INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures

[EN] This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. Our developments are freely downloadable as open source components, and are already being integrated into many scientific applications.INDIGO-Datacloud has been funded by the European Commision H2020 research and innovation program under grant agreement RIA 653549.Salomoni, D.; Campos, I.; Gaido, L.; Marco, J.; Solagna, P.; Gomes, J.; Matyska, L.... (2018). INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures. Journal of Grid Computing. 16(3):381-408. https://doi.org/10.1007/s10723-018-9453-3S381408163García, A.L., Castillo, E.F.-d., Puel, M.: Identity federation with VOMS in cloud infrastructures. In: 2013 IEEE 5Th International Conference on Cloud Computing Technology and Science, pp 42–48 (2013)Chadwick, D.W., Siu, K., Lee, C., Fouillat, Y., Germonville, D.: Adding federated identity management to OpenStack. Journal of Grid Computing 12(1), 3–27 (2014)Craig, A.L.: A design space review for general federation management using keystone. In: Proceedings of the 2014 IEEE/ACM 7th International Conference on Utility and Cloud Computing, pp 720–725. IEEE Computer Society (2014)Pustchi, N., Krishnan, R., Sandhu, R.: Authorization federation in iaas multi cloud. In: Proceedings of the 3rd International Workshop on Security in Cloud Computing, pp 63–71. ACM (2015)Lee, C.A., Desai, N., Brethorst, A.: A Keystone-Based Virtual Organization Management System. In: 2014 IEEE 6Th International Conference On Cloud Computing Technology and Science (Cloudcom), pp 727–730. IEEE (2014)Castillo, E.F.-d., Scardaci, D., García, A.L.: The EGI Federated Cloud e-Infrastructure. Procedia Computer Science 68, 196–205 (2015)AARC project: AARC Blueprint Architecture, see https://aarc-project.eu/architecture . Technical report (2016)Oesterle, F., Ostermann, S., Prodan, R., Mayr, G.J.: Experiences with distributed computing for meteorological applications: grid computing and cloud computing. Geosci. Model Dev. 8(7), 2067–2078 (2015)Plasencia, I.C., Castillo, E.F.-d., Heinemeyer, S., García, A.L., Pahlen, F., Borges, G.: Phenomenology tools on cloud infrastructures using OpenStack. The European Physical Journal C 73(4), 2375 (2013)Boettiger, C.: An introduction to docker for reproducible research. ACM SIGOPS Operating Systems Review 49(1), 71–79 (2015)Docker: http://www.docker.com (2013)Gomes, J., Campos, I., Bagnaschi, E., David, M., Alves, L., Martins, J., Pina, J., Alvaro, L.-G., Orviz, P.: Enabling rootless linux containers in multi-user environments: the udocker tool. Computing Physics Communications. https://doi.org/10.1016/j.cpc.2018.05.021 (2018)Zhang, Z., Chuan, W., Cheung, D.W.L.: A survey on cloud interoperability taxonomies, standards, and practice. SIGMETRICS perform. Eval. Rev. 40(4), 13–22 (2013)Lorido-Botran, T., Miguel-Alonso, J., Lozano, J.A.: A Review of Auto-scaling Techniques for Elastic Applications in Cloud Environments. Journal of Grid Computing 12(4), 559–592 (2014)Nyrén, R., Metsch, T., Edmonds, A., Papaspyrou, A.: Open Cloud Computing Interface–Core. Technical report, Open Grid Forum (2010)Metsch, T., Edmonds, A.: Open Cloud Computing Interface-Infrastructure. Technical report, Open Grid Forum (2010)Metsch, T., Edmonds, A.: Open Cloud Computing Interface-RESTful HTTP Rendering. Technical report, Open Grid Forum (2011)(Ca Technologies) Lipton, P., (Ibm) Moser, S., (Vnomic) Palma, D., (Ibm) Spatzier, T.: Topology and Orchestration Specification for Cloud Applications. Technical report, OASIS Standard (2013)Teckelmann, R., Reich, C., Sulistio, A.: Mapping of cloud standards to the taxonomy of interoperability in IaaS. In: Proceedings - 2011 3rd IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2011, pp 522–526 (2011)García, A.L., Castillo, E.F.-d., Fernández, P.O.: Standards for enabling heterogeneous IaaS cloud federations. Computer Standards & Interfaces 47, 19–23 (2016)Caballer, M., Zala, S., García, A.L., Montó, G., Fernández, P.O., Velten, M.: Orchestrating complex application architectures in heterogeneous clouds. Journal of Grid Computing 16 (1), 3–18 (2018)Hardt, M., Jejkal, T., Plasencia, I.C., Castillo, E.F.