Scientific Computing and Data Management

FAIRSCAPE provides a framework for creating FAIR and reproducible biomedical analytics by generating machine-interpretable provenance metadata for computational results.

The paper introduces Galaxy-ML, a web-based platform for reproducible and scalable supervised machine learning in biomedicine, extending the Galaxy computational workbench.

Easyreporting simplifies implementing reproducible research layers in R software by enabling report creation without R Markdown knowledge and automatic tracking of analysis steps.

runBioSimulations provides a web platform to execute diverse computational models, enabling easier access to simulation tools and promoting reproducibility in modeling.

GGD provides a fast, reproducible way to install standardized data recipes for genomics research, addressing challenges in data collection, transformation, and integration.

The paper introduces the HASTE Toolkit, a cloud-native toolkit for intelligent data pipelines that prioritize resource usage based on data content, demonstrating it in microscopy imaging case studies.

The paper evaluates workflow management systems for a bioinformatics project using rapid prototyping and selects Nextflow for its workflow.

The paper introduces the BioContainers Registry and API to improve the findability, accessibility, interoperability, and reusability of bioinformatics tools and containers.

The paper investigates reproducibility of systems biology models, finding that 49% of 455 models could not be reproduced due to missing data or inconsistencies.

SIMON is an open-source platform that enables biomedical researchers to apply machine learning algorithms to high-dimensional data without requiring advanced programming skills.

The paper provides strategies for using workflow systems to streamline biological data analysis, emphasizing reproducibility and scalability in high-throughput sequencing projects.

OpenStats improves speed and scalability for high-throughput phenotypic data analysis, showing significant performance gains in the International Mouse Phenotyping Consortium.

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

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.

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

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

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.

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.

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.