Batch Scripts Research Articles

A novel methodology for analysing dental implant positional changes from virtual planning to placement without CBCT.

Introduction This paper introduces a novel methodology for analysing dental implant positioning in vivo, advancing beyond traditional methods that rely on post-placement cone beam computed tomography (CBCT) scans.Method The core of the methodology is comparing stereolithography (STL) files, representing pre-planned and actual post-placement implant positions. These STL files, exported from guided surgery planning and computer-aided design software, focus on clinically significant key points, like the apical and coronal midpoints. Additionally, the method uses pose detection, differing fundamentally from CBCT scan approximations.Discussion Relying on pose detection instead of scanner resolution, this method aligns with international standards and overcomes CBCT and intra-oral scanner limitations. It allows for a more precise and accurate assessment of implant positions, independent of scanner technology constraints. Further refinements include potential detailed reporting of apical deviations, enhancing implant placement accuracy.Conclusion This research has significant implications for dental implantology, enhancing implant placement precision and overall procedure success. Introducing an automated process for report generation through a batch script improves efficiency and precision, streamlining the analysis process. This innovation sets the stage for future technological advancements, improving both the accuracy and reliability of implant placement assessments.

GCDkit.Mineral: A customizable, platform-independent R-language environment for recalculation, plotting, and classification of electron probe microanalyses of common rock-forming minerals

Abstract GCDkit.Mineral is a platform-independent (Windows/Mac/Linux) freeware for recalculation, plotting, and statistical treatment of mineral data obtained by microbeam techniques, typically an electron microprobe. It is written in R, a language providing a feature-rich environment for statistics and data visualization. This new program imports compositional data in various commonly used file formats or retrieves them from the clipboard. Routines are available for data management, i.e., grouping, searching, and generation of subsets, using regular expressions and Boolean logic. Raw compositional data (wt%) are recalculated to atoms per formula unit (apfu) based on a required number of O equivalents, atoms, or charges, with or without FeII/FeIII estimation by various methods. Analyses may then be recast to structural formulae, i.e., the atoms are distributed into appropriate crystallographic sites. For minerals forming solid solutions, the molar percentages of end-members are computed. All the data may be treated statistically, either by built-in functions for descriptive and multivariate statistics or using the wealth of tools provided by the wide R community. Raw and recalculated mineral data may be plotted on assorted binary and ternary plots and boxplots. Most are defined as internal templates that provide a means to make later changes to the plot (zooming and scaling, adding comments or legend, identifying data points, altering the size or color of the plotting symbols, etc.). The publication-ready graphics may be saved into several vector-(PostScript, PDF, and WMF) and bitmap-based (e.g., PNG, TIF, and JPG) formats, ready to be imported into a professional graphical, presentation, or desktop publishing software. Importantly, the graphical templates are used as a basis for classification. The general classification routine looks for the name of the polygon within the diagram (= graphical template), into which the analysis falls according to its x–y coordinates. The outcome may be either the name of a mineral or a link to another diagram in the case of more complex classification schemes. Following the rules of the International Mineralogical Association (IMA), in some cases, the classification is not done graphically but using prescribed algorithms. The class mechanism in R provides an elegant solution to the computational problems presented by the differing requirements of each mineral group. By assigning each mineral species to a particular class, all algorithms may be implemented as mutually independent but mineral group-specific methods. The default recalculation options for each mineral class are stored externally in a small and simple text file. The program is designed to cater to three potential user groups. For users with no familiarity with R, the program is fully menu-driven and contains embedded default recalculation options for many common rock-forming minerals. More experienced users may easily tweak these parameters, as they are saved in a logically structured plain text file. Seasoned R users may invoke GCDkit.Mineral in command line mode, use batch scripts or Python-driven notebooks (e.g., of project Jupyter), or modify and develop new recalculations or plugins. The lucid, open, and modular design thus makes GCDkit.Mineral a versatile workbench for everyday use, as well as a promising platform for community-driven development. The GCDkit family of R tools, including GCDkit. Mineral, is distributed through the WWW. The current version may be downloaded from http://mineral.gcdkit.org.

