Graphical User Interface Version 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.

SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic datasets.

Phylogenetic studies now routinely require manipulating and summarizing thousands of data files. For most of these tasks, currently available software requires considerable computing resources and substantial knowledge of command-line applications. We develop an ultrafast and memory-efficient software, SEGUL, that performs common phylogenomic dataset manipulations and calculates statistics summarizing essential data features. Our software is available as standalone command-line interface (CLI) and graphical user interface (GUI) applications, and as a library for Rust, R and Python, with possible support of other languages. The CLI and library versions run native on Windows, Linux and macOS, including Apple ARM Macs. The GUI version extends support to include mobile iOS, iPadOS and Android operating systems. SEGUL leverages the high performance of the Rust programming language to offer fast execution times and low memory footprints regardless of dataset size and platform choice. The inclusion of a GUI minimizes bioinformatics barriers to phylogenomics while SEGUL's efficiency reduces economic barriers by allowing analysis on inexpensive hardware. Our support for mobile operating systems further enables teaching phylogenomics where access to computing power is limited.

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.

SMap: Evolution of independent, dependent and conditioned discrete characters in a Bayesian framework

Abstract Trait evolution analyses enable the comparison of characters amongst different species—a useful technique when inferring ancestral phenotypes based on a phylogeny of living taxa. The evolution of discrete characters can be mapped on the branches of a phylogenetic tree using stochastic mapping. Here we present sMap, a new program to perform stochastic mapping analyses. Key features characterising sMap are: a wide variety of models and prior distributions; the ability to use a posterior distribution of trees and to compute marginal likelihoods to perform model selection analyses; and the implementation of three kinds of characters: ‘independent’ characters, which do not interact with each other; ‘dependent’ characters, which co‐evolve at the same time; and ‘conditioned’ characters, whose state is determined by the state of other characters. Here we present two examples that show how sMap can be used to perform stochastic mapping analyses, produce robust results and answer new kinds of questions. sMap is freely available and distributed under a GPL licence, in a command‐line and Graphical User Interface version; a detailed user manual with examples and tutorials is also provided. The wide variety of algorithms implemented in sMap enables accurate analyses of the evolution of discrete characters. Conditioned characters can be used to study the interaction of simple traits to produce complex phenotypes. As a multiplatform and open‐source project, sMap can be used on a variety of systems and situations, such as academic research and teaching.

BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy data.

High‐throughput analyses of single‐cell microscopy data are a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase‐contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell‐to‐cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post‐processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP (Bacterial toolbox for Microscopy Analysis & Plotting), a command‐line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots. Furthermore, BactMAP makes it possible to perform custom analyses and change the layout of the output. Because BactMAP works independently of segmentation and detection programs, inputs from different sources can be compared within the same analysis pipeline. BactMAP complies with standard practice in R which enables the use of advanced statistical analysis tools, and its graphic output is compatible with ggplot2, enabling adjustable plot graphics in every operating system. User feedback will be used to create a fully automated Graphical User Interface version of BactMAP in the future. Using BactMAP, we visualize key cell cycle parameters in Bacillus subtilis and Staphylococcus aureus, and demonstrate that the DNA replication forks in Streptococcus pneumoniae dissociate and associate before splitting of the cell, after the Z‐ring is formed at the new quarter positions. BactMAP is available from https://veeninglab.com/bactmap.

Graphical User Interface Optimalization Based C# with Visual Studio to Operator Control Unit Rhino Robot

System of communication and data storage on the old version Graphical User Interface (GUI) can not developed or modified because it is not made in a modular way. In addition, the memory capacity is quite large because there are XNA Framework function and excessive robot control menus. Based on these problems we need to optimize GUI on the Operator Control Unit (OCU) Rhino robot. Programming language using C # with Integrated Development Environment (IDE) Visual Studio. Communication systems and data storage robots are grouped into 3 parts of the program with inheritance class. It creation use one of the IDE features of the Windows Presentation Foundation (WPF). The result of this research is program of communication system and data storage more structured so that can be developed for further research. After that, the memory capacity of the new version of GUI is 57.4 MB with an average memory usage of about 513.5 MB and the number of GUI pages as many as 8 with 3 main page details and 5 supporting pages to control robot motion.

Error-Free Data Visualization and Processing through imzML and mzML Validation.

