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3,878 results for “Molecular data”
Supporting Data for: The V30 Benchmark Set for Anharmonic Vibrational Frequencies of Molecular Dimers
<p>Intermolecular vibrations are extremely challenging to describe but are the most crucial part for determining entropy and hence free energies, and enable for instance the distinction between different crystal-packing arrangements of the same molecule via THz spectroscopy. Herein, we introduce a benchmark data set - V30 - containing 30 small molecular dimers with intermolecular interactions ranging from exclusively van-der-Waals dispersion to systems with hydrogen bonds. All calculations are performed with the gold standard of Quantum Chemistry CCSD(T). We discuss vibrational frequencies obtained via different models starting with the harmonic approximation over independent Morse oscillators up to second-order vibrational perturbation theory (VPT2), which allows a proper anharmonic treatment including coupling of vibrational modes. However, large amplitude motions present in many low-frequency intermolecular modes are problematic for VPT2. In analogy to the often used treatment for internal rotations, we replace such problematic modes by a simple one-dimensional hindered rotor model. We compare selected dimers with available experimental data or high-level calculations of potential energy surfaces and show that VPT2 in combination with hindered rotors can yield a very good description of fundamental frequencies for the discussed subset of dimers involving small and semi-rigid molecules.<br><br>This supporting dataset includes the calculated force constants, harmonic frequencies, Morse frequencies, VPT2 frequencies, and the optimized structures for the V30 dataset. See the included README.md file for more details. The related preprint can be found at <a href="https://doi.org/10.48550/arXiv.2209.04392">https://doi.org/10.48550/arXiv.2209.04392</a>.</p>
Data to Reproduce "Robust Automated Equilibration Detection for Molecular Simulations"
<p>Data to reproduce the results from "Robust Automated Equilibration Detection for Molecular Simluations" (see <a href="https://github.com/michellab/Robust-Equilibration-Detection-Paper">https://github.com/michellab/Robust-Equilibration-Detection-Paper</a> and the work linked there). These data are too large to host on GitHub, but are automatically downloaded by the workflow supplied at the above GitHub repository. </p> <p>All data were generated using the code given in the <a href="https://github.com/michellab/Robust-Equilibration-Detection-Paper">GitHub repository</a>, other than the original free energy gradient data <code>gradient_arrays_30ns.pkl</code> which were generated as described in <a title="DOI URL" href="https://doi.org/10.1021/acs.jctc.4c00806">https://doi.org/10.1021/acs.jctc.4c00806</a> (to regenerate, see the code available at: <a href="https://github.com/michellab/Automated-ABFE-Paper">https://github.com/michellab/Automated-ABFE-Paper</a>).</p> <p>The synthetic data used to test all equilibration detection heuristics are given in the <code>compute_equil_times</code> output directories (for example <code>synthetic_data_bound_vanish_with_equil_times.pkl</code>. These are supplied as pickled Python dictionaries with the structures <code>data[dataset_type][system][trace_index]["data"]</code>. For example, to access the first synthetic trace for the T4L system from the "standard" synthetic ensemble, use <code>data["standard"]["T4L"][0]["data"]</code>. For all directories, <code>_free</code> denotes the free vanish multi-window data and <code>_single</code> denotes the bound vanish single-window data - otherwise these are the standard bound vanish multi-window data. However, it is recommended that these data are used as part of the workflow given at <a href="https://github.com/michellab/Robust-Equilibration-Detection-Paper">https://github.com/michellab/Robust-Equilibration-Detection-Paper</a>, which allows the study to be reproduced from scratch.</p>
Raw data for Role of molecular damage in crack initiation mechanisms of tough elastomers, PNAS 2024 Vol. 121 e2410515121
<p>This the raw data for figures 1-5 of the paper. the images and the data sets in csv format</p>
Linked collectors and determiners for: Revision of the genus Dinotoperla Tillyard, 1921 (Plecoptera: Gripopterygidae) using morphological characters and molecular data: Establishes two new genera, three new species and updates the larval taxonomy.
