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74 results for “Materials Discovery”
Dataset - SciVisContest - Materials Discovery Challenge - version 2025
<p>This the updated version of the dataset that is made available for the SciVisContest Materials Discovery Challenge.</p> <p>The data provided for this challenge was generated for the specific use case of developing a new Al-based alloy suitable for additive manufacturing by blending different available aluminum metal scrap such as automotive Al-Si piston alloys and other alloys from different sectors. Different alloy designs were initially generated based on mixing ratios between available scrap alloys. The CALPHAD method was used to perform equilibrium and non-equilibrium calculations to predict relevant thermo-physical and mechanical variables such as the content of volatile elements like Mg and Zn, phase formation and their fractions, solidification intervals, thermo-physical parameters, yield strength and hot crack sensitivity for each alloy composition.</p>
Rapid discovery of stable materials by coordinate-free coarse graining
<p>Prospective density function theory (DFT) calculations carried out on novel material structures predicted to be stable by the Wren model. In total 5,675 materials were selected for validation. Of these converged results were obtained for 4,721 structures. Calculations were conducting using the VASP DFT code with the settings and pseudopotentials selected such that the data is compatible with the Materials Project.</p> <p>A README file is included that describes how to load the data and the contents of the DataFrame.</p>
A database of vacancy formation enthalpies for materials discovery
<p><strong>A database of vacancy formation enthalpies for materials discovery</strong></p> <p>Matthew Witman<sup>a</sup>, Anuj Goyal<sup>b</sup>, Tadashi Ogitsu<sup>c</sup>, Anthony McDaniel<sup>a</sup>, Stephan Lany<sup>b</sup></p> <p><sup>a</sup> Sandia National Laboratories, <sup>b</sup> National Renewable Energy Laboratory, <sup>c</sup> Lawrence Livermore National Laboratories</p> <p><strong>Abstract</strong></p> <p>This dataset provides DFT calculations of cation and oxygen vacancy defects in oxides which can be used to derive efficient data-driven models for vacancy formation enthalpy. DFT calculations were performed as described in <DOI: 10.26434/chemrxiv-2022-frcns>, where a graph neural network surrogate model was trained and used to screen the Materials Project for promising solar thermochemical water splitting materials. The data, models, scripts and code needed to reproduce the results in <DOI: 10.26434/chemrxiv-2022-frcns> are described below.</p> <p><strong>Data & Models</strong></p> <p>1) data_01_03_22/* corresponds to oxide compounds used in model training</p> <p>2) known_cmpds/* corresponds to known STCH compounds</p> <p>3) screeningMP/* corresponds to the screening related data</p> <ul> <li>screening_inelements/* stores only Materials Project oxides whose composition is a subset of the training elements and contains all the vacancy defect predictions</li> <li>MP_O_PDs/* stores offline PDs from Materials Project so that adjusting oxide stability metrics can be done somewhat rapidly</li> <li>MP_O_Compounds/* stores possible MP oxide compounds to screen</li> </ul> <p>In general, the above folders contain:</p> <ul> <li>DFT data/structures are included in sub-directories: poscars, magnetic moments, oxidation states, and csvs (containing the vacancy enthalpy for each unique site)</li> <li>cgcnn/* contains the processed DFT data for use in the CGCNN code (see <strong>Scripts</strong> for how to prepare this) <ul> <li>id_prop.csv.* contains [cif name, defect formation enthalpy] pairs <ul> <li>Different id_prop.csv.* files correspond to different K-fold stratifications</li> <li>in the screening directory, defect formation enthalpy is omitted since it has not been computed with DFT</li> </ul> </li> <li>model-(X1)k(X2)_(X3)_(X4) corresponds to different CV models for <ul> <li>X1 different training set sizes (i.e., try to train with only 10%, 40%, or 100% of the data)</li> <li>X2 different k folds</li> <li>X3 = "struct" or "" for "structure-wise validation" or "defect-wise validation", respectively</li> <li>X4 for different encoding strategies</li> </ul> </li> <li>structure X-Yz.cif indicates structure X, defect element Y, symmetry site z, where one instance of that site has been re-ordered to be the first atom in the cif file</li> <li>*.locals contains a one-hot encoding of oxidation states of all sites in that crystal</li> <li>*.locals_continuous contains a continuous encoding of oxidation state in that crystal</li> <li>*.globals contains global properties of the host structure</li> </ul> </li> </ul> <p><strong>Scripts</strong></p> <ul> <li>scripts/*.sh scripts to rerun the screenings for different k-folds, encodings, etc.