Management of generic and multi-platform workflows for exploiting heterogeneous environments on e-Science

Scientific Workflows (SWFs) are widely used to model applications in e-Science. In this programming model, scientific applications are described as a set of tasks that have dependencies among them. During the last decades, the execution of scientific workflows has been successfully performed in the available computing infrastructures (supercomputers, clusters and grids) using software programs called Workflow Management Systems (WMSs), which orchestrate the workload on top of these computing infrastructures. However, because each computing infrastructure has its own architecture and each scientific applications exploits efficiently one of these infrastructures, it is necessary to organize the way in which they are executed. WMSs need to get the most out of all the available computing and storage resources. Traditionally, scientific workflow applications have been extensively deployed in high-performance computing infrastructures (such as supercomputers and clusters) and grids. But, in the last years, the advent of cloud computing infrastructures has opened the door of using on-demand infrastructures to complement or even replace local infrastructures. However, new issues have arisen, such as the integration of hybrid resources or the compromise between infrastructure reutilization and elasticity, everything on the basis of cost-efficiency. The main contribution of this thesis is an ad-hoc solution for managing workflows exploiting the capabilities of cloud computing orchestrators to deploy resources on demand according to the workload and to combine heterogeneous cloud providers (such as on-premise clouds and public clouds) and traditional infrastructures (supercomputers and clusters) to minimize costs and response time. The thesis does not propose yet another WMS, but demonstrates the benefits of the integration of cloud orchestration when running complex workflows. The thesis shows several configuration experiments and multiple heterogeneous backends from a realistic comparative genomics workflow called Orthosearch, to migrate memory-intensive workload to public infrastructures while keeping other blocks of the experiment running locally. The running time and cost of the experiments is computed and best practices are suggested.Los flujos de trabajo científicos son comúnmente usados para modelar aplicaciones en e-Ciencia. En este modelo de programación, las aplicaciones científicas se describen como un conjunto de tareas que tienen dependencias entre ellas. Durante las últimas décadas, la ejecución de flujos de trabajo científicos se ha llevado a cabo con éxito en las infraestructuras de computación disponibles (supercomputadores, clústers y grids) haciendo uso de programas software llamados Gestores de Flujos de Trabajos, los cuales distribuyen la carga de trabajo en estas infraestructuras de computación. Sin embargo, debido a que cada infraestructura de computación posee su propia arquitectura y cada aplicación científica explota eficientemente una de estas infraestructuras, es necesario organizar la manera en que se ejecutan. Los Gestores de Flujos de Trabajo necesitan aprovechar el máximo todos los recursos de computación y almacenamiento disponibles. Habitualmente, las aplicaciones científicas de flujos de trabajos han sido ejecutadas en recursos de computación de altas prestaciones (tales como supercomputadores y clústers) y grids. Sin embargo, en los últimos años, la aparición de las infraestructuras de computación en la nube ha posibilitado el uso de infraestructuras bajo demanda para complementar o incluso reemplazar infraestructuras locales. No obstante, este hecho plantea nuevas cuestiones, tales como la integración de recursos híbridos o el compromiso entre la reutilización de la infraestructura y la elasticidad, todo ello teniendo en cuenta que sea