Convenient Graphical Interface Research Articles

Processing biological literature with customizable Web services supporting interoperable formats.

Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams.Database URL: http://argo.nactem.ac.uk.

A digital feedback loop and a control program for scanning tunneling microscopes

A designed software for scanning tunneling microscopes (STM), in which the feedback loop operation, STM operation control, and reception and storage of measurement results are based on a single desk top computer with a Linux Ubuntu operational system, is described. A commercial-production data acquisition unit (NI-6229) and an analog unit, consisting of five high-voltage amplifiers, a control unit of stepping piezodrives, and a separate tunneling current preamplifier, are additionally used for operation with an STM. The software was used for controlling a low-temperature (4.2 K) STM with a 3D-positioner for roughly selecting the scanning site and has a convenient graphical user interface.

The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites.

BackgroundMany Protein Data Bank (PDB) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom coordinates is not homogeneous between models or throughout the same model. To avoid basing a research project on a flawed model, we present a tool for assessing the quality of ligands and binding sites in crystallographic models from the PDB.ResultsThe Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e., users with little or no crystallography knowledge). Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed.ConclusionsVHELIBS allows inexperienced users to examine the binding site and the ligand coordinates in relation to the experimental data. This is an important step to evaluate models for their fitness for drug discovery purposes such as structure-based pharmacophore development and protein-ligand docking experiments.

Robust Optimal Design of Experiments for Model Discrimination Using an Interactive Software Tool

Mathematical modeling of biochemical processes significantly contributes to a better understanding of biological functionality and underlying dynamic mechanisms. To support time consuming and costly lab experiments, kinetic reaction equations can be formulated as a set of ordinary differential equations, which in turn allows to simulate and compare hypothetical models in silico. To identify new experimental designs that are able to discriminate between investigated models, the approach used in this work solves a semi-infinite constrained nonlinear optimization problem using derivative based numerical algorithms. The method takes into account parameter variabilities such that new experimental designs are robust against parameter changes while maintaining the optimal potential to discriminate between hypothetical models. In this contribution we present a newly developed software tool that offers a convenient graphical user interface for model discrimination. We demonstrate the beneficial operation of the discrimination approach and the usefulness of the software tool by analyzing a realistic benchmark experiment from literature. New robust optimal designs that allow to discriminate between the investigated model hypotheses of the benchmark experiment are successfully calculated and yield promising results. The involved robustification approach provides maximally discriminating experiments for the worst parameter configurations, which can be used to estimate the meaningfulness of upcoming experiments. A major benefit of the graphical user interface is the ability to interactively investigate the model behavior and the clear arrangement of numerous variables. In addition to a brief theoretical overview of the discrimination method and the functionality of the software tool, the importance of robustness of experimental designs against parameter variability is demonstrated on a biochemical benchmark problem. The software is licensed under the GNU General Public License and freely available at http://sourceforge.net/projects/mdtgui/.

OLED器件光电性能集成测试系统研制

In order to test the performance of organic light-emitting devices(OLEDs),an integrated photoelectric performance test system for OLEDs was designed and developed.The performances of the OLEDs(such as voltage-current,brightness,spectrum,chromaticity coordinates,lifetime,etc) could be measured in the same software.The communication routine between personal computers and the individual test equipments was described.The electroluminescent(EL) properties of OLEDs can be successfully obtained through simple control in a general computer.Using MFC(Microsoft Foundation Classes),a development tool of Microsoft Visual 2005,one convenient graphical user interface was successfully developed.Real-time display of the test process about the devices was realized through TeeChart(a graphical software developed by Steema).Furthermore,the characteristics of different devices could be compared by showing their curves in the same diagram.In addition,one CIE chromaticity coordinates assistant tool was developed,thus we manage to analyze the EL spectra and obtain the CIE chromaticity coordinates of the devices.

