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1. Supporting Data for Icelandic Riverine Freshwater Distribution, Offshore Export, and Alongshelf Connectivity

   https://doi.org/10.17632/yw6xcwh9md.2  

   Whitney, Michael (January 2025, Mendeley Data)

   This dataset contains the supporting data for figures in “Icelandic Riverine Freshwater Distribution, Offshore Export, and Alongshelf Connectivity,” a manuscript for Estuarine, Coastal and Shelf Science by Michael M. Whitney (affiliated with the University of Connecticut). This study simulates Iceland’s shelf and open-ocean waters to investigate riverine freshwater distributions and transports. Tracers are applied to determine flushing times and quantify exports to the open ocean relative to downshelf transports. Results have broader relevance to Iceland’s coastal ecosystems and transports on other continental shelves. The dataset includes MATLAB data files that contain all the output data presented in the corresponding figures within the manuscript. Details about variables and units are described within the figure captions and manuscript text. Modified model code, settings, and input files are included for the Regional Ocean Model System (ROMS) application. The FORTRAN code files have the modifications for tracers that allow for decay in deep waters. The manuscript contains complete descriptions of methods, analysis, and interpretation. List of MATLAB data files: Figure01_data.mat Figure02_data.mat Figure03_data.mat Figure04_data.mat Figure05_data.mat Figure06_data.mat Figure07_data.mat Figure08_data.mat List of modified ROMS code files: def_info.F mod_scalars.F read_phypar.F step3d_t.F wrt_info.F ana_passive.h ana_psource.h List of ROMS settings and input files: iceland.h roms.in boundary2km_lonlatgrid.nc rivers2km_with_additional_rivers_lonlatgrid.nc grid_iceland2km_lonlatgrid.nc iceland2km_lonlatgrid_tideforcing_M2_NA_phase010119.nc initial2km_lonlatgrid_yearend_dyes.nc windforcing2km_lonlatgrid.nc 

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2. Replication Data for: Self-Strengthening Tape Junctions Inspired by Recluse Spider Webs

   https://doi.org/10.7910/DVN/Q7LTLW  

   Skopic, Ben H.; Koebley, Sean R.; Schniepp, Hannes C. (January 2022, Harvard Dataverse)

   The raw data for the associated manuscript is organized here into three categories: 1) relating to the measurement and analysis of the native recluse spiders loop junctions, 2) raw images found in the figures throughout the manuscript, and 3) relating to the experiments testing the effect that junction angle has on the strength of two intersecting tapes. It is recommended to browse the data files in Tree mode, which will make the files appear in folders reflecting this organization. 1) Loxosceles Loop Junction Images and Analysis The folder titled, SEM Raw Images, has all of the scanning electron microscopy (SEM) images taken of the native recluse loop junctions. Some images are close-ups of individual junctions and others take a broader perspective (macro) of many loop junctions in series. Where possible several close-up images of the individual junctions are accompanied with a macro image. These images were imported into ImageJ where the junction angle was measured. The measurements for all 41 loop junctions observed are in the folder titled, Raw Data Files in the file titled, Loxosceles Loop Junction Angle Measurements.txt. The folder titled, Raw Data Files contains, in addition to the angle measurements, the raw data for analyzing the strength of individual loop junctions. The data is in native MATLAB data format. These datasets include the complete tensile data and the cross-sectional area data for each spiders silk. The MATLAB code titled, Figure_2A_2B_code, processes the raw tensile data from the natural recluse spiders loop junctions. This data is plotted as two representative curves in Figure 2A and as a complete set as a histogram in Figure 2B. The MATLAB code titled, Figure_7_code, processes and plots the loop junction data found in, Loxosceles Loop Junction Angle Measurements.txt and executed the model of a random set of recluse loops. This code can be executed to generate Figure 7. The folder titled, Raw Data Files, must be open in MATLAB to run this code! This code uses the MATLAB function, areacalculation, to calculate the junction area for a given junction angle. 2) Raw Images This folder is organized by the respective figure in the manuscript where each image can be found. Additional metadata for each image can be found accompanying each image. 3) Tensile Data and Analysis This folder contains all of the raw tensile data for all tape-tape junction experiments conducted. All of the tensile data is in the folder titled, Raw Data Test Files. Within this folder is a .txt file for each sample tested. The file names are critical to the figure codes working properly because they contain the information for the junction angle and iterations. The file names are in the format year-month-day_trialnumber_junctionangle.txt. Also in the Raw Data Test Files folder are two functions used within some of the figure codes: fbfill and areacalculation. These functions will be used in the figure codes to properly analyze the data. To generate any figure using the MATLAB code in this folder, first open the code in MATLAB. Then within MATLAB, open the folder Raw Data Test Files. Only with this folder open in MATLAB will the code be able to find the correct raw data .txt files. The rest of the contents of this folder are MATLAB codes for specific figures in the manuscript. The only exception to this is the code titled, surfaceenergy_code, which is executed to calculate the phenomenological surface energy for the tapes used in these experiments. 

