Cargando…
Evolvix BEST Names for semantic reproducibility across code2brain interfaces
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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299481/ https://www.ncbi.nlm.nih.gov/pubmed/27918836 http://dx.doi.org/10.1111/nyas.13192 |
_version_ | 1782506034134253568 |
---|---|
author | Loewe, Laurence Scheuer, Katherine S. Keel, Seth A. Vyas, Vaibhav Liblit, Ben Hanlon, Bret Ferris, Michael C. Yin, John Dutra, Inês Pietsch, Anthony Javid, Christine G. Moog, Cecilia L. Meyer, Jocelyn Dresel, Jerdon McLoone, Brian Loberger, Sonya Movaghar, Arezoo Gilchrist‐Scott, Morgaine Sabri, Yazeed Sescleifer, Dave Pereda‐Zorrilla, Ivan Zietlow, Andrew Smith, Rodrigo Pietenpol, Samantha Goldfinger, Jacob Atzen, Sarah L. Freiberg, Erika Waters, Noah P. Nusbaum, Claire Nolan, Erik Hotz, Alyssa Kliman, Richard M. Mentewab, Ayalew Fregien, Nathan Loewe, Martha |
author_facet | Loewe, Laurence Scheuer, Katherine S. Keel, Seth A. Vyas, Vaibhav Liblit, Ben Hanlon, Bret Ferris, Michael C. Yin, John Dutra, Inês Pietsch, Anthony Javid, Christine G. Moog, Cecilia L. Meyer, Jocelyn Dresel, Jerdon McLoone, Brian Loberger, Sonya Movaghar, Arezoo Gilchrist‐Scott, Morgaine Sabri, Yazeed Sescleifer, Dave Pereda‐Zorrilla, Ivan Zietlow, Andrew Smith, Rodrigo Pietenpol, Samantha Goldfinger, Jacob Atzen, Sarah L. Freiberg, Erika Waters, Noah P. Nusbaum, Claire Nolan, Erik Hotz, Alyssa Kliman, Richard M. Mentewab, Ayalew Fregien, Nathan Loewe, Martha |
author_sort | Loewe, Laurence |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5299481 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-52994812017-02-22 Evolvix BEST Names for semantic reproducibility across code2brain interfaces Loewe, Laurence Scheuer, Katherine S. Keel, Seth A. Vyas, Vaibhav Liblit, Ben Hanlon, Bret Ferris, Michael C. Yin, John Dutra, Inês Pietsch, Anthony Javid, Christine G. Moog, Cecilia L. Meyer, Jocelyn Dresel, Jerdon McLoone, Brian Loberger, Sonya Movaghar, Arezoo Gilchrist‐Scott, Morgaine Sabri, Yazeed Sescleifer, Dave Pereda‐Zorrilla, Ivan Zietlow, Andrew Smith, Rodrigo Pietenpol, Samantha Goldfinger, Jacob Atzen, Sarah L. Freiberg, Erika Waters, Noah P. Nusbaum, Claire Nolan, Erik Hotz, Alyssa Kliman, Richard M. Mentewab, Ayalew Fregien, Nathan Loewe, Martha Ann N Y Acad Sci Original Articles 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. John Wiley and Sons Inc. 2016-12-05 2017-01 /pmc/articles/PMC5299481/ /pubmed/27918836 http://dx.doi.org/10.1111/nyas.13192 Text en © 2016 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of New York Academy of Sciences. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Articles Loewe, Laurence Scheuer, Katherine S. Keel, Seth A. Vyas, Vaibhav Liblit, Ben Hanlon, Bret Ferris, Michael C. Yin, John Dutra, Inês Pietsch, Anthony Javid, Christine G. Moog, Cecilia L. Meyer, Jocelyn Dresel, Jerdon McLoone, Brian Loberger, Sonya Movaghar, Arezoo Gilchrist‐Scott, Morgaine Sabri, Yazeed Sescleifer, Dave Pereda‐Zorrilla, Ivan Zietlow, Andrew Smith, Rodrigo Pietenpol, Samantha Goldfinger, Jacob Atzen, Sarah L. Freiberg, Erika Waters, Noah P. Nusbaum, Claire Nolan, Erik Hotz, Alyssa Kliman, Richard M. Mentewab, Ayalew Fregien, Nathan Loewe, Martha Evolvix BEST Names for semantic reproducibility across code2brain interfaces |
title | Evolvix BEST Names for semantic reproducibility across code2brain interfaces |
title_full | Evolvix BEST Names for semantic reproducibility across code2brain interfaces |
title_fullStr | Evolvix BEST Names for semantic reproducibility across code2brain interfaces |
title_full_unstemmed | Evolvix BEST Names for semantic reproducibility across code2brain interfaces |
title_short | Evolvix BEST Names for semantic reproducibility across code2brain interfaces |
title_sort | evolvix best names for semantic reproducibility across code2brain interfaces |
topic | Original Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299481/ https://www.ncbi.nlm.nih.gov/pubmed/27918836 http://dx.doi.org/10.1111/nyas.13192 |
work_keys_str_mv | AT loewelaurence evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT scheuerkatherines evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT keelsetha evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT vyasvaibhav evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT liblitben evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT hanlonbret evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT ferrismichaelc evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT yinjohn evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT dutraines evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT pietschanthony evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT javidchristineg evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT moogcecilial evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT meyerjocelyn evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT dreseljerdon evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT mcloonebrian evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT lobergersonya evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT movaghararezoo evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT gilchristscottmorgaine evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT sabriyazeed evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT sescleiferdave evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT peredazorrillaivan evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT zietlowandrew evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT smithrodrigo evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT pietenpolsamantha evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT goldfingerjacob evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT atzensarahl evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT freibergerika evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT watersnoahp evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT nusbaumclaire evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT nolanerik evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT hotzalyssa evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT klimanrichardm evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT mentewabayalew evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT fregiennathan evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces AT loewemartha evolvixbestnamesforsemanticreproducibilityacrosscode2braininterfaces |