Command Options Research Articles

Bash in the Wild: Language Usage, Code Smells, and Bugs

The Bourne-again shell (Bash) is a prevalent scripting language for orchestrating shell commands and managing resources in Unix-like environments. It is one of the mainstream shell dialects that is available on most GNU Linux systems. However, the unique syntax and semantics of Bash could easily lead to unintended behaviors if carelessly used. Prior studies primarily focused on improving the reliability of Bash scripts or facilitating writing Bash scripts; there is yet no empirical study on the characteristics of Bash programs written in reality, e.g., frequently used language features, common code smells, and bugs. In this article, we perform a large-scale empirical study of Bash usage, based on analyses over one million open source Bash scripts found in Github repositories. We identify and discuss which features and utilities of Bash are most often used. Using static analysis, we find that Bash scripts are often error-prone, and the error-proneness has a moderately positive correlation with the size of the scripts. We also find that the most common problem areas concern quoting, resource management, command options, permissions, and error handling. We envision that these findings can be beneficial for learning Bash and future research that aims to improve shell and command-line productivity and reliability.

Single EMG Sensor-Driven Robotic Glove Control for Reliable Augmentation of Power Grasping

The practical operation of wearable robots requires intuitive, compact, yet reliable control interfaces. However, current myoelectric interfaces based on surface electromyography (EMG) often fail to achieve these requirements by demanding multiple sensors and exhibiting unreliable performance under limb posture changes. In this study, we show that a myoelectric interface on the musculotendinous junctions (MTJs) of the flexor digitorum superficialis (FDS) enables reliable control of a robotic glove with a single EMG sensor by identifying power grasp intentions. We found that the myoelectric signals from the MTJs of the FDS show significantly increased amplitudes exclusively when a power grasp is performed, regardless of the arm posture. We systematically verified that, in identifying power grasp intentions, the proposed single-sensor myoelectric interface even outperforms a five-sensor myoelectric interface around the proximal forearm. By exploiting the unique biological feature of the MTJs, we devised two myoelectric control methods for a robotic glove-Dual-threshold control and Morse-code control-and further showed their performances in practical operations. Dual-threshold control enables direct co-operation between the user and the robotic glove, and Morse-code control provides various command options for the user.

Integrated Control of a Motor/Generator Set Composed of Doubly Fed Induction Machines

This article considers the control problem for a motor/generator set, where a prime mover drives a generator and the electrical power produced drives a motor. Both the generator and the motor are assumed to be doubly fed induction machines with direct ac connection between their stators. The rotors are controlled by three-phase converters, so that operation is possible with motor and generator speeds that are different from each other, and not synchronized with the electrical frequency of the stator voltages. The strong couplings between the two machines motivate the design of an integrated controller. This article proposes a general framework for such a design based on a joint model of the two machines. A specific method is also developed for the control of the stator voltages and the motor velocity. In its simplest form, the proposed algorithm does not rely on current sensors. A current command option is also developed that ensures closer tracking and limiting of the rotor currents. The algorithm is relatively simple and all its parameters can be computed based on the estimates of the machine parameters. Practical implementation and testing can be performed rapidly. Experiments performed on a small-scale laboratory testbed show very good tracking performance of a speed reference profile.

FBB: a fast Bayesian-bound tool to calibrate RNA-seq aligners.

Despite RNA-seq reads provide quality scores that represent the probability of calling a correct base, these values are not probabilistically integrated in most alignment algorithms. Based on the quality scores of the reads, we propose to calculate a lower bound of the probability of alignment of any fast alignment algorithm that generates SAM files. This bound is called Fast Bayesian Bound (FBB) and serves as a canonical reference to compare alignment results across different algorithms. This Bayesian Bound intends to provide additional support to the current state-of-the-art aligners, not to replace them. We propose a feasible Bayesian bound that uses quality scores of the reads to align them to a genome of reference. Two theorems are provided to efficiently calculate the Bayesian bound that under some conditions becomes the equality. The algorithm reads the SAM files generated by the alignment algorithms using multiple command option values. The program options are mapped into the FBB reference values, and all the aligners can be compared respect to the same accuracy values provided by the FBB. Stranded paired read RNA-seq data was used for evaluation purposes. The errors of the alignments can be calculated based on the information contained in the distance between the pairs given by Theorem 2, and the alignments to the incorrect strand. Most of the algorithms (Bowtie, Bowtie 2, SHRiMP2, Soap 2, Novoalign) provide similar results with subtle variations. Current version of the FBB software is provided at https://bitbucket.org/irenerodriguez/fbb CONTACT: rhuerta@ucsd.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Integrated Assessment of no-Regret Climate Change Adaptation Options for Reservoir Catchment and Command Areas

The need for credible, salient and legitimate climate change adaptation options in the water sector, which target location specific adaptation requirements, is well recognized. In developing countries, the low-hanging fruit; no-regret options, should be identified with stakeholders and assessed against future changes in water availability and demand, for comparing effectiveness and robustness. Such integrated basin-scale assessments, including reservoir catchment and command areas, can suitably inform adaptation decision-making. In this study, we integrate participatory and modelling approaches for evaluation of reservoir catchment and command area no-regret options addressing water availability and demand in the Kangsabati river basin. Through multi-level stakeholder workshops we identify and prioritize options, followed by evaluation of two reservoir catchment options; check dams and increasing forest cover and three reservoir command options; changing cropping pattern, traditional ponds and waste water reuse, using the Water Evaluation And Planning (WEAP) model. We use four high resolution (~25 km) regional climate model simulations of future climatic factors, along with non-climatic factors affecting water demand, for forcing WEAP. We find that options have varied ability in addressing adaptation requirements. Amongst catchment options, increasing forest cover addresses adaptation requirements more suitably than check dams, while in the command areas we observe mixed abilities of options, leading to the inference that combining complementary options may be a more useful strategy. We conclude by discussing our experiences with this approach in a developing country context, in terms of benefits, limitations, lessons learnt and future research directions.

Dhreg, Xtdhreg, and Bootdhreg: Commands to Implement Double-Hurdle Regression

The dhreg command implements maximum likelihood estimation of the double-hurdle model for continuously distributed outcomes. The command includes the option to fit a p-tobit model, that is, a model that estimates only an intercept for the hurdle equation. The bootdhreg command (the bootstrap version of dhreg) may be convenient if the data-generating process is more complicated or if heteroskedasticity is suspected. The xtdhreg command is a random-effects version of dhreg applicable to panel data. However, this estimator differs from standard random-effects estimators in the sense that the outcome of the first hurdle applies to the complete set of observations for a given subject instead of applying at the level of individual observations. Command options include estimation of a correlation parameter capturing dependence between the two hurdles.

EEG-Based Mobile Robot Control Through an Adaptive Brain–Robot Interface

A major challenge in two-class brain-computer interface (BCI) systems is the low bandwidth of the communication channel, especially while communicating and controlling assistive devices, such as a smart wheelchair or a telepresence mobile robot, which requires multiple motion command options in the form of forward, left, right, backward, and start/stop. To address this, an adaptive user-centric graphical user interface referred to as the intelligent adaptive user interface (iAUI) based on an adaptive shared control mechanism is proposed. The iAUI offers multiple degrees-of-freedom control of a robotic device by providing a continuously updated prioritized list of all the options for selection to the BCI user, thereby improving the information transfer rate. Results have been verified with multiple participants controlling a simulated as well as physical pioneer robot.

The Need for a National Abortion Reporting Requirement: Why Both Sides Should Be in Support of Better Data

This paper focuses on the status of abortion reporting in the United States and how current data is inadequate. Looking to the two primary collectors of abortion statistics, the CDC and the Guttmacher Institute, this article highlights how both institutions suffer deficiencies and delays with their information gathering and how this is ultimately bad for society. Next, the paper discusses the Supreme Court's treatment of state abortion reporting statutes and how under today's Court, such legislation would likely pass constitutional muster as long as patient confidentiality was maintained. Finally, I discuss potential avenues through which better data can be achieved by Congress, characterized as the command option (legislative mandate), and the bribe option (conditional spending), respectively. I conclude that the bribe option is superior as it avoids concerns of anti-commandeering and allows the states to voluntarily cooperate with federal policy rather than passively resist it.

