GitHub Pages Research Articles

Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story.

Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript, and Python. Although Haxe is more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxe's source code conversion functionality when it comes to implementing bioinformatic software.

Automating Test Reporting: Integrating Allure Reports with GitHub Workflows for Enhanced Software Testing

Allure Reports, an open-source framework, significantly enhance the visualization and comprehensibility of test results in software testing. This paper explores the integration of Allure Reports with GitHub Workflows to automate the generation, publication, and management of detailed and interactive test reports. The primary focus is on improving communication, debugging processes, and overall testing efficiency through auto- mated, real-time reporting solutions. Key features of Allure Re- ports include interactive visualizations, comprehensive overviews, detailed test case information, customizable reports, and seamless integration with Continuous Integration/Continuous Deployment (CI/CD) pipelines. Additionally, the paper discusses the role of GitHub Pages and GitHub Artifacts in making test results accessible and supporting continuous integration and delivery processes. The implementation of this integration resulted in enhanced transparency, collaboration, and efficiency within development teams, as well as improved test result visibility and debugging capabilities. Empirical studies support our findings, highlighting improvements in task efficiency and reduced debugging time through the use of automated reporting and continuous integration practices [1- 3].

Md_harmonize: A Python Package for Atom-Level Harmonization of Public Metabolic Databases.

A major challenge to integrating public metabolic resources is the use of different nomenclatures by individual databases. This paper presents md_harmonize, an open-source Python package for harmonizing compounds and metabolic reactions across various metabolic databases. The md_harmonize package utilizes a neighborhood-specific graph coloring method for generating a unique identifier for each compound via atom identifiers based on a compound's chemical structure. The resulting harmonized compounds and reactions can be used for various downstream analyses, including the construction of atom-resolved metabolic networks and models for metabolic flux analysis. Parts of the md_harmonize package have been optimized using a variety of computational techniques to allow certain NP-complete problems handled by the software to be tractable for these specific use-cases. The software is available on GitHub and through the Python Package Index, with end-user documentation hosted on GitHub Pages.

Technology for Internet mapping of the ecological and magnetic state of soils in urban areas

The paper describes the technology of Internet mapping of the ecological and magnetic state of soils on the example of the soil cover of the town of Chusovoi in Perm Region. The ecological and magnetic state of soils reflects the results of the long-term impact of industry and transport on the urban ecosystem, and the presentation of such data in the form of maps is generally accepted in ecological soil science. However, there is a problem of availability of spatial data characterizing soil pollution, caused, on the one hand, by the placement of materials in specialized literature and reports, and, on the other hand, by digital inequality due to the specificity of geographic information. In this regard, today the process of integration of geoinformation technologies and web technologies is actively taking place. The purpose of the research is to develop the technology for creating a typical web map of the ecological and magnetic state of soils in an urbanized area. The creation of a web map of the ecological and magnetic state of soils was carried out according to the standard stages of soil mapping: preparatory, field, and final cameral. Maps of magnetic susceptibility and content of heavy metals in soils were made using the ordinary kriging. Web application development is implemented using the qgis2web module and the Brackets code editor. The web application is hosted on the GitHub Pages platform. The results of the work represent a combination of geostatistics and visualization methods based on Internet mapping technologies, which makes it possible to present a whole set of geoecological maps dedicated to the ecological and magnetic state of soils in the form of a website. The presented geotechnology greatly simplifies the development of a soil-ecological web GIS application – the work is mainly carried out in a GIS environment and therefore does not require advanced competencies of a soil-cartographer in web programming

TaxonWorks in its 10th Year: What’s new, what’s next?

TaxonWorks in its 10th Year: What’s new, what’s next?

Building and Deploying a Classification Schema using Open Standards and Technology

This tutorial offers a full introduction to Building and Deploying a Classification schema using Open Standards and Technology. Beyond accessing the command line, no prior knowledge is assumed as all the steps are described in detail. However, the tutorial will take you through some more complex technical steps. In order to profit best from the example workflows of the last chapter, it is good if you have some idea of how to work with OpenRefine and/or to have a TEI Publisher server set up to play around with. With this tutorial, you ‑ the reader ‑ should gain an understanding of: ‑ what different classification schemes can contribute to your project, ‑ what to pay attention to when building a classification scheme, ‑ how to code the classification scheme (in SKOS), ‑ how to publish the classification scheme (on GitHub pages), ‑ what some possible scenarios of using classifications schemes in actual project workflows are.

