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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 atmore » its core.« less

Authors:
 [1];  [2];  [1];  [2];  [3];  [4];  [5];  [6];  [7];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2] more »;  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [8];  [9];  [10];  [2] « less
  1. Wisconsin Institute for Discovery, Laboratory of Genetics
  2. Wisconsin Institute for Discovery
  3. Departments of Computer Sciences
  4. Statistics
  5. Wisconsin Institute for Discovery, Departments of Computer Sciences
  6. Wisconsin Institute for Discovery, Chemical and Biological Engineering University of Wisconsin‐Madison Madison Wisconsin
  7. Department of Computer Science University of Porto Porto Portugal
  8. Department of Biology Cedar Crest College Allentown Pennsylvania
  9. Department of Biology Spelman College Atlanta Georgia
  10. College of the Menominee Nation Keshena Wisconsin
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF); National Institutes of Health (NIH); NHGRI; NIGMS; University of Wisconsin-Madison; U.S. Air Force
OSTI Identifier:
1334369
Alternate Identifier(s):
OSTI ID: 1341331; OSTI ID: 1625920
Grant/Contract Number:  
DE‐AC02‐06CH11357; AC02-06CH11357; T32GM007133; 5T32HG002760; 1R01GM086445‐01; FA9550‐15‐1‐0212; 1149123
Resource Type:
Published Article
Journal Name:
Annals of the New York Academy of Sciences
Additional Journal Information:
Journal Name: Annals of the New York Academy of Sciences Journal Volume: 1387 Journal Issue: 1; Journal ID: ISSN 0077-8923
Publisher:
Wiley-Blackwell
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Science & Technology - Other Topics

Citation Formats

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, and Loewe, Martha. Evolvix BEST Names for semantic reproducibility across code2brain interfaces. United States: N. p., 2016. Web. doi:10.1111/nyas.13192.
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. United States. https://doi.org/10.1111/nyas.13192
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, and Loewe, Martha. Mon . "Evolvix BEST Names for semantic reproducibility across code2brain interfaces". United States. https://doi.org/10.1111/nyas.13192.
@article{osti_1334369,
title = {Evolvix BEST Names for semantic reproducibility across code2brain interfaces},
author = {Loewe, Laurence and Scheuer, Katherine S. and Keel, Seth A. and Vyas, Vaibhav and Liblit, Ben and Hanlon, Bret and Ferris, Michael C. and Yin, John and Dutra, Inês and Pietsch, Anthony and Javid, Christine G. and Moog, Cecilia L. and Meyer, Jocelyn and Dresel, Jerdon and McLoone, Brian and Loberger, Sonya and Movaghar, Arezoo and Gilchrist‐Scott, Morgaine and Sabri, Yazeed and Sescleifer, Dave and Pereda‐Zorrilla, Ivan and Zietlow, Andrew and Smith, Rodrigo and Pietenpol, Samantha and Goldfinger, Jacob and Atzen, Sarah L. and Freiberg, Erika and Waters, Noah P. and Nusbaum, Claire and Nolan, Erik and Hotz, Alyssa and Kliman, Richard M. and Mentewab, Ayalew and Fregien, Nathan and Loewe, Martha},
abstractNote = {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.},
doi = {10.1111/nyas.13192},
journal = {Annals of the New York Academy of Sciences},
number = 1,
volume = 1387,
place = {United States},
year = {Mon Dec 05 00:00:00 EST 2016},
month = {Mon Dec 05 00:00:00 EST 2016}
}

Journal Article:
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https://doi.org/10.1111/nyas.13192

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