Open Workflow Research Articles

Activity-based and agent-based transport model of Melbourne: an open multi-modal transport simulation model for Greater Melbourne

Activity- and agent-based models for simulating transport systems have attracted significant attention in recent years. However, building these types of models at a city-wide level and including motorized (i.e. cars and public transport) and non-motorized (i.e. walk and bicycle) modes of transport is a complicated and involved task. This paper presents an open workflow for creating large-scale multi-modal agent-based transport simulation models. The workflow brings together a number of external tools, for example, an activity-based demand generation tool and a road network generation tool, and a set of tools developed for the agent-based model parameter estimation, calibration, and simulation post-processing. We used this workflow to create an activity- and agent-based model for Melbourne and compared the output of the simulation model with observations from the real world in terms of mode share, road volume, travel time, and travel distance. Through these comparisons, we showed that our model is suitable for studying mode choice and road usage behavior of travelers. The calibrated model could be used to test road network change interventions. In addition, a similar workflow can be applied for building simulation models for other cities or could be expanded to include more complicated travel behaviors.

Scalable BIM based open workflow for structural analysis of masonry building aggregates

Masonry building aggregates are complex historical structures comprising interconnected buildings. The safety of each building depends not only on its structural integrity but also on the interactions with neighbouring structures and their collective performance. The structural assessment of such complex constructions can benefit from BIM methodology. The latter eases modelling complicated solid geometries and assigning mechanical properties information essential for developing a reliable finite element model. Thus far, BIM to finite element analysis procedures applied to historic constructions have remained laborious, semi-automatic, and based on proprietary software. This paper introduces an open-source automated solid finite element analysis method using OpenBIM data (IFC). The tool implemented automatically creates tetrahedron mesh and assigns mechanical properties, self-weights, and fixities at the structure's base. The methodology is applied to an actual masonry building aggregate to validate its capability of working with complex geometries and scalability.

OpenWorkFlow—Development of an open-source synthesis-platform for safety investigations in the site selection process

The identification of appropriate locations for secure nuclear waste disposal, a crucial aspect of Germany’s nuclear phase-out strategy (StandAG 2017), remains a significant scientific, technical, and political challenge worldwide. The selection and safety assessment of sites demand extensive applications of numerical methods. The OpenWorkFlow project, initiated by Bundesgesellschaft für Endlagerung (BGE), develops a new, open synthesis platform to virtualise repository systems. The simulation platform will evaluate far-field and near-field processes, supporting the site selection process first and the geotechnical design of repository systems later on. The project’s development philosophy adheres to the principles of continuity and innovation. Through continuous scientific development, the OpenWorkFlow platform will remain at the forefront of science and technology. Furthermore, as a digital platform, OpenWorkFlow employs up-to-date IT methods and constantly evolving software concepts. As its name suggests, OpenWorkFlow (OWF) is an open platform, developed on the basis of FAIR principles as an open-source project, inviting community participation.This paper primarily focuses on the technical aspects of OWF, with only a brief discussion of conceptual principles and modelling methods. In the second part of the manuscript, demonstration examples from different scales are presented to illustrate the current technical status of OWF and to emphasize the requirement for further development.

Integrative open workflow for confident annotation and molecular networking of metabolomics MSE/DIA data.

Liquid chromatography coupled with high-resolution mass spectrometry data-independent acquisition (LC-HRMS/DIA), including MSE, enable comprehensive metabolomics analyses though they pose challenges for data processing with automatic annotation and molecular networking (MN) implementation. This motivated the present proposal, in which we introduce DIA-IntOpenStream, a new integrated workflow combining open-source software to streamline MSE data handling. It provides 'in-house' custom database construction, allows the conversion of raw MSE data to a universal format (.mzML) and leverages open software (MZmine 3 and MS-DIAL) all advantages for confident annotation and effective MN data interpretation. This pipeline significantly enhances the accessibility, reliability and reproducibility of complex MSE/DIA studies, overcoming previous limitations of proprietary software and non-universal MS data formats that restricted integrative analysis. We demonstrate the utility of DIA-IntOpenStream with two independent datasets: dataset 1 consists of new data from 60 plant extracts from the Ocotea genus; dataset 2 is a publicly available actinobacterial extract spiked with authentic standard for detailed comparative analysis with existing methods. This user-friendly pipeline enables broader adoption of cutting-edge MS tools and provides value to the scientific community. Overall, it holds promise for speeding up metabolite discoveries toward a more collaborative and open environment for research.

