The BioExtract Server: a web-based bioinformatic workflow platform

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet

BBMS + + – basic bioinformatics meta-searcher

In this paper we present a Basic Bioinformatics Meta-searcher (BBMS), a web-based service aiming to simplify and integrate biological data searching through selected biological databases. BBMS facilitates biological data searching enabling multiple sources transparently, increasing research productivity as it avoids time consuming learning and parameterization of different search engines. As a complementary service, BBMS provides insight and links to common online bioinformatics tools. Users’ feedback when evaluating BBMS in terms of usability, usefulness and efficiency was very positive

PlantGDB: a resource for comparative plant genomics

PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies. Annotation is facilitated by the integrated yrGATE module for community curation of gene models. Novel web services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-based server for executing custom sequence analysis workflows. PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time—sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn's utility are provided herein

Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations

In this paper we introduce Armadillo v1.1, a novel workflow platform dedicated to designing and conducting phylogenetic studies, including comprehensive simulations. A number of important phylogenetic and general bioinformatics tools have been included in the first software release. As Armadillo is an open-source project, it allows scientists to develop their own modules as well as to integrate existing computer applications. Using our workflow platform, different complex phylogenetic tasks can be modeled and presented in a single workflow without any prior knowledge of programming techniques. The first version of Armadillo was successfully used by professors of bioinformatics at Université du Quebec à Montreal during graduate computational biology courses taught in 2010–11. The program and its source code are freely available at: <http://www.bioinfo.uqam.ca/armadillo>

A genome-wide association study platform built on iPlant cyber-infrastructure

We demonstrate a flexible genome-wide association study platform built upon the iPlant Collaborative Cyber-infrastructure. The platform supports big data management, sharing, and large-scale study of both genotype and phenotype data on clusters. End users can add their own analysis tools and create customized analysis workflows through the graphical user interfaces in both iPlant Discovery Environment and BioExtract server

EEG interpretation reliability and interpreter confidence: a large single-center study

The intrarater and interrater reliability (I&IR) of EEG interpretation has significant implications for the value of EEG as a diagnostic tool. We measured both I&IR of EEG interpretation based on interpretation of complete EEGs into standard diagnostic categories and rater confidence in their interpretations, and investigated sources of variance in EEG interpretations. During two distinct time intervals six board-certified clinical neurophysiologists classified 300 EEGs into one or more of seven diagnostic categories, and assigned a subjective confidence to their interpretations. Each EEG was read by three readers. Each reader interpreted 150 unique studies, and 50 studies twice to generate intrarater data. A generalizability study assessed the contribution of subjects, readers, and the interaction between subjects and readers to interpretation variance. Five of the six readers had a median confidence of ≥ 99%, and the upper quartile of confidence values was 100% for all six readers. Intrarater Cohen’s kappa (κ(c)) ranged from 0.33 to 0.73 with an aggregated value of 0.59. κ(c) ranged from 0.29 to 0.62 for the 15 reader pairs, with an aggregated Fleiss kappa of 0.44 for interrater agreement. The κ(c) were not significantly different across rater pairs (Chi-Square = 17.3, df=14, p = 0.24). Variance due to subjects (i.e. EEGs) was 65.3%, to readers was 3.9%, and to the interaction between readers and subjects was 30.8%. Experienced epileptologists have very high confidence in their EEG interpretations and low to moderate I&IR, a common paradox in clinical medicine. A necessary but insufficient condition to improve EEG interpretation accuracy is to increase intrarater and interrater reliability. This goal could be accomplished, for instance, with an automated on-line application integrated into a continuing medical education module that measures and reports EEG I&IR to individual users

Applying the CiPA approach to evaluate cardiac proarrhythmia risk of some antimalarials used off‐label in the first wave of COVID‐19

We applied a set of in silico and in vitro assays, compliant with the CiPA (Comprehensive In Vitro Proarrhythmia Assay) paradigm, to assess the risk of chloroquine or hydroxychloroquine‐mediated QT prolongation and Torsades de Pointes (TdP), alone and combined with erythromycin and azithromycin, drugs repurposed during the first wave of COVID‐19. Each drug or drug combination was tested in patch clamp assays on 7 cardiac ion channels, in in silico models of human ventricular electrophysiology (Virtual Assay®) using control (healthy) or high‐risk cell populations, and in human induced pluripotent stem cell (hiPSC)‐derived cardiomyocytes. In each assay, concentration‐response curves encompassing and exceeding therapeutic free plasma levels were generated. Both chloroquine and hydroxychloroquine showed blocking activity against some potassium, sodium and calcium currents. Chloroquine and hydroxychloroquine inhibited IKr (IC50: 1µM and 3‐7µM, respectively) and IK1 currents (IC50: 5 and 44µM, respectively). When combining hydroxychloroquine with azithromycin, no synergistic effects were observed. The two macrolides had no or very weak effects on the ion currents (IC50>300‐1000µM). Using Virtual Assay®, both antimalarials affected several TdP indicators, chloroquine being more potent than hydroxychloroquine. Effects were more pronounced in the high‐risk cell population. In hiPSC‐derived cardiomyocytes, all drugs showed early‐after‐depolarizations, except azithromycin. Combining chloroquine or hydroxychloroquine with a macrolide did not aggravate their effects. In conclusion, our integrated nonclinical CiPA dataset confirmed that, at therapeutic plasma concentrations relevant for malaria or off‐label use in COVID‐19, chloroquine and hydroxychloroquine use is associated with a proarrhythmia risk, which is higher in populations carrying predisposing factors but not worsened with macrolide combination