eficiente en el coste. La principal contribución de esta tesis es una solución ad-hoc para gestionar flujos de trabajos explotando las capacidades de los orquestadores de recursos de computación en la nube para desplegar recursos bajo demando según la carga de trabajo y combinar proveedores de computación en la nube heterogéneos (privados y públicos) e infraestructuras tradicionales (supercomputadores y clústers) para minimizar el coste y el tiempo de respuesta. La tesis no propone otro gestor de flujos de trabajo más, sino que demuestra los beneficios de la integración de la orquestación de la computación en la nube cuando se ejecutan flujos de trabajo complejos. La tesis muestra experimentos con diferentes configuraciones y múltiples plataformas heterogéneas, haciendo uso de un flujo de trabajo real de genómica comparativa llamado Orthosearch, para traspasar cargas de trabajo intensivas de memoria a infraestructuras públicas mientras se mantienen otros bloques del experimento ejecutándose localmente. El tiempo de respuesta y el coste de los experimentos son calculados, además de sugerir buenas prácticas.Els fluxos de treball científics són comunament usats per a modelar aplicacions en e-Ciència. En aquest model de programació, les aplicacions científiques es descriuen com un conjunt de tasques que tenen dependències entre elles. Durant les últimes dècades, l'execució de fluxos de treball científics s'ha dut a terme amb èxit en les infraestructures de computació disponibles (supercomputadors, clústers i grids) fent ús de programari anomenat Gestors de Fluxos de Treballs, els quals distribueixen la càrrega de treball en aquestes infraestructures de computació. No obstant açò, a causa que cada infraestructura de computació posseeix la seua pròpia arquitectura i cada aplicació científica explota eficientment una d'aquestes infraestructures, és necessari organitzar la manera en què s'executen. Els Gestors de Fluxos de Treball necessiten aprofitar el màxim tots els recursos de computació i emmagatzematge disponibles. Habitualment, les aplicacions científiques de fluxos de treballs han sigut executades en recursos de computació d'altes prestacions (tals com supercomputadors i clústers) i grids. No obstant açò, en els últims anys, l'aparició de les infraestructures de computació en el núvol ha possibilitat l'ús d'infraestructures sota demanda per a complementar o fins i tot reemplaçar infraestructures locals. No obstant açò, aquest fet planteja noves qüestions, tals com la integració de recursos híbrids o el compromís entre la reutilització de la infraestructura i l'elasticitat, tot açò tenint en compte que siga eficient en el cost. La principal contribució d'aquesta tesi és una solució ad-hoc per a gestionar fluxos de treballs explotant les capacitats dels orquestadors de recursos de computació en el núvol per a desplegar recursos baix demande segons la càrrega de treball i combinar proveïdors de computació en el núvol heterogenis (privats i públics) i infraestructures tradicionals (supercomputadors i clústers) per a minimitzar el cost i el temps de resposta. La tesi no proposa un gestor de fluxos de treball més, sinó que demostra els beneficis de la integració de l'orquestració de la computació en el núvol quan s'executen fluxos de treball complexos. La tesi mostra experiments amb diferents configuracions i múltiples plataformes heterogènies, fent ús d'un flux de treball real de genòmica comparativa anomenat Orthosearch, per a traspassar càrregues de treball intensives de memòria a infraestructures públiques mentre es mantenen altres blocs de l'experiment executant-se localment. El temps de resposta i el cost dels experiments són calculats, a més de suggerir bones pràctiques.Carrión Collado, AA. (2017). Management of generic and multi-platform workflows for exploiting heterogeneous environments on e-Science [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/86179TESI

