About a Simulation Experiment (MIASE)

The original publication is available at www.ploscompbiol.orgReproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of simulations difficult. It is therefore essential to define the core information necessary to perform simulations of those models. The Minimum Information About a Simulation Experiment describes the minimal set of information that must be provided to make the description of a simulation experiment available to others. It includes the list of models to use and their modifications, all the simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any simulation experiment. The provision of this information, along with a set of required models, guarantees that the simulation experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and simulation of biological processes.The discussions that led to the definition of MIASE benefited from the support of a Japan Partnering Award by the UK Biotechnology and Biological Sciences Research Council. DW was supported by the Marie Curie program and by the German Research Association (DFG Research Training School ‘‘dIEM oSiRiS’’ 1387/1). This publication is based on work (EJC) supported in part by Award No KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). FTB acknowledges support by the NIH (grant 1R01GM081070- 01). JC is supported by the European Commission, DG Information Society, through the Seventh Framework Programme of Information and Communication Technologies, under the VPH NoE project (grant number 223920). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Publishers versio

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

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Model-Checking CSP-OZ Specifications with FDR

CSP-OZ is a formal method integrating two different specifications formalisms into one: the formalism Object-Z for the description of static aspects, and the process algebra CSP for the description of the dynamic behaviour of systems. The semantics of CSP-OZ is failure divergence taken from the process algebra side. In this paper we propose a method for checking correctness of CSP-OZ specifications via a translation into the CSP dialect of the model checker FDR

Neighborhood Socioeconomic Environment and Sexual Network Position

Rates of sexually transmitted infections (STIs) are strongly associated with neighborhood poverty; however, the mechanisms responsible for this association remain unclear. Using a population-based study of sexual networks among urban African American adolescents, we tested the hypothesis that poverty, unemployment, and the sex ratio drive STI rates by affecting sexual network structure. Participants were categorized as being in one of three network positions that had previously been found to be strongly linked to infection with chlamydia and gonorrhea: being in a confirmed dyad (i.e., a monogamous pair), being connected to a larger network through one partner, and being in the center of a larger network. We found that only poverty was statistically significantly associated with sexual network position. Residing in the poorest third of neighborhoods was associated with 85% decreased odds of being in confirmed dyads. There was no association of sexual network position with neighborhood employment. Living in a neighborhood with an unequal number of young men and women appeared to be associated with a higher likelihood of being in a confirmed dyad; however, the differences were not statistically significant. These results suggest that poverty may impact STI rates by shaping sexual network structure, but we did not find any evidence that this association operates through unemployment or the sex ratio