Exchange Format Research Articles

RCX-an R package adapting the Cytoscape Exchange format for biological networks.

The Cytoscape Exchange (CX) format is a JSON-based data structure designed for the transmission of biological networks using standard web technologies. It was developed by the network data exchange, which itself serves as online commons to share and collaborate on biological networks. Furthermore, the Cytoscape software for the analysis and visualization of biological networks contributes structure elements to capture the visual layout within the CX format. However, there is a fundamental difference between data handling in web standards and R. A manual conversion requires detailed knowledge of the CX format to reproduce and work with the networks. Here, we present a software package to create, handle, validate, visualize and convert networks in CX format to standard data types and objects within R. Networks in this format can serve as a source for biological knowledge and also capture the results of the analysis of those while preserving the visual layout across all platforms. The RCX package connects the R environment for statistical computing with outside platforms for storage and collaboration, as well as further analysis and visualization of biological networks. RCX is a free and open-source R package, available on Bioconductor from release 3.15 (https://bioconductor.org/packages/RCX) and via GitHub (https://github.com/frankkramer-lab/RCX). Supplementary data are available at Bioinformatics Advances online.

Automatic cabin virtualization based on preliminary aircraft design data

Preliminary aircraft design and cabin design are essential and well-established steps within the product development cycle for modern passenger aircraft. In practice, the execution usually takes place sequentially, with the preliminary design defining a basic cabin layout and the detail implementation following in a subsequent step. To enable higher fidelity assessment of the cabin early in the design process—for example by means of virtual reality applications—this paper proposes an interface, which can derive detailed 3D geometry of the fuselage from preliminary design data provided in the Common Parametric Aircraft Configuration Schema (CPACS). This is a key step towards integration of cabin analysis and preliminary design in automated collaborative aircraft design chains, not only in terms of passenger comfort, but also manufacturability or crash safety. Like the TiGL Geometry Library for CPACS, the interface presented acts as a parameter engine, which translates data from CPACS into CAD geometry using the Open Cascade Technology library. However, the scope of TiGL is expanded significantly, albeit with an explicit focus on the fuselage, by including more details such as extruded frame and stringer profiles and floor structures. Furthermore, advanced knowledge management techniques are employed to detect and augment missing data. For virtual reality applications, triangulated representations of the CAD geometry can be provided in established exchange formats, creating an interface to common visualization platforms. Additionally, a new evolution of the cabin definition schema in CPACS is presented, to incorporate models of cabin components such as seats or sidewall panels enabling immersive virtual mock-ups.

Development of a Visual Assembly Planning System based on Neutral Files

Assembly planning is still a manual undertaking today. In past work, however, a novel approach was presented that allows precise assembly sequence generation on the basis of a variety of optimization criteria. This approach was integrated directly into a CAD system, which in turn results in a dependency on the CAD system. In the context of this work, it was therefore examined how the same result can be realized with a neutral approach. Therefore, it will be investigated what kind of information can be extracted directly and how the missing information can be added via a user interface. Therefore, a reverse engineering algorithm and an additional user interface were developed using a game engine. After the 3D model was analyzed, the 3D model will be imported into the user interface and the interactive disassembly of the model will begin. Thus, the product to disassemble is selected via mouse clicks and moved to its final position. Once the disassembly is finished, the generated information is saved into a neutral exchange format. Based on the exchange format, the system is able to generate automatically assembly animations and assembly videos.

Обнаружение аномалий в составных объектах в формате JSON

In this paper, we address the problem of intrusion detection for modern web applications and mobile applications with the cloud-based server side, using malicious content detection in JSON data, which is currently one of the most popular data serialization and exchange formats between client and server parts of an application. We propose a method for building a JSON model for the given set of JSON objects capable of detection of structure and type anomalies. The model is based on the models for basic data types inside JSON collection objects and schema model that generalizes objects’ structure in the collection. We performed experiments using modifications of objects’ structures and insertions of code injection attack vectors such as SQL injections, OS command injections, and JavaScript/HTML injections. The analysis showed statistical significance between the model’s predictions and the presence of anomalies in the data gathered from the real web applications’ traffic. The quality of the model’s predictions was measured using the Matthews correlation coefficient (MCC). The MCC values computed on the data were close to one which indicates the model’s high efficiency in solving the problem of anomaly detection in JSON objects.

