Graphical Analysis Tool Research Articles

Sensitivity analysis using contribution to sample variance plot: Application to a water hammer model

This paper presents “contribution to sample variance plot”, a natural extension of the “contribution to the sample mean plot”, which is a graphical tool for global sensitivity analysis originally proposed by Sinclair. These graphical tools have a great potential to display graphically sensitivity information given a generic input sample and its related model realizations. The contribution to the sample variance can be obtained at no extra computational cost, i.e. from the same points used for deriving the contribution to the sample mean and/or scatter-plots. The proposed approach effectively instructs the analyst on how to achieve a targeted reduction of the variance, by operating on the extremes of the input parameters' ranges. The approach is tested against a known benchmark for sensitivity studies, the Ishigami test function, and a numerical model simulating the behaviour of a water hammer effect in a piping system.

PlantRGS: A Web Server for the Identification of Most Suitable Candidate Reference Genes for Quantitative Gene Expression Studies in Plants

Normalization of quantitative gene expression data with a suitable reference gene is essential for accurate and reliable results. However, the availability and choice of most suitable reference gene(s) showing uniform expression across all the experimental conditions remain a drawback. We have developed a web server, PlantRGS (http://www.nipgr.res.in/PlantRGS), for the identification of most suitable candidate reference gene(s) at the whole-genome level using microarray data for quantitative gene expression studies in plants. Microarray data from more than 11 000 tissue samples for nine plant species have been included in the PlantRGS for meta-analysis. The web server provides a user-friendly graphical user interface-based analysis tool for the identification of most suitable reference genes in the selected plant species under user-defined experimental conditions. Various parameter options and output formats will help users to investigate desired number of most suitable reference genes with wide range of expression levels. Validation of results revealed that novel reference genes identified by the PlantRGS outperforms the traditionally used reference genes in terms of expression stability. We anticipate that the PlantRGS will provide a platform for the identification of most suitable reference gene(s) under given experimental conditions and facilitate quantitative gene expression studies in plants.

Fungal genome resources at NCBI

The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank, and sequence analysis tool BLAST (basic local alignment search tool). However, NCBI integrates many types of biomolecular data from a variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez System. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap, and UniGene DDD (found via UniGene Homepage). Genome Project and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid, and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.

Performance analysis of multi‐level parallelism: inter‐node, intra‐node and hardware accelerators

SUMMARYThe advent of multi‐core processors has made parallel computing techniques mandatory on mainstream systems. With the recent rise in hardware accelerators, hybrid parallelism adds yet another dimension of complexity to the process of software development. The inner workings of a parallel program are usually difficult to understand and verify. This paper presents a tool for graphical program flow analysis of hardware accelerated parallel programs. It monitors the hybrid program execution to record and visualize many performance relevant events along the way. Representative real‐world applications written for both IBM's Cell processor and NVIDIA's CUDA API are studied exemplarily. With our combined monitoring and visualization approach for hardware accelerated multi‐core and multi‐node systems we take the next step in tool evolution towards a highly improved level of detail, precision, and completeness. The contents of this paper is of interest to developers of hardware accelerated applications as well as performance tool architects. Copyright © 2011 John Wiley & Sons, Ltd.

Effect of muffler mounting bracket designs on durability

Automotive industries perform durability tests on vehicles in the end-user environment to reduce failures and warranty costs in the end-user hands. In this paper we present the failure analysis of muffler mounting brackets of three-wheeler vehicles observed during the durability test. Cracks at the weld location between the engine cradle and brackets were observed in all the vehicles at an average distance of 10,000 km. Many possible causes of the failures are identified using fishbone diagram. The fishbone diagram is a graphical analysis tool that provides a systematic way of looking at effects and the causes that contribute to those effects. Statistical analysis of the failure data was conducted using Weibull distribution for durability life prediction. Further investigations were carried out on the design using finite element method (FEM). A FEM model was developed for the engine cradle assembly in which engine and muffler were modeled as point mass. Vertical forces were applied on the assembly using ‘4 g’ criterion, where g is the acceleration due to gravity. The applied force accounts for the high impact forces that act on the structure during durability testing. Results show high magnitude of stresses and strain energy at the weld location. Analysis of the design suggests that bracket was acting as a cantilever beam with one-plane welding mounted on the engine cradle. Modified design, though eliminated the above failure, shifted the failure mode to the bush-bracket region. Various design modifications were carried out and its effect on durability has been discussed. FEM analysis on the final design shows significant reduction in stresses at the critical locations. The new design of the bush-bracket system passed the durability target of 1,00,000 km.

