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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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The challenges of theory-software translation.

Caroline Jay1, Robert Haines1, Daniel S Katz2

  • 1University of Manchester, Manchester, UK.

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|November 20, 2020
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Summary

Translating scientific theory into research software presents significant challenges in design, infrastructure, and culture. Addressing these issues through a new field of theory-software translation can improve scientific integrity and accelerate research progress.

Keywords:
high performance computingresearch softwareresearch software engineeringscientific computingscientific softwarescientific software development

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Area of Science:

  • Scientific computing
  • Computational science
  • Research software engineering

Background:

  • Software is integral to modern research, requiring it to represent complex theoretical constructs.
  • Ensuring the robustness of theory-software translation is critical for scientific integrity.
  • Challenges in this translation process have been historically under-explored.

Purpose of the Study:

  • To identify and categorize challenges in translating scientific theory into research software.
  • To explore the implications of these challenges for scientific advancement.
  • To propose a new research area focused on theory-software translation.

Main Methods:

  • Thematic analysis of discussion sessions from the Theory-Software Translation Workshop 2019.
  • Involved academic researchers and research software engineers from diverse domains.
  • Focused on expertise in high-performance computing.

Main Results:

  • Identified a broad spectrum of challenges in implementing scientific theories within research software.
  • Categorized challenges into emergent themes: design, infrastructure, and culture.
  • Mapped identified challenges to specific research questions.

Conclusions:

  • Systematic investigation of research software construction and output utilization can enhance robustness.
  • Propose the establishment of theory-software translation as a new research area.
  • This new field has the potential to advance both scientific knowledge and practice.