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325 results for “network structure”
Fast and long-term super-resolution imaging of ER nano-structural dynamics in living cells using a neural network
<p>Datasets acquired and generated for the manuscript "Fast and long-term super-resolution imaging of ER nano-structural dynamics in living cells using a neural network". The datasets include test, training and time series datasets each containing the raw data and the predicted data where it applies. </p>
Structural brain network of gifted children
Open the record for dataset details and reuse information.
Fine-scale structure of the 2016-2017 Central Italy Seismic Sequence from data recorded at the Italian National Network
<p><strong>Data Set </strong></p> <p>Catalog of 33,983 earthquakes located during the 2016-2017 Central Italy seismic sequence. The velocity model used is the 1D gradient P- and S-wave velocity models (after Carannante et al., 2013). We used the highest quality P- and S-wave arrival times manually picked by analysts of the National Institute of Geophysics and Volcanology (INGV) seismic monitoring room, having an uncertainty lower than 0.6 s. </p> <p>Events were located by means of a 2-step procedure: the INGV routine absolute locations computation for all events with ML ≥ 1.5 that occurred in the study area between August 2016 and January 2018, using the method described in Chiaraluce et al. (2017); the determination of relative locations by applying the HypoDD code (Waldhauser, 2001) to the catalog picks and phase delay times measured from waveform cross correlation.</p> <p>The time domain cross-correlation method (Schaff et al., 2004; Schaff and Waldhauser, 2005) was applied to seismograms of all pairs of events separated by 3 km or less and recorded at common stations. Seismograms were filtered in the 1-15 Hz frequency range using a 4 pole, zero phase band‐pass Butterworth filter. The correlations measurements were performed on 0.7 s long window for P-waves and 1 s windows for S-waves. Only measurements with correlation coefficients greater than 0.7 were kept, resulting in a total of ~4.4 million P and ~1.1 million S wave delay times. </p> <p>We sub-divided the entire dataset in 18 rectangular boxes, containing a maximum of 6000 earthquakes, orthogonal to and centered on the mean strike of the seismic sequence. The overlap between neighboring boxes is 50% with respect to the NW-SE extension. HypoDD is run separately on each box. Resulting relative locations from all boxes were combined into a single catalog, computing the weighted mean of double hypocenters in the overlapping regions (Waldhauser and Schaff, 2008).</p> <p>The final double-difference catalog includes 33,982 events occurring between 24<sup>th</sup> of August 2016 and 18<sup>th</sup> of January 2018.</p> <p>The catalog is in csv format, semicolon separator, ordered by origin time and the header content is the following:</p> <ul> <li>Id-ingv: ingv eventid, useful to link to the QuakeML phase file through the INGV fdsnws/event webservice (<a href="https://meet.google.com/linkredirect?authuser=0&dest=http%3A%2F%2Fwebservices.ingv.it%2Fswagger-ui%2Fdist%2F%3Furl%3Dhttps%3A%2F%2Fingv.github.io%2Fopenapi%2Ffdsnws%2Fevent%2F0.0.1%2Fevent.yaml">http://webservices.ingv.it/swagger-ui/dist/?url=https://ingv.github.io/openapi/fdsnws/event/0.0.1/event.yaml</a>) and to the reported magnitude;</li> <li>Latitude(°) expressed in decimal degrees;</li> <li>Longitude(°) expressed in decimal degrees;</li> <li>Depth(km) hypocentral depth expressed in kilometers;</li> <li>Year of origin time in the format yyyy;</li> <li>Month of origin time in the format mm;</li> <li>Day of origin time in the format dd; </li> <li>Hour of origin time in the format hh;</li> <li>Minute of origin time in the format min;</li> <li>Second of origin time in the format ??.?????? s;</li> <li>Magnitude: the value available at the phases downloading time (see Id-ingv fdsnws/event)</li> </ul> <p> </p> <p> </p> <p> </p> <p><br> </p>
Charting nanocluster structures via convolutional neural networks