A Layered Architecture and Taxonomy for Blockchain-empowered Reputation-based Reward Systems

Blockchain based rating and review systems have changed the operational structure of the traditional market by introducing characteristics like immutability, security, anonymity etc. to liberate users from potential malicious acts of sellers such as altering and hiding ratings or reviews, collusion with users or service providers. The lack of standardization for developing decentralized applications does not depict flow of information and cataloguing of specific functions and roles for a particular set of tasks. The development of decentralized applications for e-commerce systems is in its immature age of progress and has lack of interoperable sharing of data and workflows for new innate systems. Thus, it is significant to catalogue blockchain-based rating and review systems by identifying key parameters to generate a taxonomy and develop a conceptual layered framework for identifying core components and their interaction. This manuscript presents a substantial analysis of existing blockchain-empowered reputation-based reward systems. It uses an iterative approach following observed to rational and rational to observed for taxonomy development. The analysis results identify 11 key parameters for categorizing systems and propose a 4 layered architecture to signify IPFS, P2P network, Blockchain and DApps. The proposed model identifies underlying subsystems, their services, and their interaction. The new taxonomy identifies natural roadmaps in system development process. This study is key because it allows developers to design new reputation-based reward framework in different dimensions by following an open workflow with a common understanding of underlying core entities.

A Layered Architecture and Taxonomy for Blockchain-empowered Reputation-based Reward Systems

Blockchain based rating and review systems have changed the operational structure of the traditional market by introducing characteristics like immutability, security, anonymity etc. to liberate users from potential malicious acts of sellers such as altering and hiding ratings or reviews, collusion with users or service providers. The lack of standardization for developing decentralized applications does not depict flow of information and cataloguing of specific functions and roles for a particular set of tasks. The development of decentralized applications for e-commerce systems is in its immature age of progress and has lack of interoperable sharing of data and workflows for new innate systems. Thus, it is significant to catalogue blockchain-based rating and review systems by identifying key parameters to generate a taxonomy and develop a conceptual layered framework for identifying core components and their interaction. This manuscript presents a substantial analysis of existing blockchain-empowered reputation-based reward systems. It uses an iterative approach following observed to rational and rational to observed for taxonomy development. The analysis results identify 11 key parameters for categorizing systems and propose a 4 layered architecture to signify IPFS, P2P network, Blockchain and DApps. The proposed model identifies underlying subsystems, their services, and their interaction. The new taxonomy identifies natural roadmaps in system development process. This study is key because it allows developers to design new reputation-based reward framework in different dimensions by following an open workflow with a common understanding of underlying core entities.

Frugivoria: A trait database for birds and mammals exhibiting frugivory across contiguous Neotropical moist forests

