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5 results for “pergola”
C. elegans data sample for Pergola documentation
<p>C. elegans data sample for Pergola documentation (<a href="http://cbcrg.github.io/pergola/quick_start.html">http://cbcrg.github.io/pergola/quick_start.html</a>). The sample data set consists in two folders: One named "worm_speeds" containing a CSV file for each of the tracked worms. From the several measures that can be found in the individual files, in this example we will use mid-body speed. The "mapping" folder contains the "worm_speed2pergola.txt", which sets the mappings between the information represented in the worm_speed files and the pergola ontology.</p>
Mouse data sample for Pergola documentation - Shiny visualization
<p>Data sample of feeding and drinking behavior recorded during three weeks of C57BL6/J male mice. The data correspond to 2 groups (9 control mice and 8 high-fat diet mice). Each animal was tracked individually on Phecomp cages for 9 weeks. During the first experimental week all animals were given <em>ad libitum</em> access to a standard chow (habituation phase). After this first week, control mice continued with the same diet regime while high-fat mice were exclusively given <em>ad libitum</em> access to a high-fat chow. Data was used originally in this publication <a href="http://onlinelibrary.wiley.com/doi/10.1111/adb.12595/abstract">10.1111/adb.12595.</a> The recordings were processed using Pergola to BED and BedGraph file formats.</p> <p>The data set consist in:</p> <p>- a exp_info.txt file setting mouse membership to the control or the HF mice.</p> <p>- a files folder containing BED and BedGraph files of mouse feeding behavior.</p>
Pergola: boosting visualization and analysis of longitudinal data by unlocking genomic analysis tools - Mouse feeding behavior dataset
<p>Dataset contains feeding and drinking behavioral recordings of C57BL6/J male mice. Mice were distributed into 2 groups (9 control mice and 8 high-fat diet mice) and tracked individually on Phecomp cages for 9 weeks. During the first experimental week all animals were given <em>ad libitum</em> access to a standard chow (habituation phase). After this first week, control mice continued with the same diet regime while high-fat mice were exclusively given <em>ad libitum</em> access to a high-fat chow. Data was used originally in this publication <a href="http://onlinelibrary.wiley.com/doi/10.1111/adb.12595/abstract">10.1111/adb.12595.</a></p> <p>The data set consist in:</p> <p>- a "mouse_recordings" folder containing a CSV file containing mouse recordings and the files.</p> <p>- a "mappings" folder containing all the mappings used by the pergola in the pipeline to convert data.</p> <p>- a "phases" folder containing a CSV file containing experimental phases.</p> <p>- a "chromHMM_files" folder containing a cellmarkfiletable table used by chromHMM to learn a HMM model</p>
Pergola: boosting visualization and analysis of longitudinal data by unlocking genomic analysis tools - D. melanogaster behavior dataset obtained with JAABA
<p>Dataset contains <em>Drosophila melanogaster </em>behavioral annotations of chasing. The dataset is formed by 20 GAL4 line flies group from a TrpA activation screen with increased propensity to chasing and by 19 pBDPGAL4U line (control) flies group. Ctrax motor trajectories derived from the original video-recordings (1000 seconds) were downloaded from this <a href="https://sourceforge.net/projects/jaaba/files/Sample%20Data/sampledata_v0.1.zip/download">link</a> and used to obtain the chasing behavioral annotations using <a href="http://jaaba.sourceforge.net/">JAABA</a> <a href="https://www.nature.com/articles/nmeth.2281">10.1038/nmeth.2281</a>: </p> <p>The data set consist in:</p> <p>- a "mappings" folder containing all the mappings used by the pergola in the pipeline to convert data.</p> <p>- a "perframe_TrpA" folder containing mat files with three Ctrax derived variables (dnose2ell, dtheta and velmag) from the motor trajectories of the GAL4 line.</p> <p>- a "perframe_pBDPGAL4" folder containing mat files with three Ctrax derived variables (dnose2ell, dtheta and velmag) from the motor trajectories of the control line.</p> <p>- a "scores" folder including the JAABA chasing annotations in two mat file one for each fly line.</p>
Pergola: boosting visualization and analysis of longitudinal data by unlocking genomic analysis tools - C. elegans unc-16 and N2 motion behavior dataset
<p>Dataset contains <em>Caenorhabditis</em> <em>elegans </em>motor behaviors originally used in this publication <a href="https://www.nature.com/articles/nmeth.2560">10.1038/nmeth.2560</a> and downloaded from the available <a href="http://wormbehavior.mrc-lmb.cam.ac.uk/">DB</a> which points to Zenodo. The dataset consists in two worm strains, 20 individuals from a mutant unc-16 strain with reduced mobility and 40 individuals from a control N2 strain. The behavioral measures derived from each individual worm trajectory were available in a HDF5-formatted file (Hierarchical Data Format Version 5) that has been included in this dataset.</p> <p>The data set consist in:</p> <p>- a "mappings" folder containing all the mappings used by the pergola in the pipeline to convert data.</p> <p>- a "N2" folder containing the 40 HDF5 files with the measures derived from the N2 worms.</p> <p>- a "N2" folder containing the 20 HDF5 files with the measures derived from the unc-16 worms.</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.