Multi Core Aware Java Library for Computing Protein Stability Indices – A Performance Improvement and Power Consumption Study

Data deluge in post genomic era has necessitated the development of multi-core aware software and libraries. Colossal analysis in the field of bioinformatics demands next generation bioinformatics applications/libraries which ought to be faster and energy efficient. In this work we have developed a multi-core aware java library for peptide properties calculations which are used in various active site prediction, protein stability calculations, protein lig and interactions. The library is capable to detect number of CPU cores at run time and divide the tasks accordingly. Processing time and power consumption has been measured for all methods in the developed library and Bio Java for various granularity of tasks (0.1 MB to 51.2 MB) and the results were compared. The developed library named as pBio shows improved performance upto 37 times than corresponding modules of Bio Java, and up to 6 times more energy efficient approximately than corresponding modules of Bio Java.