Graphical Interface Running Research Articles

Open-source Electrophilic Fragment Screening Platform to Identify Chemical Starting Points for UCHL1 Covalent Inhibitors

Target-based screening of covalent fragment libraries with mass spectrometry has emerged as a powerful strategy to identify chemical starting points for small molecule inhibitors or find new binding pockets on proteins of interest. These libraries span diverse chemical space with a modest number of compounds. Screening covalent fragments against purified protein targets reduces the demands on the mass spectrometer with respect to absolute throughput, detection limit, and dynamic range. Given these relaxed analytical requirements, we sought to develop an open-source, medium-throughput mass spectrometry system for target-based covalent fragment screening. Our platform comprises automated, dual LC desalting columns integrated with electrospray ionization for rapid sample introduction and mass spectrometry detection. The system is operated through a simple python graphical user interface running on commodity microcontroller boards which allow integration with diverse liquid chromatography and mass spectrometry instruments. We provide scripts for fragment pooling, construction of sample batches, along with routines for data processing and visualization. The system enables primary screening of ∼10,000 covalent fragments per day in pooled format. In a proof-of-concept study we executed primary and secondary screens to identify 27 hit fragments against UCHL1, a deubiquitinating enzyme that is emerging as a drug target of interest across multiple clinical indications. We validated and triaged these covalent compounds through a series of orthogonal biochemical and chemoproteomic assays. The most promising chloroacetamide covalent fragment inhibited UCHL1 activity in vitro (IC50 <5 µM) and exhibited dose-dependent binding along with good selectivity against 57 cellular DUBs as quantified by activity-based protein profiling.

A web-based numerical model for sustainable management of Lake Batur, Bali: Preliminary results

Lake Batur is one of The National Priority Lakes according to President Regulation Number 60/2021 with the target of restoring water quality through the pollution control program for floating net fishery (FNF), agriculture, and other anthropogenic sources around the watershed. The regulation also states several internal measures designed to restore the lake’s water quality. Unfortunately, detailed information on pollution control priorities, the amount that must be controlled for water quality improvements to be visible, and the effectiveness of internal restoration efforts have yet to be obtained. This can hinder the lake restoration process and, furthermore, its sustainable management. This study aimed to develop a web-based numerical model as an open-source web-service for guiding restoration in Lake Batur. It is accessible via the interactive graphical user interface (GUI) running in a standard web browser and includes tools of varying complexity. The platform provides the user with features to set up some parameters, run and analyze the numerical water quality, and the possibility to set up, run and compare various lake management scenarios. The preliminary results show that the model was able to represent existing daily water quality dynamics. Hopefully, the model can be used as a tool for lake restoration and as a part of sustainable lake management.

Quantifying the dust in SN 2012aw and iPTF14hls with ORBYTS

ABSTRACT Core-collapse supernovae (CCSNe) are capable of producing large quantities of dust, with strong evidence that ejecta dust masses can grow significantly over extended periods of time. Red–blue asymmetries in the broad emission lines of CCSNe can be modelled using the Monte Carlo radiative transfer code damocles, to determine ejecta dust masses. To facilitate easier use of damocles, we present a Tkinter graphical user interface (GUI) running damocles. The GUI was tested by high school students through the Original Research By Young Twinkle Students programme, who used it to measure the dust masses formed at two epochs in Type IIP CCSNe, SN 2012aw and iPTF14hls, demonstrating that a wide range of people can contribute to scientific advancement. Bayesian methods quantified uncertainties on our model parameters. From the red scattering wing in the day 1863 Hα profile of SN 2012aw, we constrained the dust composition to large (radius &amp;gt;0.1 μm) silicate grains, with a dust mass of $6.0^{+21.9}_{-3.6}\times 10^{-4}~\mathrm{ M}_\odot$. From the day 1158 Hα profile of SN 2012aw, we found a dust mass of $3.0^{+14}_{-2.5}\times 10^{-4}$ M⊙. For iPTF14hls, we found a day 1170 dust mass of 8.1$^{+81}_{-7.6}\times 10^{-5}$ M⊙ for a dust composition consisting of 50 per cent amorphous carbon and 50 per cent astronomical silicate. At 1000 d post-explosion, SN 2012aw and iPTF14hls have formed less dust than the peculiar Type II SN 1987A, suggesting that SN 1987A may have formed a larger dust mass than typical Type IIP’s.