BIM implementation in Sarawak construction industry: Awareness, readiness and challenges

Lack of coordination and fragmentations have always existed among the stakeholders and parties involved in the implementation of planning, design and construction process of construction projects, especially in the aspects of information transfer. In the recent trends, Building Information Modelling, BIM has been introduced to address the fragmentation issues. The BIM framework is based on the notion of coordination between stakeholders in digital format for information exchange throughout the construction progress. Although BIM technology has been implemented in Malaysia for several years, low adoption is found within the Sarawak construction industry. This paper aims to assess the awareness and readiness for BIM implementation in the Sarawak construction industry. The study was carried out using questionnaire survey across the districts in the Southern Region, Central Region and Northern Region of Sarawak. There are in total 404 responses received, and it is revealed that only 14% of the participants have experience in BIM-related projects. This is still far from the goals set by the Construction Industry Development Board (CIDB) Malaysia. Meanwhile, 63% of respondents had heard of BIM and 46% of them had attended some seminar or program related on BIM. The investigation of awareness, readiness and challenges of BIM implementation has been further inferred and compiled as a foundation guideline for the proposed solution framework to increase BIM usage in the state. It is hopeful that proposed solution framework can help in overcoming BIM implementation barriers in the Sarawak Construction Industry.

Evolution of data sources for integrated data-driven urban mobility management

The aim of this paper is to perform research, propose a concept and identify conventional and emerging data sources that will be used as a base for quality data-driven decision-making in the area of urban mobility management in small/medium-sized cities. Conventional data sources have been identified and required data sets have been defined using existing standardized data protocols. In order to take advantage of emerging unconventional data sources, two potential data sources were identified that could be used for urban traffic management. These data sources include crowdsourcing data from smart city sharing economy service application and data from the mobile network operator. Since these data sources are not defined by existing standards, an exchange scope and format has been defined between data source and data consumer in order to enable data flow. The concept was tested at the prototype level and at the data exchange level during the research project in the City of Rijeka.

Greetings from the Incoming Standards VP

<fig orientation="portrait" position="float" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <graphic orientation="portrait" position="float" xlink:href="schle-3136936.tif"/> </fig> The first SMPTE standard I ever got to study was ST 377:2004—the file format specification for the beloved Material Exchange Format (MXF). That was in 2005, when I started my career as an undergraduate student at Fraunhofer IIS, Erlangen, Germany. Working there for a few hours a week, I was tasked with implementing small software tools to validate and process prototype Digital Cinema Packages (DCPs). The MXF standard was certainly no light read—I was both impressed and intimidated by its complexity. Frankly, I was quite happy about the publication of the famous <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MXF Book</i> by Bruce Devlin <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">et al.</i> when I was still wrapping my head around operational patterns, descriptors, and package types. Now, 17 years after learning about MXF and SMPTE, it is a great honor to be serving the Society as the Standards Vice President. Picking up the baton from Mr. MXF himself is very humbling, to say the least. I thank Bruce for the leadership that he has provided to the standards community during his four years as Standards Vice President and for the guidance and support I personally received from him.

Processing of the Results of Satellite Inland Positioning Transport Using Mobile Devices and Their Visualization

The issue of spatial data visualization is currently an important element in the positioning and navigation process. The constant trend in increasing the accuracy and availability of position modules affects the widespread use of the mobile devices in transport. The paper presents creation of a three-dimensional visualization model based on ground tracks recorded in NMEA (National Marine Electronics Association) and GPX (GPS Exchange Format) formats. Additionally, the study presents an analysis of the positioning accuracy including the sky obstructions presence and the instantaneous state of the satellite constellation. The significant deterioration in positioning accuracies was noted due to the presence of sky obstructions and low movement speed during data recording. The analysis of these parameters showed the dependence of the positioning accuracy with the number of visible satellites and the HDOP (Horizontal Dilution of Precision) parameter.

A survey of multi-signature schemes for XML documents

Extensible markup language (XML) is a widely used data exchange format in various fields for data transmission over the web. But due to security risk, the privacy of XML documents cannot be ensured, and hence sharing of data had become the major challenge. Web vulnerabilities cause threats to XML data confidentiality and integrity. There is a set of security mechanisms such as encryption, decryption, digital signature, and validations, which are applied to XML documents. Signing a document is the commonly used method for ensuring the authentication, non-repudiation, and integrity in which only a single signer is responsible for signing a document. But nowadays, the responsibility of signing a document is shared among multiple signers instead of a single signer which results in increasing the popularity of using multi-signature schemes. Therefore, a document may have multiple signatures and the integrity of the entire document depends upon it. This arises the need of studying various multi-signature schemes. Here, in this paper, various developments in the era of multi-signature schemes as well as its application areas are discussed.

