Script Execution Research Articles

MATLAB time-based simulations of projectile motion, pendulum oscillation, and water discharge

In addition to teaching undergraduate technical majors about theory and experiments, an important component of their instruction should be to develop proficiency in using computers for simulations and data presentation. A particularly appropriate course for this purpose is classical mechanics because one of the primary goals of that course is to simulate the motion of physical systems, which is greatly aided by visualizations that help to build students’ intuition about expected behaviors. As a demonstration of the ease with which this objective can be accomplished using the MATLAB software package, fully executable scripts are presented here for three commonly studied systems: point projectiles, simple pendula, and water flowing out of a hole in a tank. It is much easier for students to edit a functioning script than to try to write their own from scratch. However, the present scripts are sufficiently short and well-documented that instructors can readily ask their students to modify and adapt them according to their local instructional environments and purposes.

Cloud application deployment with transient failure recovery

Application deployment is a crucial operation for modern cloud providers. The ability to dynamically allocate resources and deploy a new application instance based on a user-provided description in a fully automated manner is of great importance for the cloud users as it facilitates the generation of fully reproducible application environments with minimum effort. However, most modern deployment solutions do not consider the error-prone nature of the cloud: Network glitches, bad synchronization between different services and other software or infrastructure related failures with transient characteristics are frequently encountered. Even if these failures may be tolerable during an application’s lifetime, during the deployment phase they can cause severe errors and lead it to failure. In order to tackle this challenge, in this work we propose AURA, an open source system that enables cloud application deployment with transient failure recovery capabilities. AURA formulates the application deployment as a Directed Acyclic Graph. Whenever a transient failure occurs, it traverses the graph, identifies the parts of it that failed and re-executes the respective scripts, based on the fact that when the transient failure disappears the script execution will succeed. Moreover, in order to guarantee that each script execution is idempotent, AURA adopts a lightweight filesystem snapshot mechanism that aims at canceling the side effects of the failed scripts. Our thorough evaluation indicated that AURA is capable of deploying diverse real-world applications to environments exhibiting high error probabilities, introducing a minimal time overhead, proportional to the failure probability of the deployment scripts.

Action affordances and visuo-spatial complexity in motor imagery: An fMRI study

Imagining a complex action requires not only motor-related processing but also visuo-spatial imagery. In the current study, we examined visuo-spatial complexity and action affordances in motor imagery (MI). Using functional magnetic resonance imaging, we investigated the neural activity in MI of reach-to-grasp movements of the right hand in five conditions. Thirty participants were scanned while imagining grasping an everyday object, grasping a geometrical shape, grasping next to an everyday object, grasping next to a geometrical shape, and grasping at nothing (no object involved). We found that MI of grasping next to an object recruited the visuo-spatial cognition network including posterior parietal and premotor regions more strongly than MI of grasping an object. This indicates that grasping next to an object requires additional processing resources rendering MI more complex. MI of a grasping movement involving a familiar everyday object compared to a geometrical shape yielded stronger activation in motor-related regions, including the bilateral supplementary motor area. This activation might be due to inhibitory processes preventing motor execution of motor scripts evoked by everyday objects (action affordances). Our results indicate that visuo-spatial cognition plays a significant role in MI.

Development of hierarchical goal representation in the control of script execution

Development of hierarchical goal representation in the control of script execution

An Interactive and Comprehensive Working Environment for High-Energy Physics Software with Python and Jupyter Notebooks

Today’s analyses for high-energy physics (HEP) experiments involve processing a large amount of data with highly specialized algorithms. The contemporary workflow from recorded data to final results is based on the execution of small scripts – often written in Python or ROOT macros which call complex compiled algorithms in the background – to perform fitting procedures and generate plots. During recent years interactive programming environments, such as Jupyter, became popular. Jupyter allows to develop Python-based applications, so-called notebooks, which bundle code, documentation and results, e.g. plots. Advantages over classical script-based approaches is the feature to recompute only parts of the analysis code, which allows for fast and iterative development, and a web-based user frontend, which can be hosted centrally and only requires a browser on the user side. In our novel approach, Python and Jupyter are tightly integrated into the Belle II Analysis Software Framework (basf2), currently being developed for the Belle II experiment in Japan. This allows to develop code in Jupyter notebooks for every aspect of the event simulation, reconstruction and analysis chain. These interactive notebooks can be hosted as a centralized web service via jupyterhub with docker and used by all scientists of the Belle II Collaboration. Because of its generality and encapsulation, the setup can easily be scaled to large installations.

Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.

Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels.

Developing control over the execution of scripts: The role of maintained hierarchical goal representations

The execution of a script often requires detecting and resolving conflict with a goal, particularly in nonroutine situations. To take the example of taking a bus daily to work, if someone’s usual bus is delayed and a bus for another destination comes first, the person must inhibit taking it and wait for the usual one. Young children can gradually acquire the ability to control the execution of scripts in such nonroutine situations, but few studies have explored the control process involved. In two experiments, we investigated the role of developments in the maintenance of hierarchical goal representations and in executive functions. We measured the ability to control the execution of scripts using a task in which children helped a doll select items to wear; clothing options were presented in an unexpected order in the nonroutine situations. The younger children (4-year-olds) could not flexibly control their execution of scripts in nonroutine situations, although they could exogenously detect and resolve conflict if they were prompted to maintain a subgoal. The older children (5-year-olds) endogenously controlled script execution based on a main goal, whereas subgoal maintenance led them to rigidly control their performance. In addition, children’s inhibition abilities were associated with their control of script execution. These findings indicate that the development of the control process underlying the execution of scripts in nonroutine situations is partially dependent on the ability to maintain hierarchical goal representations.

NoWorkflow

We present noWorkflow, an open-source tool that systematically and transparently collects provenance from Python scripts, including data about the script execution and how the script evolves over time. During the demo, we will show how noWorkflow collects and manages provenance, as well as how it supports the analysis of computational experiments. We will also encourage attendees to use noWorkflow for their own scripts.

A Tutorial on Pharmacodynamic Scripting Facility inSimcyp.

The Simcyp Simulator provides a framework for mechanistic Physiologically‐Based Pharmacokinetic/Pharmacodynamic modeling of potentially interacting drugs. It also provides a scripting facility, using the Lua language, for developing customized pharmacodynamic and toxicity models driven by drug concentrations at the site of action. We present an overview of the scripting facility including the scripting language, the editor, and how scripts are embedded within the Simulator. Examples incorporating differential equations and including inter‐individual variability on parameters are presented.

Python Executable Script for Estimating Two Effective Parameters to Individualize Brain-Computer Interfaces: Individual Alpha Frequency and Neurophysiological Predictor.

A brain-computer interface (BCI) aims to establish communication between the human brain and a computing system so as to enable the interaction between an individual and his environment without using the brain output pathways. Individuals control a BCI system by modulating their brain signals through mental tasks (e.g., motor imagery or mental calculation) or sensory stimulation (e.g., auditory, visual, or tactile). As users modulate their brain signals at different frequencies and at different levels, the appropriate characterization of those signals is necessary. The modulation of brain signals through mental tasks is furthermore a skill that requires training. Unfortunately, not all the users acquire such skill. A practical solution to this problem is to assess the user probability of controlling a BCI system. Another possible solution is to set the bandwidth of the brain oscillations, which is highly sensitive to the users' age, sex and anatomy. With this in mind, NeuroIndex, a Python executable script, estimates a neurophysiological prediction index and the individual alpha frequency (IAF) of the user in question. These two parameters are useful to characterize the user EEG signals, and decide how to go through the complex process of adapting the human brain and the computing system on the basis of previously proposed methods. NeuroIndeX is not only the implementation of those methods, but it also complements the methods each other and provides an alternative way to obtain the prediction parameter. However, an important limitation of this application is its dependency on the IAF value, and some results should be interpreted with caution. The script along with some electroencephalographic datasets are available on a GitHub repository in order to corroborate the functionality and usability of this application.