<p>The repository contains a notebook for the training of the autoencoder for the RDFs for structural classification. The notebook describes the procedure going from RDFs calculation to clustering of the reduced space. In the folder are contained Au147 structures, together with the associated pretrained AE, the 3D chart and the different clustering performed varying mean shift bandwidth.</p> <p>Files:</p> <p>- ChartAu147.ipynb: notebook</p> <p>- Configurations: directory with the dataset divided according to the CNA classification of the structures, xyz format with no headers, every 147 lines is a single structure</p> <p>- Libraries: directory with functions imported in the notebook</p> <p>- Precomputed: directory with the precomputed outputs</p> <p> - rdfs.npy: preocmputed RDFs of the data stored in configurations, npy format to load with NumPy</p> <p> - labels.npy: CNA labels of the RDFs, npy format to load with NumPy</p> <p> - model_au147.pth: pretrained model for au147</p> <p> - scaler_au147.pkl: minmax scaler of the RDFs</p> <p> - chart_3d.dat: 3d space generated via the encoder on the au147 dataset</p> <p> - ae_reconstructions.npy: reconstructions of the rdfs of the model (model_au147.pth)</p> <p> - MSscanbw: pretrained mean shift clustering with different bandwidths, the file "clus_vs_bw.dat" reports the number of clusters associated to each bandwidth</p>
Networking nutrients: how nutrition determines the structure of ecological networks - Dataset
<p>Raw sequencing data and other metadata files are associated with Cuff et al. (2021a, 2022a), available at https://doi.org/10.5281/zenodo.4708418</p> <p>Data/code relating to the macronutrient contents and delineation of tropho-species clusters are associated with Cuff et al. (2021b, 2022b), available at https://doi.org/10.5281/zenodo.5738016</p> <p>Cuff, Jordan P. (2021a). A molecular analysis of the diet and biocontrol potential of spiders in cereal crops - Dataset. <em>Zenodo</em>. doi: 10.5281/zenodo.4708419</p> <p>Cuff, Jordan Patrick, Tercel, M. P., Vaughan, I. P., Drake, L. E., Wilder, S. M., Bell, J. R., … Symondson, W. O. (2021b). Evidence for nutrient-specific foraging of predators under field conditions. <em>Zenodo</em>. doi: 10.5281/zenodo.5738015</p> <p>Cuff, Jordan P., Tercel, M. P. T. G., Drake, L. E., Vaughan, I. P., Bell, J. R., Orozco-terWengel, P., … Symondson, W. O. C. (2022a). Density-independent prey choice, taxonomy, life history and web characteristics determine the diet and biocontrol potential of spiders (Linyphiidae and Lycosidae) in cereal crops. <em>Environmental DNA</em>, in press. doi: 10.1002/edn3.272</p> <p>Cuff, Jordan P., Tercel, M. P. T. G., Vaughan, I. P., Drake, L. E., Wilder, S. M., Bell, J. R., … Symondson, W. O. C. (2022b). Evidence for nutrient-specific foraging of predators under field conditions. <em>Authorea</em>. doi: 10.22541/au.164908092.21266343/v1</p>
HEroBM: a deep equivariant graph neural network for high-fidelity backmapping from coarse-grained to all-atom structures
<p><span>Molecular simulations play a pivotal role in chemistry, biology, and material sciences, enabling the</span><br><span>study of complex dynamic properties within systems. Coarse-grained (CG) techniques have emerged</span><br><span>as indispensable tools in this domain, facilitating the sampling of large-scale systems and extending</span><br><span>simulation timescales by simplifying system representation. However, CG approaches involve a trade-</span><br><span>off: they sacrifice atomistic details that may be crucial for understanding the underlying processes.</span><br><span>To address this challenge, a recommended strategy is to identify key CG conformations and employ</span><br><span>backmapping methods to retrieve atomistic coordinates. Currently, rule-based methods often yield</span><br><span>suboptimal geometries and rely on energy relaxation, resulting in less-than-optimal outcomes. In</span><br><span>contrast, machine learning techniques offer higher accuracy but may lack transferability between</span><br><span>systems or be tied to specific CG mappings. In this study, we present HEroBM, a dynamic and scalable</span><br><span>method that utilizes deep equivariant graph