Code/Data for: Multi-omic Dissection of Oncogenically Active Epiproteomes Identifies Drivers of Proliferative and Invasive Breast Tumors
Contributors: John Wrobel
... R scripts and data files for analysis of TCGA and METABRIC datasets for Wrobel et al. (2019). Multi-omic Dissection of Oncogenically Active Epiproteomes Identifies Drivers of Proliferative and Invasive Breast Tumors. iScience. DOI: https://doi.org/10.1016/j.isci.2019.07.001
Contributors: Ping He, Charles Mader, Joaquim Martins, Kevin Maki
... This data set contains files and instructions to reproduce the results in the following paper: Ping He, Charles A. Mader, Joaquim R. R. A. Martins, and Kevin J. Maki. DAFoam: An open source adjoint framework for multidisciplinary design optimization with OpenFOAM. In this paper, we use an open source adjoint framework (DAFoam; see the link below) to perform optimizations that cover a wide range of disciplines (aerodynamics, heat transfer, structures, and radiation), configurations (wings, aircraft, turbine cooling channels, compressor blades), and conditions (incompressible, subsonic, and transonic). The following files are the meshes and flow and optimization configurations to reproduce the optimization results. - UAV_Aero_Opt.tar.gz: Multipoint aerodynamic optimization for a UAV wing at low speed. - DPW4_Aero_Opt.tar.gz: Trimmed aerodynamic optimization for a transonic aircraft configuration. - UBend_AeroTherm_Opt.tar.gz: Aerothermal optimization for a turbine internal cooling channel. - Rotor67_AeroStruct_Opt.tar.gz: Aerostructural optimization for an axial compressor rotor. The Code_Version.txt file contains the required codes to reproduce the results, including their links and GIT versions.
Data for: Dose response analysis program (DREAP): a user-friendly program for the analyses of radiation-induced biological responses utilizing established deterministic models at cell population and organ scales.
Contributors: Kyung-Nam Lee
... DREAP stands for dose response analysis program, a user-friendly program for analysis of radiation-induced biological responses such as survival fraction, relative biological effectiveness, normal tissue complication probability, and tumor control probability. 1. DREAP_source_code.zip: including m-files 2. How to execute DREAP: explaining how to use and some requirements of the DREAP at first 3. sample_input.zip: sample input files 4. sample_output.zip: sample output files from the DREAP 5. Validation study data: results of validation study on accuracy and speed
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Contributors: Denis Mikryukov
... Here we store the coefficients of the planetary disturbing function in computer-readable form. These were obtained by Maxima computer algebra system. The method is described by Laskar and Robutel (CMDA, 62, 193-217, 1995). We should note that our coefficients of secular Hamiltonian up to degree 4 coincide with those presented by Laskar and Robutel (see Section 7, CMDA, 62, 193-217, 1995). Therefore we hope that our expansions are error free. We plan to provide more thorough and complete comments on all of these data in the near future.
Sensory-to-category transformation via dynamic reorganization of ensemble structures in mouse auditory cortex. Xin et al
Contributors: Ning-long Xu
... Dataset for the study by Xin et al., "Sensory-to-category transformation via dynamic reorganization of ensemble structures in mouse auditory cortex." 1. The folder "Behavior Dataset for Figure 1" contains the behavioral data that can be used to reproduce the results in Figure 1 2. The folder "Dataset for Figures 2, 4, 6, 7, 8" contains 21 sessions calcium imaging data acquired during behavioral task. All the raw data are included in the folder and each session was saved as a separate file. Please refer to the note before data loading. 3. The folder "Dataset for Figure 3" contains calcium imaging data that can be used to reproduce the results in Figure 3. 4. The folder "Dataset for Figure 5" contains calcium imaging data that can be used to reproduce the results in Figure 5, which shows results of the experiments with two different behavior contexts. The subfolder "4_16Sess" contains data for the 4-16kHz imaging sessions. The subfolder "7_28Sess" contains data for for 7-28kHz imaging session. Files within different folders but sharing same file names (e.g. "Sess1_data_save.mat" contains data from session 1) are for the same imaging field of view.
Contributors: Marsel Rabaev, Handy Pratama, Ka Ching Chan
... This data set was generated using Arena Simulation
Contributors: Damian Matuszewski, Carolina Wählby, Jordi Carreras-Puigvert, Ida-Maria Sintorn
... PopulationProfiler – is light-weight cross-platform open-source tool for data analysis in image-based screening experiments. The main idea is to reduce per-cell measurements to per-well distributions, each represented by a histogram. These can be optionally further reduced to sub-type counts based on gating (setting bin ranges) of known control distributions and local adjustments to histogram shape. Such analysis is necessary in a wide variety of applications, e.g. DNA damage assessment using foci intensity distributions, assessment of cell type specific markers, and cell cycle analysis. The software imports measurements from a simple text file, visualizes population distributions in a compact and comprehensive way, and can create gates for subpopulation classes based on control samples. The simple graphical user interface (GUI) allows selection of multiple csv files with image-based screening data. Each file is treated as a separate plate (i.e. independent experiment) with rows representing cell measurements. One measurement is processed at a time and cells are grouped based on well labels. The measurement is selected by the user from a drop-down list created from the csv file header (first row). The GUI also allows selection of control wells based on the treatment labels. If such labels are not available, the user can select control wells manually. The corresponding data is pooled and stored as a separate record in the output csv file. PopulationProfiler thereafter calculates and displays the distribution of the selected measurement as a histogram for each well. A vector representation of each well’s histogram is saved in the output file, and can be used as input for e.g., cluster analysis, elsewhere. The cell count for each well is also saved as a measure of statistical relevance of population effects. Cite this software as: Matuszewski, D.J., Wählby, C., Puigvert, J.C., Sintorn, I.-M. (2016) PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data. PloS one, 11(3), e0151554. The Python source code, sample data and user manual are available free of charge.
Contributors: Laurent Remusat
... Dataset from heating experiment on Orgueil IOM. NanoSIMS, FTIR, XANES and Raman data.
Contributors: juan Zuluaga
... Project Objectives In the field of construction there are some operators called crane helpers which indicate to the crane operator through some hand signals what he has to do and of course there are some other operators that work on other activities But they have to be aware about the crane activities so they constantly must see the signals performed by the crane helpers. And all these activities represent an imminent risk and not only for the crane operator but also for the people close to him The main point of our project is create an application based on activity recognition through smartphone sensors to detect the signal performed by a human operator or a crane helper through a machine learning algorithm. Sensors used: Two cell phones are used, of which the accelerometer and the gyroscope are used. Location of the sensors: The sensors are located in the hands and one at the height of the bicep Collection mechanism: For the collection of the data, five series were made, in each of the series 6 signals were made defined for the experiment, for the exercise 5 people were used.
Data for: An approach to fabricate high performance cooler with nearly ideal emissive spectrum for above ambient radiative cooling
Contributors: YuXiang Zheng
... These are the research data files of "An approach to fabricate high performance cooler with nearly ideal emissive spectrum for above ambient radiative cooling".