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies

BackgroundMost software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot.ResultsUsing the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool.ConclusionsOur programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.

ViSim: A user-friendly graphical simulation tool for performance analysis of MANET routing protocols

The task of simulation is often complicated, and naive users often look for relatively easier solutions. In many cases, simulations are done with no visual output which makes them non-attractive. In this paper, we present ViSim; a new simulation tool that has a user-friendly graphical interface. ViSim could be useful for researchers, students, teachers in their work, and for the demonstration of various wireless network scenarios on computer screens. It could make the task of simulation more exciting and enhance the interest of the users by avoiding the need to use a complex command-only text interface. ViSim is not a simulation engine, rather it calls ns-2 simulations in the background and makes the task easy for the users to visualize the simulation in a Windows environment. Though ViSim is mainly a simulation demonstration tool, any user with knowledge of ns-2 and Tcl scripting also has the provision to make the necessary modifications and rapid configuration for any other MANET routing scenario. Using our simulation tool, we measured the performances of several Mobile Ad-hoc Network (MANET) routing protocols. In this paper, we present the performance analysis of three prominent MANET routing protocols (DSDV, DSR and AODV) using our tool. Details of the various features of ViSim, brief descriptions of the selected routing protocols and their comparisons, and details about the experiments performed and the results obtained are presented in this work.

RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae

BackgroundRoot and bulb vegetables (RBV) include carrots, celeriac (root celery), parsnips (Apiaceae), onions, garlic, and leek (Alliaceae)—food crops grown globally and consumed worldwide. Few data analysis platforms are currently available where data collection, annotation and integration initiatives are focused on RBV plant groups. Scientists working on RBV include breeders, geneticists, taxonomists, plant pathologists, and plant physiologists who use genomic data for a wide range of activities including the development of molecular genetic maps, delineation of taxonomic relationships, and investigation of molecular aspects of gene expression in biochemical pathways and disease responses. With genomic data coming from such diverse areas of plant science, availability of a community resource focused on these RBV data types would be of great interest to this scientific community.DescriptionThe RoBuST database has been developed to initiate a platform for collecting and organizing genomic information useful for RBV researchers. The current release of RoBuST contains genomics data for 294 Alliaceae and 816 Apiaceae plant species and has the following features: (1) comprehensive sequence annotations of 3663 genes 5959 RNAs, 22,723 ESTs and 11,438 regulatory sequence elements from Apiaceae and Alliaceae plant families; (2) graphical tools for visualization and analysis of sequence data; (3) access to traits, biosynthetic pathways, genetic linkage maps and molecular taxonomy data associated with Alliaceae and Apiaceae plants; and (4) comprehensive plant splice signal repository of 659,369 splice signals collected from 6015 plant species for comparative analysis of plant splicing patterns.ConclusionsRoBuST, available at http://robust.genome.com, provides an integrated platform for researchers to effortlessly explore and analyze genomic data associated with root and bulb vegetables.

AAMI's Benchmarking Solution: Analysis of Cost of Service Ratio and Other Metrics

AMI's Benchmarking Solution (ABS) is a new online tool designed specifically to help clinical engineering (CE) departments measure their practices, policies, and procedures against similar depart- ments at other facilities; monitor their progress through- out the year; and share best practices. The tool includes an online survey with more than 100 benchmarking and best practice questions, both qualitative and quantitative, and a set of graphical analysis tools to help CE depart- ments analyze benchmarking data results against other facilities of particular demographics. The survey tool—developed by a software company, NeuraMetrics, with the guidance of a team of clinical engineering experts hired by AAMI—is structured to en- courage both numeric and non-numeric responses, allow- ing those departments that do not have all the numeric information to participate and enter the data that they do have. This overcomes the problem of some prior clinical engineering benchmarking studies which required many numeric responses that were difficult for some potential participants to provide. Although a very new product, ABS already has a high participation rate. This study looks at the first set of ABS data focusing on and further analyzing some of the quantitative mea- surements available. One key statistical analysis technique used in this study is linear correlation. Linear correlation quantifies the strength of a linear relationship between two variables. When there is no correlation between the two variables, then there is no tendency for the values of one quantity to increase or decrease with the values of the second quantity. When there is 100% correlation, every increase or decrease in one variable has an equivalent in- crease or decrease in the other one. Linear correlation is typically represented by a number between 0.00 (no cor- relation) and ± 1.00 (100% correlation). Sample size in lin- ear correlation studies is relevant; one of the weaknesses of some prior studies 1 is their small sample size. ABS has overcome the small sample size issue with more than 100 institutions subscribing in less than one year of operation. At the time of this analysis (April 2010), 86 organiza- tions had entered data into the ABS database. The pro- cess for data analysis included the following:

