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UNLABELLED Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of systems biology. Two of the most critical steps in this approach are to construct dynamical models of biochemical reaction networks for large datasets and complex experimental conditions and to perform efficient and reliable parameter(More)
DNA repair and other chromatin-associated processes are carried out by enzymatic macromolecular complexes that assemble at specific sites on the chromatin fiber. How the rate of these molecular machineries is regulated by their constituent parts is poorly understood. Here we quantify nucleotide-excision DNA repair in mammalian cells and find that, despite(More)
Non-ribosomal peptide synthetases (NRPSs) are enzymes that catalyze ribosome-independent production of small peptides, most of which are bioactive. NRPSs act as peptide assembly lines where individual, often interconnected modules each incorporate a specific amino acid into the nascent chain. The modules themselves consist of several domains that function(More)
1 Purpose The purpose of this RFC is to introduce a standardized framework for the engineering of customizable non-ribosomal peptide synthetases (NRPS) and their application for in vivo and in vitro synthesis of short non-ribosomal peptides (NRPs) of user-defined sequence and structure. 2 Relation to other BBF RFCs BBF RFC100 updates RFC57 describing the "(More)
For a long time the biggest challenges in modeling cellular signal transduction networks has been the inference of crucial pathway components and the qualitative description of their interactions. As a result of the emergence of powerful high-throughput experiments, it is now possible to measure data of high temporal and spatial resolution and to analyze(More)
Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of systems biology. Two of the most critical steps in this approach are to construct dynamical models of biochemical reaction networks for large datasets and complex experimental conditions and to perform efficient and reliable parameter estimation for(More)
The Data2Dynamics modeling environment is MATLAB-based, open source and freely available. MATLAB R2012 or later is recommended, the MATLAB Optimization Toolbox and the Symbolic Math Toolbox are required. Windows, Mac and Linux operating systems are supported. For MATLAB mex-compilation under Windows systems, the freely available Windows SDK 7.1 is required.(More)
Aims. An efficient algorithm for calculating radiative transfer on massively parallel computers using domain decomposition is presented. Methods. The integral formulation of the transfer equation is used to divide the problem into a local but compute-intensive part for calculating the intensity and optical depth integrals, and a nonlocal part for(More)
The synthetic feasibility of any compound library used for virtual screening is critical to the drug discovery process. TIN, a recursive acronym for 'TIN Is Not commercial', is a virtual combinatorial database enumeration of diversity-orientated multicomponent syntheses (MCR). Using a 'one-pot' synthetic technique, 12 unique small molecule scaffolds were(More)
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