Tools of the Trade: A Survey of Various Agent Based Modeling Platforms

Agent Based Modeling (ABM) toolkits are as diverse as the community of people who use them. With so many toolkits available, the choice of which one is best suited for a project is left to word of mouth, past experiences in using particular toolkits and toolkit publicity. This is especially troublesome for projects that require specialization. Rather than using toolkits that are the most publicized but are designed for general projects, using this paper, one will be able to choose a toolkit that already exists and that may be built especially for one's particular domain and specialized needs. In this paper, we examine the entire continuum of agent based toolkits. We characterize each based on 5 important characteristics users consider when choosing a toolkit, and then we categorize the characteristics into user-friendly taxonomies that aid in rapid indexing and easy reference.Agent Based Modeling, Individual Based Model, Multi Agent Systems

Enriching conflict resolution environments with the provision of context information

It is a common affair to settle disputes out of courts nowadays, through negotiation, mediation or any other mean. This has also been implemented over telecommunication means under the so-called Online Dispute Resolution methods. However, this new technology-supported approach is impersonal and cold, leaving aside important issues such as the disputants’ body language, stress level or emotional response while being based on forms, e-mails or chat rooms. To overcome this shortcoming in this paper it is proposed the creation of intelligent environments for conflict resolution that can complement the existing tools with important knowledge about the context of interaction. This will allow decisionmakers to take better framed decisions based not only on figures but also on important contextual information, similarly to what happens when parties communicate in the physical presence of each other.This work is part-funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT - Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project FCOMP-01-0124-FEDER-028980 (PTDC/EEI-SII/1386/2012) and PEst-OE/ EEI/UI0752/2011. The work of Davide Carneiro is also supported by a doctoral grant by FCT (SFRH/BD/64890/2009).info:eu-repo/semantics/publishedVersio

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

<p>Abstract</p> <p>Background</p> <p>The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.</p> <p>Results</p> <p>Panseq was used to identify <it>Escherichia coli </it>O157:H7 and <it>E. coli </it>K-12 genomic islands. Within a population of 60 <it>E. coli </it>O157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs) of six <it>L. monocytogenes </it>strains were extracted with Panseq and hierarchically clustered and visualized. The nucleotide core and binary accessory data were also used to construct maximum parsimony (MP) trees, which were compared to the MP tree generated by multi-locus sequence typing (MLST). The topology of the accessory and core trees was identical but differed from the tree produced using seven MLST loci. The Loci Selector module found the most variable and discriminatory combinations of four loci within a 100 loci set among 10 strains in 1 s, compared to the 449 s required to exhaustively search for all possible combinations; it also found the most discriminatory 20 loci from a 96 loci <it>E. coli </it>O157:H7 SNP dataset.</p> <p>Conclusion</p> <p>Panseq determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters. It readily extracts regions unique to a genome or group of genomes, identifies SNPs within shared core genomic regions, constructs files for use in phylogeny programs based on both the presence/absence of accessory regions and SNPs within core regions and produces a graphical overview of the output. Panseq also includes a loci selector that calculates the most variable and discriminatory loci among sets of accessory loci or core gene SNPs.</p> <p>Availability</p> <p>Panseq is freely available online at <url>http://76.70.11.198/panseq</url>. Panseq is written in Perl.</p

INNOVATIVE CITY IN WEST CHINA CHONGQING

This working paper offers insights on science and technology in China with supporting official and interview data. The paper, as evidenced from the title, is indicating the future role of Chongqing and its evolution primarily focusing on the period of rapid development of the Municipality after Chongqing became a political entity on the same level as provinces of China. This has coincided with the planning, construction and completion of the Three Gorges Dam Project involving the resettlement of 1,000,000 people – most them coming to the rural areas Chongqing Municipality. Three major sub-themes are highlighted. First, the city played important role during more than 2000 years of its history (in 1981, for example it became first inland port in China open for foreign commerce). In the XX century Chongqing was national capital during the Second World War and the Japanese invasion (Nationalists government). Since then it enjoyed higher political status and economic independence than any other city of the same size in whole western China. Second, the municipality’s geographical position and demographic condition makes it quite unique in West China. It has a population of 31 million, an area of 82 square km, a population density of 379 persons per km2 and a location at the upper reaches of Chang (Yangtze) River. This makes it the gate of Southwest China. Third, Chongqing has a strong basic multi-faced economy in the region. Central investment since the 1950s has assisted the development of a relatively strong modern industrial base in the city. Despite the post-Mao reform era’s impact on social and economic disparities as between the coastal areas and the west, Chongqing remains one of the China’s strongest city economies. Its industrial output value ranked 11th among the 35 biggest city economies in China in 2000, though it ranked behind the top ten most industrialized coastal cities, all of which had attracted much greater foreign investment during the reform era. The campaign to Open up the West provides Chongqing with the opportunity to act as the growth pole for a number of less industrialized provincial-level units in north-west and south-west China. Fourth, the initiatives by central authorities and the extraordinary task of Three Gorges Dam project required among other great tasks also relocation of over 1,2 million people, the rebuilding of two cities, eleven county towns and one hundred sixteen townships from the site of Three Gorges Dam water reservoir. Until 2005 there were already almost one million residents resettled. Less than 20 per cent moved outside Chongqing municipality and the majority was to be accommodated within the region of Chongqing Municipality.Regional development; clusters; Regional innovation System (RIS); Development block; competence block; technology system; High Technology Parks; Overview of Science and Technology; FDI

