OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans.

The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole. The OpenWorm Foundation is an independent research organization working towards an integrative simulation of the nematode Caenorhabditis elegans, with the aim of providing a powerful new tool to understand how the organism's behaviour arises from its fundamental biology. In this perspective, we give an overview of the history and philosophy of OpenWorm, descriptions of the constituent sub-projects and corresponding open-science management practices, and discuss current achievements of the project and future directions.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.

Unit testing, model validation, and biological simulation.

The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models.

Inability to ventilate while using a silicone-based endotracheal tube.

We present a complication associated with herniation of a specially designed silicone-based endotracheal tube (ETT) cuff used for laryngeal nerve monitoring (electromyographic [EMG] ETT). Lung ventilation in our patient was initially unimpeded. However, 30 minutes after initiation of anesthesia with desflurane and nitrous oxide, there was a sudden inability to ventilate due to the herniation of the ETT cuff presumably caused by diffusion of nitrous oxide into the silicone-based cuff. In vitro testing has shown that the increase in intracuff pressure during ventilation with nitrous oxide in the silicone-based EMG ETT is much greater (approximately 50 mmHg) than that in the polyvinyl chloride-based ETT (approximately 10 mmHg) routinely used in our department.