Simulation of P systems with active membranes on CUDA

P systems or Membrane Systems provide a high-level computational modelling framework that combines the structure and dynamic aspects of biological systems in a relevant and understandable way. They are inherently parallel and non-deterministic computing devices. In this article, we discuss the motivation, design principles and key of the implementation of a simulator for the class of recognizer P systems with active membranes running on a (GPU). We compare our parallel simulator for GPUs to the simulator developed for a single central processing unit (CPU), showing that GPUs are better suited than CPUs to simulate P systems due to their highly parallel nature.Ministerio de Educación y Ciencia TIN2006-13425Junta de Andalucía P08–TIC-0420

ChlamyNET: a Chlamydomonas gene co-expression network reveals global properties of the transcriptome and the early setup of key co-expression patterns in the green lineage

Background Chlamydomonas reinhardtii is the model organism that serves as a reference for studies in algal genomics and physiology. It is of special interest in the study of the evolution of regulatory pathways from algae to higher plants. Additionally, it has recently gained attention as a potential source for bio-fuel and bio-hydrogen production. The genome of Chlamydomonas is available, facilitating the analysis of its transcriptome by RNA-seq data. This has produced a massive amount of data that remains fragmented making necessary the application of integrative approaches based on molecular systems biology. Results We constructed a gene co-expression network based on RNA-seq data and developed a web-based tool, ChlamyNET, for the exploration of the Chlamydomonas transcriptome. ChlamyNET exhibits a scale-free and small world topology. Applying clustering techniques, we identified nine gene clusters that capture the structure of the transcriptome under the analyzed conditions. One of the most central clusters was shown to be involved in carbon/nitrogen metabolism and signalling, whereas one of the most peripheral clusters was involved in DNA replication and cell cycle regulation. The transcription factors and regulators in the Chlamydomonas genome have been identified in ChlamyNET. The biological processes potentially regulated by them as well as their putative transcription factor binding sites were determined. The putative light regulated transcription factors and regulators in the Chlamydomonas genome were analyzed in order to provide a case study on the use of ChlamyNET. Finally, we used an independent data set to cross-validate the predictive power of ChlamyNET. Conclusions The topological properties of ChlamyNET suggest that the Chlamydomonas transcriptome posseses important characteristics related to error tolerance, vulnerability and information propagation. The central part of ChlamyNET constitutes the core of the transcriptome where most authoritative hub genes are located interconnecting key biological processes such as light response with carbon and nitrogen metabolism. Our study reveals that key elements in the regulation of carbon and nitrogen metabolism, light response and cell cycle identified in higher plants were already established in Chlamydomonas. These conserved elements are not only limited to transcription factors, regulators and their targets, but also include the cis-regulatory elements recognized by them.España, Ministerio de Economía y Competitividad CSD2007-00057España, Ministerio de Economía y Competitividad BIO2011-28847-C02-00España, Ministerio de Economía y Competitividad BIO2014-52425-

Simulating a P system based efficient solution to SAT by using GPUs

P systems are inherently parallel and non-deterministic theoretical computing devices defined inside the field of Membrane Computing. Many P system simulators have been presented in this area, but they are inefficient since they cannot handle the parallelism of these devices. Nowadays, we are witnessing the consolidation of the GPUs as a parallel framework to compute general purpose applications. In this paper, we analyse GPUs as an alternative parallel architecture to improve the performance in the simulation of P systems, and we illustrate it by using the case study of a family of P systems that provides an efficient and uniform solution to the SAT problem. Firstly, we develop a simulator that fully simulates the computation of the P system, demonstrating that GPUs are well suited to simulate them. Then, we adapt this simulator to the GPU architecture idiosyncrasies, improving the performance of the previous simulator.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08–TIC-0420

An integrated model of structural equations with cognitive and environmental factors for the study of active commuting

This work was partially supported with funds from the FEDER Projects /Ministry for Science and Innovation, ECO2017-89452-R, and PGC2018-095786-B-I00, Spain.Introduction: The active commuting can be defined as the action of displacement to the educa-tional or work centre by way of any non-motorised means of transport, usually by walking or cycling. The aim of this study is to identify and evaluate cognitive and environmental factors for the active commuting. Methods: In order to propose a set of beliefs and attitudes that explain the main possible moti-vations for an individual to carry out the active commuting, a model based on the Theory of Planned Behaviour, health and environment is developed. To compute the results, a structural equations model is proposed instead of another standard regression technique, due to the use of multiple indicators for each latent construct. The proposed model permits to evaluate each of the aspects and to quantify their contribution to the global behavioural intention. Results: The computation of the structural equations model concludes that, for the intention to practise active commuting, the most influential variable is attitude, followed by health and environmental awareness. It is interesting to see that perceived behavioural control exerts a negative influence on the intention, while the subjective norm has no significant effect. Conclusions: From the results of this study can be induced that the perceived behavioural control, health, and environmental awareness exert a significant influence on attitude and intention to practice active commuting. Furthermore, the results also show that attitude influences as a pre-cursor to the intention of practicing and permit to rank the relative weight of each aspect: atti-tude, health and environmental awareness. Hence, political measures that publicise the benefits of active commuting in these particular aspects should have significant results in the promotion of this activity.Universidad Pablo de Olavid