neural networks and a hierarchical approach to achieve</span><br><span>high-resolution backmapping. HEroBM is capable of handling any type of CG mapping, providing a</span><br><span>versatile and efficient protocol for reconstructing atomistic structures with high accuracy. Grounded</span><br><span>in local principles, HEroBM spans the entire chemical space and can be applied across systems of</span><br><span>varying composition and sizes. We demonstrate the versatility of our framework through a range of</span><br><span>biological systems, including a complex real-case scenario. Here, our end-to-end backmapping approach</span><br><span>accurately generates atomistic coordinates for a G protein-coupled receptor bound to an organic small</span><br><span>molecule within a cholesterol/phospholipid bilayer. The high-fidelity HEroBM backmapping enables</span><br><span>researchers to effortlessly transition between CG and all-atom simulations, opening unprecedented</span><br><span>avenues for molecular investigations.</span></p>
Structure and dynamics of growing networks of Reddit threads
<p>Data used in the paper "<a href="https://doi.org/10.1007/s41109-024-00654-y" target="_blank" rel="noopener">Structure and dynamics of growing networks of Reddit threads</a>".</p> <p>This dataset is made of 6366 threads collected from the r/AmITheAsshole community on Reddit. The dataset contains a total of 6,372,251 comments. The collected threads constitute the “top” submissions — those having the highest score, measured as the difference between upvotes and downvotes of a post. We downloaded them using PRAW, running 10 different queries across various temporal scopes, and then cleaning the obtained dataset by removing duplicated threads. Please refer to the paper, specifically to <a href="https://appliednetsci.springeropen.com/articles/10.1007/s41109-024-00654-y/tables/3" target="_blank" rel="noopener">Table 3</a>, for more details about the dataset.</p> <p><strong>If you use this data, please cite the following source:</strong> Goglia, D., Vega, D. Structure and dynamics of growing networks of Reddit threads. Appl Netw Sci 9, 48 (2024). https://doi.org/10.1007/s41109-024-00654-y</p>
5D-NP-FABTECH_ALD - Open Dataset for: "ZnO vapor phase infiltration into photo-patternable polyacrylate networks for the microfabrication of hybrid organic-inorganic structures"
<p>This is the open dataset for the paper: "L. Demelius, L. Zhang, A. M. Coclite and M. D. Losego, ZnO vapor phase infiltration into photo-patternable polyacrylate networks for the microfabrication of hybrid organic–inorganic structures, <em>Mater. Adv.</em>, 2024, <strong>5</strong>, 8464–8474."</p> <p>This includes the supplementary information and all the source material that was used for the paper preparation.</p> <p>For each folder (sub-dataset), there exists a corresponding readme file describing the content and including material.</p>
NUT01 Nutrient Network: Investigating the roles of nutrient availability and vertebrate herbivory on grassland structure and function at Konza Prairie
The goals and focal research questions are copied below from the Nutrient Network website. More information can be found at nutnet.org. NutNet focal research questions: (1) How general is our current understanding of productivity-diversity relationships? (2) To what extent are plant production and diversity co-limited by multiple nutrients in herbacoues-dominated communities? (3) Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? NutNet goals: (1) To collect data from a broad range of sites in a consistent manner to allow direct comparisons of environment-productivity-diversity relationships among systems around the world. This is currently occurring at each site in the network and, when these data are compiled, will allow us to provide new insights into several important, unanswered questions in ecology. (2) To implement a cross-site experiment requiring only nominal investment of time and resources by each investigator, but quantifying community and ecosystem responses in a wide range of herbaceous-dominated ecosystems (i.e., desert grasslands to arctic tundra).
