Linking Unit Tests and Properties

QuickCheck allows us to verify software against particular proper- ties. A property can be regarded as an abstraction over many unit tests. QuickCheck uses generated random input data to test such properties. If a counterexample is found, it becomes immediately clear what we have tested. This is not the case when all tests pass, since we do not (and shall not) see the actual generated test cases. How can we be sure about what is tested? QuickCheck has the ability to gather statistics about the test cases, which is insightful. But still it does not tell us whether the particular unit test scenarios we have in mind are included. For this reason, we have developed a tool that can answer this question. It checks if a given unit test can be generated by a property, making it easier to judge the property’s quality. We have applied our tool to an industrial use case of testing the AUTOSAR basic software modules and shows that it can handle complex models and large unit tests

Endemic Sexual Violence and Abuse: Contexts and Dispositions

Endemic sexual violence and abuse has been observed in a number of specific circumstances, most notably conflict zones, remote and marginalised communities, and religious and state institutions. In this article we examine several documented examples and argue that a similar set of causal processes are at work in all of these otherwise apparently disparate circumstances. Rather than construing the problem as ‘organised’ sexual abuse, we present the problem in terms of the breakdown (or disorganisation) of usual individual, situational and ecological constraints

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution

Testing Safety PLCs Using QuickCheck

The testing of safety-related industrial systems is usually carried out by means of checklists. A tester has a list of scenarios that he or she manually applies to the system to check whether the system behaves according to its specification. However, operators behave unpredictably. Their behavior may not be covered by the set of scenarios tested and may lead to dangerous situations. To avoid this, randomized test case generation can be useful as it allows for unanticipated scenarios. The presented framework uses a tool for randomized test case generation, QuickCheck, to trigger event sequences that are then applied to a Safety Programmable Logic Controller (Safety PLC). Experiments show that this concept is capable of finding errors in safety code or increasing the tester\u27s confidence in the correctness of the code by exhibiting a large number of passing test cases. While this concept proves to be powerful, it does not require much effort from the tester as the execution of test cases is done without user interaction

A community-driven global reconstruction of human metabolism

Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the reconstruction has improved topological and functional features, including ~2× more reactions and ~1.7× more unique metabolites. Using Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically generated a compendium of 65 cell type–specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/

Coming out of conflict: How migrant entrepreneurs utilise human and social capital

This paper examines how human and social capital influences the entrepreneurial activity of migrant entrepreneurs, with special reference to forced migrants due to conflict. The study uses Riinvest Migrant’s Survey data collected at the end of 2008 and beginning of 2009 to estimate the probability of entrepreneurial activity among Kosovan migrants. The findings demonstrate that host networking (foreign spouse and foreign language fluency) exerts a positive effect on entrepreneurial activity of migrants, while co-ethnic networking is found not to be important. We show that migration experience has a positive impact on the probability of entrepreneurship. Exposure to host country (both measured as years in migration and age) increases probability to start a business. Educational qualifications in the country of origin before migration do not have any influence on entrepreneurship, while specific business training in the country of residence has a positive impact. Contributions to scholarship on migrant entrepreneurship and policy approaches to mobilise them are discussed