Chaste: a test-driven approach to software development for biological modelling

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud \ud Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling

The Genomic HyperBrowser: inferential genomics at the sequence level

The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical analysis of sequence-level genomic information. We provide a growing collection of generic biological investigations that query pairwise relations between tracks, represented as mathematical objects, along the genome. The Genomic HyperBrowser implements the approach and is available at http://hyperbrowser.uio.no

iTETRIS: An Integrated Wireless and Traffic Platform for Real-Time Road Traffic Management Solutions

Wireless vehicular cooperative systems have been identified as an attractive solution to improve road traffic management, thereby contributing to the European goal of safer, cleaner, and more efficient and sustainable traffic solutions. V2V-V2I communication technologies can improve traffic management through real-time exchange of data among vehicles and with road infrastructure. It is also of great importance to investigate the adequate combination of V2V and V2I technologies to ensure the continuous and costefficient operation of traffic management solutions based on wireless vehicular cooperative solutions. However, to adequately design and optimize these communication protocols and analyze the potential of wireless vehicular cooperative systems to improve road traffic management, adequate testbeds and field operational tests need to be conducted. Despite the potential of Field Operational Tests to get the first insights into the benefits and problems faced in the development of wireless vehicular cooperative systems, there is yet the need to evaluate in the long term and large dimension the true potential benefits of wireless vehicular cooperative systems to improve traffic efficiency. To this aim, iTETRIS is devoted to the development of advanced tools coupling traffic and wireless communication simulators

Simulation of droplet-based microfluidic lab-on-a-chip applications

This paper was presented at the 3rd Micro and Nano Flows Conference (MNF2011), which was held at the Makedonia Palace Hotel, Thessaloniki in Greece. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, Aristotle University of Thessaloniki, University of Thessaly, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute.Miniaturization of biological and chemical assays in lab-on-a-chip systems is a highly topical field of research. Droplet-based microfluidic chips are types of these miniaturized systems. They expand the capability of assays with special features that are unreached by traditional workflows. In particular, small sample volumes, independent separated reaction units, high throughput, automation and parallelization of assays are prominent features of droplet-based microfluidic devices. Full custom centric design of droplet-based microfluidic lab-on-a-chip technology implicates a high system integration level and design complexity. Therefore advanced development methodologies are needed, comparable with the methods in electronic design automation. Our design and simulation toolkit meets these requirements for an agile and low-risk development of custom lab-on-a-chip devices. The system simulation approach enables a fast and precise prediction of complex microfluidic networks. This fact is confirmed by reference and benchmark experiments. The results show that the simulation correctly reproduces the experimental measurements.The German BMBF and the EU in the projects DiNaMiD, signature 0315591B and NoE Photonics4Life, Grant Agreement number: 224014