basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method

Standardized DNA assembly methods utilizing modular components provide a powerful framework to explore design spaces and iterate through Design-Build-Test-Learn cycles. Biopart Assembly Standard for Idempotent Cloning (BASIC) DNA assembly uses modular parts and linkers, is highly accurate, easy to automate, free for academic and commercial use, while enabling simple hierarchical assemblies through an idempotent format. These attributes facilitate various applications including pathway engineering, ribosome binding site tuning, fusion protein synthesis and multiplex gRNA expression. In this work we present basicsynbio, an open-source software encompassing a Web App (https://basicsynbio.web.app/) and Python Package (https://github.com/LondonBiofoundry/basicsynbio). With basicsynbio, users can access commonly used BASIC parts and linkers while robustly designing new parts and assemblies with exception handling for common design errors. Furthermore, users can export sequence data and create build instructions for manual or automated workflows. The generation of build instructions relies on the BasicBuild Open Standard which is easily parsed for bespoke workflows and is serialised in Java Script Object Notation for transfer and storage. We demonstrate basicsynbio by assembling a collection of 30 BASIC-compatible vectors using various sequences including modules from the Standard European Vector Architecture (SEVA). The BASIC SEVA collection encompasses plasmids containing six antibiotic resistance markers and five origins of replication from different compatibility groups, including a temperature-sensitive variant. We deposit the collection on Addgene under an OpenMTA agreement, making them available. Furthermore, these sequences are accessible from within the basicsynbio application programming interface along with other collections of parts and linkers, providing an ideal environment to design BASIC DNA assemblies for bioengineering applications.

A BIM Based Framework for Damage Segmentation, Storage, and Visualization

Current bridge inspection practices rely on paper-based data acquisition, digitization, and multiple conversions in between incompatible formats to facilitate data exchange. This practice is time-consuming, error-prone, cumbersome, and leads to information loss. One aim for future inspection procedures is to have a fully digitized workflow that achieves loss-free data exchange, which lowers costs and offers higher efficiency. On the one hand, existing studies proposed methods to automatize data acquisition and visualization for inspections. These studies lack an open standard to make the gathered data available for other processes. On the other hand, several studies discuss data structures for exchanging damage information through out different stakeholders. However, those studies do not cover the process of automatic data acquisition and transfer. This study focused on a framework that incorporates automatic damage data acquisition, transfer, and a damage information model for data exchange. This enables inspectors to use damage data for subsequent analyses and simulations. The proposed framework shows the potentials for a comprehensive damage information model and related (semi-)automatic data acquisition and processing.

OPC UA TSN: a next-generation network for Industry 4.0 and IIoT

Purpose The purpose of this paper is to describe how emerging open standards are replacing traditional industrial networks. Current industrial Ethernet networks are not interoperable; thus, limiting the potential capabilities for the Industrial Internet of Things (IIoT). There is no forthcoming new generation fieldbus standard to integrate into the IIoT and Industry 4.0 revolution. The open platform communications unified architecture (OPC UA) time-sensitive networking (TSN) is a potential vendor-independent successor technology for the factory network. The OPC UA is a data exchange standard for industrial communication, and TSN is an Institute of Electrical and Electronics Engineers standard for Ethernet that supports real-time behaviour. The merging of these open standard solutions can facilitate cross-vendor interoperability for Industry 4.0 and IIoT products. Design/methodology/approach A brief review of the history of the fieldbus standards is presented, which highlights the shortcomings for current industrial systems in meeting converged traffic solutions. An experimental system for the OPC UA TSN is described to demonstrate an approach to developing a three-layer factory network system with an emphasis on the field layer. Findings From the multitude of existing industrial network schemes, there is a convergence pathway in solutions based on TSN Ethernet and OPC UA. At the field level, basic timing measurements in this paper show that the OPC UA TSN can meet the basic critical timing requirements for a fieldbus network. Originality/value This paper uniquely focuses on the specific fieldbus standards elements of industrial networks evolution and traces the developments from the early history to the current developing integration in IIoT context.

IFC AND CITYGML SEMANTIC TRANSFORMATION FOR 3D GIS

Building information modelling (BIM) and geographical information systems (GIS) domains immensely contribute to a digital representation of architectural and environmental bodies respectively. BIM is endorsed in order to enhance the Architecture Engineering and Construction (AEC) industry process to save time, cost and speed up the project, and more so, to minimise the frequent requests of information by the stakeholders within the industry. On the other hand, the Geographic Information System (GIS) has been increasingly used to generate detailed 3D data, geolocation and spatial analysis. Both BIM and GIS provide 3D data for the development of 3D city models, digital twin, smart city, AEC etc. However, there are significant diverse between the two in terms of their characteristics, scope of interest and focus that makes it difficult to easily be achieved. The amalgamation of the two worlds provides a clear picture of a built environment based on data (geometry and semantics) integration, which reinforces the enhancement of the three-dimensional (3D) applications in general into the digital world. This paper presents a methodology that semantically integrates the two worlds through their standards that is the Industry Foundation Classes (IFC) which is an open standard, selected because it is the typical free standard to exchange data in the BIM world and City Geography Markup Language (CityGML) is the most leading 3D city model standard in 3D GIS. This is carried out by performing a semantic mapping between the two standards, converting the encoding that the two standards use from STEP in IFC(BIM) to XML in CityGML (3D GIS), by providing a basic implementation created using Python to combine the above tasks.

