JournalTOCs

Journal of Open Research Software
Number of Followers: 4

This is an Open Access Journal

Open Access journal
ISSN (Online) 2049-9647
Published by Ubiquity Press Limited

[40 journals]

Plots.jl – A User Extendable Plotting API for the Julia
Programming Language
- Abstract: There are many excellent plotting libraries. Each excels at a specific use case: one is particularly suited for creating printable 2D figures for publication, another for generating interactive 3D graphics, while a third may have excellent LATEX integration or be ideal for creating dashboards on the web. The aim of Plots.jl is to enable the user to use the same syntax to interact with a range of different plotting libraries, making it possible to change the library that does the actual plotting (the backend) without needing to touch the code that creates the content – and without having to learn multiple application programming interfaces (API). This is achieved by separating the specification of the plot from the implementation of the graphical backend. This plot specification is extendable by a recipe system that allows package authors and users to create new types of plots, as well as to specify how to plot any type of object (e.g. a statistical model, a map, a phylogenetic tree or the solution to a system of differential equations) without depending on the Plots.jl package. This design supports a modular ecosystem structure for plotting and yields a high code reuse potential across the entire Julia package ecosystem. Plots.jl is publicly available at https://github.com/JuliaPlots/Plots.jl. Published on 2023-02-14 12:39:42
pyHomogeneity: A Python Package for Homogeneity Test of Time Series Data
- Abstract: The pyHomogeneity package is a pure python package for performing homogeneity tests. The homogeneity test is applied to detect one (or more) change-point/breakpoint in the time series or sequential data. It is one of the essential tests for time series data (e.g. financial time series, hydrology, climate study, etc.). However, till now, there is no Python package available for the homogeneity test. This is where the pyHomogeneity package comes in. Currently, Pettitt’s Test, four variants of Buishand’s Test, and SNHT Test can be performed using this package. The package is freely available for public use. Published on 2023-02-14 12:28:21
Fan-Slicer: A Pycuda Package for Fast Reslicing of Ultrasound Shaped
Planes
- Abstract: Fan-Slicer (https://github.com/UCL/fan-slicer) is a Python package that enables the fast sampling (slicing) of 2D ultrasound-shaped images from a 3D volume. To increase sampling speed, CUDA kernel functions are used in conjunction with the Pycuda package. The main features include functions to generate images from both 3D surface models and 3D volumes. Additionally, the package also allows for the sampling of images from curvilinear (fan shaped planes) and linear (rectangle shaped planes) ultrasound transducers. Potential uses of Fan-slicer include the generation of large datasets of 2D images from 3D volumes and the simulation of intra-operative data among others. Published on 2023-02-08 11:30:35
ExpressInHost: A Codon Tuning Tool for the Expression of Recombinant
Proteins in Host Microorganisms
- Abstract: ExpressInHost (https://gitlab.com/a.raguin/expressinhost) is a GTK/C++ based user friendly graphical interface that allows tuning the codon sequence of an mRNA for recombinant protein expression in a host microorganism. Heterologous gene expression is widely implemented in biotechnology companies and academic research laboratories. However, expression of recombinant proteins can be challenging. On the one hand, maximising translation speed is important, especially in scalable production processes relevant to biotechnology companies, but on the other hand, solubility problems often arise as a consequence, since translation ‘pauses’ might be key to allow the nascent polypeptide chain to fold appropriately. To address this challenge, we have developed a software that offers three distinct modes to tune codon sequences using the genetic code redundancy. The tuning strategies implemented take into account the specific tRNA resources of the host and that of the native organism. They balance rapid translation and native speed mimicking, which might be important to allow proper protein folding, thereby avoiding protein solubility problems. Published on 2023-02-01 11:30:00
Taskfarm: A Client/Server Framework for Supporting Massive Embarrassingly
Parallel Workloads
- Abstract: Taskfarm is a client/server framework that can be used to keep track of massive embarrassingly parallel workloads. The system is split up into two packages: (1) a flask server that hands out new tasks via HTTP and (2) a python client that requests and updates tasks. The server stores task progress in a database. This system has been designed to manage a satellite data processing workflow with hundreds of thousands of tasks with variable compute costs. It can be used for any problem that can be solved using a task farm. Published on 2023-01-12 10:58:40
What Do We (Not) Know About Research Software Engineering'
