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109 documents, page 1 of 11

ConfBuster: Open-Source Tools for Macrocycle Conformational Search and Analysis

Barbeau, Xavier; Vincent, Antony T.; Lagüe, Patrick (2018)
Macrocycles are cyclic macromolecules that have gained an increased interest in drug development. To our knowledge, the current bioinformatics tools that are available to investigate and predict macrocycles 3D conformations are limited in their availability. In this paper, we introduce ConfBuster, a suite of tools written in Python with the goal of sampling the lower energy conformations of macrocycles. The suite also includes tools for the analysis and visualisation of the conformational sea...

PyPSA: Python for Power System Analysis

Brown, Thomas; Hörsch, Jonas; Schlachtberger, David (2018)
Python for Power System Analysis (PyPSA) is a free software toolbox for simulating and optimising modern electrical power systems over multiple periods. PyPSA includes models for conventional generators with unit commitment, variable renewable generation, storage units, coupling to other energy sectors, and mixed alternating and direct current networks. It is designed to be easily extensible and to scale well with large networks and long time series. In this paper the basic functionality of P...

An Octave/MATLAB® Interface for Rapid Processing of SMOS L1C Full Polarization Brightness Temperature

Saavedra, Pablo; Simmer, Clemens (2018)
A tool to process the SMOS microwave radiometer level 1C polarized brightness temperatures data product has been developed. The SMOS L1C science product contains the dual and full (Stokes vector) polarization brightness temperatures at L-band for multiple incidence angles. In order to use the L1C product, the measurements are processed by a number of procedures including radio frequency interference (RFI) filters, conversion of the polarization plane from the antenna (X- & Y-pol) to the E...

Quandle and Biquandle Homology Calculation in R

Fenn, Roger; Wenzel, Ansgar (2018)
In knot theory several knot invariants have been found over the last decades. This paper concerns itself with invariants of several of those invariants, namely the Homology of racks, quandles, biracks and biquandles. The software described in this paper calculates the rack, quandle and degenerate homology groups of racks and biracks. It works for any rack/quandle with finite elements where there are homology coefficients in Zk. The up and down actions can be given either as a function of the ...

A Random-Dot Kinematogram for Web-Based Vision Research

Rajananda, Sivananda; Lau, Hakwan; Odegaard, Brian (2018)
Web-based experiments using visual stimuli have become increasingly common in recent years, but many frequently-used stimuli in vision research have yet to be developed for online platforms. Here, we introduce the first open access random-dot kinematogram (RDK) for use in web browsers. This fully customizable RDK offers options to implement several different types of noise (random position, random walk, random direction) and parameters to control aperture shape, coherence level, the number of...

ImageSURF: An ImageJ Plugin for Batch Pixel-Based Image Segmentation Using Random Forests

O'Mara, Aidan; King, Anna E.; Vickers, James C.; Kirkcaldie, Matthew T. K. (2017)
Image segmentation is a necessary step in automated quantitative imaging. ImageSURF is a macro-compatible ImageJ2/FIJI plugin for pixel-based image segmentation that considers a range of image derivatives to train pixel classifiers which are then applied to image sets of any size to produce segmentations without bias in a consistent, transparent and reproducible manner. The plugin is available from ImageJ update site http://sites.imagej.net/ImageSURF/ and source code from https://github.com/o...

pyObs: Open-Source Software for Computer-Assisted Behavioral Observation Coding

Griffin, William A. (2018)
pyObs is a computer-assisted behavioral observation coding system used to record social interaction among children in classroom and playground settings. Its flexible architecture allows it to be useful for capturing behaviors occurring in settings that vary across age group or context. Written in Python, pyObs has a cross-platform GUI using drop down menus and check boxes along with audio and visual cues that increase coder reliability. Time-stamped GIS maps record subject location. And data ...

Jug: Software for Parallel Reproducible Computation in Python

Coelho, Luis Pedro (2017)
As computational pipelines become a bigger part of science, it is important to ensure that the results are reproducible, a concern which has come to the fore in recent years. All developed software should be able to be run automatically without any user intervention.In addition to being valuable to the wider community, which may wish to reproduce or extend a published analysis, reproducible research practices allow for better control over the project by the original authors themselves. For ex...

DSCImageCalc – Software for Determining Similarity Coefficients for the Analysis of Image Segmentations

Lawton, Tom (2017)
DSCImageCalc is free software for calculating similarity coefficients on segmented images. It is written in Visual BASIC .NET and is available at: https://doi.org/10.6084/m9.figshare.894428.It presently calculates Sørensen-Dice Coefficient, Jaccard Coefficient, Proportional Agreement, Cohen’s Kappa, Goodman & Kruskal’s Gamma, and Rogot-Goldberg Agreement. It also calculates segment centroids and the distance between them.Whilst it was originally designed for calculating Dice coefficients ...

OpenOpticalFlow: An Open Source Program for Extraction of Velocity Fields from Flow Visualization Images

Liu, Tianshu (2017)
This paper describes OpenOpticalFlow, an open source optical flow program in Matlab for extraction of high-resolution velocity fields from various flow visualization images. This program is a useful tool for researchers to use the optical flow method in various flow measurements. The principles of the optical flow method are concisely described, including the physics-based optical flow equation, the variational solution, and errors. The central part of this paper is the descriptions of the ma...