Scientific Computing and Data Management

Bio-medical Big Data Operating System (Bio-OS): An Integrated Data Mining Environment for Data Intensive Scientific Research

BioOS provides a cloud-native platform for reproducible biomedical research by integrating data, code, tools, and environments into workspaces, enhancing data integrity and accessibility.

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.

scGNN+: Adapting ChatGPT for Seamless Tutorial and Code Optimization

scGNN+ integrates ChatGPT with graph neural networks to improve code optimization, tutorial generation, and visualization in single-cell research.

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.

BMAP: a comprehensive and reproducible biomedical data analysis platform

BMAP provides a platform for managing and analyzing biomedical data, improving reproducibility and efficiency in research workflows.

Maloja: simple and scalable Snakemake workflow orchestration in the cloud

Maloja simplifies cloud deployment of Snakemake workflows by automatically scaling AWS resources, tested on ecological genomics tasks.

Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows from a Network of Microservices

The paper introduces a web-based platform for building bioinformatics workflows using APIs, enabling hypothesis generation across multiple data sources.

Improving the Reliability and Quality of Nextflow Pipelines with nf-test

The paper introduces nf-test, a testing framework for Nextflow pipelines that improves reliability, reduces test time, and enhances software quality through modular and efficient testing.

BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow

This paper introduces BIA, an intelligent agent using LLMs to automate bioinformatics tasks, demonstrating its effectiveness with scRNA-seq data and outlining strategies for improvement.

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.

Replicating a High-Impact Scientific Publication Using Systems of Large Language Models

This study attempts to reproduce a high-impact publication using a multi-agent system of LLMs, highlighting both capabilities and challenges in automating scientific research.

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.

Spyglass: a framework for reproducible and shareable neuroscience research

Spyglass provides a reproducible and shareable framework for neuroscience research, enabling data reuse and analysis across labs using standardized formats and pipelines.

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.

Enabling AI in Synthetic Biology through Construction File Specification

This paper introduces a standardized Construction File specification for synthetic biology, enabling AI integration to automate experiment design and reduce errors.

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

ILIAD automates genomic data processing into VCF files for downstream applications using Snakemake, Singularity, and Docker, improving efficiency and reproducibility.

BioMANIA: Simplifying bioinformatics data analysis through conversation

BioMANIA provides a codeless, AI-driven bioinformatics pipeline that simplifies omics data analysis by interpreting natural language instructions and integrating existing tools.

Flow: a web platform and open database to analyse, store, curate and share bioinformatics data at scale

Flow provides a web platform and database for managing and analyzing large-scale bioinformatics data, addressing challenges in data processing, quality, and accessibility.

Building an Open Representation for Biological Protocols

The paper introduces PAML, an open protocol representation language for biological protocols, enabling precise interpretation, automation, and reuse across different contexts.

A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object

The paper develops a multi-omics data analysis workflow packaged as a FAIR Digital Object to improve reproducibility and reuse in computational research.

BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse

This paper introduces a protocol to create a FAIR collection of machine learning models in life sciences and medicine, aiming to improve reproducibility and reuse through community curation.

QuNex -- An Integrative Platform forReproducible Neuroimaging Analytics

QuNex provides a platform for reproducible neuroimaging analytics, integrating multi-modal tools and enabling scalable, high-throughput processing across species and datasets.

The ENCODE Uniform Analysis Pipelines

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

Planemo is a command-line toolkit for developing, deploying, and executing Galaxy tools and workflows, promoting best practices in scientific data analysis.

Minuteman - A versatile cloud computational platform for collaborative research

Minuteman provides a secure cloud platform for collaborative biomedical data analysis with features for data management, access control, and interactive exploration.