AutomationML as Seamless Data Exchange Format for Integration of Automated Planning Tools for Assembly Line Design

The design of assembly lines is a demanding task, whose outcome is highly dependent on the production engineers’ knowledge and experience. Additionally, it is very time-consuming when performed manually. For this reason, many approaches exist to automate the required planning phases with their sub-tasks. This paper presents an integrated modeling approach using AutomationML as seamless data exchange format for the sequentially required tasks to design and configure an assembly line against multiple user-defined criteria. In its simple form, the design of an assembly line requires the assignment of processes to a set of resources and workstations (conceptual design), and decisions about the spatial arrangement of workstations and their connection through a conveyor or AGV system (physical layout). After every planning phase the model is extended and enriched with additional information required for the next phase and its automated tools.

ACCOUNTING IN THE CONTEXT OF THE MODERN DEVELOPMENT OF THE DIGITAL ECONOMY

Purpose. The aim of the article is to substantiate the need for the development of digitalization of modern accounting and financial reporting. Methodology of research. The study was conducted using a dialectical approach to the study of the current state of development of the digital economy. General scientific and special methods were used, in particular: analytical - when reviewing normative sources; monographic - when studying literary sources on issues of digital economy and accounting; system and analytical method - when processing the received information. Findings. It was determined that in the conditions of digitization of business processes, introduction and development of new business concepts, approaches to reporting methodology are changing, the need to create a new accounting concept is increasing. It is substantiated that digitalization contributes to the change in the functioning of management services and their responsibilities in all divisions of the business entity, and in the accounting department, in particular. It was revealed that the result of the development of digital technologies will be the transformation of the organizational structure and management services of the accounting department, including due to the reduction of the staff and the review of the functionality, the introduction of new technologies for processing primary documents and information, the modernization of accounting processes and accounting policy in general; strengthening requirements for professional skills of users. Origination. Directions for the development of digitalization of the organizational structure of the company’s accounting service are proposed in the article. The introduction of a single electronic data exchange format for financial reporting as a strategic tool for accounting harmonization is substantiated. Practical value. The obtained results of the research will contribute to increasing the efficiency of the formation and development of accounting in the conditions of the digital economy and will become the basis for further scientific developments in this field. Key words: digitalization, information technologies, accounting, financial reporting, digital accounting, digital technologies, business process.

EnzymeML-a data exchange format for biocatalysis and enzymology.

EnzymeML is an XML-based data exchange format that supports the comprehensive documentation of enzymatic data by describing reaction conditions, time courses of substrate and product concentrations, the kinetic model, and the estimated kinetic constants. EnzymeML is based on the Systems Biology Markup Language, which was extended by implementing the STRENDA Guidelines. An EnzymeML document serves as a container to transfer data between experimental platforms, modeling tools, and databases. EnzymeML supports the scientific community by introducing a standardized data exchange format to make enzymatic data findable, accessible, interoperable, and reusable according to the FAIR data principles. An application programming interface in Python supports the integration of software tools for data acquisition, data analysis, and publication. The feasibility of a seamless data flow using EnzymeML is demonstrated by creating an EnzymeML document from a structured spreadsheet or from a STRENDA DB database entry, by kinetic modeling using the modeling platform COPASI, and by uploading to the enzymatic reaction kinetics database SABIO-RK.

CAD-BASED AUTOMATED G-CODE GENERATION FOR DRILLING OPERATIONS

The automated generation of G-code for machining processes is a valuable tool at the hands of every engineer and machinist. Nowadays, many software systems exist that provide automated functions related to G-code generation. Most free software require the import of a Drawing Exchange Format (DXF) file and cannot work directly on a 3D part. On the contrast, the equivalent commercially-available software systems are feature-rich and can provide a variety of automated processes, but are usually highly priced. The presented application aims to supplement the existing free Computer Aided Manufacturing (CAM) systems by providing a way of generating G-code for drilling operations, using already owned commercial 3D Computer Aided Design (CAD) systems such as SolidWorksTM. Thus, in the case of 3D part drilling, a standard 3D CAD system is sufficient since the code can be adopted by most modern CAD software with minor changes. Moreover, no specialized CAM software is required. In order to achieve this automation, the Application Programming Interface (API) of SolidWorks™ 2018 was utilized, which allows for the design of visualized User Interfaces (UI) and the development of code under the Visual Basic for Applications (VBA™) programming language. The available API methods are employed to recognize the features that were used to design the part, as well as extract the geometric parameters of each of these features. In addition, an embedded calculator automatically defines the cutting conditions (cutting speed, feed and tool) based on the user selections. Finally, the application generates the Computer Numerical Control (CNC) code for the summary of the discovered holes according to the standardized G-code commands; the output can be a typical TXT or NC file that can be easily converted to the preference of the user if necessary.