AbstractMotivationBiodiversity in many areas is rapidly declining because of global change. As such, there is an urgent need for new tools and strategies to help identify, monitor and conserve biodiversity hotspots. This is especially true for frugivores, species consuming fruit, because of their important role in seed dispersal and maintenance of forest structure and health. One way to identify these areas is by quantifying functional diversity, which measures the unique roles of species within a community and is valuable for conservation because of its relationship with ecosystem functioning. Unfortunately, the functional trait information required for these studies can be sparse for certain taxa and specific traits and difficult to harmonize across disparate data sources, especially in biodiversity hotspots. To help fill this need, we compiled Frugivoria, a trait database containing ecological, life‐history, morphological and geographical traits for mammals and birds exhibiting frugivory. Frugivoria encompasses species in contiguous moist montane forests and adjacent moist lowland forests of Central and South America—the latter specifically focusing on the Andean states. Compared with existing trait databases, Frugivoria harmonizes existing trait databases, adds new traits, extends traits originally only available for mammals to birds also and fills gaps in trait categories from other databases. Furthermore, we create a cross‐taxa subset of shared traits to aid in analysis of mammals and birds. In total, Frugivoria adds 8662 new trait values for mammals and 14,999 for birds and includes a total of 45,216 trait entries with only 11.37% being imputed. Frugivoria also contains an open workflow that harmonizes trait and taxonomic data from disparate sources and enables users to analyse traits in space. As such, this open‐access database, which aligns with FAIR data principles, fills a major knowledge gap, enabling more comprehensive trait‐based studies of species in this ecologically important region.Main Types of Variable ContainedEcological, life‐history, morphological and geographical traits.Spatial Location and GrainNeotropical countries (Mexico, Guatemala, Costa Rica, Panama, El Salvador, Belize, Nicaragua, Ecuador, Colombia, Peru, Bolivia, Argentina, Venezuela and Chile) with contiguous montane regions.Time Period and GrainIUCN spatial data: obtained February 2023, spanning range maps collated from 1998 to 2022. IUCN species data: obtained June 2019–September 2022. Newly included traits: span 1924 to 2023.Major Taxa and Level of MeasurementClasses Mammalia and Aves; 40,074 species‐level traits; 5142 imputed traits for 1733 species (mammals: 582; birds: 1147) and 16 sub‐species (mammals).Software Format.csv; R.

Human populations in the world's mountains: Spatio-temporal patterns and potential controls.

Changing climate and human demographics in the world's mountains will have increasingly profound environmental and societal consequences across all elevations. Quantifying current human populations in and near mountains is crucial to ensure that any interventions in these complex social-ecological systems are appropriately resourced, and that valuable ecosystems are effectively protected. However, comprehensive and reproducible analyses on this subject are lacking. Here, we develop and implement an open workflow to quantify the sensitivity of mountain population estimates over recent decades, both globally and for several sets of relevant reporting regions, to alternative input dataset combinations. Relationships between mean population density and several potential environmental covariates are also explored across elevational bands within individual mountain regions (i.e. "sub-mountain range scale"). Globally, mountain population estimates vary greatly-from 0.344 billion (<5% of the corresponding global total) to 2.289 billion (>31%) in 2015. A more detailed analysis using one of the population datasets (GHS-POP) revealed that in ∼35% of mountain sub-regions, population increased at least twofold over the 40-year period 1975-2015. The urban proportion of the total mountain population in 2015 ranged from 6% to 39%, depending on the combination of population and urban extent datasets used. At sub-mountain range scale, population density was found to be more strongly associated with climatic than with topographic and protected-area variables, and these relationships appear to have strengthened slightly over time. Such insights may contribute to improved predictions of future mountain population distributions under scenarios of future climatic and demographic change. Overall, our work emphasizes that irrespective of data choices, substantial human populations are likely to be directly affected by-and themselves affect-mountainous environmental and ecological change. It thereby further underlines the urgency with which the multitudinous challenges concerning the interactions between mountain climate and human societies under change must be tackled.

