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4,489 results for “transitivity”
MD simulations files for: Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning
<p>Here's a rephrased version of the README file:</p> <p>#### Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning</p> <p>**Authors:** Mingyuan Zhang, Hao Wu, Yong Wang</p> <p>This repository contains the official implementation for the paper "Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning" by Mingyuan Zhang, Hao Wu, and Yong Wang. Included are all trajectories from our MD simulations in the form of PLUMED COLVAR files, as well as all analysis scripts and files needed to replicate the results and figures presented in both the main text and Supporting Information (SI) of the paper.</p> <p>The paper features two examples: Ala2 and Ala10. For each, we have organized all the associated simulation files as they were during our automated simulation pipeline. The directory structure is the same for both examples. Here, we use Ala2, found in the `Ala2` folder, as an example:</p> <p>### Key Components</p> <p>- **Automated Pipeline Implementation:** The pipeline is implemented in `Ala2/7-adaptive-40ps/ala2.ipynb`. This implementation is ready to use once all required packages are installed, and gmx/gmx_mpi/plumed are callable within the notebook. After configuring the environment and specifying parameters like `gpu_id`, `ntomp`, and `n_sim` according to your hardware, running the blocks will replicate the entire pipeline.</p> <p>- **Analysis Scripts:** The scripts to replicate the results or figures from the main text or SI are organized in three files: `Ala2/7-adaptive-40ps/AdaptiveSamplingAnalysis.ipynb`, `Ala2/7-adaptive-40ps/compare_with_msm.ipynb`, and `Ala2/7-adaptive-40ps/opes/COLVAR/analysis.ipynb`.</p> <p>### Directory Structure</p> <p>Under the `Ala2` main directory, there are seven subdirectories:</p> <p>- **`Ala2/1-topol/`**: Contains files generated during system construction, including the final Gromacs topology file `topol.top`, which is necessary for running the automated simulation script.</p> <p>- **`Ala2/2-em/`, `Ala2/3-nvt/`, `Ala2/4-npt/`**: These directories store files generated during energy minimization and NVT/NPT equilibration. The `Ala2/4-npt/npt.gro` file is required to run the automated simulation script.</p> <p>- **`Ala2/mdp/`**: Contains all mdp files used, including `Ala2/mdp/md_detail.mdp`, which is necessary for running the automated simulation script.</p> <p>- **`Ala2/7-adaptive-40ps/`**: Contains all simulation and analysis scripts, along with files required to replicate the study related to the automated pipeline.</p> <p> 1. **`Ala2/7-adaptive-40ps/CV/`**: Stores all COLVAR files from adaptive sampling simulations.<br> <br> 2. **`Ala2/7-adaptive-40ps/opes/`**: Contains all files related to OPES simulations, including raw data for the final FES plots found in `Ala2/7-adaptive-40ps/opes/COLVAR/`. The script for replicating OPES and FES estimation figures is located in `Ala2/7-adaptive-40ps/opes/COLVAR/analysis.ipynb`.<br> <br> 3. **`Ala2/7-adaptive-40ps/figures/`**: Includes all original figures from the main text and SI, saved at 600 dpi.<br> <br> 4. **`Ala2/7-adaptive-40ps/traj_and_dat/`**: Stores all PLUMED `*.dat` files for the `DRIVER` utility in adaptive sampling simulations, a topology file `input.pdb` for PLUMED `MOLINFO`, and a topology file `seed_ref.pdb` for MDAnalysis adaptive sampling seed `*.gro` generation. Note that all `*.xtc` files from adaptive sampling were deleted to reduce the package size.<br> <br> 5. **Seed Index Files:** Seed indices for each round are stored as `Ala2/7-adaptive-40ps/round{i}_seed.txt`, necessary for figure replication.<br> <br> 6. **Automated Pipeline Notebook:** Implemented in `Ala2/ala2.ipynb`. Ensure that all imported packages are installed and gromacs (both gmx and gmx_mpi)/plumed can be called within the Jupyter notebook.