Straightforward Interface Research Articles

Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis.

BackgroundRNA interference (RNAi) is an effective and important tool used to study gene function. For large-scale screens, RNAi is used to systematically down-regulate genes of interest and analyze their roles in a biological process. However, RNAi is associated with off-target effects (OTEs), including microRNA (miRNA)-like OTEs. The contribution of reagent-specific OTEs to RNAi screen data sets can be significant. In addition, the post-screen validation process is time and labor intensive. Thus, the availability of robust approaches to identify candidate off-targeted transcripts would be beneficial.ResultsSignificant efforts have been made to eliminate false positive results attributable to sequence-specific OTEs associated with RNAi. These approaches have included improved algorithms for RNAi reagent design, incorporation of chemical modifications into siRNAs, and the use of various bioinformatics strategies to identify possible OTEs in screen results. Genome-wide Enrichment of Seed Sequence matches (GESS) was developed to identify potential off-targeted transcripts in large-scale screen data by seed-region analysis. Here, we introduce a user-friendly web application that provides researchers a relatively quick and easy way to perform GESS analysis on data from human or mouse cell-based screens using short interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs), as well as for Drosophila screens using shRNAs. Online GESS relies on up-to-date transcript sequence annotations for human and mouse genes extracted from NCBI Reference Sequence (RefSeq) and Drosophila genes from FlyBase. The tool also accommodates analysis with user-provided reference sequence files.ConclusionOnline GESS provides a straightforward user interface for genome-wide seed region analysis for human, mouse and Drosophila RNAi screen data. With the tool, users can either use a built-in database or provide a database of transcripts for analysis. This makes it possible to analyze RNAi data from any organism for which the user can provide transcript sequences.

A flexible user-interface for audiovisual presentation and interactive control in neurobehavioral experiments

A major problem facing behavioral neuroscientists is a lack of unified, vendor-distributed data acquisition systems that allow stimulus presentation and behavioral monitoring while recording neural activity. Numerous systems perform one of these tasks well independently, but to our knowledge, a useful package with a straightforward user interface does not exist. Here we describe the development of a flexible, script-based user interface that enables customization for real-time stimulus presentation, behavioral monitoring and data acquisition. The experimental design can also incorporate neural microstimulation paradigms. We used this interface to deliver multimodal, auditory and visual (images or video) stimuli to a nonhuman primate and acquire single-unit data. Our design is cost-effective and works well with commercially available hardware and software. Our design incorporates a script, providing high-level control of data acquisition via a sequencer running on a digital signal processor to enable behaviorally triggered control of the presentation of visual and auditory stimuli. Our experiments were conducted in combination with eye-tracking hardware. The script, however, is designed to be broadly useful to neuroscientists who may want to deliver stimuli of different modalities using any animal model.

GeneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification

BackgroundThe diagnosis and prognosis of several diseases can be shortened through the use of different large-scale genome experiments. In this context, microarrays can generate expression data for a huge set of genes. However, to obtain solid statistical evidence from the resulting data, it is necessary to train and to validate many classification techniques in order to find the best discriminative method. This is a time-consuming process that normally depends on intricate statistical tools.ResultsgeneCommittee is a web-based interactive tool for routinely evaluating the discriminative classification power of custom hypothesis in the form of biologically relevant gene sets. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. Provided with a straightforward and intuitive interface, geneCommittee is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.ConclusionsgeneCommittee allows the enrichment of microarrays raw data with gene functional annotations, producing integrated datasets that simplify the construction of better discriminative hypothesis, and allows the creation of a set of complementary classifiers. The trained committees can then be used for clinical research and diagnosis. Full documentation including common use cases and guided analysis workflows is freely available at http://sing.ei.uvigo.es/GC/.

PAVIS: a tool for Peak Annotation and Visualization

We introduce a web-based tool, Peak Annotation and Visualization (PAVIS), for annotating and visualizing ChIP-seq peak data. PAVIS is designed with non-bioinformaticians in mind and presents a straightforward user interface to facilitate biological interpretation of ChIP-seq peak or other genomic enrichment data. PAVIS, through association with annotation, provides relevant genomic context for each peak, such as peak location relative to genomic features including transcription start site, intron, exon or 5'/3'-untranslated region. PAVIS reports the relative enrichment P-values of peaks in these functionally distinct categories, and provides a summary plot of the relative proportion of peaks in each category. PAVIS, unlike many other resources, provides a peak-oriented annotation and visualization system, allowing dynamic visualization of tens to hundreds of loci from one or more ChIP-seq experiments, simultaneously. PAVIS enables rapid, and easy examination and cross-comparison of the genomic context and potential functions of the underlying genomic elements, thus supporting downstream hypothesis generation.

A flexible user-interface for audiovisual presentation and interactive control in neurobehavioral experiments

A major problem facing behavioral neuroscientists is a lack of unified, vendor-distributed data acquisition systems that allow stimulus presentation and behavioral monitoring while recording neural activity. Numerous systems perform one of these tasks well independently, but to our knowledge, a useful package with a straightforward user interface does not exist. Here we describe the development of a flexible, script-based user interface that enables customization for real-time stimulus presentation, behavioral monitoring and data acquisition. The experimental design can also incorporate neural microstimulation paradigms. We used this interface to deliver multimodal, auditory and visual (images or video) stimuli to a nonhuman primate and acquire single-unit data. Our design is cost-effective and works well with commercially available hardware and software. Our design incorporates a script, providing high-level control of data acquisition via a sequencer running on a digital signal processor to enable behaviorally triggered control of the presentation of visual and auditory stimuli. Our experiments were conducted in combination with eye-tracking hardware. The script, however, is designed to be broadly useful to neuroscientists who may want to deliver stimuli of different modalities using any animal model.

ASHP eBook Collection

ASHP eBook Collection offers at present 50 titles published by the American Society of Health-System Pharmacists, a professional organization for pharmacists and pharmacy technicians. Topics range from clinical references to career advice. Institutions may purchase an annual site license or subscribe a la carte by title. Some features may cause confusion in the end-user in an otherwise straightforward interface. When compared with platforms with more robust customization features, ASHP eBook Collection has few options for tailoring it to an institution's needs. However, the specialized nature of its titles makes this platform a valuable resource to institutions serving pharmacy students, pharmacists, and pharmacy technicians.

A flexible user-interface for audiovisual presentation and interactive control in neurobehavioral experiments

A major problem facing behavioral neuroscientists is a lack of unified, vendor-distributed data acquisition systems that allow stimulus presentation and behavioral monitoring while recording neural activity. Numerous systems perform one of these tasks well independently, but to our knowledge, a useful package with a straightforward user interface does not exist. Here we describe the development of a flexible, script-based user interface that enables customization for real-time stimulus presentation, behavioral monitoring and data acquisition. The experimental design can also incorporate neural microstimulation paradigms. We used this interface to deliver multimodal, auditory and visual (images or video) stimuli to a nonhuman primate and acquire single-unit data. Our design is cost-effective and works well with commercially available hardware and software. Our design incorporates a script, providing high-level control of data acquisition via a sequencer running on a digital signal processor to enable behaviorally triggered control of the presentation of visual and auditory stimuli. Our experiments were conducted in combination with eye-tracking hardware. The script, however, is designed to be broadly useful to neuroscientists who may want to deliver stimuli of different modalities using any animal model.

A flexible user-interface for audiovisual presentation and interactive control in neurobehavioral experiments

A major problem facing behavioral neuroscientists is a lack of unified, vendor-distributed data acquisition systems that allow stimulus presentation and behavioral monitoring while recording neural activity. Numerous systems perform one of these tasks well independently, but to our knowledge, a useful package with a straightforward user interface does not exist. Here we describe the development of a flexible, script-based user interface that enables customization for real-time stimulus presentation, behavioral monitoring and data acquisition. The experimental design can also incorporate neural microstimulation paradigms. We used this interface to deliver multimodal, auditory and visual (images or video) stimuli to a nonhuman primate and acquire single-unit data. Our design is cost-effective and works well with commercially available hardware and software. Our design incorporates a script, providing high-level control of data acquisition via a sequencer running on a digital signal processor to enable behaviorally triggered control of the presentation of visual and auditory stimuli. Our experiments were conducted in combination with eye-tracking hardware. The script, however, is designed to be broadly useful to neuroscientists who may want to deliver stimuli of different modalities using any animal model.

