cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/d1.2121
title: The Mouse Action Recognition System (MARS): multi-worker behavior annotation data

description: This dataset was collected to quantify inter-annotator variability in manual labeling of social behaviors in freely interacting mice.

We provided a group of graduate students, postdocs, and technicians in the Anderson lab with written descriptions of close investigation, mounting, and attack behaviors (included below), and instructed them to score a set of ten resident-intruder videos, all taken from unoperated mice. Annotators were given front- and top-view video of social interactions, and scored behavior using either Bento or the Caltech Behavior Annotator, both of which support simultaneous display of front- and top-view video and frame-by-frame browsing and scoring. All but one annotator (Human 4) had previous experience scoring mouse behavior videos; Human 4 had previous experience scoring similar social behaviors in flies.
DOI: 10.22002/d1.20221
title: Oxnard DAS Noise Cross-Correlation

description: This is the noise cross-correlation result for the Oxnard DAS array, in stack.segy (PASSCAL SEG-Y format). The DAS array has 2496 channels in total, but in the noise cross-correlation, we only take the first 2370 ones and disregard the 126 bad channels at the end of the array. The sampling rate is 50 Hz and the maximum time lag is 30 s. The Python function load_segy in reader.py can be used to read the file.
DOI: 10.22002/d1.20193
title: Supershear rupture propagation through non-homogeneously rough surfaces

description: Data set and MATLAB scripts for studying supershear rupture propagation when roughness is not constant along the interface. Architecture is similar to the one used by V. Rubino and A. Rosakis. Readme file included for more details.
DOI: 10.22002/d1.20092
title: Dataset related to "Benzoquinones in the defensive secretion of a bug (Pamillia behrensii): a common chemical trait retrieved in the Heteroptera"

description: Behavioral and chemical data for a benzoquinone producing bug. Provided DeepLabCut project with behavioral movies, hand labeled frames for network training, neural network, and outputs from DLC and other outputs from custom machine vision pipeline. Also contains endpoint assay chemical readouts from a solid phase micro-extraction deployed during the video runs and analyzed on a GCMS.
description: Related Publication:
Benzoquinones in the defensive secretion of a bug (Pamillia behrensii): a common chemical trait retrieved in the Heteroptera

Julian M. Wagner Caltech

Thomas H. Naragon

Adrian Brückner Caltech

https://doi.org/10.1101/2020.12.11.421891
eng
DOI: 10.22002/d1.1958
title: Informed Training Set Design Enables Highly Efficient Machine Learning-Assisted Directed Protein Evolution

description: This dataset contains the information used to perform simulated machine learning-assisted directed evolution (MLDE) experiments. It also contains summary statistics for all simulations performed in the accompanying work. Detailed information on the contents of the data can be found in the README  that accompanies the download.
DOI: 10.22002/d1.1936
title: SUGARseq_TMG_Opt_cDNA_FASTQ

description: FASTQ files for transcriptome
DOI: 10.22002/d1.1928
title: Data for "Signal Amplification in Synthetic Bacterial Communication"

description: The files provided here contain the data and Python code referenced in the PhD thesis entitled "Signal Amplification in Synthetic Bacterial Communication". Python analysis and simulation files are in the tar archive `analysis.tgz`, in which the top-level directories `platereader`, `microscopy`, and `omnitray-modeling` correspond respecting order to platereader experiments, microscopy experiments, and simulations. Microscopy data are stored in tar archives and are labeled by date codes as YYMMDD.tgz. When these archives are extracted to the directory `microscopy/data` they can be accessed by the `viewing_aquisitions.ipynb` or `200626_analysis.ipynb` Jupyter Notebooks. The time lapse microscopy images are unprocessed TIFF files. Raw and processed platereader data are in the `biotek_data.tgz` tar archive and related MCMC walker traces are in `mcmc_outputs.tgz'. 