<br> <br> 7. **Adaptive Sampling Analysis:** Scripts for analyzing adaptive sampling trajectories are found in `Ala2/AdaptiveSamplingAnalysis.ipynb`. This notebook contains scripts to replicate all figures related to adaptive sampling.<br> <br> 8. **MSM Comparison:** Analysis scripts for MSM comparison are located in `Ala2/compare_with_msm.ipynb`. This notebook contains scripts to replicate figures used for MSM/OPES comparison.</p> <p>- **`Ala2/8-adaptive-400ps/`**: Contains all simulation files (except xtc) for an additional adaptive sampling dataset computed for MSM comparison.</p> <p>### Contact Information</p> <p>We are continuing to test and improve the pipeline, so a tutorial is not yet available. Please feel free to reach out with any questions related to the implementation via email at mingyuanzhang@zju.edu.cn or by raising an issue on our GitHub page: https://github.com/yongwangCPH/papers/tree/main/2024/ALICE.</p>
Multi Room Transition Dataset
<h2>Introduction</h2> <p>We present a dataset of room impulse response (RIR) measurements with a focus on covering a broad spectrum of room-acoustic conditions. A central motivation was to collect data from complex, real-world multi-room environments in which acoustic energy decay functions (EDFs) are characterized by multiple decay slopes. The dataset is accompanied by positional information and visual documentation in the form of 360˚ photographs. A total of 4032 room impulse responses were measured throughout three complex indoor environments using a KEMAR head and torso simulator, and a Zoom H3 ambisonics microphone array.</p> <h3>Acoustic environments</h3> <p>In each of the three environments considered in the dataset (hallways-lecturehall, offices, workshops), four loudspeakers were placed and remained stationary throughout all measurements. A mobile measurement platform was then moved along a predefined path that covered various measurement positions. At each position, the Room Impulse Responses (RIRs) between the mobile platform and each of the four loudspeakers were recorded.</p> <h3>Mobile measurement platform</h3> <p>The mobile recording platform consisted of a head and torso simulator (GRAS 45BB KEMAR), fitted with binaural microphones, and a four-channel tetrahedral microphone array (Zoom H3-VR), placed on top of the head simulator.</p> <h3>Signals</h3> <p>All measurements were conducted at a sampling rate of 48 kHz (24-bit), for ease-of-use, we provide the signals in the dataset in two formats: as a pickled <a href="https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.html">pandas dataframe</a> (<code>mrtd_dataframe.pkl</code>) and as <a href="https://www.sofaconventions.org/mediawiki/index.php/SOFA_(Spatially_Oriented_Format_for_Acoustics)">SOFA</a> files.</p> <p>-------------------------------------------------------------------------------------------------------------------------------------------------------------------</p> <div> <h3>Publication</h3> <p>A more detailled description of the dataset and a method for the blind estimation of Energy Decay Functions can be found in our IWAENC 2024 paper:</p> </div> <p>Philipp Götz, Georg Götz, Nils Meyer-Kahlen, Kyung Yun Lee, Karolina Prawda, Emanuël A. P. Habets, and Sebastian J. Schlecht: <em>A Multi-Room Transition Dataset for Blind Estimation of Energy Decay, </em>IWAENC 2024, Aalborg, Denmark</p> <p>The accompanying code repository can be found at <a href="https://github.com/audiolabs/blind-multi-room-model">GitHub</a>.</p>
Reproduction package for the paper "The open-source sunbather code: Modeling escaping planetary atmospheres and their transit spectra"
