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  • Research software . 2021
    Restricted English
    Authors: 
    Joustra, Jelle; Balkenende, Ruud; van der Grinten, Bram;
    Publisher: Zenodo
    Project: EC | ECOBULK (730456), EC | ECOBULK (730456)

    Fastener finder toolbox developed by TUDelft to support in the decision of which fastener best fits the circular products.

  • Open Access
    Authors: 
    Toni Martinez del Hoyo Guri; Marc Vila Gómez; José Gorchs Morillas; Ignasi Garcia-Milà Vidal;
    Publisher: Zenodo
    Project: EC | STOP-IT (740610), EC | STOP-IT (740610)

    First version of the Public Warning Notification System (PWNS) for the STOP-IT project. General documentation of the module is available at https://stop-it-project.eu/results/public-warning-notification-system/

  • Open Access
    Authors: 
    Sievers, Silvan; Wehrle, Martin;
    Publisher: Zenodo
    Project: EC | TAILOR (952215), EC | BDE (817639), EC | TAILOR (952215), EC | BDE (817639)

    This bundle contains code, scripts and benchmarks for reproducing all experiments reported in the paper. It also contains the data generated for the paper. sievers-wehrle-ijcai2021-fast-downward.zip contains the implementation based on Fast Downward. It also contains the experiment scripts compatible with Lab 6.3 for reproducing all experiments of the paper, under experiments/weak-stubborn-sets. The scripts 2021-05-10-CRC-* contain configurations for running the experiments and the script paper-tables.py gathers the data and produces plots and tables. (Note that some adjustments to the scripts would need to be done because, e.g., the entire tree is not a repository anymore.) sievers-wehrle-ijcai2021-benchmarks.zip contains the benchmarks. It consists of the STRIPS IPC benchmarks used in all optimal sequential tracks of IPCs up to 2018 (suite optimal_strips from https://github.com/aibasel/downward-benchmarks). sievers-wehrle-ijcai2021-lab.tar.gz contains a copy of Lab 6.3 (https://github.com/aibasel/lab). sievers-wehrle-ijcai2021-data.zip contains the experimental data. Directories without the "-eval" ending contain raw data, distributed over a subdirectory for each experiment. Each of these contain a subdirectory tree structure "runs-*" where each planner run has its own directory. For each run, there are symbolic links to the input PDDL files domain.pddl and problem.pddl (can be resolved by putting the benchmarks directory to the right place), the run log file "run.log" (stdout), possibly also a run error file "run.err" (stderr), the run script "run" used to start the experiment, and a "properties" file that contains data parsed from the log file(s). Directories with the "-eval" ending contain a "properties" file, which contains a JSON directory with combined data of all runs of the corresponding experiment. In essence, the properties file is the union over all properties files generated for each individual planner run. Note on license: we chose GPL v3.0 or later mainly because we consider our implementation based on Fast Downward the main contribution of this package, and Fast Downward comes with GPL v3.0. We only include a copy of Lab and the benchmarks for convenience.

  • Open Access
    Authors: 
    Esther van Kleef; Nantasit Luangasanatip; Marc JM Bonten; Ben S Cooper;
    Publisher: Zenodo
    Project: EC | R-GNOSIS (282512), EC | R-GNOSIS (282512)

    This release contains additional sensitivity analysis showing the impact of changing the degree of bacterial inference and mixing. This model simulates the transmission dynamics of two competing strains, i.e. a hospital-adapted resistant strain and a community-adapted sensitive strain, in the hospital and its catchment area. It has been argued that since infection control measures, such as hand hygiene, should affect resistant and sensitive strains equally, observed discordant changes must have largely resulted from other factors, such as changes in antibiotic use. This model is used to test the validity of this reasoning. model_functions.R contains all functions including the model, plotting functions and functions to calculate R0. run_model.R contains the code to run the model and generate output. Parameters listed are those at baseline. plot_output.R contains the code to plot the model output. run_model_cdi.R contains the code to run the model and generate output for the Lancet ID correspondence to Dingle et al 2017 (DOI: http://dx.doi.org/10.1016/S1473-3099(16)30514-X). Parameters listed are those used to generate the plot. plot_model_cdi.R contains the code to generate the figure in the Lancet ID correspondence.

