Related Experiment Video
Updated: Dec 22, 2025
10:41
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
Published on: May 9, 2017
9.5K
Better together: Elements of successful scientific software development in a distributed collaborative community
Julia Koehler Leman1,2, Brian D Weitzner3,4,5,6, P Douglas Renfrew1
1Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, United States of America.
Plos Computational Biology
|May 5, 2020
Summary
Scientific software development thrives through community collaboration. Practices in version control, testing, and community building, as seen with the Rosetta software suite, ensure sustainability and maintainability in computational research.
Area of Science:
- Computational biology
- Scientific software engineering
- Macromolecular modeling
Background:
- Scientific disciplines increasingly rely on computational tools for research.
- Academic researchers often develop software without formal software engineering training, impacting tool sustainability.
- The Rosetta software suite is a large-scale example of scientific software developed in an academic setting.
Purpose of the Study:
- To use the Rosetta software and its community as a case study for successful scientific software development.
- To demonstrate how modern software development principles can be applied effectively in academic environments.
- To illustrate transferable practices for building sustainable and maintainable scientific software in distributed communities.
Main Methods:
- Analysis of the RosettaCommons community's development practices over two decades.
- Examination of technical aspects including version control, testing, and maintenance.
- Review of community-building strategies, diversity initiatives, software dissemination, and user support.
Main Results:
- Rosetta has been successfully developed and maintained by a global community of over 60 institutions.
- Effective technical practices and community engagement strategies have ensured the software's longevity and widespread use.
- The development model demonstrates the viability of collaborative, distributed scientific software creation.
Conclusions:
- Modern computational research can flourish within distributed, collaborative communities.
- The practices employed by the RosettaCommons are adaptable to other scientific software development efforts.
- Adopting these principles can enhance the sustainability and maintainability of academic software tools.
Related Concept Videos
01:25Distribution Reliability and Automation
436
Distribution reliability in electrical power systems is critical for ensuring an uninterrupted power supply to consumers at minimal cost. According to IEEE Standard Terms, reliability is the probability that a device will function without failure over a specified time period or amount of usage. For electric power distribution, this translates to maintaining continuous power supply and addressing customer concerns over power outages. Several indices, as defined by IEEE Standard 1366-2012, are...
436
01:21Distributed Loads: Problem Solving
1.0K
Beams are structural elements commonly employed in engineering applications requiring different load-carrying capacities. The first step in analyzing a beam under a distributed load is to simplify the problem by dividing the load into smaller regions, which allows one to consider each region separately and calculate the magnitude of the equivalent resultant load acting on each portion of the beam. The magnitude of the equivalent resultant load for each region can be determined by calculating...
1.0K
01:21Development of Analytical Methods
1.5K
An analytical methodology can be divided into four sequential steps: technique, method, procedure, and protocol. A technique is a scientific principle that rationalizes a specific phenomenon through chemical measurements. Adapting a technique for analyzing a sample of interest is termed a method. The procedure outlines the directions for performing the analysis via an analytical method. The protocol is the detailed guidelines on the procedure, which should be strictly followed to obtain the...
1.5K
01:13Principle of Virtual Work: Problem Solving
1.5K
The principle of virtual work is an essential concept in the field of mechanics and engineering. This is used to solve problems related to the equilibrium of a structure or system. It is based on the assumption that if a system is in equilibrium, the work done by all the forces during a virtual displacement is zero. This principle is applied by considering virtual displacements of the system and the corresponding work done by internal and external forces.
To apply the principle of virtual work,...
To apply the principle of virtual work,...
1.5K
01:32The Scientific Method
255.0K
The scientific method is a detailed, empirical problem-solving process used by biologists and other scientists. This iterative approach involves formulating a question based on observation, developing a testable potential explanation for the observation (called a hypothesis), making and testing predictions based on the hypothesis, and using the findings to create new hypotheses and predictions.
Generally, predictions are tested using carefully-designed experiments. Based on the outcome of these...
Generally, predictions are tested using carefully-designed experiments. Based on the outcome of these...
255.0K
02:40The Scientific Method
64.5K
Research is what makes the difference between facts and opinions. Facts are observable realities, and opinions are personal judgments, conclusions, or attitudes that may or may not be accurate. In the scientific community, facts can be established only using evidence collected through empirical research.
64.5K