Powerful Graphical Interface Research Articles

Development and application of a second-generation multilingual tool for invasion risk screening of non-native terrestrial plants

Under the increasing threat to native ecosystems posed by non-native species invasions, there is an urgent need for decision support tools that can more effectively identify non-native species likely to become invasive. As part of the screening (first step) component in non-native species risk analysis, decision support tools have been developed for aquatic and terrestrial organisms. Amongst these tools is the Weed Risk Assessment (WRA) for screening non-native plants. The WRA has provided the foundations for developing the first-generation WRA-type Invasiveness Screening Kit (ISK) tools applicable to a range of aquatic species, and more recently for the second-generation ISK tools applicable to all aquatic organisms (including plants) and terrestrial animals. Given the most extensive usage of the latter toolkits, this study describes the development and application of the Terrestrial Plant Species Invasiveness Screening Kit (TPS-ISK). As a second-generation ISK tool, the TPS-ISK is a multilingual turnkey application that provides several advantages relative to the WRA: (i) compliance with the minimum standards against which a protocol should be evaluated for invasion process and management approaches; (ii) enhanced questionnaire comprehensiveness including a climate change component; (iii) provision of a level of confidence; (iv) error-free computation of risk scores; (v) multilingual support; (vi) possibility for across-study comparisons of screening outcomes; (vii) a powerful graphical user interface; (viii) seamless software deployment and accessibility with improved data exchange. The TPS-ISK successfully risk-ranked five representative sample species for the main taxonomic groups supported by the tool and ten angiosperms previously screened with the WRA for Turkey. The almost 20-year continuous development and evolution of the ISK tools, as opposed to the WRA, closely meet the increasing demand by scientists and decision-makers for a reliable, comprehensive, updatable and easily deployable decision support tool. For terrestrial plant screening, these requirements are therefore met by the newly developed TPS-ISK.

Abstract 5398: Optimization generator app (OpGen) for radiotherapy treatment planning using case-based reasoning

Abstract Case-based reasoning (CBR) means adopting previous experiences (i.e, data from previous patients) to meet new demands (new patients). In this scenario, we developed an application named OpGen to generate optimization objective values for head and neck radiotherapy inverse treatment planning, using the previously treated patient with an acceptable outcome. OpGen will be helpful in radiotherapy treatment planning automation and efficiently reducing the required time to reach the target goals and improving the quality and safety of the treatment.OpGen has been developed in Python and has four main modules: 1- Analyzing radiotherapy treatment planning parameters of the previous patients in the database. We have developed (a) a powerful graphical user interface (GUI) that allows quantitative and qualitative analysis of the previous knowledge, including the type of frequently used objective parameter (Min Dose, Max Dose, Min DVH dose, etc.); (b) The range of values used for each specific objective type, and (c) Histogram of the number of patients vs. values used for a specific objective type. 2- Importing patients from treatment planning and retrieving a user-defined number of treatment planning information from the previously treated patients in the database corresponding to the given patient using the user-defined quantitative features (geometrical, distance or geo-distance) and retrieval algorithms (k-Nearest Neighbor and Random Forest). 3- Generating optimization objective values based on the following available options: (a) The most similar patient in the database; (b)- Average or median value over the number of patients retrieved from the database; and (c) Deep learning generated values using a model trained over 100 similar cases retrieved from the database. 4- Generate a portable database of the objective values and patient geometric information for any inter- or intra-institutional usage of the algorithm. OpGen is compatible with RayStation (RaySearch Laboratories™) treatment planning and can retrieve, analyze and generate treatment planning optimization parameters in less than 3 minutes. OpGen can potentially increase the quality and safety of radiotherapy treatment planning by improving the efficiency of the optimization process. Citation Format: Reza Reiazi, Surendra Prajapati, Abdallah Sherif Mohamed, Clifton David Fuller, Mohammad Salehpour. Optimization generator app (OpGen) for radiotherapy treatment planning using case-based reasoning. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5398.

Global Repeat Map (GRM) Application: Finding All DNA Tandem Repeat Units

Tandem repeats (TRs) are important components of eukaryotic genomes; they have both structural and functional roles: (i) they form essential chromosome structures such as centromeres and telomeres; (ii) they modify chromatin structure and affect transcription, resulting in altered gene expression and protein abundance. There are established links between variations in TRs and incompatibilities between species, evolutionary development, chromosome mis-segregation, aging, cancer outcomes and different diseases. Given the importance of TRs, it seemed essential to develop an efficient, sensitive and automated application for the identification of all kinds of TRs in various genomic sequences. Here, we present our new GRM application for identifying TRs, which is designed to overcome all the limitations of the currently existing algorithms. Our GRM algorithm provides a straightforward identification of TRs using the frequency domain but avoiding the mapping of the symbolic DNA sequence into numerical sequence, and using key string matching, but avoiding the statistical methods of locally optimizing individual key strings. Using the GRM application, we analyzed human, chimpanzee and mouse chromosome 19 genome sequences (RefSeqs), and showed that our application was very fast, efficient and simple, with a powerful graphical user interface. It can identify all types of TRs, from the smallest (2 bp) to the very large, as large as tens of kilobasepairs. It does not require any prior knowledge of sequence structure and does not require any user-defined parameters or thresholds. In this way, it ensures that a full spectrum of TRs can be detected in just one step. Furthermore, it is robust to all types of mutations in repeat copies and can identify TRs with various complexities in the sequence pattern. From this perspective, we can conclude that the GRM application is an efficient, sensitive and automated method for the identification of all kinds of TRs.

CellExplorer: A framework for visualizing and characterizing single neurons

The large diversity of neuron types provides the means by which cortical circuits perform complex operations. Neuron can be described by biophysical and molecular characteristics, afferent inputs, and neuron targets. To quantify, visualize, and standardize those features, we developed the open-source, MATLAB-based framework CellExplorer. It consists of three components: a processing module, a flexible data structure, and a powerful graphical interface. The processing module calculates standardized physiological metrics, performs neuron-type classification, finds putative monosynaptic connections, and saves them to a standardized, yet flexible, machine-readable format. The graphical interface makes it possible to explore the computed features at the speed of a mouse click. The framework allows users to process, curate, and relate their data to a growing public collection of neurons. CellExplorer can link genetically identified cell types to physiological properties of neurons collected across laboratories and potentially lead to interlaboratory standards of single-cell metrics.

ANALYSIS AND DESIGN OF G+4 RESIDENTIAL BUILDING USING ETABS

ETABS stands for Extended Three-Dimensional Analysis of Building Systems. ETABS is commonly used to analyze: Skyscrapers, concrete structures, low and high rise buildings, and portal frame structures. The case study in this paper mainly emphasizes on structural behavior of multi-storey building for different plan configurations like rectangular, C, L and I-shape. Modelling of 15-storeys R.C.C. framed building is done on the ETABS software for analysis ETABS issue, for analysis and design for building systems. ETABS features are contain powerful graphical interface coupled with unmatched modeling, analytical, and design procedures, all integrated using a common database. STAAD and ETABS both of the software are well equipped and very much capable of handling different shape of the structures, static and dynamic loadings and different material properties.

CellExplorer, a Framework for Visualizing and Characterizing Single Neurons

The large diversity of neuron types of the brain, provides the means by which cortical circuits perform complex operations. Neuron types can be described by a broad set of electrophysiological characteristics, afferent inputs, neuron targets and molecular features. To quantify, visualize, and standardize these features, we developed the open-source Matlab-based framework, CellExplorer. It consists of three components: a processing module, a flexible data structure, and a powerful graphical interface. The processing module calculates standardized physiological metrics, performs neuron type classification from electrophysiological features, finds putative monosynaptic connections and saves it to a standardized yet flexible machine-readable format. The graphical interface makes it possible to explore any combination of computed features at the speed of a mouse click. The framework allows users to process, curate and relate their data to a growing publicly available collection of neurons. In addition to data mining, CellExplorer can link genetically identified cell types to physiological properties of tens of thousands of single neurons collected across laboratories, potentially leading to interlaboratory standards of single cell metrics.

Computational design applied to equilibrium-staged and rate-based absorption processes

Simulators are of great interest in Chemical Engineering because they facilitate process optimization and help evaluate different solutions through the so-called �what-if� approach. They include the most advanced thermodynamical models and complete libraries for the calculation of physicochemical properties and estimation of phase equilibria data which are successfully integrated in the process design. Moreover, simulators allow addressing both stationary and batch operations. For this reason, their use in the design of Industrial Chemistry processes has gained much acceptance in the last decades. Even so, simulations should be accompanied by another computational tool which allows the professionals to implement specific algorithms which relate inputs and outputs, so as to get the most out of the computing power. We herein exemplify how Aspen Plus and Mathcad Prime software packages were successfully integrated in a case study on the removal of carbon disulphide by contact with a paraffinic oil in an absorption tower. This absorption operation was studied in both trayed and packed columns. Regarding the first contact type, i.e. trays, Mathcad�s powerful programming tool and graphical interface enabled to corroborate and to better understand the effect of temperature on the number of theoretical stages previously observed with Aspen Plus.

Virtual Instrumentation in Electrical Engineering Applications

This paper presents the applications of LabVIEW tools in the field of electrical engineering for student-centric learning such as power factor measurement, AC-to-DC converters, speed control of induction and DC motor drive. LabVIEW is a powerful graphical interface and user-friendly tool designed specifically for test, measurement and control. The power factor of resistive and inductive loads, the performance parameters of fully controlled converters and speed control of induction motor are performed in LabVIEW with DAQ device USB 6009. The speed control of a DC motor is performed with PI-speed controller using LabVIEW control and simulation toolkit and fuzzy logic controller. Measurement results are presented to validate the feasibility of system.

Macromodeling of in- and out-of-plane behavior of unreinforced masonry infill walls

Surveys on damaged and collapsed reinforced concrete (RC) buildings following recent earthquakes indicated that poor performance is associated with the influence of unreinforced masonry (URM) infill walls. In the event of an earthquake, a typical URM infill wall is subjected to a three-dimensional acceleration field and undergoes simultaneous in-plane (IP) and out-of-plane (OoP) loading. Depending on the direction of the seismic action, the observed damage mechanisms for URM infill walls may be classified as IP and OoP performance failures or a combination of both. Since the turn of the millennium, there have been a number of distinct experimental studies in the field of infilled frames, addressing the OoP response of URM infill walls. This has led to a number of numerical macro models able to represent the OoP behavior of the URM infill wall. The main limitation of the proposed models is the difficulty in using them as practical models, since all the proposed models were implemented in software tools without a graphical user interface (GUI), such as OpenSees. In this paper, one of the recently presented models is utilized and a methodology presented for a more practical and user-friendly implementation. The model previously validated using OpenSees is recalibrated and revalidated using the computer software SAP2000, which has a powerful GUI utilizing the material models and numerical elements available in the program library. The model considers the IP and OoP response as well as their interaction. For the determination of failure patterns, respective local damage grades for primary (frame) and secondary (infill wall) elements are defined. Finally, a four-story RC frame structure with URM infill walls, which was tested in the European Laboratory for Structural Assessment considering the IP response only, is used to assess the combined failure mechanism of URM infill walls through the concept of interaction curves.

VMS-ROT: A New Module of the Virtual Multifrequency Spectrometer for Simulation, Interpretation, and Fitting of Rotational Spectra.

