Design and evaluation of a genomics variant analysis pipeline using GATK Spark tools

Scalable and efficient processing of genome sequence data, i.e. for variant discovery, is key to the mainstream adoption of High Throughput technology for disease prevention and for clinical use. Achieving scalability, however, requires a significant effort to enable the parallel execution of the analysis tools that make up the pipelines. This is facilitated by the new Spark versions of the well-known GATK toolkit, which offer a black-box approach by transparently exploiting the underlying Map Reduce architecture. In this paper we report on our experience implementing a standard variant discovery pipeline using GATK 4.0 with Docker-based deployment over a cluster. We provide a preliminary performance analysis, comparing the processing times and cost to those of the new Microsoft Genomics Services

Portability of Scientific Workflows in NGS Data Analysis: A Case Study

The analysis of next-generation sequencing (NGS) data requires complex computational workflows consisting of dozens of autonomously developed yet interdependent processing steps. Whenever large amounts of data need to be processed, these workflows must be executed on a parallel and/or distributed systems to ensure reasonable runtime. Porting a workflow developed for a particular system on a particular hardware infrastructure to another system or to another infrastructure is non-trivial, which poses a major impediment to the scientific necessities of workflow reproducibility and workflow reusability. In this work, we describe our efforts to port a state-of-the-art workflow for the detection of specific variants in whole-exome sequencing of mice. The workflow originally was developed in the scientific workflow system snakemake for execution on a high-performance cluster controlled by Sun Grid Engine. In the project, we ported it to the scientific workflow system SaasFee that can execute workflows on (multi-core) stand-alone servers or on clusters of arbitrary sizes using the Hadoop. The purpose of this port was that also owners of low-cost hardware infrastructures, for which Hadoop was made for, become able to use the workflow. Although both the source and the target system are called scientific workflow systems, they differ in numerous aspects, ranging from the workflow languages to the scheduling mechanisms and the file access interfaces. These differences resulted in various problems, some expected and more unexpected, that had to be resolved before the workflow could be run with equal semantics. As a side-effect, we also report cost/runtime ratios for a state-of-the-art NGS workflow on very different hardware platforms: A comparably cheap stand-alone server (80 threads), a mid-cost, mid-sized cluster (552 threads), and a high-end HPC system (3784 threads)

Programming Languages for Data-Intensive HPC Applications: a Systematic Mapping Study

A major challenge in modelling and simulation is the need to combine expertise in both software technologies and a given scientific domain. When High-Performance Computing (HPC) is required to solve a scientific problem, software development becomes a problematic issue. Considering the complexity of the software for HPC, it is useful to identify programming languages that can be used to alleviate this issue. Because the existing literature on the topic of HPC is very dispersed, we performed a Systematic Mapping Study (SMS) in the context of the European COST Action cHiPSet. This literature study maps characteristics of various programming languages for data-intensive HPC applications, including category, typical user profiles, effectiveness, and type of articles. We organised the SMS in two phases. In the first phase, relevant articles are identified employing an automated keyword-based search in eight digital libraries. This lead to an initial sample of 420 papers, which was then narrowed down in a second phase by human inspection of article abstracts, titles and keywords to 152 relevant articles published in the period 2006–2018. The analysis of these articles enabled us to identify 26 programming languages referred to in 33 of relevant articles. We compared the outcome of the mapping study with results of our questionnaire-based survey that involved 57 HPC experts. The mapping study and the survey revealed that the desired features of programming languages for data-intensive HPC applications are portability, performance and usability. Furthermore, we observed that the majority of the programming languages used in the context of data-intensive HPC applications are text-based general-purpose programming languages. Typically these have a steep learning curve, which makes them difficult to adopt. We believe that the outcome of this study will inspire future research and development in programming languages for data-intensive HPC applications.Additional co-authors: Sabri Pllana, Ana Respício, José Simão, Luís Veiga, Ari Vis