Macchess: Unique Opportunities for Structural Biology at a Synchrotron Source

MacCHESS (“Macromolecular diffraction at CHESS”) is an NIH funded facility at the Cornell High Energy Synchrotron Source; we provide a user facility with exceptional staff support. A special MacCHESS strength is developing new x-ray methods to benefit the entire structural biology community.Crystallography - High-flux monochromatic beamlines equipped with large CCD detectors, air bearing-based goniometers, selection of 100-µm or 20-µm beam size, cryocooling, excellent crystal centering systems, and crystal automounters are available. BSL-2 biohazards can be handled. Methods for collecting and processing multi-crystal data sets are under development.BioSAXS - A dedicated beamline features a dual SAXS/WAXS setup using 2 Pilatus detectors and an integrated computer-controlled flow system including robotic sample loading from 96-well trays, a capillary cell with a replaceable insert, and a convenient graphical interface. An HPLC system allows sample preparation immediately before taking data. Microfluidic “lab-on-a-chip” units are under development. Periodic workshops are held to educate users in the intricacies of BioSAXS.Pressure cryocooling - A new method for cryocooling crystals under pressure reduces both cooling-induced degradation and the need for penetrating cryoprotectants, and can stabilize mobile ligands and possibly reaction intermediates. We offer pressure-cooling as a service to CHESS users, while continuing to develop the method. Several sample mounting techniques are now available, and the technique has promise for use with biological samples other than crystals.More information - To request beamtime, fill out a simple on-line proposal form at http://www.chess.cornell.edu. Mail-in service is available for crystallography. We welcome a chance to collaborate on “non-standard” experiments. For more information, contact User Administrator Kathy Dedrick (kd73@cornell.edu).

SlicerRT: Radiation therapy research toolkit for 3D Slicer

Interest in adaptive radiation therapy research is constantly growing, but software tools available for researchers are mostly either expensive, closed proprietary applications, or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we propose SlicerRT, a customizable, free, and open-source radiation therapy research toolkit. SlicerRT aspires to be an open-source toolkit for RT research, providing fast computations, convenient workflows for researchers, and a general image-guided therapy infrastructure to assist clinical translation of experimental therapeutic approaches. It is a medium into which RT researchers can integrate their methods and algorithms, and conduct comparative testing. SlicerRT was implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. SlicerRT provides functionality specifically designed for radiation therapy research, in addition to the powerful tools that 3D Slicer offers for visualization, registration, segmentation, and data management. The feature set of SlicerRT was defined through consensus discussions with a large pool of RT researchers, including both radiation oncologists and medical physicists. The development processes used were similar to those of 3D Slicer to ensure software quality. Standardized mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The testing and validation environment was configured to automatically launch a regression test upon each software change and to perform comparison with ground truth results provided by other RT applications. Modules have been created for importing and loading DICOM-RT data, computing and displaying dose volume histograms, creating accumulated dose volumes, comparing dose volumes, and visualizing isodose lines and surfaces. The effectiveness of using 3D Slicer with the proposed SlicerRT extension for radiation therapy research was demonstrated on multiple use cases. A new open-source software toolkit has been developed for radiation therapy research. SlicerRT can import treatment plans from various sources into 3D Slicer for visualization, analysis, comparison, and processing. The provided algorithms are extensively tested and they are accessible through a convenient graphical user interface as well as a flexible application programming interface.

QCanvas: An Advanced Tool for Data Clustering and Visualization of Genomics Data

We developed a user-friendly, interactive program to simultaneously cluster and visualize omics data, such as DNA and protein array profiles. This program provides diverse algorithms for the hierarchical clustering of two-dimensional data. The clustering results can be interactively visualized and optimized on a heatmap. The present tool does not require any prior knowledge of scripting languages to carry out the data clustering and visualization. Furthermore, the heatmaps allow the selective display of data points satisfying user-defined criteria. For example, a clustered heatmap of experimental values can be differentially visualized based on statistical values, such as p-values. Including diverse menu-based display options, QCanvas provides a convenient graphical user interface for pattern analysis and visualization with high-quality graphics.

Source term characterization program for the decommissioning waste from a CANDU reactor

An automatic source term characterization program was developed, and its structure, logic, and function are explained here in detail. Called the CANDU Activated Source Term Evaluator (CASE), the developed program is equipped with a convenient graphical user interface; it uses MCNP for the neutron transport calculation and ORIGEN2 for activation analysis. CASE can prepare the MCNP input and run MCNP to obtain the neutron flux and the cross section. It can also prepare the ORIGEN2 input for the activation analysis of the region of interest, process the ORIGEN2 output, and compare the estimated specific activity of activated waste with the waste classification standard. CASE is expected to be very useful for reducing the engineering time, minimizing human error, and enhancing the reliability of source term evaluations of decommissioning waste from CANDU reactors.

Accurate and rapid estimation of phosphene thresholds (REPT).

To calibrate the intensity of transcranial magnetic stimulation (TMS) at the occipital pole, the phosphene threshold is used as a measure of cortical excitability. The phosphene threshold (PT) refers to the intensity of magnetic stimulation that induces illusory flashes of light (phosphenes) on a proportion of trials. The existing PT estimation procedures lack the accuracy and mathematical rigour of modern threshold estimation methods. We present an improved and automatic procedure for estimating the PT which is based on the well-established Ψ Bayesian adaptive staircase approach. To validate the new procedure, we compared it with another commonly used procedure for estimating the PT. We found that our procedure is more accurate, reliable, and rapid when compared with an existing PT measurement procedure. The new procedure is implemented in Matlab and works automatically with the Magstim Rapid2 stimulator using a convenient graphical user interface. The Matlab program is freely available for download.

