Publications related to Scientific workflow system

Orchestrating chromosome conformation capture analysis with Bioconductor

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

Data and Workflow to: Three-dimensional buoyant hydraulic fractures: finite volume release (Möri and Lecampion, (2023))

Brice Tanguy Alphonse Lecampion, Andreas Möri

This upload contains the relevant scripts, notebooks, and datasets to reproduce the numerically obtained results of the Journal article "Three-dimensional buoyant hydraulic fractures: finite volume release" by Möri and Lecampion, (2023). ...

Zenodo2023

Building a Knowledge Graph of Chinese Kung Fu Masters From Heterogeneous Bilingual Data

Lin Yuan, Yumeng Hou

Various endeavours into semantic web technologies and ontology engineering have been made within the organisation of cultural data, facilitating public access to digital assets. Although models for conceptualising objects have reached a certain level of ma ...

2023

A Robust Framework for Generating Adsorption Isotherms to Screen Materials for Carbon Capture

Berend Smit, Elias Moubarak, Susana Garcia Lopez, Seyedmohamad Moosavi

To rank the performanceof materials for a given carbon captureprocess, we rely on pure component isotherms from which we predictthe mixture isotherms. For screening a large number of materials,we also increasingly rely on isotherms predicted from molecular ...

AMER CHEMICAL SOC2023

Towards high-throughput many-body perturbation theory: efficient algorithms and automated workflows

Giovanni Pizzi, Antimo Marrazzo, Junfeng Qiao, Miki Bonacci, Andrea Ferretti

The automation of ab initio simulations is essential in view of performing high-throughput (HT) computational screenings oriented to the discovery of novel materials with desired physical properties. In this work, we propose algorithms and implementations ...

NATURE PORTFOLIO2023

AiiDA-defects: an automated and fully reproducible workflow for the complete characterization of defect chemistry in functional materials

Nicola Marzari, Sokseiha Muy, Conrad Johnston

Functional materials that enable many technological applications in our everyday lives owe their unique properties to defects that are carefully engineered and incorporated into these materials during processing. However, optimizing and characterizing thes ...

IOP Publishing Ltd2023

Interactive design with optimum matchmaking of reused structural elements – a software implementation

Corentin Jean Dominique Fivet, Jonas Warmuth, Jan Friedrich Georg Brütting

Structural systems are a significant contributor to buildings’ embodied carbon and reusing structural elements in new load-bearing applications is one strategy to reduce this impact. However, integrating this approach into existing design workflows without ...

International Association for Shell and Spatial Structures (IASS)2023

Formation of carbonyl compounds during ozonation of lake water and wastewater: Development of a non-target screening method and quantification of target compounds

Urs von Gunten, Joanna Maria Houska

Ozonation of natural waters is typically associated with the formation of carbonyl compounds (aldehydes, ketones and ketoacids), a main class of organic disinfection byproducts (DBPs). However, the detection of carbonyl compounds in water and wastewater is ...

PERGAMON-ELSEVIER SCIENCE LTD2023

Data and Workflow to: Three-dimensional buoyant hydraulic fracture growth: constant release from a point source (Möri and Lecampion, (2022))

Brice Tanguy Alphonse Lecampion, Andreas Möri

This upload contains the relevant scripts, notebooks, and datasets to reproduce the numerically obtained results of the Journal article "Three-dimensional buoyant hydraulic fracture growth: constant release from a point source" by Möri and Lecampion, (2022 ...

2022

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows

Daniel Keller

Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system work ...

2022

A Collaborative Workflow to Automate the Design, Analysis, and Construction of Integrally-Attached Timber Plate Structures

Yves Weinand, Nicolas Henry Pierre Louis Rogeau, Aryan Rezaei Rad, Petras Vestartas, Pierre Latteur

This paper introduces a computational framework that fosters collaboration between architects, engineers, and contractors by bridging the gap between architectural design, structural analysis, and digital construction. The present research is oriented towa ...

CAADRIA2022

Augmented-reality-assisted timber drilling with smart retrofitted tools

Yves Weinand, Julien Gamerro, Andrea Settimi

An ordinary electric drill was integrated into a context-aware augmented reality (AR) framework to assist in timber-drilling tasks. This study is a preliminary evaluation to detail technical challenges, potential bottlenecks, and accuracy of the proposed o ...

2022

Policy-based Exploration of Equilibrium Representations (PEER): A topology grammar for generative conceptual structural design

Ioannis Mirtsopoulos

Design exploration is a creative process that consists of the incremental generation of design candidates. Supported by digital means or not, the process handles the ill-structured nature of design and allows creativity to flourish through diversity of des ...

EPFL2022

Proteomics of Human Milk: Definition of a Discovery Workflow for Clinical Research Studies

Loïc Dayon

Milk is a complex biological fluid composed mainly of water, carbohydrates, lipids, proteins, and diverse bioactive factors. Human milk represents a unique tailored source of nutrients that adapts during lactation to the specific needs of the developing in ...

2021

A conceptual simulation workflow to guide design decisions regarding the effects of daylight on occupants' alertness

Marilyne Andersen, Clotilde Marie A Pierson, Victoria Eugenia Soto Magán

Recent developments in the lighting research field have demonstrated the importance of a proper exposure to light to mediate several of our behavioral and physiological responses. However, we spend nowadays around 90% of our time indoors with an often quit ...

IOP PUBLISHING LTD2021

Clouseau: Blockchain-based Data Integrity for HDFS Clusters

Ioannis Mytilinis

As the volume of produced data is exponentially increasing, companies tend to rely on distributed systems to meet the surging demand for storage capacity. With the business workflows becoming more and more complex, such systems often consist of or are acce ...

IEEE COMPUTER SOC2021

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

Vassily Hatzimanikatis, Jasmin Maria Hafner

Plant natural products (PNPs) and their derivatives are important but underexplored sources of pharmaceutical molecules. To access this untapped potential, the reconstitution of heterologous PNP biosynthesis pathways in engineered microbes provides a valua ...

Nature Research2021

AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance

Nicola Marzari, Giovanni Pizzi, Nicolas Frank Mounet, Martin Uhrin, Andrea Cepellotti, Boris Kozinsky, Fernando Gargiulo, Christoph Leopold Talirz, Leonid Kahle, Aliaksandr Yakutovich, Sebastiaan Philippe Huber, Snehal Pramod Kumbhar, Andrius Merkys, Conrad Johnston, Casper Welzel Andersen, Spyros Zoupanos, Elsa Passaro, Carl Simon Adorf, Francisco Fernando Ramirez

The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and d ...

2020

Workflows in AiiDA: Engineering a high-throughput, event-based engine for robust and modular computational workflows

Nicola Marzari, Giovanni Pizzi, Martin Uhrin, Sebastiaan Philippe Huber

Over the last two decades, the field of computational science has seen a dramatic shift towards incorporating high-throughput computation and big-data analysis as fundamental pillars of the scientific discovery process. This has necessitated the developmen ...

2020

Scaling Out Bioinformatics in the Data Center

Sam David Whitlock

Whole Genome Sequencing is a process in the field of bioinformatics that transforms biological samples of DNA into an electronic dataset of genetic bases. The process consists of two sequential components. First, the laboratory process of sequencing transf ...

EPFL2019