Development of CAM system based on industrial robotic servo controller without using robot language

This paper describes the development of a robotic CAM system for an articulated industrial robot RV1A from the view point of robotic servo controller. It is defined here that the CAM system includes an important function which allows an industrial robot to move along cutter location data (CL data) consisting of position and orientation components. In addition, the developed CAM system has a high applicability to other industrial robots whose servo systems are technically opened to end-users. The developed robotic CAM system works as a straightforward interface between a general CAD/CAM and an industrial robot. At the present stage, the relationship between CAD/CAM and industrial robots is not well established compared to NC machine tools that are widely spread in manufacturing industries. The CAM systems for NC machine tools are already established, however, the CAM system for industrial robots has not been sufficiently considered and developed yet. A teaching pendant is generally used to obtain position and orientation data of the arm tip before an industrial robot works. Here, in order to enhance the relationship between a conventional CAD/CAM system and an industrial robot, a simple and straightforward CAM system without using any robot language is developed and implemented. The basic design of the robotic CAM system and the experimental results are presented in this paper.

Biophysical modeling of brain tumor progression: From unconditionally stable explicit time integration to an inverse problem with parabolic PDE constraints for model calibration

A novel unconditionally stable, explicit numerical method is introduced to the field of modeling brain cancer progression on a tissue level together with an inverse problem (IP) based on optimal control theory that allows for automated model calibration with respect to observations in clinical imaging data. Biophysical models of cancer progression on a tissue level are in general based on the assumption that the spatiotemporal spread of cancerous cells is determined by cell division and net migration. These processes are typically described in terms of a parabolic partial differential equation (PDE). In the present work a parallelized implementation of an unconditionally stable, explicit Euler (EE(⋆)) time integration method for the solution of this PDE is detailed. The key idea of the discussed EE(⋆) method is to relax the strong stability requirement on the spectral radius of the coefficient matrix by introducing a subdivision regime for a given outer time step. The performance is related to common implicit numerical methods. To quantify the numerical error, a simplified model that has a closed form solution is considered. To allow for a systematic, phenomenological validation a novel approach for automated model calibration on the basis of observations in medical imaging data is developed. The resulting IP is based on optimal control theory and manifests as a large scale, PDE constrained optimization problem. The numerical error of the EE(⋆) method is at the order of standard implicit numerical methods. The computing times are well below those obtained for implicit methods and by that demonstrate efficiency. Qualitative and quantitative analysis in 12 patients demonstrates that the obtained results are in strong agreement with observations in medical imaging data. Rating simulation success in terms of the mean overlap between model predictions and manual expert segmentations yields a success rate of 75% (9 out of 12 patients). The discussed EE(⋆) method provides desirable features for image-based model calibration or hybrid image registration algorithms in which the model serves as a biophysical prior. This is due to (i) ease of implementation, (ii) low memory requirements, (iii) efficiency, (iv) a straightforward interface for parameter updates, and (v) the fact that the method is inherently matrix-free. The explicit time integration method is confirmed via experiments for automated model calibration. Qualitative and quantitative analysis demonstrates that the proposed framework allows for recovering observations in medical imaging data and by that phenomenological model validity.

EasyModeller: A graphical interface to MODELLER

BackgroundMODELLER is a program for automated protein Homology Modeling. It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently.FindingsThe study was designed with an aim to develop of "EasyModeller" tool as a frontend graphical interface to MODELLER using Perl/Tk, which can be used as a standalone tool in windows platform with MODELLER and Python preinstalled. It helps inexperienced users to perform modeling, assessment, visualization, and optimization of protein models in a simple and straightforward way.ConclusionEasyModeller provides a graphical straight forward interface and functions as a stand-alone tool which can be used in a standard personal computer with Microsoft Windows as the operating system.