MzDOCK: A free ready-to-use GUI-based pipeline for molecular docking simulations.

Molecular docking is by far the most preferred approach in structure-based drug design for its effectiveness to predict the scoring and posing of a given bioactive small molecule into the binding site of its pharmacological target. Herein, we present MzDOCK, a new GUI-based pipeline for Windows operating system, designed with the intent of making molecular docking easier to use and higher reproducible even for inexperienced people. By harmonic integration of python and batch scripts, which employs various open source packages such as Smina (docking engine), OpenBabel (file conversion) and PLIP (analysis), MzDOCK includes many practical options such as: binding site configuration based on co-crystallized ligands; generation of enantiomers from SMILES input; application of different force fields (MMFF94, MMFF94s, UFF, GAFF, Ghemical) for energy minimization; retention of selectable ions and cofactors; sidechain flexibility of selectable binding site residues; multiple input file format (SMILES, PDB, SDF, Mol2, Mol); generation of reports and of pictures for interactive visualization. Users can download for free MzDOCK at the following link: https://github.com/Muzatheking12/MzDOCK.

Automated workflows using Quantitative Colour Pattern Analysis (QCPA): a guide to batch processing and downstream data analysis

Animal and plant colouration presents a striking dimension of phenotypic variation, the study of which has driven general advances in ecology, evolution, and animal behaviour. Quantitative Colour Pattern Analysis (QCPA) is a dynamic framework for analysing colour patterns through the eyes of non-human observers. However, its extensive array of user-defined image processing and analysis tools means image analysis is often time-consuming. This hinders the full use of analytical power provided by QCPA and its application to large datasets. Here, we offer a robust and comprehensive batch script, allowing users to automate many QCPA workflows. We also provide a complimentary set of useful R scripts for downstream data extraction and analysis. The presented batch processing extension will empower users to further utilise the analytical power of QCPA and facilitate the development of customised semi-automated workflows. Such quantitatively scaled workflows are crucial for exploring colour pattern spaces and developing ever-richer frameworks for analysing organismal colouration accounting for visual perception in animals other than humans. These advances will, in turn, facilitate testing hypotheses on the function and evolution of vision and signals at quantitative and qualitative scales, which are otherwise computationally unfeasible.

Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline.

Skyline Batch is a newly developed Windows forms application that enables the easy and consistent reprocessing of data with Skyline. Skyline has made previous advances in this direction; however, none enable seamless automated reprocessing of local and remote files. Skyline keeps a log of all of the steps that were taken in the document; however, reproducing these steps takes time and allows room for human error. Skyline also has a command-line interface, enabling it to be run from a batch script, but using the program in this way requires expertise in editing these scripts. By formalizing the workflow of a highly used set of batch scripts into an intuitive and powerful user interface, Skyline Batch can reprocess data stored in remote repositories just by opening and running a Skyline Batch configuration file. When run, a Skyline Batch configuration downloads all necessary remote files and then runs a four-step Skyline workflow. By condensing the steps needed to reprocess the data into one file, Skyline Batch gives researchers the opportunity to publish their processing along with their data and other analysis files. These easily run configuration files will greatly increase the transparency and reproducibility of published work. Skyline Batch is freely available at https://skyline.ms/batch.url.

3Dscript.server: true server-side 3D animation of microscopy images using a natural language-based syntax.

SummaryCreating 3D animations from microscopy data is computationally expensive and requires high-end hardware. We therefore developed 3Dscript.server, a 3D animation software that runs as a service on dedicated, shared workstations. Using 3Dscript as the underlying rendering engine, it offers unique features not found in existing software: rendering is performed completely server-side. The target animation is specified on the client without the rendering engine, eliminating any hardware requirements client-side. Still, defining an animation is intuitive due to 3Dscript’s natural language-based animation description. We implemented a new OMERO web app to utilize 3Dscript.server directly from the OMERO web interface; a Fiji client to use 3Dscript.server from Fiji for integration into image processing pipelines; and batch scripts to run 3Dscript.server on compute clusters for large-scale visualization projects.Availability and implementationSource code and documentation is available at https://github.com/bene51/omero_3Dscript, https://github.com/bene51/3Dscript.server and https://github.com/bene51/3Dscript.cluster.Supplementary information Supplementary data are available at Bioinformatics online.