Collaborative Workflow in an HBIM Project for the Restoration and Conservation of Cultural Heritage

ABSTRACT A restoration and conservation project for a building with heritage values requires an increasingly efficient and sustainable methodology. Based on a collaborative ‘Teamwork’ HBIM (Historic Building Information Modelling) project, this paper aims to describe the technical processes applied to a 16th-century historic building to support an open and interoperable workflow between the participating agents. The process is transparent and controllable by operators and disciplines, ensuring direct and continuous access to project data. The study focuses on implementing effective procedures for the identification and classification of heritage architecture. The first stage comprises the analysis of the geometry and materiality of the existing architecture, using data acquisition technologies such as Terrestrial Laser Scanning (TLS) and Structure-from-Motion (SfM) photogrammetry. The information modelling of the historic building begins with a medium level of knowledge, based on the metric survey and enriched by the materiality of the textures deriving from the point cloud. This enables a modelling approach that fits building components to the real geometry of the historic building, considering the deformations and irregularities that occur over time. In the next phase, the BIM project is developed through the analysis of the construction characteristics, materials, and architectural structuring in the historical evolution of the building. The difference between intervening in architectural heritage and new construction lies in the search for the transposition of construction techniques in walls with a long history, thus requiring classification and sectorisation of the various systems used. It is then required to segment the construction systems based on a semantic study of the walls that make up the envelope of the historic architecture. Programming objects in Python within the BIM platform enables the automated identification processes. The method is applied in the identification of the integrating elements of a larger construction entity, such as the stone ashlars of the masonry wall, and the classification by their construction-temporal dating. The main novelty of this research is the use of the object-oriented programming language (OOP), which automates operations based on an open-source structure and allows the operability of cataloguing, classification, and reuse characteristics.

An open workflow to gain insights about low‐likelihood high‐impact weather events from initialized predictions

AbstractLow‐likelihood weather events can cause dramatic impacts, especially when they are unprecedented. In 2020, amongst other high‐impact weather events, UK floods caused more than £300 million damage, prolonged heat over Siberia led to infrastructure failure and permafrost thawing, while wildfires ravaged California. Such rare phenomena cannot be studied well from historical records or reanalysis data. One way to improve our awareness is to exploit ensemble prediction systems, which represent large samples of simulated weather events. This ‘UNSEEN’ method has been successfully applied in several scientific studies, but uptake is hindered by large data and processing requirements, and by uncertainty regarding the credibility of the simulations. Here, we provide a protocol to apply and ensure credibility of UNSEEN for studying low‐likelihood high‐impact weather events globally, including an open workflow based on Copernicus Climate Change Services (C3S) seasonal predictions. Demonstrating the workflow using European Centre for Medium‐Range Weather Forecasts (ECMWF) SEAS5, we find that the 2020 March–May Siberian heatwave was predicted by one of the ensemble members; and that the record‐shattering August 2020 California‐Mexico temperatures were part of a strong increasing trend. However, each of the case studies exposes challenges with respect to the credibility of UNSEEN and the sensitivity of the outcomes to user decisions. We conclude that UNSEEN can provide new insights about low‐likelihood weather events when the decisions are transparent, and the challenges and sensitivities are acknowledged. Anticipating plausible low‐likelihood extreme events and uncovering unforeseen hazards under a changing climate warrants further research at the science‐policy interface to manage high impacts.

A Method for Verifying the Behavioral Consistency between Public Business Process and Private Business Process Based on Environment

The cross-organizational business process is characterized by privacy, collaboration, autonomy, dynamic interaction structure, etc. It is necessary to model and analyze the cross-organizational business process in order to ensure the accuracy and consistency of process interaction among different organizations. The open workflow net proposed on the basis of Petri net is used as a tool to model the cross-organizational business process. The cross-organizational business process is divided into two parts, namely private process and public process. The private process is regarded as the internal view of the organization, and the public process is regarded as the external view of the interaction between an organization and other organizations. The interaction behavior of model verification is regarded as the starting point with regard to the behavioral consistency problem of the model. A method for verifying the behavioral consistency based on environment is proposed, which is more relaxed than the existing method for verifying the behavioral consistency based on mutual simulation and more consistent with the asynchronous communication among organizations.