-d., Jackson, A., Weiland, M., Palak, B., Plociennik, M., Nielsson, D.: Transparent Access to Scientific and Commercial Clouds from the Kepler Workflow Engine. Computing and Informatics 31(1), 119 (2012)Fakhfakh, F., Kacem, H.H., Kacem, A.H.: Workflow Scheduling in Cloud Computing a Survey. In: IEEE 18Th International Enterprise Distributed Object Computing Conference Workshops and Demonstrations (EDOCW), 2014, Vol. 71, pp. 372–378. Springer, New York (2014)Stockton, D.B., Santamaria, F.: Automating NEURON simulation deployment in cloud resources. Neuroinformatics 15(1), 51–70 (2017)Plóciennik, M., Fiore, S., Donvito, G., Owsiak, M., Fargetta, M., Barbera, R., Bruno, R., Giorgio, E., Williams, D.N., Aloisio, G.: Two-level Dynamic Workflow Orchestration in the INDIGO DataCloud for Large-scale, Climate Change Data Analytics Experiments. Procedia Computer Science 80, 722–733 (2016)Moreno-Vozmediano, R., Montero, R.S., Llorente, I.M.: Multicloud deployment of computing clusters for loosely coupled mtc applications. IEEE transactions on parallel and distributed systems 22(6), 924–930 (2011)Katsaros, G., Menzel, M., Lenk, A.: Cloud Service Orchestration with TOSCA, Chef and Openstack. In: Ic2e (2014)Garcia, A.L., Zangrando, L., Sgaravatto, M., Llorens, V., Vallero, S., Zaccolo, V., Bagnasco, S., Taneja, S., Dal Pra, S., Salomoni, D., Donvito, G.: Improved Cloud resource allocation: how INDIGO-DataCloud is overcoming the current limitations in Cloud schedulers. J. Phys. Conf. Ser. 898(9), 92010 (2017)Singh, S., Chana, I.: A survey on resource scheduling in cloud computing issues and challenges. Journal of Grid Computing, pp. 1–48 (2016)García, A.L., Castillo, E.F.-d., Fernández, P.O., Plasencia, I.C., de Lucas, J.M.: Resource provisioning in Science Clouds: Requirements and challenges. Software: Practice and Experience 48(3), 486–498 (2018)Chauhan, M.A., Babar, M.A., Benatallah, B.: Architecting cloud-enabled systems: a systematic survey of challenges and solutions. Software - Practice and Experience 47(4), 599–644 (2017)Somasundaram, T.S., Govindarajan, K.: CLOUDRB A Framework for scheduling and managing High-Performance Computing (HPC) applications in science cloud. Futur. Gener. Comput. Syst. 34, 47–65 (2014)Sotomayor, B., Keahey, K., Foster, I.: Overhead Matters: A Model for Virtual Resource Management. In: Proceedings of the 2nd International Workshop on Virtualization Technology in Distributed Computing SE - VTDC ’06, p 5. IEEE Computer Society, Washington (2006)SS, S.S., Shyam, G.K., Shyam, G.K.: Resource management for Infrastructure as a Service (IaaS) in cloud computing SS Manvi A survey. J. Netw. Comput. Appl. 41, 424–440 (2014)INDIGO-DataCloud consortium: Initial requirements from research communities - d2.1, see https://www.indigo-datacloud.eu/documents/initial-requirements-research-communities-d21 https://www.indigo-datacloud.eu/documents/initial-requirements-research-communities-d21 https://www.indigo-datacloud.eu/documents/initial-requirements-research-communities-d21 . Technical report (2015)Europen open science cloud: https://ec.europa.eu/research/openscience (2015)Proot: https://proot-me.github.io/ (2014)Runc: https://github.com/opencontainers/runc (2016)Fakechroot: https://github.com/dex4er/fakechroot (2015)Pérez, A., Moltó, G., Caballer, M., Calatrava, A.: Serverless computing for container-based architectures Future Generation Computer Systems (2018)de Vries, K.J.: Global fits of supersymmetric models after LHC run 1. Phd thesis Imperial College London (2015)Openstack: https://www.openstack.org/ (2015)See http://argus-documentation.readthedocs.io/en/stable/argus_introduction.html (2017)See https://en.wikipedia.org/wiki/xacml (2013)See http://www.simplecloud.info (2014)Opennebula: http://opennebula.org/ (2018)Redhat openshift: http://www.opencityplatform.eu (2011)The cloud foundry foundation: https://www.cloudfoundry.org/ (2015)Caballer, M., Blanquer, I., Moltó, G., de Alfonso, C.: Dynamic management of virtual infrastructures. Journal of Grid Computing 13(1), 53–70 (2015)See http://www.infoq.com/articles/scaling-docker-with-kubernetes http://www.infoq.com/articles/scaling-docker-with-kubernetes (2014)Prisma project: http://www.ponsmartcities-prisma.it/ (2010)Opencitiy platform: http://www.opencityplatform.eu (2014)Onedata: https://onedata.org/ (2018)Dynafed: http://lcgdm.web.cern.ch/dynafed-dynamic-federation-project http://lcgdm.web.cern.ch/dynafed-dynamic-federation-project (2011)Fts3: https://svnweb.cern.ch/trac/fts3 (2011)Fernández, P.O., García, A.L., Duma, D.C., Donvito, G., David, M., Gomes, J.: A set of common software quality assurance baseline criteria for research projects, see http://hdl.handle.net/10261/160086 . Technical reportHttermann, M.: Devops for developers Apress (2012)EOSC-Hub: ”Integrating and managing services for the European Open Science Cloud” Funded by H2020 research and innovation pr ogramme under grant agreement No. 777536. See http://eosc-hub.eu (2018)Apache License: author = https://www.apache.org/licenses/LICENSE-2.0 (2004)INDIGO Package Repo: http://repo.indigo-datacloud.eu/ (2017)INDIGO DockerHub: https://hub.docker.com/u/indigodatacloud/ https://hub.docker.com/u/indigodatacloud/ (2015)Indigo gitbook: https://indigo-dc.gitbooks.io/indigo-datacloud-releases https://indigo-dc.gitbooks.io/indigo-datacloud-releases (2017)Van Zundert, G.C., Bonvin, A.M.: Disvis: quantifying and visualizing the accessible interaction space of distance restrained biomolecular complexes. Bioinformatics 31(19), 3222–3224 (2015)Van Zundert, G.C., Bonvin, A.M.: Fast and sensitive rigid–body fitting into cryo–em density maps with powerfit. AIMS Biophys. 2(0273), 73–87 (2015

