SeqImprove: Machine-Learning-Assisted Curation of Genetic Circuit Sequence Information.

The progress and utility of synthetic biology is currently hindered by the lengthy process of studying literature and replicating poorly documented work. Reconstruction of crucial design information through post hoc curation is highly noisy and error-prone. To combat this, author participation during the curation process is crucial.

Advancing reuse of genetic parts: progress and remaining challenges.

Issues with data reuse have been recognized in synthetic biology and the broader scientific community. Policies and standards fall short as machine reasoning is not emphasised and enforcement is lacking. We discuss the progress, remaining challenges, and possible solutions.

Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories.

Accelerating the development of synthetic biology applications requires reproducible experimental findings. Different standards and repositories exist to exchange experimental data and metadata. However, the associated software tools often do not support a uniform data capture, encoding, and exchange of information.

Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa.

Standards support synthetic biology research by enabling the exchange of component information. However, using formal representations, such as the Synthetic Biology Open Language (SBOL), typically requires either a thorough understanding of these standards or a suite of tools developed in concurrence with the ontologies. Since these tools may be a barrier for use by many practitioners, the Excel-SBOL Converter was developed to facilitate the use of SBOL and integration into existing workflows.

Building an Artificial Plant Cell Wall on a Lipid Bilayer by Assembling Polysaccharides and Engineered Proteins.

The cell wall constitutes a fundamental structural component of plant cells, providing them with mechanical resistance and flexibility. Mimicking this wall is a critical step in the conception of an experimental model of the plant cell. The assembly of cellulose/hemicellulose in the form of cellulose nanocrystals and xyloglucans as a representative model of the plant cell wall has already been mastered; however, these models lacked the pectin component.

Sequence-Based Searching for SynBioHub Using VSEARCH.

The ability to search for a part by its sequence is crucial for a large repository of parts. Prior to this work, however, this was not possible on SynBioHub. Sequence-based search is now integrated into SynBioHub, allowing users to find a part by a sequence provided in plain text or a supported file format.

Synthetic Biology Curation Tools (SYNBICT).

Much progress has been made in developing tools to generate component-based design representations of biological systems from standard libraries of parts. Most biological designs, however, are still specified at the sequence level. Consequently, there exists a need for a tool that can be used to automatically infer component-based design representations from sequences, particularly in cases when those sequences have minimal levels of annotation.

Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA.

In synthetic biology, combinational circuits are used to program cells for various new applications like biosensors, drug delivery systems, and biofuels. Similar to asynchronous electronic circuits, some combinational genetic circuits may show unwanted switching variations () caused by multiple input changes. Depending on the biological circuit, glitches can cause irreversible effects and jeopardize the circuit's functionality.

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.

Synthetic Biology Knowledge System.

The Synthetic Biology Knowledge System (SBKS) is an instance of the SynBioHub repository that includes text and data information that has been mined from papers published in ACS Synthetic Biology. This paper describes the SBKS curation framework that is being developed to construct the knowledge stored in this repository. The text mining pipeline performs automatic annotation of the articles using natural language processing techniques to identify salient content such as key terms, relationships between terms, and main topics.

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.

Extending SynBioHub's Functionality with Plugins.

SynBioHub is a repository for synthetic genetic designs represented in the (SBOL). To integrate SynBioHub into more synthetic biology workflows, its data processing capabilities need to be expanded. To this end, a plugin interface has been developed.

A heuristic approach to handling missing data in biologics manufacturing databases.

The biologics sector has amassed a wealth of data in the past three decades, in line with the bioprocess development and manufacturing guidelines, and analysis of these data with precision is expected to reveal behavioural patterns in cell populations that can be used for making predictions on how future culture processes might behave. The historical bioprocessing data likely comprise experiments conducted using different cell lines, to produce different products and may be years apart; the situation causing inter-batch variability and missing data points to human- and instrument-associated technical oversights. These unavoidable complications necessitate the introduction of a pre-processing step prior to data mining.

Near-infrared spectroscopy for detection of a significant patent ductus arteriosus.

Background: Near-infrared spectroscopy (NIRS) may assist with characterization of a hemodynamically significant patent ductus arteriosus (hsPDA) by measuring cerebral and renal saturation (Csat and Rsat) levels. We hypothesized that Csat and Rsat in preterm infants with an hsPDA would be decreased compared to those with no PDA or nonsignificant PDA.

Methods: This non a-priori designed study retrospectively investigated clinical and ECHO characteristics of preterm infants <29 wk gestation who underwent routine NIRS monitoring.

Impact of ambient conditions on SMP elimination and rejection in MBRs.

The widespread application of the membrane-assisted activated sludge process is restricted by membrane fouling, which increases investment and operating costs. Soluble microbial products (SMPs) are currently considered as the major cause of membrane fouling in membrane bioreactors (MBRs). This study aims at elucidating and quantifying the effects of varying environmental conditions on SMP elimination and rejection based on findings in a pilot MBR and in well-defined lab trials.

Movement characteristics of persons with prader-willi syndrome rising from supine.

Purpose: The purposes of this study were to: 1) determine if previously published descriptors of the supine to stand rising task in healthy individuals could be applied to the movements of persons with Prader-Willi Syndrome (PWS); and 2) assess upper extremity (UE), axial region (AX), and lower extremity (LE) movements among subjects with PWS compared with controls.

Methods: Nine subjects with PWS (seven-36 years of age) and matched controls were videotaped performing 10 rising trials. The UE, AX, and LE movements were classified using published descriptors.

Reversal of cardiac hypertrophy in transgenic disease models by calcineurin inhibition.

Heart disease remains one of the leading causes of morbidity and mortality in the industrialized nations of the world. Intense investigation has centered around identifying and manipulating intracellular signaling pathways that direct hypertrophic and myopathic responses in an attempt to intervene in the progression or reverse certain forms of heart disease. We show here that cyclosporin A-mediated inhibition of the calcium-regulated phosphatase, calcineurin (PP2B), reverses cardiac hypertrophy and myopathic dilation in two transgenic mouse models of cardiomyopathy.