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COMPUTERS & CHEMICAL ENGINEERING 1998年第12期22卷 1745-1747页

作者： Spotnitz, R Hoechst Celanese Corp Charlotte NC 28273 USA

An application of literate programming methodology using WEB tools to chemical engineering is provided. literate programming produces beautifully typeset manuscripts that combine textual explanation and fragments of computer code. literate programming is especially useful for technical programming because the possibility for errors is reduced when the textual explanation and code are combined. (C) 1998 Elsevier Science Ltd. All rights reserved.

关键词： WEB literate programming technical programming

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ActinoMation: A literate programming approach for medium-throughput robotic conjugation of Streptomyces spp

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SYNTHETIC AND SYSTEMS BIOTECHNOLOGY 2025年第2期10卷 667-676页

作者： Moller, Tenna A. Booth, Thomas J. Shaw, Simon Moller, Vilhelm K. Frandsen, Rasmus J. N. Weber, Tilmann Tech Univ Denmark Novo Nordisk Fdn Ctr Biosustainabil Lyngby Denmark Tech Univ Denmark DTU Bioengn Lyngby Denmark

The genus Streptomyces are valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineering tools, such as CRISPR, have provided some access to the metabolic potential of Streptomyces, but efficient genetic engineering of strains is hindered by laborious and slow manual transformation protocols. In this paper, we present a semi-automated medium-throughput workflow for the introduction of recombinant DNA into Streptomyces spp. using the affordable and open-sourced Opentrons (OT-2) robotics platform. To increase the accessibility of the workflow we provide an open-source protocolcreator, ActinoMation. ActinoMation is a literate programming environment using Python in Jupyter Notebook. We validated the method by transforming Streptomyces coelicolor (M1152 and M1146), S. albidoflavus (J1047), and S. venezuelae (DSM40230) with the plasmids pSETGUS and pIJ12551. We demonstrate conjugation efficiencies of 3.33*10-3/0.33 % for M1152 with pSETGUS and pIJ12551;2.96*10-3/0.29 % for M1146 with pSETGUS and pIJ12551;1.21*10-5/0.0012 % for J1047 with pSETGUS and 4.70*10-4/0.047 % with pIJ12551, and 4.97*10-2/4.97 % for DSM40230 with pSETGUS and 6.13*10-2/6.13 % with pIJ12551 with a false positive rate between 8.33 % and 54.54 %. Automation of the conjugation workflow facilitates a streamlined workflow on a larger scale without any evident loss of conjugation efficiency.

关键词： Streptomyces Conjugation literate programming High-throughput Liquid handling

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literate programming ON A TEAM PROJECT

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SOFTWARE-PRACTICE & EXPERIENCE 1991年第7期21卷 677-683页

作者： RAMSEY, N MARCEAU, C ODYSSEY RES ASSOCIATES ITHACANY 14850

We used literate programming on a team project to write a 33,000 line program for the Synthesizer Generator. The program, Penelope, was written using WEB, a tool designed for writing literate programs. Unlike other WEB programs, many of which have been written by WEB's developer or by individuals, Penelope was not intended to be published. We used WEB in the hope that both our team and its final product would benefit from the advantages often attributed to literate programming. The WEB source served as good internal documentation throughout development and maintenance, and it continues to document Penelope's design and implementation. Our experience also uncovered a number of problems with WEB.

关键词： literate programming WEB

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literate programming in quantum chemistry: A simple example

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INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2005年第4期104卷 430-445页

作者： Quiney, HM Wilson, S Rutherford Appleton Lab Oxford 0X11 0QX England

literate programming methods have not been widely used in computational molecular structure theory. We argue that significant advantages would result from the use of literate programming methods in the computational molecular sciences and, indeed, in computational science, in general. Our arguments are illustrated by a simple example of literate programming methods in ab initio electronic structure theory is described. We distinguish text-embedded code, or literate programs, from code-embedded text and suggest that the latter may form a more useful vehicle for publication than literate programs. (c) 2005 Wiley Periodicals, Inc.

关键词： literate programming quantum chemistry helium atom

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literate programming and documentation reuse

Literate programming and documentation reuse

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4th International Conference on Software Reuse

作者： Childs, B Sametinger, J TEXAS A&M UNIV DEPT COMP SCICOLLEGE STNTX 77843

ISBN: (纸本)0818673036

Object-oriented programming has brought many advantages to the software engineering community. The reuse of existing software components and application frameworks can improve the productivity in software development considerably. The same object-oriented techniques, i.e., inheritance and information hiding, that ease reusing software, can be applied to documentation and thus, enable its reuse. One can document each software component-regardless of what a component is-from scratch. This leads to multiple documentation of features that are multiply reused. One can also describe a component's differences to other components. This seems logical for the systems documentation of object-oriented software. However, as will be shown, this kind of reuse can not only be applied to source-code related documentation, but also to documentation, where there is no source code involved at all, e.g., user documentation. In this paper we describe the concepts for documentation reuse, how these concepts can be realized with a literate programming tool, and the application of documentation reuse.

关键词： documentation reuse reuse of software engineering artifacts object-oriented programming literate programming noweb

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Supporting tailorable program visualisation through literate programming and fisheye views

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INFORMATION AND SOFTWARE TECHNOLOGY 2001年第13期43卷 745-758页

作者： Cockburn, A Univ Canterbury Dept Comp Sci Christchurch 1 New Zealand

This paper describes the 'Jaba' program editor and browser that allows users to tailor the level of abstraction at which they visualise, browse, edit and document object-oriented programs. Its design draws on concepts from literate programming, holophrasting displays, fisheye visualisation and hypertext to allow programmers to rapidly move between abstract and detailed views of Java classes. The paper focuses on the motivation for, and user interface issues surrounding, the integration of these facilities in Jaba. Limitations in the current tools and theories for programming support are identified, and modifications are proposed and demonstrated. Examples include overcoming the static post-hoc documentation support provided by Javadoc, and normalising Fumas's 'degree of interest' fisheye visualisation formula to avoid excessive suppression of program segments. (C) 2001 Elsevier Science B.V. All rights reserved.

关键词： literate programming documentation fisheye visualisation hypertext programming environments Java

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markdoc: literate programming in Stata

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STATA JOURNAL 2016年第4期16卷 964-988页

作者： Haghish, E. F. Univ Freiburg Ctr Med Biometry & Med Informat Freiburg Germany Odense Univ Dept Math & Comp Sci Odense Denmark

Rigorous documentation of the analysis plan, procedure, and computer codes enhances the comprehensibility and transparency of data analysis. Documentation is particularly critical when the codes and data are meant to be publicly shared and examined by the scientific community to evaluate the analysis or adapt the results. The popular approach for documenting computer codes is known as literate programming, which requires preparing a trilingual script file that includes a programming language for running the data analysis, a human language for documentation, and a markup language for typesetting the document. In this article, I introduce markdoc, a software package for interactive literate programming and generating dynamic-analysis documents in Stata. markdoc recognizes Markdown, LATEX, and HTML markup languages and can export documents in several formats, such as PDF, Microsoft Office. docx, OpenOffice and LibreOffice. odt, LATEX, HTML, ePub, and Markdown.

关键词： pr0064 markdoc Markdown HTML LATEX literate programming dynamic documents reproducible research log file translator

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Rethinking literate programming in statistics

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STATA JOURNAL 2016年第4期16卷 938-963页

作者： Haghish, E. F. Univ Freiburg Ctr Med Biometry & Med Informat Freiburg Germany Odense Univ Dept Math & Comp Sci Odense Denmark

literate programming is becoming increasingly trendy for data analysis because it allows the generation of dynamic-analysis reports for communicating data analysis and eliminates untraceable human errors in analysis reports. Traditionally, literate programming includes separate processes for compiling the code and preparing the documentation. While this workflow might be satisfactory for software documentation, it is not ideal for writing statistical analysis reports. Instead, these processes should run in parallel. In this article, I introduce the weaver package, which examines this idea by creating a new log system in HTML or LATEX that can be used simultaneously with the Stata log system. The new log system provides many features that the Stata log system lacks;for example, it can render mathematical notations, insert figures, create publication-ready dynamic tables, and style text, and it includes a built-in syntax highlighter. The weaver package also produces dynamic PDF documents by converting the HTML log to PDF or by typesetting the LATEX log and thus provides a real-time preview of the document without recompiling the code. I also discuss potential applications of the weaver package.

关键词： pr0063 weave div img txt tbl weaver weaving literate programming dynamic documents reproducible research log HTML LATEX

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Integrated literate programming for Structured Light Camera Calibration

Integrated Literate Programming for Structured Light Camera ...

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Joint Conference on New Trends in Audio and Video And Signal Processing - Algorithms, Architectures, Arrangements and Applications (NTAV/SPA)

作者： Skarbek, Wladyslaw Warsaw Univ Technol Fac Elect & Informat Technol PL-00661 Warsaw Poland

ISBN: (纸本)9788372835024

literate programming is a concept initially conceived by Professor Donald Knuth who had applied it in practice while developing his TEX formatting system. In my integrated approach I advocate the concept of literate programming in a single book, i.e. all levels of a created application ( including the descriptions of new algorithms) are joined together with all source codes in one PDF document, which is created from a tree of Latex documents. The code granularity can be of any detail. Even a single line of code is possible, surrounded by necessary comments, if needed. Codes can be composed sequentially and hierarchically. The presented paper will discuss advantages of the proposed programming methodology for developing software prototypes of applications within digital media one the example of calibration algorithms for a structured light camera system.

关键词： literate programming software documentation structured light method camera calibration

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A HYPERTEXT FOR literate programming

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INTERNATIONAL CONF ON COMPUTING AND INFORMATION ( ICCI 90 )

作者： BROWN, M CZEJDO, B Department of Computer Science University of Alabama Box 870290 Tuscaloosa 35487-0290 AL United States Department of Mathematical Sciences Loyola University New Orleans 77004 LA United States

ISBN: (纸本)3540535047

In this paper we describe a hypertext presentation for the WEB system for literate programming. The requirements for an environment for modern literate programming are analyzed and the WEB hypertext system is proposed. Different types of windows for displaying text, indices and graphical representations are discussed. All semantic links and operators using them are analyzed. The proposed architecture of the WEB hypertext system includes a general purpose relational database management system. Mapping between hypertext queries and relational database queries is provided. The system allows the user to define new hypertext operations by providing the corresponding SQL queries for the underlying relational database. The described system can be easily extended by many other types of queries and applications. © Springer-Verlag Berlin Heidelberg 1990.

关键词： literate programming HYPERTEXT DATABASE

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