Generic Mapping Tools: Improved Version Released

Generic Mapping Tools (GMT) is an open‐source software package for the analysis and display of geoscience data, helping scientists to analyze, interpolate, filter, manipulate, project, and plot time series and gridded data sets. The GMT toolbox includes about 80 core and 40 supplemental program modules sharing a common set of command options, file structures, and documentation. Its power to process data and produce publication‐quality graphic presentations has made it vital to a large scientific community that now includes more than 25,000 individual users. GMT's website (http://gmt.soest.hawaii.edu/) exceeds 20,000 visits per month, and server logs show roughly 2000 monthly downloads.

The Remote Sensing and GIS Software Library (RSGISLib)

Key to the successful application of remotely sensed data to real world problems is software that is capable of performing commonly used functions efficiently over large datasets, whilst being adaptable to new techniques. This paper presents an open source software library that was developed through research undertaken at Aberystwyth University for environmental remote sensing, particularly in relation to vegetation science. The software was designed to fill the gaps within existing software packages and to provide a platform to ease the implementation of new and innovative algorithms and data processing techniques. Users interact with the software through an XML script, where XML tags and attributes are used to parameterise the available commands, which have now grown to more than 300. A key feature of the XML interface is that command options are easily recognisable to the user because of their logical and descriptive names. Through the XML interface, processing chains and batch processing are supported. More recently a Python binding has been added to RSGISLib allowing individual XML commands to be called as Python functions. To date the Python binding has over 100 available functions, mainly concentrating on image utilities, segmentation, calibration and raster GIS. The software has been released under a GPL3 license and makes use of a number of other open source software libraries (e.g., GDAL/OGR), a user guide and the source code are available at http://www.rsgislib.org.

Control-display mapping in brain–computer interfaces

Event-related potential (ERP) based brain–computer interfaces (BCIs) employ differences in brain responses to attended and ignored stimuli. When using a tactile ERP-BCI for navigation, mapping is required between navigation directions on a visual display and unambiguously corresponding tactile stimuli (tactors) from a tactile control device: control-display mapping (CDM). We investigated the effect of congruent (both display and control horizontal or both vertical) and incongruent (vertical display, horizontal control) CDMs on task performance, the ERP and potential BCI performance. Ten participants attended to a target (determined via CDM), in a stream of sequentially vibrating tactors. We show that congruent CDM yields best task performance, enhanced the P300 and results in increased estimated BCI performance. This suggests a reduced availability of attentional resources when operating an ERP-BCI with incongruent CDM. Additionally, we found an enhanced N2 for incongruent CDM, which indicates a conflict between visual display and tactile control orientations. Practitioner Summary: Incongruency in control-display mapping reduces task performance. In this study, brain responses, task and system performance are related to (in)congruent mapping of command options and the corresponding stimuli in a brain–computer interface (BCI). Directional congruency reduces task errors, increases available attentional resources, improves BCI performance and thus facilitates human–computer interaction.

Decoding of multichannel EEG activity from the visual cortex in response to pseudorandom binary sequences of visual stimuli

