Scientific Computing and Data Management

The Labbing Project: A database management application for neuroimaging research

The Labbing Project presents a web application for neuroimaging data aggregation and preprocessing, designed to simplify data management for researchers with limited programming experience.

MXP: Modular eXpandable framework for building bioinformatics Pipelines

The paper introduces MXP, a framework for building bioinformatics pipelines, and demonstrates its flexibility and utility in GWAS and post-GWAS analysis.

A workflow reproducibility scale for automatic validation of biological interpretation results.

The paper introduces a reproducibility scale to evaluate the reproducibility of biological interpretation results from data analysis workflows.

Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows

The paper introduces Yevis, a system that automatically validates and tests workflows to improve their reusability when shared.

An accessible infrastructure for artificial intelligence using a docker-based Jupyterlab in Galaxy

The paper presents a docker-based Jupyterlab infrastructure in Galaxy for AI development, enabling remote training and management of AI projects with GPU support and version control.

Trecode: a FAIR eco-system for the analysis and archiving of omics data in a combined diagnostic and research setting

Trecode provides a FAIR-compliant platform for managing and analyzing omics data in clinical and research settings, ensuring reproducibility and data reuse.

Dissecting Complexity: The Hidden Impact of Application Parameters on Bioinformatics Research

This paper examines the impact of application parameters on bioinformatics tools and proposes a methodology to systematically explore these parameters across different tools and scientific inquiries.

Snakeobjects: an object-oriented workflow management system

Snakeobjects extends Snakemake to simplify workflow development, improve readability, and maintain portability and scalability.

H3AGWAS : A portable workflow for Genome Wide Association Studies

H3AGWAS provides a scalable and portable workflow for conducting GWAS, enabling pre-association, association testing, and post-association analysis with containerized software.

Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability

This paper meta-analyzes single-cell method benchmarks to identify challenges in extensibility, interoperability, and reproducibility.

saks-nf: A json solution for Nextflow pipeline construction

saks-nf simplifies Nextflow pipeline creation using JSON, enabling non-programmers to build and manage complex workflows without coding.

Microbench: Automated metadata management for systems biology benchmarking and reproducibility in Python

Microbench automates metadata capture for reproducibility in computational systems biology by recording execution details and environment information.

Harmonizing and integrating the NCI Genomic Data Commons through accessible, interactive, and cloud-enabled workflows

The paper converts GDC SOPs into reproducible, containerized workflows to harmonize datasets across repositories and improve data interpretation.

Neuroscience Cloud Analysis As a Service

This paper introduces a cloud-based platform that provides automated, reproducible, and accessible data analysis tools for neuroscience, improving efficiency and reducing infrastructure barriers.

Accelerated and Reproducible Fiji for image processing using GPUs on the cloud

The paper presents a cloud-based Fiji platform with GPU acceleration for image processing, achieving 29x faster execution with reproducible results across AWS and IBM clouds.

Snaq: A Dynamic Snakemake Pipeline for Microbiome data analysis with QIIME2

Snaq automates 16S microbiome data analysis with QIIME2 using a Snakemake pipeline, reducing manual effort and parameter confusion through a single command-line instruction.

NeuroCI: Continuous Integration of Neuroimaging Results Across Software Pipelines and Datasets

NeuroCI evaluates result variability across neuroimaging pipelines and datasets using continuous integration to improve reproducibility.

FAIRsoft - A practical implementation of FAIR principles for research software

The paper proposes FAIRsoft, a framework to assess software quality in Life Sciences research based on FAIR principles, to be implemented in OpenEBench.

PEGR: a flexible management platform for reproducible epigenomic and genomic research

PEGR is a web-based platform that manages epigenomic and genomic research projects, ensuring reproducibility across experimental and computational workflows.

Organizing laboratory information to analyze the reproducibility of experimental workflows

The paper analyzes the reproducibility of experimental workflows by structuring data and applying statistical tests to identify factors affecting variation in plasmid purification and cell culture processes.

Deploying genomics workflows on high performance computing (HPC) platforms: storage, memory, and compute considerations

This paper provides infrastructure recommendations for optimizing genomics workflows on HPC platforms through benchmarking and profiling.

LPMX: A pure rootless composable container system

LPMX is a rootless container system that enables composability and cross-site usability for genome analysis tools.

FAIRly big: A framework for computationally reproducible processing of large-scale data

The paper introduces a framework for reproducible processing of large-scale data that complies with FAIR principles, demonstrating its performance on brain imaging and data sharing datasets.

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software

This paper evaluates factors predicting bioinformatic software accuracy and finds that sustained development, not citations or journal impact, is most indicative of accuracy.

Versioning Biological Cells for Trustworthy Cell Engineering

The paper introduces a version control system for cell engineering that combines cloud-based software with molecular barcoding to enhance transparency and traceability.

STENCIL: A web templating engine for visualizing and sharing life science datasets

STENCIL is a web templating engine that organizes, visualizes, and shares life science datasets, enabling interactive and customizable data dissemination.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.

Expanding the Galaxy's reference data

The paper describes integrating refgenie into Galaxy to manage and share reference datasets, with tools for retrieval and a global repository for easy access.

FaDA: A Shiny web application to accelerate common lab data analyses

FaDA is a web application that enables biologists to perform common lab data analyses with statistical tests and visualizations without bioinformatics expertise.

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

The paper presents a framework for ensuring reproducibility in bio-macromolecular modeling through automated benchmarks and a test server, demonstrating its utility for Rosetta and other tools.