Related papers: SBMLDiagrams: A python package to process and visu…
In this technical report, we describe a new version of SimpleSBML which provides an easier to use interface to python-libSBML allowing users of Python to more easily construct, edit, and inspect SBML based models. The most commonly used…
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…
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…
Motivation: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard…
Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results:…
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…
We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implements S-system representations, a canonical power-law…
Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often…
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…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
This paper describes an an open-source software system for the automatic conversion of NLP event representations to system biology structured data interchange formats such as SBML and BioPAX. It is part of a larger effort to make results of…
Antimony is a high-level, human-readable text-based language designed for defining and sharing models in the systems biology community. It enables scientists to describe biochemical networks and systems using a simple and intuitive syntax.…
PyMilo is an open-source Python package that addresses the limitations of existing Machine Learning (ML) model storage formats by providing a transparent, reliable, and safe method for exporting and deploying trained models. Current…
Summary: The DynaSig-ML (Dynamical Signatures - Machine Learning) Python package allows the efficient, user-friendly exploration of 3D dynamics-function relationships in biomolecules, using datasets of experimental measures from large…
PiML (read $\pi$-ML, /`pai`em`el/) is an integrated and open-access Python toolbox for interpretable machine learning model development and model diagnostics. It is designed with machine learning workflows in both low-code and high-code…
semanticSBML 2.0 is an online collection of services for the work with biochemical network models in SBML format.
We describe a binding schema markup language (BSML) for describing data interchange between scientific codes. Such a facility is an important constituent of scientific problem solving environments (PSEs). BSML is designed to integrate with…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Machine learning is revolutionizing image-based diagnostics in pathology and radiology. ML models have shown promising results in research settings, but their lack of interoperability has been a major barrier for clinical integration and…
Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges…