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Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.
Pjotr Prins1, Naohisa Goto, Andrew Yates
1Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands. pjotr.prins@wur.nl
Methods in Molecular Biology (Clifton, N.J.)
|March 9, 2012
Summary
Sharing software components across programming languages in bioinformatics is crucial. Call stack methods generally outperform remote procedure calls and native Bio* implementations for improved efficiency.
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Area of Science:
- Bioinformatics
- Computational Biology
- Software Engineering
Background:
- Open-source software (OSS) facilitates code reuse in programming.
- Bioinformatics utilizes diverse languages (C/C++, Perl, Python, Java, R) and Bio* projects (BioPerl, Biopython, BioJava, BioRuby, R/Bioconductor).
- Sharing software components across these languages and projects is essential to avoid redundant development.
Purpose of the Study:
- To compare the performance of different approaches for sharing software components between programming languages in bioinformatics.
- To evaluate strategies for inter-language communication within Bio* projects.
- To provide practical examples and a testable environment for cross-language bioinformatics software sharing.
Main Methods:
- Comparison of two primary software sharing approaches: Remote Procedure Call (RPC) and local call stack.
- Implementation and performance measurement of various inter-language communication methods, including RSOAP, Rserve, RPy, native Bio* interfaces, and call stack bindings.
- Cross-language sequence translation examples were used for performance testing.
- A downloadable BioNode image with all necessary tools and libraries was provided for reproducible testing.
Main Results:
- Call stack approaches generally demonstrate superior performance compared to native Bio* implementations.
- Native Bio* implementations outperform RPC-based approaches.
- Specific performance variations were observed across different interface types (e.g., RPy vs. Rserve).
Conclusions:
- Local call stack methods offer a more efficient strategy for inter-language software sharing in bioinformatics compared to RPC.
- Optimizing software component sharing across diverse programming languages can significantly enhance development efficiency in bioinformatics.
- The provided BioNode image facilitates further research and practical application of these findings.