Scientific Computing and Data Management

Bashing irreproducibility with shournal

The paper introduces shournal, a tool that automatically records Linux shell activity to improve reproducibility of computational workflows.

A validation framework for neuroimaging software: the case of population receptive fields

The paper introduces a framework for validating neuroimaging software using ground-truth testing, applied to population receptive field analysis in fMRI data.

Implementation of Genomic Variant Calling: A Novel Approach

The paper proposes a cloud-based genomic variant calling workflow using GATK4 and SPARK for automation and scalability.

Executable Simulation Model of the Liver

The paper introduces an executable simulation model (EXSIMO) to improve reproducibility in computational modeling and applies it to replicate a study on hepatic glucose metabolism.

TraIT, Translational research IT bridging the valley of death in translational medicine

TraIT provides an IT platform for translational research, supporting data management and workflows with training, and has been widely adopted as a demonstrator for Health-RI.

intern: Integrated Toolkit for Extensible and Reproducible Neuroscience

The paper introduces a toolkit called intern to unify computational backends and abstract computer science challenges in neuroscience data analysis.

BioViz Connect: Web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser

BioViz Connect links CyVerse science gateways to the Integrated Genome Browser for interactive genomic visualization and analysis.

Advanced Research Infrastructure for Experimentation in genomicS (ARIES): a lustrum of Galaxy experience

The paper describes the development and growth of the ARIES platform over five years as a Galaxy-based system for genomic and epidemiological data analysis in molecular epidemiology.

DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

DolphinNext provides a graphical interface for creating, deploying, and executing Nextflow pipelines to improve reproducibility and portability in genomic data analysis.

Bio-Node - Bioinformatics in the Cloud

Bio-Node is a cloud-based platform for bioinformatics analysis that improves performance, cost, and reproducibility of workflows through automated clustering and metagenome annotation.

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

The paper describes the development of a cloud-based platform for managing, analyzing, and distributing MaizeCODE data, enhancing reproducibility and accessibility.

figureComposer: A web-based interactive multi-panel bio- infographic designing tool

figureComposer is a web-based tool that allows users to create multi-panel publication-quality figures without programming skills.

BioTracs: A transversal framework for computational workflow standardization and traceability

BioTracs provides a framework for standardizing and tracing computational workflows in bioinformatics, implemented in MATLAB and available on GitHub.

Chloe: Flexible, Efficient Data Provenance and Management

Chloe is a flexible, modular system for managing data provenance and reducing manual effort in experiments across various fields.

Galaxy External Display Applications: Closing a dataflow interoperability loop

The paper introduces GEDA, a framework enabling interoperability between Galaxy user data and external resources by accepting URLs pointing to user data.

Bioinformatics Pipeline using JUDI: Just Do It

The paper introduces JUDI, a bioinformatics pipeline framework that reduces scripting effort for parameterized workflows by leveraging DBMS principles, demonstrating a fivefold reduction in scripting for HT-SELEX data analysis.

Bio-DIA: A web-based tool for data and algorithms integration

Bio-DIA is a web-based tool that integrates data and algorithms for data science workflows, enabling collaboration and reusability without requiring specific computer science skills.

Arteria: An automation system for a sequencing core facility

Arteria provides an automation system for sequencing core facilities using modular, open-source micro-services.

uap: Reproducible and Robust HTS Data Analysis

The paper introduces uap, a workflow management system for reproducible and robust HTS data analysis, addressing reproducibility challenges in complex bioinformatic pipelines.

Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines.

The paper introduces a scalable approach for reproducible proteomics and metabolomics analysis using BioContainers and workflows engines like Galaxy and Nextflow.

Building containerized workflows using the BioDepot-workflow-builder (Bwb)

The paper introduces Bwb, a tool for creating and executing reproducible bioinformatics workflows via a drag-and-drop interface using Docker containers.

Creating reproducible pharmacogenomic analysis pipelines

The paper develops reproducible pharmacogenomic analysis pipelines using Common Workflow Language to process breast cancer datasets and share them with a Digital Object Identifier.

Shared Data Science Infrastructure for Genomics Data

The paper introduces BoaG, a data science infrastructure for genomic research, demonstrating its ability to efficiently explore RefSeq data and reveal species-specific assembly quality variations.

Query Combinators: Domain Specific Query Languages for Medical Research

The paper introduces Query Combinators, a framework for creating domain-specific query languages to facilitate data processing and analysis in medical research.

Bioshake: a Haskell EDSL for bioinformatics pipelines

Bioshake is a Haskell EDSL for bioinformatics pipelines that enables static error checking and robust execution through type-level properties and integration with Shake.

Managing genomic variant calling workflows with Swift/T

The paper describes a Swift/T wrapper for the GATK variant calling workflow to improve portability and maintainability across cluster environments.

CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language

CWL-Airflow extends Apache Airflow to support Common Workflow Language, enabling portable and reproducible computational workflows across various environments.

xml2jupyter: Mapping parameters between XML and Jupyter widgets

xml2jupyter maps XML configuration files to Jupyter widgets, enabling interactive simulation parameter tuning.

Pipeliner: A Nextflow-based framework for the definition of sequencing data processing pipelines

Pipeliner provides a Nextflow-based framework for creating flexible and reproducible sequencing data processing pipelines, supporting bulk RNA-seq, scRNA-seq, and DGE data.

A comprehensive framework to capture the arcana of neuroimaging analysis

This paper introduces Arcana, a framework for creating adaptable neuroimaging workflows that can be reused across different computing environments and data sources.