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’.

Following the simple observation that the interconnection of a set of quantum optical input–output devices can be specified using structural mode VHSIC hardware description language, we demonstrate a computer-aided schematic capture workflow for modelling and simulating multi-component photonic circuits. We describe an algorithm for parsing circuit descriptions to derive quantum equations of motion, illustrate our approach using simple examples based on linear and cavity-nonlinear optical components, and demonstrate a computational approach to hierarchical model reduction.

We examine a proposal by Sherson and Mølmer to generate polarization-squeezed light in terms of quantum stochastic calculus (QSC). We investigate the statistics of the output field and confirm their results using the QSC formalism. In addition, we study the atomic dynamics of the system and find that this setup can produce up to 3 dB of atomic spin squeezing.

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.

We propose a model, based on a quantum stochastic differential equation (QSDE), to describe the scattering of polarized laser light by an atomic gas. The gauge terms in the QSDE account for the direct scattering of the laser light into different field channels. Once the model has been set, we can rigorously derive quantum filtering equations for balanced polarimetry and homodyne detection experiments, study the statistics of output processes, and investigate a strong driving, weak coupling limit.