 The analysis code includes Jupyter Notebooks, Python modules, and SLURM job scripts. The job scripts are unchanged and unsuitable for the out-of-the box use. However,  a user may need to adapt these scripts in order to perform processing or simulation before exploring data or generating figures in a Jupyter Notebook.
DOI: 10.22002/d1.1898
title: Rover Relocalization for Mars Sample Return by Virtual Template Synthesis and Matching

description: We consider the problem of rover relocalization in the context of the notional Mars Sample Return campaign. In this campaign, a rover (R1) needs to be capable of autonomously navigating and localizing itself within an area of approximately 50 x 50 m using reference images collected years earlier by another rover (R0). We propose a visual localizer that exhibits robustness to the relatively barren terrain that we expect to find in relevant areas, and to large lighting and viewpoint differences between R0 and R1. The localizer synthesizes partial renderings of a mesh built from reference R0 images and matches those to R1 images. We evaluate our method on a dataset totaling 2160 images covering the range of expected environmental conditions (terrain, lighting, approach angle). Experimental results show the effectiveness of our approach. This work informs the Mars Sample Return campaign on the choice of a site where Perseverance (R0) will place a set of sample tubes for future retrieval by another rover (R1).
description: A set of 2178 stereo images with calibration parameters and ground-truth pose provided by a motion capture system.
See included README.pdf file for file structure.
Cleared for release with URS number URS299897.
description: Related Publication:
Rover Relocalization for Mars Sample Return by Virtual Template Synthesis and Matching

Pham, Tu-Hoa JPL
eng
description: Contact person: Pham, Tu-Hoa tu-hoa.pham@jpl.nasa.gov
DOI: 10.22002/d1.1882
title: Synthetic multistability in mammalian cells

description: Data and code repository for paper "Synthetic multistability in mammalian cells"
DOI: 10.22002/d1.1658
title: Programming Boundary Deformation Patterns in Active Networks

description: This the  dataset for the Programming Boundary Deformation Patterns in Active Networks.
DOI: 10.22002/d1.1657
title: Persistent fluid flows defined by active matter boundaries

description: Experimental data for active matter (microtubule and kinesin motor) contraction and fluid flow. Hollow square cases.
DOI: 10.22002/d1.1441
title: Data related to Li et al. (2020). Current Biology.

description: This is data and codes related to Li et al. (2020). Functional Architecture of Motion Direction in the Mouse Superior Colliculus. Current Biology.
description: Related Publication:
Functional Architecture of Motion Direction in the Mouse Superior Colliculus

Li, Ya-tang Division of Biology and Biological Engineering, California Institute of Technology

Turan, Zeynep  Division of Biology and Biological Engineering, California Institute of Technology

Meister, Markus Division of Biology and Biological Engineering, California Institute of Technology

Current Biology
eng
description: Contact person: Meister, Markus meister@caltech.edu
DOI: 10.22002/d1.1303
title: Data for "In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription "

description: This dataset provides the raw and analyzed data as well as the code to recreate results reported in the paper "In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription". The dataset is organized based on the figures and figure panels of the paper, with the codes provided as Matlab and R scripts. Please contact the corresponding author for any questions or comments regarding the data, the code, the methods, or the reagents used here.
description: Related Publication:
In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription

Askary, Amjad  Caltech

Nature Biotechnology

https://doi.org/10.1038/s41587-019-0299-4
eng
DOI: 10.22002/d1.1222
title: Simulated radiance and retrieved variables (XCO2 and SIF) for the Orbiting Carbon Observatory-3 (OCO-3) Mission

description: This is a pre-launch simulated dataset for OCO-3 (Orbiting Carbon Observatory-3). Simulated satellite measurements from the ISS include the radiances observed in 3 bands (~765nm, 1.6 microns, and 2.1 microns) are provided along with the results from two cloud screening algorithms. The L2 retrievals of carbon dioxide dry air mole fraction (XCO2) and solar induced fluorescence (SIF) are included. The meteorology and surface properties used in the simulation are also archived.
description: Related Publication:
The OCO-3 mission; measurement objectives and expected performance based on one year of simulated data

Annmarie Eldering, Thomas E. Taylor, Christopher W. O'Dell, Ryan Pavlick Jet Propulsion Laboratory/ Caltech (Eldering and Pavlick) and Cooperative Institute for Research in theAtmosphere, Colorado State University (Taylor and O'Dell)

Atmospheric Measurement Techniques

2019-04-30

https://doi.org/10.5194/amt-12-2341-2019
eng
DOI: 10.22002/d1.1160
title: Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries

description: Data for Fig 1c,d,e,f:
Form*.tif - microscopy images of forming microtubule created by disks of various diameters.

