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complete genome.fas The sequence of complete genome of the Phauda flammans. We checked by manual proofreading according to its relative species. tree.fas The dateset is what we used in the tree reconstruction.
Data Types:
  • Sequencing Data
  • Dataset
The dataset consists of 1,431 UAV-acquired construction site images and 8,601 captions describing the regions of the images. It contains five types of text information on construction resources, as well as their identification and position information.
Data Types:
  • Dataset
  • File Set
In vitro electrophysiology of iPSC-derived cortical neural networks (healthy vs. induced proteinopathy) using customised microfluidic chips interfaced with 60-electrode microelectrode arrays. The recordings were obtained using the M2100 Multichannel Systems platform.
Data Types:
  • Document
  • Dataset
  • File Set
In vitro electrophysiology of iPSC-derived cortical neural networks (healthy vs. induced proteinopathy) using customised microfluidic chips interfaced with 60-electrode microelectrode arrays. The recordings were obtained using the M2100 Multichannel Systems platform.
Data Types:
  • Document
  • Dataset
  • File Set
The version 3.01 of ELMAG, a Monte Carlo program for the simulation of electromagnetic cascades initiated by high-energy photons and electrons interacting with extragalactic background light (EBL), is presented. Pair production and inverse Compton scattering on EBL photons as well as synchrotron losses are implemented using weighted sampling of the cascade development. New features include, among others, the implementation of turbulent extragalactic magnetic fields and the calculation of three-dimensional electron and positron trajectories, solving the Lorentz force equation. As final result of the three-dimensional simulations, the program provides two-dimensional source images as function of the energy and the time delay of secondary cascade particles.
Data Types:
  • Dataset
  • File Set
MiTMoJCo (Microscopic Tunneling Model for Josephson Contacts) is C code which aims to assist modeling of superconducting Josephson contacts based on the microscopic tunneling theory. The code offers implementation of a computationally demanding part of this calculation, that is evaluation of superconducting pair and quasiparticle tunnel currents from the given tunnel current amplitudes (TCAs) which characterize the junction material. MiTMoJCo comes with a library of pre-calculated TCAs for frequently used Nb-AlOx-Nb and Nb-AlN-NbN junctions, a Python module for developing custom TCAs, supplementary optimum filtration module for extraction of a constant component of a sinusoidal signal and examples of modeling few common cases of superconducting Josephson contacts.
Data Types:
  • Dataset
  • File Set
We present JeLLyFysh-Version1.0, an open-source Python application for event-chain Monte Carlo (ECMC), an event-driven irreversible Markov-chain Monte Carlo algorithm for classical N-body simulations in statistical mechanics, biophysics and electrochemistry. The application’s architecture mirrors the mathematical formulation of ECMC. Local potentials, long-ranged Coulomb interactions and multi-body bending potentials are covered, as well as bounding potentials and cell systems including the cell-veto algorithm. Configuration files illustrate a number of specific implementations for interacting atoms, dipoles, and water molecules.
Data Types:
  • Dataset
  • File Set
Variant calls for the in vivo and in vitro studies of virus diversity and genetic stability reported in the manuscript, "A new live-attenuated polio vaccine constructed by rational design improves safety by preventing reversion to virulence", by Yeh, et al.
Data Types:
  • Sequencing Data
  • Tabular Data
  • Dataset
Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine.
Data Types:
  • Document
  • Dataset
  • File Set
This files contains all codes, data as well as descriptions of its use accompanied with reproducible examples.
Data Types:
  • Dataset
  • File Set
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