ESM01 Fire and grazing modulate the structure and resistance of plant-floral visitor networks in a tallgrass prairie
Data from the study: Welti, E.A.R. and Joern, A. 2017. Fire and Grazing modulate the structure and resistance of plant-floral visitor networks in a tallgrass prairie. Oecologia 186: 447-458. EMS011 dataset contains counts of blooming inflorescences of plant species on 12 Konza watersheds in June-July of 2014; ESM012 dataset contains associations between flower-visiting insects and insect-pollinated flowering plants on 12 Konza watersheds collected in May-July of 2014; ESM013 dataset describes insects belonging to the orders of Coleoptera, Diptera, Lepidoptera and Hymenoptera collected in pantrap transects on 12 Konza watersheds collected in June - July of 2014.
Modifications of the plant-pollinator network structure and species' roles along a gradient of urbanization
<p>This file includes data and codes used in the article titled: " Modifications of the plant-pollinator network structure and species’ roles along a gradient of urbanization".</p> <p>Data include plant-pollinator interactions sampled in each site (1-12) at each sampling event (6 events) in the three urbanization classes (low, medium, high). Each row is a single insect pollinator X plant interaction. Full species names and abbreviations used in figures in the Supplementary Information are reported.<br> The data file is .txt with tab-separated values.</p>
NoSyms: A neural network approach to detecting data structures in raw memory
<p>This data was used for a experiments with graph convolutional neural networks for memory forensics as part of a bachelor thesis (included as pdf).<br> <br> Abstract:<br> <br> This work presents a neural network based approach for data structure detection in raw memory that does not require an entirely matching description of the target data structure. Instead, it’s merely necessary to provide multiple descriptions of data structures similar to the target as training data in the form of debugging symbols. The core contribution of this work is a formal description and implementation of encoding data structure definitions as well as raw memory contents such that they can be processed by graph convolutional neural networks. A description and implementation of a neural network meant to detect data structures in the memory contents of a Linux Kernel demonstrates the practical applicability of the described approach.<br> <br> The Code is available on GitHub <a href="https://github.com/NiklasBeierl/nosyms">https://github.com/NiklasBeierl/nosyms</a>.<br> <br> nokaslr_dump is the qemu memory snapshot used to test the model.<br> nokaslr.raw is the "raw" form of the snapshot as produced by Volatility 3's layerwriter plugin.<br> symbols-training-data contains the Volatility symbol JSON files from which training data was derived.<br> nokaslr_pointers.csv lists the kernel space pointers in the snapshot and<br> nokaslr_tasks.csv lists task structs in the snapshot. Both were extracted via a Volatility plugins that are included in the GitHub Repo.<br> vmlinux-5.4.0-58-generic.json is the symbol file for the kernel the snapshot was taken from.<br> other-symbols.zip contains symbol files I generated vor various other kernels but did not end up using, use at your own discretion.</p>
Deep neural networks and humans both benefit from compositional language structure
<p>This dataset holds the results generated in the paper:</p> <p>Deep neural networks and humans both benefit from compositional language structure</p> <p>by L. Galke, Y. Ram, and L. Raviv.</p>
Robust Method for Property Prediction via Artificial Neural Networks: Incorporating Key Structural Features for Carbon Dioxide – Ionic Liquid Mixtures
