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855 results for “model system”
Multi-state modeling of the PhoQ two-component system
<p>This directory contains the input data, protocols and output model for the modeling of the PhoQ homodimer, using cysteine crosslinking and multi-state Bayesian modeling in IMP.</p> <p>For more information about how to reproduce this modeling, see https://salilab.org/phoq or the README file.</p>
Learning stochastic process-based models of dynamical systems from knowledge and data - Libraries, incomplete models and data
<p>The archive contains all libraries of domain knowledge, the incomplete models and the data used in the experiments described in the manuscript titled "Learning stochastic process-based models of dynamical systems from knowledge and data" pubilshed in BMC Systems Biology</p>
Model systems with GPCRs embedded in multicomponent membranes
<p>Files required to run coarse-grained simulations on various lipid membranes with embedded adenosine A_2A and dopamine D_2 receptors. These simulations were performed to study the effect of the presence of polyunsaturated fatty acid on GPCR oligomerization. The detailed description of the aims, methodologies and results of this study are explained in the research paper [1]. The composition and purpose of each simulated system will also be explained in this paper [1].</p> <p>The Martini force field [2,3] was employed in the study, and the simulations were performed with version 4.5.x of the GROMACS package [4].</p> <p>For each system the following (in GROMACS compatible format) is provided:</p> <p>1) Initial structure (*Start.gro)</p> <p>2) Topology file (*.top)</p> <p>3) Index file (*.ndx)</p> <p>In addition, for systems other than those containing only one protein, the final structure is given (*End.gro).</p> <p>Other files required to run the simulations, which are common for all the systems, are also provided:</p> <p>4) Simulation parameter file (.mdp)</p> <p>5) Force field parameters (.itp)</p> <p> </p> <p><strong>References:</strong></p> <p> </p> <p>[1] Guixà-González et al., Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors. <em>Scientific Reports</em> <strong>6</strong>, Article number: 19839 (2016) <strong>DOI:</strong>10.1038/srep19839</p> <p>[2] Marrink et al., The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations.<em> Journal of Physical Chemistry B </em><strong>111</strong>, 7812–7824 (2007), <strong>DOI:</strong>10.1021/jp071097f</p> <p>[3] Monticelli et al., The MARTINI Coarse-Grained Force Field: Extension to Proteins. <em>Journal of Chemical Theory and Computation </em><strong>4</strong>, 819–834 (2008), <strong>DOI:</strong>10.1021/ct700324x</p> <p>[4] Pronk et al., GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. <em>Bioinformatics </em><strong>29</strong> 845-854 (2013), <strong>DOI:</strong>10.1093/bioinformatics/btt055</p>
WESSBAS: Extraction of Probabilistic Workload Specifications for Load Testing and Performance Prediction - A Model-Driven Approach for Session-Based Application Systems.
<p>Supplementary material for the paper: "WESSBAS: Extraction of Probabilistic Workload Specifications for Load Testing and Performance Prediction".</p> <p>Included in the supplementary material are the evaluation results.</p> <p>The WESSBAS software relevant to the paper is available via https://github.com/Wessbas/</p> <p>The WESSBAS UI is available as a password-protected (password: wessbasui) ZIP file:</p> <p>https://dl.dropboxusercontent.com/u/81621779/wessbas.ui.zip (--- WESSBAS GUI (license confirmation pending, i.e., not on GitHub, yet))</p>
Data for "Fractal analysis of urban catchments and their representation in semi-distributed models: imperviousness and sewer system"
<p>The data set corresponds the data used in the paper : “Fractal analysis of urban catchments and their representation in semi-distributed models: imperviousness and sewer system”, published in 2017 in the Journal “Hydrology and Earth System Sciences” (http://www.hydrol-earth-syst-sci.net/).</p> <p>More precisely it corresponds to the matrices that are used in the fractal and multi-fractal analysis of the ten urban areas investigated in the paper.</p> <p> </p> <p>For each catchment, it is organised as follow:</p> <p>- catchment_name_conduit.asc : the matrix describing the sewer system.</p> <p>- catchment_name_OSM.asc : the matrix describing the impervious areas (roads and buildings) obtained via Open Street Map (www.openstreetmap.org)</p> <p>- catchment_name_OSM_house_only.asc : the matrix describing the “building” areas obtained via Open Street Map (www.openstreetmap.org)</p> <p>- catchment_name_imperviousness.asc : the matrix describing the representation of imperviousness in operational semi-distributed models.</p> <p> </p> <p>More details can be found in the paper.</p>