</li> <li>scripts/*.ipynb to analyze results</li> <li>scripts/prepare_cgcnn.py for translating the data in (poscars/*, csvs/*, oxstate/*, mags/*) to the ML input needed in cgcnn/*</li> </ul> <p><strong>Code</strong></p> <ul> <li>Install CGCNN and its defect modifications from https://github.com/mwitman1/cgcnndefect</li> </ul> <p><strong>Questions/Collaborations</strong></p> <ul> <li>Please contact <a href="mailto:mwitman@sandia.gov">mwitman@sandia.gov</a></li> </ul> <p><strong>Acknowledgements</strong></p> <ul> <li>This material is based upon work supported by the U.S. Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy (EERE), specifically the Hydrogen and Fuel Cell Technologies Office. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. Part of the work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under contract No.~DE- AC52-07NA27344. The National Renewable Energy Laboratory (NREL) is operated by the Alliance for Sustainable Energy, LLC, for the DOE under Contract No.~DE-AC36-08GO28308. This work used High-Performance Computing resources at NREL, sponsored by DOE-EERE. The views expressed in this article do not necessarily represent the views of the U.S. Department of Energy or the United States Government.</li> </ul>
Workshop Material - 3D-e-Chem Structural Cheminformatics Workflows for Computer-Aided Drug Discovery
<p>The workshop at the KNIME user meeting (Berlin 9th of March 2018) is set up to stimulate participants with varying degrees of experience in cheminformatics to learn and apply the different structural cheminformatics tools and workflows developed within the context of the 3D-e-Chem project. You will learn how to construct and apply integrated cheminformatics workflows using the 3D-e-Chem KNIME nodes for the exploitation of G protein-coupled receptor and kinase data (two important pharmaceutical target classes) to obtain useful information for drug discovery.</p> <p>Information on the 3D-e-Chem KNIME nodes and workflows can be found online:</p> <p>3D-e-Chem GitHub website: <a href="http://3d-e-chem.github.io/">http://3d-e-chem.github.io/</a></p>
Radio and gamma-ray timing of TRAPUM L-band Fermi pulsar survey discoveries - Supplementary material
<p>Timing ephemerides for the redback pulsar J1803-6707 (published in <em>"Radio and gamma-ray timing of TRAPUM L-band \textit{Fermi} pulsar survey discoveries"</em>, Burgay et al 2024, A&A) covering 15 years of Fermi data. The ephemeris are provided both in "ORBIFUNC" (to be used with timing software <a href="https://bitbucket.org/psrsoft/tempo2/src/master/" target="_blank" rel="noopener">tempo2</a>) and "ORBWAVES" (with <a href="https://github.com/nanograv/PINT" target="_blank" rel="noopener">PINT</a>) formats. The ORBIFUNC parameters are a time-domain interpolating function describing the orbital phase variations over time, while the ORBWAVES parameters are the Fourier-domain representation of the same function.</p>
Supplementary materials for "High-Throughput Discovery of Substrate Peptide Sequences for E3 Ubiquitin Ligases Using a cDNA Display Method."
<p>The next-generation sequencing (NGS) data of the 5th rounds' samples for LX9 library and p53deg library. The csv files contain DNA sequences read out, amino acid sequences and their read counts in descending order. </p>
Supplementary material 1 from: Pourmoghaddam MJ, Lambert C, Surup F, Khodaparast SA, Krisai-Greilhuber I, Voglmayr H, Stadler M (2020) Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture. MycoKeys 66: 105-133. https://doi.org/10.3897/mycokeys.66.50946
Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon species towards the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture
FIGURE 1–4 in Discovery and redescription of type material of Nausithoe simplex (Kirkpatrick, 1890), comb. nov. (Cnidaria: Scyphozoa: Coronatae: Nausithoidae) from the North Atlantic
FIGURE 1–4. Nausithoe simplex (Kirkpatrick, 1890), comb. nov. 1. Original figures published in 1890; showing habit of polyp and detail of tube; adapted from the original. 2. Lectotype (NHM 1878.3.26.11a) on the left and specimen numbered NHM 1878.3.26.11c on the right (note that this specimen is only a basal part of the tube). Scale bar = 2 mm. 3. Scanning electronic microscopy of tube surface (NHM 1878.3.26.11d). Scale bar = 100 µm. 4. Scanning electronic microscopy of internal whorl of cusps (NHM 1878.3.26.11d). Scale bar = 100 µm.
