A comparison of common programming languages used in bioinformatics

-
The electronic version of this article is the complete one and can be found online at:http://www.biomedcentral.com/1471-2105/9/82

Abstract

Background

The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python.

Results

Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found.
Source code and additional information are available from http://www.bioinformatics.org/benchmark/webcite

Conclusion

This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

Share |

Comments

Post a Comment

Popular posts from this blog

Abbott Laboratories Buys Piramal Healthcare Limited Biz for $3.72B

-
Abbott May 21 announced a definitive agreement with Piramal Healthcare Limited to acquire full ownership of Piramal's Healthcare Solutions business (Domestic Formulations), a leader in the Indian branded generics market, for an up-front payment of $2.12 billion , plus $400 million annually for the next four years, giving Abbott the No. 1 position in the Indian pharmaceutical market. This further accelerates Abbott's emerging markets growth following the recent acquisition of Solvay Pharmaceuticals and announcements last week of Abbott's collaboration with Zydus Cadila as well as the creation of a new stand-alone Established Products Division to focus on expanding the global markets for its leading branded generics portfolio. "This strategic action will advance Abbott into the leading market position in India , one of the world's most attractive and rapidly growing markets," said Miles D. White , chairman and chief executive officer, Abbott. ...
Read more

Top 25 Indian Bioinformatics Companies

-
Here is another, quite interesting blog page with a list of Top 25 Indian Bioinformatics Companies by a fellow blogger Nabeel Basheer, while there is no actual criteria behind listing these 25 companies. It is a good handy list just in alphabetic order for all those job seekers. More so a good chronicle of the local informatics industry as well. 1. Accelrys Software Solution Pvt Ltd. 12th Floor, Discover, ITPL, White Field, Bangalore-65. www.accelrys.com 2. Apticraft Systems (P) Ltd. 142, Electronics Complex, Pardeshipura, Indore – 452010 (M.P.), India www.apticraft.com 3. Aptuit Informatics Plot No. 100-103, Export Promotion Industrial Park, White Field, Bangalore-560066 www.aptiuit.com 4. Bigtec J. K. Towers, 8th Block, Sangam Circle,46th Cross, Bangalore-560082. www.bigtec.org 5. Bijam Biosciences Private Limited Nagarjuna Hills, Hyderabad 500 082, India www.nagarjunagroup.com 6. Bio Base Databases India Pvt Ltd. Crescent Towers, 4th Floor, No : 32/1, Crescent Road, Bnagalore -...
Read more