Search results for "SBML"
showing 3 items of 3 documents
A Method of Three-Dimensional Visualization of Molecular Processes of Apoptosis
2014
Apoptosis or programmed cell death plays an important role in many physiological states and diseases. Detection of apoptotic cells, tracing the development of apoptosis, drug development and regulation of apoptosis are an important parts of basic research in medicine. A large number of models have been developed that are based on the differential equations of the chemical kinetics, and can be expressed in a uniform notation using some XML-based languages, such as SBML and CellML. We describe the CellML and the simulation environment OpenCell herein. These tools can display models schematically and output results in the form of graphs showing time dependencies of component concentrations. Ho…
EFMviz
2020
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1…
Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows
2020
AbstractMany computer-aided design tools are available for synthetic biology and metabolic engineering. Yet, these tools can be difficult to apprehend, sometimes requiring a level of expertise that limits their use by a wider community. Furthermore, some of the tools, although complementary, rely on different input and output formats and cannot communicate with one another. Scientific workflows address these shortcomings while offering a novel design strategy. Among the workflow systems available, Galaxy is a web-based platform for performing findable and accessible data analyses for all scientists regardless of their informatics expertise, along with interoperable and reproducible computat…