Análisis y caracterización de trabajos BLAST para la planificación eficiente en entorno Grid y Supercomputación

La ejecución de experimentos con BLAST, una de las herramientas bioinformáticas más utilizadas, requiere recursos computacionales que exceden los recursos de la mayoría de centros de investigación. Esta tesis se centra en desarrollar técnicas para la ejecución eficiente de estos experimentos tanto en infraestructuras Grid como en Supercomputación.Carrión Collado, AA. (2010). Análisis y caracterización de trabajos BLAST para la planificación eficiente en entorno Grid y Supercomputación. http://hdl.handle.net/10251/1385

Further Results on the Total Roman Domination in Graphs

[EN] Let G be a graph without isolated vertices. A function f:V(G)-> {0,1,2} is a total Roman dominating function on G if every vertex v is an element of V(G) for which f(v)=0 is adjacent to at least one vertex u is an element of V(G) such that f(u)=2 , and if the subgraph induced by the set {v is an element of V(G):f(v)>= 1} has no isolated vertices. The total Roman domination number of G, denoted gamma tR(G) , is the minimum weight omega (f)=Sigma v is an element of V(G)f(v) among all total Roman dominating functions f on G. In this article we obtain new tight lower and upper bounds for gamma tR(G) which improve the well-known bounds 2 gamma (G)<= gamma tR(G)<= 3 gamma (G) , where gamma (G) represents the classical domination number. In addition, we characterize the graphs that achieve equality in the previous lower bound and we give necessary conditions for the graphs which satisfy the equality in the upper bound above.Cabrera Martínez, A.; Cabrera García, S.; Carrión García, A. (2020). Further Results on the Total Roman Domination in Graphs. Mathematics. 8(3):1-8. https://doi.org/10.3390/math8030349S1883Henning, M. A. (2009). A survey of selected recent results on total domination in graphs. Discrete Mathematics, 309(1), 32-63. doi:10.1016/j.disc.2007.12.044Henning, M. A., & Yeo, A. (2013). Total Domination in Graphs. Springer Monographs in Mathematics. doi:10.1007/978-1-4614-6525-6Henning, M. A., & Marcon, A. J. (2016). Semitotal Domination in Claw-Free Cubic Graphs. Annals of Combinatorics, 20(4), 799-813. doi:10.1007/s00026-016-0331-zHenning, M. . A., & Marcon, A. J. (2016). Vertices contained in all or in no minimum semitotal dominating set of a tree. Discussiones Mathematicae Graph Theory, 36(1), 71. doi:10.7151/dmgt.1844Henning, M. A., & Pandey, A. (2019). Algorithmic aspects of semitotal domination in graphs. Theoretical Computer Science, 766, 46-57. doi:10.1016/j.tcs.2018.09.019Cockayne, E. J., Dreyer, P. A., Hedetniemi, S. M., & Hedetniemi, S. T. (2004). Roman domination in graphs. Discrete Mathematics, 278(1-3), 11-22. doi:10.1016/j.disc.2003.06.004Stewart, I. (1999). Defend the Roman Empire! Scientific American, 281(6), 136-138. doi:10.1038/scientificamerican1299-136Chambers, E. W., Kinnersley, B., Prince, N., & West, D. B. (2009). Extremal Problems for Roman Domination. SIAM Journal on Discrete Mathematics, 23(3), 1575-1586. doi:10.1137/070699688Favaron, O., Karami, H., Khoeilar, R., & Sheikholeslami, S. M. (2009). On the Roman domination number of a graph. Discrete Mathematics, 309(10), 3447-3451. doi:10.1016/j.disc.2008.09.043Liu, C.-H., & Chang, G. J. (2012). Upper bounds on Roman domination numbers of graphs. Discrete Mathematics, 312(7), 1386-1391. doi:10.1016/j.disc.2011.12.021González, Y., & Rodríguez-Velázquez, J. (2013). Roman domination in Cartesian product graphs and strong product graphs. Applicable Analysis and Discrete Mathematics, 7(2), 262-274. doi:10.2298/aadm130813017gLiu, C.-H., & Chang, G. J. (2012). Roman domination on strongly chordal graphs. Journal of Combinatorial Optimization, 26(3), 608-619. doi:10.1007/s10878-012-9482-yAhangar Abdollahzadeh, H., Henning, M., Samodivkin, V., & Yero, I. (2016). Total Roman domination in graphs. Applicable Analysis and Discrete Mathematics, 10(2), 501-517. doi:10.2298/aadm160802017aAmjadi, J., Sheikholeslami, S. M., & Soroudi, M. (2019). On the total Roman domination in trees. Discussiones Mathematicae Graph Theory, 39(2), 519. doi:10.7151/dmgt.2099Cabrera Martínez, A., Montejano, L. P., & Rodríguez-Velázquez, J. A. (2019). Total Weak Roman Domination in Graphs. Symmetry, 11(6), 831. doi:10.3390/sym1106083

Total Roman Domination Number of Rooted Product Graphs

[EN] Let G be a graph with no isolated vertex and f:V(G)->{0,1,2} a function. If f satisfies that every vertex in the set {v is an element of V(G):f(v)=0} is adjacent to at least one vertex in the set {v is an element of V(G):f(v)=2}, and if the subgraph induced by the set {v is an element of V(G):f(v)>= 1} has no isolated vertex, then we say that f is a total Roman dominating function on G. The minimum weight omega(f)= n-ary sumation v is an element of V(G)f(v) among all total Roman dominating functions f on G is the total Roman domination number of G. In this article we study this parameter for the rooted product graphs. Specifically, we obtain closed formulas and tight bounds for the total Roman domination number of rooted product graphs in terms of domination invariants of the factor graphs involved in this product.Cabrera Martinez, A.; Cabrera García, S.; Carrión García, A.; Hernandez Mira, FA. (2020). Total Roman Domination Number of Rooted Product Graphs. Mathematics. 8(10):1-13. https://doi.org/10.3390/math8101850S11381