The IceCube Neutrino Observatory - Contributions to ICRC 2017 Part VI: IceCube-Gen2, the Next Generation Neutrino Observatory

Papers on research & development towards IceCube-Gen2, the next generation neutrino observatory at South Pole, submitted to the 35th International Cosmic Ray Conference (ICRC 2017, Busan, South Korea) by the IceCube-Gen2 Collaboration

The occurrence and dissemination of methicillin and vancomycin-resistant Staphylococcus in samples from patients and health professionals of a university hospital in Recife, State of Pernambuco, Brazil

Introduction Methicillin-resistant Staphylococcus aureus (MRSA) strains have been responsible for many nosocomial outbreaks. Within hospitals, colonized employees often act as reservoirs for the spread of this organism. This study collected clinical samples of 91 patients admitted to the intensive care unit (ICU), hemodialysis/nephrology service and surgical clinic, and biological samples from the nasal cavities of 120 professionals working in those environments, of a University Hospital in Recife, in the State of Pernambuco, Brazil. The main objective of this study was to determine the occurrence and dissemination of methicillin- and vancomycin-resistant Staphylococcus spp. Methods The isolates obtained were tested for susceptibility to oxacillin and vancomycin and detection of the mecA gene. In addition, the isolates were evaluated for the presence of clones by ribotyping-polymerase chain reaction (PCR). Results MRSA occurrence, as detected by the presence of the mecA gene, was more prevalent among nursing technicians; 48.1% (13/27) and 40.7% (11/27) of the isolates were from health professionals of the surgical clinic. In patients, the most frequent occurrence of mecA-positive isolates was among the samples from catheter tips (33.3%; 3/9), obtained mostly from the hemodialysis/nephrology service. Eight vancomycin-resistant strains were found among the MRSA isolates through vancomycin screening. Based on the amplification patterns, 17 ribotypes were identified, with some distributed between patients and professionals. Conclusions Despite the great diversity of clones, which makes it difficult to trace the source of the infection, knowledge of the molecular and phenotypic profiles of Staphylococcus samples can contribute towards guiding therapeutic approaches in the treatment and control of nosocomial infections

