scholarly journals CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis

2021 ◽  
Author(s):  
Xintao Qiu ◽  
Avery S. Feit ◽  
Ariel Feiglin ◽  
Yingtian Xie ◽  
Nikolas Kesten ◽  
...  
Keyword(s):  
Bioinformatics Workflow

scholarly journals Identification of candidate repurposable drugs to combat COVID-19 using a signature-based approach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sinead M. O’Donovan ◽  
Ali Imami ◽  
Hunter Eby ◽  
Nicholas D. Henkel ◽  
Justin Fortune Creeden ◽  
...  
Keyword(s):  
Infected Cell ◽  
Mek Inhibitor ◽  
Therapeutic Agents ◽  
The Novel ◽  
Integrated Network ◽  
Candidate Drug ◽  
Novel Targets ◽  
Additional Support ◽  
Bioinformatics Workflow

AbstractThe COVID-19 pandemic caused by the novel SARS-CoV-2 is more contagious than other coronaviruses and has higher rates of mortality than influenza. Identification of effective therapeutics is a crucial tool to treat those infected with SARS-CoV-2 and limit the spread of this novel disease globally. We deployed a bioinformatics workflow to identify candidate drugs for the treatment of COVID-19. Using an “omics” repository, the Library of Integrated Network-Based Cellular Signatures (LINCS), we simultaneously probed transcriptomic signatures of putative COVID-19 drugs and publicly available SARS-CoV-2 infected cell lines to identify novel therapeutics. We identified a shortlist of 20 candidate drugs: 8 are already under trial for the treatment of COVID-19, the remaining 12 have antiviral properties and 6 have antiviral efficacy against coronaviruses specifically, in vitro. All candidate drugs are either FDA approved or are under investigation. Our candidate drug findings are discordant with (i.e., reverse) SARS-CoV-2 transcriptome signatures generated in vitro, and a subset are also identified in transcriptome signatures generated from COVID-19 patient samples, like the MEK inhibitor selumetinib. Overall, our findings provide additional support for drugs that are already being explored as therapeutic agents for the treatment of COVID-19 and identify promising novel targets that are worthy of further investigation.

scholarly journals aCLImatise: automated generation of tool definitions for bioinformatics workflows

2020 ◽  
Author(s):  
Michael Milton ◽  
Natalie Thorne
Keyword(s):  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Supplementary Data ◽  
Automated Generation ◽  
Base Camp ◽  
Python Package ◽  
Bioinformatics Workflow ◽  
Bioinformatics Workflows

Abstract Summary aCLImatise is a utility for automatically generating tool definitions compatible with bioinformatics workflow languages, by parsing command-line help output. aCLImatise also has an associated database called the aCLImatise Base Camp, which provides thousands of pre-computed tool definitions. Availability and implementation The latest aCLImatise source code is available within a GitHub organisation, under the GPL-3.0 license: https://github.com/aCLImatise. In particular, documentation for the aCLImatise Python package is available at https://aclimatise.github.io/CliHelpParser/, and the aCLImatise Base Camp is available at https://aclimatise.github.io/BaseCamp/. Supplementary information Supplementary data are available at Bioinformatics online.

Abstract 830: New bioinformatics workflow of genome-wide CRISPR-Cas9 knockout screens

2020 ◽  
Author(s):  
Yue Zhao ◽  
Xue Wu ◽  
Yuru Wang ◽  
Kin Fai Au ◽  
Lijun Cheng ◽  
...  
Keyword(s):  
Genome Wide ◽  
Bioinformatics Workflow

scholarly journals Snakemake--a scalable bioinformatics workflow engine

2012 ◽  
Vol 28 (19) ◽  
pp. 2520-2522 ◽  
Author(s):  
J. Koster ◽  
S. Rahmann
Keyword(s):  
Workflow Engine ◽  
Bioinformatics Workflow

scholarly journals Flexible selection of heterogeneous and unreliable services in large-scale grids