SU‐F‐T‐399: Migration of Treatment Planning Systems Without Beam Data Measurement

Purpose:Data acquisition for commissioning is steered by Treatment Planning System (TPS) requirements which can be cumbersome and time consuming involving significant clinic downtime. The purpose of this abstract is to answer if we could circumvent this by extracting data from existing TPS and speed up the process.Methods:Commissioning beam data was obtained from a clinically commissioned TPS (Pinnacle™) using Matlab™ generated Pinnacle™ executable scripts to commission a secondary 3D dose verification TPS (Eclipse™). Profiles and output factors for commissioning as required by Eclipse™ were computed on a 50 cm3 water phantom at a dose grid resolution of 2mm3. Verification doses were computed and compared to clinical TPS dose profiles as per TG‐106 guidelines. Standard patient plans from Pinnacle™ including IMRT and VMAT plans were re‐computed keeping the same monitor units (in order to perform true comparison) using Eclipse™. Computed dose was exported back to Pinnacle for comparison to original plans. This methodology enables us to alleviate all ambiguities that arise in such studies.Results:Profile analysis using in‐house software for 6x, showed that for all field sizes including small MLC generated fields, 100% of infield and penumbra data points of Eclipse™ match Pinnacle™ generated and measured profiles with 2%/2 mm gamma criteria. Excellent agreement was observed in the penumbra regions, with all data points passing DTA criteria for complex C‐shaped and S‐shaped profiles. Patient plan dose volume histograms (DVHs) and isodose lines agreed well to within a 1.5% for target coverage.Conclusion:Secondary 3D dose checking is of utmost importance with advanced techniques such as IMRT and VMAT. Migration of TPS is possible without compromising accuracy or enduring the cumbersome measurement of commissioning data. Economizing time for commissioning such a verification system or for migration of TPS can add great QA value and minimize downtime

Optimisation of automatic variable graphic layout and imposition

Original scientific paper The benefit of automation in graphic prepress lies primarily in an increase of efficiency in the production of layout and imposition of repetitive tasks by shortening lead time. Another benefit is cost reduction, since more work can be done with fewer staff members. One way of automating is by using scripts. Scripts can be written to execute just one task, complex scripts can perform multiple tasks and some scripts automate the entire publishing process. With scripts that execute complex tasks execution period can be time consuming. This paper describes the script that was made to automate variable data layout, imposition and to number digital printing. Quantitative research was carried out in this paper to determine achieved automation and time reduction by using automated processes. This paper also deals with written script optimization in order to shorten the time of its execution and to identify factors that affect the script execution time.

Schinus Terebinthifolius Raddi, Popular Use, Chemical Composition, and Biological Activity: A Systematic Review

Introduction: The advance of quantitative and qualitative research has been proving the use of plants as medic ine. Considering that many people are adept at popular practices and Schinus terebinthifolis Raddi is native to South America, abundant in the coastal regions of Brazil, where it is popularly known as ‘aroeira’ (Brazilian peppertree). Objective: Identify the primary studies regarding the popular use, chemical composition, and the main biological activities of Schinus terebinthifolis Raddi. Metodology: This study attempted to identified, through a previous defined methodology, the systematic review, primary studies regarding the popular use, chemical composition, and the main biological activities of Schinus terebinthifolis Raddi. The survey was conducte d in virtual libraries commonly accessed by the scientific community following a script execution and inclusion of some articles. Results: After all steps of selection, we obtained a total of eighty - one, a number of studies on popular use, the chemical co mposition, and biological activities of the plant were achieved. The biological activity found and described for this plant is quite extensive. Thirty - eight works surveyed demonstrate that are several scientifically proven recommendations for using differe nt parts of the plant. Conclusion: This review enabled to systematize the knowledge produced on the main popular use, the main researches related to biological activity, and the range of chemical constituents of Schinus terebinthifolius Raddi already isola ted.

Safe reconfiguration of Coqcots and Pycots components

Software systems have to face evolutions of their running context and users. Therefore, the so-called dynamic reconfiguration has been commonly adopted for modifying some components and/or the architecture at runtime. Traditional approaches typically stop the needed components, apply the changes, and restart the components. However, this scheme is not suitable for critical systems and degrades user experience. This paper proposes to switch from the stop/restart scheme to dynamic software updating(DSU) techniques. Instead of stopping a component, its implementation is replaced by another one specifically built to apply the modifications while maintaining the best quality of service possible. The major contributions of this work are: (i) the integration of DSU techniques in a component model; (ii) a reconfiguration development process including specification, proof of correctness using Coq, and; (iii) a systematic method to produce the executable script. In this perspective, the use of DSU techniques brings higher quality of service when reconfiguring component-based software. Moreover, the formalization allows ensuring the safety and consistency of the reconfiguration process.

