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11,506 results for “Dynamics”
Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC
<p><strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in water.</p> <p><strong>Number of DMPC: </strong>64.<br> <strong>Number of DMTAP:</strong> 64.<br> <strong>Number of Cl--ions:</strong> 64.<br> <strong>Number of waters:</strong> 5336.</p> <p><strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 149 ns.<br> <strong>Previously equilibrated for:</strong> 41 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm.</p> <p><strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.</p>
Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC in 0.1 M NaCl
<p><strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in 0.1 M NaCl solution.</p> <p><strong>Number of DMPC:</strong> 64.<br> <strong>Number of DMTAP:</strong> 64.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 10.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 74.<br> <strong>Number of waters:</strong> 5316.</p> <p><strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 190 ns.<br> <strong>Previously equilibrated for:</strong> 21 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm.</p> <p><strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.</p>
Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 0.1 M NaCl
<p><strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in 0.1 M NaCl solution.</p> <p><strong>Number of DMPC:</strong> 32.<br> <strong>Number of DMTAP:</strong> 96.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 10.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 106.<br> <strong>Number of waters:</strong> 5476.</p> <p><strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 110 ns.<br> <strong>Previously equilibrated for:</strong> 11 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm.</p> <p><strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.</p>
Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC in 0.5 M NaCl
<p><strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in 0.5 M NaCl solution.</p> <p><strong>Number of DMPC:</strong> 32.<br> <strong>Number of DMTAP:</strong> 96.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 49.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 145.<br> <strong>Number of waters:</strong> 5398.</p> <p><strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 110 ns.<br> <strong>Previously equilibrated for:</strong> 11 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm.</p> <p><strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.</p>
Molecular dynamics simulation trajectory of a cationic lipid bilayer: 75/25 mol% DMTAP/DMPC
<p><strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 75 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 25 mol-%) lipids in water.</p> <p><strong>Number of DMPC:</strong> 32.<br> <strong>Number of DMTAP:</strong> 96.<br> <strong>Number of Cl--ions:</strong> 96.<br> <strong>Number of waters:</strong> 5496.</p> <p><strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 109 ns.<br> <strong>Previously equilibrated for:</strong> 31 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm.</p> <p><strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.</p>
Dynamics of oculomotor direction discrimination
<p>Dataset relative to the following publication:</p> <p>Braun, D.I. & Gegenfurtner, K.R. (2016) Dynamics of oculomotor direction discrimination. <strong>Journal of Vision</strong>, 16(13):4. http://www.journalofvision.org/16/13/4.</p> <p>See the file README.rtf for further information.</p> <p> </p>
Data for S. Grandi et al., "Quantum dynamics of a driven two-level molecule with variable dephasing", arXiv:1607.02112, to appear in Phys. Rev. A.
<p>Data for S. Grandi et al., "Quantum dynamics of a driven two-level molecule with variable dephasing", arXiv:1607.02112, to appear in Phys. Rev. A. We include raw data, a Mathematica notebook, and read me files describing the files.</p>
Data for Wind Energy Science paper "Modal dynamics of structures with bladed isotropic rotors and its complexity for 2-bladed rotors"
<p>The files are data files with model input and Matlab files with model parameters and function that sets up the block matrices of the dynamic model used in the paper. The Matlab script "test_repo.m" shows how to this function with all input.</p>
Simulation snapshots of complex I molecular dynamics simulation
<p>These are snapshots from the molecular dynamics simulations of complex I (setups I and II). These can be loaded in the VMD software for visualization, and 'segname' keyword can be used to distinguish the different parts of the protein.</p>
Supplementary material 2: Seu Nico Community Dynamics from: Tree Diversity and Dynamics of the Forest of Seu Nico, Viçosa, Minas Gerais, Brazil - Biodiversity Data Journal 3: e5425 (31 July 2015) https://doi.org/10.3897/BDJ.3.e5425
2868 tree occurrences from two census within 100 plots of 10x10 m in the Forest of Seu Nico (FSN), Viçosa municipality, Minas Gerais, Brazil, including measurements of each tree as well as environmental data from all 100 plots. Dataset consists of seven independent files
Figure 1. from: Tree Diversity and Dynamics of the Forest of Seu Nico, Viçosa, Minas Gerais, Brazil - Biodiversity Data Journal 3: e5425 (31 July 2015) https://doi.org/10.3897/BDJ.3.e5425
Figure 1. - The Forest of Seu Nico (FSN) covers the bottom and the slopes of a small valley on the Bom Sucesso Farm in Viçosa, Minas Gerais, Brazil. Photograph by M. Gastauer from northeastern direction.