On the Outer-Independent Roman Domination in Graphs

[EN] Let G be a graph with no isolated vertex and f:V(G)->{0,1,2} a function. Let V-i={v is an element of V(G):f(v)=i} for every i is an element of{0,1,2}. The function f is an outer-independent Roman dominating function on G if V0 is an independent set and every vertex in V-0 is adjacent to at least one vertex in V-2. The minimum weight omega(f)= Sigma v is an element of V(G)f(v) among all outer-independent Roman dominating functions f on G is the outer-independent Roman domination number of G. This paper is devoted to the study of the outer-independent Roman domination number of a graph, and it is a contribution to the special issue "Theoretical Computer Science and Discrete Mathematics" of Symmetry. In particular, we obtain new tight bounds for this parameter, and some of them improve some well-known results. We also provide closed formulas for the outer-independent Roman domination number of rooted product graphs.Cabrera Martínez, A.; Cabrera García, S.; Carrión García, A.; Grisales Del Rio, AM. (2020). On the Outer-Independent Roman Domination in Graphs. Symmetry (Basel). 12(11):1-12. https://doi.org/10.3390/sym12111846S1121211Goddard, W., & Henning, M. A. (2013). Independent domination in graphs: A survey and recent results. Discrete Mathematics, 313(7), 839-854. doi:10.1016/j.disc.2012.11.031Cockayne, E. J., Dreyer, P. A., Hedetniemi, S. M., & Hedetniemi, S. T. (2004). Roman domination in graphs. Discrete Mathematics, 278(1-3), 11-22. doi:10.1016/j.disc.2003.06.004Abdollahzadeh Ahangar, H., Chellali, M., & Samodivkin, V. (2017). Outer independent Roman dominating functions in graphs. International Journal of Computer Mathematics, 94(12), 2547-2557. doi:10.1080/00207160.2017.1301437Cabrera Martínez, A., Kuziak, D., & Yero, G. I. (2021). A constructive characterization of vertex cover Roman trees. Discussiones Mathematicae Graph Theory, 41(1), 267. doi:10.7151/dmgt.2179Godsil, C. D., & McKay, B. D. (1978). A new graph product and its spectrum. Bulletin of the Australian Mathematical Society, 18(1), 21-28. doi:10.1017/s000497270000776

Glositis romboidal: localización atípica: caso clínico y diagnóstico diferencial

La glositis romboidal media (GRM) es una alteración benigna, poco frecuente, que afecta ligeramente más a los varones. Suele localizarse en la línea media del dorso de la lengua por delante de la 'V' lingual, en forma de área rojiza, romboidal, plana como una mácula o a veces exofítica, mamelonada, que puede sobresalir de 2 a 5 mm, en la que no se observan papilas filiformes. Se presenta el caso clínico de un varón de 61 años de edad que consulta por presentar una lesión exofítica asintomática en dorso de lengua, situada a nivel paramedial izquierdo. El estudio histopatológico es compatible con glositis romboidal. Se debe realizar el diagnóstico diferencial con otras lesiones exofíticas frecuentes en esta localización como: hemangioma o lesión vascular, granuloma piogénico, amiloidosis, tumor de células granulares y carcinoma de células escamosas, analizando tanto los aspectos clínicos como histopatológicos de cada una de ellas. A través de este caso clínico comprobamos que la GRM puede tener una localización paramedial, que denominamos atípica.Median rhomboid glossitis (MRG) is an uncommon benign abnormality of the tongue, most frequently affecting men. It is typically located around the midline of the dorsum of the tongue, anterior to the lingual 'V', appearing as a reddish, rhomboid area, depapillated, flat maculate or mamillated and raised by 2 - 5 mm. This paper reports a case of rhomboid glossitis in a 61- year-old man who consulted for a painless raised lesion on the dorsum of the tongue, in left paramedial (not medial) location. Histopathological findings were compatible with rhomboid glossitis. Other diagnoses considered but ruled out on the basis of the clinical and histopathological findings were haemangioma, pyogenic granuloma, amyloidosis, granular cell tumour, and squamous cell carcinoma. This case confirms that rhomboid glossitis may occur in paramedial locations

Managing Workflows on top of a Cloud Computing Orchestrator for using heterogeneous environments on e-Science

[EN] Scientific workflows (SWFs) are widely used to model processes in e-Science. SWFs are executed by means of workflow management systems (WMSs), which orchestrate the workload on top of computing infrastructures. The advent of cloud computing infrastructures has opened the door of using on-demand infrastructures to complement or even replace local infrastructures. However, new issues have arisen, such as the integration of hybrid resources or the compromise between infrastructure reutilisation and elasticity. In this article, we present an ad hoc solution for managing workflows exploiting the capabilities of cloud orchestrators to deploy resources on demand according to the workload and to combine heterogeneous cloud providers (such as on-premise clouds and public clouds) and traditional infrastructures (clusters) to minimise costs and response time. The work does not propose yet another WMS but demonstrates the benefits of the integration of cloud orchestration when running complex workflows. The article shows several configuration experiments from a realistic comparative genomics workflow called Orthosearch, to migrate memory-intensive workload to public infrastructures while keeping other blocks of the experiment running locally. The article computes running time and cost suggesting best practices.This paper wants to acknowledge the support of the EUBrazilCC project, funded by the European Commission (STREP 614048) and the Brazilian MCT/CNPq N. 13/2012, for the use of its infrastructure. The authors would like also to thank the Spanish 'Ministerio de Economia y Competitividad' for the project 'Clusters Virtuales Elasticos y Migrables sobre Infraestructuras Cloud Hibridas' with reference TIN2013-44390-R.Carrión Collado, AA.; Caballer Fernández, M.; Blanquer Espert, I.; Kotowski, N.; Jardim, R.; Dávila, AMR. (2017). Managing Workflows on top of a Cloud Computing Orchestrator for using heterogeneous environments on e-Science. International Journal of Web and Grid Services. 13(4):375-402. doi:10.1504/IJWGS.2017.10003225S37540213

