How to SNIFF out Good Scientific Software

Ten quick tips to SNIFF out sustainable and secure scientific software

Modern computational biology depends heavily on open-source software tools, analysis pipelines, and containerized workflows developed and shared by the research community. While there is extensive guidance (including Quick Tips and Simple Rules articles) on how to build robust and sustainable scientific software, far less has been written for researchers in the role of software users evaluating whether an existing tool is reliable, secure, and sustainable enough for their work. Here we present ten quick tips to help researchers critically assess the tools they adopt. Our tips are organized around a framework that centers on key evaluation features: source, network, interaction, fit, and fragility (SNIFF). These dimensions prompt researchers to consider who maintains a tool and why, whether it is embedded in a broader ecosystem, how actively its developers and users engage, whether it matches the intended use case and licensing requirements, and how robust its dependencies and security practices are. By applying these tips, researchers can make more informed decisions, reduce the risk of relying on abandoned or insecure software, and contribute to a more sustainable scientific software ecosystem.

Linking the world's research to the code it runs on - OpenAlex blog

Research relies on software. Software written by scientists, for science, runs through the entire modern research stack: NumPy and SciPy, R and ggplot2, Jupyter, BLAST, ImageJ, AlphaFold. Yet in the scholarly record, that software is nearly invisible. Software is not usually cited formally in publications and is usually just mentioned in the text, which means […]

Introducing COSIG: The Collection of Open Science Integrity Guides

Investigating the integrity of published scientific papers is key to the scientific process, but the necessary knowledge is in short supply. We present COSIG, an open collection of meta-scientific guides enabling anyone to perform forensic peer review.

The Bazaar of Scientific Knowledge | shishyko!

Is the current form of the scientific paper still optimal in 2025? How do we preserve, and efficiently leverage, the uncut gems of the scientific process?

SCI — Software Carbon Intensity | Green Software Foundation

The global standard for calculating and reducing the carbon emissions of your software. ISO/IEC 21031:2024.

oss-security - Dirty Frag: Universal Linux LPE

Please check out the Open Source Software Security Wiki, which is counterpart to this mailing list.

Scimeto - Automated Manuscript Integrity Checker

Upload your academic manuscript and get instant analysis of citations, references, statistics, retractions, and more. 21 plugins, 9 citation styles, free for researchers.

The Fraud Bowl

An idea for how to incentivize best practices combatting scientific fraud

Introducing the Open-Source Codex Security CLI

Codex Security helps security and engineering teams find, confirm, and fix vulnerabilities. Use its command-line interface (CLI) to scan repositories you own or have permission to assess, review findings over time, and check changes before they land. Quickstart Guide for an interactive scan Cloud set-up for connected GitHub repositories Link to the public repo: Codex Security This is an early release, and we’re listening to your feedback as we continue improving it. The Codex Security CLI ...

Improving Science That Uses Code

Abstract. As code is now an inextricable part of science it should be supported by competent Software Engineering, analogously to statistical claims being

SciOS

Facilitating infrastructure for open science

SciOS

Facilitating infrastructure for open science

VaultGemma: The world's most capable differentially private LLM

Amer Sinha, Software Engineer, and Ryan McKenna, Research Scientist, Google Research

SciToolAgent: a knowledge-graph-driven scientific agent for multitool integration

Scientific research increasingly relies on specialized computational tools, yet effectively utilizing these tools requires substantial domain expertise. While large language models show promise in tool automation, they struggle to seamlessly integrate and orchestrate multiple tools for complex scientific workflows. Here we present SciToolAgent, a large language model-powered agent that automates hundreds of scientific tools across biology, chemistry and materials science. At its core, SciToolAgent leverages a scientific tool knowledge graph that enables intelligent tool selection and execution through graph-based retrieval-augmented generation. The agent also incorporates a comprehensive safety-checking module to ensure responsible and ethical tool usage. Extensive evaluations on a curated benchmark demonstrate that SciToolAgent outperforms existing approaches. Case studies in protein engineering, chemical reactivity prediction, chemical synthesis and metal–organic framework screening further demonstrate SciToolAgent’s capability to automate complex scientific workflows, making advanced research tools accessible to both experts and nonexperts.

Hypercerts: Recognizing and Rewarding Impact – ATProto Implementation

Hi all, excited to share some of what we’ve been building and to introduce hypercerts to the ATProto community. Where we started The hypercerts project began at Protocol Labs with a simple goal: improve how we fund public goods. Many of the contributions society relies on most—open-source software, scientific R&D, and ecological regeneration—remain underfunded because their value is hard to see, coordinate around, and reward. What are hypercerts Hypercerts address this by serving as digital im...