Scientific Workflows: Moving Across Paradigms

Modern scientific collaborations have opened up the opportunity to solve complex problems that require both multidisciplinary expertise and large-scale computational experiments. These experiments typically consist of a sequence of processing steps that need to be executed on selected computing platforms. Execution poses a challenge, however, due to (1) the complexity and diversity of applications, (2) the diversity of analysis goals, (3) the heterogeneity of computing platforms, and (4) the volume and distribution of data. A common strategy to make these in silico experiments more manageable is to model them as workflows and to use a workflow management system to organize their execution. This article looks at the overall challenge posed by a new order of scientific experiments and the systems they need to be run on, and examines how this challenge can be addressed by workflows and workflow management systems. It proposes a taxonomy of workflow management system (WMS) characteristics, including aspects previously overlooked. This frames a review of prevalent WMSs used by the scientific community, elucidates their evolution to handle the challenges arising with the emergence of the “fourth paradigm,” and identifies research needed to maintain progress in this area

Scalable and efficient whole-exome data processing using workflows on the cloud

Dataflow-style workflows offer a simple, high-level programming model for flexible prototyping of scientific applications as an attractive alternative to low-level scripting. At the same time, workflow management systems (WFMS) may support data parallelism over big datasets by providing scalable, distributed deployment and execution of the workflow over a cloud infrastructure. In theory, the combination of these properties makes workflows a natural choice for implementing Big Data processing pipelines, common for instance in bioinformatics. In practice, however, correct workflow design for parallel Big Data problems can be complex and very time-consuming. In this paper we present our experience in porting a genomics data processing pipeline from an existing scripted implementation deployed on a closed HPC cluster, to a workflow-based design deployed on the Microsoft Azure public cloud. We draw two contrasting and general conclusions from this project. On the positive side, we show that our solution based on the e-Science Central WFMS and deployed in the cloud clearly outperforms the original HPC-based implementation achieving up to 2.3× speed-up. However, in order to deliver such performance we describe the importance of optimising the workflow deployment model to best suit the characteristics of the cloud computing infrastructure. The main reason for the performance gains was the availability of fast, node-local SSD disks delivered by D-series Azure VMs combined with the implicit use of local disk resources by e-Science Central workflow engines. These conclusions suggest that, on parallel Big Data problems, it is important to couple understanding of the cloud computing architecture and its software stack with simplicity of design, and that further efforts in automating parallelisation of complex pipelines are required.</p

Scalable and efficient whole-exome data processing using workflows on the cloud

Dataflow-style workflows offer a simple, high-level programming model for flexible prototyping of scientific applications as an attractive alternative to low-level scripting. At the same time, workflow management systems (WFMS) may support data parallelism over big datasets by providing scalable, distributed deployment and execution of the workflow over a cloud infrastructure. In theory, the combination of these properties makes workflows a natural choice for implementing Big Data processing pipelines, common for instance in bioinformatics. In practice, however, correct workflow design for parallel Big Data problems can be complex and very time-consuming. In this paper we present our experience in porting a genomics data processing pipeline from an existing scripted implementation deployed on a closed HPC cluster, to a workflow-based design deployed on the Microsoft Azure public cloud. We draw two contrasting and general conclusions from this project. On the positive side, we show that our solution based on the e-Science Central WFMS and deployed in the cloud clearly outperforms the original HPC-based implementation achieving up to 2.3× speed-up. However, in order to deliver such performance we describe the importance of optimising the workflow deployment model to best suit the characteristics of the cloud computing infrastructure. The main reason for the performance gains was the availability of fast, node-local SSD disks delivered by D-series Azure VMs combined with the implicit use of local disk resources by e-Science Central workflow engines. These conclusions suggest that, on parallel Big Data problems, it is important to couple understanding of the cloud computing architecture and its software stack with simplicity of design, and that further efforts in automating parallelisation of complex pipelines are required.</p

Automatic deployment and reproducibility of workflow on the Cloud using container virtualization

