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575 results for “Modeling Codes”
Data and code from: A spectral three-dimensional color space model of tree crown health
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Methyl bromide atmosphere-ocean box model code, inputs, and outputs
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SLABCC: Total energy correction code for charged periodic slab models
<p>Test set for SLABCC (SLAB Charge Correction) including the input files, input parameters and the expected output.<br> The geometries correspond to the positively charged Cl-vacancy on the surface of the NaCl slab with different vacuum thickness. The compiler type/compilation flags, linked libraries, and the hardware architecture may influence the optimization results but the effects on the correction energies should be negligible.</p> <p>The latest version of SLABCC can be downloaded from <a href="https://github.com/MFTabriz/slabcc">https://github.com/MFTabriz/slabcc</a></p> <p> </p>
Data and code for "Predicting evaporation in stream temperature models – Penman, Dalton or something else?"
<p>The uploaded files contain the data set and code used in an empirical evaluation of the application of the Penman equation for predicting evaporation from streams.</p> <ul> <li>Fishtrap_for_stream_evap_analysis.csv - data set used in the analysis</li> <li>streamEvapAnalysis_final.r - code used to analyse the data</li> </ul>
Improved representation of clouds in the atmospheric component LMDZ6A of the IPSL Earth system model IPSL-CM6A : Source codes and supporting files
<p>Source codes and supporting files of the paper by J-B Madeleine et al., 2020, entitled "Improved representation of clouds in the atmospheric component LMDZ6A of the IPSL Earth system model IPSL-CM6A" published in the Journal of Advances in Modeling Earth Systems. See the README file for more information.</p>
Dataset and codes for "BaHSYM: parsimonious Bayesian Hierarchical Model to predict river Sediment Yield"
<p>This folder contains:</p> <ul> <li>R project file</li> <li>R code for Best Fit model</li> <li>R code for temporal cross-validation</li> <li>R code for spatial cross-validation</li> <li>R code for cluster analysis</li> <li>dataset containing all input variables for the river gauges (and catchments) used for the development and testing of the BaHSYM model in Austria</li> </ul> <p>It also contains the same codes and datasets adapted to reproduce the model by de Vente et al. (2011), i.e. with the same structure but with the variables used in such model.</p>
A model of the optimal selection of crypto assets - simulation code
<p>In the modelling we assume that crypto assets differ by two essential features: security (technological) and stability (governance). Investors make choices over crypto assets similarly to how they make choices by using a recommender app: the app presents each investor with a pair of crypto assets with certain security-stability characteristics to be compared. Each investor submits its preference for adopting one of the two assets to the app. The app, in turn, provides a recommendation on whether the proposed adoption is sensible given the assets' essential features, information about the adoption choices of all other investors, and expected future economic benefits of adoption. Investors continue making their adoption choices over all pairs of crypto assets until their expected future economic benefits can no longer be improved upon. This constitutes an optimal selection decision. We simulate optimal selection decisions considering the behaviour of different types of investors, driven by their attitudes towards assets' features. We find a variety of possible emergent outcomes for the investments in the crypto-ecosystem and the future adoption of the crypto assets.</p>
The performance of permutations and exponential random graph models when analysing animal networks (R code and data)
<p>Social network analysis is a suite of approaches for exploring relational data. Two approaches commonly used to analyse animal social network data are permutation-based tests of significance and exponential random graph models. However, the performance of these approaches when analysing different types of network data has not been simultaneously evaluated. Here we test both approaches to determine their performance when analysing a range of biologically realistic simulated animal social networks. We examined the false positive and false negative error rate of an effect of a two-level explanatory variable (e.g. sex) on the number and combined strength of an individual's network connections. We measured error rates for two types of simulated data collection methods in a range of network structures, and with/without a confounding effect and missing observations. Both methods performed consistently well in networks of dyadic interactions, and worse on networks constructed using observations of individuals in groups. Exponential random graph models had a marginally lower rate of false positives than permutations in most cases. Phenotypic assortativity had a large influence on the false positive rate, and a smaller effect on the false negative rate for both methods in all network types. Aspects of within- and between-group network structure influenced error rates, but not to the same extent. In grouping-event based networks, increased sampling effort marginally decreased rates of false negatives, but increased rates of false positives for both analysis methods. These results provide guidelines for biologists analysing and interpreting their own network data using these methods.</p>
