Abstract: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g., enable in-silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models.Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems.In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2 -compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate, and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialised SBML simulators.SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica

Abstract: Stress is a risk factor for impaired general, mental and reproductive health. The role of physiological and supraphysiological estradiol concentrations in stress perception and stress processing is less well understood. We therefore, conducted a prospective observational study to investigate the association between estradiol, stress perception and stress-related cognitive performance within serial measurements either during the natural menstrual cycle or during fertility treatment, where estradiol levels are strongly above the physiological level of a natural cycle and consequently, represent a good model to study dose-dependent effects of estradiol. Data from 44 women receiving in vitro fertilization at the Department of Reproductive Endocrinology in Zurich, Switzerland was compared to data from 88 women with measurements during their natural menstrual cycle. The german version of the Perceived Stress Questionnaire (PSQ) and the Cognitive Bias Test (CBT), in which cognitive performance is tested under time stress were used to evaluate subjective and functional aspects of stress. Estradiol levels were investigated at four different time points during the menstrual cycle and at two different time points during a fertility treatment. Cycle phase were associated with PSQ worry and cognitive bias in normally cycling women, but different phases of fertility treatment were not associated with subjectively perceived stress and stress-related cognitive bias. PSQ lack of joy and PSQ demands related to CBT in women receiving fertility treatment but not in women with a normal menstrual cycle. Only strong changes of the estradiol level during fertility treatment were weakly associated with CBT, but not with subjectively experienced stress. Our research emphasises the multidimensional character of stress and the necessity to adjust stress research to the complex nature of stress perception and processing. Infertility is associated with an increased psychological burden in patients. However, not all phases of the process to overcome infertility do significantly increase patient stress levels. Also, research on the psychological burden of infertility should consider that stress may vary during the different phases of fertility treatment.

Abstract: The NRL Pump protocol defines a multilevel secure component whose goal is to minimize leaks of information from high level systems to lower level systems, without degrading average time performances. We define a probabilistic model for the NRL Pump and show how a probabilistic model checker (FHP-mur$\varphi$) can be used to estimate the capacity of a probabilistic covert channel in the NRL Pump. We are able to compute the probability of a security violation as a function of time for various configurations of the system parameters (e.g. buffer sizes, moving average size, etc). Because of the model complexity, our results cannot be obtained using an analytical approach and, because of the low probabilities involved, it can be hard to obtain them using a simulator.

Abstract: Fuzzy control is well known as a powerful technique for designing and realizing control systems. However, statistical evidence for their correct behavior may be not enough, even when it is based on a large number of samplings. In order to provide a more systematic verification process, the cell-to-cell mapping technology has been used in a number of cases as a verification tool for fuzzy control systems and, more recently, to assess their optimality and robustness. However, cell-to-cell mapping is typically limited in the number of cells it can explore. To overcome this limitation, in this paper we show how model checking techniques may be instead used to verify the correct behavior of a fuzzy control system. To this end, we use a modified version of theMurphi verifier, which ease the modeling phase by allowing to use finite precision real numbers and external C functions. In this way, also already designed simulators may be used for the verification phase. With respect to the cell mapping technique, our approach appears to be complementary; indeed, it explores a much larger number of states, at the cost of being less informative on the global dynamic of the system.