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Mathematica script

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Mathematica script is a powerful computational software that provides a versatile platform for mathematical, technical, and scientific computing. Its core function is to enable users to perform a wide range of calculations, data analysis, and visualization tasks through the use of a concise and expressive programming language.

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Mathematica (333 citations)

3 protocols using mathematica script

1

Quantifying Powdery Mildew Infection in Plants

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The presence of On symptoms was assessed by visual inspection at 8, 13, and 15 days post-inoculation (dpi), according to Bai et al. (2008) (link). Plants were photographed with a Casio Exilim EX-Z85 digital camera and images were analyzed with a dedicated Wolfram Mathematica script (Long Hanborough, UK). Depending on the stage of symptoms developed, the area of infection on individual leaves was quantified either considering the PM colonized region (white color) or the necrotic one (brown color), based on changes deduced from the RGB (red, green, and blue) values. The disease index (DI) was assessed at the same time points and on the same leaflets, using a scale from 0 to 4, according to Bai et al. (2008) (link) and Patil et al (Patil and Bodhe, 2011 ), as follows: 0, apparently not infected; 1, 0%–25% leaf area infected; 2, 25%–50% leaf area infected; 3, 50%–75% leaf area infected; 4 >75% leaf area infected.
D’Errico C., Forgia M., Pisani M., Pavan S., Noris E, & Matić S. (2023). Overexpression of the C4 protein of tomato yellow leaf curl Sardinia virus increases tomato resistance to powdery mildew. Frontiers in Plant Science, 14, 1163315.
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2

Quantitative Protein Mapping via Binarized Imaging

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Thresholded, binarized maps were given as input to a custom Mathematica script (Wolfram Research, 2020 ). The Mathematica script calculated the segmented difference maps between all maps and calculated the molecular weights of the differences maps (in kilodaltons) using Equation 1(Ludtke, 2016 ):
MW =npixels∗pixelsize3∗ρ/1000
Density (ρ) is 0.81 daltons/Å3. The MW difference matrix was clustered using the Euclidean distance metric and Ward’s linkage and displayed in a dendrogram. Similar maps were averaged together after hierarchical clustering analysis using EMAN2 ((Ludtke, 2016 ).
Rabuck-Gibbons J.N., Lyumkis D, & Williamson J.R. (2022). Quantitative Mining of Compositional Heterogeneity in Cryo-EM Datasets of Ribosome Assembly Intermediates. Structure (London, England : 1993), 30(4), 498-509.e4.
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3

Quantifying Cell Adhesion Dynamics

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Cell area and FA size, elongation and number per cell were determined using a custom-built Mathematica script (version 11.1, Wolfram Research Inc., USA), as previously described by Buskermolen et al. [57] (link). Single cells were selected in the software for analysis. FAs between 0.1 μm 2 and 11 μm 2 were used for further analysis. Elongation was determined as 1 -(FA length/FA width) -1 , thereby a perfect circle has an elongation of 0. Per condition approximately 10-20 single cells were selected and analyzed in each of the four replicates (n = 40-58).
van Gaal R.C., Buskermolen A.B.C., Ippel B.D., Fransen P.K.H., Zaccaria S., Bouten C.V.C, & Dankers P.Y.W. (2019). Functional peptide presentation on different hydrogen bonding biomaterials using supramolecular additives. Biomaterials, 224.
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