Material description for textile draping simulation: data structure, open data exchange formats and system for automatic analysis of experimental series

The simulative development of clothing and other textile products requires a complete set of material parameters to be provided. Currently, different simulation software providers users with different values and formats for these parameters. This paper provides an overview about the most important values and proposed structures for storing both the raw data and the extracted parameters. The structure is implemented in both JSON and XML formats, allowing integration in proven formats for three-dimensional worlds such as gltf and x3d. Finally, a structure for organization of the raw data of the testing devices is described. Following this structure allows automatic processing, normalization and extraction of the parameters in short time. The goal of the paper is to simplify and unify the exchange of material parameters for textile fabrics.

An updated version of the global interior ocean biogeochemical data product, GLODAPv2.2021

Abstract. The Global Ocean Data Analysis Project (GLODAP) is a synthesis effort providing regular compilations of surface-to-bottom ocean biogeochemical bottle data, with an emphasis on seawater inorganic carbon chemistry and related variables determined through chemical analysis of seawater samples. GLODAPv2.2021 is an update of the previous version, GLODAPv2.2020 (Olsen et al., 2020). The major changes are as follows: data from 43 new cruises were added, data coverage was extended until 2020, all data with missing temperatures were removed, and a digital object identifier (DOI) was included for each cruise in the product files. In addition, a number of minor corrections to GLODAPv2.2020 data were performed. GLODAPv2.2021 includes measurements from more than 1.3 million water samples from the global oceans collected on 989 cruises. The data for the 12 GLODAP core variables (salinity, oxygen, nitrate, silicate, phosphate, dissolved inorganic carbon, total alkalinity, pH, CFC-11, CFC-12, CFC-113, and CCl4) have undergone extensive quality control with a focus on systematic evaluation of bias. The data are available in two formats: (i) as submitted by the data originator but updated to World Ocean Circulation Experiment (WOCE) exchange format and (ii) as a merged data product with adjustments applied to minimize bias. For this annual update, adjustments for the 43 new cruises were derived by comparing those data with the data from the 946 quality controlled cruises in the GLODAPv2.2020 data product using crossover analysis. Comparisons to estimates of nutrients and ocean CO2 chemistry based on empirical algorithms provided additional context for adjustment decisions in this version. The adjustments are intended to remove potential biases from errors related to measurement, calibration, and data handling practices without removing known or likely time trends or variations in the variables evaluated. The compiled and adjusted data product is believed to be consistent with to better than 0.005 in salinity, 1 % in oxygen, 2 % in nitrate, 2 % in silicate, 2 % in phosphate, 4 µmol kg−1 in dissolved inorganic carbon, 4 µmol kg−1 in total alkalinity, 0.01–0.02 in pH (depending on region), and 5 % in the halogenated transient tracers. The other variables included in the compilation, such as isotopic tracers and discrete CO2 fugacity (fCO2), were not subjected to bias comparison or adjustments. The original data, their documentation, and DOI codes are available at the Ocean Carbon Data System of NOAA NCEI (https://www.ncei.noaa.gov/access/ocean-carbon-data-system/oceans/GLODAPv2_2021/, last access: 7 July 2021). This site also provides access to the merged data product, which is provided as a single global file and as four regional ones – the Arctic, Atlantic, Indian, and Pacific oceans – under https://doi.org/10.25921/ttgq-n825 (Lauvset et al., 2021). These bias-adjusted product files also include significant ancillary and approximated data and can be accessed via https://www.glodap.info (last access: 29 June 2021). These were obtained by interpolation of, or calculation from, measured data. This living data update documents the GLODAPv2.2021 methods and provides a broad overview of the secondary quality control procedures and results.

Building models for coupled thermo elastic problems in different software architectures using a new model exchange format

AbstractTo reduce the energy consumption of machine tools while preserving the productivity and quality, the deformation caused by thermal loads must be taken into account. Two approaches to reach this goal are the integration of model predictive error correction algorithms into the machine controller and a machine design that mitigates unwanted thermo‐elastic behaviour.Both approaches demand a profound understanding of the machine behaviour under different thermal load scenarios by simulation. The computation of representative distortions requires accurate models of the machine components, relevant physical phenomena and appropriate numerical methods, ranging from adaptive finite element discretization to model order reduction methods. In most cases, these methods and models are developed independently by different scientific groups, whereas the total goal of an improved operation of the machine tool demands the joint knowledge of all teams within the same machine model.This contribution, introduces an open source format for a seamless model exchange between the scientific groups. It bases on the standardized and machine readable JSON format. The JSON scheme comprises of all necessary model information. The main use cases, benefits and drawbacks are outlined. The file structure is briefly described. Design decisions and problems are discussed. After that, a work flow using the new format to calculate the thermal behaviour of a machine tool is shown. Different modelling approaches to calculate the thermal field are compared. Finally the next development steps and further use cases for the format will be outlined.

RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data

BackgroundThe abundance of glycomics data that have accumulated has led to the development of many useful databases to aid in the understanding of the function of the glycans and their impact on cellular activity. At the same time, the endeavor for data sharing between glycomics databases with other biological databases have contributed to the creation of new knowledgebases. However, different data types in data description have impeded the data sharing for knowledge integration. To solve this matter, Semantic Web techniques including Resource Description Framework (RDF) and ontology development have been adopted by various groups to standardize the format for data exchange. These semantic data have contributed to the expansion of knowledgebases and hold promises of providing data that can be intelligently processed. On the other hand, bench biologists who are experts in experimental finding are end users and data producers. Therefore, it is indispensable to reduce the technical barrier required for bench biologists to manipulate their experimental data to be compatible with standard formats for data sharing.ResultsThere are many essential concepts and practical techniques for data integration but there is no method to enable researchers to easily apply Semantic Web techniques to their experimental data. We implemented our procedure on unformatted information of E.coli O-antigen structures collected from the web and show how this information can be expressed as formatted data applicable to Semantic Web standards. In particular, we described the E-coli O-antigen biosynthesis pathway using the BioPAX ontology developed to support data exchange between pathway databases.ConclusionsThe method we implemented to semantically describe O-antigen biosynthesis should be helpful for biologists to understand how glycan information, including relevant pathway reaction data, can be easily shared. We hope this method can contribute to lower the technical barrier that is required when experimental findings are formulated into formal representations and can lead bench scientists to readily participate in the construction of new knowledgebases that are integrated with existing ones. Such integration over the Semantic Web will enable future work in artificial intelligence and machine learning to enable computers to infer new relationships and hypotheses in the life sciences.

PDBe-KB: collaboratively defining the biological context of structural data.

The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

An FSKX compliant source attribution model for salmonellosis and a look at its major hidden pitfalls

To reduce the burden of human society that is caused by zoonotic diseases, it is important to attribute sources to human illnesses. One powerful approach in supporting any intervention decision is mathematical modelling. This paper presents a source attribution model which considers five sources (broilers, laying hens, pigs, turkeys) for salmonellosis and uses two datasets from Germany collected over two time periods; one from 2004 to 2007 and one from 2010 to 2011. The model uses a Bayesian modelling approach derived from the so-called Hald model and is based on microbial subtyping. In this case, Salmonella isolates from humans and animals were subtyped with respect to serovar and phage type. Based on that typing, the model estimates how many human salmonellosis cases can be attributed to each of the considered sources. A reference description of the model is available under DOI: 10.1111/zph.12645. Here, we present this model as a ready-to-use resource in the Food Safety Knowledge Exchange (FSKX) format. This open information exchange format allows to re-use, modify, and further develop the model and uses model metadata and controlled vocabulary to harmonise the annotation. In addition to the model, we discuss some technical pitfalls that might occur when running this Bayesian model based on Markov chain Monte Carlo calculations. As source attribution of zoonotic disease is one useful tool for the One Health approach, our work facilitates the exchange, adjustment, and re-usage of this source attribution model by the international and multi-sectoral community.

A ReRAM Memory Compiler for Monolithic 3D Integrated Circuits in a Carbon Nanotube Process

We present a ReRAM memory compiler for monolithic 3D (M3D) integrated circuits (IC). We develop ReRAM architectures for M3D ICs using 1T-1R bit cells and single and multiple tiers of transistors for access and peripheral circuits. The compiler includes an automated flow for generation of subarrays of different dimensions and larger arrays of a target capacity by integrating multiple subarrays. The compiler is demonstrated using an M3D process design kit (PDK) based on a Carbon Nanotube Transistor technology. The PDK includes multiple layers of transistors and back-end-of-the-line integrated ReRAM. Simulations show the compiled ReRAM macros with multiple tiers of transistors reduces footprint and improves performance over the macros with single-tier transistors. The compiler creates layout views that are exported into library exchange format or graphic data system for full-array assembly and schematic/symbol views to extract per-bit read/write energy and read latency. Comparison of the proposed M3D subarray architectures with baseline 2D subarrays, generated with a custom-designed set of bit cells and peripherals, demonstrate up to 48% area reduction and 13% latency improvement.