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103 documents, page 1 of 11

Web Tool for Navigating and Plotting SomaLogic ADAT Files

SOMAscan™ is a complex proteomic platform created by SomaLogic. Experimental data resulting from the assay is provided by SomaLogic in a proprietary text-based format called ADAT. This manuscript describes a user-friendly point and click open source, platform-independent software tool designed to be used for navigating and plotting data from an ADAT file. This tool was used either alone or in conjunction with other tools as a first pass analysis of the data on several different on-going resea...

GENESIS – The GENEric SImulation System for Modelling State Transitions

This software implements a discrete time Markov chain model, used to model transitions between states when the transition probabilities are known a priori. It is highly configurable; the user supplies two text files, a “state transition table” and a “config file”, to the Perl script genesis.pl. Given the content of these files, the script generates a set of C++ classes based on the State design pattern, and a main program, which can then be compiled and run. The C++ code generated is based on...

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

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...

Xanthos – A Global Hydrologic Model

Xanthos is an open-source hydrologic model, written in Python, designed to quantify and analyse global water availability. Xanthos simulates historical and future global water availability on a monthly time step at a spatial resolution of 0.5 geographic degrees. Xanthos was designed to be extensible and used by scientists that study global water supply and work with the Global Change Assessment Model (GCAM). Xanthos uses a user-defined configuration file to specify model inputs, outputs and p...

The Giles Ecosystem – Storage, Text Extraction, and OCR of Documents

In the digital humanities, there is a constant need to turn images and PDF files into plain text to apply analyses such as topic modelling, named entity recognition, and other techniques. However, although there exist different solutions to extract text embedded in PDF files or run OCR on images, they typically require additional training (for example, scholars have to learn how to use the command line) or are difficult to automate without programming skills. The Giles Ecosystem is a distribu...

GIFT-Grab: Real-time C++ and Python multi-channel video capture, processing and encoding API

GIFT-Grab is an open-source API for acquiring, processing and encoding video streams in real time. GIFT-Grab supports video acquisition using various frame-grabber hardware as well as from standard-compliant network streams and video files. The current GIFT-Grab release allows for multi-channel video acquisition and encoding at the maximum frame rate of supported hardware – 60 frames per second (fps). GIFT-Grab builds on well-established highly configurable multimedia libraries including FFmp...

Jug: Software for Parallel Reproducible Computation in Python

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...

VScope — Data Acquisition and Analysis for Voltage-sensitive Dye Imaging Using Multiple Cameras and Electrophysiology

VScope is a software package for the acquisition and analysis of data from multiple cameras as well as electrophysiology. Its main intended purpose is to record fluorescent traces from neurons loaded with voltage-sensitive dyes along with associated electrophysiology. VScope can record simultaneously from any number of cameras and frame rates can be set independently for each camera. VScope can also record synchronized electrophysiology traces and digital channels. VScope is mainly intended t...

ATUS-Commuting: Stata Code to Calculate Commuting Time in the American Time Use Survey

The American Time Use Survey (ATUS) provides extensive information on how Americans spend their time, and has been of particular interest to economists, sociologists, and other researchers. Researchers have sought to study commuting behavior using the ATUS, but its stock time use measures do not measure commuting satisfactorily. This package provides Stata code to implement the previously described trip tour methodology, constructing an appropriate measure of commuting from ATUS activity-leve...

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

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 ...