From Transparency to Transactive Memory System: How Do Newsrooms’ GitHub Pages Shape News Outlet Credibility?

Amid the rise of computational and data-driven journalism, many newsrooms are using GitHub as a platform for collaborative work on news products. Despite the growing importance of GitHub in journalism, little is known about how a newsroom’s information disclosure on GitHub shapes audiences’ credibility judgment of the news outlet. Integrating theoretical insights from the transactive memory system and journalistic transparency, we conducted two online experiments in the United States. Study 1 (N = 225) explored whether newsrooms’ producer- and production-disclosure on GitHub impact news outlet credibility. The results show that production transparency could directly predict credibility whereas producer transparency could only indirectly boost credibility via perceived transparency. Study 2 (N = 210) examined how the two key indicators of TMS operation: team expertise diversity and experience diversity affected news outlet credibility. It was revealed that team expertise diversity could indirectly enhance news outlet credibility via perceived team specialization; team experience diversity could indirectly foster news outlet credibility via perceived team coordination. We discussed the theoretical significance and practical implications for newsrooms on using GitHub as an emerging space to practice transparency and build trust with audiences.

APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data.

SummaryDNA metabarcoding is an emerging approach to assess and monitor biodiversity worldwide and consequently the number and size of data sets increases exponentially. To date, no published DNA metabarcoding data processing pipeline exists that is (i) platform independent, (ii) easy to use [incl. graphical user interface (GUI)], (iii) fast (does scale well with dataset size) and (iv) complies with data protection regulations of e.g. environmental agencies. The presented pipeline APSCALE meets these requirements and handles the most common tasks of sequence data processing, such as paired-end merging, primer trimming, quality filtering, clustering and denoising of any popular metabarcoding marker, such as internal transcribed spacer, 16S or cytochrome c oxidase subunit I. APSCALE comes in a command line and a GUI version. The latter provides the user with additional summary statistics options and links to GUI-based downstream applications.Availability and implementationAPSCALE is written in Python, a platform-independent language, and integrates functions of the open-source tools, VSEARCH (Rognes et al., 2016), cutadapt (Martin, 2011) and LULU (Frøslev et al., 2017). All modules support multithreading to allow fast processing of larger DNA metabarcoding datasets. Further information and troubleshooting are provided on the respective GitHub pages for the command-line version (https://github.com/DominikBuchner/apscale) and the GUI-based version (https://github.com/TillMacher/apscale_gui), including a detailed tutorial.Supplementary information Supplementary data are available at Bioinformatics online.

CLIENT-SIDE WEB MAPPING SYSTEM FOR VINEYARD SUITABILITY ASSESSMENT

Abstract. Currently, several types of geospatial data are provided as open data and/or map tile data. This implies that geospatial data have become more barrier-free than older data with traditional licenses and formats. In this study, we used open geospatial data to develop a client-side web mapping system for assessment of site suitability for vineyards. As the research area for testing the system, we selected Nagano Prefecture, where many farmers recently started viticulture. The data used in the system are geology, soil, slope gradient, slope aspect, annual mean temperature, and annual maximum and minimum temperatures. These data were converted to a Grid PNG tile, which was developed by The Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology. FOSS4G tools, such as QGIS, TileMill, and MBUtil were used to prepare Grid PNG tile data. Map algebra functions were implemented using the WebGL. Web mapping systems developed in this research do not require server-side systems and/or middleware and can be operated using only a web browser. This means that various entities can be operated on the same system at low cost, or on a free web service such as GitHub pages.

Py-fmas: A python package for ultrashort optical pulse propagation in terms of forward models for the analytic signal

We present a flexible, open-source Python package for the accurate simulation of the z-propagation dynamics of ultrashort optical pulses in nonlinear waveguides, especially valid for few-cycle pulses and their interaction. The simulation approach is based on unidirectional propagation equations for the analytic signal. The provided software allows to account for dispersion, attenuation, four-wave mixing processes including, e.g., third-harmonic generation, and features various models for the Raman response. The propagation equations are solved on a periodic temporal domain. For z-propagation, a selection of pseudospectral methods is available. Propagation scenarios for a custom propagation constant and initial field pulses can either be specified in terms of a HDF5 based input file format or by direct implementation using a python script. We demonstrate the functionality for a test-case for which an exact solution is available, by reproducing exemplary results documented in the scientific literature, and a complex propagation scenario involving multiple pulses. Program summaryProgram Title: py-fmasCPC Library link to program files:https://doi.org/10.17632/7s2cv9kjfs.1Developer's repository link:https://github.com/omelchert/py-fmasCode Ocean capsule:https://codeocean.com/capsule/8221780Licensing provisions: MITProgramming language: Python3Supplementary material: Reference manual, extended user guide, and usage examples are hosted on gitHub pages under https://omelchert.github.io/py-fmas.Nature of problem: Solves for the z-propagation dynamics of spectrally broad ultrashort optical pulses in single mode nonlinear waveguides in terms of propagation models for the analytic signal of the optical field [1–3]. The implemented models include, e.g., third-harmonic generation and the Raman effect.Solution method: The initial real-valued optical field is defined on a periodic one-dimensional temporal grid and converted to the complex-valued analytic signal. z-stepping is performed via spectral methods. The software implements a selection of algorithms with fixed or adaptive stepsize, commonly used in nonlinear optics for solving nonlinear Schrödinger type equations.Additional comments including restrictions and unusual features: The range of applicability of the provided software is equivalent to that of the forward Maxwell equation [4]. For reasonably chosen initial conditions, it can be used beyond the unidirectional approximation as a bidirectional model for a complex field, allowing to describe forward and backward waves coupled through nonlinear interactions [1]. The software implements various models for the Raman response and allows to calculate spectrograms, detailing the time-frequency composition of the analytic signal. Additionally, a convenience class for analyzing propagation constants is provided.

Building a static website with Jekyll and GitHub Pages

Esta lección te ayudará a crear un sitio web seguro completamente gratuito, fácil de mantener y sobre el que tendrás control total, como un blog académico, un sitio web de proyectos o un portafolio en línea.

Designing Trojan Detectors in Neural Networks Using Interactive Simulations.

This paper addresses the problem of designing trojan detectors in neural networks (NNs) using interactive simulations. Trojans in NNs are defined as triggers in inputs that cause misclassification of such inputs into a class (or classes) unintended by the design of a NN-based model. The goal of our work is to understand encodings of a variety of trojan types in fully connected layers of neural networks. Our approach is (1) to simulate nine types of trojan embeddings into dot patterns, (2) to devise measurements of NN states, and (3) to design trojan detectors in NN-based classification models. The interactive simulations are built on top of TensorFlow Playground with in-memory storage of data and NN coefficients. The simulations provide analytical, visualization, and output operations performed on training datasets and NN architectures. The measurements of a NN include (a) model inefficiency using modified Kullback-Liebler (KL) divergence from uniformly distributed states and (b) model sensitivity to variables related to data and NNs. Using the KL divergence measurements at each NN layer and per each predicted class label, a trojan detector is devised to discriminate NN models with or without trojans. To document robustness of such a trojan detector with respect to NN architectures, dataset perturbations, and trojan types, several properties of the KL divergence measurement are presented. For the general use, the web-based simulations is deployed via GitHub pages at https://github.com/usnistgov/nn-calculator.

GitHub and Jekyll for Publishing GIS Workshop Content

In this article, we describe GitHub in simple terms and demonstrate its practical value as a platform for delivering workshop instruction. This article stems from a virtual pre-conference workshop we delivered at the 2020 annual meeting of the Western Association of Map Libraries (WAML). We describe an easily replicated workflow for publishing workshop materials and documentation to the web using GitHub Pages and provide a GitHub repository that readers of this article can copy and customize to suit their own workshop needs.

How to create an interactive dashboard using R: the example of the Queensland COVID-19 tracker

Background Interactive tools like data dashboards enable users both to view and interact with data. In today’s data-driven environment it is a priority for researchers and practitioners alike to be able to develop interactive data visualisation tools easily and where possible at a low cost.
 Aims Here, we provide a guide on how to develop and create an interactive online data dashboard in R, using the COVID-19 tracker for Health and Hospital Regions in Queensland, Australia as an example. We detail a series of steps and explain choices made to design, develop, and easily maintain the dashboard and publish it online.
 Data and methods The dashboard visualises publicly available data from the Queensland Health web page. We used the programming language R and its free software environment. The dashboard webpage is hosted publicly on GitHub Pages updated via GitHub Desktop.
 Results Our interactive dashboard is available at https://qcpr.github.io/.
 Conclusions Interactive dashboards have many applications such as dissemination of research and other data. This guide and the supplementary material can be adjusted to develop a new dashboard for a different set of data and needs.