AbstractElectroencephalography (EEG) signals have been an attractive choice to build noninvasive brain computer interfaces (BCIs) for nearly three decades. Depending on the stimuli, there are different responses which one could get from EEG signals. One of them is the P300 response which is a visually evoked response that has been widely studied. Steady state visually evoked potential (SSVEP) is the response to an oscillating stimulus with fixed frequency, which is detectable from the visual cortex. However, there exists some work on using an m‐sequence with different lags as the control sequence of the flickering stimuli. In this study, we used several m‐sequences instead of one with the intent of increasing the number of possible command options in a BCI setting. We also tested two different classifiers to decide between the m‐sequences and study the performance of multi channel classifiers versus single channel classifiers. The study is done over two different flickering frequencies, 15 and 30 Hz to investigate the effect of flickering frequency on the accuracy of the classification methods. Our study shows that the EEG channels are correlated, and although all the channels contain some useful information, but combining them with a multi channel classifier based on the assumption of having conditional independence will not improve the classification accuracy. In addition, we were able to get reasonably good results using the 30 Hz flickering frequency comparing with 15 Hz flickering frequency that will give us the ability of having a shorter training and decision making time. © 2011 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 21, 139–147, 2011

Interactive graphics return to protein science

Visualization of molecular images is an important means of interpreting structural and other data and of communicating scientific results in the field of protein science. Long-time readers of the journal Protein Science will recall that early issues of the journal were accompanied by a floppy disk containing graphical images in the pioneering kinemage format developed by David C. Richardson and Jane S. Richardson (The kinemage: A tool for scientific communication, Protein Science (1992) 1, 3-9.). Unfortunately, kinemages disappeared from Protein Science a decade ago. In this issue, a Commentary by Li and Palmer (Protein Science (2009) 18, 678-681) returns interactive computer graphics to Protein Science. This article incorporates interactive figures, based on the open-source Jmol package (http://jmol.sourceforge.net/), that are viewable using any World-Wide-Web browser through embedded links within the electronic version of the paper. These figures are of two types. First, authors can generate figures specially designed to enhance the information presented in the article (see below). Second, any Protein Data Bank (PDB) code quoted in the manuscript will be linked to the FirstGlance in Jmol viewer (http://molvis.sdsc.edu/fgij/index.htm). This will allow the reader to immediately and interactively visualize the structure in question. No additional files or programs need to be downloaded or installed on a reader's computer in order to view these figures. The molecular images can be manipulated, either using command options provided within the figures (which requires no knowledge of Jmol) or by opening the Jmol console window (which requires a modicum of familiarity with molecular graphics packages). Jmol has been adopted by a number of other journals and organizations, including ACS Chemical Biology, Biochemical Journal, and the International Union of Crystallography, as a platform for “enhanced” figures. The level of interactivity provided by Jmol is the major benefit over animations or embedded movies; of course, animations and movies prepared in standard formats, using for example other molecular graphics software packages, also can be included as supplementary material to a paper in Protein Science. Interactive figures in Protein Science are prepared by incorporating user-generated Jmol scripts and hyertext markup language (html) content into html templates. This hybrid approach simplifies the process of generating figures for new users, but provides flexibility for more expert authors. We emphasize that this initiative is continuing to be developed. The commentary of Li and Palmer is intended to provide readers with a flavor of the system that we have in mind. Feedback is welcome. During the initial “learning phase”, authors wishing to include interactive figures in their papers in Protein Science should contact the Editor for additional information. The re-incorporation of interactive graphics into Protein Science is a long-awaited return of the journal to its roots and an exciting opportunity for authors to augment the usefulness of their papers for readers.

Making Holes and Windows in Surfaces

In this article, we demonstrate makehole, a program which removes points from any Graphics or Graphics3D picture whose coordinates satisfy a stated condition. We also demonstrate transparent and makewindow, programs which make an entire or a specific portion of an opaque surface into a transparent mesh. We use these programs to view the region of integration for a triple integral. This article uses Mathematica 5.2, but with minor modifications all three programs work in Mathematica 6, as well as earlier versions. The makehole program duplicates some of the functionality of the RegionPlot3D command and RegionFunction option of the ParametricPlot3D command in Version 6, while the transparent program behaves like the PlotStyle O None option of the Plot3D command (see Editor’s Note for a demonstration of the Mathematica 6 code).