Natural history specimen data linked to collectors and determiners held within, "Revision of the genus Dinotoperla Tillyard, 1921 (Plecoptera: Gripopterygidae) using morphological characters and molecular data: Establishes two new genera, three new species and updates the larval taxonomy". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e57764ce-8c26-4ab9-a6d2-0b8a324f828c">https://bionomia.net/dataset/e57764ce-8c26-4ab9-a6d2-0b8a324f828c</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e57764ce-8c26-4ab9-a6d2-0b8a324f828c">https://gbif.org/dataset/e57764ce-8c26-4ab9-a6d2-0b8a324f828c</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: A cybertaxonomic revision of the new dung beetle tribe Parachoriini (Coleoptera: Scarabaeidae: Scarabaeinae) and its phylogenetic assessment using molecular and morphological data.
Natural history specimen data linked to collectors and determiners held within, "A cybertaxonomic revision of the new dung beetle tribe Parachoriini (Coleoptera: Scarabaeidae: Scarabaeinae) and its phylogenetic assessment using molecular and morphological data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/7e33ec7d-211b-4042-8d07-344364ee805d">https://bionomia.net/dataset/7e33ec7d-211b-4042-8d07-344364ee805d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/7e33ec7d-211b-4042-8d07-344364ee805d">https://gbif.org/dataset/7e33ec7d-211b-4042-8d07-344364ee805d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Taxonomic revision of the speckled crabs, genus Arenaeus Dana, 1851 (Brachyura: Portunidae) based on morphological and molecular data.
Natural history specimen data linked to collectors and determiners held within, "Taxonomic revision of the speckled crabs, genus Arenaeus Dana, 1851 (Brachyura: Portunidae) based on morphological and molecular data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/5e87f718-703c-4280-8ca9-f8b6d0f3b402">https://bionomia.net/dataset/5e87f718-703c-4280-8ca9-f8b6d0f3b402</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/5e87f718-703c-4280-8ca9-f8b6d0f3b402">https://gbif.org/dataset/5e87f718-703c-4280-8ca9-f8b6d0f3b402</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status.
Natural history specimen data linked to collectors and determiners held within, "Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d">https://bionomia.net/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d">https://gbif.org/dataset/53780a8e-66fa-4263-8542-ff9c540ab37d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: A taxonomic revision of Anthothela (Octocorallia: Scleraxonia: Anthothelidae) and related genera, with the addition of new taxa, using morphological and molecular data.
Natural history specimen data linked to collectors and determiners held within, "A taxonomic revision of Anthothela (Octocorallia: Scleraxonia: Anthothelidae) and related genera, with the addition of new taxa, using morphological and molecular data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3b9bd2c4-7dee-46a3-a36d-80077b88a78b">https://bionomia.net/dataset/3b9bd2c4-7dee-46a3-a36d-80077b88a78b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3b9bd2c4-7dee-46a3-a36d-80077b88a78b">https://gbif.org/dataset/3b9bd2c4-7dee-46a3-a36d-80077b88a78b</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: FBIP: One baobab species or two-morphological and molecular data to address this question.
Natural history specimen data linked to collectors and determiners held within, "FBIP: One baobab species or two-morphological and molecular data to address this question". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3c7c79f0-4ee6-4ea0-bc96-1c347d63cb67">https://bionomia.net/dataset/3c7c79f0-4ee6-4ea0-bc96-1c347d63cb67</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3c7c79f0-4ee6-4ea0-bc96-1c347d63cb67">https://gbif.org/dataset/3c7c79f0-4ee6-4ea0-bc96-1c347d63cb67</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Resurrection of Oxythyrea abigailoides Mikšić, 1978 (Coleoptera: Scarabaeidae: Cetoniinae) based on new morphological, morphometrical and molecular data.
