Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework.

Background: Computational approaches to support rare disease diagnosis are challenging to build, requiring the integration of complex data types such as ontologies, gene-to-phenotype associations, and cross-species data into variant and gene prioritisation algorithms (VGPAs). However, the performance of VGPAs has been difficult to measure and is impacted by many factors, for example, ontology structure, annotation completeness or changes to the underlying algorithm. Assertions of the capabilities of VGPAs are often not reproducible, in part because there is no standardised, empirical framework and openly available patient data to assess the efficacy of VGPAs - ultimately hindering the development of effective prioritisation tools.

Detecting Respiratory Viruses Using a Portable NIR Spectrometer-A Preliminary Exploration with a Data Driven Approach.

Respiratory viruses' detection is vitally important in coping with pandemics such as COVID-19. Conventional methods typically require laboratory-based, high-cost equipment. An emerging alternative method is Near-Infrared (NIR) spectroscopy, especially a portable one of the type that has the benefits of low cost, portability, rapidity, ease of use, and mass deployability in both clinical and field settings.

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research.

Disposable Paper-Based Biosensors: Optimizing the Electrochemical Properties of Laser-Induced Graphene.

Laser-induced graphene (LIG) on paper substrates is a desirable material for single-use point-of-care sensing with its high-quality electrical properties, low fabrication cost, and ease of disposal. While a prior study has shown how the repeated lasing of substrates enables the synthesis of high-quality porous graphitic films, however, the process-property correlation of lasing process on the surface microstructure and electrochemical behavior, including charge-transfer kinetics, is missing. The current study presents a systematic in-depth study on LIG synthesis to elucidate the complex relationship between the surface microstructure and the resulting electroanalytical properties.

A Simple Standard for Sharing Ontological Mappings (SSSOM).

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction).

Curation Principles Derived from the Analysis of the SBOL iGEM Data Set.

As an engineering endeavor, synthetic biology requires effective sharing of genetic design information that can be reused in the construction of new designs. While there are a number of large community repositories of design information, curation of this information has been limited. This in turn limits the ways in which design information can be put to use.

VisBOL2-Improving Web-Based Visualization for Synthetic Biology Designs.

VisBOL is a web-based visualization tool used to depict genetic circuit designs. This tool depicts simple DNA circuits adequately, but it has become increasingly outdated as new versions of SBOL Visual were released. This paper introduces VisBOL2, a heavily redesigned version of VisBOL that makes a number of improvements to the original VisBOL, including proper functional interaction rendering, dynamic viewing, a more maintainable code base, and modularity that facilitates compatibility with other software tools.

High-isolation antenna array using SIW and realized with a graphene layer for sub-terahertz wireless applications.

This paper presents the results of a study on developing an effective technique to increase the performance characteristics of antenna arrays for sub-THz integrated circuit applications. This is essential to compensate the limited power available from sub-THz sources. Although conventional array structures can provide a solution to enhance the radiation-gain performance however in the case of small-sized array structures the radiation properties can be adversely affected by mutual coupling that exists between the radiating elements.

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering.

The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of DNA-based components and their sub-components, SBOL can now be used to represent knowledge across multiple scales and throughout the entire synthetic biology workflow, from the specification of a single molecule or DNA fragment through to multicellular systems containing multiple interacting genetic circuits. The third major iteration of the SBOL standard, SBOL3, is an effort to streamline and simplify the underlying data model with a focus on real-world applications, based on experience from the deployment of SBOL in a variety of scientific and industrial settings.

Nanophotonic-Carbohydrate Lab-on-a-Microneedle for Rapid Detection of Human Cystatin C in Finger-Prick Blood.

Miniaturized total analysis systems, for the rapid detection of disease biomarkers, with features including high biomarker sensitivity, selectivity, biocompatibility, and disposability, all at low cost are of profound importance in the healthcare sector. Within this frame of reference, we developed a lab-on-a-carbohydrate-microneedle biodevice by integrating localized surface plasmon resonance (LSPR) paper-based substrates with biocompatible microneedles of high aspect ratio (>60:1 length:width). These microneedles are completely fabricated with carbohydrate (maltose) and further coated with poly lactic--glycolic acid (PLGA), which together serves the purpose of fluid channels.

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL).

Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization.

Synthetic biology open language (SBOL) version 3.0.0.

Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions.

ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL).

The Synthetic Biology Open Language (SBOL) is an emerging synthetic biology data exchange standard, designed primarily for unambiguous and efficient machine-to-machine communication. However, manual editing of SBOL is generally difficult for nontrivial designs. Here, we describe ShortBOL, a lightweight SBOL scripting language that bridges the gap between manual editing, visual design tools, and direct programming.

Sensitivity Enhancement of Point-of-Care for Cardiac Markers Detection using Micro-Impedimetric Immunosensor Arrays.

This paper describes the development and characterisation of a novel, electrical impedance spectroscopy-based (EIS) immunosensor array for point-of-care applications. EIS is a highly sensitive, label-free, real time technique suitable for single use, point-of-care cardiac marker detection devices. However, the underlying source of the observed change in EIS immunoassay response has not been well characterised or understood.

Effective Utilization of Waste Red Mud for High Performance Supercapacitor Electrodes.

In recent years, metal oxide-based, inexpensive, stable electrodes are being explored as a potent source of high performance, sustainable supercapacitors. Here, the employment of industrial waste red mud as a pseudocapacitive electrode material is reported. Mechanical milling is used to produce uniform red mud nanoparticles, which are rich in hematite (FeO), and lower amounts of other metal oxides.

Communicating Structure and Function in Synthetic Biology Diagrams.

Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about the functional relationships between features of these sequences and/or other molecular species. A number of conventions and practices have begun to emerge within synthetic biology for creating such diagrams, and the Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard to organize, systematize, and extend such conventions in order to produce a coherent visual language.

SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information.

Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent information about genetic circuits, and it is based on capturing data using graphs. The language provides the syntax using a free text document that is accessible to humans only.

sboljs: Bringing the Synthetic Biology Open Language to the Web Browser.

The Synthetic Biology Open Language (SBOL) is a data standard for the representation of engineered biological systems. SBOL is implemented in the form of software libraries which can be used to add SBOL support to both new and existing software tools. While existing libraries allow for software to be developed that runs on a server or is installed locally, they lack the capability to create SBOL software that runs directly in a Web browser.

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs.

Synthetic Biology Open Language (SBOL) Version 2.2.0.

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories.

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.

The SynBioHub repository ( https://synbiohub.org ) is an open-source software project that facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical user interface that enables users to search for and share designs in a Web browser.

A standard-enabled workflow for synthetic biology.

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs.