Systems biology in animal sciences

Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes and animal traits are not yet frequently used. This paper aims to explain what systems biology is and which areas of animal sciences could benefit from systems biology approaches. Systems biology aims to understand whole biological systems working as a unit, rather than investigating their individual components. Therefore, systems biology can be considered a holistic approach, as opposed to reductionism. The recently developed ‘omics’ technologies enable biological sciences to characterize the molecular components of life with ever increasing speed, yielding vast amounts of data. However, biological functions do not follow from the simple addition of the properties of system components, but rather arise from the dynamic interactions of these components. Systems biology combines statistics, bioinformatics and mathematical modeling to integrate and analyze large amounts of data in order to extract a better understanding of the biology from these huge data sets and to predict the behavior of biological systems. A ‘system’ approach and mathematical modeling in biological sciences are not new in itself, as they were used in biochemistry, physiology and genetics long before the name systems biology was coined. However, the present combination of mass biological data and of computational and modeling tools is unprecedented and truly represents a major paradigm shift in biology. Significant advances have been made using systems biology approaches, especially in the field of bacterial and eukaryotic cells and in human medicine. Similarly, progress is being made with ‘system approaches’ in animal sciences, providing exciting opportunities to predict and modulate animal traits

TaBooN -- Boolean Network Synthesis Based on Tabu Search

Recent developments in Omics-technologies revolutionized the investigation of biology by producing molecular data in multiple dimensions and scale. This breakthrough in biology raises the crucial issue of their interpretation based on modelling. In this undertaking, network provides a suitable framework for modelling the interactions between molecules. Basically a Biological network is composed of nodes referring to the components such as genes or proteins, and the edges/arcs formalizing interactions between them. The evolution of the interactions is then modelled by the definition of a dynamical system. Among the different categories of network, the Boolean network offers a reliable qualitative framework for the modelling. Automatically synthesizing a Boolean network from experimental data therefore remains a necessary but challenging issue. In this study, we present taboon, an original work-flow for synthesizing Boolean Networks from biological data. The methodology uses the data in the form of Boolean profiles for inferring all the potential local formula inference. They combine to form the model space from which the most truthful model with regards to biological knowledge and experiments must be found. In the taboon work-flow the selection of the fittest model is achieved by a Tabu-search algorithm. taboon is an automated method for Boolean Network inference from experimental data that can also assist to evaluate and optimize the dynamic behaviour of the biological networks providing a reliable platform for further modelling and predictions

Dimensions of Timescales in Neuromorphic Computing Systems

This article is a public deliverable of the EU project "Memory technologies with multi-scale time constants for neuromorphic architectures" (MeMScales, https://memscales.eu, Call ICT-06-2019 Unconventional Nanoelectronics, project number 871371). This arXiv version is a verbatim copy of the deliverable report, with administrative information stripped. It collects a wide and varied assortment of phenomena, models, research themes and algorithmic techniques that are connected with timescale phenomena in the fields of computational neuroscience, mathematics, machine learning and computer science, with a bias toward aspects that are relevant for neuromorphic engineering. It turns out that this theme is very rich indeed and spreads out in many directions which defy a unified treatment. We collected several dozens of sub-themes, each of which has been investigated in specialized settings (in the neurosciences, mathematics, computer science and machine learning) and has been documented in its own body of literature. The more we dived into this diversity, the more it became clear that our first effort to compose a survey must remain sketchy and partial. We conclude with a list of insights distilled from this survey which give general guidelines for the design of future neuromorphic systems

The ecology of suffering: developmental disorders of structured stress, emotion, and chronic inflammation

'Punctuated equilibrium' models of cognitive process, adapted from the Large Deviations Program of probability theory, are applied to the interaction between immune function and emotion in the context of culturally structured psychosocial stress. The analysis suggests: (1) Chronic inflammatory diseases should be comorbid and synergistic with characteristic emotional dysfunction, and may form a collection of joint disorders most effectively treated at the individual level using multifactorial 'mind/body' strategies. (2) Culturally constructed psychosocial stress can literally write an image of itself onto the punctuated etiology and progression of such composite disorders, beginning a trajectory to disease in utero or early childhood, and continuing throughout the life course, suggesting that, when moderated by 'social exposures', these are developmental disorders. (3) At the community level of organization, strategies for prevention and control of the spectrum of emotional/inflammatory developmental disorders must include redress of cross-sectional and logitudinal (i.e. historical) patterns of inequality and injustice which generate structured psychosocial stress. Evidence further suggests that within 'Westernized' or 'market economy' societies, such stress will inevitably entrain high as well as lower stutus subopulations into a unified ecology of suffering

MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data

A new computational tool is presented that allows the integration of high-throughput experimental results with the probabilistic modeling of previously obtained information about cellular systems. The tool (MetaReg) is demonstrated on the leucine biosynthesis system in S.cerevisiae