Natural history specimen data linked to collectors and determiners held within, "Resurrection of Oxythyrea abigailoides Mikšić, 1978 (Coleoptera: Scarabaeidae: Cetoniinae) based on new morphological, morphometrical and molecular data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/14aeff19-f503-43f4-af68-bc55aa4adb9a">https://bionomia.net/dataset/14aeff19-f503-43f4-af68-bc55aa4adb9a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/14aeff19-f503-43f4-af68-bc55aa4adb9a">https://gbif.org/dataset/14aeff19-f503-43f4-af68-bc55aa4adb9a</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: A taxonomic revision of the ecologically important Ochna holstii (Ochnaceae) complex using molecular and morphological data.
Natural history specimen data linked to collectors and determiners held within, "A taxonomic revision of the ecologically important Ochna holstii (Ochnaceae) complex using molecular and morphological data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/954f96c0-684a-41ff-a23a-8287ce9f7e81">https://bionomia.net/dataset/954f96c0-684a-41ff-a23a-8287ce9f7e81</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/954f96c0-684a-41ff-a23a-8287ce9f7e81">https://gbif.org/dataset/954f96c0-684a-41ff-a23a-8287ce9f7e81</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: A new subgenus of Sonchus (Asteraceae: Cichorieae) inferred from molecular data.
Natural history specimen data linked to collectors and determiners held within, "A new subgenus of Sonchus (Asteraceae: Cichorieae) inferred from molecular data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/b9ea8044-2429-43a3-be7d-ad9201326aff">https://bionomia.net/dataset/b9ea8044-2429-43a3-be7d-ad9201326aff</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/b9ea8044-2429-43a3-be7d-ad9201326aff">https://gbif.org/dataset/b9ea8044-2429-43a3-be7d-ad9201326aff</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data.
Natural history specimen data linked to collectors and determiners held within, "Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/b7ec7b7c-5b54-401f-a513-7776957b6a09">https://bionomia.net/dataset/b7ec7b7c-5b54-401f-a513-7776957b6a09</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/b7ec7b7c-5b54-401f-a513-7776957b6a09">https://gbif.org/dataset/b7ec7b7c-5b54-401f-a513-7776957b6a09</a>. Formatted as a Frictionless Data package.
Code and data for molecular dating benchmark based on real and simulated Primates gene trees
<p>Benchmark of molecular clock dating applied to single gene trees separately, whose results are described in “Factors influencing the accuracy and precision in dating single gene trees” by Guillaume Louvel and Hugues Roest Crollius.</p> <ol> <li>Real Primates gene trees are analyzed to identify what characteristics of a gene tree are related to the precision of dating; </li> <li>alignments are also simulated on the tree of Primates to measure the accuracy of dating under controlled parameters such as the degree of rate variation and the length of the alignment.</li> </ol> <p><strong>Content</strong></p> <p><code>Louvel_Accuracy-dating_results_2024.tar.gz</code>:<br> - <code>notebook/</code>: statistical analyses in Python;<br> - <code>outputs/</code>: html reports with figures/tables resulting from the analysis;<br> - <code>lib/</code>: required libraries.<br> - <code>data/</code>: intermediate data needed for the final analysis (dates, gene tree features);</p> <p><code>Louvel_Accuracy-dating_dating-source_2024.tar.gz</code>:<br> - <code>dating-source/</code>: input data and config files necessary to reproduce <code>data</code>;</p> <p><code>Louvel_Accuracy-dating_raw-data-preparation_2024.tar.gz</code>:<br> - <code>raw-data-preparation/</code>: raw data and steps to produce <code>dating-source</code>.<br><br><strong>Requirements</strong><br><br>This code requires the libraries developed in the lab for this project,<br>available at <a href="https://github.com/DyogenIBENS/">github.com/DyogenIBENS/</a>, but also included here in <code>lib/</code>.<br><br>- <a href="https://github.com/DyogenIBENS/Phylorgs">Phylorgs</a><br>- <a href="https://github.com/DyogenIBENS/LibsDyogen_py3">LibsDyogen_py3</a><br>- <a href="https://github.com/DyogenIBENS/ToolsDyogen_py3">ToolsDyogen_py3</a>.</p>
