BOL: September 2013

Upcoming R Webinar

Jitendra Narayan — Wed, 11 Sep 2013 10:30:16 -0500

This webinar will describe an R based approach to considerably speed GWAS computation time on a notebook book computer.

More http://www.extension.org/pages/68354/upcoming-webinar:-fast-semi-parallel-linear-and-logistic-regression-for-genome-wide-association-studi#.UjCL9azyPqV

A fast package to parse BLAST

Jitendra Narayan — Tue, 10 Sep 2013 16:58:56 -0500

In current era, we are handling huge amount of genomics data, and analysing it to make some biological sense out of it. Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. There are several BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to single results, and performing logical operations over them.

Massimiliano Orsini and Simone Carcangiu develope a new and fast fast package "BlaSTorage" to parse and store BLAST results. BlaSTorage shows comparable speed of more basic parser written in compiled languages as C++ and can be easily integrated into web applications or software pipelines.

Find more @ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571973/

http://biowiki.crs4.it/biowiki/MassimilianoOrsini

Fourth Branch of Life

Jitendra Narayan — Mon, 09 Sep 2013 21:48:37 -0500

Scientist have found the biggest viruses known, pandoraviruses which opened up entirely /completely... new questions questions and raise objections to in science. It even suggesting a fourth domain of life.

The new visrus are about one micron—a thousandth of a millimeter—in length, the newfound genus Pandoravirus dwarfs other viruses, which range in size from about 50 nanometers up to 100 nanometers. A genus is a taxonomic ranking between species and family.

Find more at @ http://www.nature.com/scitable/blog/viruses101/newly_found_pandoraviruses_hint_at

http://news.nationalgeographic.co.uk/news/2013/07/130718-viruses-pandoraviruses-science-biology-evolution/

RCSB PDB Sept'13 Release

Jitendra Narayan — Thu, 05 Sep 2013 15:07:48 -0500

RCSB PDB Sept'13 Release offers following new features:

- New tools to search for drugs and drug targets
- Improved interface for 3D visualisation using Jmol/JSmol
- An update to the representation of protein symmetry and stoichiometry.
- Improvements when performing sequence searches.

Reference

http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1308

4273π: Bioinformatics education on low cost ARM hardware

Jitendra Narayan — Mon, 02 Sep 2013 07:02:43 -0500

Are you teaching bioinformatics at universities and found it complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. Hmm don't worry there is one new OS for the rescue. 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. It provides an attractive, general-purpose computing environment, within which the course 4273π Bioinformatics for Biologists is embedded.

Though far slower than current desktop and laptop computers, the Raspberry Pi is notably faster than the Cray 1 supercomputer, a marvel of computer speed in its day. The Raspberry Pi approach includes all the benefits of the laptop approach, above, but at lower cost. In addition, the Raspberry Pi is a new and exciting computer system, which in itself can add interest to the course.

As the Raspbian operating system, Raspberry Pi firmware and hardware and 4273π Bioinformatics for Biologists teaching material develop, further releases of 4273π will be made available. It is anticipated that there will be a minimum of two releases per year during the next four years.

4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

Descriptive paper @ http://www.biomedcentral.com/1471-2105/14/243

Image source: BMC Bioinformatics