PhD ThesisCloud computing is a service-oriented approach to distributed computing that has many attractive features, including on-demand access to large compute resources. One type of cloud applications are scientific work ows, which are playing an increasingly important role in building applications from heterogeneous components. Work ows are increasingly used in science as a means to capture, share, and publish computational analysis. Clouds can offer a number of benefits to work ow systems, including the dynamic provisioning of the resources needed for computation and storage, which has the potential to dramatically increase the ability to quickly extract new results from the huge amounts of data now being collected. However, there are increasing number of Cloud computing platforms, each with different functionality and interfaces. It therefore becomes increasingly challenging to de ne work ows in a portable way so that they can be run reliably on different clouds. As a consequence, work ow developers face the problem of deciding which Cloud to select and - more importantly for the long-term - how to avoid vendor lock-in. A further issue that has arisen with work ows is that it is common for them to stop being executable a relatively short time after they were created. This can be due to the external resources required to execute a work ow - such as data and services - becoming unavailable. It can also be caused by changes in the execution environment on which the work ow depends, such as changes to a library causing an error when a work ow service is executed. This "work ow decay" issue is recognised as an impediment to the reuse of work ows and the reproducibility of their results. It is becoming a major problem, as the reproducibility of science is increasingly dependent on the reproducibility of scientific work ows. In this thesis we presented new solutions to address these challenges. We propose a new approach to work ow modelling that offers a portable and re-usable description of the work ow using the TOSCA specification language. Our approach addresses portability by allowing work ow components to be systematically specifed and automatically - v - deployed on a range of clouds, or in local computing environments, using container virtualisation techniques. To address the issues of reproducibility and work ow decay, our modelling and deployment approach has also been integrated with source control and container management techniques to create a new framework that e ciently supports dynamic work ow deployment, (re-)execution and reproducibility. To improve deployment performance, we extend the framework with number of new optimisation techniques, and evaluate their effect on a range of real and synthetic work ows.Ministry of Higher Education and Scientific Research in Iraq and Mosul Universit

Linguagens para a Computação de Alto Desempenho, utilizadas no processamento de Big Data: Um Estudo de Mapeamento Sistemático

Big Data são conjuntos de informação de alto Volume, Velocidade e/ou Variedade que exigem formas inovadoras e económicas de processamento, que permitem uma melhor percepção, tomada de decisões e automação de processos. Desde 2002, a taxa de melhoria do desempenho em processadores simples diminuiu bruscamente. A fim de aumentar o poder dos processadores, foram utilizados múltiplos cores, em paralelo, num único chip. Para conseguir beneficiar deste tipo de arquiteturas, é necessário reescrever os programas sequenciais. O objetivo da Computação de Alto Desempenho (CAD) é estudar as metodologias e técnicas que permitem a exploração destas arquiteturas. O desafio é a necessidade de combinar o desenvolvimento de Software para a CAD com a gestão e análise de Big Data. Quando a computação paralela e distribuída é obrigatória, o código torna-se mais difícil. Para tal, é necessário saber quais são as linguagens a utilizar para facilitar essa tarefa. Pelo facto da literatura existente sobre o tópico da CAD se encontrar muito dispersa, foi conduzido um Estudo de Mapeamento Sistemático (EMS), que agrega caraterísticas sobre as diferentes linguagens encontradas (categoria; natureza; perfis de utilizador típicos; eficácia; tipos de artigos publicados na área), no processamento de Big Data, auxiliando estudantes, investigadores, ou outros profissionais que necessitem de uma introdução ou uma visão panorâmica sobre este tema. A pesquisa de artigos foi efetuada numa busca automatizada, baseada em palavraschave, nas bases de dados de 8 bibliotecas digitais selecionadas. Este processo resultou numa amostra inicial de 420 artigos, que foi reduzida a 152 artigos, publicados entre Janeiro de 2006 e Março de 2018. A análise manual desses artigos permitiu-nos identificar 26 linguagens em 33 publicações incluídas. Sumarizei e comparei as informações com as opiniões de profissionais. Os resultados indicaram que a maioria destas linguagens são Linguagem de Propósito Geral (LPG) em vez de Linguagem de Domínio Específico (LDE), o que nos leva a concluir que existe uma oportunidade de investigação aplicada de linguagens que tornem a codificação mais fácil para os especialistas do domínio