Research data supporting "Multiscale Molecular Modelling of ATP-Fueled Supramolecular Polymerisation and Depolymerisation"
<p>Raw research data supporting the publication Perego C. et al., <em>ChemSystemsChem</em> <strong>2021</strong>, DOI: <a href="https://doi.org/10.1002/syst.202000038">https://doi.org/10.1002/syst.202000038</a></p>
Data from: Andriollo T., Michaux J.R., Ruedi M. (2021). Food for everyone: differential feeding habits of cryptic bat species inferred from DNA metabarcoding. Molecular Ecology
<p><strong>Supporting data for:</strong> Andriollo T., Michaux J.R., Ruedi M. (2021). Food for everyone: differential feeding habits of cryptic bat species inferred from DNA metabarcoding. Molecular Ecology. https://doi.org/ 10.1111/mec.16073</p> <p>Raw DNA sequences of prey of <em>Plecotus auritus</em>, <em>P. austriacus</em> and <em>P. macrobullaris</em> with complete sampling information and taxonomic assignations. Data separated by semicolums as follows:</p> <p>Sample name; Dataset; Colony; Bat species; Date; Season; Read numbers (Size); DNA sequence; Lowest taxonomic identification (ID_MOTU); Family; Order; Class; Is the sequence attributable to the diet or not (Diet)</p>
Figure 3 in Use of morphological and molecular data to identify three new sibling species of the genus Munida Leach, 1820 (Crustacea, Decapoda, Galatheidae) from New Caledonia
Figure 3. Munida pectinata sp. nov., ovigerous female 6.9 mm, holotype from stn 1727 (NORFOLK 1). (A) Carapace, dorsal view; (B) sternal plastron; (C) ventral view of cephalic region, showing antennular and antennal peduncles; (D) right third maxilliped, lateral view; (E) right cheliped, dorsal view; (F) right first walking leg, lateral view; (G) dactylus of right first walking leg, lateral view.
Figure 2 in Use of morphological and molecular data to identify three new sibling species of the genus Munida Leach, 1820 (Crustacea, Decapoda, Galatheidae) from New Caledonia
Figure 2. Munida simulatrix sp. nov., male 7.7 mm, holotype from stn 1721 (NORFOLK 1). (A) Carapace, dorsal view; (B) sternal plastron; (C) ventral view of cephalic region, showing antennular and antennal peduncles; (D) right third maxilliped, lateral view; (E) right cheliped, dorsal view; (F) right first walking leg, lateral view; (G) dactylus of right first walking leg, lateral view.
Figure 1 in Use of morphological and molecular data to identify three new sibling species of the genus Munida Leach, 1820 (Crustacea, Decapoda, Galatheidae) from New Caledonia
Figure 1. Munida parile sp. nov., ovigerous female 3.7 mm, holotype from stn 1701 (NORFOLK 1). (A) Carapace, dorsal view; (B) sternal plastron; (C) ventral view of cephalic region, showing antennular and antennal peduncles; (D) left third maxilliped, lateral view; (E) right cheliped, dorsal view; (F) left first walking leg, lateral view; (G) dactylus of left first walking leg, lateral view.
Fig. 5 in Two new species of the genus Mystilus Distant (Hemiptera: Miridae: Mirinae) from Vietnam, with discussion on morphological variation based on molecular data, and a revised key for Mystilus species
Fig. 5. Modified Neighbor-Joining tree based on a total of 25 COI sequences of six Mystilus species and other 19 species in the subfamily Mirinae in this study. Coloured squares next to the Mystilus species names indicate character states for three characters.
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.