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A Search Space Exploration Framework for e-Science Applications 面向电子科学应用的搜索空间探索框架
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/bresci.2018.3276
Eric B. Gauch, Bruno E. C. Milanesi, B. Silva, Renato L. F. Cunha, M. Netto
{"title":"A Search Space Exploration Framework for e-Science Applications","authors":"Eric B. Gauch, Bruno E. C. Milanesi, B. Silva, Renato L. F. Cunha, M. Netto","doi":"10.5753/bresci.2018.3276","DOIUrl":"https://doi.org/10.5753/bresci.2018.3276","url":null,"abstract":"High Performance Computing (HPC) has always been a fundamental component to conduct scientific experiments. Model calibrations/simulations often require several executions of scientific applications by changing their input parameters. This process is a common practice in research even though it represents a tedious and error-prone task. In this paper we propose Copper framework which employs a black-box strategy and contains a set of plugins to accelerate user experiments for exploring search spaces in HPC parametric applications. Copper has been used to conduct scientific experiments in different areas including, agriculture, oil gas, flood simulation, and bioinformatics.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"365 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115471520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modelagem de um Data Mart para Leituras do Fluxo de Múons Captadas pelos Telescópios New-Tupi 新图皮望远镜观测到的介子通量读数的数据市场建模
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/bresci.2018.3272
Lucas Bertelli, M. N. D. Oliveira, N. Ferreira, C. E. Navia, Daniel de Oliveira
{"title":"Modelagem de um Data Mart para Leituras do Fluxo de Múons Captadas pelos Telescópios New-Tupi","authors":"Lucas Bertelli, M. N. D. Oliveira, N. Ferreira, C. E. Navia, Daniel de Oliveira","doi":"10.5753/bresci.2018.3272","DOIUrl":"https://doi.org/10.5753/bresci.2018.3272","url":null,"abstract":"O muon e a particula carregada mais abundante da radiacao cosmica secundaria ao nivel do mar. Por meio da leitura do fluxo de muons, fisicos sao capazes de analisar e identificar eventos solares transientes, que podem gerar impactos em nosso planeta. Os telescopios New-Tupi sao telescopios capazes de efetuar a leitura do fluxo de muons que chegaa Terra. Esses telescopios geram um grande volume de dados que precisa ser consultado pelos fisicos. Entretanto, atualmente tais telescopios armazenam todas as leituras realizadas em arquivos binarios, o que dificulta a elaboracao de consultas sobre os dados e sua posterior analise. O objetivo deste artigo e propor um Data Mart para os dados do telescopio New-Tupi, possibilitando aos fisicos realizarem consultas mais complexas de forma facil e com desempenho aceitavel sem ter que recorrera scripts ou programas de terceiros para implementar as consultas sobre os arquivos.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"28 12","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"113944546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Uma Plataforma Computacional para a Construção de Bancos de Dados para Experimentos de Neurociência 为神经科学实验建立数据库的计算平台
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/bresci.2018.3275
Kelly Rosa Braghetto, Evandro Rocha, C. Ribas, Cassiano Reinert Novais dos Santos, Sueli S. Rabaça, Margarita Ruiz Olazar
{"title":"Uma Plataforma Computacional para a Construção de Bancos de Dados para Experimentos de Neurociência","authors":"Kelly Rosa Braghetto, Evandro Rocha, C. Ribas, Cassiano Reinert Novais dos Santos, Sueli S. Rabaça, Margarita Ruiz Olazar","doi":"10.5753/bresci.2018.3275","DOIUrl":"https://doi.org/10.5753/bresci.2018.3275","url":null,"abstract":"Open scientific data is fundamental to support better quality and higher impact reproducible science. The creation of open scientific databases involves a number of challenges, such as the creation of standardized representations of data and metadata from different domains of knowledge, as well as the development of computational resources to assist scientists in collecting and maintaining high-quality data. This paper presents a free software computational platform for the management and sharing of data from Neuroscience experiments. This platform allows to register data and metadata of experiments in a safe and user-friendly way, integrating data records of different types, such as clinical, electrophysiological and behavioral.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"47 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128811808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Integração de Dados na Detecção de Alvos para Fármacos de Schistosoma mansoni 曼氏血吸虫药物靶点检测中的数据集成
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/BRESCI.2018.3271
F. P. Garcia, Kele T. Belloze
