BioSimulators: a central registry of simulation engines and services for recommending specific tools

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations

libCellML - 10th CellML Conference

Presentation on libCellML at the 10th CellML Workshop, Auckland, New Zealand

GET: Generalised Epithelial Transport

<p>The presentation I gave at the 8th International CellML Workshop introducing my suite of tools for modelling epoithelial transport using CellML.</p

OpenCMISS-Zinc: Visualising Research

<p>OpenCMISS-Zinc is a software library for creating interactive graphical modelling applications.  Suitable for, but not limited to, representing biological finite element models.  OpenCMISS-Zinc uses OpenGL and is available on Windows, Mac and Linux via a C, C++ or Python API.</p

PMR2: supporting collaborative, reproducible, and discoverable science

<p>My poster from the ICSB 2014 meeting.</p> <p> ABSTRACT:</p> <p>Background: PMR2 is the software framework supporting the Physiome Repository (https://models.physiomeproject.org). All content of the Physiome Repository is stored in version-controlled workspaces and specific revisions of a workspace can be exposed with a persistent URL and customisable presentation via the web interface. Access control is a key part of PMR2 and users of the Physiome Repository are able to choose to keep their data private, shared with specific collaborators, or public.</p> <p>Method: Recent developments in the PMR2 software stack have seen the inclusion of semantic web technologies and the provision of new web services that are able to leverage the semantic content of the Physiome Repository to enhance the ability of application developers to discover, access, and modify data contained in the Physiome Repository.</p> <p>Results: Users of the Physiome Repository are now able to flag specific items in their workspaces as annotations to be indexed in the semantic knowledgebase of the repository. When new versions of these items are pushed into the workspace, the knowledgebase is automatically updated. Application developers are able to make use of PMR2 web services to access this semantic knowledgebase to discover data matching their requirements.</p> <p>Conclusion: PMR2 provides a framework encouraging the collaborative development and evolution of mathematical models and associated data. Recent innovation in the PMR2 framework has significantly improved the ability of application developers and repository users to discover content that meets their requirements.</p

Developing the Virtual Physiological Human: tools, techniques, and best practices for data exchange, storage, and publication

<p>Poster from the IEEE EMBS Conference 2015, held in Milan, Italy. Introduces some key technologies enabling the development of the Virtual Physiological Human as well as some new material being developed to introduce new doctoral students to computational physiology.</p

CellML 2.0.1

We present here CellML 2.0.1, an XML-based language for describing and exchanging mathematical models of physiological systems. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of reusable components, each with variables and equations giving relationships between those variables. Models may import other models to create systems of increasing complexity. CellML 2.0.1 is defined by the normative specification presented here, prescribing the CellML syntax and the rules by which it should be used. The normative specification is intended primarily for the developers of software tools which directly consume CellML syntax. Users of CellML models may prefer to browse the informative rendering of the specification (https://cellml.org/specifications/cellml_2.0/) which extends the normative specification with explanations of the rules combined with examples of their usage. This version improves the identification of rule statements and corrects errata present in the CellML 2.0 specification

CellML 2.0

We present here CellML 2.0, an XML-based language for describing and exchanging mathematical models of physiological systems. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of reusable components, each with variables and equations giving relationships between those variables. Models may import other models to create systems of increasing complexity. CellML 2.0 is defined by the normative specification presented here, prescribing the CellML syntax and the rules by which it should be used. The normative specification is intended primarily for the developers of software tools which directly consume CellML syntax. Users of CellML models may prefer to browse the informative rendering of the specification (https://cellml.org/specifications/cellml_2.0/) which extends the normative specification with explanations of the rules combined with examples of their usage

cellml/libcellml: v0.4.0-rc.2

&lt;p&gt;This is a development release of libCellML v0.4.0-rc.2&lt;/p&gt

cellml/libcellml: v0.3.99

&lt;p&gt;This is an official release of libCellML v0.3.99&lt;/p&gt