Cholesteryl Ester Transfer Protein Polymorphism (TaqIB) Associates With Risk in Postinfarction Patients With High C-Reactive Protein and High-Density Lipoprotein Cholesterol Levels

To investigate the roles of inflammation and a cholesteryl ester transfer protein (CETP) polymorphism potentially related to recent findings demonstrating coronary risk with increasing high-density lipoprotein cholesterol (HDL-C) level. A novel graphical exploratory data analysis tool allowed the examination of coronary risk in postinfarction patients relating to HDL-C and C-reactive protein levels. Results demonstrated a high-risk subgroup, defined by high HDL-C and C-reactive protein levels, exhibiting larger HDL particles and lower lipoprotein-associated phospholipaseA(2) levels than lower-risk patients. Subgroup CETP-associated risk was probed using a functional CETP polymorphism (TaqIB, rs708272). In the high-risk subgroup, multivariable modeling revealed greater risk for B2 allele carriers (less CETP activity) versus B1 homozygotes (hazard ratio, 2.41; 95% CI, 1.04 to 5.60; P=0.04). Within the high-risk subgroup, B2 allele carriers had higher serum amyloid A levels than B1 homozygotes. Evidence also demonstrates that CETP genotypic differences in HDL subfraction distributions regarding non-HDL-C and lipoprotein-associated phospholipaseA(2) may potentially relate to impaired HDL remodeling. Postinfarction patients with high HDL-C and C-reactive protein levels demonstrate increased risk for recurrent events. Future studies should aim at characterizing altered HDL particles from such patients and at elucidating the mechanistic details related to inflammation and HDL particle remodeling. Such patients should be considered in drug trials involving an increase in HDL-C level.

Inflammation reduces HDL protection against primary cardiac risk

We recently reported high high-density lipoprotein (HDL) cholesterol as a predictor of recurrent risk in a subgroup of postinfarction patients defined by hypercholesterolemia and high C-reactive protein (CRP) levels. We investigated whether a similar high-risk subgroup might exist for incident cardiovascular disease. A graphical exploratory data analysis tool was used to identify high-risk subgroups in a male population-based cohort (n = 3405) from the prevention of renal and vascular end-stage disease study by generating 3-dimensional mappings of risk over the HDL-cholesterol/CRP domain with subsequent use of Kaplan-Meier analysis to verify high-risk. Within-subgroup risk was assessed using Cox proportional hazards regression and Kaplan-Meier analysis. Mappings revealed two high-risk subgroups: a low HDL-cholesterol/high CRP subgroup and a high HDL-cholesterol/high CRP subgroup. The low HDL-cholesterol subgroup demonstrated a pattern of metabolic syndrome dyslipidemia contrasted with a predominantly unremarkable biomarker pattern for the high HDL-cholesterol subgroup. However, in the high HDL-cholesterol subgroup, CRP levels were higher than the low HDL-cholesterol subgroup; and within the high HDL-cholesterol subgroup, CRP predicted risk. Moreover, in the high HDL-cholesterol subgroup, risk was associated with lower triglyceride levels in conjunction with presumptively larger HDL particles. High HDL-cholesterol and high CRP levels define a subgroup of men at high-risk for incident cardiovascular disease. High HDL cholesterol-associated risk likely relates to impaired HDL particle remodelling in the setting of inflammation. This approach may facilitate identification of additional inflammation-related mechanisms underlying high HDL cholesterol-associated risk; and potentially influence management of such patients.