Monsoon Mission Coupled Forecast System Version 2.0: Model Description and Indian Monsoon Simulations Figures
<p>Monsoon Mission Coupled Forecast System Version 2.0: Model Description and Indian Monsoon Simulations Figures</p>
Simulation data for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly"
<p>This is the original simulation data sets for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly".</p>
PyPSA-PL: Sectorally-integrated modelling of the Polish energy system until 2040
<p>This record contains all the scripts and data from the PyPSA-PL modelling exercise that supported the report:</p><ul><li>Kubiczek, P., Smoleń, M., Żelisko, W. (2023). Polska prawie bezemisyjna. Cztery scenariusze transformacji energetycznej do 2040 r. Instrat Policy Paper 06/2023. <a href="https://www.instrat.pl/polska-2040">https://www.instrat.pl/polska-2040</a></li></ul><p>The record structure is based on the PyPSA-PL repository <a href="https://github.com/instrat-pl/pypsa-pl">https://github.com/instrat-pl/pypsa-pl</a> (v2.1).</p>
A multi-omics systems vaccinology resource to develop and test computational models of immunity: 1st challenge dataset and submissions
<p>The goal of the CMI-PB prediction contest is to foster a collaborative research community that can collectively tackle challenges and accelerates scientific progress beyond the capabilities of individual researchers or groups. The CMI-PB consortium has curated multi-source data from multiple individuals, encompassing Ab titers (around four antibodies/features), cell frequency (approximately 20 cell types/features), gene expression (roughly 50,000 RNA transcripts/features), and plasma proteomics (around 50 proteins/features). The challenge requires integrating these diverse data sources to predict different immune responses or tasks. Specifically, you will utilize multi-source data from several individuals on day 0 (baseline) to predict specific immune responses at later time points (1, 3, 7, and 14 days post-booster vaccination).</p> <p>The first CMI-PB challenge, which is an internal challenge, was conducted using datasets from 2020 (train) and 2021 (test). In the following sections, we provide detailed information on the datasets, challenge tasks, submission format, descriptions, and access to the necessary data files for participants to develop their models and make predictions.</p> <p><br><strong>A) Multiomics CMI-PB dataset:</strong></p> <p>We propose a study design that enables a systems-level understanding of the immune responses through computational modeling. Our cohort comprises aP vs. wP infancy-primed subjects boosted with Tdap. We recruit individuals born before 1995 (wP) and after 1996 (aP), collect baseline plasma and blood samples, and then at 1, 3, 7 and 14 days post booster vaccination.</p> <p>With the obtained samples processed, we generated omics data by:</p> <ul> <li> <p>Bulk PBMCs transcriptomics,</p> </li> <li> <p>Plasma proteomics using Olink, which provides a quantitative readout of cytokines, chemokines, and other immune factors,</p> </li> <li> <p>Cell frequency in PBMCs using flow cytometry,</p> </li> <li> <p>Tdap-specific antibodies levels</p> </li> </ul> <p><strong>B) List of tasks can be accessed using the “List of tasks for challenge 1.docx” file, and submissions need to submit in provided format here: “submission template challenge 1.tsv”</strong></p> <p><strong>C) Datasets for model building and making predictions:</strong></p> <p> Data files are divided into two categories: 1) raw dataset and 2) computable matrices.</p> <ol> <li> <p><strong>Raw dataset: </strong>This raw-most dataset is divided into training and test datasets. </p> </li> <li> <p><strong>Computable matrices: </strong>There are three different types of computable matrices. a) Full: These files are generated by dividing raw files into sub-files specific to planned days specific to vaccination. b) harmonized: These are generated by preserving only overlapping features between train and test datasets. b) imputed: MICE imputation is performed to impute missing values in the dataset.</p> </li> </ol> <p><strong>D) Submission evaluation</strong></p> <p>This folder contains all submitted models with ranking files and code for evaluating these models.</p> <p><strong>To learn more about the CMI-PB prediction challenge, visit our website at www.cmi-pb.org.</strong></p>
Code generation for classical-quantum software systems modelled in UML - Dataset and EGL Transformation
