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1. Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets

   https://doi.org/10.1186/s12864-021-07791-z  

   Koonchanok, Ratanond ; Daulatabad, Swapna Vidhur ; Mir, Quoseena ; Reda, Khairi ; Janga, Sarath Chandra ( July 2021 , BMC Genomics)

   Direct-sequencing technologies, such as Oxford Nanopore’s, are delivering long RNA reads with great efficacy and convenience. These technologies afford an ability to detect post-transcriptional modifications at a single-molecule resolution, promising new insights into the functional roles of RNA. However, realizing this potential requires new tools to analyze and explore this type of data.

   Here, we present Sequoia, a visual analytics tool that allows users to interactively explore nanopore sequences. Sequoia combines a Python-based backend with a multi-view visualization interface, enabling users to import raw nanopore sequencing data in a Fast5 format, cluster sequences based on electric-current similarities, and drill-down onto signals to identify properties of interest. We demonstrate the application of Sequoia by generating and analyzing ~ 500k reads from direct RNA sequencing data of human HeLa cell line. We focus on comparing signal features from m6A and m5C RNA modifications as the first step towards building automated classifiers. We show how, through iterative visual exploration and tuning of dimensionality reduction parameters, we can separate modified RNA sequences from their unmodified counterparts. We also document new, qualitative signal signatures that characterize these modifications from otherwise normal RNA bases, which we were able to discover from the visualization.

   Sequoia’s interactive features complement existing computational approaches in nanopore-based RNA workflows. The insights gleaned through visual analysis should help users in developing rationales, hypotheses, and insights into the dynamic nature of RNA. Sequoia is available athttps://github.com/dnonatar/Sequoia.

    

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2. Cosmic-CoNN: A Cosmic-Ray Detection Deep-learning Framework, Data Set, and Toolkit

   https://doi.org/10.3847/1538-4357/ac9d91  

   Xu 许, Chengyuan 程远 ; McCully, Curtis ; Dong 董, Boning 泊宁 ; Howell, D. Andrew ; Sen, Pradeep ( January 2023 , The Astrophysical Journal)

   Rejecting cosmic rays (CRs) is essential for the scientific interpretation of CCD-captured data, but detecting CRs in single-exposure images has remained challenging. Conventional CR detectors require experimental parameter tuning for different instruments, and recent deep-learning methods only produce instrument-specific models that suffer from performance loss on telescopes not included in the training data. We present Cosmic-CoNN, a generic CR detector deployed for 24 telescopes at the Las Cumbres Observatory, which has been made possible by the three contributions in this work: (1) We build a large and diverse ground-based CR data set leveraging thousands of images from a global telescope network. (2) We propose a novel loss function and a neural network optimized for telescope imaging data to train generic CR-detection models. At 95% recall, our model achieves a precision of 93.70% on Las Cumbres imaging data and maintains a consistent performance on new ground-based instruments never used for training. Specifically, the Cosmic-CoNN model trained on the Las Cumbres CR data set maintains high precisions of 92.03% and 96.69% on Gemini GMOS-N/S 1 × 1 and 2 × 2 binning images, respectively. (3) We build a suite of tools including an interactive CR mask visualization and editing interface, console commands, and Python APIs to make automatic, robust CR detection widely accessible by the community of astronomers. Our data set, open-source code base, and trained models are available athttps://github.com/cy-xu/cosmic-conn.

    

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3. BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

   https://doi.org/10.1186/s40168-023-01625-8  

   Pavia, Michael J. ; Chede, Abhinav ; Wu, Zijun ; Cadillo-Quiroz, Hinsby ; Zhu, Qiyun ( August 2023 , Microbiome)

   Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure.

   We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time.

   In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset.

   BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted athttps://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

    

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4. Contact.engineering—Create, analyze and publish digital surface twins from topography measurements across many scales

   https://doi.org/10.1088/2051-672X/ac860a  

   Röttger, Michael C. ; Sanner, Antoine ; Thimons, Luke A. ; Junge, Till ; Gujrati, Abhijeet ; Monti, Joseph M. ; Nöhring, Wolfram G. ; Jacobs, Tevis D. B. ; Pastewka, Lars ( September 2022 , Surface Topography: Metrology and Properties)

   The optimization of surface finish to improve performance, such as adhesion, friction, wear, fatigue life, or interfacial transport, occurs largely through trial and error, despite significant advancements in the relevant science. There are three central challenges that account for this disconnect: (1) the challenge of integration of many different types of measurement for the same surface to capture the multi-scale nature of roughness; (2) the technical complexity of implementing spectral analysis methods, and of applying mechanical or numerical models to describe surface performance; (3) a lack of consistency between researchers and industries in how surfaces are measured, quantified, and communicated. Here we present a freely-available internet-based application (available athttps://contact.engineering) which attempts to overcome all three challenges. First, the application enables the user to upload many different topography measurements taken from a single surface, including using different techniques, and then integrates all of them together to create a digital surface twin. Second, the application calculates many of the commonly used topography metrics, such as root-mean-square parameters, power spectral density (PSD), and autocorrelation function (ACF), as well as implementing analytical and numerical calculations, such as boundary element modeling (BEM) for elastic and plastic deformation. Third, the application serves as a repository for users to securely store surfaces, and if they choose, to share these with collaborators or even publish them (with a digital object identifier) for all to access. The primary goal of this application is to enable researchers and manufacturers to quickly and easily apply cutting-edge tools for the characterization and properties-modeling of real-world surfaces. An additional goal is to advance the use of open-science principles in surface engineering by providing a FAIR database where researchers can choose to publish surface measurements for all to use.

    

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5. VITALSE: visualizing eye tracking and biometric data

   https://doi.org/10.1145/3377812.3382154  

   Roy, Devjeet ; Fakhoury, Sarah ; Arnaoudova, Venera ( June 2020 , ICSE '20: Proceedings of the ACM/IEEE 42nd International Conference on Software Engineering: Companion Proceedings)

   null (Ed.)

   Recent research in empirical software engineering is applying techniques from neurocognitive science and breaking new grounds in the ways that researchers can model and analyze the cognitive processes of developers as they interact with software artifacts. However, given the novelty of this line of research, only one tool exists to help researchers represent and analyze this kind of multi-modal biometric data. While this tool does help with visualizing temporal eyetracking and physiological data, it does not allow for the mapping of physiological data to source code elements, instead projecting information over images of code. One drawback of this is that researchers are still unable to meaningfully combine and map physiological and eye tracking data to source code artifacts. The use of images also bars the support of long or multiple code files, which prevents researchers from analyzing data from experiments conducted in realistic settings. To address these drawbacks, we propose VITALSE, a tool for the interactive visualization of combined multi-modal biometric data for software engineering tasks. VITALSE provides interactive and customizable temporal heatmaps created with synchronized eyetracking and biometric data. The tool supports analysis on multiple files, user defined annotations for points of interest over source code elements, and high level customizable metric summaries for the provided dataset. VITALSE, a video demonstration, and sample data to demonstrate its capabilities can be found at http://www.vitalse.app. 

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