Scientific Computing and Data Management

ZARP: An automated workflow for processing of RNA-seq data

ZARP is an RNA-seq analysis workflow that automates data processing using Snakemake, reducing hands-on time for users by integrating best practices and generating detailed reports.

Design considerations for workflow management systems use in production genomics research and the clinic

This paper evaluates workflow management systems for genomics research and clinical use, comparing their features and suitability across different environments and use cases.

Cloud-enabled Fiji for reproducible, integrated and modular image processing

The paper introduces a cloud-enabled platform for reproducible and modular image processing workflows that integrates interactive graphics with software containers.

BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment

The paper presents BioCompute Objects (BCOs) as a standardized framework for communicating computational analyses, demonstrating their use in a viral detection pipeline for regulatory environments.

Simplifying the development of portable, scalable, and reproducible workflows

The paper introduces ToolJig, a web application that simplifies creating and validating Common Workflow Language (CWL) documents for reproducible bioinformatics workflows.

Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses

Eoulsan 2 updates a workflow manager to support bulk, long-read, and single-cell transcriptomics analyses with improved infrastructure and module development.

Data Representation in the DARPA SD2 Program

The paper describes challenges in scientific collaboration and presents a flexible data-sharing model to improve information flow and experimentation in multidisciplinary research.

Relating simulation studies by provenance--Developing a family of Wnt signaling models

The paper develops a provenance ontology for simulation models of Wnt signaling and applies it to 19 models, showing how they are related through shared entities and activities.

Reproducibility and reusability limitations in Regulatory Circuits: analysis and solutions

The paper analyzes reproducibility issues in the Regulatory Circuits project and proposes solutions for improving reusability and reproducibility of its data integration pipeline.

COPILOT: a Containerised wOrkflow for Processing ILlumina genOtyping daTa

COPILOT automates GWAS quality control for Illumina genotyping data, improving sample call rates and identifying data issues across two cohorts.

Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node

This paper demonstrates how software engineering techniques improve reproducibility of a mathematical model of the atrioventricular node by implementing automated testing, version control, and modular design.

FAIRSCAPE: A Framework for FAIR and Reproducible Biomedical Analytics

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

Accessible, Reproducible, and Scalable Machine Learning for Biomedicine

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 the implementation of Reproducible Research Layers in R software

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

runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

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

Enabling the execution of large scale workflows for molecular dynamics simulations

The paper presents a workflow management system to enable complex molecular dynamics simulations across different computational platforms and large-scale supercomputing infrastructures.

Go Get Data (GGD): simple, reproducible access to scientific data

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

DataJoint Elements: Data Workflows for Neurophysiology

The paper introduces DataJoint Elements, a resource providing modular workflow designs for organizing data and computations in neurophysiology experiments.

Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit

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.

Using rapid prototyping to choose a bioinformatics workflow management system

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

BioContainers Registry: searching for bioinformatics tools, packages and containers

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

Linking Labs: Interconnecting Experimental Environments

The paper introduces LabLinking, a framework for connecting experimental labs across different institutions and disciplines to enable borderless experimentation.

Reproducibility in systems biology modelling

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

Evidence Graphs: Supporting Transparent and FAIR Computation, with Defeasible Reasoning on Data, Methods and Results

SIMON: open-source knowledge discovery platform

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

Streamlining Data-Intensive Biology With Workflow Systems

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

OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput Phenotypic Data

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

Adding software to package management systems can increase their citation by 280%

This study shows that publishing software in package management systems increases its cited scholarly papers by 280%.

Strengthening the BioCompute Standard by Crowdsourcing on PrecisionFDA

The paper describes a crowdsourced challenge on precisionFDA to improve the BioCompute standard by gathering feedback and demonstrating BCO creation tools.

SoftWipe - a tool and benchmark to assess scientific software quality

SoftWipe ranks 51 computational tools across research areas to assess scientific software quality, aiding in software selection and review processes.