PyMOL is often used to generate images of biomolecular structures. Hundreds of parameters in PyMOL provide precise control over the appearance of structures. We developed 241 Python functions—called ...“shortcuts”—that extend and ease the use of PyMOL. A user runs a shortcut by entering its name at the PyMOL prompt. We clustered the shortcuts by functionality into 25 groups for faster look‐up. One set of shortcuts generates new styles of molecular representation. Another group saves files with time stamps in the file names; the unique filenames avoid overwriting files that have already been developed. A third group submits search terms in the user's web browser. The help function prints the function's documentation to the command history window. This documentation includes the PyMOL commands that the user can reuse by copying and pasting onto the command line or into a script file. The shortcuts should save the average PyMOL user many hours per year searching for code fragments in their computer or on‐line.
Statement for Lay Public
Computer‐generated images of protein structures are vital to the interpretation of and communication about the molecular structure of proteins. PyMOL is a popular computer program for generating such images. We made a large collection of macros or shortcuts that save time by executing complex operations with a few keystrokes.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Teachers often complain about the quality of students' written essays in higher education. This study explores the relations between scripted online peer feedback processes and quality of written ...argumentative essay as they occur in an authentic learning situation with direct practical relevance. Furthermore, the effects of the online argumentative peer feedback script on students' written argumentative essay are studied. A pre-test, post-test design was used with 189 undergraduate students who were assigned to groups of three. They were asked to explore various perspectives, and the ‘pros and cons’ on the topic of ‘Genetically Modified Organisms (GMOs)’ in order to write an argumentative essay in the field of biotechnology. The findings reveal that successful students and groups differ in terms of their feedback quality than less-successful students and groups. This implies that when students engage in high-quality, elaborated and justified peer feedback processes, they write high-quality argumentative essays. Furthermore, the results show that the online argumentative peer feedback script enhances the quality of students' written argumentative essay. Explanations for these results, limitations, and recommendations for further research are provided.
•Learning argumentation is a prerequisite for higher education students.•Online peer feedback script can improve students' quality of written essays.•Online peer feedback script can improve students' quality of feedback.•Successful students differ in terms of their feedback quality than less-successful students.•Online peer feedback script provokes students for engaging in high-quality feedback.
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► The Swift parallel scripting language is described in detail. ► Swift provides an implicitly parallel functional data flow computation model that simplifies parallel scripting. ► Swift scripts ...describe parallel execution patterns for running independent serial or parallel programs. ► Swift scales from multicore workstations to petascale systems, using parallel and distributed resources, including clusters, grids, and clouds.
Scientists, engineers, and statisticians must execute domain-specific application programs many times on large collections of file-based data. This activity requires complex orchestration and data management as data is passed to, from, and among application invocations. Distributed and parallel computing resources can accelerate such processing, but their use further increases programming complexity. The Swift parallel scripting language reduces these complexities by making file system structures accessible via language constructs and by allowing ordinary application programs to be composed into powerful parallel scripts that can efficiently utilize parallel and distributed resources. We present Swift’s implicitly parallel and deterministic programming model, which applies external applications to file collections using a functional style that abstracts and simplifies distributed parallel execution.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been ...redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages.
Multiphysics simulations of solid oxide cell (SOC) require extensive experience and can be labor intensive. This paper reports the first successful implementation of automated multiphysics simulation ...process for industrial-scale planar SOC stacks. The automation is realized through Python based Ansys SpaceClaim scripting for building geometric model, Python based Ansys Workbench Meshing scripting for setting numerical grids, and Scheme based Ansys Fluent TUI commands for performing multiphysics simulations. The model building process allows for customized dimensions of all stack components and the corresponding edge grid counts. The automation of simulations streamlines all the computational steps in multiphysics modeling. The multiphysics model is shown to agree well with the experimental data. The automated tool is illustrated in a parametric analysis of SOC operations, illuminating the influences of size, shape and thermal boundary on the stack performance. The automation makes the simulations simple and efficient, invaluable for the SOC design and operation analysis.
•First realization of automated multiphysics modeling of production-scale SOC stacks.•Techniques for automated high-fidelity geometry model building and mesh creation.•Simulation of 6 different sized kW-scale stacks & with different thermal conditions.•Mechanism for the influences of stack size and shape on physical fields revealed.
