MEXPRESS : visualizing expression, DNA methylation and clinical TCGA data

Background: In recent years, increasing amounts of genomic and clinical cancer data have become publically available through large-scale collaborative projects such as The Cancer Genome Atlas (TCGA). However, as long as these datasets are difficult to access and interpret, they are essentially useless for a major part of the research community and their scientific potential will not be fully realized. To address these issues we developed MEXPRESS, a straightforward and easy-to-use web tool for the integration and visualization of the expression, DNA methylation and clinical TCGA data on a single-gene level (http://mexpress.be). Results: In comparison to existing tools, MEXPRESS allows researchers to quickly visualize and interpret the different TCGA datasets and their relationships for a single gene, as demonstrated for GSTP1 in prostate adenocarcinoma. We also used MEXPRESS to reveal the differences in the DNA methylation status of the PAM50 marker gene MLPH between the breast cancer subtypes and how these differences were linked to the expression of MPLH. Conclusions: We have created a user-friendly tool for the visualization and interpretation of TCGA data, offering clinical researchers a simple way to evaluate the TCGA data for their genes or candidate biomarkers of interest

RealCoins: A Case Study of Enhanced Model Driven Development for Pervasive Games

Model Driven Development (MDD) and Domain Specific Modeling (DSM) have been widely used in information system domains and achieved success in many open or in-house scenarios. But its application in the game domain is seldom and immature. In our research, we identified three issues that should be considered carefully in order to play the strength of MDD in the game development environment to a larger extend: 1) structured domain analysis should be done to assure the size and familiarity of the domain; 2) adapted process should be designed to save cost and support evolution; and 3) proper tools (especially language workbenches) should be evaluated and utilized to ease DSM tasks and accelerate iterations. In this paper, we explain these three issues and illustrate our solutions to them by presenting the development details (both technical and procedural) of one pervasive game case. We evaluate the gains and costs by involving MDD into the game development process. We reflect on the issues we have met, and discuss possible future works as well.an open access journa

Virtual Communication Stack: Towards Building Integrated Simulator of Mobile Ad Hoc Network-based Infrastructure for Disaster Response Scenarios

Responses to disastrous events are a challenging problem, because of possible damages on communication infrastructures. For instance, after a natural disaster, infrastructures might be entirely destroyed. Different network paradigms were proposed in the literature in order to deploy adhoc network, and allow dealing with the lack of communications. However, all these solutions focus only on the performance of the network itself, without taking into account the specificities and heterogeneity of the components which use it. This comes from the difficulty to integrate models with different levels of abstraction. Consequently, verification and validation of adhoc protocols cannot guarantee that the different systems will work as expected in operational conditions. However, the DEVS theory provides some mechanisms to allow integration of models with different natures. This paper proposes an integrated simulation architecture based on DEVS which improves the accuracy of ad hoc infrastructure simulators in the case of disaster response scenarios.Comment: Preprint. Unpublishe

The dicode workbench: A flexible framework for the integration of information and web services

Aiming to address requirements concerning integration of services in the context of ?big data?, this paper presents an innovative approach that (i) ensures a flexible, adaptable and scalable information and computation infrastructure, and (ii) exploits the competences of stakeholders and information workers to meaningfully confront information management issues such as information characterization, classification and interpretation, thus incorporating the underlying collective intelligence. Our approach pays much attention to the issues of usability and ease-of-use, not requiring any particular programming expertise from the end users. We report on a series of technical issues concerning the desired flexibility of the proposed integration framework and we provide related recommendations to developers of such solutions. Evaluation results are also discussed

Light on horizontal interactive surfaces: Input space for tabletop computing

In the last 25 years we have witnessed the rise and growth of interactive tabletop research, both in academic and in industrial settings. The rising demand for the digital support of human activities motivated the need to bring computational power to table surfaces. In this article, we review the state of the art of tabletop computing, highlighting core aspects that frame the input space of interactive tabletops: (a) developments in hardware technologies that have caused the proliferation of interactive horizontal surfaces and (b) issues related to new classes of interaction modalities (multitouch, tangible, and touchless). A classification is presented that aims to give a detailed view of the current development of this research area and define opportunities and challenges for novel touch- and gesture-based interactions between the human and the surrounding computational environment. © 2014 ACM.This work has been funded by Integra (Amper Sistemas and CDTI, Spanish Ministry of Science and Innovation) and TIPEx (TIN2010-19859-C03-01) projects and Programa de Becas y Ayudas para la Realización de Estudios Oficiales de Máster y Doctorado en la Universidad Carlos III de Madrid, 2010

Design and Cost Analysis of a Self-contained Mobile Laboratory for Commercial-scale Aquatic Species Cryopreservation

