相关论文: SBMLtoOdin and Menelmacar: Interactive visualisati…
Artificial intelligence (AI) techniques are widely applied in the life sciences. However, applying innovative AI techniques to understand and deconvolute biological complexity is hindered by the learning curve for life science scientists to…
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…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
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…
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…
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…
The R package merlin performs flexible joint modelling of hierarchical multi-outcome data. Increasingly, multiple longitudinal biomarker measurements, possibly censored time-to-event outcomes and baseline characteristics are available.…
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…
This paper presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for omics data analysis, with a special focus on metabolomics-based methods. It builds on the…
Real-time visualization of computational simulations running over graphics processing units (GPU) is a valuable feature in modern science and technological research, as it allows researchers to visually assess the quality and correctness of…
Summary: More sophisticated models are needed to address problems in bioscience, synthetic biology, and precision medicine. To help facilitate the collaboration needed for such models, the community developed the Simulation Experiment…
Detecting microbial biomarkers used to predict disease phenotypes and clinical outcomes is crucial for disease early-stage screening and diagnosis. Most methods for biomarker identification are linear-based, which is very limited as…
Visualizations have become an indispensable part of the scientific process. A vibrant ecosystem of visualization tools exists, catering to a wide variety of different needs. Real-time visualizations of numerical simulations offer scientists…
OpenML is an online machine learning platform where researchers can easily share data, machine learning tasks and experiments as well as organize them online to work and collaborate more efficiently. In this paper, we present an R package…
Understanding complex scientific and mathematical concepts, particularly those presented in dense research papers, poses a significant challenge for learners. Dynamic visualizations can greatly enhance comprehension, but creating them…
The past decade has witnessed a dramatic increase in the size and scope of biological and behavioral experiments. These experiments are providing an unprecedented level of detail and depth of data. However, this increase in data presents…
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 present vivid, an R package for visualizing variable importance and variable interactions in machine learning models. The package provides a range of displays including heatmap and graph-based displays for viewing variable importance and…
Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions. However, mathematical models are still most often created de novo, based on reading the literature and…
Inverse problem for the identification of the parameters for large-scale systems of nonlinear ordinary differential equations (ODEs) arising in systems biology is analyzed. In a recent paper in \textit{Mathematical Biosciences, 305(2018),…