{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2afa2ea9222a7bc8d1d960207fd95d1f1/testusersimtech", "tags" : [ "EXC2075","PNX","darus" ], "intraHash" : "afa2ea9222a7bc8d1d960207fd95d1f1", "interHash" : "429ca4547b67ad5b620be2e97ff85e10", "label" : "Harvester-Curator, a tool to elevate metadata provision in data and/or software repositories", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2024", "url": "", "author": [ "Sarbani Roy","Fangfang Wang","Dennis Gläser" ], "authors": [ {"first" : "Sarbani", "last" : "Roy"}, {"first" : "Fangfang", "last" : "Wang"}, {"first" : "Dennis", "last" : "Gläser"} ], "abstract": "Harvester-Curator is a tool, designed to elevate metadata provision in data repositories. In the first phase, Harvester-Curator acts as a scanner, navigating through user code and/or data repositories to identify suitable parsers for different file types. It collects metadata from each of the files by applying corresponding parsers and then compiles this information into a structured JSON file, providing researchers with a seamless and automated solution for metadata collection. Moving to the second phase, Harvester-Curator transforms into a curator, leveraging the harvested metadata to populate metadata fields in a target repository. By automating this process, it not only relieves researchers of the manual burden but also ensures the accuracy and comprehensiveness of the metadata. Beyond its role in streamlining the intricate task of metadata collection, this tool contributes to the broader objective of elevating data accessibility and interoperability within repositories.", "affiliation" : "Roy, Sarbani/Universität Stuttgart, Wang, Fangfang/Universität Stuttgart, Gläser, Dennis/Universität Stuttgart", "orcid-numbers" : "Roy, Sarbani/0000-0002-5990-0076, Gläser, Dennis/0000-0001-9646-881X", "doi" : "10.18419/darus-3785", "bibtexKey": "roy2024harvestercurator" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2cdd13dd38e0b03302d9ecb41c4bc7f2a/testusersimtech", "tags" : [ "EXC2075","PN6","darus" ], "intraHash" : "cdd13dd38e0b03302d9ecb41c4bc7f2a", "interHash" : "3ca8f1b169c650ca2cb27512d841fcd4", "label" : "Input-Output Dataset for Physics-inspired Artificial Neural Network for Dynamic System", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 5, "pub-type": "misc", "year": "2020", "url": "", "author": [ "Timothy Praditia" ], "authors": [ {"first" : "Timothy", "last" : "Praditia"} ], "note": "Related to: Praditia, T., Walser, T., Oladyshkin, S. and Nowak, W.: Improving Thermochemical Energy Storage dynamics forecast with Physics-Inspired Neural Network architecture. Energies 2020","abstract": "This dataset contains two .mat files, one pre-processed (direct simulation results) and the other one is with added noise. The simulated problem is a thermochemical energy storage problem using CaO/Ca(OH)2 as the material choice. This dataset is used as input-output data pairs necessary for training, validating, and testing the ANN. The input data consist of CaO density, Ca(OH)2 density, CaO specific heat capacity, Ca(OH)2, porosity, permeability, reaction rate constant, initial and outlet pressure, initial temperature, inlet temperature, N2 molar inflow rate, H2O molar inflow rate, and specific reaction enthalpy. The output data consist of pressure, temperature, CaO volume fraction, and H2O molar fraction. Additionally, there is an automated script file for the DuMuX run.", "affiliation" : "Praditia, Timothy/Universität Stuttgart", "orcid-numbers" : "Praditia, Timothy/0000-0003-3619-9122", "doi" : "10.18419/darus-633", "bibtexKey": "praditia2020inputoutput" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2393c10d2ba974038c33a52b60956feb0/testusersimtech", "tags" : [ "EXC2075","PN4","darus" ], "intraHash" : "393c10d2ba974038c33a52b60956feb0", "interHash" : "c379a61ab4ddeb1c66e0d8763c959a21", "label" : "A Data Set for Research on Data-based Methods for an Omnidirectional Mobile Robot", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 6, "pub-type": "misc", "year": "2021", "url": "", "author": [ "Hannes Eschmann" ], "authors": [ {"first" : "Hannes", "last" : "Eschmann"} ], "abstract": "The intend of this data set is the cooperation within SimTech. It will be particularly interesting for data-based modeling and control which is a key area of the research of project network 4. We are proud to provide real-world data, which is essential for the benchmark of any data-based method. Additionally, we are able to provide reference solutions in order to evaluate the predictive quality of the methods tested. Finally, an example on how this data set can be used with Gaussian process (GP) regression in order to predict the systematic mismatches of the mobile robot is given. The data set contains input-output data of an omnidirectional mobile robot. The inputs to the mobile robots are the desired speeds in the plane as well as an angular velocity of the robot around its vertical axis. The corresponding outputs are the position in the plane and the robots orientation in an inertial frame of reference. The data set is provided in the Matlab *.mat format.", "affiliation" : "Eschmann, Hannes/Universität Stuttgart", "orcid-numbers" : "Eschmann, Hannes/0000-0001-8924-1908", "doi" : "10.18419/darus-1845", "bibtexKey": "eschmann2021research" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2343eceaf3167b093b7537d3963c49274/testusersimtech", "tags" : [ "EXC2075","PNX","darus" ], "intraHash" : "343eceaf3167b093b7537d3963c49274", "interHash" : "13972096182f175c582d60c0c4b0abe6", "label" : "Replication Data for: Constraint-aware neural networks for Riemann problems", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2024", "url": "", "author": [ "Jim M. Magiera" ], "authors": [ {"first" : "Jim M.", "last" : "Magiera"} ], "note": "Related to: Jim Magiera, Deep Ray, Jan S. Hesthaven, Christian Rohde, Constraint-aware neural networks for Riemann problems, Journal of Computational Physics, Volume 409, 2020, 109345. doi: 10.1016/j.jcp.2020.109345","abstract": "Data sets of the article \"Constraint-aware neural networks for Riemann problems\", consisting of training and test data sets for Riemann solutions of the cubic flux model, an isothermal two-phase model, and the Euler equations for an ideal gas. You can find detailed information in the README.md.", "affiliation" : "Magiera, Jim M./Universität Stuttgart", "orcid-numbers" : "Magiera, Jim M./0000-0001-9807-0784", "doi" : "10.18419/darus-3869", "bibtexKey": "magiera2024replication" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/22b58ea3f5c19661e59e9fe0e6cac098d/testusersimtech", "tags" : [ "EXC2075","PNX","darus" ], "intraHash" : "2b58ea3f5c19661e59e9fe0e6cac098d", "interHash" : "b673577efe95c0d908359b2178b8b64d", "label" : "PDEBench Pretrained Models : Pretrained models for \"PDEBench: An Extensive Benchmark for Scientific Machine Learning\"", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 7, "pub-type": "misc", "year": "2022", "url": "", "author": [ "Makoto Takamoto","Timothy Praditia","Raphael Leiteritz","Dan MacKinlay","Francesco Alesiani","Dirk Pflüger","Mathias Niepert" ], "authors": [ {"first" : "Makoto", "last" : "Takamoto"}, {"first" : "Timothy", "last" : "Praditia"}, {"first" : "Raphael", "last" : "Leiteritz"}, {"first" : "Dan", "last" : "MacKinlay"}, {"first" : "Francesco", "last" : "Alesiani"}, {"first" : "Dirk", "last" : "Pflüger"}, {"first" : "Mathias", "last" : "Niepert"} ], "note": "Related to: Takamoto, M., Praditia, T., Leiteritz, R., MacKinlay, D., Alesiani, F., Pflüger, D. and Niepert, M.: PDEBench: An Extensive Benchmark for Scientific Machine Learning. submitted to the 36th Conference on Neural Information Processing Systems (NeurIPS 2022) Track on Datasets and Benchmarks","abstract": "This dataset contains the pretrained baseline models, namely FNO, U-Net, and PINN. These models are trained on different PDEs, such as 1D advection, 1D Burgers', 1D and 2D diffusion-reaction, 1D diffusion-sorption, 1D, 2D, and 3D compressible Navier-Stokes, 2D Darcy flow, and 2D shallow water equation. In addition the dataset contains the pre-trained model for the 1D Inverse problem for FNO and U-Net. These models are stored using the same structure as the dataset they trained on. All the files are saved in .pt files, the default file type for the PyTorch library.More detailed information are also provided in our Github repository (https://github.com/pdebench/PDEBench) and our submitting paper to NeurIPS 2022 Benchmark track.", "affiliation" : "Takamoto, Makoto/NEC Labs Europe, Praditia, Timothy/Universität Stuttgart, Leiteritz, Raphael/Universität Stuttgart, MacKinlay, Dan/CSIRO's Data61, Alesiani, Francesco/NEC Labs Europe, Pflüger, Dirk/Universität Stuttgart, Niepert, Mathias/Universität Stuttgart", "orcid-numbers" : "Takamoto, Makoto/0000-0001-7192-1956, Praditia, Timothy/0000-0003-3619-9122, Leiteritz, Raphael/0000-0001-8070-2384, MacKinlay, Dan/0000-0001-6077-2684, Alesiani, Francesco/0000-0003-4413-7247, Pflüger, Dirk/0000-0002-4360-0212, Niepert, Mathias/0000-0002-8401-3751", "doi" : "10.18419/darus-2987", "bibtexKey": "takamoto2022pdebench" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2172197a719dfb8148f9a999a0a5cf4aa/testusersimtech", "tags" : [ "EXC2075","PNX","darus" ], "intraHash" : "172197a719dfb8148f9a999a0a5cf4aa", "interHash" : "caade020b959958fad6ee3cea50e9ed8", "label" : "Raw Simulation Datasets for Extending Heat Plumes", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2024", "url": "", "author": [ "Julia Pelzer" ], "authors": [ {"first" : "Julia", "last" : "Pelzer"} ], "abstract": "These data sets serve as training and testing data for modelling the extension of temperature field emanating from one groundwater heat pump. There are simulated with Pflotran and saved in h5 format. The data set for training is called \"dataset_medium_k_3e-10_1000dp\".It contains 999 simulation runs, each simulated until a near steady state is reached. Each data point measures 320 m x 6400 m with 64 x 1280 cells. The varying parameters of the data set are pressure and permeability. Both are constant within the domain, but vary across the data set. A longer data set for testing is called \"dataset_long_k_3e-10_7dp\". It