skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
Abstract Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.  more » « less
Award ID(s):
1929237
PAR ID:
10354896
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more » ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; « less
Date Published:
Journal Name:
Nature Communications
Volume:
12
Issue:
1
ISSN:
2041-1723
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; (, IEEE International Conference on Cluster Computing, CLUSTER 2021)
    IEEE Computer Society (Ed.)
    Scientists using the high-throughput computing (HTC) paradigm for scientific discovery rely on complex software systems and heterogeneous architectures that must deliver robust science (i.e., ensuring performance scalability in space and time; trust in technology, people, and infrastructures; and reproducible or confirmable research). Developers must overcome a variety of obstacles to pursue workflow interoperability, identify tools and libraries for robust science, port codes across different architectures, and establish trust in non-deterministic results. This poster presents recommendations to build a roadmap to overcome these challenges and enable robust science for HTC applications and workflows. The findings were collected from an international community of software developers during a Virtual World Cafe in May 2021. 
    more » « less
  2. ; ; ; ; ; ; ; ; ; ; et al (, Geoscientific Model Development)
    Abstract. Computational modeling occupies a unique niche in Earth and environmental sciences. Models serve not just as scientific technology and infrastructure but also as digital containers of the scientific community's understanding of the natural world. As this understanding improves, so too must the associated software. This dual nature – models as both infrastructure and hypotheses – means that modeling software must be designed to evolve continually as geoscientific knowledge itself evolves. Here we describe design principles, protocols, and tools developed by the Community Surface Dynamics Modeling System (CSDMS) to promote a flexible, interoperable, and ever-improving research software ecosystem. These include a community repository for model sharing and metadata, interface and ontology standards for model interoperability, language-bridging tools, a modular programming library for model construction, modular software components for data access, and a Python-based execution and model-coupling framework. Methods of community support and engagement that help create a community-centered software ecosystem are also discussed. 
    more » « less
  3. ; (, Computing in Science & Engineering)
    Testing scientific software is a difficult task due to their inherent complexity and the lack of test oracles. In addition, these software systems are usually developed by end user developers who are neither normally trained as professional software developers nor testers. These factors often lead to inadequate testing. Metamorphic testing is a simple yet effective testing technique for testing such applications. Even though MT is a well-known technique in the software testing community, it is not very well utilized by the scientific software developers. The objective of this article is to present MT as an effective technique for testing scientific software. To this end, we discuss why MT is an appropriate testing technique for scientists and engineers who are not primarily trained as software developers. Especially, how it can be used to conduct systematic and effective testing on programs that do not have test oracles without requiring additional testing tools. 
    more » « less
  4. ; (, Computing in science engineering)
    Testing scientific software is a difficult task due to their inherent complexity and the lack of test oracles. In addition, these software systems are usually developed by end-user developers who are not normally trained as professional software developers nor testers. These factors often lead to inadequate testing. Metamorphic testing (MT) is a simple yet effective testing technique for testing such applications. Even though MT is a well known technique in the software testing community, it is not very well utilized by the scientific software developers. The objective of this paper is to present MT as an effective technique for testing scientific software. To this end, we discuss why MT is an appropriate testing technique for scientists and engineers who are not primarily trained as software developers. Specifically, how it can be used to conduct systematic and effective testing on programs that do not have test oracles without requiring additional testing tools. 
    more » « less
  5. ; ; ; (, Conference on Computer Supported Cooperative Work and Social Computing)
    Sharing scientific data, software, and instruments is becoming increasingly common as science moves toward large-scale, distributed collaborations. Sharing these resources requires extra work to make them generally useful. Although we know much about the extra work associated with sharing data, we know little about the work associated with sharing contributions to software, even though software is of vital importance to nearly every scientific result. This paper presents a qualitative, interview-based study of the extra work that developers and end users of scientific software undertake. Our findings indicate that they conduct a rich set of extra work around community management, code maintenance, education and training, developer-user interaction, and foreseeing user needs. We identify several conditions under which they are likely to do this work, as well as design principles that can facilitate it. Our results have important implications for future empirical studies as well as funding policy. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Text Encoded Conversion
  • XML
  • Save / Share this Record
  • Send to Email