Find research datasets worth reusing

opencc-by-4.0Apr 2020View details →

CrocO: manuscript Dataset

This archive includes the dataset associated with the release of CrocO_v1.0 snowpack ensemble data assimilation system in the submitted manuscript: <blockquote> CrocO : a Particle Filter to assimilate snowpack observations in a spatialised framework, Bertrand Cluzet, Matthieu Lafaysse, Emmanuel Cosme, Clement Albergel, Louis-François Meunier, and Marie Dumont, Geoscientific Model development, 2021, doi:10.5194/gmd-14-1595-2021. </blockquote> CrocO_toolbox, the python code used to launch the simulations and produce this dataset is available on github: <a href="https://github.com/bertrandcz/CrocO">https://github.com/bertrandcz/CrocO</a>_toolbox, tag CrocO_v1.0, and at the associated zenodo archive: https://doi.org/10.5281/zenodo.3784980  The model source code and required librairies (open-source) are archived at: https://doi.org/10.5281/zenodo.3774861 This archive includes the several directories : <ul> <li>namelist_conf : the original namelists and configuration files used to perform the assimilation experiments</li> <li>notebooks : notebooks to produce the figures of the article and select the openloop members used as synthetic observations</li> <li> s2m/12/* :  <ul> <li>simulation outputs required to reproduce the article figures (openloop simulation and assimilation experiments</li> <li>spinup: files used to initialize the simulations</li> </ul> </li> <li>safran/12/* : <ul> <li>reference forcing before perturbations, originating from SAFRAN reanalyses (<a href="https://doi.org/10.25326/37">https://doi.org/10.25326/37</a>).</li> <li>original impurities forcing file from MOCAGE model and extracted by F.Tuzet at the Col du Lautaret.</li> </ul> </li> <li>scores : the scores used in Figs. 6-7 of the manuscript.</li> </ul>

opencc-by-4.0Jun 2020View details →

Dataset and script for the manuscript Lobet et al. 2020 presenting the QuoVidi web interface

Dataset and scripts used for the figure of the manuscript "QuoVidi : a open-source web application for the organisation of large scale biological treasure hunt" by Guillaume Lobet, Charlotte Descamps, Lola Leveau, Alain Guillet and  Jean-François Rees (2020)

opencc-by-4.0Jun 2020View details →

Extended data for Manuscript: Precision medicine implementation and research-practice partnerships: implications of measurement scale differential item functioning (DIF)

This is the extended data for the manuscript submitted to F1000 Research titled: Precision medicine implementation and research-practice partnerships: implications of measurement scale differential item functioning (DIF). File 1 is the redacted survey responses from a card sort exercise carried out to find out how the study participants sorted and ranked various measures of factors thought to influence precision medicine implementation at health systems level. File 2 consists of the study package as described in the article

opencc-by-4.0Aug 2020View details →

Data supporting manuscript "Effect of cold front-induced waves along wetlands boundaries" submitted to JGR Oceans

This directory contains simulation data used in the manuscript "Effect of cold front-induced waves along wetlands boundaries" submitted to jGR Oceans. 1. Matlab codes for wind input generation    (From NCEP Reanalysis data and NOAA weather station to Delft3D space-varying wind input) 2. Wave Power Calculator     (Wave number calculation by the dispersion relation Including Newton–Raphson codes, Shallow and Deep-water approximation availability check) Data are intended for the reviewers and may be updated until the review process is complete.

opencc-by-4.0Sep 2020View details →

Data for GRL manuscript "Vertical Coordinate and Resolution Dependence of the Second Moment Turbulent Closure Models"

The zipped directory contains data used for analysis and figures in the GRL manuscript "Vertical Coordinate and Resolution Dependence of the Second Moment Turbulent Closure Models" ### OSP observations: Air Temperature: airt50n145w_hr.ascii    Ocean Temperature: t50n145w_hr.ascii  Ocean Salinity: s50n145w_hr.ascii Total Heat Flux:  heatflux_papa.dat 10m Wind Speed: wspd_papa.dat u and v components of Stokes drift velocity hourly time series given on vertical grid vertical_grid_128: uvstk_papa.dat ### NCOM simulation results out_Model_LayerGrid.dat Model:   h15 - use harcourt (2015)     kc04 - use Kantha & Clayson (2004)   myl2p5 - use Mellor & Yamda (1982) level 2.5 Layer:   030, 040, 050, 080, 100 Grid:   s - uniform stretched grid   u - uniform grid   y - mixed layer enhanced grid The following variables are provied in all out_*.dat files as given in their headers  depth (m) tke (cm2/s2) dis (cm2/s3) tl (cm)  zkm (cm2/s)  zkh (cm2/s) T (C) S (psu) pd (kg/m3) z-mid (m) ### LES output Eddy viscosity computed using LES model   LES simulation with all foring - Km_les_AllForcing.dat   LES simulation without Stokes drift - Km_les_NoStk.dat   LES simulation without Heat Flux - Km_les_NoHF.dat