<p>This Dataset comprises two sub-sets of information:</p> <ul> <li>Database and Results of the work present in the paper "Robust Method for Property Prediction via Artificial Neural Networks: Incorporating Key Structural Features for Carbon Dioxide – Ionic Liquid Mixtures" published in The Journal of Physical Chemistry B (https://doi.org/10.1021/acs.jpcb.4c04432).</li> <li>Sample of the code used, in order to reproduce any of the results presented above. This can be found in the previous version of this Dataset (v1.0 https://zenodo.org/records/11216901)</li> </ul> <p> </p> <p>Regarding the sample code, an example for all ANN Models used in this work is provided. This includes the three models used:</p> <ol> <li>One based only on Critical Properties of Ionic Liquids (CRT Model)</li> <li>One based only on Structural Properties of Ionic Liquids (STR Model)</li> <li>One combination of the previous models, taking into account both Critical and Structural Properties (COMB Model)</li> </ol> <p>In this manner, it is possible to observe the differences between the performance of the different models, either through statiscal analysis or using graphical representation. This allows for the benchmarking to be done in a more concise way.</p>
Data for "Unfolding the structural stability of nanoalloys via symmetry-constrained genetic algorithm and neural network potential"
<p><strong>PtNi_alloy_eam.db</strong> is the dataset (ase.db object) consisting of 55982 intially sampled Pt-Ni alloy structures with EAM energies and forces.</p> <p><strong>PtNi_alloy_dft.db</strong> is the dataset (ase.db object) consisting of the final 6828 resampled Pt-Ni alloy structures with DFT energies and forces calculated by VASP. This is the training set for the NNP, and could be very useful for fitting other machine learning models.</p> <p><strong>PtNi_nanoalloy_vertices_nnp.db</strong> is the dataset (ase.db object) consisting of all the vertices (stable structures) on the convex hulls obtained from NNP-based SCGA runs on 36 Pt-Ni nanoalloy systems. The energies are given by the NNP. Additional information such as mixing energy, motif and symmetry axis are also saved in the dataset and can be queried by the 'data' keyword. An xyz format trajectory of these stable structures is also uploaded.</p> <p>All the input files and scripts for hybrid MC-MD simulations, QBC resampling, DFT calculations, NNP training, NNP-based SCGA runs and convex hull analysis are provided in <strong>inputs_and_scripts.zip</strong>.</p>
Accelerated Mechanophore Activation and Drug Release in Network Core-Structured Star Polymers Using High-Intensity Focused Ultrasound
<div>Data of the associated manuscript and supporting information sorted after Figures, Schemes, and Tables.</div>
Assemblies, synapse clustering and network topology interact with plasticity to explain structure-function relationships of the cortical connectome
<p>Dataset linked to the article with the same title</p> <p>The model itself is very similar to its non-plastic counterpart under the following DOI: <a href="../record/7930275">10.5281/zenodo.7930275</a>, i.e. a 1.5 mm diameter cortical tissue comprising 211,712 neurons and their connectivity in the front limb and jaw subregions and the dysgranular zone of the Paxinos & Watson rat brain atlas. It's formatted in the open <a href="https://github.com/AllenInstitute/sonata">SONATA</a> standard and contains neuron locations and their properties (such as morphological types, cortical layer, etc.), their detailed morphologies, and synaptic connectivity (with all their anatomical and physiological parameters). The main difference from the non-plastic version is the addition of plasticity related parameters to <em>O1/S1nonbarrel_neurons__S1nonbarrel_neurons__chemical/edges.h5. </em>Extrinsic synaptic connections from the thalamus are included in this release, but for inputs from neurons in the remainder of non-barrel somatosensory cortex please see the non-plastic version of the circuit.</p> <p><strong>Analyzing the model</strong></p> <p>The model can be analyzed in terms of its anatomy, physiology and connectivity using the packages <a href="https://neurom.readthedocs.io/en/stable/">NeuroM</a>, <a href="https://bluebrainsnap.readthedocs.io/en/stable/">BlueBrain SNAP</a> and <a href="https://github.com/BlueBrain/ConnectomeUtilities">ConnectomeUtilities</a>. (see first Jupyter notebook)</p> <p><strong>Simulating the model</strong></p> <p>To simulate the model we'd recommend using out using our open-source simulator <a href="https://github.com/BlueBrain/neurodamus">Neurodamus</a>. The reference version is the branch <em>nbS1-2023</em>, which is archived under the following DOI: <a href="http://doi.org/10.5281/zenodo.8075202">10.5281/zenodo.8075202</a>. Instructions on how to use the simulator are provided on the GitHub page linked above. Briefly, you'll first have to <a