Supplementary Materials for: Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China
<p>Supplementary Materials for</p><p><strong>Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China</strong></p><p>Adrian Jones, Daoyu Zhang, Steven E. Massey, Yuri Deigin, Louis R. Nemzer, Steven C. Quay</p>
Supplementary material 4 from: Chen H-P, Kikuchi N, Shiao S-F (2024) Discovery of a new Pseudalomya Telenga, 1930 (Hymenoptera, Ichneumonidae, Ichneumoninae) species from Taiwan and its implications for the systematic position of this genus. Journal of Hymenoptera Research 97: 277-296. https://doi.org/10.3897/jhr.97.119470
Complete maximum likelihood trees reconstructed using the COI, 28S, 18S, and concatenated 18S+28S+COI datasets
Discovery of a Cold Giant Planet and Mass Measurement of a Hot Super-Earth in the Multi-Planetary System WASP-132 Supplementary Material
<p>Supplementary Material for the publication in Astronomy & Astrohpysics: Discovery of a Cold Giant Planet and Mass Measurement of a Hot Super-Earth in the Multi-Planetary System WASP-132.</p>
FIGURE 1 in Re-discovery of the type material of Leptoseris fragilis (Cnidaria, Anthozoa Scleractinia) from the upper mesophotic in La Réunion, a taxonomic puzzle
FIGURE 1. The Leptoseris fragilis type material puzzle; a Plate 29 (partim) by Rousseau (1854) in which the largest specimen was appended as 1 (dashed grey line), while drawings of smaller specimens and radial elements (r.e.) details by 1a-e and 1f-h, respectively. The original codes were re-drawn with larger font size for readability. Additionally, the multiple coralla on 1 (di) are here appended as 1i-l (in bold); b MNHN468 (later re-catalogued as MNHN-IK-2010-494), 1 in a; c MNHN470, four Cycloseris wellsi specimens bearing the tags of the L. fragilis holotype by multiple hands, including Chevalier's (J.P.C.). The smaller are juveniles and correspond to the 1b, 1d-e in a, the largest, absent from b, has the typical species morphology (inset, see Benzoni et al., 2016: Fig. 6); d specimen 1 in a and b. The biogenic block is substrate for three Leptoseris (1i-j, l) and one antipatharian (1k); e specimen 1l; f detail of 1l; g detail of 1l; h specimen 1i; i specimens 1j (left) and 1l (right). Grey arrows point to central protocorallite (red *) and secondary corallites (turquoise *); dashed blue rectangles (larger side is 10mm) show the corallum surface where r.e. counts were performed. Pictures b-h, by F. Benzoni (2010), i, © A. Andouche/MNHN (2014).
Supplementary material 21 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
Video 8 : Explanation note: Zasphinctus wilsoni sp. n. holotype worker (MCZ-ENT-00512764). 3D rotation video of volumetric surface rendering of head (antennae virtually removed).
Supplementary material 17 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
Video 4 : Explanation note: Zasphinctus sarowiwai sp. n. holotype worker (CASENT0764654). 3D rotation video of volumetric surface rendering of head (antennae virtually removed).
Supplementary material 22 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
Video 9 : Explanation note: Zasphinctus wilsoni sp. n. holotype worker (MCZ-ENT-00512764). 3D rotation video of volumetric surface rendering of mesosoma (head and metasoma mostly virtually removed).
Supplementary material 3 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
3D PDF 3 : Explanation note: Zasphinctus obamai sp. n. paratype worker (CASENT0764127). 3D PDF of volumetric surface rendering model of mesosoma (head and metasoma mostly virtually removed).
Supplementary material 16 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
Video 3 : Explanation note: Zasphinctus obamai sp. n. paratype worker (CASENT0764127). 3D rotation video of volumetric surface rendering of metasoma (virtually separated from mesosoma and most of legs virtually removed).
Supplementary material 1 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
3D PDF 1 : Explanation note: Zasphinctus obamai sp. n. holotype worker (CASENT0764125). 3D PDF of volumetric surface rendering model of full body.
Supplementary material 2 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
3D PDF 2 : Explanation note: Zasphinctus obamai sp. n. paratype worker (CASENT0764127). 3D PDF of volumetric surface rendering model of head (most of antennae virtually removed).
Supplementary material 4 from: Hita Garcia F, Fischer G, Liu C, Audisio TL, Economo EP (2017) Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics. ZooKeys 693: 33-93. https://doi.org/10.3897/zookeys.693.13012
3D PDF 4 : Explanation note: Zasphinctus obamai sp. n. paratype worker (CASENT0764127). 3D PDF of volumetric surface rendering model of metasoma (virtually separated from mesosoma and most of legs virtually removed).
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.