Find research datasets worth reusing

opencc-zeroMar 2024View details →

Processed data for the analysis of human mobility changes from COVID-19 lockdown on bird occupancy in North Carolina, USA

The COVID-19 pandemic lockdown worldwide provided a unique research opportunity for ecologists to investigate the human-wildlife relationship under abrupt changes in human mobility, also known as Anthropause. Here we chose 15 common non-migratory bird species with different levels of synanthrope and we aimed to compare how human mobility changes could influence the occupancy of fully synanthropic species such as House Sparrow (Passer domesticus) versus casual to tangential synanthropic species such as White-breasted Nuthatch (Sitta carolinensis). We extracted data from the eBird citizen science project during three study periods in the spring and summer of 2020 when human mobility changed unevenly across different counties in North Carolina. We used the COVID-19 Community Mobility reports from Google to examine how community mobility changes towards workplaces, an indicator of overall human movements at the county level, could influence bird occupancy.

opencc-by-4.0Feb 2024View details →

Statistical analysis of data determining minimal selective concentration of Amoxicillin, doxycycline and enrofloxacin

This repository is containing the datasets with statistical analysis of the paper: "Selection for amoxicillin, doxycycline and enrofloxacin resistant Escherichia coli at  concentrations lower tha nthe ECOFF in rich media and in broiler-derived fecal fermenations." The phenotypic analysis <ul> <li>Phenotypic amoxicillin <ul> <li>R-file: Phenotypic Amox mixed models, CSV-file: Phenotypic data Amox</li> </ul> </li> <li>Phenotypic doxycycline <ul> <li>R-file: Phenotypic Dox mixed models, CSV-file: Phenotypic data Dox</li> </ul> </li> <li>Phenotypic enrofloxacin <ul> <li>R-file: Phenotypic Enro mixed models, CSV-file: Phenotypic data Enro</li> </ul> </li> </ul> The resistome analysis  <ul> <li>two CSV-files: Resistoom workfile and resistome_reference_file</li> <li>one R-file: Resistome_analysis_antimicrobial_classes</li> </ul> Microbiome analysis <ul> <li>Alpha- and beta-diversity analysis <ul> <li>R-file Biom analysis, CSV-file: metadata2, biom-file: reads_fermentation</li> </ul> </li> <li>Microbial abundance analysis <ul> <li>R-file: Abundance plot, CSV-file: metadata2. biom-file: reads_fermentation2.biom</li> </ul> </li> </ul>

Data from: Dietary partitioning among three cryptobentic reef fish mesopredators revealed by visual analysis, metabarcoding of gut content, and stable isotope analysis

Understanding how mesopredators partition their diet and the identity of consumed prey can assist in understanding the ecological role predators and prey play in ecosystem trophodynamics. Here, we assessed the diet of three common coral reef mesopredators; Pseudochromis flavivertex, Pseudochromis fridmani, and Pseudochromis olivaceus from the family Pseudochromidae, commonly known as dottybacks, using a combination of i) visual stomach content analysis, ii) stomach content DNA metabarcoding (18S, COI), and iii) stable isotope analysis (δ15N, δ13C). In addition, P. flavivertex is found in two distinct color morphs in the Red Sea, providing an opportunity to analyze intra-morph differences. These techniques revealed partitioning in the dietary composition and resource use among species. Arthropods comprised the main dietary component of P. flavivertex (18S > 60%; COI > 10%), and P. olivaceus (18S = 57.2%) while P. fridmani ingested predominantly mollusks (18S = 51.3%, COI = 24.6%). Despite being small predators, microplastics were found in the gut content of some of these fishes. Stable isotope analysis showed differences in species' isotopic niche breadth and trophic position. Pseudochromis olivaceus presented the largest isotopic niche (SEAC = 1.61‰2), while P. fridmani showed the smallest isotopic niche (SEAC = 0.45‰2) among species. Although the two techniques used for stomach content analysis did not show differences in the diet within color morphs of P. flavivertex, they differed in the isotopic niche and resource use. Despite our limited sampling, our findings provide evidence of species-specific differences in the trophic ecology of dottybacks and demonstrate their important role as predators of cryptic invertebrates and small fishes. This study highlights the importance of combining several approaches (short-term: visual analysis and DNA metabarcoding; and long-term: isotope analysis) when assessing the feeding habits of coral reef fish, as they provide complementary information necessary to delimit their niches and understand the role that small mesopredators play in coral reef ecosystems.

