Scientific Computing and Data Management

Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data

The paper introduces the Microbiology Galaxy Lab, a community-driven platform for reproducible and FAIR microbial data analysis, offering tools for various omics data types and use cases.

BenchHub enables an inclusive and transparent ecosystem for community-focused benchmarking in computational biology

BenchHub provides a modular ecosystem for community-focused benchmarking in computational biology by linking datasets, metrics, and ground truth to improve reproducibility and sustainability.

A metadata managed FAIR end-to-end workflow for microbial community Omics data analysis

The paper presents a metadata-managed FAIR end-to-end workflow for microbial community Omics data analysis, demonstrating its reliability and reproducibility through mock datasets.

BioMaster: Multi-agent System for Automated Bioinformatics Analysis Workflow

BioMaster automates complex bioinformatics workflows using a multi-agent system, improving accuracy, efficiency, and scalability across tasks like RNA-seq and Hi-C processing.

Multiscale Cloud-based Pipeline for Neuronal Electrophysiology Analysis and Visualization

The paper presents a cloud-based pipeline for analyzing and visualizing neuronal electrophysiology data from HD-MEAs, demonstrating its utility in simplifying data analysis and understanding neural activity.

MOAflow: how re-design a pipeline with Nextflow streamlines data analysis

The paper redesigns an existing MOA-seq analysis pipeline using Nextflow to improve scalability and efficiency, resulting in a containerized and reproducible workflow.

CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts

CBIcall provides a configuration-driven framework for standardized variant calling across large sequencing cohorts, ensuring reproducibility and consistency in pipeline execution.

QuNex Recipes: Executable, Human-Readable Workflows for Reproducible Neuroimaging Research

QuNex Recipes provide a framework for creating executable, human-readable workflows to ensure reproducibility in neuroimaging research.

Verification and reproducible curation of the BioModels repository

The paper updates and corrects SED-ML files for 1055 models in BioModels to improve reproducibility and verification across simulation engines.

CloneCoordinate: Open-source software for collaborative DNA construction

CloneCoordinate is an open-source electronic lab notebook for DNA cloning that improves collaboration and efficiency through task management and data standardization.

Distributed Collaboration for Data, Analysis Pipelines, and Results in Single-Cell Omics

The paper introduces a web platform for no-code single-cell omics analysis pipelines, enabling sharing of data, pipelines, and results to improve accessibility and reproducibility.

Empowering bioinformatics communities with Nextflow and nf-core

This paper discusses the adoption of Nextflow and nf-core frameworks to standardize bioinformatics pipelines, improving collaboration and interoperability across research communities.

SIMPROV : Provenance capturing for simulation studies

SIMPROV captures comprehensive provenance for simulation studies by integrating data from multiple software tools into a coherent graph.

Leveraging large language models for data analysis automation

This paper introduces mergen, an R package using LLMs to automate data analysis by generating and executing code based on user descriptions, showing promise but highlighting challenges in complex tasks.

OT-Mation: an open-source code for parsing CSV files into python scripts for control of OT-2 liquid handling robotics

OT-Mation converts CSV files into Python scripts to control OT-2 liquid handling robots, enabling efficient and reproducible experimental setups.

Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis

The paper introduces g2nb, a notebook environment integrating bioinformatics platforms into a unified interface for genomics analysis.

Software System Design to Support Scale in Mammalian Cell Line Engineering.

The paper describes the development of software systems and automation to increase the throughput of mammalian cell line engineering workflows by threefold.

VueGen: Automating the generation of scientific reports

VueGen automates report generation from bioinformatics outputs, enabling non-experts to create reports with minimal coding experience.

cOmicsArt - a customizable Omics Analysis and reporting tool

cOmicsArt provides a customizable tool for omics analysis and reporting, integrating GUI-based analysis with R for reproducibility and customization.

Curating models from BioModels: Developing a workflow for creating OMEX files

The paper curates 50 BioModels by reproducing results with Tellurium and creating OMEX files for reproducibility.

An AI Agent for Fully Automated Multi-omic Analyses

AutoBA is an AI agent that automates multi-omic analyses using large language models, offering adaptability and security across various sequencing and omics data types.

EMhub: a web platform for data management and on-the-fly processing in scientific facilities

EMhub is a web platform for managing scientific facility operations and data processing, with applications in CryoEM and other centers.

Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story

The paper demonstrates the use of Haxe for rewriting a bioinformatics tool, SeqPHASE, to improve security and maintainability.

BTR: A Bioinformatics Tool Recommendation System

BTR is a deep learning model that recommends bioinformatics tools based on workflow context and tool descriptions, outperforming existing systems.

Nextflow vs. plain Bash: Different Approaches to the Parallelisation of SNP Calling from the Whole Genome Sequence Data

This paper compares SNP calling workflow parallelisation using plain Bash and Nextflow, finding that multi-process Nextflow is faster but uses more RAM and disk space.

Reducing the efforts to create reproducible analysis code with FieldTrip

This paper introduces a strategy to automate the creation of standardized MATLAB scripts for EEG/MEG analysis using the FieldTrip toolbox, improving reproducibility with minimal user effort.

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Neurodesk provides a portable and reproducible neuroimaging analysis platform using software containers to enable accessible and flexible data analysis pipelines.

Performing highly parallelized and reproducible GWAS analysis on biobank-scale data

The paper presents a Nextflow pipeline for scalable and reproducible GWAS analysis on large biobank datasets, validated against published datasets and tested on HPC and cloud infrastructures.

A reproducible and generalizable software workflow for analysis of large-scale neuroimaging data collections using BIDS Apps

The paper introduces BABS, a Python package for reproducible and scalable neuroimaging data processing using BIDS Apps and HPC systems.

OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data.

The paper introduces ORCA, an open-source Shiny application for semi-automated analysis of cellular biology experiments, promoting reproducibility and open science practices.