The Virtual Multifrequency Spectrometer (VMS) is a tool that aims at integrating a wide range of computational and experimental spectroscopic techniques with the final goal of disclosing the static and dynamic physical–chemical properties “hidden” in molecular spectra. VMS is composed of two parts, namely, VMS-Comp, which provides access to the latest developments in the field of computational spectroscopy, and VMS-Draw, which provides a powerful graphical user interface (GUI) for an intuitive interpretation of theoretical outcomes and a direct comparison to experiment. In the present work, we introduce VMS-ROT, a new module of VMS that has been specifically designed to deal with rotational spectroscopy. This module offers an integrated environment for the analysis of rotational spectra: from the assignment of spectral transitions to the refinement of spectroscopic parameters and the simulation of the spectrum. While bridging theoretical and experimental rotational spectroscopy, VMS-ROT is strongly integrated with quantum-chemical calculations, and it is composed of four independent, yet interacting units: (1) the computational engine for the calculation of the spectroscopic parameters that are employed as a starting point for guiding experiments and for the spectral interpretation, (2) the fitting-prediction engine for the refinement of the molecular parameters on the basis of the assigned transitions and the prediction of the rotational spectrum of the target molecule, (3) the GUI module that offers a powerful set of tools for a vis-à-vis comparison between experimental and simulated spectra, and (4) the new assignment tool for the assignment of experimental transitions in terms of quantum numbers upon comparison with the simulated ones. The implementation and the main features of VMS-ROT are presented, and the software is validated by means of selected test cases ranging from isolated molecules of different sizes to molecular complexes. VMS-ROT therefore offers an integrated environment for the analysis of the rotational spectra, with the innovative perspective of an intimate connection to quantum-chemical calculations that can be exploited at different levels of refinement, as an invaluable support and complement for experimental studies.

Development and Implementation of Advanced Fitting Methods for the Calculation of Accurate Molecular Structures.

The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical-chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of dynamical and environmental effects in tuning their overall behavior. For this purpose the so-called semiexperimental approach, based on a nonlinear least-squares fit of the moments of inertia associated with a set of available isotopologues, allows one to obtain very accurate results, without the unfavorable computational cost characterizing high-level quantum chemical methods. In the present work the MSR (Molecular Structure Refinement) software for the determination of equilibrium structures by means of the semiexperimental approach is presented, and its implementation is discussed in some detail. The software, which is interfaced with a powerful graphical user interface, includes different optimization algorithms, an extended error analysis, and a number of advanced features, the most remarkable ones concerning the choice of internal coordinates and the method of predicate observations. In particular, a new black-box scheme for defining automatically a suitable set of nonredundant internal coordinates of A1 symmetry in place of the customary Z-matrix has been designed and tested. Finally, the implementation of the method of the predicate observations is discussed and validated for a set of test molecules. As an original application, the method is employed for the determination of the semiexperimental structure for the most stable conformer of glycine.

A Novel Pre-processing and Kernel Based Support Vector Machine Classifier with Discriminative Dictionary Learning for Bone Age Assessment

Aim of this study: Bone age assessment and X-ray assessment on hand radiographs is an expensive and time consuming process in radiology. This research work presents a powerful Graphical User Interface (GUI) for IRMA that gives exceptional medical image retrieval results. Methods: This study gives complete details regarding the execution of a novel Discriminative Dictionary Learning (DDL) for the purpose of matching query and input medical image samples. In order to further boost the quality of the medical images, Principal Component Analysis (PCA) based noise level estimation scheme is introduced. This helps to eliminate noises included in the medical images. Furthermore, to enhance the performance, a new relevance score scheme via Kernel Support Vector Machine (KSVM) is formulated, which efficiently make use of medical images features in order to discriminate the images accurately. This system initiated a new discriminative name called ‘pairwise similarity measurement’ for the discriminativeness of pairs of query and input medical database images and subsequently integrate it with the classification error for discriminativeness in classifier production to generate a unified objective function. Results: Experimentation results assessed the proposed DDL in IRMA framework on a numerous medical images like BAA images and X-Ray skull images and results confirm that DDL performs far better than the state-of the-art approaches significantly in terms of precision, recall, sensitivity, specificity and accuracy. Conclusion: The resulting DDL has a considerable impact on medical CBIR applications.