StateLens: A Reverse Engineering Solution for Making Existing Dynamic Touchscreens Accessible

Blind people frequently encounter inaccessible dynamic touchscreens in their everyday lives that are difficult, frustrating, and often impossible to use independently. Touchscreens are often the only way to control everything from coffee machines and payment terminals, to subway ticket machines and in-flight entertainment systems. Interacting with dynamic touchscreens is difficult non-visually because the visual user interfaces change, interactions often occur over multiple different screens, and it is easy to accidentally trigger interface actions while exploring the screen. To solve these problems, we introduce StateLens - a three-part reverse engineering solution that makes existing dynamic touchscreens accessible. First, StateLens reverse engineers the underlying state diagrams of existing interfaces using point-of-view videos found online or taken by users using a hybrid crowd-computer vision pipeline. Second, using the state diagrams, StateLens automatically generates conversational agents to guide blind users through specifying the tasks that the interface can perform, allowing the StateLens iOS application to provide interactive guidance and feedback so that blind users can access the interface. Finally, a set of 3D-printed accessories enable blind people to explore capacitive touchscreens without the risk of triggering accidental touches on the interface. Our technical evaluation shows that StateLens can accurately reconstruct interfaces from stationary, hand-held, and web videos; and, a user study of the complete system demonstrates that StateLens successfully enables blind users to access otherwise inaccessible dynamic touchscreens.Comment: ACM UIST 201

From Network to Web dimension in supply chain management

Cette thèse soutient que la dimension réseau, étant actuellement la portée du domaine de la gestion de chaîne logistique, contraint l’avancement de ce domaine et restreint des innovations conceptuelles et fondamentales capables d’adresser les grands défis économiques, environnementaux et sociaux. Les concepts de chaîne et de réseau ne reflètent pas la complexité des flux physiques, informationnels et financiers générés par les interactions qui ont lieu dans des réseaux interconnectés. Ces concepts n’offrent pas les fondations théoriques pour supporter des interventions allant au-delà d’un seul réseau et laissent échapper des opportunités nécessitant une vision multi-réseau. Ainsi, la dimension “web”, celle des réseaux de réseaux, est proposée comme une extension de la dimension réseau. Cette extension peut être vue comme l’étape naturelle suivante dans la progression qui a commencé par le niveau de gestion des opérations internes, est passée au niveau de la chaîne logistique et se trouve actuellement au niveau du réseau logistique. Après l’investigation théorique des raisons et de la façon d’intégrer la dimension web dans le domaine de la gestion de la chaîne logistique, la thèse étudie des implications importantes de cette intégration sur la collaboration inter-organisationnelle et le processus de prise de décision dans des environnements de webs logistiques. Elle démontre, en exploitant l’exemple des réseaux interconnectés ouverts, des potentialités inimaginables sans une vision web. Une méthodologie de conception d’un modèle de simulation permettant l’évaluation et la comparaison des webs ouverts par rapport aux webs existants est proposée. Puisque l’aide à la décision est une composante importante de la gestion de la chaîne logistique, la thèse contribue à déterminer les besoins des gestionnaires et à identifier les lignes directrices de la conception des outils d’aide à la décision offrant le support adéquat pour faire face aux défis et à la complexité des webs logistiques. Ces lignes directrices ont été compilées dans un cadre de conception des logiciels d’aide à la décision supportant la dimension web. Ce cadre est exploité pour développer quatre applications logicielles offrant aux praticiens et aux chercheurs des outils nécessaires pour étudier, analyser et démêler la complexité des webs logistiques.This thesis argues that the network dimension as the current scope of supply chain management is confining the evolution of this field and restricting the conceptual and fundamental innovations required for addressing the major challenges imposed by the evolution of markets and the increased intricacies of business relationships. The concepts of chain and network are limitative when attempting to represent the complexity of physical, informational and financial flows resulting from the interactions occurring in overlapping networks. They lack the theoretical foundations necessary to explain and encompass initiatives that go beyond a single chain or network. They also lead to overlook substantial opportunities that require beyond a network vision. Therefore, the “web” dimension, as networks of networks, is proposed as an extension to the network dimension in supply chain management. This new scope is the natural next step in the progression from the internal operations management level to the supply chain level and then to the supply network level. After a theoretical investigation of why and how the web dimension should be integrated into the supply chain management field, the thesis studies and discusses important implications of this integration on inter-organisational collaboration and of the decision-making processes in the logistic web environments. It demonstrates through the example of open interconnected logistic webs some of the potentials that cannot be imagined without a web vision. A methodology for designing a simulation model to assess the impact of such open webs versus existing webs is proposed. Since decision support is a key element in supply chain management, the thesis contributes to determine the needs of supply chain managers and identify the important axes for designing decision support systems that provide adequate assistance in dealing with the challenges and complexity presented by logistic web environments. The identified elements result in the establishment of a foundation for designing software solutions required to handle the challenges revealed by the web dimension. This conceptual framework is applied to the prototyping of four applications that have the potential of providing practitioners and researchers with the appropriate understanding and necessary tools to deal with the complexity of logistics webs