Networks of Shared Manuscript Transmission for Medieval European Vernacular Languages

Codices that compile different textual units in the same physical object were common in the European Middle Ages. Many reasons guided scribes when collecting a variety of works and their analysis can offer scholars insight into scribal practices and the circulation of medieval works. In order to study this shared transmission of medieval texts, methods from network analysis offer the possibility of researching the phenomenon from a general perspective and discover fundamental trends. This paper deals with the methodological and practical foundations for such an approach.   Modern digital databases of medieval manuscripts provide a big amount of relevant data for this type of research. In this presentation, I consider three online databases, each dealing with textual witnesses in vernacular languages: Handschriftencensus (German) Jonas (French and Occitan) and Philobiblon (Iberian languages). Each of these has different criteria on data collection and data modelling. For this reason, their analysis and comparison offers insight not only on medieval manuscripts and texts, but also on the consequences of different approaches when cataloguing and describing medieval manuscripts.

From Networks of Texts to Networks of Genres? On the Classification of Texts in Compilations with a View towards Manuscript Transmission

At the end of the 14th century, Jakob Twinger von Königshofen, a cleric from Strasbourg, composed a chronicle in the vernacular that spread widely – up to today nearly 130 manuscripts are known that contain the text, wholly or in parts, and that were produced not only in Strasbourg, but as far as Cologne, Augsburg, or Tyrol. About thirty qualify as true copies, while in the big majority of the witnesses, the text is altered in various ways: abbreviated, augmented, updated, corrected, put in a dierent order, and more often than not combined with other texts, either with distinct text boundaries or resulting in new compositions made of several texts. In several manuscripts, a combination of historiographical texts – chronicles, annals, lists, etc. – can be observed, leading to the assumption that Twinger’s work was preferably copied for historiographical compilations and that its structure facilitated some historiographical activity of the recipients. But this view puts a big weight on the genre of Twinger’s work, making it a filter through which all the other texts in a codex are seen. As I have been working on the chronicle transmission, the attribute in common of the known manuscripts is of course the appearance of at least some lines of the Twinger chronicle; but the attempt to look at a single codex as objectively as possible, without giving preference to a particular text, can not only reveal connections between different manuscripts, but also the fluidity and flexibility of medieval texts. The classification of a work as part of a certain genre does not necessarily hold true for its entire transmission, for the manifestation of a distinct text – what is, on the one hand, a nuisance, but on the other a chance to better understand medieval text transmission, manuscript production and the transfer of knowledge. The co-occurrence of certain texts in several manuscripts hints towards intentional copying processes that are reflecting particular interests not only of one individual scribe or commissioner; multiple occurrences of particular compilations can reveal networks that go unseen if the content of a codex is not regarded as a whole. While a text-based analysis often faces difficulties that result from insufficient manuscript descriptions, a broader view that would compare less particular texts, but more areas of interest or fields of knowledge, has to deal with problems regarding the classification of the single texts: Apart from an inevitable subjectivity, questions about the criteria and levels of classification have to be addressed, while the danger of over- or under-representation is always lurking. Discussing these issues and the applicability and usefulness of the comparison of codices from a kind-of-genre-perspective could be fruitful to develop a better understanding for the transmission of manuscripts, of texts and of knowledge.