Open data formats are key to facilitating data processing, sharing, and integration. The imzML format ( http://imzml.org/ ) has drastically improved these aspects of mass spectrometry imaging data. Efficient processing of data depends on data sets which are consistent and adhere to the specifications; however, this is not always the case. Here we present a validation tool for data stored in both imzML and the HUPO-PSI mass spectrometery counterpart, mzML, to identify any deviations from the published (i)mzML standard which could cause issues for the user when visualizing or processing data. The tool is released in two forms, a graphical user interface (GUI) for ease of use, and a command line version to fit into existing workflows and pipelines. When certain known issues are encountered, such as the presence of negative values for the location of the binary data, the validator resolves the issue automatically upon saving. The GUI version of the validator also allows editing of the metadata included within the (i)mzML files in order to resolve inconsistencies. We also present a means of performing conditional validation on the metadata within (i)mzML files, where user-defined rules are validated against depending on whether specific metadata are present (or not). For example, if the MALDI term is present, then additional rules related to MALDI (such as the requirement of inclusion of laser parameters) can be validated against this. This enables a flexible and more thorough automated validation of (i)mzML data. Such a system is necessary for validating data against more comprehensive sets of metadata such as minimum reporting guidelines or metadata requirements prior to submission and acceptance of data to data repositories. We demonstrate how this tool can be used to validate against the proposed minimum reporting guidelines in MSI as well as institute specific metadata criteria. The validator tool is endorsed for validation of imzML ( http://imzml.org/ ) and mzML ( http://www.psidev.info/mzml ) and is made available through the respective Web sites. The validator is also released as open source under Mozilla Public License 2.0 at https://gitlab.com/imzML/imzMLValidator .

Dr. Probe: A software for high-resolution STEM image simulation

The Dr. Probe software for multislice simulations of STEM images is introduced, and reference is given of the applied methods. Major program features available with the graphical user interface version are demonstrated by means of a few examples for bright-field and dark-field STEM imaging as well as simulations of diffraction patterns. The numerical procedure applied for the simulation of thermal-diffuse scattering by the frozen-lattice approach is described in detail. Intensity variations occurring in simulations with atomic-column resolution due to frozen-lattice variations are discussed in the context of atom counting. It is found that a significant averaging over many lattice configurations with different random atomic displacements is required to prevent atom-counting bias from simulations. A strategy is developed for the assessment of the amount of required averaging based on the estimated signal variance and the expected signal gain per atom in a column.

ATPP: A Pipeline for Automatic Tractography-Based Brain Parcellation.

There is a longstanding effort to parcellate brain into areas based on micro-structural, macro-structural, or connectional features, forming various brain atlases. Among them, connectivity-based parcellation gains much emphasis, especially with the considerable progress of multimodal magnetic resonance imaging in the past two decades. The Brainnetome Atlas published recently is such an atlas that follows the framework of connectivity-based parcellation. However, in the construction of the atlas, the deluge of high resolution multimodal MRI data and time-consuming computation poses challenges and there is still short of publically available tools dedicated to parcellation. In this paper, we present an integrated open source pipeline (https://www.nitrc.org/projects/atpp), named Automatic Tractography-based Parcellation Pipeline (ATPP) to realize the framework of parcellation with automatic processing and massive parallel computing. ATPP is developed to have a powerful and flexible command line version, taking multiple regions of interest as input, as well as a user-friendly graphical user interface version for parcellating single region of interest. We demonstrate the two versions by parcellating two brain regions, left precentral gyrus and middle frontal gyrus, on two independent datasets. In addition, ATPP has been successfully utilized and fully validated in a variety of brain regions and the human Brainnetome Atlas, showing the capacity to greatly facilitate brain parcellation.

DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information.

Glycan or carbohydrate structures can be pictorially represented using symbolic nomenclatures. The symbol nomenclature for glycans (SNFG) contains 67 different monosaccharides represented using various colors and geometric shapes. A simple tool to convert International Union of Pure and Applied Chemistry (IUPAC) format text to SNFG will be useful for sketching glycans and glycopeptides. Such code can also enable the development of more sophisticated applications, where the visual representation of carbohydrate structures is necessary. To address this need, the current manuscript describes DrawGlycan-SNFG, a freely available, platform-independent, open-source tool. It allows: i. the display of glycans and glycopeptides from IUPAC-condensed text inputs and ii. the depiction of glycan and glycopeptide fragments. The online version of this program is provided with a user-friendly web interface at www.virtualglycome.org/DrawGlycan. Downloadable, stand-alone GUI (Graphical User Interface) version and the program source code are also available from this repository. DrawGlycan-SNFG will be useful for experimentalists looking for a ready to use, simple program for sketching carbohydrates and for software developers interested in incorporating SNFG into their program suite.

With practice, keyboard shortcuts become faster than menu selection: A crossover interaction.

It is widely believed that a graphical user interface (GUI) is superior to a command line interface (CLI) for novice users, but less efficient than the CLI after practice. However, there appears to be no detailed study of the crossover interaction that this implies. The rate of learning may shed light on the reluctance of experienced users to adopt keyboard shortcuts, even though, when mastered, shortcut use would reduce task completion times. We report 2 experiments examining changes in the efficiency of and preference for keyboard input versus GUI with practice. Experiment 1 had separate groups of subjects make speeded choice responses to words on a 20-item list either by clicking on a tab in a dropdown menu (GUI version) or by entering a preassigned keystroke combination (CLI version). The predicted crossover was observed after approximately 200 responses. Experiment 2 showed that following training all but 1 subject in the CLI-trained group chose to continue using shortcuts. These results suggest that frequency of shortcut use is a function of ease of retrieval, which develops over the course of multiple repetitions of the command. We discuss possible methods for promoting shortcut learning and the practical implications of our results.