Data from: A qualitative analysis of an Aβ-monomer model with inflammation processes for Alzheimer's disease

We introduce and study a new model for the progression of Alzheimer's disease incorporating the interactions of Aβ-monomers, oligomers, microglial cells and interleukins with neurons through different mechanisms such as protein polymerization, inflammation processes and neural stress reactions. In order to understand the complete interactions between these elements, we study a spatially-homogeneous simplified model that allows to determine the effect of key parameters such as degradation rates in the asymptotic behavior of the system and the stability of equilibriums. We observe that inflammation appears to be a crucial factor in the initiation and progression of Alzheimer's disease through a phenomenon of hysteresis, which means that there exists a critical threshold of initial concentration of interleukins that determines if the disease persists or not in the long term. These results give perspectives on possible anti-inflammatory treatments that could be applied to mitigate the progression of Alzheimer's disease. We also present numerical simulations that allow to observe the effect of initial inflammation and concentration of monomers in our model.

opencc-by-4.0Apr 2024View details →

Data and code for the publication "Multi-method analysis of microplastic distribution by flood frequency and local topography in Rhine floodplains"

Background The dataset contains data on soil properties and microplastic abundance in soil samples taken in the floodplains Langel-Merkenich, Poller Wiesen and Westhovener Aue (Cologne, Germany). They were analysed in the paper by M. Rolf, H. Laermanns, J. Horn, L. Kienzler, C. Pohl, G. Dierkes, S. Kernchen, C. Laforsch, M.G.J. Löder and C. Bogner, “Multi-method analysis of microplastic distribution by flood frequency and local topography in Rhine floodplains” <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.scitotenv.2024.171927" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.scitotenv.2024.171927</a>) published in Science of the Total Environment.

opencc-by-4.0Jan 2024View details →

MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data

This repository contains the data required to run the example notebooks and to reproduce the figures from the paper :  <div> <div>MUFFIN : A suite of tools for the analysis of functional sequencing data</div> </div> <div>Pierre de Langen, Benoit Ballester</div> <div>bioRxiv 2023.12.11.570597; doi: <a href="https://doi.org/10.1101/2023.12.11.570597" target="_blank" rel="noopener">https://doi.org/10.1101/2023.12.11.570597</a></div> <div> </div> <div>Source code is located here :</div> <div><a href="https://github.com/pdelangen/Muffin" target="_blank" rel="noopener">https://github.com/pdelangen/Muffin</a></div> <div> </div> <ul> <li>10k_pbmc_gene/ contains the data for 10k pbmc dataset in standard 10x sparse count table format.</li> <li>genome_annot/ contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)</li> <li>GO_files/ contains gene set information retrieved from the g:ProfileR website.</li> <li>immune_chip/ contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.</li> <li>tcga_atac/ contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.</li> <li>scATAC/  contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.</li> </ul> <div> </div>

Data from: Building functional and sustainable pharmacovigilance systems - an analysis of pharmacovigilance development across high-, middle- and low-income countries

