SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems

by   Filippo Maggioli, et al.

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 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:



page 1

page 2

page 3

page 4


Development of a General Purpose Sentiment Lexicon for Igbo Language

There are publicly available general purpose sentiment lexicons in some ...

JuxtaPiton: Enabling Heterogeneous-ISA Research with RISC-V and SPARC FPGA Soft-cores

Energy efficiency has become an increasingly important concern in comput...

Reconciling interoperability with efficient Verification and Validation within open source simulation environments

A Cyber-Physical System (CPS) comprises physical as well as software sub...

BioADAPT-MRC: Adversarial Learning-based Domain Adaptation Improves Biomedical Machine Reading Comprehension Task

Motivation: Biomedical machine reading comprehension (biomedical-MRC) ai...

The MosaicSim Simulator (Full Technical Report)

As Moore's Law has slowed and Dennard Scaling has ended, architects are ...

Enso: A general-purpose virtual machine

In this paper we introduce Enso, a virtual machine designed to be used a...

GzScenic: Automatic Scene Generation for Gazebo Simulator

Testing robotic and cyberphysical systems in simulation require specific...
This week in AI

Get the week's most popular data science and artificial intelligence research sent straight to your inbox every Saturday.