POINeT: protein interactome with sub-network analysis and hub prioritization

BackgroundProtein-protein interactions (PPIs) are critical to every aspect of biological processes. Expansion of all PPIs from a set of given queries often results in a complex PPI network lacking spatiotemporal consideration. Moreover, the reliability of available PPI resources, which consist of low- and high-throughput data, for network construction remains a significant challenge. Even though a number of software tools are available to facilitate PPI network analysis, an integrated tool is crucial to alleviate the burden on querying across multiple web servers and software tools.ResultsWe have constructed an integrated web service, POINeT, to simplify the process of PPI searching, analysis, and visualization. POINeT merges PPI and tissue-specific expression data from multiple resources. The tissue-specific PPIs and the numbers of research papers supporting the PPIs can be filtered with user-adjustable threshold values and are dynamically updated in the viewer. The network constructed in POINeT can be readily analyzed with, for example, the built-in centrality calculation module and an integrated network viewer. Nodes in global networks can also be ranked and filtered using various network analysis formulas, i.e., centralities. To prioritize the sub-network, we developed a ranking filtered method (S3) to uncover potential novel mediators in the midbody network. Several examples are provided to illustrate the functionality of POINeT. The network constructed from four schizophrenia risk markers suggests that EXOC4 might be a novel marker for this disease. Finally, a liver-specific PPI network has been filtered with adult and fetal liver expression profiles.ConclusionThe functionalities provided by POINeT are highly improved compared to previous version of POINT. POINeT enables the identification and ranking of potential novel genes involved in a sub-network. Combining with tissue-specific gene expression profiles, PPIs specific to selected tissues can be revealed. The straightforward interface of POINeT makes PPI search and analysis just a few clicks away. The modular design permits further functional enhancement without hampering the simplicity. POINeT is available at .

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

Most biological membranes are composed of many different kinds of lipid, and can be characterized by the composition of the lipids. Although more and more researchers have shown their interests in molecular dynamics simulation of lipid bilayer or protein-membrane complex system, the setup of such system remains quite challenging for even relatively experienced researchers. In the previous work [1], we have shown that the setup of molecular dynamics simulation for protein-membrane complex can be dramatically simplified by automating the process and providing intuitive and straightforward user interface. In this work, we have further elaborated the process to include 25 different kinds of lipid, which makes it possible to build more biologically relevant lipid bilayers, and we also added the facility to make a lipid bilayer system alone. The efficacy of the web interface at the CHARMM-GUI website [2] has been tested by building and simulating lipid bilayer systems that resemble yeast membrane, which is composed of cholesterol, DPPC, DOPC, POPE, POPA, and POPS. In this work, we will present the usages of the mixed bilayer generation in Membrane Builder and the simulation results of the yeast membrane systems.

Render2MPEG: A Perception‐based Framework Towards Integrating Rendering and Video Compression

AbstractCurrently 3D animation rendering and video compression are completely independent processes even if rendered frames are streamed on‐the‐fly within a client‐server platform. In such scenario, which may involve time‐varying transmission bandwidths and different display characteristics at the client side, dynamic adjustment of the rendering quality to such requirements can lead to a better use of server resources. In this work, we present a framework where the renderer and MPEG codec are coupled through a straightforward interface that provides precise motion vectors from the rendering side to the codec and perceptual error thresholds for each pixel in the opposite direction. The perceptual error thresholds take into account bandwidth‐dependent quantization errors resulting from the lossy com‐pression as well as image content‐dependent luminance and spatial contrast masking. The availability of the discrete cosine transform (DCT) coefficients at the codec side enables to use advanced models of the human visual system (HVS) in the perceptual error threshold derivation without incurring any significant cost. Those error thresholds are then used to control the rendering quality and make it well aligned with the compressed stream quality. In our prototype system we use the lightcuts technique developed by Walter et al., which we enhance to handle dynamic image sequences, and an MPEG‐2 implementation. Our results clearly demonstrate many advantages of coupling the rendering with video compression in terms of faster rendering. Furthermore, temporally coherent rendering leads to a reduction of temporal artifacts.

Exploratory Visual Analysis of Statistical Results from Microarray Experiments Comparing High and Low Grade Glioma

The biological interpretation of gene expression microarray results is a daunting challenge. For complex diseases such as cancer, wherein the body of published research is extensive, the incorporation of expert knowledge provides a useful analytical framework. We have previously developed the Exploratory Visual Analysis (EVA) software for exploring data analysis results in the context of annotation information about each gene, as well as biologically relevant groups of genes. We present EVA as a flexible combination of statistics and biological annotation that provides a straightforward visual interface for the interpretation of microarray analyses of gene expression in the most commonly occuring class of brain tumors, glioma. We demonstrate the utility of EVA for the biological interpretation of statistical results by analyzing publicly available gene expression profiles of two important glial tumors. The results of a statistical comparison between 21 malignant, high-grade glioblastoma multiforme (GBM) tumors and 19 indolent, low-grade pilocytic astrocytomas were analyzed using EVA. By using EVA to examine the results of a relatively simple statistical analysis, we were able to identify tumor class-specific gene expression patterns having both statistical and biological significance. Our interactive analysis highlighted the potential importance of genes involved in cell cycle progression, proliferation, signaling, adhesion, migration, motility, and structure, as well as candidate gene loci on a region of Chromosome 7 that has been implicated in glioma. Because EVA does not require statistical or computational expertise and has the flexibility to accommodate any type of statistical analysis, we anticipate EVA will prove a useful addition to the repertoire of computational methods used for microarray data analysis. EVA is available at no charge to academic users and can be found at http://www.epistasis.org .