Background Pharmacovigilance (PV) is an essential component of health systems. Functional PV systems protect and promote public health by supporting the safe and effective use of medicinal products through the prevention and mitigation of harm. With increased simultaneous introduction of innovative products in high-, middle- and low-income countries, e.g., COVID-19 vaccines, or solely in low- and middle-income countries (LMIC), e.g., malaria vaccines, PV systems in LMIC must be able to detect safety signals and ensure adequate safety surveillance. This research aims to analyse the development of PV systems across high-, middle- and low-income countries and to carve out essential elements for implementing functional and sustainable PV systems in LMIC. Methods A convergent parallel mixed-methods design, consisting of qualitative and quantitative methods was used. Qualitative research consisted of semi-structured interviews. To expand the breadth and range of the study, a quantitative survey was conducted, focusing on the same thematic questions as the semi-structured interviews. Results Twelve key informants from nine countries were interviewed and 52 respondents from 36 countries completed an online questionnaire. Four major themes consisting of 12 categories emerged from the data. Based on these, the following elements essential for building functional and sustainable pharmacovigilance systems in LMIC were identified: understanding the drivers of PV development; adequately resolving core system challenges; implementing an efficient organisational structure and procedures for PV; investing in activities beyond reporting of adverse drug reactions; identifying alternate sources of financing; having a national strategy with a vision and mission for PV; adequately leveraging the health system; and effectively integrating the pharmaceutical sector in the national PV system. Conclusions Findings from this research revealed progress in PV systems in LMIC in the last decade, though significant efforts are still needed to develop these systems to meet global standards. Developing the different areas emerging from this research, which necessitates implementing functional PV structures and processes, adequately leveraging the health system and effectively engaging the pharmaceutical sector, through the mechanisms proposed, would enable a comprehensive progression from basic to stable, functional and thus sustainable PV systems in LMIC.

Data from: the great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographic range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugiam, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear "islands of differentiation", even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow

Red deer (Cervus elaphus) throughout central Europe are impacted by different anthropogenic activities including habitat fragmentation, selective hunting, and translocations. This has substantial influences on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess the genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, and anthropogenic infrastructures) has led to comparably low levels of genetic diversity. The mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. Based on these findings, we suggest that connectivity among existing management units needs to be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.

opencc-by-4.0Apr 2024View details →

Data on soil variables (with plot IDs) and grassland species traits used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. Journal of Vegetation Science, 35, e13259. Available from: https://doi.org/10.1111/jvs.13259

File <a href="../api/records/10983049/draft/files/Plot_IDs_990ua.txt/content" target="_blank" rel="noopener noreferrer">Plot_IDs_990ua.txt</a> contains the IDs of the 1-m2 plots used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. The plot data are stored in the sPlot database (PPBio South Brazilian Grassland Database). File <a href="../api/records/10983049/draft/files/E_990ua_21SoilVar.txt/content" target="_blank" rel="noopener noreferrer">E_990ua_21SoilVar.txt</a> contains data on soil variables evaluated in the 250 m transects, but here expanded to the 990 1-m2 plots (each transect was sampled using 10 1-m2 pots). File <a href="../api/records/10983049/draft/files/B_769spp_4t.txt/content" target="_blank" rel="noopener noreferrer">B_769spp_4t.txt</a> is the species trait database collected in the framework of several research projects in the Quantitative Ecology Lab (EcoQua) and Grassland Vegetation Studies Lab (LevCamp) of Universidade Federal do Rio Grande do Sul (UFRGS). Data gaps were filled by compiled from the TRY database and data imputation.

opencc-by-4.0Apr 2024View details →

Data used by Bouchez-Zacria et al. in "Analysis of the Usutu episode of summer 2018 in birds in France."

