Verifiability in computer-aided research: the role of digital scientific notations at the human-computer interface

@article{Hinsen2018VerifiabilityIC,
  title={Verifiability in computer-aided research: the role of digital scientific notations at the human-computer interface},
  author={Konrad Hinsen},
  journal={PeerJ Computer Science},
  year={2018},
  volume={4}
}
  • K. Hinsen
  • Published 23 July 2018
  • Computer Science
  • PeerJ Computer Science
Most of today’s scientific research relies on computers and software for processing scientific information. Examples of such computer-aided research are the analysis of experimental data or the simulation of phenomena based on theoretical models. With the rapid increase of computational power, scientific software has integrated more and more complex scientific knowledge in a black-box fashion. As a consequence, its users do not know, and do not even have a chance of finding out, which… 

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References

SHOWING 1-10 OF 55 REFERENCES

Computer Simulations and Computational Models in Science

TLDR
Providing a satisfactory and fruitful definition of computer simulations turns out to be more difficult than expected, partly because this notion is at the crossroads of difficult questions like the nature of representation and computation or the success of scientific inquiries.

Functional declarative language design and predicate calculus: a practical approach

TLDR
The proposed alternative combines a language of utmost simplicity (four constructs only) that is devoid of the defects of common mathematical conventions, with a set of convenient calculation rules that is sufficiently comprehensive to make it practical for everyday use in most (if not all) domains of interest.

The Role of Programming in the Formulation of Ideas

TLDR
This work uses computational techniques to communicate a deeper understanding of Classical Mechanics by formulating a method as a computerexecutable program and debugging that program.

User interfaces for computational science: A domain specific language for OOMMF embedded in Python

TLDR
A domain specific language for micromagnetics that is embedded in the Python language, and allows users to define the micromagnetic simulations they want to carry out in a flexible way and is implemented together with a computational backend that executes the simulation task using the Object Oriented MicroMagnetic Framework.

Computational science: shifting the focus from tools to models

TLDR
It is argued that this emphasis on software tools over models and data is detrimental to science in the long term, and a means by which this can be reversed is proposed.

A Primer on Scientific Programming with Python

TLDR
The book serves as a first introduction to computer programming of scientific applications, using the high-level Python language, and teaches "Matlab-style" and procedural programming as well as object-oriented programming.

Computational science: ...Error

TLDR
E-mails from the Climatic Research Unit (CRU) at the University of East Anglia in Norwich, UK, last year revealed another problem — one described by a CRU employee named “Harry”, who often wrote of his wrestling matches with wonky computer software.

Computer Science and its Relation to Mathematics

TLDR
A personal view of how this subject interacts with Mathematics is given, by discussing the similarities and differences between the two fields, and by examining some of the ways in which they help each other.

Journal of Open Source Software (JOSS): design and first-year review

TLDR
The motivation, design, and progress of the Journal of Open Source Software is described, which has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit.

(Position Paper) Applying software engineering methods and tools to CSE research projects

...