XGlycScan: An Open-source Software For N-linked Glycosite Assignment, Quantification and Quality Assessment of Data from Mass Spectrometry-based Glycoproteomic Analysis.

Mass spectrometry based glycoproteomics has become a major means of identifying and characterizing previously N-linked glycan attached loci (glycosites). In the bottom-up approach, several factors which include but not limited to sample preparation, mass spectrometry analyses, and protein sequence database searches result in previously N-linked peptide spectrum matches (PSMs) of varying lengths. Given that multiple PSM scan map to a glycosite, we reason that identified PSMs are varying length peptide species of a unique set of glycosites. Because associated spectra of these PSMs are typically summed separately, true glycosite associated spectra counts are lost or complicated. Also, these varying length peptide species complicate protein inference as smaller sized peptide sequences are more likely to map to more proteins than larger sized peptides or actual glycosite sequences. Here, we present XGlycScan. XGlycScan maps varying length peptide species to glycosites to facilitate an accurate quantification of glycosite associated spectra counts. We observed that this reduced the variability in reported identifications of mass spectrometry technical replicates of our sample dataset. We also observed that mapping identified peptides to glycosites provided an assessment of search-engine identification. Inherently, XGlycScan reported glycosites reduce the complexity in protein inference. We implemented XGlycScan in the platform independent Java programing language and have made it available as open source. XGlycScan's source code is freely available at https://bitbucket.org/paiyetan/xglycscan/src and its compiled binaries and documentation can be freely downloaded at https://bitbucket.org/paiyetan/xglycscan/downloads. The graphical user interface version can also be found at https://bitbucket.org/paiyetan/xglycscangui/src and https://bitbucket.org/paiyetan/xglycscangui/downloads respectively.

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. http://www.megasoftware.net/.

A new tool for modeling dune field evolution based on an accessible, GUI version of the Werner dune model

Research into aeolian dune form and dynamics has benefited from simple and abstract cellular automata computer models. Many of these models are based upon a seminal framework proposed by Werner (1995). Unfortunately, most versions of this model are not publicly available or are not provided in a format that promotes widespread use. In our view, this hinders progress in linking model simulations to empirical data (and vice versa). To this end, we introduce an accessible, graphical user interface (GUI) version of the Werner model. The novelty of this contribution is that it provides a simple interface and detailed instructions that encourage widespread use and extension of the Werner dune model for research and training purposes. By lowering barriers for researchers to develop and test hypotheses about aeolian dune and dune field patterns, this release addresses recent calls to improve access to earth surface models.

FITDisk: A Cataclysmic Variable Accretion Disk Demonstration Tool

ABSTRACTWe present the software tool FITDisk, a precompiled‐binary Windows graphical user interface version of our smoothed particle hydrodynamics research code for cataclysmic variable accretion disks. Cataclysmic variables are binary star systems in which a compact stellar remnant, typically a white dwarf star, is stripping mass from a lower main‐sequence companion star by way of an accretion disk. Typically, the disk is the brightest component of the system, because the plasma is heated dramatically as it spirals down in the gravitational well of the primary white dwarf star. The shortest‐period systems can display disk “superhump” oscillations driven by the rotating tidal field of the secondary star. FITDisk models these accretion disk phenomena using a fully three‐dimensional hydrodynamics calculation, and data can be visualized as they are computed or stored to hard drive for later playback at a fast frame rate. Simulations are visualized using OpenGL graphics, and the viewing angle can be changed interactively. Pseudo–light curves of simulated systems can be plotted along with the associated Fourier amplitude spectrum. FITDisk is available for free and can be downloaded from the Florida Institute of Technology Web site.

The generalized earthquake-location (GENLOC) package: an earthquake-location library

We describe a library and associated set of applications for locating seismic events. The library is called the GENeralized LOCation (GENLOC) library because it is a general library that implements most methods commonly used for single event locations. The library has a flexible implementation of the standard Gauss–Newton method with many options for weighting schemes, inversion methods, and algorithms for choosing an initial location estimate. GENLOC also has a grid-search algorithm that makes no assumptions about the geometry of the grid it is searching returning only the point with a best fit solution for the specified residual norm. GENLOC supports both arrival time and array slowness vector measurements. A unique feature is the strong separation between the travel time/earth model problem and the location estimations. GENLOC can utilize data from any seismic phase for which the user can supply an earth model and method to compute theoretical travel times and/or slowness values. The GENLOC library has been used in five different working applications: (1) a simple command line program, (2) an interactive graphical user interface version used in an analyst information system, (3) a database-driven relocation program, (4) a recent implementation of the progressive multiple event location method, and (5) a real-time location program. We ran a validation test against LOCSAT and found reasonable consistency in estimated locations. We attribute observed differences in the solutions to roundoff errors in different calculators used by the two programs.