Patterns of Knowledge Circulation in Early Modern East-Central Europe: Tracing Jewish Kabbalistic Textual Units in Multiple-Text Manuscripts

This presentation will provide initial insights into the first comprehensive study of the networks of production and circulation of Jewish esoteric texts in early modern East-Central Europe (1500-1750). This study, which is funded by the German Research Foundation and has begun in 2019, aims to collect datasets and quantitatively analyse the transmission and reception of Jewish esoteric traditions recorded in manuscript form. In doing so, the study makes use of network analysis methods and utilises digital database environment (provided by LAB 1100) that facilitates analysis and visualisation of data with complex temporal, geographical and relational attributes. The scholarship on Jewish books, both in manuscripts and in print, and kabbalah has centred chiefly on studying individual figures, narrowing the focus of study to singular individuals and groups. Such an approach, although important, stops short of unearthing broader patterns and dissemination of ideas, which could be available through analysis of a larger selection of sources. Virtually no study has been to date devoted to examining broader networks of esoteric textual knowledge exchange from the perspective of the material evidence of such interactions. Such examination may offer a more comprehensive view on East-Central European dynamics of creating, transmitting, and re-appropriating kabbalistic and esoteric sources. Of special interest is the phenomenon of copying, transcription and compiling of kabbalistic textual units in multiple-text manuscripts, often of complex codicological structure, which abound as the most universal medium of dissemination for esoteric (kabbalistic) texts. In recent years, substantial methodological changes occurred in the field of manuscript studies, which emphasise positioning and contextualizing manuscripts as material objects within their social and cultural milieus, and rediscovers the network of ‘manuscript cultures,’ i.e. ‘the urban micro-cultures,’ which left their imprints on both the external aspects and the contents of the codices. The current presentation will highlight potentials and challenges of network analysis for the study of circulation of textual units and their variants in multiple complex and composite manuscripts, whose transcription gives evidence to conscious decisions of those involved in their dissemination and subsequent transmission in East-Central Europe. As the study will have run for just over one year by the date of the conference, the presentation will refrain from offering final conclusions, but remain open to discussions and suggestions from scholars deploying similar methods to the study of manuscripts and manuscript cultures.

opencc-by-4.0Apr 2020View details →

SALAMI - Subjective Assessments of Legibility in Ancient Manuscript Images

We introduce a novel dataset of Subjective Assessments of Legibility in Ancient Manuscript Images (SALAMI) to serve as a ground truth for the development of quantitative evaluation metrics in the field of digital text restoration. This dataset consists of 250 images of 50 manuscript regions with corresponding spatial maps of mean legibility and uncertainty, which are based on a study conducted with 20 experts of philology and paleography. Description of files: <ul> <li>images <ul> <li>input - rated test images</li> <li>mean_score_maps - spatial maps of mean legibility</li> <li>std_maps - spatial maps of uncertainty (standard deviation of legibility)</li> </ul> </li> <li>src <ul> <li>images.json - definition of source images contained in the dataset</li> <li>users.json - list of participants with their respective properties</li> <li>assessments.json - the main data generated by our experiments.</li> <li>salami_proc.py - contains python functions to process the .json files named above</li> <li>salami_proc_usage.py - uses the functions from salami_proc.py to reproduce the output images and statistical results described in the accompanying paper</li> <li>salami_llm.R - documents the linear mixed models analysis performed in R</li> </ul> </li> </ul>

Data associated to the manuscript "Computational Screening of the Physical Properties of Water-in-Salt Electrolytes"

Contains input files and data used to generate the figures of the article: Computational Screening of the Physical Properties of Water-in-Salt Electrolytes Trinidad Mendez-Morales, Zhujie Li and Mathieu Salanne, *ChemRxiv*, 13012646v2, 2020 [https://doi.org/10.26434/chemrxiv.13012646.v2](https://doi.org/10.26434/chemrxiv.13012646.v2) *WiS-inputs.zip* contains typical [LAMMPS](https://lammps.sandia.gov/) input files for all the systems. The folder *transport_coefficients* contains the computed viscosities, conductivities and diffusion coefficients for all the systems. The folder *radial_distribution_functions* contains all the partial radial distribution functions for all the systems. The nomenclature of the atoms of the anion is provided in the file *figureS1.pdf* and the atoms from the water molecules are labelled Ow and Hw.