EPILAB: A software package for studies on the prediction of epileptic seizures

Abstract A Matlab ® -based software package, EPILAB, was developed for supporting researchers in performing studies on the prediction of epileptic seizures. It provides an intuitive and convenient graphical user interface. Fundamental concepts that are crucial for epileptic seizure prediction studies were implemented. This includes, for example, the development and statistical validation of prediction methodologies in long-term continuous recordings. Seizure prediction is usually based on electroencephalography (EEG) and electrocardiography (ECG) signals. EPILAB is able to process both EEG and ECG data stored in different formats. More than 35 time and frequency domain measures (features) can be extracted based on univariate and multivariate data analysis. These features can be post-processed and used for prediction purposes. The predictions may be conducted based on optimized thresholds or by applying classifications methods such as artificial neural networks, cellular neuronal networks, and support vector machines. EPILAB proved to be an efficient tool for seizure prediction, and aims to be a way to communicate, evaluate, and compare results and data among the seizure prediction community.

IGTP: A software package for large-scale gene tree parsimony analysis

BackgroundThe ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle.ResultsWe introduce iGTP, a platform-independent software program that implements state-of-the-art algorithms that greatly speed up species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves the functionality and performance of existing gene tree parsimony software and offers advanced features such as building effective initial trees using stepwise leaf addition and the ability to have unrooted gene trees in the input. Moreover, iGTP provides a user-friendly graphical interface with integrated tree visualization software to facilitate analysis of the results.ConclusionsiGTP enables, for the first time, gene tree parsimony analyses of thousands of genes from hundreds of taxa using the duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient graphical user interface.

SPARK

Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform for Agent-based Representation of Knowledge), a framework for agent-based modeling specifically designed for systems-level biomedical model development. SPARK is a stand-alone application written in Java. It provides a user-friendly interface, and a simple programming language for developing Agent-Based Models (ABMs). SPARK has the following features specialized for modeling biomedical systems: 1) continuous space that can simulate real physical space; 2) flexible agent size and shape that can represent the relative proportions of various cell types; 3) multiple spaces that can concurrently simulate and visualize multiple scales in biomedical models; 4) a convenient graphical user interface. Existing ABMs of diabetic foot ulcers and acute inflammation were implemented in SPARK. Models of identical complexity were run in both NetLogo and SPARK; the SPARK-based models ran two to three times faster.

An Effective Information Support System for Medical Management: Indicator Based Intelligence System

A medical organization is a complex body comprising different units and processes which unequivocally pose dilemmas related to hospital management. In this study, we summarize the requirements emerging from hospital indicators as they relate to medical management and propose a new architecture that can effectively support these requirements. The most important characteristics of this indicator based BI (BI) system are: (1) indicator data collection automation, (2) demonstration of a simplified BI key performance indicator (KPI) model using the Taiwan Quality Indicator (TQIP ) project, (3) provision of a convenient and effective graphical user interface, and (4) support for outer feedback information being rejoined into a Data Warehouse for indicator comparison analysis.

A visual programming system for automated problem solving

Although new AI planning algorithms and techniques are being developed and improved rapidly, there is a lack of efficient and easy to use systems able to incorporate and utilize them. Furthermore, while visual representation facilitates design, maintenance and comprehension of planning domains and problems, very few systems incorporate it. This paper presents VLEPPO, an integrated system aiming at visually modeling planning domains and problems through a convenient graphical interface, while maintaining compatibility with the Planning Domain Definition Language (PDDL), with import and export features. Solutions to planning problems can be obtained by invoking different planners employing the web services technology. The demonstration of the system is performed through a case study involving web service composition viewed as a planning problem.

General Theoretical/Computational Tool for Interpreting NMR Spin Relaxation in Proteins

We developed in recent years the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS is a two-body coupled rotator model which accounts rigorously for mode-coupling between the global motion of the protein and the local motion of the spin-bearing probe and allows for general properties of the second rank tensors involved. We showed that a general tool of data analysis requires both capabilities. Several important functionalities were missing in our previous implementations of SRLS in data fitting schemes, and in some important cases, the calculations were tedious. Here we present a general implementation which allows for asymmetric local and global diffusion tensors, distinct local ordering and local diffusion frames, and features a rhombic local potential which includes Wigner matrix element terms of ranks 2 and 4. A recently developed hydrodynamics-based approach for calculating global diffusion tensors has been incorporated into the data-fitting scheme. The computational efficiency of the latter has been increased significantly through object-oriented programming within the scope of the C++ programming language, and code parallelization. A convenient graphical user interface is provided. Currently autocorrelated (15)N spin relaxation data can be analyzed effectively. Adaptation to any autocorrelated and cross-correlated relaxation analysis is straightforward. New physical insight is gleaned on largely preserved local structure in solution, even in chain segments which experience slow local motion. Prospects associated with improved dynamic models, and new applications made possible by the current implementation of SRLS, are delineated.

