SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems

Motivation 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. Results 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 specialized SBML simulators. Availability and implementation SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica.

TRuML: A Translator for Rule-Based Modeling Languages

ABSTRACTRule-based modeling languages, such as the Kappa and BioNetGen languages (BNGL), are powerful frameworks for modeling the dynamics of complex biochemical reaction networks. Each language is distributed with a distinct software suite and modelers may wish to take advantage of both toolsets. This paper introduces a practical application called TRuML that translates models written in either Kappa or BNGL into the other language. While similar in many respects, key differences between the two languages makes translation sufficiently complex that automation becomes a useful tool. TRuML accommodates the languages’ complexities and produces a semantically equivalent model in the alternate language of the input model when possible and an approximate model in certain other cases. Here, we discuss a number of these complexities and provide examples of equivalent models in both Kappa and BNGL.CCS CONCEPTS• Applied computing → Systems biology; • Computing methodologies → Simulation languages;

Cyber-Physical System Development Environment for Energy Applications

Cyber-physical systems (CPS) are smart systems that include engineered interacting networks of physical and computational components. The tight integration of a wide range of heterogeneous components enables new functionality and quality of life improvements in critical infrastructures such as smart cities, intelligent buildings, and smart energy systems. One approach to study CPS uses both simulations and hardware-in-the-loop (HIL) to test the physical dynamics of hardware in a controlled environment. However, because CPS experiment design may involve domain experts from multiple disciplines who use different simulation tool suites, it can be a challenge to integrate the heterogeneous simulation languages and hardware interfaces into a single experiment. The National Institute of Standards and Technology (NIST) is working on the development of a universal CPS environment for federation (UCEF) that can be used to design and run experiments that incorporate heterogeneous physical and computational resources over a wide geographic area. This development environment uses the High Level Architecture (HLA), which the Department of Defense has advocated for co-simulation in the field of distributed simulations, to enable communication between hardware and different simulation languages such as Simulink® and LabVIEW®. This paper provides an overview of UCEF and motivates how the environment could be used to develop energy experiments using an illustrative example of an emulated heat pump system.

A new type of hydraulic cylinder system controlled by the new-type hydraulic transformer

In order to enhance the efficiency of the hydraulic system, one new-type hydraulic transformer is presented in this paper. First, the basic structure and the principle of the new-type hydraulic transformer are explained. Then, the mathematical models including both the inner and outer loops are analyzed. Moreover, two kinds of control methods are discussed corresponding to the two loops, respectively. Furthermore, the proposed strategies are translated into the simulation languages, and the simulation is made in Simulink. Finally, the prototypes of new-type hydraulic transformer and the test rig are constructed to test the performance. Both the simulated and experimental results show that the new-type hydraulic transformer can be used in the practical condition, and the proposed control algorithm is suitable.