Automation Process to Support an Information System on Extreme Weather Warning

Hydrometeorological hazard early warning system has been developed in order to support public society in anticipating the extreme weather in Indonesia. Meanwhile, the early warning system in Indonesia still produced locally and need arduous human resources to process the enormous size data to have a good quality early warning. Therefore, in order to increase the effectivity, efficiency, and efficacy of the early warning system to produce the desired result, the automatic process was needed. This study will explain further the mechanism of process automation from the weather forecast to the output of warning displayed in an information system. The automation process combines several scripting in Python and batch script for GIS processing, as well as process scheduling using task scheduler. The output of extreme weather warning is in form of JSON files stored in organized folder directory. The automated process proven to be more useful in increasing the effectivity, efficiency, and efficacy of the early warning system to produce the desired result and later the automated process could be enhanced further to boost the lead time and reducing the arduous task in producing the early warning system.

Mothulity Facilitates 16S/ITS Amplicon Diversity Analysis.

We present Mothulity-a novel interface for Mothur, a well-established tool for 16S/ITS biodiversity analysis. Although Mothur is a well-documented and virtually complete software suite, its proper execution might be challenging for first-time users, and editing the Mothur batch scripts is time consuming even for experienced users. Mothur produces little to no graphical output, leaving the generation of plots to the user. Mothulity minimizes the chance of human error through a minimalistic yet powerful interface, with most of the analysis parameters predefined or adjusted automatically. Time spent on running the analysis is drastically reduced, since Mothulity produces an HTML report with publication-quality figures. Finally, Mothulity can be conveniently used with the SLURM workload manager, and is thereby suitable for a range of computing facilities. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Standard operational procedure (SOP) Basic Protocol 2: Generating report on pre-processed data.

LBtrans-Bot: A Latin-to-Balinese Script Transliteration Robotic System based on Noto Sans Balinese Font

Balinese script writing, as one of Balinese cultural richness, is going to extinct because of its decreasing use. This research is one of the ways to preserve Balinese script writing using technological approach. Through collaboration between Computer Science and Balinese Language discipline, this research focused on the development of a Latin-to-Balinese script transliteration robotic system that was called LBtrans-Bot. LBtrans-Bot can be used as a learning system to give the transliteration knowledge as one aspect of Balinese script writing. In this research area, LBtrans-Bot was known as the first system that utilize Noto Sans Balinese font and was developed based on the identified seventeen kinds of special word. LBtrans-Bot consists of the transliterator web application, the transceiver console application, and the robotic arm with its GUI controller application. The transliterator used the Model-View-Controller architectural pattern, where each of them was implemented by using MySQL database (as the repository for the words belong to the seventeen kinds of special word), HTML, PHP, CSS, and Bootstrap (mostly for the User Interface responsive design), and JavaScript (mostly for the transliteration algorithm and as the controller between the Model and the View). <em>Dictionary</em> data structure was used in the transliterator memory as a place to hold data (words) from the Model. The transceiver used batch script and AutoIt script to receive and trasmit data from the transliterator to the GUI controller, which control the Balinese script writing of the robotic arm. The robotic arm with its GUI controller used open-source mDrawBot Arduino Robot Building platform. Through the experiment, LBtrans-Bot has been able to write the 34-pixel font size of the Noto Sans Balinese font from HTML 5 canvas that has been setup with additional 10-pixel length of the width and the height of the Balinese script writing area. Its transliterator gave the accuracy result up to 91% (138 of 151) testing cases of The Balinese Alphabet writing rules and examples document by Sudewa. This transliterator result outperformed the best result of the known existing transliterator based on Bali Simbar font, i.e. Transliterasi Aksara Bali, that only has accuracy up to 68% (103 of 151) cases of the same testing document. In the future work, LBtrans-Bot could be improved by: 1) Accommodating more complex Balinese script with trade off to the limited writing area of robotic system; 2) Enhancing its transliterator to accommodating the rules and/or examples from the testing document that recently cannot be handled or gave incorrect transliteration result; enriching the database consists of words belong to the seventeen kinds of special word; and implementing semantic relation transliteration.