<p>This is a reproduction package for the paper "The open-source sunbather code: modeling escaping planetary atmospheres and their transit spectra" by Dion Linssen, Jim Shih, Morgan MacLeod & Antonija Oklopčić (2024). It provides a front-to-end reproduction script to reproduce the results and Figures 1-5 of the paper. Figures 6&7 can be reproduced with the example notebook found in the sunbather installation.</p>
Data and code for "Design Principles for Energy Transfer in the Photosystem II Supercomplex from Kinetic Transition Networks"
<p>Data and code for "Design Principles for Energy Transfer in the Photosystem II Supercomplex from Kinetic Transition Networks".</p>
Statistical trends in JWST transiting exoplanet atmospheres
<p>Spectra shown in Figure 1</p> <p>Columns are: Wavelength(micron), Wavelength err(micron), Transit Depth, Transit Depth err</p>
Replication Data for: Entanglement transition in random rod packings
<p>This repository includes the data and source code used to generate figures for </p> <p>Yeonsu Jung, Thomas Plumb-Reyes, Hao-Yu Greg Lin, L. Mahadevan<br>Entanglement transition in random rod packings.</p> <p>Please refer to the README.md file in each zip archive for a detailed description.</p> <ul> <li><strong>rod-packing-data-code.zip:</strong> Contains experimental and numerical data, along with source codes for plotting figures.</li> <li><strong>rod-packing-rod-segmentation-example.zip:</strong> Contains MATLAB functions and scripts demonstrating the image segmentation process.</li> </ul>
FIGURE 4 in Arthrobrachus crassicornis sp. nov (Coleoptera: Melyridae), a new species from the South American Transition Zone in Argentina
FIGURE 4: Arthrobrachus crassicornis sp. nov. Male, abdomen (a), v: V ventrite, pa: abdominal process; vi: VI ventrite and lt: last tergite, Scale 1 mm. Segment 9 (b). Scale 1 mm.
FIGURE 3 in Arthrobrachus crassicornis sp. nov (Coleoptera: Melyridae), a new species from the South American Transition Zone in Argentina
FIGURE 3: Arthrobrachus crassicornis sp. nov. Female, abdomen (a), v: V ventrite, vi: VI ventrite, and lt: last tergite. Scale 1 mm. Ovipositor, ventral view (b), bo: baculi oblique, bv: ventral baculi, vl: ventral lamina; dorsal view (c), dl: dorsal lamina, bp: proctiger baculi. Scale 1 mm.
FIGURE 6 in Arthrobrachus crassicornis sp. nov (Coleoptera: Melyridae), a new species from the South American Transition Zone in Argentina
FIGURE 6: Distribution map of Arthrobrachus crassicornis sp. nov. (*) in the biogeographic provinces of the South America transition zone (colored in green), according to Morrone et al. (2022).
FIGURE 5 in Arthrobrachus crassicornis sp. nov (Coleoptera: Melyridae), a new species from the South American Transition Zone in Argentina
FIGURE 5: Arthrobrachus crassicornis sp. nov. Male genitalia. Tegmen and parameres: dorsal view (a), p: parameres; ventral view (b); lateral view (c) ap: apodeme, Scale 1 mm. Median lobe: dorsal view (d), pha: phallotreme; ventral view (e); lateral view (f), ap: apodeme. Scale 1 mm.
Dataset for: Dynamic transition and Galilean relativity of current-driven skyrmions
<p>This data repository contains the experimental data utilised to produce the figures shown in the article "Dynamic transition and Galilean relativity of current-driven skyrmions" by Max Birch, Ilya Belopolski, Yukako Fujishiro, Minoru Kawamura, Akiko Kikkawa, Yasujiro Taguchi, Max Hirschberger, Naoto Nagaosa and Yoshinori Tokura.</p> <p>All data are in the typical .dat file format from a Quantum Design PPMS. The data are organised according to each main/extended/supplementary figure in the article. This means that same data files may appear in more than one figure folder. Files are labelled according to which device was measured, with additional information on the sample environment (temperature/field/current etc) included where relevant.</p>
Unveiling the mechanism of CO2 electroreduction to C1 and C2 products on ordered double transition metal MXenes.