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Measurement of the inclusive cross-section for the production of jets in association with a Z boson in proton-proton collisions at 8 TeV using the ATLAS detector

The inclusive cross-section for jet production in association with a Z boson decaying into an electron–positron pair is measured as a function of the transverse momentum and the absolute rapidity of jets using 19.9 fb −1 of s√=8 TeV proton–proton collision data collected with the ATLAS detector at the Large Hadron Collider. The measured Z + jets cross-section is unfolded to the particle level. The cross-section is compared with state-of-the-art Standard Model calculations, including the next-to-leading-order and next-to-next-to-leading-order perturbative QCD calculations, corrected for non-perturbative and QED radiation effects. The results of the measurements cover final-state jets with transverse momenta up to 1 TeV, and show good agreement with fixed-order calculations

Reciprocity between membranous and nuclear expression of beta-catenin in colorectal tumours.

beta-Catenin has a central role not only in linking the cadherin-mediated cell adhesion system but also in the intercellular signalling pathway. To investigate alterations of beta-catenin in the development of colorectal carcinoma, the pattern of beta-catenin expression was studied using immunohistochemistry in 74 sporadic colorectal adenomas, in histologically normal mucosa adjacent to 65 of these adenomas, and in 52 carcinomas arising in adenomas. All normal epithelia displayed cell boundary staining for beta-catenin. Adenomas and carcinomas showed varying degrees of membranous staining. However, some tumours also showed nuclear staining of beta-catenin protein. Decreased membranous and increased nuclear beta-catenin staining were associated with increasing degrees of dysplasia in adenomas (P < 0.005, P < 0.05, respectively). Carcinomas manifested significantly reduced membranous, but enhanced nuclear beta-catenin expression compared with their associated adenomas (P < 0.001, P < 0.005, respectively). An inverse correlation was found between decreased membranous and increased nuclear staining of beta-catenin in both adenomas and carcinomas (P < 0.025, P < 0.05, respectively). The data confirm that reduced membranous and increased nuclear expression of beta-catenin is associated with the progression of colorectal adenomas to carcinomas. Our results also suggest that decreased membranous expression of beta-catenin may result from aberrant localisation of the protein in the cell nucleus

Reduced expression of molecules of the cadherin/catenin complex in the transition from colorectal adenoma to carcinoma.

E-cadherin is crucial to the intercellular adherens junctions which are involved in the organisation and maintenance of epithelial structure and suppression of tumour invasion. E-cadherin is associated with the actin cytoskeleton via cytoplasmic proteins, including alpha-, beta- and gamma-catenins, which together form the cadherin/catenin complex. To evaluate changes of the molecules of the cadherin/catenin complex in colorectal carcinogenesis, seventy-four sporadic adenomas, samples of histologically normal epithelium adjacent to 65 adenomas, and 52 carcinomas arising in adenomas were investigated by immunohistochemistry. All normal epithelial cells showed a uniform membranous staining pattern for E-cadherin, alpha-, beta-, and gamma-catenin. Decreased expression of all 4 proteins occurred in parallel in adenomas and carcinomas (in all cases, p &lt; 10(-5). Decreased expression of the cadherin/catenin complex in adenomas was associated with increasing severity of dysplasia (p &lt; 0.001, for E-cadherin, alpha-, and gamma-catenin, p &lt; 0.005 for beta-catenin). Carcinomas displayed significantly reduced expression of the cadherin/catenin complex compared with their associated adenomas (all p &lt; 0.001). The results directly confirm that colorectal tumour progression and invasion is associated with disruption of the cadherin/catenin complex and suggest that the genetic changes and transcriptional modulation of catenins underlying this progression may affect all members of the complex