Bacatá: a language parametric notebook generator (tool demo)

Merino, Mauricio Verano; Vinju, Jurgen; Storm, Tijs van der

doi:10.1145/3276604.3276981

Cited by 5 publications

(2 citation statements)

References 17 publications

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“…These include, for example, Google Colab 8 and MyBinder. 9 Papermill 10 facilitates the sequential execution of cells within a Jupyter Notebook, while Bacatá 11 provides a framework for generating notebook interfaces for domain-specific languages. XML2Jupyter 12 dynamically generates Jupyter widgets from XML descriptions.…”

Section: Introductionmentioning

confidence: 99%

Appyters: Turning Jupyter Notebooks into data-driven web apps

et al. 2021

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Summary Jupyter Notebooks have transformed the communication of data analysis pipelines by facilitating a modular structure that brings together code, markdown text, and interactive visualizations. Here, we extended Jupyter Notebooks to broaden their accessibility with Appyters. Appyters turn Jupyter Notebooks into fully functional standalone web-based bioinformatics applications. Appyters present to users an entry form enabling them to upload their data and set various parameters for a multitude of data analysis workflows. Once the form is filled, the Appyter executes the corresponding notebook in the cloud, producing the output without requiring the user to interact directly with the code. Appyters were used to create many bioinformatics web-based reusable workflows, including applications to build customized machine learning pipelines, analyze omics data, and produce publishable figures. These Appyters are served in the Appyters Catalog at https://appyters.maayanlab.cloud . In summary, Appyters enable the rapid development of interactive web-based bioinformatics applications.

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Section: Introductionmentioning

confidence: 99%

Appyters: Turning Jupyter Notebooks into data-driven web apps

et al. 2021

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“…In this paper, we present an extended version of Bacatá [72,74], and a Feature-Oriented Domain Analysis (FODA) of computational notebooks. Bacatá 1 is a languageparametric kernel generator that hides the complexity of Jupyter's low-level wire protocol.…”

Section: Introductionmentioning

confidence: 99%

Bacatá: Notebooks for DSLs, Almost for Free

2020

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Context: Computational notebooks are a contemporary style of literate programming, in which users can communicate and transfer knowledge by interleaving executable code, output, and prose in a single rich document. A Domain-Specific Language (DSL) is a software language tailored for an application domain. Usually, DSL users are domain experts that may not have a software engineering background. Therefore, they might not be familiar with Integrated Development Environments (IDEs). In brief, the development of tools that offer different interfaces for interacting with a DSL is relevant.Inquiry: However, DSL designers' resources are limited. We want to leverage General-purpose Languages (GPLs) tooling in the context of DSLs. Computational notebooks are an example of such tools. Then, our main question is: What is an efficient and effective method of designing and implementing notebook interfaces for DSLs? By addressing this question, we might be able to speed up the development of DSL tools, and ease the interaction between end-users and DSLs.Approach: In this paper, we present Bacatá, a mechanism for generating notebook interfaces for external DSLs in a language-parametric fashion. This mechanism is designed in a way in which language engineers can reuse as many language components as possible (e.g., language processors, type checkers, code generators). In addition, we present a Feature-Oriented Domain Analysis that depicts language dependent and language independent features of computational notebooks.Knowledge: Our results show that notebook interfaces generated by Bacatá can be used with little manual configuration. However, there are a few considerations and caveats that should be addressed by language engineers that rely on language design aspects. The creation of a notebook for a DSL with Bacatá becomes a matter of writing the code that wires existing language components in the Rascal language workbench with the Jupyter platform.Grounding: We evaluate Bacatá by generating functional computational notebook interfaces for three different non-trivial DSLs, namely: a small subset of Halide (a DSL for digital image processing), SweeterJS (an extended version of JavaScript), and QL (a DSL for questionnaires). Additionally, it is relevant to generate notebook implementations rather than implementing them manually. To illustrate this, we measured and compared the number of source lines of code that we reused from existing implementations of those languages.Importance: The adoption of notebooks by novice-programmers and end-users has made them very popular in several domains such as exploratory programming, data science, data journalism, and machine learning. Why are they popular? In (data) science, it is essential to make results reproducible as well as understandable. However, notebooks are only available for GPLs. This paper opens the notebook metaphor for DSLs to improve the end-user experience when interacting with code and to increase DSLs adoption. ACM CCS 2012Software and its engineering → Domain specific lang...

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