<p>This dataset contains all the elements necessary for carry out the EGL transformation from UML models to Hybrid and Quantum code, as well as to carry its validation. </p> <blockquote> <p><em>Quantum computing is gaining an increasing interest since it can solve certain problems exponentially faster than classical computing. Thus, many organizations are researching and launching investments for integrating quantum software into their existing systems. Software modernization (as based on Model-Driven Engineering) has been proposed to migrate from/to the so-called hybrid software systems, which integrate classical and quantum software. In that process, both, reverse engineering and restructuring phases, have already been investigated. However, forward engineering phase for generating hybrid source code from high-level design models has not yet been addressed. Thus, this research proposes a quantum code generation technique from extended UML design models. It consists of a set of Model-to-Text transformations (defined through Epsilon Generation Language) to generate both Python and Qiskit code, which respectively integrate classical and quantum code. The transformation has been validated through a multi-case study with 7 hybrid software systems modelled in UML, which demonstrated that the transformation is effective and efficient. The implication of this work is that the software modernization process for hybrid software systems can be completed by tackling forward engineering phase, and that Model-Driven Engineering can therefore globally facilitate industry adoption of quantum software.</em></p> </blockquote>
Data from the micrometeorological tower of the Antarctic Modeling Observation System (ATMOS) project of the 40th Brazilian Antarctic Operation (OPERANTAR XL) to calculate the CO2 flux (FCO2)
<p>Micrometeorological tower data obtained by the "Antarctic Modeling Observation System" (ATMOS) project. These data were collected in the southern summer of 2021/2022 during the 40th Brazilian Antarctic Operation (OPERANTAR XL) and were used to calculate CO2 fluxes (FCO2).</p> <p>A 9 m high metal micrometeorological tower was installed on the bow of the Polar Ship Almirante Maximiano, 8.75 m above sea level, for sampling atmospheric variables. In the tower, the Motion Pack II was installed, on the main shaft of the tower, to determine the ship's movement in the orthogonal directions xp, yp and zp of the platform's coordinate system, at a frequency of 20 Hz. As well as, a GPS (Global Positioning System) and an electronic compass, to determine the ship's geographic position and speed. The movement of the ship influences wind speed measurements, and as a solution, a wind speed correction was carried out.<br>An IRGASON sensor (Campell Scientific®) was placed on the secondary shaft of the tower, configured to perform measurements at 20 Hz. The IRGASON has an open path infrared gas analyzer that measures the concentrations of CO2 and water vapor (H2O), a three-dimensional sonic anemometer, which measures the 3 vector components of the wind, and a thermohygrometer that measures air temperature and humidity. From the IRGASON collections, it is possible to calculate the CO2 flux using the Vortex Covariance method.</p>
LI-COR (LI-850) sensor data obtained by the Antarctic Modeling Observation System (ATMOS) project during the 40th Brazilian Antarctic Operation (OPERANTAR XL) and were used to calculate the partial pressure of CO2 (pCO2)
<p>LI-COR (LI 850) sensor data obtained by the "Antarctic Modeling Observation System" (ATMOS) project. These data were collected in the southern summer of 2021/2022 during the 40th Brazilian Antarctic Operation (OPERANTAR XL) and were used to calculate the partial pressure of seawater CO2 (pCO2sea)</p> <p>The LI-850 carbon dioxide analyzer was installed in the laboratory aft of H41 together with a balancer to measure the CO2 concentration of the water. The collection system occurs as follows: the ship's saltwater piping system collects seawater, when this water enters the balancer it generates turbulence. The turbulence generated causes the CO2 present in the water to come into balance with the air. The air that comes out of the balancer is pumped into the LI-850, by its internal pump, and thus, the equipment measures the concentration of CO2 present in the water. To ensure that the air inside the balancer is actually balanced with the seawater, the air leaving the LI-850 is pumped back into the balancer, closing the circuit. From these data it is possible to calculate pCO2sea.</p>
On the prediction of the time-varying behaviour of dynamic systems by interpolating state-space models