RHAMNETIN IS A BETTER INHIBITOR OF SARS-COV-2 2’-O-METHYLTRANSFERASE THAN DOLUTEGRAVIR: A COMPUTATIONAL PREDICTION

Background: The 2’-O-methyltransferase is responsible for the capping of SARS-CoV-2 mRNA and consequently the evasion of the host’s immune system. This study aims at identifying prospective natural inhibitors of the active site of SARS-CoV-2 2’O-methyltransferase (2’-OMT) through an in silico approach. Materials and Method: The target was docked against a library of natural compounds obtained from edible African plants using PyRx - virtual screening software. The antiviral agent, Dolutegravir which has a binding affinity score of -8.5 kcal mol−1 with the SARS-CoV-2 2’-OMT was used as a standard. Compounds were screened for bioavailability through the SWISSADME web server using their molecular descriptors. Screenings for pharmacokinetic properties and bioactivity were performed with PKCSM and Molinspiration web servers respectively. The PLIP and Fpocket webservers were used for the binding site analyses. The Galaxy webserver was used for simulating the time-resolved motions of the apo and holo forms of the target while the MDWeb web server was used for the analyses of the trajectory data. Results: The Root-Mean-Square-Deviation (RMSD) induced by Rhamnetin is 1.656A0 as compared to Dolutegravir (1.579A0). The average B-factor induced by Rhamnetin is 113.75 while for Dolutegravir is 78.87; the Root-Mean-Square-Fluctuation (RMSF) for Rhamnetin is 0.75 and for Dolutegravir is 0.67. Also at the active site, Rhamnetin also has a binding affinity score of -9.5 kcal mol−1 and forms 7 hydrogen bonds as compared to Dolutegravir which has -8.5 kcal mol−1 and forms 4 hydrogen bonds respectively. Conclusion: Rhamnetin showed better inhibitory activity at the target’s active site than Dolutegravir

FROM CONCEPT, TO DESIGN, EVALUATION AND FIRST IN VIVO DEMONSTRATION OF A TELE-OPERATED CATHETER NAVIGATION SYSTEM

Percutaneous transluminal catheter (PTC) intervention is a medical technique used to assess and treat vascular and cardiac diseases, including electrophysiological conditions. A Interventional specialists use the vasculature as a passageway to guide the catheter to the site of interest, using fluoroscopic x-ray imaging for image-guidance. Common PTC procedures include: vascular angiography, inflating balloons and stents, depositing coils, and the treatment of cardiac arrhythmia via catheter ablation. Catheter ablation has gained prevalence over the last two decades, as the treatment success rate for atrial fibrillation reaches 100%. The close proximity between the interventionalist and the radiation source combined with the increased number of procedures performed annually has lead to increased lifetime exposure; escalating the interventionalist probability of developing cancer, cataracts or passing genetic defects to offspring. Furthermore, the lead garments that protect the interventionalist can lead to musculoskeletal injury. Both these factors have lead to increased occupational risk. Catheter navigation systems are commercially available to reduce these risks. Lack of intuitive design is a common failing among these systems. iii This thesis presents the design and validation of a remote catheter navigation system (RCNS) that utilizes dexterous skills of the interventionalist during remote navigation, by keeping the catheter in their hands of the interventionalist during remote navigation. For remote catheter manipulation, the interventionalist pushes, pulls, and twists an input catheter, which is placed inside an electromechanical sensor (CS). Position changes of the input catheter are transferred to a second electromechanical (CM) that replicates the sensed motion with a second, remote catheter. Design of this system begins with understanding the dynamic forces applied to the catheter during intravascular navigation. These dynamics were quantified and then used as operating parameters in the mechanical design of the CM. In a laboratory setting, motion sensed and replicated by the RCNS was found to be 1 mm in the axial direction, 1° in the radial direction, with a latency of 180 ms. In a multi-operator, comparative study using a specially constructed multi-path vessel phantom, comparable navigation efficacy was demonstrated between the RCNS and conventional catheter manipulation, with the RCNS requiring only 9s longer to complete the same tasks. Finally, remote navigation was performed in vivo to fully demonstrate the application of this system towards the diagnosis and treatment of cardiac arrhythmia

Wearable Computing for Health and Fitness: Exploring the Relationship between Data and Human Behaviour

Health and fitness wearable technology has recently advanced, making it easier for an individual to monitor their behaviours. Previously self generated data interacts with the user to motivate positive behaviour change, but issues arise when relating this to long term mention of wearable devices. Previous studies within this area are discussed. We also consider a new approach where data is used to support instead of motivate, through monitoring and logging to encourage reflection. Based on issues highlighted, we then make recommendations on the direction in which future work could be most beneficial