Plann: A command-line application for annotating plastome sequences.

Premise of the study:Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on a similar, well-annotated plastome.Methods and Results:Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann’s output can be used in the National Center for Biotechnology Information’s tbl2asn to create a Sequin file for GenBank submission.Conclusions:Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved.

A Mobile Cloud Computing System for Mathematical Computation

This paper is aimed at proposing a mobile cloud computing system called M2C (Mobile Math Cloud). This system provides users with an APP to accelerate the execution of MATLAB instructions and scripts on their Android-based mobile devices by taking advantage of diverse processors including CPUs and GPUs available in clouds. On the other hand, it supports time-sharing license management to reduce the user time of waiting system services and increase the resource utilization of clouds. Moreover, it supports parallel computing and optimal resource configurations for maximizing the performance of user applications, and faulty tolerance for recovering the contexts of user programs from system faults. With these supports, M2C provides a reliable and efficient service for mobile users to perform massive mathematical computation anytime anywhere.

Integrating task planning, execution and monitoring for a domestic service robot

Abstract Embodied artificial agents operating in dynamic, real-world environments need architectures that support the special requirements that exist for them. Architectures are not always designed from scratch and the system then implemented all at once, but rather, a step-wise integration of components is often made to increase functionality. In order to increase flexibility and robustness, a task planner was integrated into an existing architecture and the planning process was coupled with the pre-existing execution and the basic monitoring processes. This involved the conversion of monolithic SMACH scenario scripts (state-machine execution scripts) into modular states that can be called dynamically based on the plan that was generated by the planning process. The procedural knowledge encoded in such state machines was used to model the planning domain for two RoboCup@Home scenarios on a Care-O-Bot 3 robot. This was done for the JSHOP2 hierarchical task network (HTN) planner. A component which iterates through a generated plan and calls the appropriate SMACH states was implemented, thus enabling the scenarios. Crucially, individual monitoring actions which enable the robot to monitor the execution of the actions were designed and included, thus providing additional robustness.

SALOON: a platform for selecting and configuring cloud environments

SummaryMigrating legacy systems or deploying a new application to a cloud environment has recently become very trendy, because the number of cloud providers available is still increasing. These cloud environments provide a wide range of resources at different levels of functionality, which must be appropriately configured by stakeholders for the application to run properly. Handling this variability during the configuration and deployment stages is known as a complex and error‐prone process, usually made in anad hocmanner. In this paper, we proposeSALOON, asoftware product lines‐based platform to face these issues. We describe the architecture of theSALOONplatform, which relies on feature models combined with a domain model used to select among cloud environments a well‐suited one.SALOONsupports stakeholders while configuring the selected cloud environment in a consistent way and automates the deployment of such configurations through the generation of executable configuration scripts. This paper also reports on some experiments, showing that usingSALOONsignificantly reduces time to configure a cloud environment compared with a manual approach and provides a reliable way to find a correct and suitable configuration. Moreover, our empirical evaluation shows that our approach is effective and scalable to properly deal with a significant number of cloud environments. Copyright © 2015 John Wiley & Sons, Ltd.

A new generation of online laboratories for teaching automatic control

Traditionally, online control education labs are designed and implemented with the purpose of teaching on a specific topic: controller tuning, stability, etc. These tools usually have a monolithic design: there is a strong binding between the model and the control. Usually, there is a built-in controller that may have a set of modifiable parameters, but the controller itself cannot be changed. Also, it cannot be easily translated to other system, for example to compare the performance. In other words, the system subject of study is not very configurable, which unnecessarily constrains the possibilities of these tools. Though this approach may be adequate for some situations, it would be interesting to have more flexible and versatile online laboratories, for instance, in Master courses, where students are expected to design and test advanced control laws. This paper proposes a new paradigm to develop such tools. An element has been deployed and allows the dynamic execution of scripts written in different programming languages, such as Java, Javascript, or Matlab. The final aim is to provide students with a tool to promote an active participation in the practice, writing their own controller code and freely experimenting with the system. The paradigm is illustrated with some examples of these new generation online laboratories.

Bioanalytical laboratory automation development: why should we and how could we collaborate?

Bioanalytical laboratory automation development: why should we and how could we collaborate?