contains only 7 simulation runs with a larger domain of 320 m x 10.240 m with 64 x 2048 cells.A third data set, with varying permeability within the domain, is called \"dataset_medium_100dp_vary_perm\". It contains 100 simulation runs. Each data point measures 320 m x 6400 m with 64 x 1280 cells. Other parameters that define the data set, such as porosity, are chosen to be as close as possible to reality and defined in the simulation input files \"inputs/pflotran.in\". Source: \"Die hydraulischen Grundwasserverhältnisse des quartären und des oberflächennahen tertiären Grundwasserleiters im Großraum München\", Geologica Bavarica Volume 122.Generated with scripts from https://github.com/JuliaPelzer/Phd_simulation_groundtruth (commit a3777510c) with arguments given in inputs/args.yaml.", "affiliation" : "Pelzer, Julia/Universität Stuttgart", "orcid-numbers" : "Pelzer, Julia/0009-0003-1727-9626", "doi" : "10.18419/darus-4133", "bibtexKey": "pelzer2024simulation" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2890357c5a9c65e510e9d1ac0c24c5c7b/testusersimtech", "tags" : [ "EXC2075","PNX","darus" ], "intraHash" : "890357c5a9c65e510e9d1ac0c24c5c7b", "interHash" : "2dc736fd7080034f6d24fb700976ce12", "label" : "Dataset: Single Heat Pump Simulation - Prepared \"Learn Params\", 100 Data Points", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2023", "url": "", "author": [ "Julia Pelzer" ], "authors": [ {"first" : "Julia", "last" : "Pelzer"} ], "abstract": "This data set serves as training data for modelling the temperature field emanating from a groundwater heat pump. It is simulated with Pflotran, preprocessed with python and saved in pt-format. It contains 100 data points, each consisting of one simulation run after 5 years - so not necessarily in steady state. Each datapoint measures 100 m x 1280 m with 20 x 256 cells. The varying parameters of the data set are pressure and permeability. Both are constant within a data point, but vary across the data set. Other parameters that define the data set, such as porosity, are chosen to be as close as possible to reality. Generated with scripts from https://github.com/JuliaPelzer/Phd_simulation_groundtruth (commit 94daf52) with arguments given in inputs/args.yaml. The prepared dataset contains two input options: full fields in Inputs folder or reduced input of 4 parameters per datapoint in InputParams; and two label options: full fields in Labels and 4 parameters in LearnableParams.More information about the specific parameters are in the readme file.", "affiliation" : "Pelzer, Julia/Universität Stuttgart", "orcid-numbers" : "Pelzer, Julia/0009-0003-1727-9626", "doi" : "10.18419/darus-3653", "bibtexKey": "pelzer2023dataset" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2a8f6962137b231bbba6b4b949abc17cd/testusersimtech", "tags" : [ "EXC2075","PN6","darus" ], "intraHash" : "a8f6962137b231bbba6b4b949abc17cd", "interHash" : "ca09e8cf904f081df27bf7cd6d3ec935", "label" : "Pre-trained and fine-tuned ANI models for: Transfer learning for chemically accurate interatomic neural network potentials", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2023", "url": "", "author": [ "Viktor Zaverkin","David Holzmüller","Luca Bonfirraro","Johannes Kästner" ], "authors": [ {"first" : "Viktor", "last" : "Zaverkin"}, {"first" : "David", "last" : "Holzmüller"}, {"first" : "Luca", "last" : "Bonfirraro"}, {"first" : "Johannes", "last" : "Kästner"} ], "note": "Related to: Viktor Zaverkin, David Holzmüller, Luca Bonfirraro, Johannes Kästner. Transfer learning for chemically accurate interatomic neural network potentials, Phys. Chem. Chem. Phys., 2023, 25, 5383-5396. doi: 10.1039/D2CP05793J","abstract": "Pre-trained and fine-tuned ANI models using the Gaussian Moments Neural Network (GM-NN) approach. Code for GM-NN implemented within the Tensorflow framework, including the respective documentation and tutorials, can be found on GitLab. The data represents TensorFlow v2 checkpoints and stores the metadata for the checkpoint and parameters for the model. Checkpoints can be read by the source code provided on GitLab. A detailed description for reproducing the results and employing pre-trained and fine-tuned models during a simulation is provided in the GM-NN Documentation.", "affiliation" : "Zaverkin, Viktor/Universität Stuttgart, Holzmüller, David/Universität Stuttgart, Bonfirraro, Luca/Universität Stuttgart, Kästner, Johannes/Universität Stuttgart", "orcid-numbers" : "Zaverkin, Viktor/0000-0001-9940-8548, Holzmüller, David/0000-0002-9443-0049, Bonfirraro, Luca/0000-0003-4799-2986, Kästner, Johannes/0000-0001-6178-7669", "doi" : "10.18419/darus-3299", "bibtexKey": "zaverkin2023pretrained" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/23c18ff6580575dbbdc6e0f12d266cf9d/testusersimtech", "tags" : [ "EXC2075","PN7","darus" ], "intraHash" : "3c18ff6580575dbbdc6e0f12d266cf9d", "interHash" : "8255ce94bee8751857302fc0d36a7d29", "label" : "Replication Code for: Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 6, "pub-type": "misc", "year": "2024", "url": "", "author": [ "Philipp Luca Reiser","Javier Enrique Aguilar","Anneli Guthke","Paul-Christian Bürkner" ], "authors": [ {"first" : "Philipp Luca", "last" : "Reiser"}, {"first" : "Javier Enrique", "last" : "Aguilar"}, {"first" : "Anneli", "last" : "Guthke"}, {"first" : "Paul-Christian", "last" : "Bürkner"} ], "note": "Related to: Reiser P., Aguilar J. E., Guthke A., & Bürkner P. C. (2023). Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference. ArXiv preprint 2312.05153. arXiv: 2312.05153","abstract": "This code allows to replicate key experiments from our paper: Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference. For further details, please refer to the README.md.", "affiliation" : "Reiser, Philipp/Universität Stuttgart, Aguilar, Javier Enrique/TU Dortmund, Guthke, Anneli/Universität Stuttgart, Bürkner, Paul-Christian/TU Dortmund", "orcid-numbers" : "Reiser, Philipp/0000-0002-5553-1007, Guthke, Anneli/0000-0003-2901-1603, Bürkner, Paul-Christian/0000-0001-5765-8995", "doi" : "10.18419/darus-4093", "bibtexKey": "reiser2024replication" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2571e60f37742bb502a1a08d4c78149cd/testusersimtech", "tags" : [ "EXC2075","PN4","darus" ], "intraHash" : "571e60f37742bb502a1a08d4c78149cd", "interHash" : "1616ff4e212ba8ce9f4887b6337cad1e", "label" : "Replication Data for: On the Accurate Estimation of Information-Theoretic Quantities from Multi-Dimensional Sample Data", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 6, "pub-type": "misc", "year": "2024", "url": "", "author": [ "Manuel Alvarez Chaves","Hoshin Gupta","Uwe Ehret","Anneli Guthke" ], "authors": [ {"first" : "Manuel", "last" : "Alvarez Chaves"}, {"first" : "Hoshin", "last" : "Gupta"}, {"first" : "Uwe", "last" : "Ehret"}, {"first" : "Anneli", "last" : "Guthke"} ], "note": "Related to: Álvarez Chaves, Manuel, Gupta, Hoshin V., Ehret, Uwe and Guthke, Anneli. On the Accurate Estimation of Information-Theoretic Quantities from Multi-Dimensional Sample Data. Entropy 2024, 26(5), 387. doi: 10.3390/e26050387","abstract": "Non-Parametric Estimation in Information Theory1. Introduction: This is a repository for our paper on: \"Evaluating Density- and Nearest Neighbor-based Methods to Accurately Estimate Information-Theoretic Quantities from Multi-Dimensional Sample Data\". Installation: Code was written in Python 3.11.5 but should be compatible with later and earlier versions of Python down to Python 3.6. Check the requirements.txt file for any dependency issues. Usage is recommended by cloning the repository to a local directory and setting up the required environment using venv and pip: python -m venv .venv, source .venv/Scripts/activate, pip install -r requirements.txt3. Generating Data: Initially data is generated and stored in the data_evaluation/data directory using the script in the data_generation/ directory. The data for the experiments is stored as an HDF5 database. From the root directory: python data_generation/data_generation.py. Note: as the data.hdf5 file is ~123 GB, it is recommended to be locally generated. This process takes about ~12 hrs in an Intel Xeon E5-26280 v2 but shouldn't vary too much in any modern CPU. 4. Conducting an Evaluation: The scripts in the directory data_evaluation/ are used to read the data and perform the experiments. Results are stored in the results/ directory.Again, from the root directory: python data_evaluation/eval_bin_entropy.py. All of the names of the scripts have the format eval_estimator_quantity.py. In total, 12 scripts must be run, tree for each estimator: binning, KDE, numerical integration of KDE and k-NN. The notebooks/ directory serves as an archive of the development of the workflow to test each estimator. The contents of each notebook are generally the same as the code in the scripts. Log files describe the history of the project. 5. Visualizing Results: The analysis_results directory contains a notebook to create the plots used in the paper, as well as a script to read the log files and calculate the time per iteration of the different experiments.The plots are generated using the results from the data_evaluation/results directory. Results are read from .hdf5 files. All results produced using the UNITE Toolbox.", "affiliation" : "Alvarez Chaves, Manuel/Universität Stuttgart, Gupta, Hoshin/The University of Arizona, Ehret, Uwe/Karlsruhe Institute of Technology, Guthke, Anneli/Universität Stuttgart", "orcid-numbers" : "Alvarez Chaves, Manuel/0009-0002-8990-3785, Gupta, Hoshin/0000-0001-9855-2839, Ehret, Uwe/0000-0003-3454-8755, Guthke, Anneli/0000-0003-2901-1603", "doi" : "10.18419/darus-4087", "bibtexKey": "alvarezchaves2024replication" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2f3eebc1f7916a0c6ca29d5494e6bb216/testusersimtech", "tags" : [ "EXC2075","PNX","darus" ], "intraHash" : "f3eebc1f7916a0c6ca29d5494e6bb216", "interHash" : "0236e13613439e60bc74e229afc65590", "label" : "Replication Code for: Rayleigh invariance allows the estimation of effective CO2 fluxes due to convective dissolution into water-filled fractures", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 9, "pub-type": "misc", "year": "2024", "url": "", "author": [ "Leon Keim","Holger Class" ], "authors": [ {"first" : "Leon", "last" : "Keim"}, {"first" : "Holger", "last" : "Class"} ], "abstract": "This dataset consists of software code associated with the publication titled \"Rayleigh Invariance Enables Estimation of Effective CO2 Fluxes Resulting from Convective Dissolution in Water-Filled Fractures.