- Abstract: As recognition of the vital importance of software for contemporary research is increasing, Research Software Engineering (RSE) is emerging as a discipline in its own right. We present an inventory of relevant research questions about RSE as a basis for future research and initiatives to advance the field, highlighting selected literature and initiatives. This work is the outcome of a RSE community workshop held as part of the 2020 International Series of Online Research Software Events (SORSE) which identified and prioritized key questions across three overlapping themes: people, policy and infrastructure. Almost half of the questions focus on the people theme, which addresses issues related to career paths, recognition and motivation; recruitment and retention; skills; and diversity, equity and inclusion. However, the people and policy themes have the same number of prioritized questions. We recommend that different types of stakeholders, such as RSE employers and policy makers, take responsibility for supporting or encouraging answering of these questions by organizations that have an interest. Initiatives such as the International Council of RSE Associations should also be engaged in this work. Published on 2022-12-26 09:58:58
Rho: Application to Analyze Electrical Resistivity
- Abstract: Electrical resistivity measurements of metals often use the four-wire method, where data acquisition alternates between temperature and voltage. The temperature and voltage values are similar and manual selection of each set of measurements is time consuming. Rho is intended to make electrical resistivity data analysis faster and more reliable by automatically selecting the temperature and voltage measurements using signal processing. The time required to process 52 data points (which consists of approximately 6000 measurements) using Rho is less than one minute compared to up to 4 hours for manual processing. Rho is stored in FigShare and can be used by any research group conducting alternate temperature and voltage measurements to obtain electrical resistivity at either ambient or extreme conditions. Published on 2022-12-13 11:43:13
Uavnoma: A UAV-NOMA Network Model under Non-Ideal Conditions
- Abstract: Uavnoma is a set of Python functions and a front-end script for modeling, studying, and analyzing the communication system composed by an unmanned aerial vehicle (UAV) and two ground users. We assume that the UAV acts as an aerial base station to serve the users according to non-orthogonal multiple access (NOMA) principles. For more practical insights, residual hardware impairments (RHI) and imperfect successive interference cancellation (ipSIC) are considered. More specifically, uavnoma allows the modelers to study and visualize the system performance in terms of achievable rate and outage probability. Additionally, the package produces figures and tables showcasing results from the specified performance metrics. Published on 2022-10-17 00:00:00
DST (Dynamic Synchronization Toolbox): A MATLAB Implementation of the
Dynamic Phase-Locking Pipeline from Stimulus Transformation into Motor
Action: Dynamic Graph Analysis Reveals a Posterior-to- Anterior Shift in
Brain Network Communication of Older Subjects
- Abstract: The Dynamic Synchronization Toolbox allows the calculation of dynamic graphs based on phase synchronization in experimental data. This enables an analysis of the time-development of network connectivity between multiple recording sites (e.g. in electroencephalography (EEG) or magnetoencephalography (MEG) data) with a high temporal resolution. Optionally, the toolbox offers the possibility to compute several graph metrics (such as cluster dynamics, node degree, HUB nodes) via the Brain Connectivity toolbox. Published on 2022-08-01 12:39:10
Guaranteed Automatic Integration Library (GAIL): An Open-Source MATLAB
Library for Function Approximation, Optimization, and Integration
- Abstract: Function approximation, integration, and optimization are three fundamental mathematical problems. They are especially challenging when the functions involved fluctuate wildly in certain parts of the domain, or if the domain is high dimensional. Ideally, algorithms to solve these problems should possess a rigorous mathematical framework, data-based (probabilistic) error bounds, and advanced sampling strategies for efficiency.The Guaranteed Automatic Integration Library (GAIL) is our multi-year research effort addressing these aforementioned challenges. GAIL is a free, open-source MATLAB software library with nine main algorithms undergirded by over a dozen peer-reviewed publications. GAIL solves problems in univariate and multivariate integration, and in univariate function approximation and optimization. GAIL algorithms adaptively sample data values of the input function and automatically stop when the error tolerance has been reached. In some cases, GAIL algorithms are proven to have asymptotically optimal computational cost. We consistently employ good software development practices for GAIL such as unit tests, searchable online documentation, and Git version control. GAIL is available at https://gailgithub.github.io/GAIL_Dev/. Published on 2022-07-29 11:34:00