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  • Simulation Data associated with the paper: Supercharging enables organized assembly of synthetic biomolecules

    Work
    Creator: Ramasubramani, Vyas
    Description: The goal of the work is to elucidate the stability of a complex experimentally observed structure of proteins. We found that supercharged GFP molecules spontaneously assemble into a complex 16-mer structure that we term a protomer, and that under the right conditions an even larger assembly is observed. The protomer structure is very well defined, and we performed simulations to try and understand the mechanics underlying its behavior. In particular, we focused on understanding the role of electrostatics in this system and how varying salt concentrations would alter the stability of the structure, with the ultimate goal of predicting the effects of various mutations on the stability of the structure. There are two separate projects included in this repository, but the two are closely linked. One, the candidate_structures folder, contains the atomistic outputs used to generate coarse-grained configurations. The actual coarse-grained simulations are in the rigid_protein folder, which pulls the atomistic coordinates from the other folder. All data is managed by signac and lives in the workspace directories, which contain various folders corresponding to different parameter combinations. The parameters associated with a given folder are stored in the signac_statepoint.json files within each subdirectory. The atomistic data uses experimentally determined protein structures as a starting point; all of these are stored in the ConfigFiles folder. The primary output is the topology files generated from the PDBs by GROMACS; these topologies are then used to parametrize the Monte Carlo simulations. In some cases, atomistic simulations were actually run as well, and the outputs are stored alongside the topology files. In the rigid_protein folder, the ConfigFiles folder contains MSMS, the software used to generate polyhedral representations of proteins from the PDBs in the candidate_structures folder. All of the actual polyhedral structures are also stored in the ConfigFiles folder. The actual simulation trajectories are stored as general simulation data (GSD) files within each subdirectory of the workspace, along with a single .pos file that contains the shape definition of the (nonconvex) polyhedron used to represent a protein. The logged quantities, such as energies and MC move sizes, are stored in .log files. The logic for the simulations in the candidate_structures project is in the Python scripts project.py, operations.py, and scripts/init.py. The rigid_protein folder also includes the notebooks directory, which contains Jupyter notebooks used to perform analyses, as well as the Python scripts used to actually perform the simulations and manage the data space. In particular, the project.py, operations.py and scripts/init.py scripts contain most of the logic associated with the simulations.
  • Belt fit Manikin Representing a Two-Year-Old Child

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    Creator: Reed, Matthew P., Boyle, K.
    Description: This is the first physical anthropomorphic test device to be based both on statistical body shape models as well as 3D printing.
  • Dataset of live-cell movies of single PolC-PAmCherry molecules in Bacillus subtilis cells with high and low fluorescent backgrounds.

    Work
    Creator: Isaacoff, Benjamin P., Li, Yilai, Lee, Stephen A., and Biteen, Julie S.
    Description: This is the experimental data referenced in our manuscript entitled “SMALL-LABS: An algorithm for measuring single molecule intensity and position in the presence of obscuring backgrounds .” These live-cell single-molecule imaging movies were used as a test of the SMALL-LABS single-molecule image analysis algorithm. The dataset comprises two movies; each one is provided both as a .tif stack and as an .avi file. The movie called “low_bg” has a standard low background, and the movie called “high_bg” includes a high fluorescent background produced by an external 488-nm laser.
  • Downloaded IAAF Sprint Results in all Heats for 2004 - 2016 Olympics for both Men and Women

    Work
    Creator: Mirshams Shahshahani, Payam
    Description: Investigating minimum human reaction times is often confounded by the motivation, training, and state of arousal of the subjects. We used the reaction times of athletes competing in the shorter sprint events in the Athletics competitions in recent Olympics (2004-2016) to determine minimum human reaction times because there's little question as to their motivation, training, or state of arousal. The reaction times of sprinters however are only available on the IAAF web page for each individual heat, in each event, at each Olympic. Therefore we compiled all these data into two separate excel sheets which can be used for further analyses.
  • Multi-Stage Attack Graph Security Games: Heuristic Strategies, with Empirical Game-Theoretic Analysis --- Dataset

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    Creator: Nguyen, Thanh H., Wright, Mason, Wellman, Michael P., and Singh, Satinder
    Description: In this work , we study the problem of allocating limited security countermeasures to protect network data from cyber-attacks, for scenarios modeled by Bayesian attack graphs. We consider multi-stage interactions between a network administrator and cybercriminals, formulated as a security game. We propose parameterized heuristic strategies for the attacker and defender and provide detailed analysis of their time complexity. Our heuristics exploit the topological structure of attack graphs and employ sampling methods to overcome the computational complexity in predicting opponent actions. Due to the complexity of the game, we employ a simulation-based approach and perform empirical game analysis over an enumerated set of heuristic strategies. Finally, we conduct experiments in various game settings to evaluate the performance of our heuristics in defending networks, in a manner that is robust to uncertainty about the security environment.
  • Supporting data and scripts for the paper "Variability in the location of High Frequency Oscillations during prolonged intracranial EEG recordings"

    Work
    Creator: Gliske, Stephen V and Stacey, William C
    Description: This data is part of a large program to translate detection and interpretation of HFOs into clinical use. A zip file is included which contains hfo detections, metadata, and Matlab scripts. The matlab scripts analyze this input data and produce figures as in the referenced paper (note: the blind source separation method is stochastic, and so the figures may not be exactly the same). A file "README.txt" provides more detail about each individual file within the zip file.
  • Magneto-inductive sensor characterization data

    Work
    Creator: Regoli, Leonardo H.
    Description: The data contained in the file comprises those collected during the characterization of the sensor as described in the article "Investigation of a low-cost magneto-inductive magnetometer for space science applications" (cited below). This includes: , - Resolution , - Stability , - Linearity , - Frequency response, and Curation note: Addendum to README added June 1, 2018 regarding several files not used in preparing the manuscript with which the dataset is associated.
  • TCCIII Near-Wall Flow

    Work
    Creator: Sick, Volker , Reuss, David L, and Greene, Mark L
    Description: This archive contains data files from spark-ignited homogeneous combustion internal combustion engine experiments. Included are high-resolution two-dimensional two-component velocity fields acquired at two 5 x 6 mm regions, one near the head and one near the piston. Crank angle resolved heat flux measurements were made at a third location in the head. The engine was operated at 40 kPa, 500 and 1300 RPM, motor and fired. Included are in-cylinder pressure measurements, external pressure and temperature data, as well as details on the geometry of the optical engine to enable setups of simulation configurations.
  • Data for "Using sensor data to dynamically map large-scale models to site-scale forecasts: A case study using the National Water Model"

    Work
    Creator: Fries, Kevin J
    Description: This data is in support of the publication in review "Using sensor data to dynamically map large-scale models to site-scale forecasts: A case study using the National Water Model". It is all the raw data extracted from the NWM flow forecasts for Iowa and the IFIS stage readings. For the NWM data, each date has it's own tab-delimited file with columns being the time (hrs) and rows being the NHD site. For the IFIS gages, each tab delimited file is for a single site for the period of record.
  • Computer Data from Ross Thesis

    Work
    Creator: Mathews, Elizabeth and Verhoff, Frank
    Description: Each pdf is an electronic version of the paper output for each experiment. Each text file is the electronic version of the data on the computer cards for each experiment. These text files are directly readable by Excel. Once in Excel, the data can be manipulated as desired. Additional information is in the theses.