<p><span>we use rigorous first principles simulations to comprehensively screen and explore the CO<sub>2</sub> reduction activity of twelve different two-dimensional ordered double transition metal MXenes. Our results indicate that all the twelve MXenes show metallic characteristics and can activate CO<sub>2</sub> significantly with strong binding energy.The electronic structure analysis reveals the charge redistribution from MXene catalysts to the antibonding states of CO<sub>2</sub> results in strong hybridization between CO<sub>2 </sub>orbitals and surface metal orbitals. The strong CO<sub>2</sub> binding is further affirmed by the enhanced charge transfer from MXene to the adsorbed CO<sub>2</sub> molecule. Simulations based on the free energy pathways show that Mo<sub>2</sub>TaC<sub>2</sub> and Mo<sub>2</sub>TiC<sub>2 </sub>possess superior catalytic activity for conversion of CO<sub>2</sub> to methanol and methane with very low limiting potential values of <span><span>-0.35 and -0.39 V respectively where as Mo<sub>2</sub>TaC<sub>2</sub> and Mo<sub>2</sub>VC<sub>2</sub> were found to display excellent performance for ethanol formation with record low limiting potential of -0.32 V and -0.42 V respectively.</span></span></span></p>
Using Multi-Modal Path-Specific Transit Trips in Transportation Social Sustainability Analysis: Case Study in Atlanta, GA
Open the record for dataset details and reuse information.
Force-Activated Spin-Crossover in Fe2+ and Co2+ Transition Metal Mechanophores
<p>Data associated with the manuscript titled "Force-Activated Spin-Crossover in Fe2+ and Co2+ Transition Metal Mechanophores"</p>
Data for "Topological grain boundary segregation transitions"
<p>Cite as: Vivek Devulapalli et al. ,Topological grain boundary segregation transitions.Science386,420-424(2024). DOI:10.1126/science.adq4147<br><br>This repository contains the raw data from STEM imaging, EDS, and EELS experiments, the code used for GB simulations and theoretical calculations presented in the paper. </p> <p>=========================================================</p> <p>MDMC-SGC directory contains the MD/MC simulation in the semi-grand-canonical<br>ensemble (Fig. 4 of the paper).</p> <p><br>Fe-Ti-phase-diagram<br>===================</p> <p>First, the bulk concentration of Fe in Ti is calculated as a function<br>of the chemical potential difference Δµ between Fe and Ti. This is<br>required to calculate the grain boundary excess over the bulk.</p> <p>Here, it turns out that the bulk concentration is approximately zero<br>in the range of Δµ investigated.</p> <p><br>MD/MC simulations of grain boundaries<br>=====================================</p> <p>The following sample names map to the naming in the paper:</p> <p>* ABC: Ti ground state structure<br>* large-1cage-2300000: isolated cage<br>* larger-2cages-3200000: double cage<br>* large-02-10000220: one layer of cages<br>* large-01-10000367: second layer of cages forming</p> <p>Each directory contains subdirectories for all investigated Δµ. The<br>subdirectory `final-states` contains the final snapshots for each Δµ.</p> <p>The script `prepare.py` was used to set up the simulations (template<br>for the LAMMPS input file is `lmp.in.template`). The script<br>`collect.py` was used to extract the thermodynamic excess properties<br>of the grain boundaries, stored in the file `T_0300K.excess.dat` in<br>each subdirectory.</p> <p>The notebook `plot-excess.ipynb` can be used to plot the excess data.</p> <p>=========================================================</p> <p># GRand canonical Interface Predictor (GRIP)</p> <p>_Authors: [Enze Chen](https://enze-chen.github.io/) (Stanford University) and<br>[Timofey Frolov](https://people.llnl.gov/frolov2) (Lawrence Livermore National Laboratory)_ <br>_Version: 0.1.2024.01.21_</p> <p>An algorithm for performing grand canonical optimization (GCO) of interfacial<br>structure (e.g., grain boundaries) in crystalline materials.