DEVELOPMENT OF A SIMPLIFIED MODEL FOR ANALYZING THE PERFORMANCE OF KALIMER-600 COUPLED WITH A SUPERCRITICAL CARBON DIOXIDE BRAYTON ENERGY CONVERSION CYCLE

A KALIMER-600 concept which is a type of sodium-cooled fast reactor, has been developed at KAERI. It uses sodium as a primary coolant and is a pool-type reactor to enhance safety. Also, a supercritical carbon dioxide (CO₂) Brayton cycle is considered as an alternative to an energy conversion system to eliminate the sodium water reaction and to improve efficiency. In this study, a simplified model for analyzing the thermodynamic performance of the KALIMER-600 coupled with a supercritical CO₂ Brayton cycle was developed. To develop the analysis model, a commercial modular modeling system (MMS) was adopted as a base engine, which was developed by nHance Technology in USA. It has a convenient graphical user interface and many component modules to model the plant. A new user library for thermodynamic properties of sodium and supercritical CO₂ was developed and attached to the MMS. In addition, some component modules in the MMS were modified to be appropriate for analysis of the KALIMER-600 coupled with the supercritical CO₂ cycle. Then, a simplified performance analysis code was developed by modeling the KALIMER-600 plant with the modified MMS. After evaluating the developed code with each component data and a steady state of the plant, a simple power reduction and recovery event was evaluated. The results showed an achievable capability for a performance analysis code. The developed code will be used to develop the operational strategy and some control logics for the operation of the KALIMER-600 with a supercritical CO₂ Brayton cycle after further studies of analyzing various operational events.

”Performance Modeling of Computer Networks: Special Issue in Memory of Dr. Gunter Bolch” (Eulogies and Editorials)

CINSim is a simulator for modeling a great variety of interconnection networks that are composed of switches, buffers, sources, and destinations. This includes regular networks as well as irregular ones. Steady-state simulation can be applied as well as terminating simulation to observe transient behavior of interconnection networks. Due to the involved stochastic events, e.g. randomly generated traffic, confidence levels and estimated precisions are calculated to determine the accuracy of the results. Additionally, quantiles are provided allowing to estimate the distribution of results. Dynamic reconfiguration of interconnection networks can also be modeled by this simulator. Thus, the reconfiguration process can be observed to investigate the particular network behavior during this time interval. CINSim can be executed on parallel or distributed systems to speed up simulations. To the best of the authors’ knowledge, CINSim is the first simulator that combines those features with a convenient graphical user interface.

TOPPView: An Open-Source Viewer for Mass Spectrometry Data

Visualization of complex mass spectrometric data sets is becoming increasingly important in proteomics and metabolomics. We present TOPPView, an integrated data visualization and analysis tool for mass spectrometric data sets. TOPPView allows the visualization and comparison of individual mass spectra, two-dimensional LC-MS data sets and their accompanying metadata. By supporting standardized XML-based data exchange formats, data import is possible from any type of mass spectrometer. The integrated analysis tools of the OpenMS Proteomics Pipeline (TOPP) allow efficient data analysis from within TOPPView through a convenient graphical user interface. TOPPView runs on all major operating systems and is available free of charge under an open-source license at http://www.openms.de.

The modeling power of CINSim: Performance evaluation of interconnection networks

CINSim is a simulator for modeling a great variety of interconnection networks that are composed of switches, buffers, sources, and destinations. This includes regular networks as well as irregular ones. Steady-state simulation can be applied as well as terminating simulation to observe transient behavior of interconnection networks. Due to the involved stochastic events, e.g. randomly generated traffic, confidence levels and estimated precisions are calculated to determine the accuracy of the results. Additionally, quantiles are provided allowing to estimate the distribution of results. Dynamic reconfiguration of interconnection networks can also be modeled by this simulator. Thus, the reconfiguration process can be observed to investigate the particular network behavior during this time interval. CINSim can be executed on parallel or distributed systems to speed up simulations. To the best of the authors’ knowledge, CINSim is the first simulator that combines those features with a convenient graphical user interface.