<p>In this article, a local Linear Parameter Varying (LPV) model identification approach is exploited to analyze the dynamic behaviour of a structure whose dynamics varies over time. This structure is composed by two aluminum crosses connected by a rubber mount. To observe time-dependent variations on the dynamics of this assembly, it is placed in a climate chamber and submitted to a six minute temperature run-up. During this run-up the structure is continuously excited by a shaker. The load provided by this device is measured by a load cell, while six accelerometers are measuring the responses of the system. The temperatures of the air inside the climate chamber and at the surface of the mount are also continuously measured. It is found that during the performed temperature run-up, the rubber mount temperature increased from, roughly, 14℃ to, approximately, 35.2℃. By using the measured load provided by the shaker and the measured accelerations, Frequency Response Functions (FRFs) at five different rubber mount temperatures are computed. From each of these sets of FRFs, state-space models are estimated. Afterwards, these models are used to define an interpolating LPV model, which enables the computation of interpolated state-space models representative of the dynamics of the system at each time sample. It is found that by feeding the interpolated state-space models with the measured load, an accurate simulation of the measured accelerations is obtained. Moreover, by exploiting a joint input state estimation algorithm with the interpolated state-space models and with the measured accelerations, a very good prediction of the applied load can be obtained. It is also shown that if the time dependency of the dynamics of the system is ignored, the results are less accurate.</p>
Input data and modelling files for a model of the Finnish energy system with focus on cascade hydropower and the addition of a hydrogen storage system realised in Backbone
<p>The files show the input data and modelling files used for the publication "Cascade hydropower integration in a techno-economic power system model: A study of Finnish hydropower plants" (Kiehle et al., 2025 - submitted). The paper's <a title="Preprint on SSRN" href="https://dx.doi.org/10.2139/ssrn.4971685" target="_blank" rel="noopener">preprint</a> is available. A model of the Finnish energy system in 2022 was built in the techno-economic modelling framework Backbone (available on GitLab: https://gitlab.vtt.fi/backbone/backbone). The focus was on implementing cascading hydropower plants in a power system model, including individual reservoirs, generation and spillage capacities. </p> <p>"ModellingFiles_Debug" are GAMS-based data that can be used to run the scenario in Backbone or display the results. "ModellingResults" are gdx files that purely list the results. Those are also presented in more detail in the scientific paper. The Excel files present the input data used for modelling and can also be used to run the model. </p>
The processing results, dataset and original codes of Coral reef PtCloud segmentation model (based on proposed underwater camera systems)
<p><strong># Data Introduction</strong><br>The proposed camera system includes three operation modes: Surface Mode, Horizontal Mode, and Curved Mode.</p> <ul> <li><strong>Surface Mode</strong>: Provides 3D reconstructions (point cloud), DEM, and orthophoto maps of the seabed (covering a line of 70m in length).</li> <li><strong>Horizontal Mode</strong>: Provides 3D reconstructions (point cloud and mesh) and orthophoto maps of a single transect line.</li> <li><strong>Curved Mode</strong>: Offers 3D reconstructions (mesh) of various targets, including artificial coral reefs, coral reefs with snails, and coral reefs with starfish.</li> </ul> <p>All mesh results are saved in <code>.FBX</code> format, and point cloud results are saved in <code>.TXT</code> format.</p> <p><strong># Code Introduction</strong><br>The backbone of our point cloud segmentation model is the KPConv model.<br>If you encounter any issues during code deployment, please refer to the original KPConv repository (<a href="https://github.com/HuguesTHOMAS/KPConv" target="_new" rel="noopener">Original Code: https://github.com/HuguesTHOMAS/KPConv</a>).<br>We provide our modified code (customized for our task) along with the complete point cloud dataset.</p>
Output files for Variable-Resolution Community Earth System Model (VR-CESM) simulations with highest resolutions over the Euro-Mediterranean
<p>Output files for Variable-Resolution Community Earth System Model (VR-CESM) simulations with highest resolutions over the Euro-Mediterranean and notebooks created for analyses and visualization.</p> <p>Configuration names:</p> <ul> <li>ne30_n</li> <li>ne30x4_n</li> <li>ne30x4_t</li> <li>ne30x8_t</li> </ul> <p>Variables at single level: PHIS,PRECC,PRECL,PS,TREFHT,LHFLX,SWCF,LWCF,TMQ,SNOWHLND</p> <p>Variables at pressure levels:U,V,OMEGA,RELHUM,Z3,Q</p>
