A Maintainable Software Architecture for Fast and Modular Bioinformatics Sequence Search

Archuleta, Jeremy; Tilevich, Eli; Feng, Wu-chun

doi:10.1109/icsm.2007.4362627

Cited by 6 publications

(4 citation statements)

References 11 publications

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“…The preferred implementation language for bioinformatics libraries-C++complicates such a refactoring undertaking and automated refactoring support for C++ remains scarce. Despite the proven benefits of systematic refactoring [5], this software development process has not been applied systematically to the numerous bioinformatics software tools and libraries.…”

Section: Introductionmentioning

confidence: 99%

Poster: Diagnosing and treating code-duplication problems in bioinformatics libraries

Hasan

Tithi

Tilevich

et al. 2016

2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

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As computing is an enabling tool of bioinformatics, software quality can influence not only the efficiency of the research process, but also the degree of confidence in scientific findings. As we discovered, popular bioinformatics C++ libraries suffer from problems that make their code hard to maintain, finetune, and extend. In particular, code duplication caused by the ubiquitous copy-and-paste development practice, substantially complicates software maintenance and evolution. The presence of multiple clones of the same code snippet multiples the amount of effort required to modify or extend it. In this paper, we present the results of a systematic study we have conducted to understand the code quality of popular bioinformatics libraries. Based on the results of our study, we developed an automated tool that systematically identifies and consolidates duplicated code blocks. Here we describe our tool-ReBio 1-and the results of applying it to improve the quality of several commonly used C++ libraries, including SeqAn, BEDtools, and NCBI C++ Toolkit. Our results reveal that these libraries indeed suffer from poor maintainability, and that our automated tool can effectively improve their quality.

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Section: Introductionmentioning

confidence: 99%

Poster: Diagnosing and treating code-duplication problems in bioinformatics libraries

Hasan

Tithi

Tilevich

et al. 2016

2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

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“…The details of this analysis are beyond the scope of this paper; the interested reader can learn about our experiences in [14]. However, the primary reason for using "mixin layers with refined roles" is that this design provides maintainable and extensible high-performance through plug-in replaceable and reusable software components that can be easily mixed and matched.…”

Section: B Implementationmentioning

confidence: 99%

“…Our framework is a good fit for unit testing due to the low coupling it exhibits. Additional details of the software engineering rationale behind our framework can be found in [14].…”

Section: ) Modularitymentioning

confidence: 99%

A Pluggable Framework for Parallel Pairwise Sequence Search

Archuleta

Feng

Tilevich

2007

2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society

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Abstract-The current and near future of the computing industry is one of multi-core and multi-processor technology. Most existing sequence-search tools have been designed with a focus on single-core, single-processor systems. This discrepancy between software design and hardware architecture substantially hinders sequence-search performance by not allowing full utilization of the hardware. This paper presents a novel framework that will aid the conversion of serial sequence-search tools into a parallel version that can take full advantage of the available hardware. The framework, which is based on a software architecture called mixin layers with refined roles, enables modules to be plugged into the framework with minimal effort. The inherent modular design improves maintenance and extensibility, thus opening up a plethora of opportunities for advanced algorithmic features to be developed and incorporated while routine maintenance of the codebase persists.

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“…mpiBLAST has been known to assist in the process of scientific discovery in domains as diverse as new drug development and classifying new virus species. mpiBLAST 2.0 is written in C++ [2], with MPI as the communication middleware. In this case study, we reimplemented the hand-written marshaling functionality of mpiBLAST by using both the Boost libraries and our automated tool.…”

Section: Mpiblast 20mentioning

confidence: 99%