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Publications

2017

Development of a Quantum Particle in Cell algorithm in GPU for solving Maxwell-Bloch equations

Authors
Gomes, M; Costa, JC; Alves, RA; Silva, NA; Guerreiro, A;

Publication
THIRD INTERNATIONAL CONFERENCE ON APPLICATIONS OF OPTICS AND PHOTONICS

Abstract
In this paper we report on the development of a numerical solver for Vlasov equations based on heterogeneous supercomputing using GPGPUs. The solver adapts techniques from many-body simulation, namely the particlein-cell approach, to describe the interaction between the electromagnetic field and atomic gas whose internal state can be described by the multilevel Bloch equations. We also present the benchmark and performance analysis of the code. We investigate the interaction between two coherent light beams, as a case of study to demonstrate the validation of the code.

2017

Fish Farming Autonomous Calibration System

Authors
Lopes, F; Silva, H; Almeida, JM; Pinho, C; Silva, E;

Publication
OCEANS 2017 - ABERDEEN

Abstract
The fish farming industry is becoming widespread all over the world. By 2039 most of the fish we eat will come from the fish farming industry. In this work, we propose an autonomous robotic solution for indoor fish farming biomass estimation. Our proposed system moves silently on top of the tank borders using differential wheels and a structured light vision system (SLS). The SLS system is composed by a camera and two line lasers (projectors) equipped with a line beam that allows to obtain the fish depth profile present in the tank to perform biomass estimation. Results in laboratory and in real aquaculture environment with live fish are presented.

2017

Certification of Workflows in a Component-Based Cloud of High Performance Computing Services

Authors
Dantas, ABD; de Carvalho, FH; Barbosa, LS;

Publication
FORMAL ASPECTS OF COMPONENT SOFTWARE (FACS 2017)

Abstract
The orchestration of high performance computing (HPC) services to build scientific applications is based on complex workflows. A challenging task consists of improving the reliability of such workflows, avoiding faulty behaviors that can lead to bad consequences in practice. This paper introduces a certifier component for certifying scientific workflows in a certification framework proposed for HPC Shelf, a cloud-based platform for HPC in which different kinds of users can design, deploy and execute scientific applications. This component is able to inspect the workflow description of a parallel computing system of HPC Shelf and check its consistency with respect to a number of safety and liveness properties specified by application designers and component developers.

2017

Teaching/Learning PBL Activity: Gantry Crane Control System Implementation

Authors
Correia, A; Amaro, B; Junior, E; Barbosa, J; Pinto, T; Bicho, E; Soares, F; Oliveira, PM;

Publication
2017 25TH MEDITERRANEAN CONFERENCE ON CONTROL AND AUTOMATION (MED)

Abstract
This paper presents a teaching/learning experiment running in the laboratorial curricular unit Project I of the 4th year of the Integrated Master in Industrial Electronics and Computers Engineering at the University of Minho. Project specifications were defined by the three teachers involved in the experience and students were encouraged to look on different solutions for a real-word problem. In a concurrent way, students designed, developed and implemented didactic rigs to control a gantry crane system. The control was performed in open-loop, based on the Posicast feedforward technique, and in closed-loop, using a two-degrees of freedom configuration. The experiment procedure and the project outcomes of two solutions proposed by the students are presented.

2017

The development process of a metadata application profile for the social and solidarity economy

Authors
Malta, MC; Baptista, AA;

Publication
Developing Metadata Application Profiles

Abstract
This chapter presents the process of developing a Metadata Application Profile for the Social and Solidarity Economy (DCAP-SSE) using Me4MAP, a method for developing Application Profiles that was being put forth by the authors. The DCAPSSE and Me4MAP were developed iteratively, feeding new developments into each other. This paper presents how the DCAP-SSE was developed showing the steps followed through the development of the activities and the techniques used, and the final deliverables obtained at the end of each activity. It also presents the work-team and how each profile of the team contributed for the DCAP-SSE development process. The DCAP-SSE has been endorsed by the SSE community and new perspectives of SSE activities have been defined for future enlargement of the DCAP-SSE. At the time of writing this chapter, Linked Open SSE Data is being published, they are the first examples of use of the DCAP-SSE. © 2017, IGI Global.

