Design of a combinatorial DNA microarray for protein-DNA interaction studies

BACKGROUND: Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently, double-stranded protein-binding microarrays were developed as a potentially scalable approach to tackle transcription factor binding site identification. RESULTS: Here we present an algorithmic approach to experimental design of a microarray that allows for testing full specificity of a transcription factor binding to all possible DNA binding sites of a given length, with optimally efficient use of the array. This design is universal, works for any factor that binds a sequence motif and is not species-specific. Furthermore, simulation results show that data produced with the designed arrays is easier to analyze and would result in more precise identification of binding sites. CONCLUSION: In this study, we present a design of a double stranded DNA microarray for protein-DNA interaction studies and show that our algorithm allows optimally efficient use of the arrays for this purpose. We believe such a design will prove useful for transcription factor binding site identification and other biological problems

Timed runtime monitoring for multiparty conversations

We propose a dynamic verification framework for protocols in real-time distributed systems. The framework is based on Scribble, a tool-chain for design and verification of choreographies based on multiparty session types, which we have developed with our industrial partners. Drawing from recent work on multiparty session types for real-time interactions, we extend Scribble with clocks, resets, and clock predicates in order to constrain the times inwhich interactions occur.We present a timedAPI for Python to programdistributed implementations of Scribble specifications. A dynamic verification framework ensures the safe execution of applications written with our timed API: we have implemented dedicated runtime monitors that check that each interaction occurs at a correct timing with respect to the corresponding Scribble specification. To demonstrate the practicality of the proposed framework, we express and verify four categories of widely used temporal patterns from use cases in literature.We analyse the performance of our implementation via benchmarking and show negligible overhead

Evaluating the Impact of an Integrated Urban Design of Transport Infrastructure and Public Space on Human Behavior and Environmental Quality: A Case Study in Beijing

Urban transport infrastructure can result in the physical, psychological and environmental separation of neighborhoods, public spaces and pedestrian networks, leading to negative impacts on citizens’ daily commutes, social activities and the quality of the ecosystem. An integrated design of transport infrastructure and public space is beneficial for mediating these negative impacts. In this paper, we propose an integrated methodology, which combines urban design, computational scenario evaluation and decision-making processes, based on a conceptual model of human and ecological needs-driven planning. To evaluate the impacts of the road network and public space design on individual outdoor activities, travel behavior and air pollution, an agent-based model is demonstrated. This model is then applied to a case study in Beijing, leading to hourly traffic volume maps and car-related air pollution heat maps of a baseline road network-public space design