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3. COAWST model simulations of warm and cool nearshore rip-current plumes

   https://doi.org/10.5281/zenodo.4272080  

   Moulton, Melissa (January 2020, Zenodo)

   This archive contains COAWST model input, grids and initial conditions, and output used to produce the results in a submitted manuscript. The files are:</p> model_input.zip: input files for simulations presented in this paper   ocean_rip_current.in: ROMS ocean model input file   swan_rip_current.in: SWAN wave model input file (example with Hs=1m)   coupling_rip_current.in: model coupling file   rip_current.h: model header file    model_grids_forcing.zip: bathymetry and initial condition files      hbeach_grid_isbathy_2m.nc: ROMS bathymetry input file      hbeach_grid_isbathy_2m.bot: SWAN bathymetry input file      hbeach_grid_isbathy_2m.grd: SWAN grid input file      hbeach_init_isbathy_14_18_17.nc: Initial temperature, cool surf zone dT=-1C case      hbeach_init_isbathy_14_18_19.nc: Initial temperature, warm surf zone dT=+1C case      hbeach_init_isbathy_14_18_16.nc: Initial temperature, cool surf zone dT=-2C case      hbeach_init_isbathy_14_18_20.nc: Initial temperature, warm surf zone dT=+2C case      hbeach_init_isbathy_14_18_17p5.nc: Initial temperature, cool surf zone dT=-0.5C case      hbeach_init_isbathy_14_18_18p5.nc: Initial temperature, warm surf zone dT=+0.5C case</p> model_output files: model output used to produce the figures      netcdf files, zipped      variables included:           x_rho (cross-shore coordinate, m)           y_rho (alongshore coordinate, m)           z_rho (vertical coordinate, m)           ocean_time (time since initialization, s, output every 5 mins)           h (bathymetry, m)           temp (temperature, Celsius)           dye_02 (surfzone-released dye)           Hwave (wave height, m)           Dissip_break (wave dissipation W/m2)            ubar (cross-shore depth-average velocity, m/s, interpolated to rho-points)      Case_141817.nc: cool surf zone dT=-1C Hs=1m      Case_141819.nc: warm surf zone dT=+1C Hs=1m      Case_141816.nc: cool surf zone dT=-2C Hs=1m      Case_141820.nc: warm surf zone dT=-2C Hs=1m      Case_141817p5.nc: cool surf zone dT=-0.5C Hs=1m      Case_141818p5.nc: warm surf zone dT=+0.5C Hs=1m      Case_141817_Hp5.nc: cool surf zone dT=-1C Hs=0.5m      Case_141819_Hp5.nc: warm surf zone dT=+1C Hs=0.5m      Case_141817_Hp75.nc: cool surf zone dT=-1C Hs=0.75m      Case_141819_Hp75.nc: warm surf zone dT=+1C Hs=0.75m</p> COAWST is an open source code and can be download at https://coawstmodel-trac.sourcerepo.com/coawstmodel_COAWST/. Descriptions of the input and output files can be found in the manual distributed with the model code and in the glossary at the end of the ocean.in file.</p> Corresponding author: Melissa Moulton, mmoulton@uw.edu</p> 

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4. Dataset: A numerical simulation of the ocean, sea ice and ice shelves in the Amundsen Sea (Antarctica) over the period 2006-2022 and its associated code and input files

   https://doi.org/10.25773/bt54-sj65  

   St-Laurent, Pierre (January 2023, William & Mary. Virginia Institute of Marine Science)

   A three-dimensional numerical model of the Amundsen Sea (Antarctica) was used to simulate the period Jan.2006-Mar.2022 under consistent atmospheric/oceanic forcings, bathymetry/ice shelf topography, and model equations/parameters. The model is an implementation of the Regional Ocean Modeling System (ROMS, https://www.myroms.org/) with extensions for sea ice (Budgell 2005) and ice shelves (Dinniman et al. 2011). It simulates the ocean hydrography and circulation, sea ice thermodynamics and dynamics, and the basal melt of the ice shelves, with a uniform horizontal mesh of 1.5km and 20 topography-following vertical levels. Forcings include the ERA5 reanalysis (3-hourly), 10 tidal constituents from CATS 2008, and ocean/sea ice conditions at the edges of the model domain taken from the 5km-resolution circumpolar model of Dinniman et al. 2020 and from daily SSM/I satellite images. The model outputs are divided into nine directories each containing two years worth of model results (run661-669) in the NetCDF format. Each directory contains: daily-averaged model fields (roms_avg_xxxx.nc), instantaneous snapshots every 3 hours for select fields (roms_qck_xxxx.nc), and instantaneous snapshots every 30 days (roms_his_xxxx.nc). All the metadata information necessary for the interpretation of the model outputs (dimensions, units, etc) is included inside the NetCDF files. The NetCDF files follow the CF conventions and can be opened with various software that are open source and freely available over the Internet. In addition to the model outputs, this archive includes the computer code as well as the input files necessary for reproducing the model outputs of this archive. 