Code for Individual Based Model to assess impact of KHV release on carp population
<p><b>1: </b>Common carp (<i>Cyprinus carpio</i>) is one of the top global invasive vertebrates and can cause significant ecological damage. The Australian Government's National Carp Control Program (NCCP) proposes to release Koi Herpesvirus (KHV) to eradicate feral carp in one of the largest ecological interventions ever attempted. Ecological and human health risks have been highlighted regarding the release of a highly pathogenic viral biocontrol for an aquatic species. The efficacy of KHV has also been questioned, and it has not been demonstrated to produce lasting population reductions.</p> <p> </p> <p>2. We developed an individual-based model (IBM) to examine the ecological and evolutionary response of a carp population after KHV release. This simulated the interaction between fish life history, viral epidemiology, host genetic resistance and population demography to critically evaluate the impact of KHV release under optimal conditions and a "best case scenario" for disease transmission.</p> <p> </p> <p>3. KHV will rarely result in prolonged reductions or population extinctions. Crucially, realistic scenarios result in a rapidly rebounding population of resistant individuals. Additional measures aimed to reduce carp population recovery rate (e.g. with genetic engineering) require rapid efficacy to significantly reduce carp numbers alongside KHV.<br> </p> <p>4. Fish fecundity has an overwhelming influence on viral efficacy as a biocontrol agent when combined with genetic resistance within a population. A high probability of population extinction is only met when carp fecundity is reduced to 1% of biological observations.<br> </p> <p><span>5.<i> Synthesis and applications. </i></span>We use an individual-based model to evaluate the efficacy of Koi Herpesvirus biocontrol in Common <a>Ca</a>rp, and find that high host fecundity combined with genetic resistance results in rapid population rebound after initial large fish-kills. Biocontrol approaches relying on natural selection lose efficacy over successive generations as resistance genes increases in frequency. Given the intense logistical effort and risks to ecosystems and human health associated with large fish kills after viral release, we suggest that sustained manual removal, alongside ecological restoration to favour recovery of native species, provides a risk-free approach to reducing populations.<br> </p>
Vesuvius deformation modeling, Comsol numerical model code
<p>The java file represenst a set of coherent procedures that allow a multiparametric analysis in the computing environment of the commercial package Comsol. </p> <p>The files .txt and .dat are files needed by the code to run the model. They represents the data related to our model.</p>
Data and code from: Growth strategies of a model picoplankter depend on social milieu and pCO2
<p><span><span><span><span><span><span><span><span><span><span><span>Aquatic microbial primary producers exist in genetically diverse populations, but are often studied as single lineages, so that interpreting single lineage studies relies critically on understanding how microbial growth differs with social milieu. The properties of lineages grown alone often fail to predict the growth of these same lineages in the presence of conspecifics, and this discrepancy points towards an opportunity to improve our understanding of how multilineage assemblages of a species are shaped. We demonstrate that different lineages of a marine picoplankter modulate their lineage growth rate in response to the presence of non-self conspecifics, even when resource competition is effectively absent. This explains why growth rates of lineages in isolation do not reliably predict their growth rates in mixed culture, or the lineage composition of assemblages. The diversity of growth strategies observed are thus consistent with lineage-specific energy-allocation that depends on social milieu. Since lineage growth is only one of many traits determining fitness in natural assemblages, we propose that in all but the poorest quality environments where allocating maximum energy to growth is the only viable strategy, we should expect intraspecific variation in growth strategies, with more strategies possible in ameliorated environments, such as high CO<sub>2</sub> for many marine picoplankton. </span></span></span></span></span></span></span></span></span></span></span></p>