Models and output datasets for OSeMOSYS Bolivia electricity system paper
<p>These are files with the outputs for each scenario in the paper "Analyzing Carbon Emissions Policies for the Bolivian Electric Sector" submitted to the journal Renewable and Sustainable Energy Transition.</p>
SESMG model scenarios of the study "Indicators for the optimization of sustainable urban energy systems based on energy system modeling"
<p>This folder contains the model scenarios belonging to the publication "<strong>Indicators for the optimization of sustainable urban energy systems based on energy system modeling</strong>" (<a href="https://doi.org/10.1186/s13705-021-00323-3">https://doi.org/10.1186/s13705-021-00323-3</a>).</p> <p>The individual scenarios can be executed and evaluated with the <strong>Spreadsheet Energy System Model Generator (<a href="https://github.com/chrklemm/SESMG">SESMG</a>)</strong> <a href="https://doi.org/10.5281/zenodo.5412027">v0.0.4</a>, respectively <a href="https://doi.org/10.5281/zenodo.5520513">v0.2.0</a>.</p> <p>The file names are to be understood as follows:</p> <p><em>"scenario name"_"(dispatch) optimization criterion"_"scenario concretization"_"further scenario concretization"_"associated program version"</em>.xlsx.</p> <p>For example, the title name "<em>Scenario3_C_4MW_Biogas_SESMGv0.0.4.xlsx</em>" contains the following information:<br> - This file belongs to scenario 3 (see main publication for details).<br> - Dispatch optimized according to energy costs C (see main publication for details).<br> - The scenario contains 4 MW biogas CHP capacity (see main publication for details)<br> - The scenario is to be executed with SESMG version v0.0.4.</p> <p>Another example. The title name "<em>optimization_C_80PercentDemand_70PercentEmissions_SESMGv0.1.1.xlsx</em>" contains the following information:<br> - This file belongs to the optimization scenario (see main publication for details).<br> - The primary optimization criterion is energy costs C (see main publication for details).<br> - Energy demand was capped at 80 percent and emissions at 70 percent of baseline (see main publication for details)<br> - The scenario is to be executed with SESMG version v0.1.1.<br> </p> <p><strong>Acknowledgements:</strong></p> <p>The authors would like to thank Prof. Dr. Peter Vennemann (Münster University of Applied Sciences) for the constructive discussion regarding this article. This research has been conducted within the R2Q project, funded by the German Federal Ministry of Education and Research (BMBF) - grant number 033W102A and the junior research group energy sufficiency funded by the German Federal Ministry of Education and Research (BMBF) as part of its Social-Ecological Research funding priority, funding number 01UU2004A. </p>
The prediction data analyzed in the article: "An improved regional coupled modeling system for Arctic sea ice simulation and prediction: a case study for 2018"
<p>The outputs of seasonal predictions with the Coupled Arctic Prediction System version 1 analyzed in the article, "An improved regional coupled modeling system for Arctic sea ice simulation and prediction: a case study for 2018", including:</p> <p>Sea ice concentration (SIC)</p> <p>Sea ice thickness (SIT)</p> <p>Sea surface temperature (SST)</p> <p>Ice mass budget diagnostics</p> <p>Accumulated downward shortwave radiation at the surface (ASWDN)</p> <p>Accumulated downward longwave radiation at the surface (ALWDN)</p> <p>Near surface air temperature (T2) </p> <p>Temperature and salinity profile of the upper ocean under sea ice </p>
Global Socio-Economic and Environmental data for PyPSA-Earth: An Open Optimisation Model of the Earth Energy System.
<p><strong>PyPSA-Earth </strong>is an open model dataset of the global power system at different network levels that cover our Earth. The African model can be built using the code provided at <a href="https://github.com/pypsa-meets-africa/pypsa-africa">https://github.com/pypsa-meets-africa/pypsa-africa</a>. Other regions follow soon under the same code base.</p> <p>Since the GitHub codebase is not suited for handling large changing files, we provide here separate <strong>data bundles and cutouts</strong> to be downloaded and extracted as noted in the <a href="https://pypsa-meets-africa.readthedocs.io/en/latest/index.html">documentation</a></p> <p>The below-provided<strong> data files </strong>contain various open data for improving energy system modelling decisions. A thorough description with license restrictions will follow soon.</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.