Using social network analysis tools in ecology: Markov process transition models applied to the seasonal trophic network dynamics of the Chesapeake Bay

Ecosystem components interact in complex ways and change over time due to a variety of both internal and external influences (climate change, season cycles, human impacts). Such processes need to be modeled dynamically using appropriate statistical methods for assessing change in network structure. Here we use visualizations and statistical models of network dynamics to understand seasonal changes in the trophic network model described by Baird and Ulanowicz [Baird, D., Ulanowicz, R.E., 1989. Seasonal dynamics of the Chesapeake Bay ecosystem. Ecol. Monogr. 501 (59), 329–364] for the Chesapeake Bay (USA). Visualizations of carbon flow networks were created for each season by using a network graphic analysis tool (NETDRAW). The structural relations of the pelagic and benthic compartments (nodes) in each seasonal network were displayed in a two-dimensional space using spring-embedder analyses with nodes color-coded for habitat associations (benthic or pelagic). The most complex network was summer, when pelagic species such as sea nettles, larval fishes, and carnivorous fishes immigrate into Chesapeake Bay and consume prey largely from the plankton and to some extent the benthos. Winter was the simplest of the seasonal networks, and exhibited the highest ascendency, with fewest nodes present and with most of the flows shifting to the benthic bacteria and sediment POC compartments. This shift in system complexity corresponds with a shift from a pelagic- to benthic-dominated system over the seasonal cycle, suggesting that winter is a mostly closed system, relying on internal cycling rather than external input. Network visualization tools are useful in assessing temporal and spatial changes in food web networks, which can be explored for patterns that can be tested using statistical approaches. A simulation-based continuous-time Markov Chain model called SIENA was used to determine the dynamic structural changes in the trophic network across phases of the annual cycle in a statistical as opposed to a visual assessment. There was a significant decrease in outdegree (prey nodes with reduced link density) and an increase in the number of transitive triples (a triad in which i chooses j and h, and j also chooses h, mostly connected via the non-living detritus nodes in position i), suggesting the Chesapeake Bay is a simpler, but structurally more efficient, ecosystem in the winter than in the summer. As in the visual analysis, this shift in system complexity corresponds with a shift from a pelagic to a more benthic-dominated system from summer to winter. Both the SIENA model and the visualization in NETDRAW support the conclusions of Baird and Ulanowicz [Baird, D., Ulanowicz, R.E., 1989. Seasonal dynamics of the Chesapeake Bay ecosystem. Ecol. Monogr. 501 (59), 329–364] that there was an increase in the Chesapeake Bay ecosystem's ascendancy in the winter. We explain such reduced complexity in winter as a system response to lowered temperature and decreased solar energy input, which causes a decline in the production of new carbon, forcing nodes to go extinct; this causes a change in the structure of the system, making it simpler and more efficient than in summer. It appears that the seasonal dynamics of the trophic structure of Chesapeake Bay can be modeled effectively using the SIENA statistical model for network change.

On the sensitivity of the control structure selection problem in large-scale multivariable systems

In complex manufacturing processes, control structure selection poses a serious challenge for the control engineer. Such systems are typically interacting, large scale and may comprise many loops. Choosing a correct control structure is not often a straightforward process, especially, if as it often is the case, one is faced with the challenge of having to integrate additional proposed control systems into an already existing plant-wide control system. Current approaches to the control structure selection problem rely either on the control engineer's experience and intuition or on solutions of difficult and non-convex combinatorial optimisation problems. A set of new computationally inexpensive graphical analysis tools based on basis pursuit regularisation methods are presented that provide significant insight into the control structure selection problem. The tools presented build a centralised controller by incrementally adding one loop at a time to the structure of a baseline decentralised controller. There are no constraints as to where new loops can be added which results in a rich class of sparse controllers. With the aid of an example, it is shown that how these tools are used directly to assess the local structural sensitivity of the problem and to identify key and important connections within the controller.

Analysis of outcomes in radiation oncology: An integrated computational platform

Radiotherapy research and outcome analyses are essential for evaluating new methods of radiation delivery and for assessing the benefits of a given technology on locoregional control and overall survival. In this article, a computational platform is presented to facilitate radiotherapy research and outcome studies in radiation oncology. This computational platform consists of (1) an infrastructural database that stores patient diagnosis, IMRT treatment details, and follow-up information, (2) an interface tool that is used to import and export IMRT plans in DICOM RT and AAPM/RTOG formats from a wide range of planning systems to facilitate reproducible research, (3) a graphical data analysis and programming tool that visualizes all aspects of an IMRT plan including dose, contour, and image data to aid the analysis of treatment plans, and (4) a software package that calculates radiobiological models to evaluate IMRT treatment plans. Given the limited number of general-purpose computational environments for radiotherapy research and outcome studies, this computational platform represents a powerful and convenient tool that is well suited for analyzing dose distributions biologically and correlating them with the delivered radiation dose distributions and other patient-related clinical factors. In addition the database is web-based and accessible by multiple users, facilitating its convenient application and use.