{"title":"Integração de Dados na Detecção de Alvos para Fármacos de Schistosoma mansoni","authors":"F. P. Garcia, Kele T. Belloze","doi":"10.5753/BRESCI.2018.3271","DOIUrl":"https://doi.org/10.5753/BRESCI.2018.3271","url":null,"abstract":"A esquistossomose causada pelo organismo Schistosoma mansoni e uma doenca negligenciada importante pela ocorrencia no mundo. Contudo, existe umunico medicamento recomendado pela Organizacao Mundial de Saude para o seu tratamento. Logo, pesquisas por alvos para farmacos alternativos no combatea doenca sao importantes. Este trabalho tem como objetivo identificar possiveis novos alvos para farmacos de S. mansoni. A metodologia adota uma abordagem baseada em ortologia e homologia fazendo uso de proteinas essenciais de organismos modelo e proteinas ja conhecidas como alvos de farmacos, e integracao destes dados. Resultados preliminares apontam uma lista de 91 proteinas candidatas a alvos para farmaco.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116120345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Avaliação do uso eficiente de algoritmos paralelos de filogenia em supercomputadores 评估并行系统发育算法在超级计算机中的有效使用
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/BRESCI.2018.3278
Kary A. C. S. Ocaña, J. Alves, Micaella Coelho, Marcelo Galheigo, C. Osthoff
{"title":"Avaliação do uso eficiente de algoritmos paralelos de filogenia em supercomputadores","authors":"Kary A. C. S. Ocaña, J. Alves, Micaella Coelho, Marcelo Galheigo, C. Osthoff","doi":"10.5753/BRESCI.2018.3278","DOIUrl":"https://doi.org/10.5753/BRESCI.2018.3278","url":null,"abstract":"Bioinformatics, especially the areas of phylogeny and evolution of organisms, requires high performance computing (HPC) environments. The present work presents a behavioral analysis of the RAxML phylogeny tool in HPC environments. RAxML implements parallelism and task distribution by using threads and MPI libraries. Executions were performed in the Santos Dumont (SDumont) supercomputer. Efficiency results show the impact is generated by the variation in configuration, coupling and use of RAxML and SDumont. This information will allow a better understanding and efficient use of these specialized environments.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"96 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130375807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Towards an e-infrastructure for Open Science in Soils Security 面向土壤安全开放科学的电子基础设施
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/BRESCI.2018.3273
Sérgio Manuel Serra da Cruz, M. Ceddia, E. Schmitz, Gabriel Rizzo, R. C. T. Miranda, Sabrina O. Cruz, Ana Clara Correa, Felipe Klinger, É. Marinho, P. V. Cruz
{"title":"Towards an e-infrastructure for Open Science in Soils Security","authors":"Sérgio Manuel Serra da Cruz, M. Ceddia, E. Schmitz, Gabriel Rizzo, R. C. T. Miranda, Sabrina O. Cruz, Ana Clara Correa, Felipe Klinger, É. Marinho, P. V. Cruz","doi":"10.5753/BRESCI.2018.3273","DOIUrl":"https://doi.org/10.5753/BRESCI.2018.3273","url":null,"abstract":"Soils Security is a critical and growing global concern. The OpenSoils´ objective is to host, connect and share large amounts of curated soil data and knowledge at the Brazilian and South America level. The e-infrastructure consists of several layers of services, a database of soil profiles, a cloud-based computational framework to compute and share soil data integrated with a map visualization tools. OpenSoils is open, elastic, provenance-oriented and lightweight computational e-infrastructure that collects, stores, describes, curates, harmonizes and directs to various soil resource types: large datasets of soils profiles, services/applications, documents, projects and external links. OpenSoils is the first open science-based computational framework of soils security in the literature.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128881376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Functional Requirements for Developing ERAS - A Portal to Support Collaborative Geomechanical Simulations* 开发ERAS的功能需求-一个支持协同地质力学模拟的门户*
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/bresci.2018.3270
Maria Julia Dias De Lima, M. Lemos, F. L. Pereira, Rodnei Couto, D. Roehl
