Synthetic biology and microdevices : a powerful combination

Recent developments demonstrate that the combination of microbiology with micro-and nanoelectronics is a successful approach to develop new miniaturized sensing devices and other technologies. In the last decade, there has been a shift from the optimization of the abiotic components, for example, the chip, to the improvement of the processing capabilities of cells through genetic engineering. The synthetic biology approach will not only give rise to systems with new functionalities, but will also improve the robustness and speed of their response towards applied signals. To this end, the development of new genetic circuits has to be guided by computational design methods that enable to tune and optimize the circuit response. As the successful design of genetic circuits is highly dependent on the quality and reliability of its composing elements, intense characterization of standard biological parts will be crucial for an efficient rational design process in the development of new genetic circuits. Microengineered devices can thereby offer a new analytical approach for the study of complex biological parts and systems. By summarizing the recent techniques in creating new synthetic circuits and in integrating biology with microdevices, this review aims at emphasizing the power of combining synthetic biology with microfluidics and microelectronics

FragViz: visualization of fragmented networks

BACKGROUND Researchers in systems biology use network visualization to summarize the results of their analysis. Such networks often include unconnected components, which popular network alignment algorithms place arbitrarily with respect to the rest of the network. This can lead to misinterpretations due to the proximity of otherwise unrelated elements. RESULTS We propose a new network layout optimization technique called FragViz which can incorporate additional information on relations between unconnected network components. It uses a two-step approach by first arranging the nodes within each of the components and then placing the components so that their proximity in the network corresponds to their relatedness. In the experimental study with the leukemia gene networks we demonstrate that FragViz can obtain network layouts which are more interpretable and hold additional information that could not be exposed using classical network layout optimization algorithms. CONCLUSIONS Network visualization relies on computational techniques for proper placement of objects under consideration. These algorithms need to be fast so that they can be incorporated in responsive interfaces required by the explorative data analysis environments. Our layout optimization technique FragViz meets these requirements and specifically addresses the visualization of fragmented networks, for which standard algorithms do not consider similarities between unconnected components. The experiments confirmed the claims on speed and accuracy of the proposed solution

Cheating for Problem Solving: A Genetic Algorithm with Social Interactions

We propose a variation of the standard genetic algorithm that incorporates social interaction between the individuals in the population. Our goal is to understand the evolutionary role of social systems and its possible application as a non-genetic new step in evolutionary algorithms. In biological populations, ie animals, even human beings and microorganisms, social interactions often affect the fitness of individuals. It is conceivable that the perturbation of the fitness via social interactions is an evolutionary strategy to avoid trapping into local optimum, thus avoiding a fast convergence of the population. We model the social interactions according to Game Theory. The population is, therefore, composed by cooperator and defector individuals whose interactions produce payoffs according to well known game models (prisoner's dilemma, chicken game, and others). Our results on Knapsack problems show, for some game models, a significant performance improvement as compared to a standard genetic algorithm.Comment: 7 pages, 5 Figures, 5 Tables, Proceedings of Genetic and Evolutionary Computation Conference (GECCO 2009), Montreal, Canad

Defusing Ideological Defenses in Biology

Ideological language is widespread in theoretical biology. Evolutionary game theory has been defended as a worldview and a leap of faith, and sexual selection theory has been criticized for what it posits as basic to biological nature. Views such as these encourage the impression of ideological rifts in the field. I advocate an alternative interpretation, whereby many disagreements between different camps of biologists merely reflect methodological differences. This interpretation provides a more accurate and more optimistic account of the state of play in the field of biology. It also helps account for biologists' tendency to embrace ideological positions

UT’s Tech Team Moves the Needle Toward Building Optimization

Values at Work Series: Facilities Services developed our core values of Service, Integrity, Teamwork, Excellence, and Stewardship (collectively referred to as SITES) based on the way we approach our work. Our values can be found throughout our areas of services in many ways.Through a series of articles, the Values at Work Series is devoted to providing a closer look at how our values are hard at work. Each article focuses on an area of service and how that group incorporates our values in a significant way. We are proud of our employees who continue to serve as an example of “walking the talk” every day.After facilities managers address their client’s unplanned maintenance issues, provide the necessary preventive maintenance on building systems and manage energy conservation efforts, how do they also find a way to optimize the performance of the buildings on campus so the systems run as well as they ought to...and do it all with limited resources? Building Operations Manager Mark White provides insights into how The University of Texas at Austin, with the help of its Building Optimization Team (BOT), is moving the needle toward impactful facilities optimization on a university campus.Facilities Service