The INOWAS platform: A web-based numerical groundwater modelling approach for groundwater management applications

The INOWAS Decision Support System (DSS) is an open-source web-service for groundwater management applications, in particular managed aquifer recharge. It is accessible via the interactive graphical user interface (GUI) running in a standard web browser and includes tools of varying complexity. The platform provides the user with features to set up, run and analyse numerical groundwater flow and transport models based on the USGS MODFLOW family and the possibility to set up, run and compare various groundwater management scenarios. The applicability of the web-based approach is demonstrated by the simulation of groundwater flow at a case study site in Pirna, Germany.

NEST Desktop, an Educational Application for Neuroscience.

Simulation software for spiking neuronal network models matured in the past decades regarding performance and flexibility. But the entry barrier remains high for students and early career scientists in computational neuroscience since these simulators typically require programming skills and a complex installation. Here, we describe an installation-free Graphical User Interface (GUI) running in the web browser, which is distinct from the simulation engine running anywhere, on the student’s laptop or on a supercomputer. This architecture provides robustness against technological changes in the software stack and simplifies deployment for self-education and for teachers. Our new open-source tool, NEST Desktop, comprises graphical elements for creating and configuring network models, running simulations, and visualizing and analyzing the results. NEST Desktop allows students to explore important concepts in computational neuroscience without the need to learn a simulator control language before. Our experiences so far highlight that NEST Desktop helps advancing both quality and intensity of teaching in computational neuroscience in regular university courses. We view the availability of the tool on public resources like the European ICT infrastructure for neuroscience EBRAINS as a contribution to equal opportunities.

A Low-Cost Automated Digital Microscopy Platform for Automatic Identification of Diatoms

Currently, microalgae (i.e., diatoms) constitute a generally accepted bioindicator of water quality and therefore provide an index of the status of biological ecosystems. Diatom detection for specimen counting and sample classification are two difficult time-consuming tasks for the few existing expert diatomists. To mitigate this challenge, in this work, we propose a fully operative low-cost automated microscope, integrating algorithms for: (1) stage and focus control, (2) image acquisition (slide scanning, stitching, contrast enhancement), and (3) diatom detection and a prospective specimen classification (among 80 taxa). Deep learning algorithms have been applied to overcome the difficult selection of image descriptors imposed by classical machine learning strategies. With respect to the mentioned strategies, the best results were obtained by deep neural networks with a maximum precision of 86% (with the YOLO network) for detection and 99.51% for classification, among 80 different species (with the AlexNet network). All the developed operational modules are integrated and controlled by the user from the developed graphical user interface running in the main controller. With the developed operative platform, it is noteworthy that this work provides a quite useful toolbox for phycologists in their daily challenging tasks to identify and classify diatoms.

Shape Memory Materials Database Tool—A Compendium of Functional Data for Shape Memory Materials

A database tool is developed for archiving and exploring shape memory materials including shape memory alloys (SMAs), superelastic alloys, magnetic SMAs, shape memory polymers, and shape memory ceramics. Over 750 000 data points and their pedigree metadata are extracted and stored into records. Data are handled via a graphical user interface running in a web application. The tool provides interactive menus for the selection of material types, properties, and filters, culminating with a visualization panel. Data are displayed in three forms, consisting of pie charts, 2D scatter plots, and ternary diagrams, all of which provide unique information pertinent to the materials and properties being explored. This database tool is a major stepping stone toward building an information system where an entire continuum of material novices to experts can have an infrastructure to explore and discover these multifunctional materials.

FumeBot: A Deep Convolutional Neural Network Controlled Robot

This paper describes the development of a convolutional neural network for the control of a home monitoring robot (FumeBot). The robot is fitted with a Raspberry Pi for on board control and a Raspberry Pi camera is used as the data feed for the neural network. A wireless connection between the robot and a graphical user interface running on a laptop allows for the diagnostics and development of the neural network. The neural network, running on the laptop, was trained using a supervised training method. The robot was put through a series of obstacle courses to test its robustness, with the tests demonstrating that the controller has learned to navigate the obstacles to a reasonable level. The main problem identified in this work was that the neural controller did not have memory of past actions it took and a past state of the world resulting in obstacle collisions. Options to rectify this issue are suggested.

Development of scanning single port free space measurement setup for imaging reflection loss of microwave absorbing materials

This paper proposes a scanning free-space measurement (SFSM) setup for the evaluation of microwave absorption properties of microwave absorbing materials. The system comprises of a vector network analyzer (VNA), focused horn antennas attached to the VNA for transmitting/receiving microwave signals, a dual-axis automated translation stage for raster scanning of the specimen and a standard personal computer. A graphical user interface (GUI) running on the computer manages the configuration and synchronization of the VNA and the stage system, measurement reception from VNA and compilation of results for display to the user. The GUI is created in C++ using Qt framework and Qt Widgets for Technical applications. It is designed with a minimalistic approach to promote usability and adaptability.