Alveolar bone loss, platelet and glycosylated haemoglobin levels in 239 patients. A clinical study

The relation between periodontal disease and systemic pathologies is still not widespread among general practitioners. The aim of our study is to evaluate whether or not periodontal radiological diagnosis can aid the detection of blood alterations associated with acquired systemic diseases. This is a cross sectional study. All of the participants underwent a panoramic radiograph and a complete blood test. Morphological bone loss was considered as positive in those patients who showed radiographically more than 1 tooth with bone loss greater than or equal to the middle third of the root. The statistical analysis was performed by comparing the variables using the ANOVA or U-Mann-Whitney tests for independent samples with normal conditions. The correlation coefficient was analysed using the Pearson test. 239 patients were included in our study (96 men and 143 women) with an average age of 64.40 years. 59.04% of the patients were determined as morphological bone loss positive and had on average 4 teeth less than negative patients (p <0.0001). Also the average platelet levels in positive patients were lower (p = 0.024) and mean levels of HBA1c (p = 0.009) were higher. Morphological bone loss parameter can be useful both for dentists and general practitioners to refer, subsequently, to periodontal specialist

Characterisation of the ex vivo virulence of Leishmania infantum isolates from Phlebotomus perniciosus from an outbreak of human leishmaniosis in Madrid, Spain

BACKGROUND: Since mid 2009, an outbreak of human leishmaniosis in Madrid, Spain, has involved more than 560 clinical cases. Many of the cases occurred in people who live in areas around a newly constructed green park (BosqueSur). This periurban park provides a suitable habitat for sand flies (the vectors of Leishmania infantum). Indeed, studies of blood meals from sand flies captured in the area showed a strong association between the insect vector, hares or rabbits, and humans in the area. Interestingly, up to 70% of cases have been found in immunocompetent patients (aged between 46-60 years). This study was designed to evaluate the ex vivo virulence of the L. infantum isolates from Phlebotomus perniciosus captured in this area of Madrid. METHODS: Murine macrophages and dendritic cells were infected ex vivo with L. infantum strain BCN150, isolate BOS1FL1, or isolate POL2FL7. At different times after infection, the infection indices, cytokine production (IL-12p40 and IL-10), NO release and arginase activities were evaluated. RESULTS: Using an ex vivo model of infection in murine bone marrow-derived cells, we found that infection with isolates BOS1FL1 and POL2FL7 undermined host immune defence mechanisms in multiple ways. The main factors identified were changes in both the balance of iNOS versus arginase activities and the equilibrium between the production of IL-12 and IL-10. Infection with isolates BOS1FL1 and POL2FL7 also resulted in higher infection rates compared to the BCN150 strain. Infection index values at 24 h were as follows: BCN150-infected cells, 110 for infected MØ and 115 for infected DC; BOS1FL1-infected cells, 300 for infected MØ and 247 for infected DC; and POL2FL7-infected cells, 275 for infected MØ and 292 for infected DC. CONCLUSIONS: Our data indicate that L. infantum isolates captured from this endemic area exhibited high virulence in terms of infection index, cytokine production and enzymatic activities involved in the pathogenesis of visceral leishmaniosis. Altogether, these data provide a starting point for the study of the virulence behaviour of parasites (BOS1FL1 and POL2FL7) isolated from P. perniciosus during the outbreak of human leishmaniosis in Madrid, Spain, and their involvement in infecting immunocompetent hosts.This study was supported by Grants AGL2010-17394 and AGL2013-44100R from the Spanish Ministry of Economy and Competitiveness and was partially funded by EU grant FP7-2011-261504 EDENext and the paper is catalogued by the EDENext Steering Committee as EDENext 276 (http://www.edenext.eu).S