opencc-by-4.0Aug 2019View details →

BPNet manuscript data 1

This repository holds the trained BPNet models and all the output files produced using the models including TF-MoDISco files and motif instances. Files: <ul> <li>output.tar.gz <ul> <li>Full output directory containing trained BPNet models, contribution scores, TF-MoDISco results, motif instances, etc.</li> <li>See <a href="https://github.com/kundajelab/bpnet-manuscript">https://github.com/kundajelab/bpnet-manuscript</a> for more information (archived at <a href="https://zenodo.org/record/4294814">https://zenodo.org/record/4294814</a> with DOI: <a href="https://doi.org/10.5281/zenodo.4294813">https://doi.org/10.5281/zenodo.4294813</a>).</li> </ul> </li> <li>bpnet.model.h5 <ul> <li>BPNet Keras model. This model can be directly used via the model repository Kipoi: <a href="http://kipoi.org/models/BPNet-OSKN">http://kipoi.org/models/BPNet-OSKN</a> . </li> </ul> </li> <li>regions.bed <ul> <li>ChIP-nexus peak regions (resized to 1 kb width) where BPNet was trained and interpreted on.</li> <li>Third column denotes the TF for which the peak was called.</li> </ul> </li> <li>motif-instances.bed <ul> <li>BPNet motif instances for 11 representative motifs</li> <li>Stored as BED file with the following columns <ul> <li>Chromosome</li> <li>Start</li> <li>End</li> <li>Motif name</li> <li>'match' score - similarity to the CWM computed using the continuous Jaccard distance metric between the CWM and L1 normalized contribution scores</li> <li>Strand</li> <li>'contrib' score - computed as the L1 norm of the contribution scores at the motif instance position</li> <li>The log odds score with respect to the PWM derived from the PFM (i.e. classical PWM score)</li> </ul> </li> </ul> </li> <li><TF>.preds.<strand>.bw <ul> <li>Model predictions in `regions.bed` for a particular TF in {Oct4, Sox2, Nanog, Klf4} and strand in {pos, neg}.</li> </ul> </li> <li><TF>.importance.counts.bw <ul> <li>Total count contribution scores for a particular TF</li> </ul> </li> <li><TF>.importance.profile.bw <ul> <li>Profile contribution scores. These were used to run TF-MoDISco and downstream analysis.</li> </ul> </li> <li>PWM,CWM,ChIP-nexus-profiles.tar.gz <ul> <li>Directory containing PFM, CWM and aggregated ChIP-nexus footprint for 11 representative motifs.</li> </ul> </li> <li>Figure-5d-periodicity.csv <ul> <li>Raw data corresponding to Figure 5d where the 10bp periodicity of contribution scores was computed for each motif.</li> </ul> </li> <li>dfabf.Oct4-Sox2-subset.parq <ul> <li>Parquet file (read with `pd.read_parquet`) of genomics motif instance pairs and along with the BPNet-predicted interaction score.</li> <li>See <a href="https://github.com/kundajelab/bpnet-manuscript/blob/dd481a04318dbbd7ea1aa9097ec3b5de8be89f93/src/figures/08-motif-interactions.genomic.ipynb">08-motif-interactions.genomic.ipynb</a> for more information on how to generate plots for Figure 5 from this data.</li> </ul> </li> </ul>

etymologiae.ms: a database of the early medieval manuscripts of the Etymologiae of Isidore of Seville

The Innovating Knowledge project is currently developing an online manuscript database that will bring together up-to-date information about the roughly 450 early medieval codices transmitting the most important medieval Latin encyclopaedia, the Etymologiae of Isidore of Seville. The objective of the database: not only to replace the outdated manuscript handlist of G.E. Anspach (the 1940s), but to work towards improved standards of digital publishing of manuscript data. Learn more about the Innovating Knowledge project at: <a href="https://www.youtube.com/redirect?redir_token=QUFFLUhqbkc1cnIySWVLTHhMNUxIMDFkVWE3UzZneUh5d3xBQ3Jtc0tseVhpZHozVkRMWG5lVTRlVExJRjc0THFnY2ItMGlYWWU0YWZPWUVkdEJkcnBpcmFrdEFRTGJ2RG1DUzJLZ0tBT0F0NUM4Z3ZuY3ZaOVRHMGRkdmI1X1JzbVUxRl94MWpkbUVnSHdzMnlVNHUyMHFKdw%3D%3D&q=https%3A%2F%2Fmittelalter.hypotheses.org%2F21234&event=video_description&v=IBIRfBHK0pU">https://mittelalter.hypotheses.org/21234</a> Presented as a Lightning Talk for the Schoenberg Symposium 2020

Coordinates and description of sample plots described in the manuscript

Coordinates and description of sample plots described in the manuscript "High canopy cover of invasive Acer negundo L. affects ground vegetation diversity" (Veselkin D.V., Dubrovin D.I., Pustovalova L.A.).