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This article examines how mortgage fraud is organised in the United Kingdom, what the crime-commissioning processes are for its occurrence and what exogenous conditions and influences support its ...existence and its capacity to reproduce. The article aims to extend understanding beyond the micro-individual-level, such as causal agency, the biographies of actors and their social relations with one another; to a level of understanding that encompasses macro-structural and facilitative factors and conditions that exist in the financial services sector. The research strategy is supported by a multiple case study design, which involves the cross-case analysis of three multi-million-pound mortgage fraud conspiracies. The study combines criminology with sociological inquiry that employs Clegg’s circuits of power theory as a conceptual framework to examine how the roles and activities of fraudsters and key professional agents are otherwise supported by the convergence of dispositional and facilitative conditions and influences in the financial services sector. It is this circuit that supports the existence of mortgage fraud and its capacity to reproduce. Crime scripting is used as a means of transposing the circuits of power framework into criminological research, as the schema is representative of the interrelationship of the causal, dispositional and facilitative powers through which the organisation of mortgage fraud is possible.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
OpenSees, an open source finite element software framework, has been used broadly in the earthquake engineering community for simulating the seismic response of structural and geotechnical systems. ...The framework allows users to perform finite element analysis with a scripting language and for developers to create both serial and parallel finite element computer applications as interpreters. For the last 15 years, Tcl has been the primary scripting language to which the model building and analysis modules of OpenSees are linked. To provide users with different scripting language options, particularly Python, the OpenSees interpreter interface was refactored to provide multi-interpreter capabilities. This refactoring, resulting in the creation of OpenSeesPy as a Python module, is accomplished through an abstract interface for interpreter calls with concrete implementations for different scripting languages. Through this approach, users are able to develop applications that utilize the unique features of several scripting languages while taking advantage of advanced finite element analysis models and algorithms.
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The Netherlands operates as a distribution hub for cocaine, due to its transit characteristics cocaine is imported from South America and distributed to the rest of Europe. To enhance the financial ...approach to organized crimes, this article proposes a new crime script: a financial crime script. With a special focus on the importing stage, 76 Dutch court rulings are analyzed to make a first financial crime script. This financial crime script provides new insight into the proceeds, costs, and means of payment of criminal organizations and therefore could aid law enforcement in calculating criminal gains.
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History is increasingly recognized as a distinctive source of competitive advantage for family businesses. Taking a rhetorical history perspective, we study how a family business leveraged the ...family’s three generations long history of entrepreneurship to sustain profitable growth over 16 years. Through our analysis, we identify three history scripting strategies—embedding, elaborating, and building family history—that created important sources of competitive advantage for the family business, facilitating acceptance by broader communities, building a reputation of continuity, and inspiring innovation through tradition. These findings advance the history-informed understanding of family firms’ idiosyncratic sources of superior performance.
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BFBNIB, FZAB, GIS, IJS, KILJ, NUK, OILJ, SAZU, SBCE, SBMB, UKNU, UL, UM, UPUK
Software applications have taken over our lives. We use and are used by software many times a day. Nevertheless, we know very little about the invisibly ubiquitous workers who write software. Who are ...they and how do they perceive their own practice? How does that shape the ways in which they collaborate to build the myriad of apps that we use every day? Coderspeak provides a critical approach to the digital transformation of our world through an engaging and thoughtful analysis of the people who write software. It is a focused and in-depth look at one programming language and its community – Ruby - based on ethnographic research at a London company and conversations with members of the wider Ruby community in Europe, the Americas and Japan. This book shows that the place people write code, the language they write it in and the stories shared by that community are crucial in questioning and unpacking what it means to be a ‘coder’. Understanding this social group is essential if we are to grasp a future (and a present) in which computer programming increasingly dominates our lives. Praise for Coderspeak 'Heurich perfectly captures the generous camaraderie, quirky spirit and intellectual curiosity at the heart of the Ruby world. Packed with tidbits of Ruby history, code snippets, and fascinating conversations, this book has something to teach every Rubyist.' Jemma Issroff, Ruby Core Team
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