The zip file contains the raw dataset used by Bouchez-Zacria et al. in their model of the usutu episode in summer 2018. The README file explains the content of this dataset.

dem files for Antarctic maps and data analysis

<div> <pre> We use BedMachine Antarctica v2, 1km resolution [https://nsidc.org/data/nsidc-0756/versions/2](https://nsidc.org/data/nsidc-0756/versions/2) (to be updated one day to v3, see below) to: * estimate the surface elevation of observation when not available: [BedMachineAntarctica_v02.nc](./data/dem/BedMachineAntarctica_v02.nc) * generate lower resolution maps of Antarctica for plots: e.g. at 10km, [ANT10km_BedMachineAntarctica_v02.nc](./data/dem/ANT10km_BedMachineAntarctica_v02.nc) You can load this data in the [./data/dem](./data/dem) from the > [!IMPORTANT] > Do not forget to cite the following articles when using this script > > #### Data Citation and Acknowledgment > As a condition of using these data, you must cite the use of this data set. Such a practice gives credit to data set producers and advances principles of transparency and reproducibility. > > * Morlighem, M. (2020). MEaSUREs BedMachine Antarctica. (NSIDC-0756, Version 2). [Data Set]. Boulder, Colorado USA. NASA National Snow and Ice Data Center Distributed Active Archive Center. https://doi.org/10.5067/E1QL9HFQ7A8M. [describe subset used if applicable]. Date Accessed 11-13-2024. > > When using this data product in a publication, please include the following citations in addition to the data product citation provided above: > > * Morlighem, M., Rignot, E., Binder, T., Blankenship, D. D., Drews, R., Eagles, G., Eisen, O., Ferraccioli, F., Forsberg, R., Fretwell, P., Goel, V., Greenbaum, J. S., Gudmundsson, H., Guo, J., Helm, V., Hofstede, C., Howat, I., Humbert, A., Jokat, W., Karlsson, N. B., Lee, W., Matsuoka, K., Millan, R., Mouginot, J., Paden, J., Pattyn, F., Roberts, J. L., Rosier, S., Ruppel, A., Seroussi, H., Smith, E. C., Steinhage, D., Sun, B., van den Broeke, M. R., van Ommen, T., van Wessem, M. & Young, D. A.. 2020. Deep glacial troughs and stabilizing ridges unveiled beneath the margins of the Antarctic ice sheet. Nature Geoscience. 13. DOI: 10.1038/s41561-019-0510-8. > > To promote open science principles and reproducibility, we encourage you to make your data citation specific to the subset used in your research. Common examples of information include spatial and temporal range and file types if relevant. You can load your favorite dem for Antarctica in [./data/dem](./data/dem): * The dem should be in the Spatial Reference System "Antarctic Polar Stereographic EPSG:3031" * E.g. the last version of BedMachine Antarctica: https://nsidc.org/data/nsidc-0756/</pre> </div>

opencc-by-4.0Jun 2024View details →

Supplementary data: Effect of genotype by environment interaction (GEI) analysis for potato tuber yield and their quality traits in organic multi-environment domains of Poland

Climate and raw data supplementary to the related publication in the journal Agriculture (ISSN 2077-0472).

Sahana et al. Supplementary Data for Global Transboundary River Research: Databases, Case Study Analysis, and Regional Statistics for Sustainable Management

This dataset supports our comprehensive review article on transboundary river research, exploring its implications for sustainable management worldwide. Utilizing machine learning, we analyzed 4,237 publications and conducted an in-depth desk review of 325 selected papers, examining a total of 4,713 case studies spanning 286 river basins globally. The study provides critical insights into upstream, midstream, and downstream regions, offering a complete view of challenges and opportunities in transboundary river management. Supplementary Data 1 contains the main database used in this study, sourced from Scopus, Web of Science, and Google Scholar. Additionally, Supplementary Data 2 and 3, included in the spreadsheet, offer statistics and further resources essential for understanding regional and cross-regional dynamics in river basin governance. These supplementary resources include key statistics, case study metadata, and tools, helping to facilitate a deeper exploration of basin-specific and global trends in transboundary water management. This collection of data and resources provides a valuable foundation for researchers and policymakers in advancing sustainable transboundary river management practices.

opencc-by-4.0Oct 2024View details →

Magic running and standing wave optical traps for Rydberg atoms - Data and code for analysis