© Copyright by the World Aquaculture Society 2018 Although aquatic species cryopreservation protocols have been studied around the world over the past 60 yr., germplasm repository development efforts and commercialization have begun only recently. The goal of this project was to develop a self-contained mobile laboratory for on-site high-throughput cryopreservation of aquatic species. The objectives of this study were to: (1) identify how a mobile laboratory would function in different operational scenarios, (2) customize an enclosed cargo trailer to function as a mobile laboratory, (3) evaluate the laboratory layout and ability of cryopreservation equipment to operate from generator power, and (4) document the investment costs for private and public groups to integrate a mobile laboratory into an existing cryopreservation facility at three levels of automation and estimate the total cost per trip based on hypothetical assumptions for two scenarios (aquaculture production and repository development). There were three operational designs identified for the mobile laboratory: (1) self-contained work inside the unit using generator power, (2) work inside the unit using external facility power, and (3) using the equipment inside of a host facility. The investment costs for a base-level mobile laboratory ranged between US$5670 and US$5787 for private groups and between US$5208 and US$5315 for public groups. With the addition of a range of automated processing equipment, total investment costs ranged from US$13,616 to US$103,529 for private groups and US$12,494 to US$94,891 for public groups. The total cost per trip to cryopreserve sperm of 59 blue catfish, Ictalurus furcatus, males to produce 6300 0.5-mL French straws was estimated to range from US$6089 to US$14,633 for private and between US$5703 and US$16,938 for public groups depending on the level of automation. Total cost per trip to cryopreserve sperm of 500 males of five different species in the genus Xiphophorus to produce 641 0.25-mL French straws was estimated to range from US$6653 to US$7640 for private and US$7582 to US$8088 for public groups depending on level of automation. Overall, a commercial-scale mobile laboratory was developed that can assist current germplasm activities and support future repository and industry development, and the layout information provided can help others to design and build comparable units

Studio Bench: the DIY Nomad and Noise Selector

This thesis asks questions about developing a holistic practice that could be termed ‘Studio Bench’ from what have been previously seen as three separate activities: DIY electronic instrument making, sound studio practice, and live electronics. These activities also take place in three very specific spaces. Firstly, the workshop with its workbench provides a way of making and exploring sound(-making) objects, and this workbench is considered more transient and expedient in relation to finding sounds, and the term DIY Nomad is used to describe this new practitioner. Secondly, the recording studio provides a way to carefully analyse sound(-making) objects that have been self-built and record music to play back in different contexts. Finally, live practice is used to bridge the gap between the workbench and studio, by offering another place for making and an opportunity to observe and listen to the sound(-making) object in another environment in front of a live audience. The DIY Nomad’s transient nature allows for free movement between these three spaces, finding sounds and making in a holistic fashion. Spaces are subverted. Instruments are built in the studio and recordings made on the workbench. From the nomadity of the musician, sounds are found and made quickly and intuitively, and it is through this recontextualisation that the DIY Nomad embraces appropriation, remixing, hacking and expediency. The DIY Nomad also appropriates cultures and the research is shaped through DJ practice - remixing and record selecting - noise music, and improvisation

Activity-Centric Computing Systems

• Activity-Centric Computing (ACC) addresses deep-rooted information management problems in traditional application centric computing by providing a unifying computational model for human goal-oriented ‘activity,’ cutting across system boundaries. • We provide a historical review of the motivation for and development of ACC systems, and highlight the need for broadening up this research topic to also include low-level system research and development. • ACC concepts and technology relate to many facets of computing; they are relevant for researchers working on new computing models and operating systems, as well as for application designers seeking to incorporate these technologies in domain-specific applications

Proceedings of International Workshop "Global Computing: Programming Environments, Languages, Security and Analysis of Systems"

According to the IST/ FET proactive initiative on GLOBAL COMPUTING, the goal is to obtain techniques (models, frameworks, methods, algorithms) for constructing systems that are flexible, dependable, secure, robust and efficient. The dominant concerns are not those of representing and manipulating data efficiently but rather those of handling the co-ordination and interaction, security, reliability, robustness, failure modes, and control of risk of the entities in the system and the overall design, description and performance of the system itself. Completely different paradigms of computer science may have to be developed to tackle these issues effectively. The research should concentrate on systems having the following characteristics: • The systems are composed of autonomous computational entities where activity is not centrally controlled, either because global control is impossible or impractical, or because the entities are created or controlled by different owners. • The computational entities are mobile, due to the movement of the physical platforms or by movement of the entity from one platform to another. • The configuration varies over time. For instance, the system is open to the introduction of new computational entities and likewise their deletion. The behaviour of the entities may vary over time. • The systems operate with incomplete information about the environment. For instance, information becomes rapidly out of date and mobility requires information about the environment to be discovered. The ultimate goal of the research action is to provide a solid scientific foundation for the design of such systems, and to lay the groundwork for achieving effective principles for building and analysing such systems. This workshop covers the aspects related to languages and programming environments as well as analysis of systems and resources involving 9 projects (AGILE , DART, DEGAS , MIKADO, MRG, MYTHS, PEPITO, PROFUNDIS, SECURE) out of the 13 founded under the initiative. After an year from the start of the projects, the goal of the workshop is to fix the state of the art on the topics covered by the two clusters related to programming environments and analysis of systems as well as to devise strategies and new ideas to profitably continue the research effort towards the overall objective of the initiative. We acknowledge the Dipartimento di Informatica and Tlc of the University of Trento, the Comune di Rovereto, the project DEGAS for partially funding the event and the Events and Meetings Office of the University of Trento for the valuable collaboration