{"title":"Functional Requirements for Developing ERAS - A Portal to Support Collaborative Geomechanical Simulations*","authors":"Maria Julia Dias De Lima, M. Lemos, F. L. Pereira, Rodnei Couto, D. Roehl","doi":"10.5753/bresci.2018.3270","DOIUrl":"https://doi.org/10.5753/bresci.2018.3270","url":null,"abstract":"One of the most important tasks in geomechanical research is executing analytical and numerical simulations to understand geomechanical phenomena. In order to attain this objective, researchers have to prepare data to perform the simulations, build the models that define the appropriate physical representation and the mathematical modeling of the problem, run a computer system capable of simulating the phenomenon, and visualize and interpret the results. This paper presents the main functional requirements to support the development of solutions that encompass the simulation of geomechanical problems, taking into account a collaborative environment with access to an efficient computer infrastructure. The paper also describes ERAS, a portal developed according to these requirements, highlighting the advantages it brings to researchers in this area.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"151 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121260717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Rumo à Otimização de Operadores sobre UDF no Spark 在Spark中优化UDF上的操作符
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/BRESCI.2018.3280
J. A. Ferreira, Fábio Porto, Rafaelli Coutinho, Eduardo S. Ogasawara
{"title":"Rumo à Otimização de Operadores sobre UDF no Spark","authors":"J. A. Ferreira, Fábio Porto, Rafaelli Coutinho, Eduardo S. Ogasawara","doi":"10.5753/BRESCI.2018.3280","DOIUrl":"https://doi.org/10.5753/BRESCI.2018.3280","url":null,"abstract":"A análise de dados em larga escala tem ganhado muita importância na comunidade científica devido ao fenômeno do Big Data. Neste contexto, funções definidas pelo usuário (UDF) são, comumente, implementadas em frameworks como Apache Spark para viabilizar a análise de dados em larga escala. No entanto, o uso de UDF traz desafios no processo de otimização de execução pois são opacas. Este trabalho propõe um método de otimização de workflows de análise de dados apoiadas em UDF sobre o Apache Spark. Tal método é baseado na API Catalyst do SparkSQL e em macros da linguagem Scala.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114742229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A volunteer computing system implemented with peer-to-peer communication optimized for small and limited environments 一个志愿者计算系统实现点对点通信优化小和有限的环境
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/BRESCI.2018.3268
C. Santiago, L. Digiampietri
{"title":"A volunteer computing system implemented with peer-to-peer communication optimized for small and limited environments","authors":"C. Santiago, L. Digiampietri","doi":"10.5753/BRESCI.2018.3268","DOIUrl":"https://doi.org/10.5753/BRESCI.2018.3268","url":null,"abstract":"The computational needs of scientific experiments often require powerful computers. One alternative way to obtain this processing power is taking advantage of the idle processing of personal computers as volunteers. This technique is known as volunteer computing and has great potential in helping scientists. However, there are several issues which can reduce the efficiency of this approach when applied to complex scientific experiments, such as, the ones with long processing time, very large input or output data, etc. In order to face these challenges, we designed a volunteer computing system based on peer-to-peer communication. When compared with the local execution of activities and traditional volunteer computing, the execution time was improved and, in some cases, there was also a reduction of the server upload bandwidth use.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124509359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Assessing the Impact of Supporting Information on the Scheduling of Scientific Workflows on Clouds 评估支持信息对云上科学工作流调度的影响
Anais do Brazilian e-Science Workshop (BreSci) Pub Date : 2018-07-06 DOI: 10.5753/BRESCI.2018.3277
Eduardo Cotrin Teixeira, Daniel Cordeiro, K. Braghetto
{"title":"Assessing the Impact of Supporting Information on the Scheduling of Scientific Workflows on Clouds","authors":"Eduardo Cotrin Teixeira, Daniel Cordeiro, K. Braghetto","doi":"10.5753/BRESCI.2018.3277","DOIUrl":"https://doi.org/10.5753/BRESCI.2018.3277","url":null,"abstract":"Executing scientific workflows in high-performance cloud computing platforms requires the use of scheduling algorithms that allow workflows execution as fast as possible, while minimizing the monetary cost of such executions. In this work we study how the use of supporting information can offer guidance to scheduling algorithms, helping them to devise more efficient execution plans in terms of the total execution time (makespan) and the total monetary cost. Using two large-scale scientific workflows, our experiments showed that simple modifications on a classical scheduling algorithm (HEFT), in conjunction with the appropriate supporting information, could reduce the monetary cost of an execution in up to 59% and reduce the makespan in up to 8.6%.","PeriodicalId":306675,"journal":{"name":"Anais do Brazilian e-Science Workshop (BreSci)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130354238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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