The roles of code in biology

Area of Science:

• Bioinformatics and Computational Biology
• Software Engineering in Life Sciences

Background:

• The perception and application of computer code in biological research have led to significant confusion.
• This confusion has resulted in suboptimal outcomes concerning reproducibility, scalability, and productivity in life science research.

Purpose of the Study:

• To address the confusion surrounding the use of computer code in biological research.
• To present a novel three-dimensional taxonomy for classifying the roles of code in the life sciences.
• To identify a "sweet spot" within this taxonomy for maximizing the value derived from code usage.

Main Methods:

• Development of a three-dimensional taxonomy to classify the diverse roles of computer code in life sciences.
• Identification of a convergence zone ("sweet spot") within the taxonomy for optimal bioinformatician effort.
• Proposal of the "inverse Conway maneuver" for structuring research teams to facilitate interaction between software engineers and researchers.

Main Results:

• A structured framework (taxonomy) is provided to understand and categorize the functions of code in biological research.
• A specific area ("sweet spot") is identified where bioinformaticians can focus efforts for maximum impact.
• The "inverse Conway maneuver" is suggested as a strategy for team organization to improve software engineering integration.

Conclusions:

• Reevaluating the relationship between life science research and software engineering is crucial.
• Adapting research structures is necessary to overcome persistent issues in bioinformatics, including reproducibility, scalability, and productivity.
• A clearer understanding and strategic application of code are essential for advancing biological research.