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42 results for “scripts and code”
Code, data and scripts to study wave dynamics in asymmetric material
<p>Supplementary data for [1] Vladislav A. Yastrebov. "Wave propagation through an elastically-asymmetric architected material", 2021, https://arxiv.org/abs/1712.06294v2</p> <p>See "Readme.md" and indivual "Readme.md" files in folders: "data", "src", "fig"</p>
Modified WRF/Chem source code, output data, and post-processing scripts for the GMD manuscript "Evaluation of WRF/Chem model (v3.9.1.1) real-time air quality forecasts over the Eastern Mediterranean"
<p>Here you will find the modified WRF/Chem code used in the simulations, the scripts used for post-processing and the model output data used in the manuscript. </p> <p>Two modifications have been made in module_aerosols_soa_vbs.F:</p> <ol> <li>ch_dust is set to1.0D-9*0.36</li> <li>The model is set not to initialize during restarts</li> </ol> <p>The model data directory includes:</p> <ol> <li>Two csv files (Winter and Summer) with the hourly concentrations of atmospheric pollutants at the locations of the ground stations. These data were used to produce Figures 4-8 in the manuscript as well as all the metrics.</li> <li>Two netcdf files (Winter and Summer) with the average ground concentrations of atmospheric pollutants over Cyprus. These data were use to produce Figure 3 in the manuscript. </li> </ol>
Mitigating Network Noise on Dragonfly Networks through Application-Aware Routing (code, data and scripts to reproduce paper results)
<p>This repository contains the data, code, and scripts required to reproduce the results of the paper "Mitigating Network Noise on Dragonfly Networks through Application-Aware Routing" by Daniele De Sensi, Salvatore Di Girolamo and Torsten Hoefler, presented at the 2019 International Conference for High Performance Computing, Networking, Storage, and Analysis. </p> <p>This repository does not contains the code of the library used to automatically tune the routing algorithm, which can be found at http://doi.org/10.5281/zenodo.3372785</p>
Board Leadership Database (U.S. Public Firms) + ML Script for Scaling Human Coded Data
<p>Files include: (1) an open sourced database of CEO duality and board chair orientations developed by scaling human coded data using supervised machine learning techniques (in both .dta and .csv formats), as well as (2) the accompanying training and scoring scripts to scale human coded data.</p> <p>Users may apply the scoring script to score the same variables from company proxy statements, or may adapt the training/scoring scripts and retrain models to scale human coded data of other constructs or measures. </p> <p>We note that early steps in the process to develop our database and script required web-scraping of company filings from SEC Edgar and text extraction from collected filings. We relied on other publicly available scripts to develop our own fetcher and extraction scripts. Users seeking to duplicate those parts of the process may benefit from the following resources from Kai Chen and pipy.org: </p> <p>For resources from Kai Chen: see <a href="https://urldefense.com/v3/__https:/www.kaichen.work/?p=681__;!!K6Z8K8YTIA!BizP9-ZnzgV0Pq7ck-UENJ1EBDrFkAkNoCaO34Ad1ezxH_okstsfxniagvxXdWudkDP44fPACbY9vaIG5A$">https://www.kaichen.work/?p=681</a> and <a href="https://urldefense.com/v3/__https:/www.kaichen.work/?p=946__;!!K6Z8K8YTIA!BizP9-ZnzgV0Pq7ck-UENJ1EBDrFkAkNoCaO34Ad1ezxH_okstsfxniagvxXdWudkDP44fPACbZhp5N_Tw$">https://www.kaichen.work/?p=946</a></p> <p>For resources from pipy.org, see <a href="https://urldefense.com/v3/__https:/pypi.org/project/sec-edgar-downloader/__;!!K6Z8K8YTIA!BizP9-ZnzgV0Pq7ck-UENJ1EBDrFkAkNoCaO34Ad1ezxH_okstsfxniagvxXdWudkDP44fPACbYxYSZGGw$">sec-edgar-downloader</a> and <a href="https://urldefense.com/v3/__https:/pypi.org/project/sec-api/__;!!K6Z8K8YTIA!BizP9-ZnzgV0Pq7ck-UENJ1EBDrFkAkNoCaO34Ad1ezxH_okstsfxniagvxXdWudkDP44fPACbZ_FwY6jw$">sec-api</a></p> <p> </p>
Network data and script accompanying the paper "Operationalizing anthropological theory: four techniques to simplify networks of co-occurring ethnographic codes"
