Scientific Computing and Data Management

Execution-aware agent harness for accessible and responsible synthetic biology automation

LabscriptAI translates natural language into robot scripts for synthetic biology, achieving high simulation accuracy and enabling secure, standardized, and traceable lab automation.

Horus: Reproducible Workflow Manager for Biomolecular Modelling

Horus provides a reproducible workflow management system for biomolecular modelling with a graphical interface and Python API, supporting remote execution and molecular visualization.

PRIME: A Multi-Agent Environment for Orchestrating Dynamic Computational Workflows in Protein Engineering

PRIME is a multi-agent system that dynamically synthesizes computational workflows for protein engineering, outperforming existing AI agents in complex tasks.

TAFFISH: shell-native command-level reproducibility for bioinformatics

TAFFISH provides a reproducibility framework for bioinformatics by packaging shell commands as executable units with versioning and validation.

Robust software development practices improve citations of RNA-seq tools

This study shows that better software development practices for RNA-seq tools lead to more citations, as evidenced by a strong statistical association between development quality and citation counts.

User-friendly scheduler Using a hybrid architecture and supercomputing for big data processing

This paper introduces a user-friendly scheduler for big data processing in bioinformatics, reducing cost and time for bulk RNA sequencing workflows using a hybrid architecture and supercomputing.

ChatMDV: Democratising Bioinformatics Analysis Using Large Language Models

ChatMDV provides a natural language interface for generating interactive visualizations of biological data using large language models and the MDV platform.

Enabling reproducible and reusable genetic demultiplexing benchmarking with Nextflow and Apptainer

The paper introduces demux_bench, a reproducible and portable pipeline for benchmarking genetic demultiplexing methods in scRNA-seq using Nextflow and Apptainer.

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.

Styx: A multi-language API Generator for Command-Line Tools

Styx and NiWrap provide language-native wrappers for command-line tools, reducing complexity in pipeline development and enhancing portability across programming languages and environments.

Interactive data analysis and reporting with SCIFR: A Single-File SPA Approach

SCIFR is a single-file interactive reporting framework that improves efficiency and usability compared to existing tools in genomics analysis.

SIMPROV : Provenance capturing for simulation studies

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

PromptBio: A Multi-Agent AI Platform for Bioinformatics Data Analysis

PromptBio introduces a multi-agent AI platform for scalable, reproducible bioinformatics analysis using generative AI and natural language interaction.

Oops: A Language for Formalizing Fallible Biological Protocols

The paper introduces a programming language to formalize biological protocols and handle errors, enabling error analysis through probabilistic inference.

Shaping a Collaborative, Sustainable, Accessible, and Reproducible Future for Computational Modeling

The paper introduces o2S2PARC, an open-source platform for computational modeling and analysis, highlighting its features, applications, and adoption.

dnaudit + Pydnaweb: A lightweight text-based planning and documentation workflow for genetic cloning with automatic verification

dnaudit and Pydnaweb provide a no-code, reproducible workflow for documenting and validating genetic cloning strategies with automated verification.

BioMedTools: a language model-powered community for biomedical computational tools

BioMedTools uses language models to create a community for biomedical computational tools, improving tool discovery and accessibility.

FAIRification of computational models in biology

The paper proposes adapting FAIR indicators to assess and improve the quality and transparency of computational models in biology.

FlowAgent: A Modular Agent-Based System for Automated Workflow Management and Data Interpretation

FlowAgent automates bioinformatics workflows with an agent-based system, improving reproducibility and accessibility through intelligent decision-making and natural language interfaces.

AIRUS: a simple workflow for AI-assisted exploration of scientific data

The paper introduces AIRUS, an AI-assisted workflow enabling scientists to use LLMs for hypothesis generation, coding, and result interpretation without extensive AI expertise.

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.

pipemake: A pipeline creation tool using Snakemake for reproducible analysis of biological datasets

pipemake creates modular Snakemake workflows for reproducible biological data analysis, reducing hands-on time and enabling flexible pipeline adaptation.

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.

Cloudgene 3: Transforming Nextflow Pipelines into Powerful Web Services

Cloudgene 3 converts Nextflow pipelines into web services, enabling easy sharing and collaboration without technical expertise.