<br>It automates sampling of slab translations and reconstructions<br>along with vacancy generation and finite temperature molecular dynamics (MD).<br>The algorithm repeatedly samples different structures in two phases:<br> 1. Structure generation and manipulation is largely handled using the<br> [Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/).<br> 2. Molecular dynamics and static relaxations are currently performed using<br> [LAMMPS](https://www.lammps.org), although in principle other energy<br> evaluation methods (e.g., density functional theory in [VASP](https://www.vasp.at))<br> may be used.</p> <p>------</p> <p>## Dependencies<br>- [Python](https://www.python.org/) (3.6+)<br>- [NumPy](https://numpy.org/) (1.23.0)<br>- [ASE](https://wiki.fysik.dtu.dk/ase/) (3.22.1)<br>- [LAMMPS](https://www.lammps.org) (stable)</p> <p>_Optional_<br>- [pandas](https://pandas.pydata.org/) (1.5.3)<br>- [Matplotlib](https://matplotlib.org/stable/index.html) (3.5.3)</p> <p><br>## Usage</p> <p>Assuming the above libraries are installed, clone the repo and make the <br>appropriate modifications in `params.yaml` (see file for detailed comments), <br>including the path to the LAMMPS binary on your system.<br>If you wish, you can supply your own slabs for the bicrystal configuration as<br>POSCAR_LOWER and POSCAR_UPPER (in the [POSCAR](https://www.vasp.at/wiki/index.php/POSCAR)<br>file format).<br>Then call:<br>```python<br>python main.py<br>```<br>If you don't have LAMMPS or just want to test the script, you can run it with the `-d` flag.<br>See the `.examples` folder for a SLURM submission script for parallel execution (preferred).</p> <p><br>## File structure<br>- `main.py`: Script to launch everything.<br>- `params.yaml`: Simulation parameters; **you'll want to edit this.**<br>- `core`: Main classes (`Bicrystal`, `Simulation`, etc.)<br>- `utility`: Main helper functions (`utils.py`, `unique.py`, etc.)<br>- `simul_files`: Files for simulations (LAMMPS input files, etc.)<br>- `best`: All relaxed structures are stored here. The naming convention is:<br>`lammps_Egb_n_X-SHIFT_Y-SHIFT_X-REPS_Y-REPS_TEMP_STEPS`</p> <p><br>Duplicate files are periodically deleted by calling `clear_best()` in `utils/unique.py`.<br>The default method cleans about 1-3% of files on average.<br>Use the `-e` flag for more aggressive cleaning (>50%).<br>Use the `-s` flag to save the processed results to CSV from a pandas DataFrame.</p> <p>Results can be visualized by running `utils/plot_gco.py` and it generates a GCO plot<br>of $E_{\mathrm{gb}}$ vs. $n$.<br>The `.examples` folder has this plot for several boundaries.<br>By default executing this file will save both the results (CSV) and the figure (PNG) <br>to the same folder as the GRIP output files.</p> <p><br>## Citation<br>If you use GRIP in your work, we would appreciate a citation to the original manuscript:</p> <p>> Enze Chen, Tae Wook Heo, Brandon C. Wood, Mark Asta, and Timofey Frolov.<br>"Grand canonically optimized grain boundary phases in hexagonal close-packed titanium."<br>_arXiv:XXXX.YYYYY [cond-mat.mtrl-sci]_, 2024.</p> <p>or in BibTeX format:</p> <p>```<br>@article{chen_2024_grip,<br> author = {Chen, Enze and Heo, Tae Wook and Wood, Brandon C. and Asta, Mark and Frolov, Timofey},<br> title = {Grand canonically optimized grain boundary phases in hexagonal close-packed titanium},<br> year = {2024},<br> journal = {arXiv:XXXX.YYYYY [cond-mat.mtrl-sci]},<br> doi = {10.48550/arXiv.XXXX.YYYYY},<br>}<br>```</p> <p>=========================================================</p> <p> </p>
Supplementary Dataset for Membrane lipid homeostasis dually regulates conformational transition of phosphoethanolamine transferase EptA
Open the record for dataset details and reuse information.