  • Open Access
    Authors: 
    Ca��ada, Pablo Mart��nez;
    Publisher: Zenodo
    Project: EC | ESNECO (893825), EC | ESNECO (893825)

    Source code to simulate the LIF and multicompartment model networks and compute EEG proxies.

  • Research software . 2022
    Open Access
    Authors: 
    Yann Pfau-Kempf; Sebastian von Alfthan; Arto Sandroos; Urs Ganse; Tuomas Koskela; Markus Battarbee; Otto Akseli Hannuksela; Ilja; Kostis Papadakis; Maxime Grandin; +4 more
    Publisher: Zenodo
    Project: EC | PRESTISSIMO (682068), EC | PRESTISSIMO (682068)

    This includes such highlights as: The new ionosphere boundary condition (New Ionosphere implementation #580) A custom hashtable for faster velociy space lookups (Replace std::unordered_map with a custom open - bucket fibonacci-hashed hashtable in vmesh. #588) Fixed maxwellian inflow conditions (Maxwellian Inflow Fix #582) Automatic simulation bailout if the vspace is too small (Vspace wall bailout #587) And many more bugfixes! Note: the old magnetospheric boundary behaviour has been renamed: It is now conductingsphere instead of ionosphere (which now denotes the proper ionosphere solver behaviour and only works for 3D simulations). For spatially 2D setups that retain the old behaviour, config files need to be updated, replacing any occurence of ionosphere by conductingsphere.

  • Research software . 2016
    Open Source SQL
    Authors: 
    Segura, Joan; Macias, Jose R.; Guerrero, Carolina Simon;
    Publisher: bio.tools
    Project: EC | EGI-Engage (654142), EC | EOSC-Life (824087), EC | INSTRUCT-ULTRA (731005), EC | CORBEL (654248), EC | ELIXIR-EXCELERATE (676559), EC | West-Life (675858), EC | iNEXT (653706)

    Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB structures and Uniprot sequences where the protein annotations stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can be explored interactively at sequence and structural level.

  • Open Access English
    Authors: 
    Ben Francis;
    Publisher: Zenodo
    Project: EC | EPIPGX (279062), EC | EPIPGX (279062)

    Release Candidate 1 with full functionality! The CRAG software provides a novel tool for the analysis of GWAS with TTE outcomes with competing risks. As CRAG is compatible with high performance parallel computing clusters, thereby allowing efficient and effective analysis of large scale GWAS datasets, without incurring memory issues. The main use of CRAG is expected to be in pharmacogenetic studies to identify genetic biomarkers of patient response to treatment, with the ultimate goal of personalising therapeutic intervention for an array of diseases.

  • Research software . 2020
    Open Access English
    Authors: 
    Chan Bukhari, Syed Ahmad; Busse, Christian E.; Christley, Scott; Corrie, Brian D.; Vander Heiden, Jason A.; Kleinstein, Steven H.; Laserson, Uri; Matsen, Frederick A 4th; Rubelt, Florian;
    Publisher: Zenodo
    Project: EC | iReceptor Plus (825821), EC | iReceptor Plus (825821)

    {"references": ["Rubelt F et al. Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. Nat Immunol 18:1274 (2017)", "Breden F et al. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol 8:1418 (2017)", "Vander Heiden JA et al. AIRR Community Standardized Representations for Annotated Immune Repertoires. Front Immunol 9:2206 (2018)", "Christley S et al. The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. Front Big Data 3:22 (2020)"]} Overview Improvements to the organization and wording of various documentation pages. Added missing deprecation tags for rearrangement_id in the Alignment schema. Modified merge_rearrangement in the airr python library so that it can handle a large number of files. Improved validation error handling in the airr python library. Full Release Notes: Schema release notes Python library release notes R library release notes

  • Open Access
    Authors: 
    benRenard;
    Publisher: Zenodo
    Project: EC | HEGS (835496), EC | HEGS (835496)

    This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 835496 This package provides a R sequencer to mix audio samples. It also defines miscellaneous related objects and methods.

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