Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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 d...

Centre for Systems and Synthetic Biology  &  Centre for Bioinformatics University of Kerala, Thiruvananthapuram, Kerala Welcome to India's First Symposium on Synthetic Biology                       The event will address several strategic issues: 1. How to design organisms from scratch ? 2. Are we ready for the Computer Aided Design of organisms ? 3. Can we design stable genetic circuits for useful applications ? 4. Have we entered the era of ordering genomes by email ? 5. Is the emergence of biohacking, the next big thing in biology ? Invite you to this first synthetic biology meeting in India . The evolving synthetic biology community in our country needs to discuss unique ideas, interest groups, synergies, funding avenues and useful applications. The key goal will be to identify areas where India has potential to take global leadership.     Welcome to BIODESIGN INDIA 1.0   Share | ...

The tables turn, it's 23andMe's turn to send a letter to FDA... Continuing the story  Reading Between Lines   slapped with cease and desist  letters . Direct-to-consumer genomics firm 23andMe has sent a letter to the heads of the US Food and Drug Administration and National Institutes of Health asking for a collaborative effort to develop guidelines for genetic testing. The firm  posted the letter  that it sent to FDA Commissioner Margaret Hamburg and NIH Director Francis Collins on its blog, The Spittoon, last night. 23andMe is one of several companies to be targeted recently by FDA, which  sent letters to several firms  saying that it believes the firms are selling unapproved diagnostic devices. The other firms that received letters were Knome, 23andMe, Decode Genetics, Navigenics, and Illumina, the last of which was cited for providing the tools that are used to provide genetic information to certain of the DTC genomics' customers. In the letter...