Distant Gatherings: A Text-Case for Digital Manuscript Collaborations

The restrictions imposed by COVID19 have challenged all who work in academia, and particularly those who work with material sources like medieval manuscripts, to reconsider normal practices of research exchange and how they might transfer to the online environment.  Rather than slavishly replicating previous in-person formats which are invariably less effective when staged virtually, we have the chance instead to think creatively about how to capitalize on the digital medium, to investigate why people already willingly dedicate so much of their time to computer-based forms of communication. By identifying and co-opting what makes some kinds of virtual exchange successful, we can inspire new forms of academic exchange that re-invent rather than mimic older forms of teaching, research, and learning.

opencc-zeroDec 2020View details →

dryad36/100

The influence of the global COVID-19 pandemic on manuscript submissions and editor and reviewer performance at six ecology journals

Government policies attempting to slow the spread of COVID-19 have reduced access to research laboratories and shifted many scholars to working from home. These disruptions will likely influence submissions to scholarly journals, and affect the time available for editors and reviewers to participate in peer review. In this editorial we examine how journal submissions, and editorial and peer review processes, have been influenced by the pandemic at six journals published by the British Ecological Society (BES). We find no evidence of a change in the geographic pattern of submissions from across the globe. We also find no evidence that submission of manuscripts by women has been more affected by pandemic disruptions than have submissions by men – the proportion of papers authored by women during the COVID period of 2020 has not changed relative to the same period in 2019. Editors handled papers just as quickly, and reviewers have agreed to review just as often, during the pandemic compared to pre-pandemic. The one notable change in peer review during the pandemic is that reviewers replied more quickly to emails inviting them to review (albeit only 4% sooner), and those that agreed to review returned their reviews more quickly (17% sooner), during the pandemic. We thus find no evidence at these six ecology journals that submissions and peer review processes have been negatively impacted by the pandemic. Also, contrary to analyses in other disciplines, we do not find evidence that there have been disproportionate impacts of the pandemic on female authors and reviewers.

dryad36/100

All simulation results, figures and code regarding the manuscript: Calibrating models of cancer invasion: parameter estimation using Approximate Bayesian Computation and gradient matching

We present two different methods to estimate parameters within a partial differential equation (PDE) model of cancer invasion. The model describes the spatio-temporal evolution of three variables -- tumour cell density, extracellular matrix density and matrix degrading enzyme concentration -- in a one-dimensional tissue domain. The first method is a likelihood-free approach associated with Approximate Bayesian Computation (ABC); the second is a two-stage gradient matching method based on smoothing the data with a Generalized Additive Model (GAM) and matching gradients from the GAM to those from the model. Both methods performed well on simulated data. To increase realism, additionally we tested the gradient matching scheme with simulated measurement error and found that the ability to estimate some model parameters deteriorated rapidly as measurement error increased.

opencc-zeroDec 2020View details →

eCodicesNL: a virtual library for medieval manuscripts in Dutch collections

This is a presentation about eCodicesNL: a new initiative to build a virtual library for medieval manuscripts in Dutch collections. The elements that go into this library are, just as in its model project e-codices Switzerland, high quality and complete images, high quality descriptions and an excellent search interface. The concept is simple, but the execution is not: what is the best model for creating such an aggregated library, and how can we deal with data that already exist? How can we facilitate collections to take care of their own material, and keep it updated within a collective system?

opencc-by-4.0Oct 2020View details →

Datasets accompanying Agiwal et al. 2020 manuscript

The following datasets accompany the publication “Constraining the Temporal Variability of Neutral Winds in Saturn's Low-Latitude Ionosphere using Magnetic Field Measurements” by O. Agiwal, H. Cao, S. W. H. Cowley, M. K. Dougherty, G. J. Hunt, I. Mueller-Wodarg, N. Achilleos. Please see READ ME file for more details.

opencc-byDec 2020View details →

Data for manuscript: An ecogeomorphic framework coupling sediment modeling with invasive riparian vegetation dynamics

Datasets (aside from the publicly available GIS datasets) used in the analyses presented in the manuscript "An ecogeomorphic framework coupling sediment modeling with invasive riparian vegetation dynamics."