Data Set: "From structure to electrochemistry: The Influence of Transition Metal Ordering on Na+/vacancy Orderings in P2-type NaxMO2 Cathode Materials for Sodium-Ion Batteries"
<p>This is the data set associated with the following publication: <strong>From structure to electrochemistry: The Influence of Transition Metal Ordering on Na+/vacancy Orderings in P2-type NaxMO2 Cathode Materials for Sodium-Ion Batteries,</strong> Lukas Fridolin Pfeiffer, Manuel Dillenz, Nora Burgard, Premysl Beran, Daniel Roscher, Maider Zarrabeitia, Paul Drews, Charles Hervoches, Daria Mikhailova, Ahmad Omar, Volodymyr Baran, Neelima Paul, Mohsen Sotoudeh, Michael Busch, Margret Wohlfahrt-Mehrens, Axel Groß, Stefano Passerini, Peter Axmann<em>, Journal of Materials Chemistry A, 2024, DOI: 10.1039/d4ta04786a<br></em></p> <p>The data set is organised along the figures of the publication.</p>
Light-Induced Polaronic Crystals in Single-Layer Transition Metal Dichalcogenides
<p>Publication set for Light-Induced Polaronic Crystals in Single-Layer Transition Metal Dichalcogenides,</p> <p>Nano Letters <span>2024</span><span>, 24</span><span>, 42</span><span>, 13179–13184, <a title="DOI URL" href="https://doi.org/10.1021/acs.nanolett.4c03065">https://doi.org/10.1021/acs.nanolett.4c03065</a></span></p> <p> </p>
Data from: 'Venus trapped, Mars transits': Cu and Fe redox chemistry, cellular topography and in situ ligand binding in terrestrial isopod hepatopancreas
Woodlice efficiently sequester copper (Cu) in 'cuprosomes' within hepatopancreatic 'S' cells. Binuclear 'B' cells in the hepatopancreas form iron (Fe) deposits; these cells apparently undergo an apocrine secretory diurnal cycle linked to nocturnal feeding. Synchrotron-based m-focus X-ray spectroscopy undertaken on thin sections was used to characterize the ligands binding Cu and Fe in S and B cells of Oniscus asellus (Isopoda). Main findings were: (i) morphometry confirmed a diurnal B-cell apocrine cycle; (ii) X-ray fluorescence (XRF) mapping indicated that Cu was co-distributed with sulfur (mainly in S cells), and Fe was co-distributed with phosphate (mainly in B cells); (iii) XRF mapping revealed an intimate morphological relationship between the basal regions of adjacent S and B cells; (iv) molecular modelling and Fourier transform analyses indicated that Cu in the reduced Cuþ state is mainly coordinated to thiol-rich ligands (Cu–S bond length 2.3 A˚ ) in both cell types, while Fe in the oxidized Fe3þ state is predominantly oxygen coordinated (estimated Fe–O bond length of approx. 2 A˚ ), with an outer shell of Fe scatterers at approximately 3.05 A˚ ; and (v) no significant differences occur in Cu or Fe speciation at key nodes in the apocrine cycle. Findings imply that S and B cells form integrated unit-pairs; a functional role for secretions from these cellular units in the digestion of recalcitrant dietary components is hypothesized.
Data from: Transition in sexual system and sex chromosome evolution in the tadpole shrimp Triops cancriformis
Transitions in sexual system and reproductive mode may affect the course of sex chromosome evolution, for instance by altering the strength of sexually antagonistic selection. However, there have been few studies of sex chromosomes in systems where such transitions have been documented. The European tadpole shrimp, Triops cancriformis, has undergone a transition from dioecy to androdioecy (a sexual system where hermaphrodites and males coexist), offering an excellent opportunity to test the impact of this transition on the evolution of sex chromosomes. To identify sex-linked markers, to understand mechanisms of sex determination and to investigate differences between sexual systems, we carried out a genome-wide association study using restriction site-associated DNA sequencing (RAD-seq) of 47 males, females and hermaphrodites from one dioecious and one androdioecious population. We analysed 22.9 Gb of paired-end sequences and identified and scored >3000 high coverage novel genomic RAD markers. Presence–absence of markers, single-nucleotide polymorphism association and read depth identified 52 candidate sex-linked markers. We show that sex is genetically determined in T. cancriformis, with a ZW system conserved across dioecious and androdioecious populations and that hermaphrodites have likely evolved from females. We also show that the structure of the sex chromosomes differs strikingly, with a larger sex-linked region in the dioecious population compared with the androdioecious population.
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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.