MATLAB code related to the thermal model of hyperthermia treatment
<p>The code attached here is used to perform the analyses on hyperthermia treatment of brain tumours that are described in the article "The interplay of blood flow and temperature in regional hyperthermia: A mathematical approach" by Jesús J. Bosque, Gabriel F. Calvo, Víctor M. Pérez-García and María Cruz Navarro. For more information turn to the article or use the readme file provided with the code.</p>
Constitutive model of erythrocyte membranes with distributions of spectrin orientations and lengths - pipette aspiration data and MatLab Code
<p>The speadsheet contains the original micropipette aspiration measurement of red blood cell membrane. There are five days of experiment each on its own tab, the first three of which are reported in the manuscript. The MatLab code used to generate theoretical predictions based on our new microstructurebased constitutive model are also included. This is the code used to generate least squared regression values for the material coefficients.</p>
Data from: A model for non-monotonic intensity coding
Peripheral neurons of most sensory systems increase their response with increasing stimulus intensity. Behavioural responses, however, can be specific to some intermediate intensity level whose particular value might be innate or associatively learned. Learning such a preference requires an adjustable trans- formation from a monotonic stimulus representation at the sensory periphery to a non-monotonic representation for the motor command. How do neural systems accomplish this task? We tackle this general question focusing on odour-intensity learning in the fruit fly, whose first- and second-order olfactory neurons show monotonic stimulus–response curves. Nevertheless, flies form associative memories specific to particular trained odour intensities. Thus, downstream of the first two olfactory processing layers, odour intensity must be re-coded to enable intensity-specific associative learning. We present a minimal, feed-forward, three-layer circuit, which implements the required transformation by combining excitation, inhibition, and, as a decisive third element, homeostatic plasticity. Key features of this circuit motif are consistent with the known architecture and physiology of the fly olfactory system, whereas alternative mechanisms are either not composed of simple, scalable building blocks or not compatible with physiological observations. The simplicity of the circuit and the robustness of its function under parameter changes make this computational motif an attractive candidate for tuneable non-monotonic intensity coding.
R code to perform distribution models of Plain Tyrannulet
<p>Archiving to Zenodo for peer-review</p>
CodeEval: Pedagogy Based Benchmark Dataset for Evaluation Of Large Language Models Trained On Code
<p>Categories has been modified to 21 from 26.</p>
Data and code from: Large language models can segment narrative events similarly to humans.
<p>Data and code supporting the paper: Large language models can segment narrative events similarly to humans.</p>
Data and R code for cluster analysis and machine learning modelling of favourite places for outdoor recreation
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Dataset of Code Context Models
<p>This is a dataset of code context models. Please refer to README for more information.</p>
Data and Code associated to the paper "Quantum simulation of the tricritical Ising model in tunable Josephson junction ladders"
<p>Modern hybrid superconductor-semiconductor Josephson junction arrays are a promising platform for analog quantum simulations. Their controllable and non-sinusoidal energy/phase relation opens the path to implement nontrivial interactions and study the emergence of exotic quantum phase transitions. Here, we propose the analysis of an array of hybrid Josephson junctions defining a 2-leg ladder geometry for the quantum simulation of the tricritical Ising phase transition. This transition provides the paradigmatic example of minimal conformal models beyond Ising criticality and its excitations are intimately related with Fibonacci non-Abelian anyons and topological order in two dimensions. We study this superconducting system and its thermodynamic phases based on bosonization and matrix-product-states techniques. Its effective continuous description in terms of a three-frequency sine-Gordon quantum field theory suggests the presence of the targeted tricritical point and the numerical simulations confirm this picture. Our results indicate which experimental observables can be adopted in realistic devices to probe the physics and the phase transitions of the model. Additionally, our proposal provides a useful one-dimensional building block to design exotic topological order in two-dimensional scalable Josephson junction arrays.</p>
ScienceDex guides
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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.