Assessing Herbarium Specimen Image Quality with FineFocus

The Mid-Atlantic Megalopolis Thematic Collections Network, a digitization project funded by the U.S. National Science Foundation, seeks to digitize ca. 800,000 herbarium specimens through imaging, transcription, and georeferencing. The use of autofocus alone in herbarium specimen imaging with a digital single-lens reflex camera does not yield consistently sharp images, even with relatively two-dimensional specimens and a proper selection of focus point. The FineFocus technique provides a way of assessing contrast, as a proxy for focus quality, through analysis of a standard text target using two freeware programs run through a batch script. By calculating a numeric value, this protocol provides an objective way to obtain a high level of focus quality for a specific imaging rig with given conditions before proceeding with imaging. Adjusting focus with FineFocus yields noticeably sharper images, allowing users to see fine details otherwise obscured by poor focus, such as secondary venation. This technique can be easily implemented in herbarium digitization workflows to improve the quality of specimen images.

CONCEPT AND IMPLEMENTATION OF AN ARCHITECTURE FOR THE IMMEDIATE PROVISION OF GEODATA IN DISASTER MANAGEMENT

Abstract. Statistics prove that the number of disasters, especially weather-related, increased during the last decades. This leads to high demands on participants in disaster management processes. To meet these requirements the provision of geodata, as a part of the information base, plays a key role. A preliminary theoretical consideration points out the evaluation of the benefits of geodata in disaster scenarios as well as the requirements for the provision of geoinformation products and systems in this field of application. There already exist several approaches that differ in the used data, the functionalities or the concept in general. As an alternative, this work introduces a new architectural concept of immediate geodata provision for disaster management based on the usage of free data and free software components. A system consisting of several free software components forms the basis of this approach. With vector data from OpenStreetMap and remote sensing data from the United States Geological Survey a batch script driven geoinformation system creates map tiles or images for end-users in disaster management within minutes.

Transition Rates Assessment of Protective Relay Reliability Models With Incomplete Data

Usually the residence intervals in various states of power equipment are known, yet information about the number of transitions from one state to another is either missing or incomplete. This is mainly caused by a difficulty in recording of the state changes in the protection equipment or poor data acquisition and recording by power utilities. The transition rates are key parameters in all power system reliability models. Partial information on protection systems poses a challenge to construct or complete a transition rate matrix for reliability assessment. This paper addresses an issue of reliability evaluation of protective relays, operating in harmonic polluted environment. It presents a solution to the problem of finding transition rate matrix for a Markov chain of a simplified digital distance relay model. In this approach, the power system network and its associated protection is designed in a graphical preprocessor to Alternative Transients Program (ATPDraw). Parametric simulations of different circuit topologies during nominal and fault conditions are executed, processed, and analyzed automatically through batch and MATLAB scripts. Statistical calculations are implemented to obtain reliability parameters. An example is used to demonstrate the interactive protection system simulation, developed using the new approach.

Automatising the analysis of stochastic biochemical time-series.

BackgroundMathematical and computational modelling of biochemical systems has seen a lot of effort devoted to the definition and implementation of high-performance mechanistic simulation frameworks. Within these frameworks it is possible to analyse complex models under a variety of configurations, eventually selecting the best setting of, e.g., parameters for a target system.MotivationThis operational pipeline relies on the ability to interpret the predictions of a model, often represented as simulation time-series. Thus, an efficient data analysis pipeline is crucial to automatise time-series analyses, bearing in mind that errors in this phase might mislead the modeller's conclusions.ResultsFor this reason we have developed an intuitive framework-independent Python tool to automate analyses common to a variety of modelling approaches. These include assessment of useful non-trivial statistics for simulation ensembles, e.g., estimation of master equations. Intuitive and domain-independent batch scripts will allow the researcher to automatically prepare reports, thus speeding up the usual model-definition, testing and refinement pipeline.

