Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics

Performance Evaluation of Hadoop based Big Data Applications with HiBench Benchmarking tool on IaaS Cloud Platforms

Cloud computing is a computing paradigm where large numbers of devices are connected through networks that provide a dynamically scalable infrastructure for applications, data and storage. Currently, many businesses, from small scale to big companies and industries, are changing their operations to utilize cloud services because cloud platforms could increase company’s growth through process efficiency and reduction in information technology spending [Coles16]. Companies are relying on cloud platforms like Amazon Web Services, Google Compute Engine, and Microsoft Azure, etc., for their business development. Due to the emergence of new technologies, devices, and communications, the amount of data produced is growing rapidly every day. Big data is a collection of large dataset, typically hundreds of gigabytes, terabytes or petabytes. Big data storage and the analytics of this huge volume of data are a great challenge for companies and new businesses to handle, which is a primary focus of this paper. This research was conducted on Amazon’s Elastic Compute Cloud (EC2) and Microsoft Azure platforms using the HiBench Hadoop Big Data Benchmark suite [HiBench16]. Processing huge volumes of data is a tedious task that is normally handled through traditional database servers. In contrast, Hadoop is a powerful framework is used to handle applications with big data requirements efficiently by using the MapReduce algorithm to run them on systems with many commodity hardware nodes. Hadoop’s distributed file system facilitates rapid storage and data transfer rates of big data among the nodes and remains operational even when a node failure has occurred in a cluster. HiBench is a big data benchmarking tool that is used for evaluating the performance of big data applications whose data are handled and controlled by the Hadoop framework cluster. Hadoop cluster environment was enabled and evaluated on two cloud platforms. A quantitative comparison was performed on Amazon EC2 and Microsoft Azure along with a study of their pricing models. Measures are suggested for future studies and research

Using big data for customer centric marketing

This chapter deliberates on “big data” and provides a short overview of business intelligence and emerging analytics. It underlines the importance of data for customer-centricity in marketing. This contribution contends that businesses ought to engage in marketing automation tools and apply them to create relevant, targeted customer experiences. Today’s business increasingly rely on digital media and mobile technologies as on-demand, real-time marketing has become more personalised than ever. Therefore, companies and brands are striving to nurture fruitful and long lasting relationships with customers. In a nutshell, this chapter explains why companies should recognise the value of data analysis and mobile applications as tools that drive consumer insights and engagement. It suggests that a strategic approach to big data could drive consumer preferences and may also help to improve the organisational performance.peer-reviewe

Database integrated analytics using R : initial experiences with SQL-Server + R

© 2016 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Most data scientists use nowadays functional or semi-functional languages like SQL, Scala or R to treat data, obtained directly from databases. Such process requires to fetch data, process it, then store again, and such process tends to be done outside the DB, in often complex data-flows. Recently, database service providers have decided to integrate “R-as-a-Service” in their DB solutions. The analytics engine is called directly from the SQL query tree, and results are returned as part of the same query. Here we show a first taste of such technology by testing the portability of our ALOJA-ML analytics framework, coded in R, to Microsoft SQL-Server 2016, one of the SQL+R solutions released recently. In this work we discuss some data-flow schemes for porting a local DB + analytics engine architecture towards Big Data, focusing specially on the new DB Integrated Analytics approach, and commenting the first experiences in usability and performance obtained from such new services and capabilities.Peer ReviewedPostprint (author's final draft

CERN openlab Whitepaper on Future IT Challenges in Scientific Research

This whitepaper describes the major IT challenges in scientific research at CERN and several other European and international research laboratories and projects. Each challenge is exemplified through a set of concrete use cases drawn from the requirements of large-scale scientific programs. The paper is based on contributions from many researchers and IT experts of the participating laboratories and also input from the existing CERN openlab industrial sponsors. The views expressed in this document are those of the individual contributors and do not necessarily reflect the view of their organisations and/or affiliates

DeapSECURE Computational Training for Cybersecurity Students: Improvements, Mid-Stage Evaluation, and Lessons Learned

DeapSECURE is a non-degree computational training program that provides a solid high-performance computing (HPC) and big-data foundation for cybersecurity students. DeapSECURE consists of six modules covering a broad spectrum of topics such as HPC platforms, big-data analytics, machine learning, privacy-preserving methods, and parallel programming. In the second year of this program, to improve the learning experience, we implemented a number of changes, such as grouping modules into two broad categories, big-data and HPC ; creating a single cybersecurity storyline across the modules; and introducing post-workshop (optional) hackshops. Two major goals of these changes are, firstly, to effectively engage students to maintain high interest and attendance in such a non-degree program, and, secondly, to increase knowledge and skill acquisition. To assess the program, and in particular the changes made in the second year, we evaluated and compared the execution and outcomes of the training in Year 1 and Year 2. The assessment data shows that the implemented changes have partially achieved our goals, while simultaneously providing indications where we can further improve. The development of a fully on-line training mode is planned for the next year, along with a reproducibility pilot study to broaden the subject domain from cybersecurity to other areas, such as computations with sensitive data