href="https://github.com/BlueBrain/neurodamus#install-neurodamus">install Neurodamus</a>. Next, build a <em>"special"</em> executable that include compiled versions of ion channel and synapse models. To do that, follow <a href="https://github.com/BlueBrain/neurodamus#build-special-with-mod-files">these instructions</a>, where <em>mod-files-from-released-circuit </em>is replaced by the location of <em>O1/mods</em> on your system. Finally, <a href="https://github.com/BlueBrain/neurodamus#examples">run a simulation</a>. The specific simulation conditions and stimuli are specified in simulation configuration files. An exemplary simulation configuration is included in this release (<em>simulation_config.zip</em>).</p> <p><strong>Analyzing simulation results</strong></p> <p>Simulation results can be analyzed with <a href="https://bluebrainsnap.readthedocs.io/en/stable/">BlueBrain SNAP</a>, <a href="https://github.com/BlueBrain/ConnectomeUtilities">ConnectomeUtilities</a>, and <a href="https://github.com/BlueBrain/assemblyfire">assemblyfire</a>. Notebooks 2-5 go though these analysis and recreate some of the panels from our article. In most cases the notebooks can be run with the shared HDF5 files and don't require running any simulations.</p> <p><strong>Version 2</strong></p> <p>Bug fix in simulation_config.json and therefore new version of results (and corresponding notebooks). The underlying circuit model (O1.xz) did not change from v1.</p> <p>--</p> <p><em>The development of this dataset was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.</em></p>
Experimental datasets of networks of nonlinear oscillators: Structure and dynamics during the path to synchronization
<p>The analysis of the interplay between structural and functional networks require experiments where both the specific structure of the connections between nodes and the time series of the underlying dynamical units are known at the same time. However, real datasets typically contain only one of the two ways (structural or functional) a network can be observed. Here, we provide experimental recordings of the dynamics of 28 nonlinear electronic circuits coupled in 20 different network configurations. For each network, we modify the coupling strength between circuits, going from an incoherent state of the system to a complete synchronization scenario. Time series containing 30000 points are recorded using a data-acquisition card capturing the analogic output of each circuit. The experiment is repeated three times for each network structure allowing to track the path to the synchronized state both at the level of the nodes (with its direct neighbors) and at the whole network. These datasets can be useful to test new metrics to evaluate the coordination between dynamical systems and to investigate to what extent the coupling strength is related to the correlation between functional and structural networks.</p> <p>We provide the times series of N=28 Rössler electronic oscillators for 20 different network configurations (compressed file with tag R1 to R20). For each network structure, we recorded the times series for 101 different coupling strengths between oscillators. Each one of the 101 corresponding files is labeled as ST_X_Y.dat where X is a value between X=0 and X=100 that corresponds, respectively, to the minimum and maximum coupling strength. The value of Y corresponds to the repetition number, which can be 1, 2 of 3 (i.e., we repeated the same experiment three times). Data files contain the second variable of the 28 nodes arranged in columns with a length of 30000 points. In a second file named Structure.zip, all the network structures are given, each file having a name Net_R.dat, where R=1, 2… 20. The degree of each node (i.e., number of output connections) is the same for all network configurations, where the specific neighbors of each node are re-arranged randomly.</p>
Database of small molecule X-ray absorption spectra, featurized structures, and neural network ensembles
