Hands-on type training of Integrated Computational Materials Engineering (ICME) is characterized by assisted application and combination of multiple simulation software tools and data. In this paper, we present recent experiences in establishing a cloud-based infrastructure to enable remote use of dedicated commercial and open access simulation tools during an interactive on-line training event. In the first part, we summarize the hardware and software requirements and illustrate how these have been met using cloud hardware services, a simulation platform environment, a suitable communication channel, common workspaces and more. The second part of the article focuses (i) on the requirements for suitable on-line hands-on training material and (ii) on details of some of the approaches taken. Eventually, the practical experiences made during three consecutive on-line training courses held in September 2020 with 35 nominal participants each, are discussed in detail.

Operational weather and also flood forecasting has been performed successfully for decades and is of great socioeconomic importance. Up to now, forecast products focus on atmospheric variables, such as precipitation, air temperature and, in hydrology, on river discharge. Considering the full terrestrial system from groundwater across the land surface into the atmosphere, a number of important hydrologic variables are missing especially with regard to the shallow and deeper subsurface (e.g. groundwater), which are gaining considerable attention in the context of global change. In this study, we propose a terrestrial monitoring/forecasting system using the Terrestrial Systems Modeling Platform (TSMP) that predicts all essential states and fluxes of the terrestrial hydrologic and energy cycles from groundwater into the atmosphere. Closure of the terrestrial cycles provides a physically consistent picture of the terrestrial system in TSMP. TSMP has been implemented over a regional domain over North Rhine-Westphalia and a continental domain over European in a real-time forecast/monitoring workflow. Applying a real-time forecasting/monitoring workflow over both domains, experimental forecasts are being produced with different lead times since the beginning of 2016. Real-time forecast/monitoring products encompass all compartments of the terrestrial system including additional hydrologic variables, such as plant available soil water, groundwater table depth, and groundwater recharge and storage.

Epidemiological surveillance and phylogenetic studies rely nowadays on processing and analysing huge volumes of data. Processing tasks consist on running and refining a series of intertwined computational tasks. And, despite of existing several web applications for data processing and interactive visualization for phylogenetic studies, integrating many different tools and algorithms, their execution is total or partially on the client side, making them unsuitable for dealing with huge volumes of data. Studies are often also not easy to reproduce. On the other hand, in recent years, data-centric workflow systems have been proposed, allowing to deal better with increasingly larger datasets. The integration of these systems within phylogenetic tools will allow to scale them as required, and will contribute also to promote studies reproducibility. We propose then the FLOWViZ middleware for facilitating the integration of a state of the art data-centric workflow system, Apache Airflow, within web applications for phylogenetic analyses. This framework abstracts contracts and a core API for defining tools and workflows, where tools are assumed to be containerized. FLOWViZ has been tested and evaluated within the PHYLOViZ web application, a tool supporting phylogenetic inference and data visualization.

Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form of isolation between processes. Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible analyses. In this manuscript we review a number of approaches to using containers as implemented in the workflow tools Nextflow, Galaxy, Pachyderm, Argo, Kubeflow, Luigi and SciPipe, when deployed in cloud environments. A particular focus is placed on the workflow tool’s interaction with the Kubernetes container orchestration framework.

Implementing High-Performance Computing to solve In-Memory Data Grid (IMDG)-based energy infrastructure resilience research problems in a heterogeneous environment presents a challenge to workflow management systems. Large-scale energy infrastructure needs multi-variant planning and tools to allocate and dispatch resources in IMDG taking into account the subject domain specificity, resource characteristics, and constraints and quotas for resource use. To that end, we propose a workflow management system using our Orlando Tools framework. To scale computing resources, we provide their integration and use corresponding software to determine key application parameters that can significantly impact the processed data size and the required number of allocated resources. We automated the IMDG cluster launch for the workflow executions. To demonstrate the advantage of our solution, we apply it to evaluate the resilience of the existing energy infrastructure model. Compared to similar approaches, our approach explores large infrastructures by modeling many simultaneously failed elements of different types up to the number of network elements. In terms of problem-solving efficiency and resource use, we achieve near-linear speedup with increasing the number of nodes of each resource.

Visual exploration of complex data helps interpretation, especially in the case of omics data analysis in life sciences and clinical research. Generating and analysing omics data requires bioinformatic skills, while they are interpreted by domain experts, for whom parsing large and complex data structures may be challenging. However, outcomes of visual analytics are often difficult to quantify, which emphasises precision and reproducibility, especially for research on human diseases. Here, we propose a workflow combining a reproducible computational environment with a dedicated visualisation functionality for systems biology diagrams. By linking the Galaxy with the MINERVA Platform, we visualise and explore COVID-19 transcriptomic data to demonstrate the utility of our workflow. Visualised data recapitulate findings of the original publication and offer new insights about the COVID-19 pathology. Our results offer a blueprint for quick prototyping of computational workflows that facilitate communication and exploration of complex data in biomedical research.

A maxillary totally edentulism was rehabilitated with one-piece implants starting from pre-existing totally removable denture. A 3D digital scan of the removable denture and upper and lower arches was performed. On this basis, a prototype with optimal esthetic and functional outcomes was re-alized and turned into a custom-made radiological stent with markers. The superimposition of STL and DICOM files allowed the virtual planning of one-piece implants ideal position. The stackable templates composed of a fixed component, namely base template, and removable components, were realized. The fixed component, once secured with anchor pins to the bone, was no longer removed. The removable components, screwed to the fixed component, were used to perform the implant surgery and the immediate prosthetic loading. A base template allowed for maintaining a fixed reference during the entire workflow, improving the transition between the digital project, the surgical procedure, and the prosthetic rehabilitation.

Configurable process models are frequently used to represent business workflows and other discrete event systems among different branches of large organizations: they unify commonalities shared by all branches and describe their differences, at the same time. The configuration of such models is usually done manually, which is challenging. On the one hand, when the number of configurable nodes in the configurable process model grows, the size of the search space increases exponentially. On the other hand, the person performing the configuration may lack the holistic perspective to make the right choice for all configurable nodes at the same time, since choices influence each other. Nowadays, information systems that support the execution of business processes create event data reflecting how processes are performed. In this article, we propose three strategies (based on exhaustive search, genetic algorithms, and greedy heuristic) that use event data to automatically derive a process model from a configurable process model that better represents the characteristics of the process in a specific branch. These strategies have been implemented in our proposed framework, and tested in both business-like event logs as recorded in a higher educational ERP system, and a real case scenario involving a set of Dutch municipalities.

Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common one has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development.