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5. Replication Data for: Protein Secondary Structure in Spider Silk Nanofibrils

   https://doi.org/10.7910/DVN/GMEEYL  

   Schniepp, Hannes C.; Wang, Qijue; McArdle, Patrick; Wang, Stephanie L.; Wilmington, Ryan L.; Xing, Zhen; Greenwood, Alexander; Cotten, Myrian L.; Qazilbash, M. Mumtaz (January 2022, Harvard Dataverse)

   This dataset contains raw data, processed data, and the codes used for data processing in our manuscript from our Fourier-transform infrared (FTIR) spectroscopy, Nuclear magnetic resonance (NMR), Raman spectroscopy, and X-ray diffraction (XRD) experiments. The data and codes for the fits of our unpolarized Raman spectra to polypeptide spectra is also included. The following explains the folder structure of the data provided in this dataset, which is also explained in the file ReadMe.txt. Browsing the data in Tree view is recommended. Folder contents Codes Raman Data Processing: The MATLAB script file RamanDecomposition.m contains the code to decompose the sub-peaks across different polarized Raman spectra (XX, XZ, ZX, ZZ, and YY), considering a set of pre-determined restrictions. The helper functions used in RamanDecomposition.m are included in the Helpers folder. RamanDecomposition.pdf is a PDF printout of the MATLAB code and output. P Value Simulation: 31_helix.ipynb and a_helix.ipynb: These two Jupyter Notebook files contain the intrinsic P value simulation for the 31-helix and alpha-helix structures. The simulation results were used to prepare Supplementary Table 4. See more details in the comments contained. Vector.py, Atom.py, Amino.py, and Helpers.py: These python files contains the class definitions used in 31_helix.ipynb and a_helix.ipynb. See more details in the comments contained. FTIR FTIR Raw Transmission.opj: This Origin data file contains the raw transmission data measured on single silk strand and used for FTIR spectra analysis. FTIR Deconvoluted Oscillators.opj: This Origin data file was generated from the data contained in the previous file using W-VASE software from J. A. Woollam, Inc. FTIR Unpolarized MultiStrand Raw Transmission.opj: This Origin data file contains the raw transmission data measured on multiple silk strands. The datasets contained in the first two files above were used to plot Figure 2a-b and the FTIR data points in Figure 4a, and Supplementary Figure 6. The datasets contained in the third file above were used to plot Supplementary Figure 3a. The datasets contained in the first two files above were used to plot Figure 2a-b, FTIR data points in Figure 4a, and Supplementary Figure 6. NMR Raw data files of the 13C MAS NMR spectra: ascii-spec_CP.txt: cross-polarized spectrum ascii-spec_DP.txt: direct-polarized spectrum Data is in ASCII format (comma separated values) using the following columns: Data point number Intensity Frequency [Hz] Frequency [ppm] Polypeptide Spectrum Fits MATLAB scripts (.m files) and Helpers: The MATLAB script file Raman_Fitting_Process_Part_1.m and Raman_Fitting_Process_Part_2.m contains the step-by-step instructions to perform the fitting process of our calculated unpolarized Raman spectrum, using digitized model polypeptide Raman spectra. The Helper folder contains two helper functions used by the above scripts. See the scripts for further instruction and information. Data aPA.csv, bPA.csv, GlyI.csv, GlyII.csv files: These csv files contain the digitized Raman spectra of poly-alanine, beta-alanine, poly-glycine-I, and poly-glycine-II. Raman_Exp_Data.mat: This MATLAB data file contains the processed, polarized Raman spectra obtained from our experiments. Variable freq is the wavenumber information of each collected spectrum. The variables xx, yy, zz, xz, zx represent the polarized Raman spectra collected. These variables are used to calculate the unpolarized Raman spectrum in Raman_Fitting_Process_Part_2.m. See the scripts for further instruction and information. Raman Raman Raw Data.mat: This MATLAB data file contains all the raw data used for Raman spectra analysis. All variables are of MATLAB structure data type. Each variable has fields called Freq and Raw, with Freq contains the wavenumber information of the measured spectra and Raw contains 5 measured Raman signal strengths. Variable XX, XZ, ZX, ZZ, and YY were used to plot and sub-peak analysis for Figure 2c-d, Raman data points in Figure 4a, Figure 5b, Supplementary Figure 2, and Supplementary Figure 7. Variable WideRange was used to plot and identify the peaks for Supplementary Figure 3b. X-Ray X-Ray.mat: This MATLAB data file contains the raw X-ray data used for the diffraction analysis in Supplementary Figure 5. 

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