Designing for Recommending Intermediate States in A Scientific Workflow Management System

To process a large amount of data sequentially and systematically, proper management of workflow components (i.e., modules, data, configurations, associations among ports and links) in a Scientific Workflow Management System (SWfMS) is inevitable. Managing data with provenance in a SWfMS to support reusability of workflows, modules, and data is not a simple task. Handling such components is even more burdensome for frequently assembled and executed complex workflows for investigating large datasets with different technologies (i.e., various learning algorithms or models). However, a great many studies propose various techniques and technologies for managing and recommending services in a SWfMS, but only a very few studies consider the management of data in a SWfMS for efficient storing and facilitating workflow executions. Furthermore, there is no study to inquire about the effectiveness and efficiency of such data management in a SWfMS from a user perspective. In this paper, we present and evaluate a GUI version of such a novel approach of intermediate data management with two use cases (Plant Phenotyping and Bioinformatics). The technique we call GUI-RISPTS (Recommending Intermediate States from Pipelines Considering Tool-States) can facilitate executions of workflows with processed data (i.e., intermediate outcomes of modules in a workflow) and can thus reduce the computational time of some modules in a SWfMS. We integrated GUI-RISPTS with an existing workflow management system called SciWorCS. In SciWorCS, we present an interface that users use for selecting the recommendation of intermediate states (i.e., modules' outcomes). We investigated GUI-RISPTS's effectiveness from users' perspectives along with measuring its overhead in terms of storage and efficiency in workflow execution.

Using prototyping to choose a bioinformatics workflow management system

Workflow management systems represent, manage, and execute multistep computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can support both incremental build and re-entrancy—the ability to selectively re-execute parts of a workflow in the presence of additional inputs or changes in configuration and to resume execution from where a workflow previously stopped. Many workflow management systems enhance portability by supporting the use of containers, high-performance computing (HPC) systems, and clouds. Most importantly, workflow management systems allow bioinformaticians to delegate how their workflows are run to the workflow management system and its developers. This frees the bioinformaticians to focus on what these workflows should do, on their data analyses, and on their science. RiboViz is a package to extract biological insight from ribosome profiling data to help advance understanding of protein synthesis. At the heart of RiboViz is an analysis workflow, implemented in a Python script. To conform to best practices for scientific computing which recommend the use of build tools to automate workflows and to reuse code instead of rewriting it, the authors reimplemented this workflow within a workflow management system. To select a workflow management system, a rapid survey of available systems was undertaken, and candidates were shortlisted: Snakemake, cwltool, Toil, and Nextflow. Each candidate was evaluated by quickly prototyping a subset of the RiboViz workflow, and Nextflow was chosen. The selection process took 10 person-days, a small cost for the assurance that Nextflow satisfied the authors’ requirements. The use of prototyping can offer a low-cost way of making a more informed selection of software to use within projects, rather than relying solely upon reviews and recommendations by others.

Overload Control in a Token Player for a Fuzzy Workflow Management System

The underlying proposal of this work is to control overload of a Token Player in a Fuzzy Workflow Management System. In order to accomplish this, possibility theory is used to measure how much the Token Player can be overloaded. The model used in this work is built using Colored Petri net and the simulation is made using CPN Tools. Finally, is possible to control overload of the Token Player in a Fuzzy Workflow Management System, nevertheless more time is spent to achieve the end of activities.

Exploitation of the MareNostrum 4 HPC using ARC-CE

The resources of the HPC centers are a potential aid to meet the future challenges of HL-LHC [1] in terms of computational requirements. Spanish HPC centers have recently been used to implement all necessary edge services to integrate resources into the LHC experiment workflow management system. In this article, we describe the integration of ATLAS with the extension plan to other LHC experiments. We chose to configure a dedicated ARC-CE [2] and interact with the HPC login and transfer nodes using ssh commands. The repository that includes a partial copy of the ATLAS experiment software on CVMFS is packaged in a singularity image to overcome network isolation for HPC nodes and reduce software requirements. ATLAS provided the initial container, and the authors adapted it to the specific HPC environment. This article shows the Spanish contribution to the simulation of experiments after the Spanish Ministry of Science agreement and the Barcelona Supercomputing Center (BSC), the center that operates MareNostrum 4. Finally, we discuss some challenges to take advantage of the next generation of HPC machines with heterogeneous architecture combining CPU and GPU.

Integrating Mobile Robots into Automated Laboratory Processes: A Suitable Workflow Management System

The general trend of automation is currently increasing in life science laboratories. The samples to be examined show a high diversity in their structures and composition as well as the determination methods. Complex automation lines such as those used in classic industrial automation are not a suitable solution with respect to the required flexibility of the systems due to changing application requirements. Rather, full automation requires the connection of several different subsystems, including manual process steps by the laboratory staff. This requires suitable workflow management systems that enable the planning and execution of complex process steps. The integration of mobile robots for transportation tasks is currently an important development trend for realizing full automation in life science laboratories. The article “Workflow Management System for the Integration of Mobile Robots in Future Labs of Life Sciences” presents the development and application of a hierarchical workflow management system (HWMS) as a top-level process management and control system. This concept combines the typical hierarchical automation structure with novel approaches for the integration of transportation tasks with variable degrees of automation. The aim is to create a general-purpose workflow management system that can be used in different areas of the life sciences, regardless of the specific device components and applications used.