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We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web…
Ontologies present an attractive technology for describing bio-medicine, because they can be shared, and have rich computational properties. However, they lack the rich expressivity of English and fit poorly with the current scientific…
Large Language Models (LLMs) have facilitated the definition of autonomous intelligent agents. Such agents have already demonstrated their potential in solving complex tasks in different domains. And they can further increase their…
Interpreting biological networks becomes challenging when molecular components, such as genes or proteins, participate in numerous interactions, resulting in densely connected regions and overlapping interactions that obscure functional…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…
Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale…
Existing human-robot interaction systems often lack mechanisms for sustained personalization and dynamic adaptation in multi-user environments, limiting their effectiveness in real-world deployments. We present HARMONI, a multimodal…
BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification…
The BioModels database is one of the premier databases for computational models in systems biology. The database contains over 1000 curated models and an even larger number of non-curated models. All the models are stored in the…
In this paper, we propose a novel system that integrates state-of-the-art, domain-specific large language models with advanced information retrieval techniques to deliver comprehensive and context-aware responses. Our approach facilitates…
Machine learning (ML) interpretability techniques can reveal undesirable patterns in data that models exploit to make predictions--potentially causing harms once deployed. However, how to take action to address these patterns is not always…
Ever-expanding volumes of biomedical text require automated semantic annotation techniques to curate and put to best use. An established field of research seeks to link mentions in text to knowledge bases such as those included in the UMLS…
Speech language models have recently demonstrated great potential as universal speech processing systems. Such models have the ability to model the rich acoustic information existing in audio signals, beyond spoken content, such as emotion,…
We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
Large language models (LLMs) are increasingly used by researchers in the social sciences and humanities (SSH) for text analysis, particularly to automate text annotation. However, many researchers still face challenges in adopting LLMs,…
This study introduces a prescriptive annotation benchmark grounded in humanities research to ensure consistent, unbiased labeling of offensive language, particularly for casual and non-mainstream language uses. We contribute two newly…
SBcoyote is an open-source cross-platform biochemical reaction viewer and editor released under the liberal MIT license. It is written in Python and uses wxPython to implement the GUI and the drawing canvas. It supports the visualization…
GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…
We present BioLunar, developed using the Lunar framework, as a tool for supporting biological analyses, with a particular emphasis on molecular-level evidence enrichment for biomarker discovery in oncology. The platform integrates Large…