CTL Model Checking of Web Services Composition based on Open Workflow Nets Modeling

Web services composition (WSC) has an enormous potential for the organizations in the B2B area. In fact, different services collaborate through the exchange of messages to implement complex business processes. BPEL is one of the most used languages to develop such cooperation. However, it has been proved that its use is complex and can require some expertise in XML syntax. Even its graphical representation is not evident to handle. This is why the authors propose to model Web services using oWF-nets, a subclass of Petri nets, and then, to translate them to BPEL. Whilst, a WSC is with added value only if the involved services are compatible. So in this context, across the translation proposed the researchers develop a verification layer of the WSC compatibility. Hence, they propose a framework named D&amp;A4WSC which allows to model the WSC by oWF-nets, to check their compatibility with the model checker NuSMV and to translate them if they are compatible in BPEL processes using the oWFN2BPEL compiler. D&amp;A4WSC permits, furthermore, to formally analyze a BPEL process.

Generic and Specific Compatibility Criteria for Web Service Composition

For automatically composing Web services in a correct manner, information about their behaviors (an abstract model) has to be published in a repository. This abstract model must be sufficient to decide whether two, or more, services are compatible (the composition is possible) is possible without including any additional information that can be used to disclose the privacy of these services. The compatibility between two Web services can be based either on some generic properties (e.g. deadlock freeness of the composite Web service) or on a specific property expressed with a formal logic. In this paper, the authors address this problem by considering these two kinds of compatibility criteria. The first criterion is defined by different variants of the well-known soundness property on open workflow nets. These properties guarantee the absence of livelocks, deadlocks and other anomalies that can be formulated without domain knowledge. The second criterion is defined by the designer formally by using the Linear Temporal Logic. The proposed approach addresses the automatic abstraction of Web services and the checking of their compatibility using their abstract models only. To abstract Web services, the authors use the symbolic observation graph (SOG) approach that preserves necessary information for service composition and hides private information. The authors show how the SOG can be adapted and used so that the verification of generic and specific compatibility criteria can be performed on the composition of the abstract models of Web services instead of the original composite service.

A Petri Net Approach to Mediation-Aided Composition of Web Services

Recently, mediation-aided composition has been widely adopted when dealing with incompatibilities of services. However, existing approaches suffer from state space explosion in compatibility verification and cannot automatically generate the BPEL code. This paper presents a Petri net approach to mediation-aided composition of Web services. First, services are modeled as open WorkFlow Nets (oWFNs) and are composed using mediation transitions (MTs). Second, the modular reachability graph (MRG) of composition is automatically constructed and the compatibility is analyzed, so that the problem of state space explosion is significantly alleviated. Furthermore, an Event-Condition-Action (ECA) rule-based technique is developed to automatically generate the BPEL code of the composition, which can significantly save the time and labor of designers. Finally, the prototype system has been developed.

New developments on the cheminformatics open workflow environment CDK-Taverna

BackgroundThe computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e.g. metabolomics or drug discovery. Pipelining or workflow tools allow for the Lego™-like, graphical assembly of I/O modules and algorithms into a complex workflow which can be easily deployed, modified and tested without the hassle of implementing it into a monolithic application. The CDK-Taverna project aims at building a free open-source cheminformatics pipelining solution through combination of different open-source projects such as Taverna, the Chemistry Development Kit (CDK) or the Waikato Environment for Knowledge Analysis (WEKA). A first integrated version 1.0 of CDK-Taverna was recently released to the public.ResultsThe CDK-Taverna project was migrated to the most up-to-date versions of its foundational software libraries with a complete re-engineering of its worker's architecture (version 2.0). 64-bit computing and multi-core usage by paralleled threads are now supported to allow for fast in-memory processing and analysis of large sets of molecules. Earlier deficiencies like workarounds for iterative data reading are removed. The combinatorial chemistry related reaction enumeration features are considerably enhanced. Additional functionality for calculating a natural product likeness score for small molecules is implemented to identify possible drug candidates. Finally the data analysis capabilities are extended with new workers that provide access to the open-source WEKA library for clustering and machine learning as well as training and test set partitioning. The new features are outlined with usage scenarios.ConclusionsCDK-Taverna 2.0 as an open-source cheminformatics workflow solution matured to become a freely available and increasingly powerful tool for the biosciences. The combination of the new CDK-Taverna worker family with the already available workflows developed by a lively Taverna community and published on myexperiment.org enables molecular scientists to quickly calculate, process and analyse molecular data as typically found in e.g. today's systems biology scenarios.