Right-Hand Side Expanding Algorithm for Maximal Frequent Itemset Mining

When it comes to association rule mining, all frequent itemsets are first found, and then the confidence level of association rules is calculated through the support degree of frequent itemsets. As all non-empty subsets in frequent itemsets are still frequent itemsets, all frequent itemsets can be acquired only by finding all maximal frequent itemsets (MFIs), whose supersets are not frequent itemsets. In this study, an algorithm, named right-hand side expanding (RHSE), which can accurately find all MFIs, was proposed. First, an Expanding Operation was designed, which, starting from any given frequent itemset, could add items using certain rules and form some supersets of given frequent itemsets. In addition, these supersets were all MFIs. Next, this operator was used to add items by taking all frequent 1-itemsets as the starting point alternately, and all MFIs were found in the end. Due to the special design of the Expanding Operation, each MFI could be found. Moreover, the path found was unique, which avoided the algorithm redundancy in temporal and spatial complexity. This algorithm, which has a high operating rate, is applicable to the big data of high-dimensional mass transactions as it is capable of avoiding the computing redundancy and finding all MFIs. In the end, a detailed experimental report on 10 open standard transaction sets was given in this study, including the big data calculation results of million-class transactions.

Evaluating Extensible 3D (X3D) Graphics For Use in Software Visualisation

<p>3D web software visualisation has always been expensive, special purpose, and hard to program. Most of the technologies used require large amounts of scripting, are not reliable on all platforms, are binary formats, or no longer maintained. We can make end-user web software visualisation of object-oriented programs cheap, portable, and easy by using Extensible (X3D) 3D Graphics, which is a new open standard. In this thesis we outline our experience with X3D and discuss the suitability of X3D as an output format for software visualisation.</p>

Evaluating Extensible 3D (X3D) Graphics For Use in Software Visualisation

<p>3D web software visualisation has always been expensive, special purpose, and hard to program. Most of the technologies used require large amounts of scripting, are not reliable on all platforms, are binary formats, or no longer maintained. We can make end-user web software visualisation of object-oriented programs cheap, portable, and easy by using Extensible (X3D) 3D Graphics, which is a new open standard. In this thesis we outline our experience with X3D and discuss the suitability of X3D as an output format for software visualisation.</p>

The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction

Background With the rapid increase in the amount of Protein-Protein Interaction (PPI) data, the establishment of an event-centered PPI ontology that contains temporal and spatial vocabularies is urgently needed to clarify PPI biological annotations. In this paper, we propose a precisely designed schema - PPIO (PPI Ontology) for representing the biological context of PPIs. Results Inspired by the event model and the distinct characteristics of PPI events, PPIO consists of six core aspects of the information required for reporting a PPI event, including the interactor (who), the biological process (when), the subcellular location (where), the interaction type (how), the biological function (what) and the detection method (which). PPIO is implemented through the integration of appropriate terms from the corresponding vocabularies/ontologies, e.g., Gene Ontology, Protein Ontology, PSI-MI/MOD, etc. To assess PPIO, an approach based on PPIO in developed to extract PPI biological annotations from an open standard corpus “BioCreAtIvE-PPI”. The experiment results demonstrate PPIO’s high performance, a precision of 0.69, a recall of 0.72 and an F-score of 0.70. Conclusions PPIO is a well-constructed essential ontology in the interpretation of PPI biological context. The results of the experiments conducted on the BioCreAtIvE corpus demonstrate that PPIO is able to facilitate PPI annotation extraction from biomedical literature effectively and enrich essential annotation for PPIs.

HBIM-GIS INTEGRATION WITH AN IFC-TO-SHAPEFILE APPROACH: THE PALAZZO TROTTI VIMERCATE PILOT CASE STUDY

The proprietary software investments in the data integration field are incrementing, and the progresses are visible in the possibility to directly open in a GIS environment a 3D software data format. Still, this is limited to the integration between the proprietary data formats and standards, ArcGIS environment shapefile multipatch and Revit 3D model, by using a proprietary software (ArcGIS). This study takes advantage of the lesson-learnt results in the proprietary data integration field, wanting to replicate a similar result using the IFC open standard, which is not directly openable by a GIS interface and needs to overcome a conversion that in most of the cases leads to semantic and geometric losses. So, an IFC-to-shapefile data conversion was performed, stressing (i) the way information is stored in the attribute table to query the geometries and perform geoprocessing, by (ii) implementing workarounds to keep the Revit instances’ shared parameters in the IFC file, (iii) meanwhile having a high Level of Detail of the HBIM. The research performed the IFC-to-shapefile data conversion through FME (Feature Manipulation Engine), benefitting of the flexibility of the shapefile format and of the IFC’ possibility to keep a high LOD in the export phase. Both allowed to properly query and manage the elements of an HBIM in a GIS (ArcGIS environment), and, using relational attributes table, retrieve the information contained in each Revit instance’ property panel, as the shared parameters that implement the BIM Level of Information (LOI).