2009 ◽  
Vol 367 (1897) ◽  
pp. 2483-2494 ◽  
Author(s):  
Sebastian Stein ◽  
Terry R. Payne ◽  
Nicholas R. Jennings
Keyword(s):  
Real World ◽  
Large Scale ◽  
Service Providers ◽  
Service Selection ◽  
Third Party ◽  
Distributed Services ◽  
On Demand ◽  
Bioinformatics Workflow ◽  
Selection Of

As grids become larger and more interconnected in nature, scientists can benefit from a growing number of distributed services that may be invoked on demand to complete complex computational workflows. However, it also means that these scientists become dependent on the cooperation of third-party service providers, whose behaviour may be uncertain, failure prone and highly heterogeneous. To address this, we have developed a novel decision-theoretic algorithm that automatically selects appropriate services for the tasks of an abstract workflow and deals with failures through redundancy and dynamic re-invocation of functionally equivalent services. In this paper, we summarize our approach, describe in detail how it can be applied to a real-world bioinformatics workflow and show that it offers a significant improvement over current service selection techniques.

Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow

2017 ◽  
Author(s):  
Dongliang Yu ◽  
Zhonghai Tang ◽  
Chaogang Shao ◽  
Xiaoxia Ma ◽  
Taihe Xiang ◽  
...  
Keyword(s):  
Bioinformatics Workflow

scholarly journals Deciphering Molecular Cascades in a Novel Acclimatization Strategy for Rapid Ascent to High Altitude

2017 ◽  
Author(s):  
Subhojit Paul ◽  
Anamika Gangwar ◽  
Kalpana Bhargava ◽  
Yasmin Ahmad
Keyword(s):  
High Altitude ◽  
Plasma Proteins ◽  
Redox Homeostasis ◽  
Redox Stress ◽  
Rapid Induction ◽  
Extreme Altitude ◽  
Two Factors ◽  
Rapid Ascent ◽  
Very High ◽  
Bioinformatics Workflow

ABSTRACTThe repercussions of hypobaric hypoxia are dependent upon two factors-time and intensity of exposure. The effects of intensity i.e. variation of altitude are yet unknown although it is a significant factor in terms of acclimatization protocols. In this study we present the effects of acute (24 h) exposure to high (10,000 ft), very high (15,000 ft) and extreme altitude (25,000 ft) zones on lung and plasma using semi-quantitative redox specific transcripts and quantitative proteo-bioinformatics workflow in conjunction with redox stress assays. Our findings indicate that very high altitude exposure elicits systemic redox homeostatic processes due to failure of lung redox homeostasis without causing mortality. We also document a rapid acclimatization protocol causing a shift from 0 to 100% survival at 25,000 ft in male SD rats upon rapid induction. Finally we posit the various processes involved and the plasma proteins that can be used to ascertain the acclimatization status of an individual.

scholarly journals Architecting a distributed bioinformatics platform with iRODS and iPlant Agave API

2015 ◽  
Author(s):  
Liya Wang ◽  
Peter Van Buren ◽  
Doreen Ware
Keyword(s):  
Large Scale ◽  
Genome Wide Association Study ◽  
Data Transfer ◽  
Genomic Analysis ◽  
The Past ◽  
Large Scale Data ◽  
Genome Wide ◽  
A Genome ◽  
Bioinformatics Workflow ◽  
Scale Data

Over the past few years, cloud-based platforms have been proposed to address storage, management, and computation of large-scale data, especially in the field of genomics. However, for collaboration efforts involving multiple institutes, data transfer and management, interoperability and standardization among different platforms have imposed new challenges. This paper proposes a distributed bioinformatics platform that can leverage local clusters with remote computational clusters for genomic analysis using the unified bioinformatics workflow. The platform is built with a data server configured with iRODS, a computation cluster authenticated with iPlant Agave system, and web server to interact with the platform. A Genome-Wide Association Study workflow is integrated to validate the feasibility of the proposed approach.

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