\" It includes a Dockerimage that contains the precompiled code for immediate use. For transparency, the Dockerfile is also provided.", "affiliation" : "Keim, Leon/Universität Stuttgart, Class, Holger/Universität Stuttgart", "orcid-numbers" : "Keim, Leon/0000-0003-2456-1809, Class, Holger/0000-0002-4476-8017", "doi" : "10.18419/darus-4089", "bibtexKey": "keim2024replication" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/256da48ba537979929bd7fe0939020a48/testusersimtech", "tags" : [ "EXC2075","PN8","darus" ], "intraHash" : "56da48ba537979929bd7fe0939020a48", "interHash" : "ba1bdd18aaea16ac35b6ca8e781865d7", "label" : "Material for the paper \"The possible role of lipid bilayer properties in the evolutionary disappearance of betaine lipids in seed plants.\"", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2023", "url": "", "author": [ "Alexander Schlaich" ], "authors": [ {"first" : "Alexander", "last" : "Schlaich"} ], "note": "Related to: The possible role of lipid bilayer properties in the evolutionary disappearance of betaine lipids in seed plants. Bolik Stéphanie, Schlaich Alexander, Mukhina Tetiana, Amato Alberto, Bastien Olivier, Schneck Emanuel, Demé Bruno, Jouhet Juliette. bioRxiv 2023.01.24.525350. doi: 10.1101/2023.01.24.525350","abstract": "Simulation input scripts to produce the data presented in the manuscript \"The possible role of lipid bilayer properties in the evolutionary disappearance of betaine lipids in seed plants.\" All simulations were carried out using the GROMACS simulation package.The folders contain the two considered lipids, 'DP-DGTS' and 'DPPC', respectively.Each folder, contains the corresponding 'topology' and the simulation inputs for the 'gel' and 'fluid' phases. Subfolders correspond to the different hydration levels (waters per lipid, 'wpl') as well as the python scripts to produce the solvated bilayers ('construct_bilayer'). The GROMACS simulation parameters are given in 'parameters'.", "affiliation" : "Schlaich, Alexander/Universität Stuttgart", "orcid-numbers" : "Schlaich, Alexander/0000-0002-4250-363X", "doi" : "10.18419/darus-2360", "bibtexKey": "schlaich2023material" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2ebf9f9471b92a818fff827d62009c8ff/testusersimtech", "tags" : [ "EXC2075","PNX","darus" ], "intraHash" : "ebf9f9471b92a818fff827d62009c8ff", "interHash" : "86ecb31a9dd966de865225856172a3bc", "label" : "Case Study Database for: Documenting Research Software in Engineering Science", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 5, "pub-type": "misc", "year": "2022", "url": "", "author": [ "Sibylle Hermann" ], "authors": [ {"first" : "Sibylle", "last" : "Hermann"} ], "note": "Related to: Hermann, S., Fehr, J. Documenting research software in engineering science. Sci Rep 12, 6567 (2022). doi: 10.1038/s41598-022-10376-9","abstract": "This dataset contains the collected data of a case study on the documentation of research software in the institutional everyday life of engineering scientists. All files beginning with \"Notes\" contain personal thoughts and transcripts. More detailed descriptions about the content of the files are located directly on the file.", "affiliation" : "Hermann, Sibylle/Universität Stuttgart", "orcid-numbers" : "Hermann, Sibylle/0000-0001-9239-8789", "doi" : "10.18419/darus-2681", "bibtexKey": "hermann2022study" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/29e1919d426fbf9a1855719f7e5c97d7c/testusersimtech", "tags" : [ "EXC2075","PN3","darus" ], "intraHash" : "9e1919d426fbf9a1855719f7e5c97d7c", "interHash" : "8d5bec6a657e2e476700c8f48e7c195b", "label" : "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2023", "url": "", "author": [ "Morris Degen","José Carlos Santos","Kristyna Pluhackova","Gonzalo Cebrero","Saray Ramos","Gytis Jankevicius","Ella Hartenian","Undina Guillerm","Stefania A. Mari","Bastian Kohl","Daniel J. Müller","Paul Schanda","Timm Maier","Camilo Perez","Christian Sieben","Petr Broz","Sebastian Hiller" ], "authors": [ {"first" : "Morris", "last" : "Degen"}, {"first" : "José Carlos", "last" : "Santos"}, {"first" : "Kristyna", "last" : "Pluhackova"}, {"first" : "Gonzalo", "last" : "Cebrero"}, {"first" : "Saray", "last" : "Ramos"}, {"first" : "Gytis", "last" : "Jankevicius"}, {"first" : "Ella", "last" : "Hartenian"}, {"first" : "Undina", "last" : "Guillerm"}, {"first" : "Stefania A.", "last" : "Mari"}, {"first" : "Bastian", "last" : "Kohl"}, {"first" : "Daniel J.", "last" : "Müller"}, {"first" : "Paul", "last" : "Schanda"}, {"first" : "Timm", "last" : "Maier"}, {"first" : "Camilo", "last" : "Perez"}, {"first" : "Christian", "last" : "Sieben"}, {"first" : "Petr", "last" : "Broz"}, {"first" : "Sebastian", "last" : "Hiller"} ], "note": "Related to: Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, \"Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death\", Nature 2023. doi: 10.1038/s41586-023-05991-z","abstract": "Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether the newly resolved cryo-electron microscopy NINJ1 filaments are capable to cap edges of membrane edges by multiscaling molecular dynamics simulations. Site-directed mutagenesis was employed to validate the function of the resulting supramolecular arrangement. The membrane protein NINJ1 is thus an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.", "affiliation" : "Degen, Morris/Biozentrum, University of Basel, Santos, José Carlos/Department of Immunobiology, University of Lausanne, Pluhackova, Kristyna/SC SimTech, University of Stuttgart, Cebrero, Gonzalo/Biozentrum, University of Basel, Ramos, Saray/Department of Immunobiology, University of Lausanne, Jankevicius, Gytis/Biozentrum, University of Basel, Hartenian, Ella/Department of Immunobiology, University of Lausanne, Guillerm, Undina/Institute of Science and Technology Austria, Mari, Stefania A./Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Kohl, Bastian/Biozentrum, University of Basel, Müller, Daniel J./Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Schanda, Paul/Institute of Science and Technology Austria, Maier, Timm/Biozentrum, University of Basel, Perez, Camilo/Biozentrum, University of Basel, Sieben, Christian/Institute for Genetics, Technische Universität Braunschweig; Nanoscale Infection Biology Group, Department of Cell Biology, Helmholtz Centre for Infection Research, Broz, Petr/Department of Immunobiology, University of Lausanne, Hiller, Sebastian/Biozentrum, University of Basel", "orcid-numbers" : "Degen, Morris/0000-0003-3762-5779, Santos, José Carlos/0000-0002-3446-4001, Pluhackova, Kristyna/0000-0002-7498-6584, Cebrero, Gonzalo/0000-0001-7171-0921, Ramos, Saray/0000-0001-6015-9310, Jankevicius, Gytis/0000-0002-0212-3923, Hartenian, Ella/0000-0001-9277-2152, Mari, Stefania A./0000-0002-6420-8578, Kohl, Bastian/0000-0001-6601-8340, Müller, Daniel J./0000-0003-3075-0665, Schanda, Paul/0000-0002-9350-7606, Maier, Timm/0000-0002-7459-1363, Perez, Camilo/0000-0002-5800-0084, Sieben, Christian/0000-0002-2836-2623, Broz, Petr/0000-0002-2334-7790, Hiller, Sebastian/0000-0002-6709-4684", "doi" : "10.18419/darus-3373", "bibtexKey": "deggen2023supplementary" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/22f49c54d5fdfb208d643d1c03ab119da/testusersimtech", "tags" : [ "EXC2075","PN4","darus" ], "intraHash" : "2f49c54d5fdfb208d643d1c03ab119da", "interHash" : "f5b3cb15f37ca659a8e4dce4cf811807", "label" : "Experiment Videos of the Force-Based Non-Prehensile Cooperative Transportation of Objects with Mobile Robots", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2023", "url": "", "author": [ "Mario Rosenfelder","Henrik Ebel","Peter Eberhard" ], "authors": [ {"first" : "Mario", "last" : "Rosenfelder"}, {"first" : "Henrik", "last" : "Ebel"}, {"first" : "Peter", "last" : "Eberhard"} ], "note": "Related to: Rosenfelder, M., Ebel, H., Eberhard, P. (2023). A Force-Based Formation Synthesis Approach for the Cooperative Transportation of Objects. In: Petrič, T., Ude, A., Žlajpah, L. (eds) Advances in Service and Industrial Robotics. RAAD 2023. Mechanisms and Machine Science, vol 135. Springer, Cham. doi: 10.1007/978-3-031-32606-6_37","abstract": "The videos provided show two experimental results of cooperative object transportation using lightweight omnidirectional mobile robots. In particular, the mobile robots shall transport two different polygonal, but non-convex, objects along predefined paths. No central decision entity is employed; the tasks are accomplished in a purely distributed manner using inter-robot communication. Novelly, the formation synthesis relies on a force-based consideration that explicitly takes into account the physical limitations of the robotic agents. Due to this, if necessary, multiple robots are placed along one edge in order to exert the desired force acting on the object. This is exemplarily shown in the video and demonstrates one crucial advantage compared to purely position-based approaches. Furthermore, an underlying hybrid position-force controller is utilized to govern the individual pushing forces of the robots. The interacting force is measured by each agent using a self-designed onboard force-sensing unit. In the videos, the direction of the unilateral force sensor is indicated by white rectangles. Moreover, the measured force is visualized by the red rectangles superimposed onto the white ones.", "affiliation" : "Rosenfelder, Mario/Universität Stuttgart, Ebel, Henrik/Universität Stuttgart, Eberhard, Peter/Universität Stuttgart", "orcid-numbers" : "Rosenfelder, Mario/0000-0003-0460-0612, Ebel, Henrik/0000-0002-2632-6960, Eberhard, Peter/0000-0003-1809-4407", "doi" : "10.18419/darus-3331", "bibtexKey": "rosenfelder2023experiment" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/285f6e4a0dcbb59ac62f6dc37b1b43fac/testusersimtech", "tags" : [ "EXC2075","PNX","darus" ], "intraHash" : "85f6e4a0dcbb59ac62f6dc37b1b43fac", "interHash" : "b0f1e7d32686177deb3f7641cc143367", "label" : "Models and Prepared Datasets for the Second Stage : based on the Two Heat Pumps Simulation Datasets", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2024", "url": "", "author": [ "Julia Pelzer" ], "authors": [ {"first" : "Julia", "last" : "Pelzer"} ], "note": "Related to: Pelzer, Julia, and Miriam Schulte. \"Efficient two-stage modeling of heat plume interactions of geothermal heat pumps in shallow aquifers using convolutional neural networks.\" Geoenergy Science and Engineering (2024): 212788. doi: 10.1016/j.geoen.2024.212788","abstract": "Models trained with 1HP_NNand datasets prepared with 1HP_NN into reasonable format + normalization etc, used for training these models. Last relevant git commit: 5d6c5eae5b00e438. Based on raw data from doi:darus-3651 and doi:darus-3652.", "affiliation" : "Pelzer, Julia/Universität Stuttgart", "orcid-numbers" : "Pelzer, Julia/0009-0003-1727-9626", "doi" : "10.18419/darus-3689", "bibtexKey": "pelzer2024models" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/20b32a4fb35cb9020a9e3da1a444a5376/testusersimtech", "tags" : [ "EXC2075","PN5","darus" ], "intraHash" : "0b32a4fb35cb9020a9e3da1a444a5376", "interHash" : "2fbd769e565133308abd183cd2042d8b", "label" : "Gaussian active learning on multi-resolution arbitrary polynomial chaos emulator : Data and Software", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2023", "url": "", "author": [ "Rebecca Kohlhaas","Ilja Kröker","Sergey Oladyshkin","Wolfgang Nowak" ], "authors": [ {"first" : "Rebecca", "last" : "Kohlhaas"}, {"first" : "Ilja", "last" : "Kröker"}, {"first" : "Sergey", "last" : "Oladyshkin"}, {"first" : "Wolfgang", "last" : "Nowak"} ], "abstract": "This folder contains the code for the aMR-PC toolbox by Ilja Kröker in the version used for the code in GALMAP_code.This toolbox was also used for Kröker et al. 2022. This folder contains inputs and simulated outputs of the CO_2 benchmark from here and referenced in Köppel et al. 2019. There are a set of 10000 random samples of inputs and corresponding simulated outputs, as well as sets of input and output samples that correspond to the roots needed for aMR-PC with different (Nr, No). Additionally the sub-folder 'DNN' contains the results of three DNN trained on the data from the benchmark. The specifics of the DNN are described in the paper. aMRPCclass.py: This file contains a class aMRPC, that makes use of the aMR-PC toolbox to implement an aMR-PC. The class can be used for creating and fitting an aMR-PC of specified polynomial degree on data, as well as refitting an existing aMR-PC on new data. data_load.py: This file contains functions that load the data from the CO_2 benchmark contained in the folder \"data\". The functions are used in the file \"run_iterative.py\". GPE.py: This file contains a variation on the Scikit GPE-implementation, which creates and fits a GPE with a standard RBF-kernel to specified data. It additionally returns the results on further, to the GPE unknown, data. PLOTS.py: This file contains functions which create the figures used in the paper. This includes representations of the CO_2 dataset, as well as the results of the iterative and active learning variations of aMR-PC and GPE. Some of the functions rely on an import of the aMRPC class.run_iterative.pyThis file can be seen as the 'main'. It runs one of the three active learning based variations on given data and outputs the results in the form of files and figures, as can be found in the folder \"results\". The desired type of variation, polynomial degree of the aMR-PC and outputs can be easily changed by setting parameters at the start of the file. This code imports aMRPCclass.py, data_load.py, GPE.py and twostep.py. twostep.py: This file contains the calculations done in the main loop from run_iterative.py. Its function run_GPE runs a GPE on given samples and returns its approximation, as well as various error measures thereof. The approximation is depicted in figures created from the function plot_twostep. Results: Results from the implementation in GALMAP_code can be found here. The results were run for the three variations GAL, GALMaP and GALMaPAT each for (Nr, No) = (1,1) and 100 iterations.", "affiliation" : "Kohlhaas, Rebecca/Universität Stuttgart, Kröker, Ilja/Universität Stuttgart, Oladyshkin, Sergey/Universität Stuttgart, Nowak, Wolfgang/Universität Stuttgart", "orcid-numbers" : "Kohlhaas, Rebecca/0000-0001-5263-5073, Kröker, Ilja/0000-0003-0360-5307, Oladyshkin, Sergey/0000-0003-4676-5685, Nowak, Wolfgang/0000-0003-2583-8865", "doi" : "10.18419/darus-2829", "bibtexKey": "kohlhaas2023gaussian" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2fd5b68cb584a7943f99c2848e6ff9e5b/testusersimtech", "tags" : [ "EXC2075","PN2","darus" ], "intraHash" : "fd5b68cb584a7943f99c2848e6ff9e5b", "interHash" : "e7b9fcbc5f5ae95133d485445c943ef4", "label" : "Replication Data for: A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2023", "url": "", "author": [ "Pablo Filipe Santana Chacon","Maria Hammer","Isabell Wochner","Johannes R. Walter","Syn Schmitt" ], "authors": [ {"first" : "Pablo Filipe", "last" : "Santana