Tarsos, a Modular Platform for Precise Pitch Analysis of Western and Non-Western Music

This paper presents Tarsos, a modular software platform used to extract and analyse pitch organization in music. With Tarsos pitch estimations are generated from an audio signal and those estimations are processed in order to form musicologically meaningful representations. Tarsos aims to offer a flexible system for pitch analysis through the combination of an interactive user interface, several pitch estimation algorithms, filtering options, immediate auditory feedback and data output modalities for every step. To study the most frequently used pitches, a fine-grained histogram that allows up to 1200 values per octave is constructed. This allows Tarsos to analyse deviations in Western music, or to analyse specific tone scales that differ from the 12 tone equal temperament, common in many non-Western musics. Tarsos has a graphical user interface or can be launched using an api—as a batch script. Therefore, it is fit for both the analysis of individual songs and the analysis of large music corpora. The interface allows several visual representations, and can indicate the scale of the piece under analysis. The extracted scale can be used immediately to tune a midi keyboard that can be played in the discovered scale. These features make Tarsos an interesting tool that can be used for musicological analysis, teaching and even artistic productions.

Integrated Development Environment for Debugging Policy-based Applications in Wireless Sensor Networks

Autonomic and customized behavior in Wireless Sensor Networks (WSN) can be facilitated through the support of policy-based programming. Currently, a facility for policy debugging and execution trace does not exist. The state of the art assumes that developers will use other methods such as static analysis, batch scripts, and the emulators/simulators to achieve debugging and testing through unsustainably complex gauntlets of manual tests. In this paper, a new approach for controlling the policy-based WSN application simulation is proposed by creating a Policy Integrated Development Environment (Policy IDE) to work interactively with the TOSSIM simulation software using a packet communication mechanism. The benefits of this approach are truly interactive simulation, granular unit testing, interactive debugging, execution trace to validate application logic, and a simplified debugging process for applications that involve policy programming.

3-D Object Projection Method of Multi-Camera Revolve Batch Rendering

3-D object recognition was different from 2-D one. In order to improve recognition rate, it was necessary to establish a full features base. With object as center, the paper offered a view space projection method of Multi-Camera Revolve Batch Rendering. Firstly, constructed three dimensional models for object, set positions for model and camera of top view. Then by the max panel stick to one of axis angle, copied camera with equal interval. Set up the moving path for hemisphere, and constraint to corresponding camera. In the last, established batch script with output parameters, automatic preservation random projection images for three dimensional objects.

ESTclean: a cleaning tool for next-gen transcriptome shotgun sequencing

BackgroundWith the advent of next-generation sequencing (NGS) technologies, full cDNA shotgun sequencing has become a major approach in the study of transcriptomes, and several different protocols in 454 sequencing have been invented. As each protocol uses its own short DNA tags or adapters attached to the ends of cDNA fragments for labeling or sequencing, different contaminants may lead to mis-assembly and inaccurate sequence products.ResultsWe have designed and implemented a new program for raw sequence cleaning in a graphical user interface and a batch script. The cleaning process consists of several modules including barcode trimming, sequencing adapter trimming, amplification primer trimming, poly-A tail trimming, vector screening and low quality region trimming. These modules can be combined based on various sequencing applications.ConclusionsESTclean is a software package not only for cleaning cDNA sequences, but also for helping to develop sequencing protocols by providing summary tables and figures for sequencing quality control in a graphical user interface. It outperforms in cleaning read sequences from complicated sequencing protocols which use barcodes and multiple amplification primers.

MCdevelop – a universal framework for Stochastic Simulations

We present MCdevelop, a universal computer framework for developing and exploiting the wide class of Stochastic Simulations (SS) software. This powerful universal SS software development tool has been derived from a series of scientific projects for precision calculations in high energy physics (HEP), which feature a wide range of functionality in the SS software needed for advanced precision Quantum Field Theory calculations for the past LEP experiments and for the ongoing LHC experiments at CERN, Geneva. MCdevelop is a “spin-off” product of HEP to be exploited in other areas, while it will still serve to develop new SS software for HEP experiments. Typically SS involve independent generation of large sets of random “events”, often requiring considerable CPU power. Since SS jobs usually do not share memory it makes them easy to parallelize. The efficient development, testing and running in parallel SS software requires a convenient framework to develop software source code, deploy and monitor batch jobs, merge and analyse results from multiple parallel jobs, even before the production runs are terminated. Throughout the years of development of stochastic simulations for HEP, a sophisticated framework featuring all the above mentioned functionality has been implemented. MCdevelop represents its latest version, written mostly in C++ (GNU compiler gcc). It uses Autotools to build binaries (optionally managed within the KDevelop 3.5.3 Integrated Development Environment (IDE)). It uses the open-source ROOT package for histogramming, graphics and the mechanism of persistency for the C++ objects. MCdevelop helps to run multiple parallel jobs on any computer cluster with NQS-type batch system. Program summary Program title: MCdevelop Catalogue identifier: AEHW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEHW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 48 136 No. of bytes in distributed program, including test data, etc.: 355 698 Distribution format: tar.gz Programming language: ANSI C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system. Operating system: Most UNIX systems, Linux. The application programs were thoroughly tested under Ubuntu 7.04, 8.04 and CERN Scientific Linux 5. Has the code been vectorised or parallelised?: Tools (scripts) for optional parallelisation on a PC farm are included. RAM: 500 bytes Classification: 11.3 External routines: ROOT package version 5.0 or higher ( http://root.cern.ch/drupal/). Nature of problem: Developing any type of stochastic simulation program for high energy physics and other areas. Solution method: Object Oriented programming in C++ with added persistency mechanism, batch scripts for running on PC farms and Autotools. Additional comments: Other requirements: • GNU compiler gcc and GNU Build System Autotools – optionally within KDevelop 3.5.3 integrated development environment. • NQS-type batch system (for running jobs in a parallel mode). Running time: For 10 6 events executed from Template 3.8 s – Intel Core 2 Duo, gcc 4.2.4 (Ubuntu 4.2.4 – lobuntu 4), single thread.

Fully Automated Processing of fMRI Data in SPM: from MRI Scanner to PACS

Here we describe the Wake Forest University Pipeline, a fully automated method for the processing of fMRI data using SPM. The method includes fully automated data transfer and archiving from the point of acquisition, real-time batch script generation, distributed grid processing, interface to SPM in MATLAB, error recovery and data provenance, DICOM conversion and PACS insertion. It has been used for automated processing of fMRI experiments, as well as for the clinical implementation of fMRI and spin-tag perfusion imaging. The pipeline requires no manual intervention, and can be extended to any studies requiring offline processing.

Web-based interfaces for simulation of coloured Petri net models

This paper describes an approach which allows users without knowledge of coloured Petri nets to control the simulation of coloured Petri net models and interpret the results obtained from simulations via web-based interfaces. We describe the architecture design of facilities in a simulation tool for making it possible to simulate a coloured Petri net model via a web-based interface. The approach is based on giving the modeller the ability to easily create a CGI script containing the entire simulator. The initial conditions of the simulator for running several simulations can then be specified via a so-called HTML form on a web page. The fact that the initial conditions of a simulation can be specified via a domain specific and user-relevant form, gives users without knowledge of coloured Petri nets and the actual simulation tool the ability to use the pre-constructed simulators for specific analysis purposes. The paper also illustrates that integrating so-called batch scripts into a CGI script has some advantages. Batch scripts give the user the ability to run several simulations after having specified initial conditions for each simulation. Thus, we will be able to first specify input via a web page and then, based on that input, run several simulations. As a representative example we show how to implement the approach in the Design/CPN tool.