Micro Hydro Potential Modelling: Integrating GIS into Energy Alternatives for Climate Change Mitigation

This research focused on integrating GIS into energy alternatives for climate change mitigation by creating a GIS-based hydrologic model that can be used to identify sites that have significant potential for micro hydropower development within the River Perkerra catchment area. Hydropower is a clean and renewable energy source that remains largely untapped in the country and its development can be used to mitigate anthropogenic climate change by reducing reliance on fossil or biomass derived fuels. This research established the extent of this resource and whether the available sites with significant micro hydropower potential within the study area were amply copious to warrant further development. Currently, such identification is done physically using means that are menial, costly and significantly time consuming. A 90-metre resolution Digital Terrain Model (DTM) data obtained from the Shuttle Radar Topography Mission and various GIS tools were used to create a hydrologic framework which was used to identify potential sites along River Perkerra that suited any desired head requirement for the purposes of locating micro hydropower plants. The derived model demonstrated that it was possible to identify sites at discrete geographic locations along any stream drainage network using GIS. In addition, the model also provides a decision support system that integrates a powerful graphical user interface, spatial database management system and a generalized river basin network flow model for the purposes of exploiting and developing micro hydropower. With sufficient data on catchment discharge and use of higher resolution DTM, the model can be further enhanced to accurately obtain the total microhydro potential of River Perkerra by aggregating the respective potentials of every steam segment.

Major upgrade of the articulated inspection arm control system to fulfill daily operation requirements

An articulated inspection arm (AIA) has been developed by CEA for visual inspection between pulses inside the Tore Supra tokamak vacuum vessel without breaking temperature and vacuum conditions. The eight meters length robot is composed of a shuttle and six articulated segments with a video camera at its end. A demonstration prototype has been achieved in 2008 at Tore Supra (Gargiulo, 2007; Houry, 2008; Perrot, 2003).A project to upgrade the AIA into a fully operational robot has been undertaken by IRFM and ASIPP in an Associated Laboratory. It will be in operation first in the EAST machine and afterwards in Tore Supra in its WEST (W/Tungsten Environment in Steady-state Tokamak) configuration where it is of paramount importance to survey possible degradation of W component surface.The control system of the robot has been extensively upgraded. The effort has been focused on three areas: (1) improvement of the arm position accuracy, (2) increase of the operational robustness, (3) use of a powerful graphical user interface including simulation of trajectories and robot deployment capabilities in a 3D viewer environment.The aim of this paper is to detail the architecture of the AIA control system.

MESMER: minimal ensemble solutions to multiple experimental restraints

Macromolecular structures and interactions are intrinsically heterogeneous, temporally adopting a range of configurations that can confound the analysis of data from bulk experiments. To obtain quantitative insights into heterogeneous systems, an ensemble-based approach can be employed, in which predicted data computed from a collection of models is compared to the observed experimental results. By simultaneously fitting orthogonal structural data (e.g. small-angle X-ray scattering, nuclear magnetic resonance residual dipolar couplings, dipolar electron-electron resonance spectra), the range and population of accessible macromolecule structures can be probed. We have developed MESMER, software that enables the user to identify ensembles that can recapitulate experimental data by refining thousands of component collections selected from an input pool of potential structures. The MESMER suite includes a powerful graphical user interface (GUI) to streamline usage of the command-line tools, calculate data from structure libraries and perform analyses of conformational and structural heterogeneity. To allow for incorporation of other data types, modular Python plugins enable users to compute and fit data from nearly any type of quantitative experimental data. Conformational heterogeneity in three macromolecular systems was analyzed with MESMER, demonstrating the utility of the streamlined, user-friendly software. https://code.google.com/p/mesmer/

Implementation of Fermi–Dirac statistics and advanced models in PC1D for precise simulations of silicon solar cells