Raw data of the experiments in "Examining the Reproducibility of Using Dynamic Loop Scheduling Techniques in Scientific Applications" (REPPAR workshop at IPDPS 2017)
<p>Raw data of the experiments in "Examining the Reproducibility of Using Dynamic Loop Scheduling Techniques in Scientific Applications" (REPPAR workshop at IPDPS 2017)</p>
Raw data of the experiments in "Towards the Reproducibility of Using Dynamic Loop Scheduling Techniques in Scientific Applications" (ISPDC 2017)
<p>Raw data of the experiments in "Towards the Reproducibility of Using Dynamic Loop Scheduling Techniques in Scientific Applications" (ISPDC 2017)</p>
Data Release: A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms
<p>The archive contains the supporting data for the results described in the paper titled "A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms".</p> <p>For more information see either the individual README files or consult the project git repository:</p> <p>https://bitbucket.org/wrs20/ppmd</p> <p> </p> <p>Copyright W.R.Saunders 2017</p>
Dynamic integration of information about salience and value for smooth pursuit eye movements
<p>Dataset from the following publication:</p> <p>Schütz, A. C., Lossin, F., & Gegenfurtner, K. R. (2015). Dynamic integration of information about salience and value for smooth pursuit eye movements. <em>Vision Research, 113</em>, 169-178. <a>doi:10.1016/j.visres.2014.08.009 <span></span></a><a></a> .</p>
Dynamics of Instagram Users
<p>These two data sets are gathered from Instagram users who were chosen randomly.</p> <p>The Main data set encompasses data for 1K users including 500 men and 500 women. The Test data set encompasses data for 100 users including 50 men and 50 women.</p> <p>Data gathered for each user includes :</p> <p>1- number of posts</p> <p>2- number of followers</p> <p>3- number of followings</p> <p>4- number of likes for the tenth previous post</p> <p>5- number of likes for the eleventh previous post</p> <p>6- number of likes for the twelfth previous post</p> <p>7- number of self-presenting posts from nine previous posts</p> <p>8- gender</p>
Epithelial cell chirality emerges through the dynamic concentric pattern of actomyosin cytoskeleton
<p>Supporting Information for</p> <p>Epithelial cell chirality emerges through the dynamic concentric pattern of actomyosin cytoskeleton</p> <p>Takaki Yamamoto, Tomoki Ishibashi, Yuko Mimori-Kiyosue, Sylvain Hiver, Naoko Tokushige, Mitsusuke Tarama, Masatoshi Takeichi, Tatsuo Shibata</p> <p>Tatsuo Shibata<br>Email: tatsuo.shibata@riken.jp</p> <p>Numerical data used for Figs. 1B, and C: </p> <p>Fig1B.csv,<br>Fig1C.csv</p> <p>Numerical data used for Fig. 1 figure supplement 1:</p> <p>Fig1S1_Collagen.csv,<br>Fig1S1_Fibronectin.csv,<br>Fig1S1_Non-coated.csv,<br>Fig1S1_PLL.csv</p> <p>Numerical data used for Figs. 2B, C and D: </p> <p>Fig2B.csv,<br>Fig2C_Blebbistatin.csv,<br>Fig2C_CK666.csv,<br>Fig2C_DMSO.csv,<br>Fig2C_Nocodazole.csv,<br>Fig2C_SMIFH2.csv,<br>Fig2D_DMSO.csv,<br>Fig2D_SMIFH2.csv</p> <p>Numerical data used for Fig. 2 figure supplement 2 A, D:</p> <p>Fig2S2A.csv,<br>Fig2S2D_NC.csv,<br>Fig2S2D_DAAM1_siRNA.csv,<br>Fig2S2D_DIAPH2_siRNA.csv</p> <p>Numerical data used for Fig. 2 figure supplement 3:</p> <p>Fig2S3A_NC.csv,<br>Fig2S3A_Myo2A_siRNA.csv,<br>Fig2S3A_Myo2B_siRNA.csv,<br>Fig2S3A_Myo2A_B_siRNA.csv,<br>Fig2S3B.csv</p> <p>Numerical data used for Fig. 2 figure supplement 4:</p> <p>Fig2S4A_NC.csv,<br>Fig2S4A_VCL_siRNA.csv,<br>Fig2S4B.csv</p> <p>Note: Fig2S2D_NC.csv, Fig2S3A_NC.csv and Fig2S4A_NC.csv represent data from the same control experiment.