E-learning technologies: employing Matlab web server to facilitate the education of mathematical programming

This paper presents new web-based educational software (webNetPro) for Linear Network Programming. It includes many algorithms for Network Optimization problems, such as shortest path problems, minimum spanning tree problems, maximum flow problems and other search algorithms. Therefore, webNetPro can assist the teaching process of courses such as Graph Theory or Network Optimization, Algorithms or Data Structures. Since the Matlab web server is part of the underlying infrastructure, the end user need not use Matlab directly. The approach exploits transparently the benefits of the Matlab programming environment through a straightforward web interface. Furthermore, webNetPro is platform independent. Thus, it can be viewed as a powerful supplement to traditional instruction techniques and can be used without significant difficulties in distance education. Benefits and drawbacks are thoroughly described in order to support the significance of this tool in distance learning.

SPEED: a molecular-evolution-based database of mammalian orthologous groups

The abundance of nucleotide sequence information available has expanded horizons of inquiry for molecular evolution; however, the full potential of whole-genome analysis has not been realized because of inadequate tools. Here, we present one of the first toolkits to aid multidisciplinary high-throughput analysis. SPEED was created to integrate molecular evolutionary data with existing genetic resources and provide a straightforward user interface to 17,352 orthologous gene groups, containing representatives from eight mammalian species and an avian outgroup. See http://bioinfobase.umkc.edu/speed/ for access.

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif

HTHquery is a web-based service to determine if a protein structure has a helix-turn-helix structural motif which could bind to DNA. It is based on a similarity with a set of structural templates, the accessibility of a putative structural motif and a positive electrostatic potential in the neighbourhood of the putative motif. A set of scores are computed, based on each template, using a linear predictor. From the training set used, the predictor has a true positive rate of 83.5% and a false positive rate of 0.8%. The emphasis for the website is on providing a straightforward interface which can be easily used by a bench-based scientist. HTHquery is implemented using a set of Perl scripts and C program and can be accessed freely on the website http://www.ebi.ac.uk/thornton-srv/databases/HTHquery.

RETROCAM: A Versatile Optical Imager for Synoptic Studies

We present RETROCAM, an auxiliary CCD camera that can be rapidly inserted into the optical beam of the MDM 2.4m telescope. The speed and ease of reconfiguring the telescope to use the imager and a straightforward user interface permit the camera to be used during the course of other observing programs. This in turn encourages RETROCAM's use for a variety of monitoring projects.

Tissue-print and print-phoresis as platform technologies for the molecular analysis of human surgical specimens: mapping tumor invasion of the prostate capsule

Molecular profiling of human biopsies and surgical specimens is frequently complicated by their inherent biological heterogeneity and by the need to conserve tissue for clinical diagnosis. We have developed a set of novel 'tissue print' and 'print-phoresis' technologies to facilitate tissue and tumor-marker profiling under these circumstances. Tissue printing transfers cells and extracellular matrix components from a tissue surface onto nitrocellulose membranes, generating a two-dimensional anatomical image on which molecular markers can be visualized by specific protein and RNA- and DNA-detection techniques. Print-phoresis is a complementary new electrophoresis method in which thin strips from the print are subjected to polyacrylamide gel electrophoresis, providing a straightforward interface between the tissue-print image and gel-based proteomic techniques. Here we have utilized these technologies to identify and characterize markers of tumor invasion of the prostate capsule, an event generally not apparent to the naked eye that may result in tumor at the surgical margins ('positive margins'). We have also shown that tissue-print technologies can provide a general platform for the generation of marker maps that can be superimposed directly onto histopathological and radiological images, permitting molecular identification and classification of individual malignant lesions.