CRYPTO-SPATIAL: AN OPEN STANDARDS SMART CONTRACTS LIBRARY FOR BUILDING GEOSPATIALLY ENABLED DECENTRALIZED APPLICATIONS ON THE ETHEREUM BLOCKCHAIN

Abstract. Blockchain is an emerging immature technology that disrupt many well established industries nowadays, like finance, supply chain, transportation, energy, official registries (identity, vehicles, …). In this contribution we present a smart contracts library, named Crypto-Spatial, written for the Ethereum Blockchain and designed to serve as a framework for geospatially enabled decentralized applications (dApps) development. The main goal of this work is to investigate the suitability of Blockchain technology for the storage, retrieval and processing of vector geospatial data. The design and the proof-of-concept implementation presented are both based on the Open Geospatial Consortium standards: Simple Feature Access, Discrete Global Grid Systems (DGGS) and Well Known Binary (WKB). Also, the FOAM protocol concept of Crypto-Spatial Coordinate (CSC) was used to uniquely identify spatial features on the Blockchain immutable ledger. The design of the Crypto-Spatial framework was implemented as a set of smart contracts using the Solidity object oriented programming language. The implemented library was assessed toward Etheruem’s best practices design patterns and known security issues (common attacks). Also, a generic architecture for geospatially enabled decentralized applications, combining blockchain and IPFS technologies, was proposed. Finally, a proof-of-concept was developed using the proposed approach which main purpose is to port the UN/FAO-SOLA to Blockchain techspace allowing more transparency and simplifying access to users communities. The smart contracts of this prototype are live on the Rinkeby testnet and the frontend is hosted on Github pages. The source code of the work presented here is available on Github under Apache 2.0 license.

Building Serverless Website on GitHub Pages

GitHub provides the environment for developing and publishing website in integrated environment. By GitHub Pages, we can host the static web easy, fast and free. It helps the developer for integrating development and deployment process, because GitHub Pages is integrating with GitHub environment that support continuous integration and continuous delivery, and also become a content delivery network (CDN), as a part of JAMstack building block. Unfortunately, the usage GitHub as web hosting and JAMstack as an approach for developing web is not very popular among developer in Indonesia. The purpose of this research is to show how implement the JAMstack approach on designing and building website and host it on the GitHub. The website we designed using JAMstack approach by implementing Hugo as static site generator (SSG) and GitHub as content delivery network (CDN). We also insert API for showing the easiness of integrating lots of components on JAMstack approach. We do several tests to check the quality of the website, such as functional test and performance test. The performance test results show that Google PageSpeed score is 97% (A) and YSlow score is 91% (A). It shows that the website can run in good performance although it connected with others services through API.

WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis

A common technique for interpreting experimentally-identified lists of genes is to look for enrichment of genes associated with particular ontology terms. The most common test uses the hypergeometric distribution; more recently, a model-based test was proposed. These approaches must typically be run using downloaded software, or on a server. We develop a collapsed likelihood for model-based gene set analysis and present WTFgenes, an implementation of both hypergeometric and model-based approaches, that can be published as a static site with computation run in JavaScript on the user's web browser client. Apart from hosting files, zero server resources are required: the site can (for example) be served directly from Amazon S3 or GitHub Pages. A C++11 implementation yielding identical results runs roughly twice as fast as the JavaScript version. WTFgenes is available from https://github.com/evoldoers/wtfgenes under the BSD3 license. A demonstration for the Gene Ontology is usable at https://evoldoers.github.io/wtfgo.

Using GitHub pages for a computer science course website

GitHub's Pages feature (https://pages.github.com) might be a convenient way for you to create and manage a website for your course, especially if you are already familiar with GitHub. In this prese...

Empirical analysis on the human dynamics of blogging behavior on GitHub

Abstract GitHub is a social collaborative coding platform on which software developers not only collaborate on codes but also share knowledge through blogs using GitHub Pages. In this article, we analyze the blogging behavior of software developers on GitHub Pages. The results show that both the commit number and the inter-event time of two consecutive blogging actions follow heavy-tailed distribution. We further observe a significant variety of activity among individual developers, and a strongly positive correlation between the activity and the power-law exponent of the inter-event time distribution. We also find a difference between the user behaviors of GitHub Pages and other online systems which is driven by the diversity of users and length of contents. In addition, our result shows an obvious difference between the majority of developers and elite developers in their burstiness property.

Building a static website with Jekyll and GitHub Pages

This lesson will help you create entirely free, easy-to-maintain, preservation-friendly, secure website over which you have full control, such as a scholarly blog, project website, or online portfolio.