Find research datasets worth reusing

Data underlying the article: Molecular insights into disease-associated glutamate transporter (EAAT1 / SLC1A3) variants using in silico

This repository contains the scripts and data for the project published in Frontiers in Molecular Biosciences under the title: Molecular insights into disease-associated glutamate transporter (EAAT1 / SLC1A3) variants using in silico and in vitro approaches (DOI <a href="https://www.frontiersin.org/articles/10.3389/fmolb.2023.1286673/full">10.3389/fmolb.2023.1286673</a>).

Replication data for "The Role of Modal Substitution in Rebound Effects Within US Freight Transportation"

There are two data files corresponding to the 2012 and 2017 Commodity Flow Survey and associated auxiliary data required for replication.

Raw data for: Structure of the human dopamine transporter and mechanisms of allosteric inhibition

This repository contains raw data related to "Structure of the human dopamine transporter and mechanisms of allosteric inhibition" by Srivastava et al. Included are molecular dynamics input parameter files, amber prmtop, production trajectories and analysis scripts. Trajectories are subsampled with one frame every 10 ns.    Contact information: Name: Md Fulbabu Sk Institution: Theoretical and Computational Biophysics Group (TCBG), Beckman Institute, University of Illinois Urbana Champaign Address: 405 N. Mathews Avenue, Urbana, Illinois 61801 Email: mfsk@illinois.edu

Mobility of magmas within the Earth: Insights from the elasticity and transport properties of hydrous albitic melts

Results from first-principles molecular dynamics simulations of anhydrous and hydrous albitic melts.

Data for "Investigating molecular transport in the human brain from MRI with physics-informed neural networks"

Data analyzed in Zapf et al. <a href="https://www.nature.com/articles/s41598-022-19157-w">Investigating molecular transport in the human brain from MRI with physics-informed neural networks</a> (Scientific Reports 2022). The data consists of CSF tracer concentrations in the brain subregions analyzed in the article. The data was pre-processed as described in S1.1 in the supplementarty materials.  In Python, load the data as numpy arrays using the nibabel package as <pre><code>import nibabel data = nibabel.load("068/concentrations/24h.mgz").get_fdata() domain_mask = nibabel.load("068/masks/roi.mgz").get_fdata().astype(bool) And view slices of the data as:</code></pre> <div> <div>plt.figure()</div> <div>plt.imshow(np.take(data, 150, 0), vmax=0.1)</div> <div>plt.figure()</div> <div>plt.imshow(np.take(data, 100, 1), vmax=0.1)</div> <div>plt.figure()</div> <div>plt.imshow(np.take(data, 100, 2), vmax=0.1)</div> <div>plt.show()</div> </div> <pre> </pre>

opencc-by-4.0Jun 2024View details →

Non-Hermitian topology of transport in Chern insulators

This repository contains our simulation data and codes used to produce the figures of the manuscript/supplementary material.

opencc-by-4.0Jun 2024View details →

Data for PhD Thesis: "Chemical and electronic structure of Cu$_2$O, NiO, and Cu$_2$O-NiO combinatorial material libraries as hole-transport material for halide perovskite solar cells"

Here, the whole data measured during the PhD time of L. CW. Bodenstein-Dresler + Labbook is uploaded. T data in the "data"-folder was measured at HZB with XPS, UPS and IPES.    The PEYS and CPD and XRD data was measured by A. Kama at BIU.

opencc-by-4.0Aug 2023View details →

The dataset for the manuscript entitled "SUPHRE: A reactive transport model with unsaturated and density-dependent flow"

This is the dataset for the manuscript entitled "SUPHRE: A reactive transport model with unsaturated and density-dependent flow".

Exploring doxorubicin transport in 2D and 3D models of MDA-MB-231 sublines: impact of hypoxia and cellular heterogeneity on doxorubicin accumulation in cells

This data set includes raw data supporting the paper "Exploring doxorubicin transport in 2D and 3D models of MDA-MB-231 sublines: impact of hypoxia and cellular heterogeneity on doxorubicin accumulation in cells". The files include the following data: 1. MTT assay results used for calculation of cell viability / EC50 values for doxorubicin in MDA-MB-231 cell line and its sublines; 2. The raw data used for calculating doxorubicin transport in 2D cells under normoxia; 3. The raw data used for calculating doxorubicin transport in 2D cells under hypoxia; 4. The raw data used for calculating doxorubicin transport in cancer spheroids (3D cultures).

opencc-by-4.0Jan 2024View details →

Investigating solute transport and reaction using a mechanistically coupled geochemical and geophysical modeling approach

This repository encompasses the acquired data for the five experiments of reactive percolation in a column with geoelectrical monitoring. The input and output files of the reactive transport simulations are also given. In addition, five movies of the reaction rate evolving with time are also part of this dataset. The files are: <ul> <li>physicochemical_data.xlsx: the ionic concentrations, alkalinity, pH, and electrical conductivity from the collected water samples, the pH monitored at two locations in the column, and the inlet and outlet water conductivity and temperature. Porosity and formation factor calculated from the measured calcium concentration are also given.</li> <li>sp-data-exp1-exp2-exp3.xlsx: the self-potential (SP) method has been used to monitor the reactive percolation for experiments 1, 2, and 3.</li> <li>sip-data-exp4.xlsx and sip-data-exp5.xlsx: the spectral induced polarization (SIP) method has been used to monitor the reactive percolation for experiments 4 and 5.</li> <li>output_expX.zip: compressed folders of all output files for the reactive transport simulations using Crunchflow software.</li> <li>1DcalciteFT_exX.in: input files for the reactive transport simulation using CrnchFlow software.</li> <li>OldRifleDatabaseLiLi_nicole.dbs: database for the reactive transport simulation using CrnchFlow software.</li> <li>video-rate-expX.avi: movies of the reaction rate along the column and evolving with time for the complete duration of each experiment.</li> </ul>

