James Lawson

The CellML Model Repository

SUMMARY The CellML Model Repository provides free access to over 330 biological models. The vast majority of these models are derived from published, peer-reviewed papers. Model curation is an important and ongoing process to ensure the CellML model is able to accurately reproduce the published results. As the CellML community grows, and more people add their models to the repository, model annotation will become increasingly important to facilitate data searches and information retrieval. AVAILABILITY The CellML Model Repository is publicly accessible at http://www.cellml.org/models.

Controlled vocabularies and semantics in systems biology

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a models longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments.

The Physiome Model Repository 2

MOTIVATION The Physiome Model Repository 2 (PMR2) software was created as part of the IUPS Physiome Project (Hunter and Borg, 2003), and today it serves as the foundation for the CellML model repository. Key advantages brought to the end user by PMR2 include: facilities for model exchange, enhanced collaboration and a detailed change history for each model. AVAILABILITY PMR2 is available under an open source license at http://www.cellml.org/tools/pmr/; a fully functional instance of this software can be accessed at http://models.physiomeproject.org/.

Standard virtual biological parts

MOTIVATION Fabrication of synthetic biological systems is greatly enhanced by incorporating engineering design principles and techniques such as computer-aided design. To this end, the ongoing standardization of biological parts presents an opportunity to develop libraries of standard virtual parts in the form of mathematical models that can be combined to inform system design. RESULTS We present an online Repository, populated with a collection of standardized models that can readily be recombined to model different biological systems using the inherent modularity support of the CellML 1.1 model exchange format. The applicability of this approach is demonstrated by modeling gold-medal winning iGEM machines. AVAILABILITY AND IMPLEMENTATION The Repository is available online as part of http://models.cellml.org. We hope to stimulate the worldwide community to reuse and extend the models therein, and contribute to the Repository of Standard Virtual Parts thus founded. Systems Model architecture information for the Systems Model described here, along with an additional example and a tutorial, is also available as Supplementary information. The example Systems Model from this manuscript can be found at http://models.cellml.org/workspace/bugbuster. The Template models used in the example can be found at http://models.cellml.org/workspace/SVP_Templates200906.

CellML metadata standards, associated tools and repositories

The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and a substantial number of models are now available in the CellML Model Repository. However, there is an urgent need to extend the current CellML metadata standard to provide biological and biophysical annotation of the models in order to facilitate model sharing, automated model reduction and connection to biological databases. This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website.

Integration of a Class-E low DV/DT rectifer in a wireless power transfer system

This paper presents the integration of a Class-E rectifier into a high frequency semi-resonant inductive power transfer system. The rectifier is used to rectify the 5.56 MHz ac output of the resonant receiving coil. End to end efficiencys exceeding 69 % are demonstrated while transferring 120 W with 30 cm coil spacing. Rectifier topologies were reviewed with their applicability to high frequency resonant IPT as a focus. A voltage driven series inductor low dv/dt resonant Class-E rectifier was selected for integration into an existing inductive power transfer system. System and rectifier efficiency is shown at 30 cm and 40 cm coil separation. Rectifier efficiency is estimated as 90.9% on the basis of the loss in overall system efficiency when using the rectifier.

Long range inductive power transfer system

We report upon a recently developed long range inductive power transfer system (IPT) designed to power remote sensors with mW level power consumption at distances up to 7 m. In this paper an inductive link is established between a large planar (1 x 1 m) transmit coil (Tx) and a small planer (170 x 170 mm) receiver coil (Rx), demonstrating the viability of highly asymmetrical coil congurations that real-world applications such as sensor networks impose. High Q factor Tx and Rx coils required for viable power transfer eciencies over such distances are measured using a resonant method. The applicability of the Class-E amplier in very low magnetic coupling scenarios and at the high frequencies of operation required for high Q operation is demonstrated by its usage as the Tx coil driver.

A Distributed Revision Control System for Collaborative Development of Quantitative Biological Models

With CellML 1.0, models are encapsulated completely by a single file. CellML 1.1 now allows a model to be decomposed into many smaller files that can represent a single component of a model that can be reused by other related models. Unfortunately, managing even just tens of models with hundreds of shared component files may be a daunting task. For instance, updating a shared component for one model may break another, or it may be difficult to locate the correct component to be included into a model that one may be building.

Position-insensitive long range inductive power transfer

This paper presents results of an improved inductive wireless power transfer system for reliable long range powering of sensors with milliwatt-level consumption. An ultra-low power flyback impedance emulator operating in open loop is used to present the optimal load to the receivers resonant tank. Transmitter power modulation is implemented in order to maintain constant receiver power and to prevent damage to the receiver electronics caused by excessive received voltage. Received power is steady up to 3 m at around 30 mW. The receiver electronics and feedback system consumes 3.1 mW and so with a transmitter input power of 163.3 W the receiver becomes power neutral at 4.75 m. Such an IPT system can provide a reliable alternative to energy harvesters for supplying power concurrently to multiple remote sensors.

Efficient artificial magnetic conductor shield for wireless power

Artificial magnetic conductors (AMC) offer a solution to increasing link efficiency in inductive power transfer (IPT) while reducing magnetic fields outside the air gap. A practical design for an artificial magnetic conductor, suitable for use as a shield for inductive power transfer, is presented. The AMC makes use of a ferrite substrate and lumped capacitor loading. A model of the plane wave behaviour of the structure is compared to simulation and the performance of the AMC compared to other shielding solutions, in an IPT scenario. The plane wave behaviour is found not to provide a good prediction of the AMC behaviour in the IPT scenario. The AMC shield is found to offer the greatest link efficiency, in the IPT scenario.