Erratum: A graphical tool for analysis and design of bi‐characteristic‐impedance transmission lines

AbstractOriginally published in Microwave Opt Technol Lett 49: 2368–2372, 2007. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1154, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24260

SimHap GUI: An intuitive graphical user interface for genetic association analysis

BackgroundResearchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool.ResultsWe have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress.ConclusionSimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.

BPMN-based business process model feasibility analysis: a petri net approach

Business process modelling has been widely applied by many companies to support the projects such as BPR or enterprize integration. In general, business modelling technique plays the role of pre-designing and evaluating the business flow before the final implementation. However, due to certain improper situations, the developed model might not be appropriate for the final analysis and evaluation. Therefore, model feasibility should be confirmed before the formal evaluation. This research proposed a Petri-net-based approach to evaluate the feasibility of a model defined by BPMN (business process modelling notation). Two kinds of invalid situations, deadlock and infinite loops, will be defined and analysed. There are four phases in the proposed approach. In problem analysis phase, a modified business process development approach would be proposed first. Then, the invalid model would be defined and classification. In the design stage, the developed BPMN model will be transferred to Modified BPEL4WS, which is an XML based language. By applying XSLT and Java, the transferred BPEL4WS will be translated to a Petri-net model specified as CPNXML (Colored Petri-net XML). In the simulation phase, the CPNXML file can be imported into a graphical simulation package CPN Tools for further analysis. Finally, in the implementation phase, the three kinds of property analysis (deadlock, infinite loops and execution time) will be evaluated in terms of the ‘liveness’, ‘reachability’ and ‘consumed time’ of the converted Petri net model.

A computational and analysis tool for proteomics research

Background Analysis Tool for Proteomics Research (ATP) is our next generation approach for processing, storing and analyzing mass spectrometry-based proteomics data base on our previously developed bioinformatics graphical comparative analysis tools (BIGCAT) software [1]. This software is being developed for the efficient management, visualization, identification, characterization and comparison of peptides and proteins from tandem mass spectrometry experiments. The basic framework of the software suite consists of a back-end relational database to store primary LC-MS/MS data and the peptide/protein identification data from various database search algorithms. The interactive front-end software applications are interfaced to the relational database for managing, visual interpreting, and analyzing the LC-MS/MS results (Figure 1). As an open source and multi-functional analysis software suite, it enables users to 1) customize source code scheme to facilitate specialized experiment aims, 2) manage and load LC-MS/ MS data and protein identification, 3) graphically display and evaluate protein identifications using various views and threshold modifications, 4) compare, merge, and run cluster results from multiple LC-MS/MS experiments, 5) search for neutral losses that are indications of modified peptides, and 6) search immunological peptide motifs. The overall goal is to increase the efficiency and simplicity of managing proteomics data while providing means of publishing and analyzing data on the web in a biologically intuitive and robust way. Acknowledgements We thank Vanderbilt University's Advanced Computing Center for Research and Education (ACCRE), which provides technique support for parallel computing service. Also, thank to Jennifer Jennings for providing from UT-ORNL-KBRIN Bioinformatics Summit 2008 Cadiz, KY, USA. 28–30 March 2008

A graphical tool for analysis and design of bi‐characteristic‐impedance transmission lines

AbstractThe bi‐characteristic‐impedance transmission lines (BCITLs) are generally lossy transmission lines that possess different complex characteristic impedances for waves propagating in forward and reverse directions. Because of complicated equations associated with BCITLs, a graphical tool is necessary in the analysis and design. In this article, the standard T‐chart developed for conjugately characteristic‐impedance transmission lines (CCITLs) is generalized to treat BCITL problems, called a generalized T‐chart. It is found that the way of using this new graphical tool is similar to that of the standard T‐chart. However, the magnitude of the voltage reflection coefficient associated with BCITLs may be greater than unity for some passive load terminations. An example of using a generalized T‐chart is provided in this paper. © 2007 Wiley Periodicals, Inc. Microwave Opt Technol Lett 49: 2368–2372, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.22801

Frequency Response Functions for Nonlinear Convergent Systems

Convergent systems constitute a practically important class of nonlinear systems that extends the class of asymptotically stable linear time-invariant systems. In this note, we extend frequency response functions defined for linear systems to nonlinear convergent systems. Such nonlinear frequency response functions for convergent systems give rise to nonlinear Bode plots, which serve as a graphical tool for performance analysis of nonlinear convergent systems in the frequency domain. The results are illustrated with an example.