Chacon"}, {"first" : "Maria", "last" : "Hammer"}, {"first" : "Isabell", "last" : "Wochner"}, {"first" : "Johannes R.", "last" : "Walter"}, {"first" : "Syn", "last" : "Schmitt"} ], "note": "Related to: P. F. S. Chacon, M. Hammer, I. Wochner, J. R. Walter and S. Schmitt. A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers. doi: 10.1080/10255842.2023.2293652","abstract": "This code/data allows you reproduce the results of the paper: \"A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers\" by P. F. S. Chacon, M. Hammer, I. Wochner, J. R. Walter and S. Schmitt. Always cite the paper together with this dataset because this dataset is not self-explanatory. More information about the dataset can be found here: README.md.", "affiliation" : "Santana Chacon, Pablo Filipe/Universität Stuttgart, Hammer, Maria/Universität Stuttgart, Wochner, Isabell/Universität Heidelberg, Walter, Johannes R./Max-Planck-Institut für Intelligente Systeme, Schmitt, Syn/Universität Stuttgart", "orcid-numbers" : "Santana Chacon, Pablo Filipe/0009-0008-9439-4747, Hammer, Maria/0000-0001-8399-9515, Wochner, Isabell/0000-0002-2820-5791, Schmitt, Syn/0000-0002-7768-8961", "doi" : "10.18419/darus-3796", "bibtexKey": "santanachacon2023replication" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2ecf8c87b4b9d1ebadb6af38afaaaef5c/testusersimtech", "tags" : [ "EXC2075","PN7","darus" ], "intraHash" : "ecf8c87b4b9d1ebadb6af38afaaaef5c", "interHash" : "f27086583ad6d368788a572f54d26155", "label" : "2023 CCN Time Window Project Code", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2023", "url": "", "author": [ "René Sebastian Skukies" ], "authors": [ {"first" : "René Sebastian", "last" : "Skukies"} ], "note": "Related to: Skukies, R., & Ehinger, B. V. (2023). The effect of estimation time window length on overlap correction in EEG data (2023.06.05.543689). bioRxiv. doi: 10.1101/2023.06.05.543689","abstract": "Notebooks/ scripts used for the time window project done for our CCN contribution in 2023. The notebooks will simulate EEG data based on a known \"ground truth\" ERP and test whether the estimation length during ERP activity estimation will have an Influence on the results. To get a first impression why this is important please have a look at our online application: http://estimationwindow.ccn2023.s-ccs.de . Used notebooks can be found in \\PlutoNB; generally, the nb_CCN2023_unfoldEstimationWindow_exploration was used during actual project work. However, nb_CCN2023_unfoldEstimationWindow.jl is a cleaned-up version and more readable. To replicate the results simply open and run the notebook in question using Pluto.jl", "affiliation" : "Skukies, René/Universität Stuttgart", "orcid-numbers" : "Skukies, René/0000-0002-4124-4584", "doi" : "10.18419/darus-3635", "bibtexKey": "skukies2023window" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2c06b14e2367463d6035f9391e7ad6fa8/testusersimtech", "tags" : [ "EXC2075","PN4","darus" ], "intraHash" : "c06b14e2367463d6035f9391e7ad6fa8", "interHash" : "c6fd673e22c25cac71c78a9a84f14fbf", "label" : "EHTM Code and Manual", "user" : "testusersimtech", "description" : "", "date" : "2024-07-03 10:45:48", "changeDate" : "2024-07-03 10:45:48", "count" : 4, "pub-type": "misc", "year": "2022", "url": "", "author": [ "Lennart Nölle","Patrick Lerge","Oleksandr Martynenko","Isabell Wochner","Fabian Kempter","Christian Kleinbach","Syn Schmitt","Jörg Fehr" ], "authors": [ {"first" : "Lennart", "last" : "Nölle"}, {"first" : "Patrick", "last" : "Lerge"}, {"first" : "Oleksandr", "last" : "Martynenko"}, {"first" : "Isabell", "last" : "Wochner"}, {"first" : "Fabian", "last" : "Kempter"}, {"first" : "Christian", "last" : "Kleinbach"}, {"first" : "Syn", "last" : "Schmitt"}, {"first" : "Jörg", "last" : "Fehr"} ], "note": "Related to: Kleinbach, C., Martynenko, O., Promies, J., Haeufle, D.F., Fehr, J., Schmitt, S., 2017. Implementation and validation of the extended hill-type muscle model with robust routing capabilities in LS-DYNA for active human body models. Biomedical engineering online 16, 109. doi: 10.1186/s12938-017-0399-7","abstract": "This Dataset contains the implementation of the four element Extended Hill-type Muscle (EHTM) model with serial damping and eccentric force\u2013velocity relation including Ca2+ dependent activation dynamics and internal methods for physiological muscle control for the finite-element solver LS-DYNA.", "affiliation" : "Nölle, Lennart/Universität Stuttgart, Lerge, Patrick/Universität Stuttgart, Martynenko, Oleksandr/Universität Stuttgart, Wochner, Isabell/Universität Stuttgart, Kempter, Fabian/Universität Stuttgart, Kleinbach, Christian/Universität Stuttgart, Schmitt, Syn/Universität Stuttgart, Fehr, Jörg/Universität Stuttgart", "orcid-numbers" : "Nölle, Lennart/0000-0001-8952-2486, Lerge, Patrick/0000-0001-6081-5226, Martynenko, Oleksandr/0000-0002-0420-0670, Wochner, Isabell/0000-0002-2820-5791, Kempter, Fabian/0000-0003-0702-2205, Kleinbach, Christian/0000-0001-9502-5910, Schmitt, Syn/0000-0002-7768-8961, Fehr, Jörg/0000-0003-2850-1440", "doi" : "10.18419/darus-1144", "bibtexKey": "nolle2022manual" } ] }