<p>This repository accompanies the paper<a href="https://rdcu.be/dbuhi"> "Operationalizing anthropological theory: four techniques to simplify networks of co-occurring ethnographic codes"</a>, by Cottica et al. It contains:</p> <ol> <li>A data file, containing networks of co-occurrence of ethnographic codes from three ethnographies. Data are pseudonymized (see the paper for details).</li> <li>A script that, when run on the data, produces simplified versions of each network. Simplifications follow four different techniques, described in the paper. Each technique relies on a tuning parameter, so that, for each network and each techniques, the script produces several simplified networks, each one associated with a unique value of the tuning parameter.</li> </ol> <p>The data file format is that of a Tulip perspective. To open, download Tulip (https://tulip.labri.fr), launch it and open the file from within the Tulip GUI.</p> <p>The script file is in Python. To run, open it from within the Tulip IDE first.</p> <p> </p>
Dataset of Jupyter Notebooks from the paper "A Large-Scale Comparison of Python Code in Jupyter Notebooks and Scripts"
<pre>This archive contains the dataset of properly-licensed Jupyter notebooks from the MSR'22 paper "A Large-Scale Comparison of Python Code in Jupyter Notebooks and Scripts". The dataset contains 847,881 notebooks stored in the PostgreSQL dump file. You can find the details about the database in the README file. To transform the notebooks into this convenient format and to calcuate the structural metrics, we used our library called Matroskin, which can be found here: <a href="https://github.com/JetBrains-Research/Matroskin">https://github.com/JetBrains-Research/Matroskin</a>. </pre>
Questionnaire, R Scripts and Response Data Set of the Survey on Functionally Similar Code Clones
<p>In 2017, we conducted an open online survey regarding functionally similar code clones with practitioners. We make the used questionnaire, the data from the response to the questionnaire and our used R script for the analysis openly available.</p>
Assets (code, scripts and datasets) for the manuscript "Correction of the Air-Sea Heat Fluxes in Ocean General Circulation Models Using Neural Networks"
<p>This dataset contains all relevant software and data related to the manuscript "Correction of the Air-Sea Heat Fluxes in Ocean General Circulation Models Using Neural Networks", submitted to AGU journals.</p>
Code, scripts and data for: Seasonality and competition select for variable germination behavior in perennials
<p class="MsoNoSpacing"><span>The occurrence of within-population variation in germination behavior and associated traits such as seed size has long fascinated evolutionary ecologists. In annuals, unpredictable environments are known to select for bet-hedging strategies causing variation in dormancy duration and germination strategies. Variation in germination timing and associated traits is also commonly observed in perennials and often tracks gradients of environmental predictability. Although bet-hedging is thought to occur less frequently in long-lived organisms, these observations suggest a role of bet-hedging strategies in perennials occupying unpredictable environments. We use complementary analytical and evolutionary simulation models of within-individual variation in germination behavior in seasonal environments to show how bet-hedging interacts with fluctuating selection, life-history traits, and competitive asymmetries among germination strategies. We reveal substantial scope for bet-hedging to produce variation in germination behavior in long-lived plants, when "false starts" to the growing season results in either competitive advantages or increased mortality risk for alternative germination strategies. Additionally, we find that lowering adult survival may, in contrast to classic bet-hedging theory, result in less spreading of germination by decreasing density-dependent competition. These models extend insights from bet-hedging theory to perennials and explore how competitive communities may be affected by ongoing changes in climate and seasonality patterns.</span></p>
Scripts and codes for G4access analysis
<p>Scripts, codes and annotations that were used for the article: <strong>"G4access identifies G-quadruplexes and their associations with open </strong><strong>chromatin and imprinting control regions "</strong></p> <p> </p>
Code, scripts and data for: Seasonality and competition select for variable germination behavior in perennials
Open the record for dataset details and reuse information.