Data, theory calculation and plotting scripts for the publication titled "Magic running and standing wave optical traps for Rydberg atoms" (<a href="https://arxiv.org/abs/2410.20901" target="_blank" rel="noopener">arXiv:2410.20901</a>).   File legend <ul> <li> <code>data_FIGx_yyy.mat</code> contains the calculated or measured data used in Figure x</li> <li> <code>calc_FIGx_yyy.py</code> is the script to calculate the theoretical data used in Figure x</li> <li> <code>plot_FIGx_yy.py</code> is the script to create the Figure x of the paper</li> <li> <code>simulation_class.py</code> is a class with theory functions</li> <li> <code>paperstyle.mplstyle</code> is a matplotlib style file</li> <li> <code>requirements.txt</code> lists all the required python packages</li> </ul>   Abstract Magic trapping of ground and Rydberg states, which equalizes the AC Stark shifts of these two levels, enables increased ground-to-Rydberg state coherence times. We measure via photon storage and retrieval how the ground-to-Rydberg state coherence depends on trap wavelength for two different traps and find different optimal wavelengths for a 1D optical lattice trap and a running wave optical dipole trap. Comparison to theory reveals that this is caused by the Rydberg electron sampling different potential landscapes. The observed difference increases for higher principal quantum numbers, where the extent of the Rydberg electron wave function becomes larger than the optical lattice period. Our analysis shows that optimal magic trapping conditions depend on the trap geometry, in particular for optical lattices and tweezers.   Theory calculation We implemented the potential arising from the Hamiltonians described in the paper. The functions are shared here in the python class <code>simulation_class.py</code>. This class is used in the calculation scripts named <code>calc_FIGx_yyy.py</code> and saves the data as <code>data_FIGx_yyy.mat</code> for the respective Figure x. In case of questions to the code or calculations, please contact Chris Nill or Lukas Ahlheit.   Experimental data The experimental data published here are photon storage and retrieval traces of 780 nm probe photons as function of storage duration. We recorded photon traces for different trap laser detunings and Rydberg states. In case of questions to the data, please contact Lukas Ahlheit or Sebastian Hofferberth.   Inkscape modification to specific figures <ul> <li>Figure 1: The plotted data is joined in Inkscape with schematic drawings</li> <li>Figure 2: The plot created by the python file is edited in Inkscape for readability</li> <li>Figure 5: We add two schematics into the figure created by the python file</li> </ul>

