skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Evolvix BEST Names for semantic reproducibility across code2brain interfaces

Journal Article · · Annals of the New York Academy of Sciences
DOI:https://doi.org/10.1111/nyas.13192· OSTI ID:1334369
 [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
+ Show Author Affiliations

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.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC); National Science Foundation (NSF); National Institutes of Health (NIH); NHGRI; NIGMS; University of Wisconsin-Madison; U.S. Air Force
Grant/Contract Number:
DE‐AC02‐06CH11357; AC02-06CH11357; T32GM007133; 5T32HG002760; 1R01GM086445‐01; FA9550‐15‐1‐0212; 1149123
OSTI ID:
1334369
Alternate ID(s):
OSTI ID: 1341331; OSTI ID: 1625920
Journal Information:
Annals of the New York Academy of Sciences, Journal Name: Annals of the New York Academy of Sciences Vol. 1387 Journal Issue: 1; ISSN 0077-8923
Publisher:
Wiley-BlackwellCopyright Statement
Country of Publication:
United States
Language:
English

References (47)

Reproducing Statistical Results journal April 2015
The case for open computer programs journal February 2012
α-Amylase Inhibitors: A Review of Raw Material and Isolated Compounds from Plant Source
  • Sales, Paloma Michelle; Souza, Paula Monteiro; Simeoni, Luiz Alberto
  • Journal of Pharmacy & Pharmaceutical Sciences, Vol. 15, Issue 1 https://doi.org/10.18433/J35S3K
journal February 2012
Implementing Reproducible Research book April 2014
Towards a whole-cell modeling approach for synthetic biology journal June 2013
Quantifying the threat of extinction from Muller's ratchet in the diploid Amazon molly (Poecilia formosa) journal January 2008
The Economics of Reproducibility in Preclinical Research journal June 2015
Evolution@home: observations on participant choice, work unit variation and low-effort global computing journal January 2007
Parallel Reproducible Summation journal July 2015
A C library for retrieving specific reactions from the BioModels database journal September 2013
Cytoscape 2.8: new features for data integration and network visualization journal December 2010
Amylase—Its Clinical Significance: a Review of the Literature journal January 1976
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models journal May 2015
Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA journal April 2006
Is salivary alpha-amylase an indicator of autonomic nervous system dysregulations in mental disorders?—A review of preliminary findings and the interactions with cortisol journal June 2013
Partitioning the UMLS semantic network journal June 2002
Reproducibility: changing the policies and culture of cell line authentication journal May 2015
Semantic reclassification of the UMLS concepts journal July 2008
A proprietary alpha-amylase inhibitor from white bean (Phaseolus vulgaris): A review of clinical studies on weight loss and glycemic control journal March 2011
Annotation and merging of SBML models with semanticSBML journal November 2009
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions journal January 2014
A data integration methodology for systems biology journal November 2005
On the potential for extinction by Muller's Ratchet in Caenorhabditis elegans journal January 2008
Overcoming an obstacle in expanding a UMLS semantic type extent journal February 2012
A Whole-Cell Computational Model Predicts Phenotype from Genotype journal July 2012
Analysis of the semantic structures of medical reference languages: Part 2. Analysis of the semantic power of MeSH, ICD and SNOMED journal January 1978
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems journal October 2014
WholeCellKB: model organism databases for comprehensive whole-cell models journal November 2012
Lazy Updating of hubs can enable more realistic models by speeding up stochastic simulations journal November 2014
Introduction book January 2012
A Review on Structure–Activity Relationship of Dietary Polyphenols Inhibiting α-Amylase journal January 2013
Systems in Evolutionary Systems Biology book January 2016
Exercise upregulates salivary amylase in humans (Review) journal January 2014
NixOS: A purely functional Linux distribution journal October 2010
Reproducible Research in Computational Harmonic Analysis journal January 2009
Corleone: hands-off crowdsourcing for entity matching
  • Gokhale, Chaitanya; Das, Sanjib; Doan, AnHai
  • SIGMOD/PODS'14: International Conference on Management of Data, Proceedings of the 2014 ACM SIGMOD International Conference on Management of Data https://doi.org/10.1145/2588555.2588576
conference June 2014
The principles of whole-cell modeling journal October 2015
A lexical metaschema for the UMLS semantic network journal January 2005
Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014 journal November 2014
WholeCellViz: data visualization for whole-cell models journal January 2013
Application of microbial α-amylase in industry - A review journal January 2010
Programming Languages shouldn't be "too Natural" journal February 2015
Titanium: a high-performance Java dialect journal September 1998
Naming and binding of objects book January 1978
Concepts and Synonymy in the UMLS Metathesaurus journal October 2009
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences journal January 2010
Accelerated discovery via a whole-cell model journal November 2013

Similar Records

A robotic framework for semantic concept learning.
Technical Report · Wed Sep 01 00:00:00 EDT 2004 · OSTI ID:1334369
NVL - a knowledge representation language based on semantic networks
Miscellaneous · Sun Jan 01 00:00:00 EST 1989 · OSTI ID:1334369
On the universal structure of human lexical semantics
Journal Article · Mon Feb 01 00:00:00 EST 2016 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1334369
+5 more

Related Subjects

97 MATHEMATICS AND COMPUTING
Science & Technology - Other Topics