Scientific Computing and Data Management

A motif for domain-specific analysis applets that are easy to learn, reuse, test, and to compose into pipelines: application to vision science

The paper introduces a framework for creating reusable, well-documented analysis tools in vision science, demonstrating their use in published research.

FlowWeb, a free, web-based platform for flow cytometry data analysis

FlowWeb provides a web-based platform for flow cytometry analysis, offering automated workflows and visualization tools comparable to commercial software.

GraphMana: graph-native data management for population genomics projects

GraphMana manages population genomics data using a graph database, enabling efficient incremental updates and export to multiple formats.

RapCluster: Bridging the Reproducibility Gap in Clustering Analysis

RapCluster provides an interactive web platform with 11 clustering algorithms to improve transparency and reproducibility in clustering analysis.

BioClaw: Human-Bot Research Collaboration Ecosystems in Group Chats

BioClaw enables human-bot collaboration in group chats to execute biomedical analyses using containerized tools and workflows across multiple domains and data types.

Pipette: Encoding scientific literature into an executable Skill Graph for multi-agent bioinformatics

Pipette is a multi-agent AI framework that generates reproducible bioinformatics workflows using a literature-derived Skill Graph, outperforming LLMs without such constraints across multiple domains.

REBEL, Reproducible Environment Builder for Explicit Library resolution

REBEL resolves dependency issues in bioinformatics by providing a reproducible environment framework that improves installation success rates and enables deterministic builds.

Benchmarking Agentic Bioinformatics Systems for Complex Protein-Set Retrieval: A Coccolithophore Calcification Case Study

This paper benchmarks three agentic bioinformatics systems for retrieving proteins related to coccolithophore calcification, finding that Codex best balances sensitivity and specificity while DeerFlow and Biomni produce larger but less relevant sets.

PopGenAgent: An Agent-Mediated Workflow for Population Genetics Analyses

PopGenAgent streamlines population genetics analyses by organizing tasks into a structured workflow, enabling reproducible and transparent multi-step analyses with preserved intermediate results.

Claw4Science: A Dataset and Platform for the OpenClaw Scientific Agent Ecosystem

The paper introduces a curated dataset and platform for the OpenClaw scientific agent ecosystem, analyzing its structure and challenges in reproducibility and governance.

A multi-agent platform for assessment and improvement of bioinformatics software documentation

This paper introduces BioGuider, a multi-agent platform that evaluates and improves bioinformatics software documentation, showing a link between documentation quality and citation frequency.

ST-Analyzer: A Packaged Web and Command-Line Interface for Simulation Trajectory Analysis

ST-Analyzer provides a CLI and GUI tool for simulation trajectory analysis, enabling reproducible insights through packaged open-source software.

PlotGDP: an AI Agent for Bioinformatics Plotting

PlotGDP provides an AI-powered web server for generating publication-quality bioinformatics plots using natural language commands without requiring coding or environment setup.

IDTrack: Time- and Namespace-Aware Identifier Harmonization for Reproducible Workflows

IDTrack harmonizes gene identifiers across time and namespaces to ensure reproducibility in computational biology workflows by tracking annotation release history and mapping decisions.

ChromSkills enables interpretable and reproducible agentic chromatin data analysis

ChromSkills provides a framework for reproducible and interpretable chromatin data analysis using domain-specific tools guided by LLMs.

BOLE: A Knowledge-Enhanced Multi-Agent Framework for Intelligent Genomic Breeding

BOLE translates high-level genomic breeding intent into validated workflows using a knowledge base and large language model reasoning.

Community Web Portal for Open Collaboration in the Martini Force Field Initiative

The paper introduces a web portal for the Martini Force Field Initiative to facilitate open collaboration and resource management in biomolecular simulations.

ToolsGenie 2.0: A Scalable and Extensible Multi-Agent System for Bioinformatics Automation

ToolsGenie 2.0 automates bioinformatics analyses using a multi-agent AI framework, achieving 68.6% accuracy on an in-house dataset and 48.3% on BixBench.

BioTrouble: A Multi-Agent Workflow for Troubleshooting Molecular Biology Techniques

BioTrouble is a multi-agent AI workflow that helps troubleshoot molecular biology techniques using a RAG framework and small language models.

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.

R2G2: A Python-R Framework for Seamless Integration of R/Bioconductor Tools into Galaxy

R2G2 automates the creation of Galaxy wrappers for R/Bioconductor packages, simplifying integration and reducing complexity for non-programmers.

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.

Notebook-based alignment of human and agentic reasoning in single-cell biology

This paper introduces kai, an agentic AI that generates analyses in computational notebooks to align human and agentic reasoning in single-cell biology, showing improved robustness and reasoning capabilities.

The Virtual Brain Ontology: A Digital Knowledge Framework for Reproducible Brain Network Modeling

The paper introduces TVB-O, a framework to improve reproducibility and comparability of brain network simulations by standardizing metadata and enabling executable code generation.

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.

Orchestrating Microbiome Analysis with Bioconductor

The paper introduces an open-source ecosystem for microbiome data science using Bioconductor, supporting modular workflows for analyzing complex, multi-modal datasets.

From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virus

The paper introduces BRC-Analytics, a browser-based platform for pathogen genomics, demonstrating its use in analyzing measles virus evolutionary dynamics and revealing asymmetric frame evolution under selective pressures.

BioFrame: Enhancing Reproducibility and Accessibility in Genomics through Web-Based Workflow Design

BioFrame provides a web-based tool for reproducible and accessible genomics workflows using containerized microservices.

Multimodal AI agents for capturing and sharing laboratory practice

This paper introduces a multimodal AI agent that captures and shares lab practice by integrating video, speech, and text analysis to improve reproducibility in proteomics.