Scientific Computing and Data Management

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

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

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

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 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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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