BioSimulators: a central registry of simulation engines and services for recommending specific tools
Myers, Chris J
Abstract
<p class="p1" style="margin: 0px; font-stretch: normal; font-size: 10px; line-height: normal; font-family: Helvetica; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: #141413;"><strong>Computational models have great potential to ac</strong><strong>celerate bioscience, bioengineering, and medicine. </strong><strong>However, it remains challenging to reproduce and </strong><strong>reuse simulations, in part, because the numerous </strong><strong>formats and methods for simulating various sub </strong><strong>systems and scales remain siloed by different soft</strong><strong>ware tools. For example, each tool must be exe</strong><strong>cuted through a distinct interface. To help investi</strong><strong>gators find and use simulation tools, we developed </strong><strong>BioSimulators </strong><strong>(https:</strong>//<strong>biosimulators.org), a central </strong><strong>registry of the capabilities of simulation tools and </strong><strong>consistent Python, command-line and containerized </strong><strong>interfaces to each version of each tool. The founda</strong><strong>tion of BioSimulators is standards, such as CellML, </strong><strong>SBML, SED-ML and the COMBINE archive format, </strong><strong>and validation tools for simulation projects and sim</strong><strong>ulation tools that ensure these standards are used </strong><strong>consistently. To help modelers find tools for partic</strong><strong>ular projects, we have also used the registry to de</strong><strong>velop recommendation services. We anticipate that </strong><strong>BioSimulators will help modelers exchange, repro</strong><strong>duce, and combine simulations.</strong>