2017

Landscape of X chromosome inactivation across human tissues

Authors
Tukiainen, T; Villani, A; Yen, A; Rivas, MA; Marshall, JL; Satija, R; Aguirre, M; Gauthier, L; Fleharty, M; Kirby, A; Cummings, BB; Castel, SE; Karczewski, KJ; Aguet, F; Byrnes, A; Aguet, F; Ardlie, KG; Cummings, BB; Gelfand, ET; Getz, G; Hadley, K; Handsaker, RE; Huang, KH; Kashin, S; Karczewski, KJ; Lek, M; Li, X; MacArthur, DG; Nedzel, JL; Nguyen, DT; Noble, MS; Segrè, AV; Trowbridge, CA; Tukiainen, T; Abell, NS; Balliu, B; Barshir, R; Basha, O; Battle, A; Bogu, GK; Brown, A; Brown, CD; Castel, SE; Chen, LS; Chiang, C; Conrad, DF; Cox, NJ; Damani, FN; Davis, JR; Delaneau, O; Dermitzakis, ET; Engelhardt, BE; Eskin, E; Ferreira, PG; Frésard, L; Gamazon, ER; Garrido-Martín, D; Gewirtz, ADH; Gliner, G; Gloudemans, MJ; Guigo, R; Hall, IM; Han, B; He, Y; Hormozdiari, F; Howald, C; Kyung Im, H; Jo, B; Yong Kang, E; Kim, Y; Kim-Hellmuth, S; Lappalainen, T; Li, G; Li, X; Liu, B; Mangul, S; McCarthy, MI; McDowell, IC; Mohammadi, P; Monlong, J; Montgomery, SB; Muñoz-Aguirre, M; Ndungu, AW; Nicolae, DL; Nobel, AB; Oliva, M; Ongen, H; Palowitch, JJ; Panousis, N; Papasaikas, P; Park, Y; Parsana, P; Payne, AJ; Peterson, CB; Quan, J; Reverter, F; Sabatti, C; Saha, A; Sammeth, M; Scott, AJ; Shabalin, AA; Sodaei, R; Stephens, M; Stranger, BE; Strober, BJ; Sul, JH; Tsang, EK; Urbut, S; van de Bunt, M; Wang, G; Wen, X; Wright, FA; Xi, HS; Yeger-Lotem, E; Zappala, Z; Zaugg, JB; Zhou, Y; Akey, JM; Bates, D; Chan, J; Chen, LS; Claussnitzer, M; Demanelis, K; Diegel, M; Doherty, JA; Feinberg, AP; Fernando, MS; Halow, J; Hansen, KD; Haugen, E; Hickey, PF; Hou, L; Jasmine, F; Jian, R; Jiang, L; Johnson, A; Kaul, R; Kellis, M; Kibriya, MG; Lee, K; Li, JB; Li, Q; Li, X; Lin, J; Lin, S; Linder, S; Linke, C; Liu, Y; Maurano, MT; Molinie, B; Montgomery, SB; Nelson, J; Neri, FJ; Oliva, M; Park, Y; Pierce, BL; Rinaldi, NJ; Rizzardi, LF; Sandstrom, R; Skol, A; Smith, KS; Snyder, MP; Stamatoyannopoulos, J; Stranger, BE; Tang, H; Tsang, EK; Wang, L; Wang, M; Van Wittenberghe, N; Wu, F; Zhang, R; Nierras, CR; Branton, PA; Carithers, LJ; Guan, P; Moore, HM; Rao, A; Vaught, JB; Gould, SE; Lockart, NC; Martin, C; Struewing, JP; Volpi, S; Addington, AM; Koester, SE; Little, AR; Brigham, LE; Hasz, R; Hunter, M; Johns, C; Johnson, M; Kopen, G; Leinweber, WF; Lonsdale, JT; McDonald, A; Mestichelli, B; Myer, K; Roe, B; Salvatore, M; Shad, S; Thomas, JA; Walters, G; Washington, M; Wheeler, J; Bridge, J; Foster, BA; Gillard, BM; Karasik, E; Kumar, R; Miklos, M; Moser, MT; Jewell, SD; Montroy, RG; Rohrer, DC; Valley, DR; Davis, DA; Mash, DC; Undale, AH; Smith, AM; Tabor, DE; Roche, NV; McLean, JA; Vatanian, N; Robinson, KL; Sobin, L; Barcus, ME; Valentino, KM; Qi, L; Hunter, S; Hariharan, P; Singh, S; Um, KS; Matose, T; Tomaszewski, MM; Barker, LK; Mosavel, M; Siminoff, LA; Traino, HM; Flicek, P; Juettemann, T; Ruffier, M; Sheppard, D; Taylor, K; Trevanion, SJ; Zerbino, DR; Craft, B; Goldman, M; Haeussler, M; Kent, WJ; Lee, CM; Paten, B; Rosenbloom, KR; Vivian, J; Zhu, J; Lappalainen, T; Regev, A; Ardlie, KG; Hacohen, N; MacArthur, DG;

Publication
Nature

Abstract
X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to one-third of X-chromosomal genes are expressed from both the active and inactive X chromosomes (Xa and Xi, respectively) in female cells, with the degree of 'escape' from inactivation varying between genes and individuals1,2. The extent to which XCI is shared between cells and tissues remains poorly characterized3,4, as does the degree to which incomplete XCI manifests as detectable sex differences in gene expression5 and phenotypic traits6. Here we describe a systematic survey of XCI, integrating over 5,500 transcriptomes from 449 individuals spanning 29 tissues from GTEx (v6p release) and 940 single-cell transcriptomes, combined with genomic sequence data. We show that XCI at 683 X-chromosomal genes is generally uniform across human tissues, but identify examples of heterogeneity between tissues, individuals and cells. We show that incomplete XCI affects at least 23% of X-chromosomal genes, identify seven genes that escape XCI with support from multiple lines of evidence and demonstrate that escape from XCI results in sex biases in gene expression, establishing incomplete XCI as a mechanism that is likely to introduce phenotypic diversity6,7. Overall, this updated catalogue of XCI across human tissues helps to increase our understanding of the extent and impact of the incompleteness in the maintenance of XCI.

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