<p>Companion data for arXiv preprint <em>Uncertainty-aware predictions of molecular X-ray absorption spectra using neural network ensembles</em> (<a href="https://arxiv.org/abs/2210.00336">https://arxiv.org/abs/2210.00336</a>), by Animesh Ghose, Mikhail Segal, Fanchen Meng, Zhu Liang, Mark S. Hybertsen, Xiaohui Qu, Eli Stavitski, Shinjae Yoo, Deyu Lu & Matthew R. Carbone.</p> <p><strong>Included</strong></p> <ul> <li>*-XANES-*.tar.bz2: raw input/output files for all molecular simulations used in the work. These inputs and outputs correspond to the structural data in the QM9 dataset.</li> <li>ml_ready.tar.bz2: machine learning-ready data (featurized spectra). Used as input to the neural network ensembles.</li> <li>XANES-220712-ACSF-*.tar.bz2: neural network ensembles used in this work.</li> </ul> <p><strong>Notes</strong></p> <ul> <li>The FEFF9 code [J. J. Rehr, J. J. Kas, F. D. Vila, M. P. Prange, and K. Jorissen, <em>Phys. Chem. Chem. Phys.</em> <strong>12</strong>, 5503 (2010)] was used to generate all X-ray absorption near-edge structure (XANES) spectra.</li> <li>All molecular structures were sourced from the QM9 database [R. Ramakrishnan, P. O. Dral, M. Rupp, and O. A. Von Lilienfeld, <em>Sci. Data</em> <strong>1</strong>, 1 (2014)].</li> </ul> <p><strong>Funding</strong></p> <p>This research is based upon work supported by the U.S. Department of Energy, Office of Science, Office Basic Energy Sciences, under Award Number FWP PS-030. This research also used theory and computational resources of the Center for Functional Nanomaterials, which is a U.S. Department of Energy Office of Science User Facility, and the Scientific Data and Computing Center, a component of the Computational Science Initiative, at Brookhaven National Laboratory under Contract No. DE-SC0012704.</p>
Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression
<p>Supplemental Data 1 is single-cell response to rapamycin count data first sequenced in this work and deposited in GEO with accession GSE242556. It is a 173348 rows × 5847 columns TSV.GZ file where the first row is a header, the first 5843 columns are integer gene counts, and the final 4 columns ('Gene', 'Replicate', 'Pool', and 'Experiment') are cell-specific metadata.</p> <p>Supplemental Data 2 is bulk response to rapamycin count data first sequenced in this work. It is a 33 rows × 5847 columns TSV.GZ file where the first row is a header, the first 5843 columns are integer gene counts, and the final 4 columns ('Oligo', 'Time', 'Replicate', and 'Sample_barcode') are sample-specific metadata.</p> <p>Supplemental Data 3 is single-cell count data published as GSE125162 and re-analyzed with the pipeline used for single-cell quantification in this work. It is a 65068 rows × 5850 columns TSV.GZ file where the first row is a header, the first 5843 columns are integer gene counts, and the final 7 columns ('Condition', 'Sample', 'Genotype_Group', 'Genotype_Individual', 'Genotype', 'Replicate', 'Cell_Barcode') are cell-specific metadata.</p> <p>Supplemental Data 4 is the four deep learning models trained in this work. It is a TAR.GZ file containing the final biophysical transcription/decay model, the pre-trained decay model, the velocity prediction model, and the count prediction model. Each model file is an h5 file containing a pytorch model that can be loaded with supirfactor\_dynamical.read().</p> <p>Supplemental Data 5 is the prior knowledge network used to constrain the models for TF interpretability. It is a 1574 rows × 204 columns [Genes x TFs] TSV.GZ file where the first row is a header with TF names, the first column is an index of gene names, and TF-gene interactions are indicated by non-zero values in the matrix. There are 2799 TF-gene interactions.</p> <p><br> Supplemental Table 6 is the oligonucleotide sequences used in this work. It is a TSV file with a header row.</p> <p>Supplemental Table 7 is the yeast strains used in this work. It is a TSV file with a header row.</p> <p>Supplemental Table 8 is gene metadata used in this work (e.g. Ribosomal Protein gene labels, etc). It is a TSV file with a header row.</p> <p>Supplemental Table 9 is FY4/5 growth curve data generated in this work. It is a 20 rows × 7 columns TSV file where the first row is a header with replicate IDs, the first column is an index of times in minutes, and values are cell densities in YPD culture, in units of 10$^6$ cells / mL.</p> <p>Supplemental Data 10 is a TAR.GZ file containing the yeast SacCer3 genome, modified to add UTR sequences, that was used to generate transcripts for kallisto pseudoalignment in this work.</p>
ScienceDex guides
Understand access before you commit
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.