Decay*.tif - microscopy images of decaying microtubule asters created by disks of various diameters.

Data for Fig 2b,c:
move*.tif - microscopy images of moving microtubule asters that follow a 25 um disk moving at various speeds.

Data for Fig 2e,f:
merge*.tif - microscopy images of merging microtubule asters created by 25 um disks separated by various distances.

Data for Fig 4c,d,e
FlowBar*.tif - microscopy images of microtubule 1D network creating flow for various activation lengths.

Data for Fig 4g
Flow*Shape*.tif - microscopy images of microtubule networks creating flow for various shaped patterns.
DOI: 10.22002/d1.963
title: Raw mass spectrometry Thermo data from "Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria"

description: This contains all Thermo .raw files.  The LacI target purification experiments were performed on a nanoflow LC system, EASY-nLC II coupled to a hybrid linear ion trap Orbitrap Classic mass spectrometer equipped with a Nanospray Flex Ion Source (Thermo Fisher Scientific). All other measurements were performed on a hybrid ion trap-Orbitrap Elite mass spectrometer (Thermo Fisher Scientific), which provided greater detection sensitivity and other fragmentation
techniques as described. The Orbitrap was operated in data-dependent acquisition mode to automatically alternate between a full scan (m/z=400–1,800) in the Orbitrap (resolution 120,000) and subsequent 5 MS/MS scans also acquired in Orbitrap with 15,000 resolution. The MS/MS spectra were acquired for the top 5 ions alternating between higher collision dissociation (HCD) and electron transfer dissociation (ETD) fragmentations that are well suited for higher charge peptides. Higher collision dissociation was performed at a normalized collision energy of 30% and electron transfer dissociation reaction time was set to 100 msec.
description: Related Publication:
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

Nathan Belliveau Caltech

Proceedings of the National Academy of Science

2018-05-04

https://doi.org/10.1073/pnas.1722055115
eng
description: Contact person: Rob Phillips phillips@pboc.caltech.edu
DOI: 10.22002/d1.962
title: Processed sequence data as .fastq from "Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria"

description: This contains all quality filtered sequence data as .fastq files (lac data are .fasta), with each sequencing bin as a unique file.
description: Related Publication:
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

Nathan Belliveau Caltech

Proceedings of the National Academy of Science

2018-05-04

https://doi.org/10.1073/pnas.1722055115
eng
description: Contact person: Rob Phillips phillips@pboc.caltech.edu
DOI: 10.22002/d1.950
title: Reconnection Stochasting Ion Heating Data and Scripts

description: The zip file contains .txt files which are simulation data sets used for verifying stochastic ion heating in magnetic reconnection. The .mat file contains Matlab data for test ion particle trajectories. These data are used in the .m Matlab scripts to plot the data.
DOI: 10.22002/d1.2046
title: OCO-3 B10 QTS Evaluation XCO2 Lite Files

description: These are lite files similar to the data products that OCO-3 delivers to NASA. This collection were produced from the testing data in B10 development (QTS), so they contain about 20% of the data record. For full documentation, look for the user's guide at the GES_DISC.
description: Contact person: Chris O'Dell Christopher.ODell@colostate.edu
DOI: 10.22002/d1.20229
title: The iNaturalist Localization 500 (iNatLoc500) Dataset

description: The iNaturalist Localization 500 (iNatLoc500) dataset. See the GitHub page (https://github.com/visipedia/inat_loc) for details.
description: Related Publication:
On Label Granularity and Object Localization

Cole, Elijah Caltech

Wilber, Kimberly Google

Van Horn, Grant Cornell University

Yang, Xuan Google

Fornoni, Marco Google

Perona, Pietro Caltech

Belongie, Serge University of Copenhagen

Howard, Andrew Google

Mac Aodha, Oisin University of Edinburgh

European Conference on Computer Vision (ECCV)

