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See detailCreation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Heirendt, Laurent UL; Arreckx, Sylvain; Pfau, Thomas UL et al

in Nature protocols (2019), 14(3), 639-702

Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of ... [more ▼]

Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods. [less ▲]

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See detailDecentralized cooperative tracking subject to motion constraints
Wang, Lin; Markdahl, Johan UL; Liu, Zhixin et al

in Automatica (2018), 96

This paper addresses the formation control problem, where three agents are tasked with moving an object cooperatively along a desired trajectory while also adjusting its posture to some desired attitudes ... [more ▼]

This paper addresses the formation control problem, where three agents are tasked with moving an object cooperatively along a desired trajectory while also adjusting its posture to some desired attitudes, i.e. position and attitude tracking. Two decentralized control laws based on locally available information are proposed. The first control law maintains constant inter-agent distances over time, i.e. the formation of agents moves as a single rigid-body. The second control law relaxes this constraint by only maintaining similarity of the agent formation as a polygon in Euclidean space. [less ▲]

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See detailA geodesic feedback law to decouple the full and reduced attitude
Markdahl, Johan UL; Hoppe, Jens; Wang, Lin et al

in System and Control Letters (2017), 102

This paper presents a novel approach to the problem of almost global attitude stabilization. The reduced attitude is steered along a geodesic path on the n−1-sphere. Meanwhile, the full attitude is ... [more ▼]

This paper presents a novel approach to the problem of almost global attitude stabilization. The reduced attitude is steered along a geodesic path on the n−1-sphere. Meanwhile, the full attitude is stabilized on SO(n). This action, essentially two maneuvers in sequel, is fused into one smooth motion. Our algorithm is useful in applications where stabilization of the reduced attitude takes precedence over stabilization of the full attitude. A two parameter feedback gain affords further trade-offs between the full and reduced attitude convergence speed. The closed loop kinematics on SO(3) are solved for the states as functions of time and the initial conditions, providing precise knowledge of the transient dynamics. The exact solutions also help us to characterize the asymptotic behavior of the system such as establishing the region of attraction by straightforward evaluation of limits. The geometric flavor of these ideas is illustrated by a numerical example. [less ▲]

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