Inexpensive Aerial Photogrammetry for Studies of Whales and Large Marine Animals

We describe a simple system enabling accurate measurement of swimming marine mammals and other large vertebrates from low-altitude single-frame photogrammetry via inexpensive modifications to a “prosumer” unmanned aerial vehicle (UAV) equipped with gimballed micro4/3 camera and 25 mm lens. Image scale is established via an independently powered LIDAR/GPS data-logging system recording altitude and GPS location at 1 Hz. Photogrammetric calibration of the camera and lens allowed distortion parameters to be rigorously accounted for during image analysis, via a custom-programmed Graphical User Interface running in MATLAB. The datalogger, camera calibration methods and measurement software are adaptable to a wide range of UAV platforms. Mean LIDAR accuracy, measured from 10 bridges 9-39 m above water, was 99.9%. We conducted 136 flights in New Zealand’s subantarctic Auckland Islands to measure southern right whales. Mean lengths of 10 individual whales, each photographed between 7 to 15 times, had CVs (SD/mean) ranging from 0.5-1.8 % (mean = 1.2 %). Repeated measurements of a floating reference target showed a mean error of c.1 %. Our system is relatively inexpensive, easily put together, produces accurate, repeatable measurements from single vertical images, and hence is applicable to a wide range of ecological questions in marine and terrestrial habitats.

The wheel of design: assessing and refining the usability of geoportals

ABSTRACTGeoportals play a major role in geospatial data distribution to end-users like researchers and engineers. For maximum effectiveness, an intuitive and comprehensive graphical user interface (GUI) is a paramount property of such portals. GeoVITe (GEOdata Visualization and Interactive Training Environment) is a geodata-sharing portal, providing ETH Zurich employees with direct access to geoinformation and geoservices. The guiding functional requirement for the GeoVITe geoportal is that a user should visually (spatially, thematically and temporally) navigate the spatial data, select the desired dataset and area and directly download the required data in a straightforward manner through a user-friendly GUI running in a standard Web browser. After several improvements that have been made to GeoVITe since its wide-spread launch in 2010, the user interface of GeoVITe was recently put under scrutiny with the help of a usability evaluation. Results showed multiple possibilities for improvement, belonging to one of three categories: (i) distribution of GUI elements, (ii) concentration on relevant functionality and (iii) improvements to the geodata download workflow. Based on these findings, three key recommendations for designing a geoportal can be made: (i) full-screen map with simple navigation, (ii) instant user feedback and (iii) multifunctional search. Further work will require an assessment of the presented redesign as a next step in the iterative process of GUI design improvement.

Implementation of a versatile research data acquisition system using a commercially available medical ultrasound scanner

This paper describes the design and implementation of a versatile, open-architecture research data acquisition system using a commercially available medical ultrasound scanner. The open architecture will allow researchers and clinicians to rapidly develop applications and move them relatively easy to the clinic. The system consists of a standard PC equipped with a camera link and an ultrasound scanner equipped with a research interface. The ultrasound scanner is an easy-to-use imaging device that is capable of generating high-quality images. In addition to supporting the acquisition of multiple data types, such as B-mode, M-mode, pulsed Doppler, and color flow imaging, the machine provides users with full control over imaging parameters such as transmit level, excitation waveform, beam angle, and focal depth. Beamformed RF data can be acquired from regions of interest throughout the image plane and stored to a file with a simple button press. For clinical trials and investigational purposes, when an identical image plane is desired for both an experimental and a reference data set, interleaved data can be captured. This form of data acquisition allows switching between multiple setups while maintaining identical transducer, scanner, region of interest, and recording time. Data acquisition is controlled through a graphical user interface running on the PC. This program implements an interface for third-party software to interact with the application. A software development toolkit is developed to give researchers and clinicians the ability to utilize third-party software for data analysis and flexible manipulation of control parameters. Because of the advantages of speed of acquisition and clinical benefit, research projects have successfully used the system to test and implement their customized solutions for different applications. Three examples of system use are presented in this paper: evaluation of synthetic aperture sequential beamformation, transverse oscillation for blood velocity estimation, and acquisition of spectral velocity data for evaluating aortic aneurysms.