CDK-Taverna: an open workflow environment for cheminformatics

BackgroundSmall molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone.ResultsHere we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios.ConclusionsThe combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.

CoopFlow: A Bottom-Up Approach to Workflow Cooperation for Short-Term Virtual Enterprises

In a context of short-term cooperation, enterprises with complementary skills are dynamically interconnected according to their needs. To deal with requirements in a such cooperation, we present in this paper CoopFlow that aims at providing a useful artifact for preservation of the privacy of workflows partners, pre-established workflows and pre-established workflow management systems. CoopFlow consists of three steps: workflow abstraction and advertisement, workflow matching and interconnection, and workflow cooperation. To preserve the privacy of partners, the first step of the approach includes an abstraction procedure allowing a partial visibility of the partners' workflows. The second step consists of interconnecting existing workflows of partners with complementary skills attributing to a matching procedure that allows checking both behaviors and business semantics of partners' workflows. Finally, the last step of CoopFlow consists of controlling the inter-enterprise workflows cooperation allowing cooperation partners to integrate the existing workflows and to check whenever they can cooperate and change their partners, which frequently leads to support spontaneous, dynamic and short-term cooperation. With this intention, we developed a platform that manages inter-operability by integrating pre-established workflow management systems. The proof of concept is provided by integrating three heterogeneous and open workflow management systems to the CoopFlow platform.

Manufacturing Grid Workflow Framework and Model

The Manufacturing Grid domain is characterized by rapid and substantial change over time. The entire process of product development can be quite complex. The activities are expected to be executed on heterogeneous resources which are geographically distributed. However, traditional modeling systems use static workflow models which can not automatically redesign the business process and mask the isomerism of the resources. In this article, an open and extensible framework of MG workflow is given, which complies with the standard of WFMC and GGF. A formalized definition workflow model is proposed including process model, organization model, resource model, and service mode. The integrated workflow model can be used to dynamically represent a business process and other aspect s of Manufacturing Grid workflow.

Workflow and CIMOSA—background and case study

For an enterprise engineering application in a low-volume microsystems production we used the two Reference Architectures: CIM Open System Architecture (CIMOSA) and Work Flow Management Coalition (WfMC). We applied the emerging WFMC standard to the microsystems worklist processing to design the workflow system InfoFlow. For the manufacturing activities of the workflow participants we used the appropriate CIMOSA constructs on the level of Machine Functional Operations fitting into the WFMC architecture. The paper describes the relation between the two reference architectures comparing their concepts and constructs. The application shows that both concepts bring benefit to the enterprise engineering task and to a large degree complement each other.

ObjectFlow: Towards a process management infrastructure

As businesses feel competitive and economic pressures to automate and streamline their operations, they examine their day-to-day business processes and look to business process reengineering pratices to provide solutions. Improved networking capabilities and the widescale adoption of open systems architectures have allowed businesses to tie their information systems together and share data across departments. The challenge now involves coordinating and automating the flow of work between people and groups in an organization. This has prompted the emergence of a new kind of infrastructure, workflow enabler, which provides a model for business processes, and a foundation on which to build solutions supporting the execution and management of business processes. This article examines the technology trends, business benefits, and requirements which have lead to this development. It describes the logical structure and an operational model of an open workflow system, and positions ObjectFlow, a software product, within this framework to illustrate the concepts.