2022
eng
DOI: 10.22002/d1.20215
title: A synthetic protein-level neural network in mammalian cells

description: Raw data and simulation code for manuscript "A synthetic protein-level neural network in mammalian cells"
DOI: 10.22002/d1.20091
title: The Cost-Accuracy Trade-Off In Operator Learning With Neural Networks

description: The repo contains data for the paper 
@article{de2022cost,
  title={The Cost-Accuracy Trade-Off In Operator Learning With Neural Networks},
  author={De Hoop, Maarten and Huang, Daniel Zhengyu and Qian, Elizabeth and Stuart, Andrew M},
  journal={arXiv preprint arXiv:2203.13181},
  year={2022}
}.
 

The data set is generated to study different neural networks for AI + engineering. 
The data set contains simulation data for the following 4 benchmark problems
1) Navier stokes equation : NavierStokes_inputs.npy  & NavierStokes_outputs.npy.  
2) Helmholtz equation : Helmholtz_inputs.npy  & Helmholtz_outputs.npy.  
3) Structural mechanics equation : StructuralMechanics_inputs.npy  & StructuralMechanics_outputs.npy. 
4) Advection equation : Advection_inputs.npy  & Advection_outputs.npy.

The data are stored as nx by ny by ndata arrays (2d problems) or nx by ndata arrays (1d problems).
DOI: 10.22002/d1.2008
title: Cone penetration simulation data from LSDEM

description: LSDEM simulation data for "Modeling Breakage Mechanics of Granular Ice Analogs for Icy Body Spacecraft Interactions." Code requires open-mpi and compiler compatible with openMP. Refer to input and output methods for details on how input and output is organized.
DOI: 10.22002/d1.20060
title: Periodic spatial patterning with a single morphogen

description: Data and code repository for paper "Periodic spatial patterning with a single morphogen"
DOI: 10.22002/d1.1989
title: Fine-grained system identification of nonlinear neural circuits

description: Data used in Bagherian et al 2021, published at KDD. Code utilizing this dataset can be found at https://github.com/dbagherian/neural-sys-id

We study the problem of sparse nonlinear model recovery of high dimensional compositional functions.  Our study is motivated by emerging opportunities in neuroscience to recover fine-grained models of biological neural circuits using collected measurement data.  Guided by available domain knowledge in neuroscience, we explore conditions under which one can recover the underlying  biological circuit that generated the training data. 
Our results suggest insights of both theoretical and practical interests.
Most notably, we find that a sign constraint on each layer of weights is a sufficient condition for system recovery (in addition to other more standard sufficient conditions, which we establish both theoretically with an identifiability guarantee and empirically on simulated biological circuits.  We conclude with a case study on retinal ganglion cell circuits using data collected from mouse retina, showcasing the practical potential of this approach.
description: Related Publication:
Fine-grained system identification of nonlinear neural circuits

Dawna Bagherian Caltech

James Gornet Caltech

Jeremy Bernstein Caltech

Yu-Li Ni Caltech

Yisong Yue Caltech

Markus Meister Caltech

KDD '21

2021-08-14
eng
DOI: 10.22002/d1.1969
title: Dataset for "Measuring Terzaghi's effective stress by decoding force transmission in fluid-saturated granular media"

description: The dataset contains data for "Measuring Terzaghi's effective stress by decoding force transmission in fluid-saturated granular media".
description: 1. Raw data
This part includes the monochrome images of the particle packing taken during the loading and draining process, the external load applied by MTS, and water pressure measured by the pressure gauge. Other parameters such as particle sizes, modulus of the particles, and friction coefficients of particles are also included.

2. Sampled data
This section contains sampled images for Digital image correlation (DIC) and Granular element method (GEM) analysis. For each of the three experiments, the first image corresponds to the undrained state, while the last image corresponds to the completely drained state.