In this work we present a modified version of the commonly used semiconductor simulation program PC1D, named cmd-PC1D 6.0, which applies Fermi–Dirac (F–D) statistics, thus improving on the existing Boltzmann approximation that is employed in the original program. Several up-to-date models for crystalline Si have been implemented in the new program, including injection dependent band gap narrowing, carrier mobility and Auger recombination. The results obtained using cmd-PC1D 6.0 are verified against well-accepted and modern simulations tools for a range of both phosphorus- and boron-doped emitters with varying surface concentration. We find a good correspondence between the simulation results obtained with the different programs, with a deviation of less than 2fA/cm2 for the calculated emitter saturation current density using F–D statistics and less than 0.8 % relative deviation in all the main solar cell parameters under 1 sun illumination. By using the correct carrier statistics and the appropriate set of models it is now possible to avoid the commonly used effective models and adapted values, thus taking a large step in bringing PC1D further towards a more general, consistent and physically meaningful simulation tool for Si solar cells. The new program can be run from a command line or within a recently developed, powerful graphical user interface. Both cmd-PC1D 6.0 and the graphical user interface are freely available for download.

On the Analysis of Soils using an Abaqus‐PANDAS Interface

AbstractThe foundation of buildings proceed from a detailed analysis of the interaction between the building and its environment in order to reduce the costs and ensure safety of the construction. A detailed and reliable analysis of the building‐foundation interaction requires suitable material definitions, an accurate description of the underground, and a model describing the geometry. Following this, a fluid‐saturated soil model, based on the the Theory of Porous Media, will be implemented into the finite‐element research‐code PANDAS, which will be connected to commercial FE package Abaqus. In this regard, one combines the powerful graphical user interface (GUI) for pre‐ and post‐processing and the algorithms of Abaqus with the convenient scripting environment for material definitions of PANDAS. Moreover, the linkage allows for a straight‐forward transfer of PANDAS material models into a well‐known and widely used commercial FE package. (© 2011 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)

EEG and MEG Data Analysis in SPM8

SPM is a free and open source software written in MATLAB (The MathWorks, Inc.). In addition to standard M/EEG preprocessing, we presently offer three main analysis tools: (i) statistical analysis of scalp-maps, time-frequency images, and volumetric 3D source reconstruction images based on the general linear model, with correction for multiple comparisons using random field theory; (ii) Bayesian M/EEG source reconstruction, including support for group studies, simultaneous EEG and MEG, and fMRI priors; (iii) dynamic causal modelling (DCM), an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses, and phase coupling. SPM8 is integrated with the FieldTrip toolbox , making it possible for users to combine a variety of standard analysis methods with new schemes implemented in SPM and build custom analysis tools using powerful graphical user interface (GUI) and batching tools.

Integrating knowledge to assess coastal vulnerability to sea-level rise: The development of the DIVA tool

This paper describes the development of the DIVA tool, a user-friendly tool for assessing coastal vulnerability from subnational to global levels. The development involved the two major challenges of integrating knowledge in the form of data, scenarios and models from various natural, social and engineering science disciplines and making this integrated knowledge accessible to a broad community of end-users. These challenges were addressed by (i) creating and applying the DIVA method, an iterative, modular method for developing integrating models amongst distributed partners and (ii) making the data, scenarios and integrated model, equipped with a powerful graphical user interface, directly and freely available to end-users.

Automatic Extraction of Heap Reference Properties in Object-Oriented Programs

We present a new technique for helping developers understand heap referencing properties of object-oriented programs and how the actions of the program affect these properties. Our dynamic analysis uses the aliasing properties of objects to synthesize a set of roles; each role represents an abstract object state intended to be of interest to the developer. We allow the developer to customize the analysis to explore the object states and behavior of the program at multiple different and potentially complementary levels of abstraction. The analysis uses roles as the basis for three abstractions: role transition diagrams, which present the observed transitions between roles and the methods responsible for the transitions; role relationship diagrams, which present the observed referencing relationships between objects playing different roles; and enhanced method interfaces, which present the observed roles of method parameters. Together, these abstractions provide useful information about important object and data structure properties and how the actions of the program affect these properties. We have implemented the role analysis and have used this implementation to explore the behavior of several Java programs. Our experience indicates that, when combined with a powerful graphical user interface, roles are a useful abstraction for helping developers explore and understand the behavior of object-oriented programs.