Model and observation data for paper "Variability of the bottom boundary layer induced by the dynamics of the cross-isobath transport over a variable shelf"

Model and observation data for paper "Variability of the bottom boundary layer induced by the dynamics of the cross-isobath transport over a variable shelf"

The conformational plasticity of structurally unrelated lipid transport proteins correlates with their mode of action

Supporting DATA files for "Conformational plasticity of structurally unrelated lipid transport proteins correlates with their mode of action". <ol> <li>zenodo_simulation_starting_files_and_result_pdbs.zip contains input files for atomistic and coarse-grained MD simulations, membrane binding interface results from coarse-grained simulations, and apo-like and holo-like conformations of lipid transfer domains arising from clustering of atomistic simulations</li> <li>zenodo_data_and_codes.zip contains the raw data and/or scripts used for the analysis of the figures of the paper as well as a README file explaining the contents. The figure caption in the manuscript indicates the folder name that contains data relevant to that particular figure.  The trajectories have not been uploaded here, in case you are interested, please ask the corresponding author (stefano.vanni@unifr.ch). </li> </ol>

An observation-based estimate of the Atlantic meridional freshwater transport

Open the record for dataset details and reuse information.

Raw data from "On the lineshapes of temperature-dependent transport measurements of superconductors under pressure"

Open the record for dataset details and reuse information.

Cumulative arrival time distribution data for "Upscaling transport in heterogeneous media featuring local-scale dispersion: flow channeling, macro-retardation and parameter prediction"

<div> <div>This archive contains arrival time CDF data for a variety of transport simulations in heterogeneous Darcy flow fields, alongside metadata describing the flow fields. The flow fields were spatially periodic, intersected by uniformly-spaced imaginary planes. Arrival times represent length of time from particle departure from one plane until arrival at the next.</div> <div> </div> <div>Consult the README.md file at the top level of the archive for more information. The file format used to store the CDF data is documented in the Python script at the top level of the archive.</div> </div>

openeupl-1.1Feb 2018View details →

Dataset for "Real-Time Hydraulic Interval State Estimation for Water Transport Networks: a Case Study"

The dataset (EPANET file) which accompanies the publication  Vrachimis, S. G., Eliades, D. G., and Polycarpou, M. M.: Real-Time Hydraulic Interval State Estimation for Water Transport Networks: a Case Study, Drink. Water Eng. Sci., 2018

openother-atJan 2018View details →

A collection of public transport network data sets for 25 cities

This dataset describes the public transport networks of 25 cities across the world in multiple easy-to-use data formats. These data formats include network edge lists, temporal network event lists, SQLite databases, GeoJSON files, and General Transit Feed Specification (GTFS) compatible ZIP-files. The source data for creating these networks has been published by public transport agencies according to the GTFS data format. To produce the network data extracts for each city, the original data have been curated for errors, filtered spatially and temporally and augmented with walking distances between public transport stops using data from OpenStreetMap.  Cities included in this dataset version: Adelaide, Belfast, Berlin, Bordeaux, Brisbane, Canberra, Detroit, Dublin, Grenoble, Helsinki, Kuopio, Lisbon, Luxembourg, Melbourne, Nantes, Palermo, Paris, Prague, Rennes, Rome, Sydney, Toulouse, Turku, Venice, and Winnipeg. Contrary to the version 1.0 of this data set, this version (1.2) does not include the cities of Antofagasta and Athens, for which non-commercial usage of the data is not allowed. Contrary to previous versions of the data set (1.0 and 1.2), in this version (1.2) the temporal filtering of the data has been slightly adapted, so that the daily and weekly data extracts cover all trips departing between from 03 AM on Monday to 03 AM on Tuesday (daily extract) or 03 AM of the Monday next week (weekly extract). Additionally, a temporal network extract covering a full week of operations has been added for each city. Documentation of the data can be found in the Data Descriptor article published in Scientific Data: http://doi.org/10.1038/sdata.2018.89  When using this dataset, please cite also the above-mentioned paper.

opencc-by-4.0Mar 2018View details →

Dataset: Mantle convection and water transport

This dataset contains simulation results used for Figures in Nakao et al. (2018, GRL) “Roles of hydrous lithospheric mantle in deep water transportation  and subduction dynamics”.

opencc-by-4.0Jun 2018View details →

Videos of electrochemiluminescence response for paper "Direct visualization of reactant transport in forced convection electrochemical cells and its application to Redox Flow Batteries"

Videos showing the real time electrochemiluminescent light production in a serpentine flow field of a redox flow battery type system. The two videos show the difference when only an ITO electrode is used compared to when an ITO and carbon paper electrode is used.