3. Results
This section contains data analysis results such as the inter-particle forces, positions of the particle centroids, and images of shear stress as well as force chains.
description: The data should be analyzed using Ncorr (for DIC) and GEM codes developed by Andrade et.al.
description: Related Publication:
Measuring Terzaghi's effective stress by decoding force transmission in fluid-saturated granular media

José E. Andarde Caltech

Zichen Gu Caltech

Siavash Monfared Caltech

Kimberley Mac Donald Caltech

Guruswami Ravichandran Caltech

Geophysical Research Letters
eng
DOI: 10.22002/d1.1871
title: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R2_04

description: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R2_04
DOI: 10.22002/d1.1870
title: Dataset cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R1_04

description: Dataset cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R1_04 from HiSeq 400
DOI: 10.22002/d1.1868
title: Dataset cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R2_03

description: Dataset cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R2_03 from HiSeq 4000
DOI: 10.22002/d1.1866
title: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R1_03

description: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R1_03 from HiSeq 4000
DOI: 10.22002/d1.1865
title: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R2_02

description: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R2_02 from HiSeq4000
DOI: 10.22002/d1.1864
title: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R1_02

description: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R1_02 from HiSeq 4000
DOI: 10.22002/d1.1863
title: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R2

description: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R2 from HiSeq 4000
DOI: 10.22002/d1.1860
title: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R1

description: cDNA Fastqs for Multiplexed Clytia Stimulation Experiment R1 from HiSeq 4000
DOI: 10.22002/d1.1855
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_08

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_08 from HiSeq 4000
DOI: 10.22002/d1.1851
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_06

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_06 from HiSeq 4000
DOI: 10.22002/d1.1850
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1_06

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1_06 from HiSeq 4000
DOI: 10.22002/d1.1849
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_05

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_05 from HiSeq 4000
DOI: 10.22002/d1.1847
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_04

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2 for HiSeq 4000
DOI: 10.22002/d1.1843
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2_02

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2 from HiSeq 4000
DOI: 10.22002/d1.1842
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1_02

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1 from HiSeq4000
DOI: 10.22002/d1.1841
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R2

description: cDNA Fastqs for Multiplexed Clytia Starvation Experiment from HiSeq4000
DOI: 10.22002/d1.1840
title: cDNA Fastqs for Multiplexed Clytia Starvation Experiment R1

description: cDNA fastqs for multiplexed Clytia starvation experiment from HiSeq 4000
DOI: 10.22002/d1.1617
title: Martian Slope Stability Data

description: This dataset provides landslide susceptibility data computed across a large part of Mars's surface. presented as a factor of safety (FOS). The factor of safety is the ratio produced by dividing the sum of forces resisting motion of a possible landslide surface by the sum of forces driving motion. These FOS values were computed using HRSC (High Resolution Stereo Camera) topographic data, and the Scoops3D software package. Full details of the method used will be provided in Roback & Ehlmann, 2020 (in prep)
description: Contact person: Bethany Ehlmann ehlmann@caltech.edu
DOI: 10.22002/d1.1451
title: Phenomenological model of motility by spatiotemporal modulation of active interactions

description: Raw data (in folder raw)
Analysis scripts used to analyze the data (in folder analysis)
Processed data for the figures (in folder figs)
README file giving more information to all data.
DOI: 10.22002/d1.1402
title: Microscopy and Growth data analyzed in "RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting"

description: This dataset contains all microscopy and growth data analyzed in the paper "RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting". It includes two smFISH datasets, four live imaging datasets, one csv file with growth data, and two csv files describing all strains and plasmids included in the image file names.
description: Related Publication:
RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting

Quintero-Cadena, Porfirio California Institute of Technology, Division of Biology and Biological Engineering

Lenstra, Tineke L The Netherlands Cancer Institute, Oncode Institute, Division of Gene Regulation, Amsterdam, the Netherlands

Sternberg, Paul W California Institute of Technology, Division of Biology and Biological Engineering

bioRxiv

2019-10-31

https://doi.org/10.1101/825299
eng
DOI: 10.22002/d1.1331
title: All MCMC inferences for expression shifts

description: All MCMC inferences for the expression shift for the Reg-Seq project .Each run has multiple chains and has 600000 total steps with a thinning factor of 60.