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custom matlab code and the bioinformatics toolbox local alignment tool  (MathWorks Inc)


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    MathWorks Inc custom matlab code and the bioinformatics toolbox local alignment tool
    Custom Matlab Code And The Bioinformatics Toolbox Local Alignment Tool, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/-coded+custom+tool/pm31740817-193-14-15
    Average 90 stars, based on 1 article reviews
    custom matlab code and the bioinformatics toolbox local alignment tool - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    other:

    Article Title: Harnessing osmotic shock for enhanced intracellular delivery of (nano)cargos.
    Article Snippet: For each condition, videos were analyzed using a custom MATLAB® code (see Supplementary Material S1).

    Article Title: Method, system and application for 3D molecular diffusion tensor measurement and structural imaging
    Article Snippet: Pre-bleaching images were averaged and subtracted from post-bleaching images, which were then analyzed with a custom MATLAB® code to calculate 2D FRAP diffusivities.

    Article Title: P-cadherin-dependent adhesions are required for single lumen formation and HGF-mediated cell protrusions during epithelial morphogenesis
    Article Snippet: The number of single cell protrusions from each cyst was analyzed using a custom-generated MATLAB code.

    Microscopy:

    Article Title: Pair correlation microscopy of intracellular molecular transport.
    Article Snippet: Pair correlation microscopy is a unique approach to fluorescence correlation spectroscopy that can track the long-range diffusive route of a population of fluorescent molecules in live cells with respect to intracellular architecture.. This method is based on the use of a pair correlation function (pCF) that, through spatiotemporal comparison of fluctuations in fluorescence intensity recorded throughout a microscope data acquisition, enables changes in a molecule’s arrival time to be spatially mapped and statistically quantified.. In this protocol, we present guidelines for the measurement and analysis of line scan pair correlation microscopy data acquired on a confocal laser scanning microscope (CLSM), which will enable users to extract a fluorescent molecule’s transport pattern throughout a living cell, and then quantify the molecular accessibility of intracellular barriers encountered or the mode of diffusion governing a molecular trafficking event.

    Fluorescence:

    Article Title: Prey capture learning drives critical period-specific plasticity in mouse binocular visual cortex
    Article Snippet: Finally, the area and volume of each Syt2 contact onto a FP + or PV + soma were obtained using the Statistics module in Imaris. .. After Suite2p, a custom Matlab code (vhlab-TwoPhoton-matlab, available on GitHub) was used to compute the change in fluorescence (ΔF/F) for each stimulus. ..



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    We developed two approaches (AD-ADOLC and AD-Recorder) to make an OpenSim function F and its forward ( F fwd ) and reverse ( F rev ) directional derivatives available within the CasADi environment for use by the NLP solver during the optimization. In the AD-ADOLC approach (top), ADOL-C’s algorithms are used in a C++ code to provide F fwd and F rev . In the AD-Recorder approach (bottom), Recorder provides the expression graph of F as MATLAB source code from which CasADi’s C-code generator generates C-code containing F , F fwd , and F rev . The AD-Recorder approach combines operator overloading, when generating the expression graph, and source code transformation, when processing the expression graph to generate C-code for F , F fwd , and F rev . In both approaches, the code comprising F , F fwd , and F rev is compiled as a Dynamic-link Library (DLL), which is imported as an external function within the CasADi environment. In our application, F represents the multi-body dynamics and is called when formulating the optimal control problem. The latter is then composed into a differentiable optimal control transcription using CasADi. During the optimization, CasADi provides the NLP solver with evaluations of the NLP objective function ( nlp f ), constraints ( nlp g ), objective function gradient ( nlp grad f ), constraint Jacobian ( nlp jac g ), and Hessian of the Lagrangian ( nlp hess l ). CasADi efficiently queries F fwd and F rev to construct the full derivative matrices.

    Journal: PLoS ONE

    Article Title: Algorithmic differentiation improves the computational efficiency of OpenSim-based trajectory optimization of human movement

    doi: 10.1371/journal.pone.0217730

    Figure Lengend Snippet: We developed two approaches (AD-ADOLC and AD-Recorder) to make an OpenSim function F and its forward ( F fwd ) and reverse ( F rev ) directional derivatives available within the CasADi environment for use by the NLP solver during the optimization. In the AD-ADOLC approach (top), ADOL-C’s algorithms are used in a C++ code to provide F fwd and F rev . In the AD-Recorder approach (bottom), Recorder provides the expression graph of F as MATLAB source code from which CasADi’s C-code generator generates C-code containing F , F fwd , and F rev . The AD-Recorder approach combines operator overloading, when generating the expression graph, and source code transformation, when processing the expression graph to generate C-code for F , F fwd , and F rev . In both approaches, the code comprising F , F fwd , and F rev is compiled as a Dynamic-link Library (DLL), which is imported as an external function within the CasADi environment. In our application, F represents the multi-body dynamics and is called when formulating the optimal control problem. The latter is then composed into a differentiable optimal control transcription using CasADi. During the optimization, CasADi provides the NLP solver with evaluations of the NLP objective function ( nlp f ), constraints ( nlp g ), objective function gradient ( nlp grad f ), constraint Jacobian ( nlp jac g ), and Hessian of the Lagrangian ( nlp hess l ). CasADi efficiently queries F fwd and F rev to construct the full derivative matrices.

    Article Snippet: First, we enabled the use of AD in OpenSim through a custom source code transformation tool and through the operator overloading tool ADOL-C. Second, we developed an interface between OpenSim and CasADi to solve trajectory optimization problems.

    Techniques: Expressing, Transformation Assay, Control, Construct