opencc-by-4.0Jun 2024View details →

msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis

This record contains example and result data of msiFlow. msiFlow is a collection of automated workflows for reproducible and scalable multimodal mass spectrometry imaging (MSI) and immunofluorescence microscopy (IFM) data processing and analysis. Using an experimental mouse model for urinary tract infection, induced by uropathogenic E.coli (UPEC), we generated data by <ul> <li>matrix-assisted laser desorption ionisation mass spectrometry imaging with laser-induced postionisation (MALDI-2 MSI) using the Bruker timsTOFfleX instrument</li> <li>transmission-mode MALDI-2 MSI (t-MALDI-2)</li> <li>immunofluorescence microscopy (IFM) using the MACSima system from Miltenyi </li> </ul> msiFlow was tested on MALDI-2 MSI, t-MALDI-2 MSI and IFM data of control and UPEC-infected mouse bladder sections. In IFM we used Ly6G and actin for staining neutrophils and the muscle layer. We validated msiFlow on MALDI MSI data of bone marrow (BM)-derived neutrophils. Tentative lipid annotations were validated by MALDI DDA MSI and MALDI MS/MS. All data used and results generated by msiFlow are included in this dataset (besides the intermediate results of the MALDI-2 preprocessing due to data size). The dataset contains the following zip files: <table> <tbody> <tr> <td>zip file</td> <td>description</td> </tr> <tr> <td>ly6g_heterogeneity.zip</td> <td>example and result data (Ly6G clusters) for molecular_heterogeneity_flow</td> </tr> <tr> <td>if_segmentation.zip</td> <td>example and result data (Ly6G segmentation) for if_segmentation_flow</td> </tr> <tr> <td>ly6g_heterogeneity_signatures.zip</td> <td>example and result data (lipids for Ly6G clusters) for molecular_signatures_flow</td> </tr> <tr> <td>ly6g_molecular_signatures.zip</td> <td>example and result data (lipids for Ly6G) for molecular_signatures_flow</td> </tr> <tr> <td>msi_if_registration.zip</td> <td>example and result data for msi_if_registration_flow</td> </tr> <tr> <td>msi_segmentation.zip</td> <td>example and result data (segmented MSI bladder data) for msi_segmentation_flow</td> </tr> <tr> <td>region_group_analysis.zip</td> <td>example and result data (regulated lipids in different bladder tissue regions) for region_group_analysis_flow</td> </tr> <tr> <td>macsima.zip</td> <td>raw IFM data of UPEC-infected bladders containing Ly6G, actin and autofluorescence images</td> </tr> <tr> <td>maldi-bm-neutrophils.zip</td> <td>raw and pre-processed MALDI MSI data of BM-derived neutrophils</td> </tr> <tr> <td>t-maldi-2.zip</td> <td>raw t-MALDI-2 MSI data of a UPEC-infected bladder section</td> </tr> <tr> <td>maldi-2-group-sampleno.zip</td> <td>raw MALDI-2 MSI data of a control/UPEC bladder section</td> </tr> <tr> <td>MALDI_DDA_MSI.zip</td> <td>raw MALDI MSI data acquired in DDA mode</td> </tr> <tr> <td>TIMS_MS_MS.zip</td> <td>raw MALDI TIMS MS/MS data</td> </tr> </tbody> </table>

BeEST single pixel data for conservative wavepacket analysis

One day of data from a single STJ pixel from the BeEST experiment.  The data file is the calibaration laser and EC signal energy spectra.  The code file produces limits on uncertainty of the energy measurement and corresponding limits on decay product wavepackets.

Data - Quantifying dynamic linkages between precipitation, groundwater recharge, and streamflow using ensemble rainfall‐runoff analysis

The data support the analysis conducted in "Quantifying Dynamic Linkages Between Precipitation, Groundwater Recharge, and Streamflow Using Ensemble Rainfall‐Runoff Analysis", accepted for publication in Water Resources Research (https://doi.org/10.1029/2024WR037821) by Huibin Gao, Qin Ju, Dawei Zhang, Zhenlong Wang, Zhenchun Hao, and James Kirchner.

opencc-by-4.0Sep 2024View details →

The mechanism of amyloid fibril growth from Φ-value analysis - data and analysis repository

Data used for analysis and figure production. Full MD-simulation dataset is available at https://github.com/Aunstrup/_2024_amyloid_PI3KSH3_Phivalues.

External cavity quantum cascade laser vibrational circular dichroism spectroscopy for fast and sensitive analysis of proteins at low concentrations (Data analysis)

This record contains a docker container image of the data evaluation shown in the publication "External cavity quantum cascade laser vibrational circular dichroism spectroscopy for fast and sensitive analysis of proteins at low concentrations". The evaluations can be accessed by running the container and accessing the contained Jupyter Lab via a browser. The calculations are contained in 'Eval_protein_D2O.ipynb'. To run the container (requires docker): 1.download 'd2o_vcd.tar' 2. in the command line, execute 'docker load -i d2o_vcd.tar'. This will return something like 'Loaded image: <image_name>' with image_name probably being "drhermann/vcd_d2o_00:trial_03" 3. then 'docker run -p 8889:8889 <image_name>' replacing the brackets with the actual name of the image, such as drhermann/vcd_d2o_00:trial_03 4.In your command line a link starting in 'http://127.0.0.1:8888/lab?token=...' will appear. Open this link in your browser to access the evaluation.