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Virtual Cell is an advanced software platform for modeling and simulating reaction kinetics, membrane transport and diffusion in the complex geometries of cells and multicellular tissues. VCell models have a hierarchical tree structure.
Windows, macOS: GPL: Collaborative project GenoCAD: A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. Linux, macOS, Windows: Apache License 2.0 GenoCAD Team (Virginia Bioinformatics Institute) Genomespace
Software design usually is directed by goals for the resulting system and involves problem-solving and planning – including both high-level software architecture and low-level component and algorithm design. In terms of the waterfall development process, software design is the activity of following requirements specification and before coding ...
pathway based data integration and visualization, easy to use and integrate into pathway analysis multiplatform (R/Bioconductor) GPL: SBMLDiagrams [2] Python API to display and edit SBML layout/render extension: multiplatform: MIT: Systrip: analysis of time-series data in the context of biological networks Windows, Linux: LGPL, GPL
The vast majority of modern systems biology modeling software support SBML, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support CellML , a standard used for representing physiological processes.
A white box (or glass box, clear box, or open box) is a subsystem whose internals can be viewed but usually not altered. [1] The term is used in systems engineering , software engineering , and in intelligent user interface design, [ 2 ] [ 3 ] where it is closely related to recent interest in explainable artificial intelligence .
A distinctive feature of Windows Aero showing "glass-like" window borders on Windows 7. Windows Aero (a backronym for Authentic, Energetic, Reflective, and Open) [1] [2] is the design language introduced in the Microsoft Windows Vista operating system. The changes introduced by Windows Aero encompassed many elements of the Windows interface ...
Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and enzymes that comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes.