title: Evolvix BEST Names for semantic reproducibility across code2brain interfaces.
abstract: Names in programming are vital for understanding the meaning of code and big data. We define code2brain (C2B) interfaces as maps in compilers and brains between meaning and naming syntax, which help to understand executable code. While working toward an Evolvix syntax for general-purpose programming that makes accurate modeling easy for biologists, we observed how names affect C2B quality. To protect learning and coding investments, C2B interfaces require long-term backward compatibility and semantic reproducibility (accurate reproduction of computational meaning from coder-brains to reader-brains by code alone). Semantic reproducibility is often assumed until confusing synonyms degrade modeling in biology to deciphering exercises. We highlight empirical naming priorities from diverse individuals and roles of names in different modes of computing to show how naming easily becomes impossibly difficult. We present the Evolvix BEST (Brief, Explicit, Summarizing, Technical) Names concept for reducing naming priority conflicts, test it on a real challenge by naming subfolders for the Project Organization Stabilizing Tool system, and provide naming questionnaires designed to facilitate C2B debugging by improving names used as keywords in a stabilizing programming language. Our experiences inspired us to develop Evolvix using a flipped programming language design approach with some unexpected features and BEST Names at its core.
authors.affiliation: Wisconsin Institute for Discovery.|Laboratory of Genetics.
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authors.affiliation: Wisconsin Institute for Discovery.
authors.forename: Katherine S
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authors.affiliation: Wisconsin Institute for Discovery.|Laboratory of Genetics.
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.affiliation: Wisconsin Institute for Discovery.|Departments of Computer Sciences.
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authors.affiliation: Wisconsin Institute for Discovery.|Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin.
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authors.affiliation: Department of Computer Science, University of Porto, Porto, Portugal.
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.lastname: Smith
authors.affiliation: Wisconsin Institute for Discovery.
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authors.lastname: Pietenpol
authors.affiliation: Wisconsin Institute for Discovery.
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authors.lastname: Goldfinger
authors.affiliation: Wisconsin Institute for Discovery.
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authors.lastname: Atzen
authors.affiliation: Wisconsin Institute for Discovery.
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authors.lastname: Freiberg
authors.affiliation: Wisconsin Institute for Discovery.
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authors.initials: NP
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authors.affiliation: Wisconsin Institute for Discovery.
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authors.lastname: Nolan
authors.affiliation: Wisconsin Institute for Discovery.
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authors.lastname: Hotz
authors.affiliation: Department of Biology, Cedar Crest College, Allentown, Pennsylvania.
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authors.lastname: Kliman
authors.affiliation: Department of Biology, Spelman College, Atlanta, Georgia.
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authors.lastname: Mentewab
authors.affiliation: College of the Menominee Nation, Keshena, Wisconsin.
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mesh_terms: D064229:Biological Ontologies; D062207:Brain-Computer Interfaces / Q000592:standards / Q000639:trends; D000067917:Cloud Computing / Q000592:standards; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods* / Q000592:standards / Q000639:trends; D057225:Data Mining / Q000639:trends; D006801:Humans; D020407:Internet; D011381:Programming Languages; D015203:Reproducibility of Results; D012984:Software; D012985:Software Design; D009626:Terminology as Topic
keywords: debugging code2brain interfaces; evolutionary systems biology simulations; flipped programming language design; fundamental modes of computing; names of identifiers in code; ontology computing; programming language paradigms and naming