</p> <p>Numerical data used for Figs. 6C and D:<br>Fig6C.xls,<br>Fig6D_1.xls,<br>Fig6D_2.xls</p> <p>Numerical data used for Figs. 6 figure supplement 1:<br>Fig6S1I.xls,<br>Fig6S1J.xls</p> <p>Note: these data were also used in Figure 7 figure supplement 2A-H.</p> <p>Numerical data used for Figs. 8D and E:<br>Fig8DE.csv: </p> <p>FreeFEM++ script to perform the numerical computation used in Fig. 7 and matlab script for Fig 7 BCDFGH, and Fig. 7 figure supplement 2I: </p> <p>caco2ActiveChiralModel.edp,<br>PlotSimulationResults.m</p>
Research data supporting: "Non-trivial stimuli-responsive collective behaviours emerging from microscopic dynamic complexity in supramolecular polymer systems"
<p>Contains the relevant simulation data and input files. See "readme.txt" for information.</p>
Datasets for the article "Emerging patterns of CO2:O2 dynamics in rivers and their link to ecosystem carbon processing "
<p>Datasets supporting the article "Emerging patterns of CO2:O2 dynamics in rivers and their link to ecosystem carbon processing". The datasets are analized using the acompanying repository in github (https://github.com/rocher-ros/O2_CO2_rivers).</p> <p> </p> <p>Currently the publication is under review, for further information and details on the analysis visit the github repository or the acompannying article. </p>
Oscillatory dynamics of mRNA metabolism and chromatin accessibility in mESCs during the cell cycle
<p>Processed single-cell RNAseq and multiome sequencing--single-nucleus RNAseq and ATACseq for mESCs</p> <table> <tbody> <tr> <td><strong>Filename</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>scrna_deepdycle.h5ad</td> <td>single-cell RNAseq data, has information about unsplcied and spliced levels and the inferred cell cycle phase</td> </tr> <tr> <td>snrna_deepdycle_rep1.h5ad</td> <td>single-nulceus RNAseq data (replicate 1), has information about unsplcied and spliced levels and the inferred cell cycle phase</td> </tr> <tr> <td>snrna_deepdycle_rep2.h5ad</td> <td>single-nulceus RNAseq data (replicate 2), has information about unsplcied and spliced levels and the inferred cell cycle phase</td> </tr> <tr> <td>body_coverage_lif1.tsv.gz</td> <td>single nucleus ATACseq data (replicate 1), counts table of ATACseq peaks mapped to the genes</td> </tr> <tr> <td>body_coverage_lif2.tsv.gz</td> <td>single nucleus ATACseq data (replicate 2), counts table of ATACseq peaks mapped to the genes</td> </tr> <tr> <td>model_predictions.zip</td> <td>gene-wise predictions for gene expression--unspliced and spliced, and mRNA metabolism rates--synthesis, splicing, export, and degradation rates for single-cell and single-nucleus data</td> </tr> </tbody> </table>
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.