Networks often contain regions of tightly connected nodes, or clusters, that highlight their shared relationships. An effective way to create a visual summary of a network is to identify clusters and ...annotate them with an enclosing shape and a summarizing label. Cytoscape provides the ability to annotate a network with shapes and labels, however these annotations must be created manually one at a time, which can be a laborious process. AutoAnnotate is a Cytoscape 3 App that automates the process of identifying clusters and visually annotating them. It greatly reduces the time and effort required to fully annotate clusters in a network, and provides freedom to experiment with different strategies for identifying and labelling clusters. Many customization options are available that enable the user to refine the generated annotations as required. Annotated clusters may be collapsed into single nodes using the Cytoscape groups feature, which helps simplify a network by making its overall structure more visible. AutoAnnotate is applicable to any type of network, including enrichment maps, protein-protein interactions, pathways, or social networks.
Geothermal energy is a renewable source of base-load power that is expected to play an important role in the transition to a low-carbon economy. In this article, we introduce a novel software ...application – named Geothermal Energy Impact Estimator – which computes the environmental impacts, including carbon emissions, of existing or future geothermal plants, using the Life Cycle Assessment (LCA) methodology. The software application is user-friendly and was designed to be used by geothermal companies and policy makers. We provide two specific use cases of the software application that represent existing plants in Iceland and in the UK.
Sequencing reads overlapping polymorphic sites in diploid mammalian genomes may be assigned to one allele or the other. This holds the potential to detect gene expression, chromatin modifications, ...DNA methylation or nuclear interactions in an allele-specific fashion. SNPsplit is an allele-specific alignment sorter designed to read files in SAM/BAM format and determine the allelic origin of reads or read-pairs that cover known single nucleotide polymorphic (SNP) positions. For this to work libraries must have been aligned to a genome in which all known SNP positions were masked with the ambiguity base 'N' and aligned using a suitable mapping program such as Bowtie2, TopHat, STAR, HISAT2, HiCUP or Bismark. SNPsplit also provides an automated solution to generate N-masked reference genomes for hybrid mouse strains based on the variant call information provided by the Mouse Genomes Project. The unique ability of SNPsplit to work with various different kinds of sequencing data including RNA-Seq, ChIP-Seq, Bisulfite-Seq or Hi-C opens new avenues for the integrative exploration of allele-specific data.
Biobtree is a bioinformatics tool to search and map bioinformatics datasets via identifiers or special keywords such as species name. It processes large bioinformatics datasets using a specialized ...MapReduce-based solution with optimum computational and storage resource usage. It provides uniform and B+ tree-based database output, a web interface, web services and allows performing chain mapping queries between datasets. It can be used via a single executable file or alternatively it can be used via the R or Python-based wrapper packages which are additionally provided for easier integration into existing pipelines. Biobtree is open source and available at
GitHub.
We have developed "Microscope-Cockpit" (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and ...elaborate bespoke microscope systems. The user environment allows next-generation near instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses "Python-Microscope" (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging.
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one ...in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
Electronic data capture systems (EDCs) have the potential to achieve efficiency and quality in collection of multisite data. We quantify the volume, time, accuracy and costs of an EDC using ...large-scale census data from the STRATAA consortium, a comprehensive programme assessing population dynamics and epidemiology of typhoid fever in Malawi, Nepal and Bangladesh to inform vaccine and public health interventions.
A census form was developed through a structured iterative process and implemented using Open Data Kit Collect running on Android-based tablets. Data were uploaded to Open Data Kit Aggregate, then auto-synced to MySQL-defined database nightly. Data were backed-up daily from three sites centrally, and auto-reported weekly. Pre-census materials’ costs were estimated. Demographics of 308,348 individuals from 80,851 households were recorded within an average of 14.7 weeks range (13-16) using 65 fieldworkers. Overall, 21.7 errors (95% confidence interval: 21.4, 22.0) per 10,000 data points were found: 13.0 (95% confidence interval: 12.6, 13.5) and 24.5 (95% confidence interval: 24.1, 24.9) errors on numeric and text fields respectively. These values meet standard quality threshold of 50 errors per 10,000 data points. The EDC’s total variable cost was estimated at US$13,791.82 per site.
In conclusion, the EDC is robust, allowing for timely and high-volume accurate data collection, and could be adopted in similar epidemiological settings.
Currently, ontologies have become the main means of formalizing and systematizing knowledge and data in scientific subject domains (SSDs). In this regard, there is an urgent need for the methods and ...software tools allowing to involve specialists from different scientific subject domains in the process of ontology building. A possible way to solve this problem is to use ontology design patterns (ODPs). The paper presents an approach to the development of a system supporting the automated construction of the SSD ontologies based on ontology design patterns, which are the formal descriptions of field-proven solutions to typical ontological modeling problems. The main components of this system are repositories of heterogeneous ODPs and basic ontologies, including concepts common to most SSDs, and editors of patterns and ontologies used to build and populate ontologies.
The report addresses the application of ADSkit approach and related software tool for creating agent-based models describing the technical state dynamics of unique mechanical systems (UMS)s. UMSs are ...manufactured in very few copies and furthermore the conditions of their exploitation can significantly diverse from each other. Also as a part of complex technical systems, UMS implements extreme technological operations. The step by step description of the ABSM development process for UMS is considered in the paper. In particular, the UMS ontology acts as a main source for model entities interpretation whereas their behavior mostly described in a rule-based or workflow manner. The testing simulations are carried out based on the ADSkit functionality related to the computational experiment management tool.
Spatial navigation is a universal behavior that varies depending on goals, experience and available sensory stimuli. Spatial navigational tasks are routinely used to study learning, memory and ...goal-directed behavior, in both animals and humans. One popular paradigm for testing spatial memory is the Morris water maze, where subjects learn the location of a hidden platform that offers escape from a pool of water. Researchers typically express learning as a function of the latency to escape, though this reveals little about the underlying navigational strategies. Recently, a number of studies have begun to classify water maze search strategies in order to clarify the precise spatial and mnemonic functions of different brain regions, and to identify which aspects of spatial memory are disrupted in disease models. However, despite their usefulness, strategy analyses have not been widely adopted due to the lack of software to automate analyses. To address this need we developed Pathfinder, an open source application for analyzing spatial navigation behaviors. In a representative dataset, we show that Pathfinder effectively characterizes the development of highly-specific spatial search strategies as male and female mice learn a standard spatial water maze. Pathfinder can read data files from commercially- and freely-available software packages, is optimized for classifying search strategies in water maze paradigms, and can also be used to analyze 2D navigation by other species, and in other tasks, as long as timestamped xy coordinates are available. Pathfinder is simple to use, can automatically determine pool and platform geometry, generates heat maps, analyzes navigation with respect to multiple goal locations, and can be updated to accommodate future developments in spatial behavioral analyses. Given these features, Pathfinder may be a useful tool for studying how navigational strategies are regulated by the environment, depend on specific neural circuits, and are altered by pathology.
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