Code and scripts used to generate results for: Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency
<p>The danger posed by infectious agents necessitates the development of new tools to both predict and manage emerging diseases. One promising approach is the development of recombinant viral vaccines that are themselves infectious. Transmissible vaccines have been shown to greatly reduce the effort required to control the spread of zoonotic pathogens in their animal reservoirs, thereby limiting the chances of human infection. While this approach can be immensely useful in combating emerging diseases, the ability to self-replicate exposes vaccines to evolutionary change. As a recombinant transmissible vaccine mutates, selection is expected to favor variants with reduced efficacy against the pathogen and increased transmission rates. This creates a trade-off in vaccine design priorities between efficacy, reduction in transmission, and evolutionary stability. Here we ask how such trade-offs influence the overall performance of transmissible vaccines. We find that evolutionary instability can dramatically reduce performance, even for vaccine candidates with ideal efficacy and transmission dynamics. One method to increase functional stability is through the inclusion of multiple redundant antigens. We show that the inclusion of a second antigen can increase functional stability in the face of evolutionary pressures. However, the benefit of genetic redundancy plus any gain in efficacy must outweigh the reduction in transmission for dual-gene designs to be effective. Our results suggest that the successful application of recombinant transmissible vaccines will require consideration of evolutionary dynamics and epistatic effects, as well as basic measurements of epidemiological features.</p>
Codes and scripts used in the Origin and de novo domestication of sweet orange
<p>Codes and scripts used in the Origin and de novo domestication of sweet orange.</p>
Data and code for "Quantum chaos on edge" (matfiles, a matlab script, and figures)
<p>The data files and matlab script to generate Figure 5,7,8 of the manuscript "Quantum chaos on edge" are uploaded.</p> <ul> <li>In 'script' folder, there is a single matlab file to generate Fig 5,7,8. </li> <li>In 'raw_data' folder, there are mat-files to be processed by the script file.</li> <li>In 'figures' folder, the generated figures are included.</li> </ul>
Coded data and R scripts for the article-Toward a dynamic behavioral profile of the Mandarin Chinese temperature term re
<p>These are the coded dataset and R scripts for the article "Towards a dynamic behavioral profile of Mandarin Chinese temperature term re: A diachronic semasiological approach".</p>
Amphibian diversity in the Amazonian floating meadows: a Hanski core-satellite species system (scripts and codes)
<p>The Amazon catchment is the largest river basin on earth, and up to 30% of its waters flow across floodplains. In its open waters, floating plants known as floating meadows abound. They can act as vectors of dispersal for their associated fauna and, therefore, can be important for the spatial structure of communities. Here, we focus on amphibian diversity in the Amazonian floating meadows over large spatial scales. We recorded 50 amphibian species over 57 sites, covering around 7,000 km along river courses. Using multi-site generalised dissimilarity modelling of zeta diversity, we tested Hanski's core-satellite (HCS) hypothesis and identified the existence of two functional groups of species operating under different ecological processes in the floating meadows. 'Core' species are associated with floating meadows, while 'satellite' species are associated with adjacent environments, being only occasional or accidental occupants of the floating vegetation. At large scales, amphibian diversity in floating meadows is mostly determined by stochastic processes, whereas at regional scales, climate and deterministic processes are central drivers. Compared with the turnover of 'core' species, the turnover of 'satellite' species increases much faster with distances and is also controlled by a wider range of climatic features. Distance is not a limiting factor for 'core' species, suggesting that they have a stronger dispersal ability even over large distances. This is probably related to the existence of passive long-distance dispersal of individuals along rivers via vegetation rafts. In this sense, Amazonian rivers can serve as corridors, facilitating dispersal especially for species associated with riverine habitats such as floating meadows.</p>
Data and code for "Experimental Observation of Topological Quantum Criticality" (matfiles, matlab script, and figures)
<p>Matlab code "zenodo_topological_quantum_criticality.m" generates Figure2 and 3 in the main script, and the Figure 2 and 3 in the Supplemental material. The generated figures are saved under folder 'figure', and the datasets used for the generation are saved under folder 'matfiles'. </p> <p>The raw measurement data (approx. 350 GB) will be shared only upon request. Please contact the Integrated Quantum Optics group (head: C. Silberhorn), Paderborn University.</p> <p>This is additional information of the publication arXiv:2301.05428 "Experimental Observation of Topological Quantum Criticality"</p>
All Your Script Are Belong to Us: Collecting and Analyzing JavaScript Code from 10K Sites for 9 Months
<p>We present a massive dataset (~2 TB) of client-side JavaScript code. Specifically, we have collected and stored on adaily basis JavaScript code from Alexa's Top 10000 web sites (~7.5 GB per day) for nine consecutive months. Our collection involved both inline scripts extracted from each web site's main page and external scripts linked from it. In order to aid researchers identify similar scripts and examine their popularity and evolution, we have produced hashes that represent the scripts' logical structure. Furthermore, we have analyzed the resulting dataset with well-established static analysis tools, generating additional metadata including reports with quality bugs and vulnerable libraries.</p>
Model source code, modified model code, and all scripts of the paper "A comprehensive estimate of the anthropogenic aerosol radiative effects using the GAMIL model with reduced complexity".
<p>Model source code, modified model code, and all scripts of the paper "A comprehensive estimate of the anthropogenic aerosol radiative effects using the GAMIL model with reduced complexity".</p>
Model source code, simulation results, and all scripts for the paper "A comprehensive estimate of the anthropogenic aerosol radiative effects using the GAMIL model with reduced complexity".
<p>FigureTable_Scripts.rar is NCL scripts used for figures and tables. <br> Model_Scripts.rar is the modified model code and scripts used for running model.<br> models.rar is the GAMIL model source code.<br> ModelResults.rar is the model results. Note that only the variables used for making plots.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.