Novel insight into the non-coding repertoire through deep sequencing analysis

Non-coding RNAs (ncRNA) account for a large portion of the transcribed genomic output. This diverse family of untranslated RNA molecules play a crucial role in cellular function. The use of ‘deep sequencing’ technology (also known as ‘next generation sequencing’) to infer transcript expression levels in general, and ncRNA specifically, is becoming increasingly common in molecular and clinical laboratories. We developed a software termed ‘RandA’ (which stands for ncRNA Read-and-Analyze) that performs comprehensive ncRNA profiling and differential expression analysis on deep sequencing generated data through a graphical user interface running on a local personal computer. Using RandA, we reveal the complexity of the ncRNA repertoire in a given cell population. We further demonstrate the relevance of such an extensive ncRNA analysis by elucidating a multitude of characterizing features in pathogen infected mammalian cells. RandA is available for download at http://ibis.tau.ac.il/RandA.

Weighted-Interaction Nestedness Estimator (WINE): A new estimator to calculate over frequency matrices

We propose a new nestedness estimator that takes into account the weight of the interactions, that is, it runs over frequency matrices. A nestedness measurement is calculated through the average distance from each matrix cell containing a link to the cell with the lowest marginal totals, in the packed matrix, using a weighted Manhattan distance. The significance of this nestedness measure is tested against a null model that constraints matrix fill to observed values and retains the distribution of number of events. This is the first methodological approach that allows for the characterization of weighted nestedness. We have developed a graphical user interface (GUI) running in Matlab to compute all these parameters. The software is also available as a script for R-package and in C++ version.

A new approach for data editing and imputation

The editing-and-imputation problem concerns the question of finding errors in a record which does not satisfy a set of consistency rules. Once some potential errors have been localizated, it is also necessary to impute new values to the associated fields. The output dataset should consist of valid records and preserve similar statistical properties as the input dataset. Most of this work is usually done manually by statistical agencies, thus consuming a great deal of human resources. This paper presents a mathematical programming model to optimally solve the problem on surveys with categorical values and particular edits. We also describe a heuristic approach to deal with the more complex surveys. The heuristic procedure follows a combination of the widely-accepted hot-deck donor scheme and the multivariate regression analysis. It has been implemented in a graphical user interface running on standard personal computers, and has been tested on real-world surveys. This paper demonstrates the satisfactory performance of our automatic procedure.

PhyloGena—a user-friendly system for automated phylogenetic annotation of unknown sequences

Phylogenomic approaches towards functional and evolutionary annotation of unknown sequences have been suggested to be superior to those based only on pairwise local alignments. User-friendly software tools making the advantages of phylogenetic annotation available for the ever widening range of bioinformatically uninitiated biologists involved in genome/EST annotation projects are, however, not available. We were particularly confronted with this issue in the annotation of sequences from different groups of complex algae originating from secondary endosymbioses, where the identification of the phylogenetic origin of genes is often more problematic than in taxa well represented in the databases (e.g. animals, plants or fungi). We present a flexible pipeline with a user-friendly, interactive graphical user interface running on desktop computers that automatically performs a basic local alignment search tool (BLAST) search of query sequences, selects a representative subset of them, then creates a multiple alignment from the selected sequences, and finally computes a phylogenetic tree. The pipeline, named PhyloGena, uses public domain software for all standard bioinformatics tasks (similarity search, multiple alignment, and phylogenetic reconstruction). As the major technological innovation, selection of a meaningful subset of BLAST hits was implemented using logic programming, mimicing the selection procedure (BLAST tables, multiple alignments and phylogenetic trees) are displayed graphically, allowing the user to interact with the pipeline and deduce the function and phylogenetic origin of the query. PhyloGena thus makes phylogenomic annotation available also for those biologists without access to large computing facilities and with little informatics background. Although phylogenetic annotation is particularly useful when working with composite genomes (e.g. from complex algae), PhyloGena can be helpful in expressed sequence tag and genome annotation also in other organisms. PhyloGena (executables for LINUX and Windows 2000/XP as well as source code) is available by anonymous ftp from http://www.awi.de/en/phylogena.

A graphical user interface for an electron monitor unit calculator using a sector‐integration algorithm and exponential curve‐fitting method

A new electron monitor unit (MU) calculator program called “eMUc” was developed to provide a convenient electron MU calculation platform for the physics and radiotherapy staff in electron radiotherapy. The program was written using the Microsoft Visual Basic.net framework and has a user‐friendly front‐end window with the following features: (1) Apart from using the well‐known polynomial curve‐fitting method for the interpolation and extrapolation of relative output factors (ROFs), an exponential curve‐fitting method was used to obtain better results. (2) A new algorithm was used to acquire the radius in each angular segment in the irregular electron field during the sector integration. (3) A comprehensive graphical user interface running on the Microsoft Windows operating system was used. (4) Importing irregular electron cutout field images to the calculator program was simplified by using only a commercial optical scanner. (5) Interlocks were provided when the input patient treatment parameters could not be handled by the calculator database accurately. (6) A patient treatment record could be printed out as an electronic file or hard copy and transferred to the patient database. The data acquisition mainly required ROF measurements using various circular cutouts for all the available electron energies and applicators for our Varian 21 EX linear accelerator. To verify and implement the calculator, the measured results using our specific designed irregular and clinical cutouts were compared to those predicted by the calculator. Both agreed well with an error of ±2%.PACS number(s): 87.53.Fs; 87.53.Hv; 87.66.‐a

CHROMA: consensus-based colouring of multiple alignments for publication.

CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to be flexible and reliable, and has a simple-to-use graphical user interface running under Microsoft Windows. Both the executables and source code for CHROMA running under Windows and Linux (portable command-line only) are freely available at http://www.lg.ndirect.co.uk/chroma. Software enquiries should be directed to CHROMA@lg.ndirect.co.uk.

OWSimu: an object-oriented and Web-based simulator for plant growth

OWSimu is a Java-based generic plant growth simulator. According to the principles of object-oriented design, Java classes were programmed for plant growth simulation as well as relevant input, output and user interfaces. The program was developed as a Java applet with a user-friendly graphical interface running on the Web. With a Java (JDK1.1)-embedded Web browser, users can link the run-time model and perform plant growth simulations at our website. OWSimu is a convenient tool for researchers, teachers and students to use in the general study of plant growth. It describes the growth of a typical plant that is free of pests and diseases. The program is currently able to simulate plant growth for more than a dozen crops and weeds under Illinois weather and three typical soil conditions. Additional data is needed to modify OWSimu so that it can have a better carbon balance model for different plant species and accommodate different varieties within a selected plant species for use in a specific crop production management system. The program source code is highly reusable for further development and for other crop modeling work.

MOVAID: a personal robot in everyday life of disabled and elderly people

The growing number of disabled and elderly citizens, on one side, and the wide spreading of technology in everyday life, on the other, has led to a consistent effort devoted to the research of technological solutions for improving the quality of life of disabled and elderly people. Technology can actually provide a wide range of solutions, at different levels of complexity and cost. The recent progress of research in advanced robotics allows robotic solutions to be applied to assist disabled and elderly people in everyday life. The MOVAID project, promoted by the European Commission within the TIDE programme, and co-ordinated by the Scuola Superiore Sant’Anna (Pisa, Italy), represents one of the first attempts to propose robotic assistance in such a personal sphere of activities as everyday life at home. Ten partners from five European countries joined the MOVAID Consortium, including Universities, validation centres, and industries. The MOVAID project proposed, applied and validated some innovative concepts for the design and development of a modular robotic solution to the problem of personal assistance, by implementing a mobile robotic system and dedicated interfaces to standard appliances. The final objective of the MOVAID project was to demonstrate two points. First, how mass consumer technological products, when accessible for disabled and elderly people, can enhance their level of autonomy in everyday activities. Second, how a robotic solution is not only technically feasible, but also acceptable from the user’s point of view, if integrated in a modular assistance system. The basic philosophy of the project relies on the concepts of ‘design for all’ and ‘user oriented approach’, as key factors for the introduction of technology in everyday activities. Such concepts were realised in the functional and physical distribution of the system in the house, including docking facilities for the mobile robotic unit. The MOVAID system consists of a number of fixed workstations (PCs), located where main activities are carried out at home, such as the kitchen and the bedroom, along with a mobile robotic unit able to navigate in the house avoiding unexpected obstacles, to grasp and manipulate common objects and to dock to the fixed workstations for data exchange and power supply. Commands to the robot are given in a high level language through a graphical interface running on the fixed workstations. On the user interface, a continuous visual feed-back from on-board cameras is also shown to the user, allowing him/her not only to monitor what the robot is doing, but also to collaborate with it, by indicating objects and positions directly on the screen. Moreover, to allow and ease access to standard technological products, interfaces for standard kitchen appliances were studied, and a prototype of a microwave oven interface, offering the oven basic functionality, was developed and tested. Typical tasks for the system, defined on the basis of identified users needs, are: to warm up some food in a microwave oven and serve it at the user’s bed; to clean the kitchen work surface; and to remove dirty sheets from a bed. The developed prototype MOVAID system has been successfully validated with potential users in Italy, France and Switzerland, both through demonstrations and user trials, carried out in a residential house for disabled people in Italy. The paper summarises the project and its achievements. The basic philosophy and the approach are introduced and a detailed description of the system is then provided, including the technical aspects related to the components design and development. Finally, the results of the validation phase on the system prototype are reported and discussed.