Implementing P Systems Parallelism by Means of GPUs

Software development for Membrane Computing is growing up yielding new applications. Nowadays, the efficiency of P systems simulators have become a critical point when working with instances of large size. The newest generation of GPUs (Graphics Processing Units) provide a massively parallel framework to compute general purpose computations. We present GPUs as an alternative to obtain better performance in the simulation of P systems and we illustrate it by giving a solution to the N-Queens problem as an example.Ministerio de Educación y Ciencia TIN2006-13425Junta de Andalucía P08–TIC-0420

Accessibility and Activity-Centered Design for ICT Users: ACCESIBILITIC Ontology

Information and communication technologies (ICTs) are involved in daily human activities. Accessibility guarantees that individuals with different abilities can interact with ICTs. User pro le models are an explicit representation of the characteristics of an individual and are used to reason about what users need. They are implemented through ontologies. After identifying common and different aspects among important ontologies in the domain of accessibility and e-inclusion, we designed and implemented the ACCESIBILITIC ontology applying the NeOn methodology, speci cally by reusing and reengineering these ontologies. The strengths of our model include the user's ability to develop a high variety of activities despite his/her disabilities, support for inference processes, and providing answers to several competency questions. ACCESIBILITIC allows the representation of suitable technical support based on the user's capabilities when interacting with ICTs. To this end, we use an activity-centered design (ACD), which allows us to identify daily activities and to match these activities with a suitable technology to perform them.This research work is funded by the Spanish Ministry of Economy and Competitiveness - Agencia Estatal de Investigación - with European Regional Development Funds (AEI/FEDER, UE) through the project ref. TIN2016-79484-R

Simulation of Recognizer P Systems by Using Manycore GPUs

Software development for cellular computing is growing up yielding new applications. In this paper, we describe a simulator for the class of recognizer P systems with active membranes, which exploits the massively parallel nature of the P systems computations by using a massively parallel computer architecture, such as Compute Unified Device Architecture (CUDA) from Nvidia, to obtain better performance in the simulations. We illustrate it by giving a solution to the N-Queens problem as an example.Ministerio de Educación y Ciencia TIN2006–13425Junta de Andalucía P08–TIC0420

A massively parallel framework using P systems and GPUs

Since CUDA programing model appeared on the general purpose computations, the developers can extract all the power contained in GPUs (Graphics Processing Unit) across many computational domains. Among these domains, P systems or membrane systems provide a high level computational modeling framework that allows, in theory, to obtain polynomial time solutions to NP-complete problems by trading time for space, and also to model biological phenomena in the area of computational systems biology. P systems are massively parallel distributed devices and their computation can be divided in two levels of parallelism: membranes, that can be expressed as blocks in CUDA programming model; and objects, that can be expressed as threads in CUDA programming model. In this paper, we present our initial ideas of developing a simulator for the class of recognizer P systems with active membranes by using the CUDA programing model to exploit the massively parallel nature of those systems at maximum. Experimental results of a preliminary version of our simulator on a Tesla C1060 GPU show a 60X of speed-up compared to the sequential code.Ministerio de Educación y Ciencia TIN2006-13425Junta de Andalucía P08–TIC-0420

A multifaceted provider-centred intervention versus usual care to improve the recognition and diagnosis of depression in primary health care: a hybrid study

Background: The aim of this study was to evaluate the impact of a multifaceted intervention to implement an adapted guideline for the management of depression in primary health care. Methods: A hybrid trial was carried out to determine the effect of a multicomponent provider centred intervention to improve the detection and diagnosis of depression in primary care, as part of the guideline implementation process, and to collect information about barriers and facilitators in a real-world context. Before the multicomponent intervention, a descriptive cross-sectional study was performed to assess the population prevalence of depression in the participating health centres and to detect possible differences. Subsequently, a quasi experimental two-phase study was carried out with a concurrent control group to assess the impact of the multicomponent intervention on the main outcomes (detection of depression, evaluation of its severity and the use of structured methods to support the diagnosis). Results: Nine-hundred seventy-four patients took part in the first phase. According to their clinical records, the prevalence of depression ranged from 7.2% to 7.9%, and there were no significant differences between the health centres scheduled to receive the intervention and those in the control group. In the experimental phase, 797 randomly selected participants received the multicomponent intervention. Adjusted multivariable analysis performed before the implementation revealed no significant differences in depression between the experimental and control groups. However, after the intervention, modest but significant differences were observed, which persisted at 1 year after the intervention. Conclusions: A multicomponent intervention for the implementation of a clinical guideline for the management of depression in primary care produced improvements in the identification of depression and in the degree of severity recorded.Funding for open access charge: Universidad de Málaga

Analysis of P systems simulation on CUDA

GPUs (Graphics Processing Unit) have been con- solidated as a massively data-parallel coprocessor to develop many general purpose computations, and en- able developers to utilize several levels of parallelism to obtain better performance of their applications. The massively parallel nature of certain computa- tions leads to use GPUs as an underlying architec- ture, becoming a good alternative to other paral- lel approaches. P systems or membrane systems are theoretical devices inspired in the way that liv- ing cells work, providing computational models and a high level computational modeling framework for biological systems. They are massively parallel dis- tributed, and non-deterministic systems. In this pa- per, we evaluate the GPU as the underlying archi- tecture to simulate the class of recognizer P systems with active membranes. We analyze the performance of three simulators implemented on CPU, CPU-GPU and GPU respectively. We compare them using a pre- sented P system as a benchmark, showing that the GPU is better suited than the CPU to simulate those P systems due to its massively parallel nature.Ministerio de Educación y Ciencia TIN2006-13425Junta de Andalucía P08–TIC0420