Human–machine interface based on muscular and brain signals applied to a robotic wheelchair

This paper presents a Human-Machine Interface (HMI) based on the signals generated by eye blinks or brain activity. The system structure and the signal acquisition and processing are shown. The signals used in this work are either the signal associated to the muscular movement corresponding to an eye blink or the brain signal corresponding to visual information processing. The variance is the feature extracted from such signals in order to detect the intention of the user. The classification is performed by a variance threshold which is experimentally determined for each user during the training stage. The command options, which are going to be sent to the commanded device, are presented to the user in the screen of a PDA (Personal Digital Assistant). In the experiments here reported, a robotic wheelchair is used as the device being commanded.

Abnormal muscle coactivation patterns during isometric torque generation at the elbow and shoulder in hemiparetic subjects.

To study abnormal spatial patterns of muscle activation in hemiparetic stroke, we compared EMG activity in paretic and contralateral elbow and shoulder muscles of 10 hemiparetic subjects during 1.5-s voluntary isometric contractions, against five to eight different loads. Isometric forces were generated in eight directions, referenced to a plane orthogonal to the long axis of the forearm, and were recorded by a three degrees of freedom load cell, mounted at the wrist. Surface and intramuscular EMGs of six elbow and six shoulder muscles were recorded from both impaired and contralateral upper extremities of each subject. The spatial characteristics of EMG activation of individual muscles were summarized using two measures. The first, called the 'net resultant EMG vector' is a new measure which calculated the vector sum of EMG magnitudes for each of the eight directions, and the second, index of EMG focus, is a measure of the range of EMG activation recorded for each load level. Use of these measures permitted us to describe spatial EMG characteristics quantitatively, which has not been done previously. We observed consistent and statistically significant shifts in the resultant EMG vector directions in the impaired limb, especially in shoulder and other proximal muscles. Significant increases in the angular range of EMG activity were also identified and were most evident at the elbow. Correlation analysis techniques were used to assess the degree of coactivation of different muscle pairs. There were consistent EMG coactivation patterns observed across all subjects (both normal and hemiparetic). However, in spasticparetic limbs, additional novel coactivational relationships were also recorded, especially between elbow flexors/shoulder abductors and elbow extensors/shoulder adductors. These novel coactivation patterns represent a reduction in the number of possible muscle combinations, or in the number of possible 'synergies' in the paretic limb of the stroke subject. This reduction in number of 'synergies' could result from a loss of descending command options; from an increased reliance on residual, descending brainstem pathways (such as the reticulospinal and vestibulospinal projections); from changes in spinal interneuronal excitability; or from a combination of several of these factors. The relative merits of these hypotheses are addressed.

Deriving Menu Structures through Modal Block Clustering: A Promising Alternative to Hierarchical Techniques

Modal block clustering (MBC) is proposed as an approach more suited to the derivation of menu structures than hierarchical clustering techniques. Problems with the application of hierarchical techniques and pairwise similarity ratings (PWSR) from which the clusters are derived are discussed. MBC defines clusters based on the pattern of common command attributes and provides an objective way to determine the composition and number of menu panels to include in a menu structure. The method also objectively defines command redundancy for the menu panels. The method of MBC was applied to the 97 commands that comprise the CMS operating system resulting in 17 menu categories. The menu categories were used to design a help menu system. The MBC procedure provides a viable methodology for complex systems, such as CMS, which derive increased functionality from numerous command options. System designers can fruitfully and efficiently apply this methodology both to current systems and to proposed systems for which there are no expert users.

Behavioral Aspects of Text Editors

article Free Access Share on Behavioral Aspects of Text Editors Authors: David W. Embley University of Nebraska, Lincoln, Nebraska University of Nebraska, Lincoln, NebraskaView Profile , George Nagy University of Nebraska, Lincoln, Nebraska University of Nebraska, Lincoln, NebraskaView Profile Authors Info & Claims ACM Computing SurveysVolume 13Issue 1March 1981 pp 33–70https://doi.org/10.1145/356835.356838Online:01 March 1981Publication History 61citation1,255DownloadsMetricsTotal Citations61Total Downloads1,255Last 12 Months18Last 6 weeks11 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF