Rice Research Data

Permanent URI for this collection

https://hdl.handle.net/1911/77660

This multidisciplinary collection contains research datasets created by members of the Rice University community. Additional information about standards and support for curating research data can be found at the Research Data Services webpage.

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Browsing Rice Research Data by Title

Now showing 1 - 20 of 26
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    Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces
    (Rice University, 2021-10-27) Ameruoso, Andrea; Department of Biosciences
    The rise of antibiotic-resistant bacteria represents a major threat to global health, creating an urgent need to discover new antibiotics. Natural products derived from the genus Streptomyces represent a rich and diverse repertoire of chemical molecules from which new antibiotics are likely to be found. However, a major challenge is that the biosynthetic gene clusters (BGCs) responsible for natural product synthesis are often poorly expressed under laboratory culturing conditions, thus preventing isolation and screening of novel chemicals. To address this, we describe a novel approach to activate silent BGCs through rewiring endogenous regulation using synthetic gene regulators based upon CRISPR-Cas. First, we create CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) systems that allow for highly programmable and effective gene repression and activation in Streptomyces. We then harness these tools to activate a silent BGC through perturbing its endogenous regulatory network. Together, this work advances the synthetic regulatory toolbox for Streptomyces and facilitates the programmable activation of silent BGCs for novel chemical discovery.
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    Analysis of Vapor-Liquid Coexistence in Colloidal Systems
    (Rice University, 2022-02-15) Biswal, Sibani Lisa; Joshi, Kedar; Chemical and Biomolecular Engineering
    This data set created in 2020 describes analysis of a superparamagnetic colloidal system forced to phase separate into a liquid-vapor coexistence. The liquid clusters and bulk particles are analyzed and modeled with classical thermodynamics.
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    Can Deep Learning Predict Complete Ruptures in Numerical Megathrust Faults?
    (Rice University, 2021-08-18) Blank, David; Morgan, Julia; Earth, Environmental and Planetary Sciences
    This dataset accompanies the paper, "Can Deep Learning Predict Complete Ruptures in Numerical Megathrust Faults?". The directory contains full python codes used to create Convolutional Neural Networks and Long Short Term Memory Recurrent Neural Networks, along with the raw data used for training, testing, and validation. Since stochastic initialization of weights in the training process will result in slightly different parameterization of models trained with identical hyperparameters, we have also included the trained models we presented in the paper with this dataset as well.
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    College Student Mental Health and Personal Impact of the COVID-19 Pandemic
    (Rice University, 2024-03-08) Nguyen, Celine; Poplin, Tate; Chen, Ying; Lesane-Brown, Chase L.; Psychological Sciences
    Undergraduate college students (N = 96) from a private southern university in the United States completed an online self-report survey through Qualtrics from early April 2021 to early May 2021. Students reported their internalizing, externalizing, and attention symptoms, personal impact of COVID-19 on their lives, fear of COVID-19, and vaccination status. Recruitment occurred over email listservs and SONA systems. Participants utilizing SONA, an online system used to manage the psychology undergraduate subject pool, received research credit for participation in this study. The study was approved by the university's Institutional Review Board. Participants were required to be at least 18 years of age. A total of 99 participants enrolled in the study, but three were excluded from analysis due to missing data. A site license was obtained to use the Brief Problem Monitor (BPM 18-59).
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    Data for the article: Pore fluid pressures and strength contrasts maintain frontal fault activity, northern Hikurangi
    (Rice University, 2020-07-29) French, Melodie; This work was funded by NSF EAR 1759127 to Melodie French and USSSP-IODP Subaward 66B(GG009393) 309 of NSF Award OCE1450528 to Julia Morgan.; Earth, Environmental, and Planetary Sciences
    This data set archives the experimental rock deformation data reported in "Pore fluid pressures and strength contrasts maintain frontal fault activity, northern Hikurangi". In this paper, we present the results of five deformation experiments conducted on samples recovered during the Intergrated Ocean Drilling Program Expedition 375.
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    Experimental and modeling data used in Yeung et al., Extreme enrichment in atmospheric 15N15N. Sci. Adv. 3, eaao6741 (2017)
    (Rice University, 2017) Yeung, Laurence Y.; Young, Edward D.; National Science Foundation (OCE-1533501, EAR-1349182, EAR-1348935, EAR-1530306), Deep Carbon Observatory, Department of Energy (BER DE-FC02-07ER64494); Earth Science
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    Grain Boundary Dynamics
    (Rice University, 2022-03-14) Biswal, Sibani Lisa; Lobmeyer, Dana; Chemical and Biomolecular Engineering
    The purpose of this study is to understand the dynamics of grain boundaries in colloidal crystals. An interfacial shear results in constant reorganization of the grain boundaries.
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    Herschel Observatory Sweep Data and Stellarium Plugin Database
    (Rice University, 2021) Mulligan, John; Center for Research Computing
    This zip file relates to the deep-space astronomical sweeps of Caroline and William Herschel, conducted in Slough, England. It was hand-transcribed from records at the Royal Astronomical Society, and could be improved upon: corrections, expansions to include missing records or John Herschel's sweeps, for instance. It contains: the transcriptions of the parameters for 1,335 sweeps, in csv format -- python scripts for -- importing this csv data into an sqlite database, useful for tracking simulations and coordinating parallel processes -- transforming this csv file into an .ini file readable by: -- a plugin written in QT5 and C++ for Stellarium 0.90, which -- ingests this .ini file -- renders sweeps projected on the night sky -- renders real-time simulations of the sweep as seen by the observer (William) -- a readme file fully documenting the work as well as installation instructions
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    Looking for Bachelors in American Silent Film
    (Rice University, 2015) Spiro, Lisa; Humanities
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    Mathematica Programs for "Automation: Wage Stagnation and Inequality" [Dataset]
    (Rice University, 2020) Curl, Robert F.; Brito, Dagobert L.; Economics
    This describes the calculations made to determine the effect of automation a developed economy and published as a working paper for Baker Institute of Public Policy. It includes two main types of calculation: 1. two folders with “workup” in the title containing the conversion of the works of others into the parameters needed for the other calculations. 2. three folders containing programs and results of calculations. The computer language chosen for all calculations is Mathematica. The paper itself is published by the Baker Institute.
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    Mechanical Strength of Water-Saturated Solnhofen Limestone at Elevated Temperatures
    (Rice University, 2021-10-07) French, Melodie; Zhu, Wenlu; Xiao, Xiaohui; Evans, Brian; Prior, David; National Science Foundation; U.S. Geological Survey; Earth, Environmental and Planetary Sciences
    The data is a record of the stress and strain during experimental deformation of Solnhofen limestone across its brittle (localized deformation) to ductile (distributed deformation) transition. We conducted conventional triaxial compression tests on both water-saturated and nominally dry cores of Solnhofen at temperatures up to 200 Celsius and effective confining pressures up to 350 MPa to evaluate the roles of pore water and temperature on the deformation mechanisms of low-porosity limestone at conditions of the upper crust.
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    Mixed heating velocity scaling input files
    (Rice University, 2020-09-29) Lenardic, Adrian; Seales, Johnny; Moore, William B.; Weller, Matthew B.; Earth, Environmental, and Planetary Sciences
    The input files were used to explore the effects of mixed heating on convective velocity scaling
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    OW1 Data InOut
    (Rice University, 2020-08-20) Seales, Johnny; Lenardic, Adrian; Earth, Environmental, and Planetary Sciences
    The parameter inputs and data outputs provided herein were used to establish the hypothesis that changes in deep water cycling lead to a multi-stage cooling of the Earth.
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    Parallelizing Interproscan with SLURM
    (Rice University, 2023-06-27) Fulk, Emily M.; Goldman, Annelise L.; Momper, Lily; Heider, Clinton; Mulligan, John; Osburn, Magdalena; Masiello, Caroline A.; Silberg, Jonathan J.; Systems, Synthetic, and Physical Biology
    This repository contains code to facilitate analysis of large numbers of proteins by Interproscan with minimum user oversight and efficient use of computational resources. It provides templates for parallelizing Interproscan with SLURM on the Rice NOTS computing cluster, following a high-throughput computing model.
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    Rational engineering of a modular bacterial CRISPR-Cas activation platform with expanded target range
    (Rice University, 2020) Chappell, James; Department of BioSciences
    CRISPR-Cas activator (CRISPRa) systems that selectively turn on transcription of a target gene are a potentially transformative technology for programming cellular function. While in eukaryotes versatile CRISPRa systems exist, in bacteria these systems suffer from a limited ability to activate different genes due to strict distance-dependent requirements of functional target binding sites, and require greater customization to optimize performance in different genetic and cellular contexts. To address this, we apply a rational protein engineering approach to create a new CRISPRa platform that is highly modular to allow for easy customization and has increased targeting flexibility through harnessing engineered Cas proteins. We first demonstrate that transcription activation domains can be recruited by CRISPR-Cas through noncovalent protein-protein interactions, which allows each component to be encoded on separate and easily interchangeable plasmid elements. We then exploit this modularity to rapidly screen a library of different activation domains, creating new systems with distinct regulatory properties. Furthermore, we demonstrate that by harnessing a library of circularly permuted Cas proteins, we can create CRISPRa systems that have different target binding site requirements, which together, allow for expanded target range.
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    Research Data Services and Center for Research Computing Needs Assessment
    (Rice University, 2024-03-25) Barber, Catherine R.; Spiro, Lisa; Cragin, Melissa; Smith, Sean; The Center for Research Computing; Fondren Library Research Data Services
    This needs assessment involved surveying the Rice University research community to determine key areas of current and projected need related to data and research computing. The results will be used to inform services and support provided by Fondren Library, Research Data Services, and the Center for Research Computing. Although the results of the needs assessment may not generalize outside of Rice, we also hope to learn about the opportunities for interdisciplinary collaboration between the library and research computing and to share those insights with the greater research community. Data were collected through an online survey administered to all faculty, research staff, and graduate students at Rice.
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    Shakespeare Passages Recommendation System
    (Rice University) Mulligan, John; Center for Research Computing
    This repository holds the code for an intertextual recommendation system that links passages in the Shakespearean dramatic corpus (as digitized by Folger) to one another based entirely on scholarly citations/quotations (as identified by JSTOR Labs in their collection of digitized works, and made available in what was called their Matchmaker API).
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    Simple ultraviolet microscope using off-the-shelf components for point-of-care diagnostics.
    (Rice University, 2019-02-12) Wong, Cindy; Bioengineering
    At the primary care setting, where there are often no or minimal laboratories, examinations often consist of self-testing and rapid diagnostics. Because of this, medical devices must be simple, robust, and easy to operate. To address these concerns, an alternate fluorescence microscope design uses ultraviolet (UV) excitation, since fluorescent dyes that are excitable in the visible region are also excitable by UV. This may allow for the removal of typical excitation, emission, and dichroic filters as optical components absorb UV wavelengths and UV is not detected by silicon based detectors. Additionally, UV has a very low penetration into samples, which may allow for controlling the depth of excitation, and thus the imaging volume. Based on these ideas, we developed a simple fluorescence microscope built completely from off-the-shelf components that uses UV to image fluorescently stained samples. The simple opto-mechanical design of the system may allow it to be more compact and easy to use, as well as decrease the overall cost of the diagnostic device. For biological validation, we imaged whole blood stained with acridine orange and performed a two-part white blood cell differential count.