Kevin Blanchard's Biotechnology Blog

July 20, 2005

Myspace users

FYI: For those of you who use , there is a new biotechnology discussion group available at

March 18, 2005

For the Live Journal users

For the people who asked. I created a Live Journal syndication feed here of this blog. If you wish to read any articles I post via LJ instead of my site, just add the lj user biotech_syn like you would any other LJ user and you can view the entries in your friends section.

Schools Biotechnology learning hub launched

An interesting article from Scoop Independent News.

A new Biotechnology learning hub is to be launched today by Associate Minister for Industry and Regional Development Pete Hodgson.

The hub will link the biotechnology sector and educators via an on-line resource and facilitate direct contact between educators and scientists.

"New Zealand biotechnology leads the world in a number of medical and agriculture applications. It is one of the most innovative and fastest growing sectors in our economy. This exciting new initiative has been set up to give students a more thorough insight into this sector," says Pete Hodgson.

The on-line resource contains case studies and examples of effective classroom and internet based teaching methodologies. It has also been set up to support live video conferencing between scientists and schools and for the archiving of such events. The Hub also enables direct contact to be established between educators, students and scientists working in the sector.

"The Hub's structure and the wealth of information available through it gives educators the opportunity to bring field of science and technology to life for students at all levels."

The Hub has been developed by a team of sector representatives and educators lead by Professor Alistair Jones of the Centre for Science and Technology Education Research at the University of Waikato in conjunction with the New Zealand Council for Education Research, e-learning company CWA New Media and staff from the University of Auckland's Education faculty. It will be managed by Cathy Buntting of the University of Waikato.

It has been designed to support the attainment of the Ministry of Education's professional development objective for teachers relating to biotechnology.

December 30, 2004

Early reviews of Xsan look good

The current issue of Bio-IT World has an early review of Apple's new enterprise-class storage file system Xsan.

Traditionally, file systems like NFS have become the bottleneck of clusters even moderately sized. NFS allows each node access to a portion of the head node's disk space on the RAID for read/write operations. The problem with this is that it does not allow full access to the entire RAID(s), only the head node's portion. Here comes Xsan to fill in those gaps.

This article goes on to explain how the tests were done on the prerelease of Xsan and the improvement achieved when implementing it on the university of Pittsburgh's 125 node cluster.

*You may also note this quote from the article for all the non-mac users running similar setups.

"This is great, but you might be asking yourself, "Am I locked into using Apple's triple-X product offering to deploy this sort of technology on my cluster?" Although Apple might prefer it if you did, the answer is no. Apple has taken an aggressive open-technology stance within this architecture. The underlying Fibre Channel technology is standards-based. You can mix and match Fibre Channel cards and switches from Brocade, QLogic, Emulex, and so on. You can use Fibre Channel storage devices other than the Xserve RAID. Xsan's underlying cluster file system is compatible with ADIC's StorNext file system, so you can even mix in Linux, Solaris, Windows, etc., clients with corollary client software from ADIC."

December 08, 2004

Received from the mpiBLAST team

mpiBLAST 1.3.0 has (finally) been released. It incorporates several major
design changes that improve reliablilty, performance, and accuracy.

Key enhancements are:
- utilizes latest NCBI Toolbox (Oct 20, 2004)
- E-value scores are exact and identical to scores reported by NCBI
BLAST by using both the effective query and effective database lengths.
(It is necessary/required to patch the NCBI Toolbox before compilation)
- Database pipelining speeds up database distribution by limiting access
to shared filesystem. Number of concurrent accesses is a run-time option
- Results pipelining reduces memory requirements for large query sets.
- Database distribution can occur through cp, scp, or rcp system
calls, through MPI function calls (MPI_Send/MPI_Recv), or not at all if you
choose to use the shared filesystem as local storage. It is a runtime
option (--copy-via).

mpiBLAST version 1.3.0 was a long time in coming, but is the fastest,
most exact, and most stable version of mpiBLAST yet.

Download it here:

December 05, 2004

Discussion: The threat from life on Mars

Original article:,,3-1385572,00.html

December 03, 2004

The threat from life on Mars
By Nigel Hawkes
Earth’s defences may need to be boosted against risk of potentially deadly microbes returning on space probes

EARTH must take precautions to avoid contamination from lifeforms that must now be presumed to exist on Mars, leading scientists gave warning yesterday.

Potentially deadly microorganisms could be returned to Earth on a probe which is being planned to collect samples from the Martian surface.

The warning comes after a detailed scientific analysis of data sent back by the roving vehicle Opportunity which landed on Mars on January 25.

Jeffrey Kargel of the US Geological Survey said that protection of our own planet from alien forms of life requires the assumption that Martian life exists. “Before proceeding with sample returns or human missions to Mars, we must review measures for planetary biological protection.”

His warning appears in Science magazine in an article accompanying the first formal publication of the mass of data from Opportunity, which continues to operate on the Martian surface.

The search for life on Mars, now more than a century old, is still not finally resolved. But the odds that life existed there and may still exist are shortening, according to planetary experts, Dr Kargel said.

Nobody any longer expects Martian life forms to be anything like those on Earth. But there remains a possibility that bacteria or other microscopic organisms may survive in regions where there is still water. On Earth, almost every imaginable habitat, including deep underground, has specialised bacteria — called extremophiles — living and thriving.

The risks are twofold: probes sent from Earth may contaminate Mars with terrestrial bacteria, wrecking future studies of Martian life; or, more important, bacteria brought back from Mars may contaminate the Earth with unpredictable effects.

Similar precautions were taken at the time of the Apollo Moon landings. Astronauts returned to Earth were kept in quarantine after they landed for fear they might be infected with a lunar bug. None was.

Although the presence of water on the red planet can be considered proved, of life there are only hints. One is the presence of the gas methane, which might be produced by forms of life. On Earth, life can exist in areas as acidic and salty as Meridiani Planum, where Opportunity landed — examples are the ancient mines of Rio Tinto in Andalucia, Spain, or the salty Permian Basin in Texas. But few earthly species survive in environments that are at the same time very cold, very acidic, and very salty — and none that do survive in such conditions produce methane.

“But maybe on Mars they do,” says Dr Kargel, the author of a recent book on the latest ideas about Mars. Or maybe, he suggests, the organisms that produced the Martian methane live in areas more hospitable than Meridiani Planum.

Analysing the data collected by Opportunity, a team led by the rovers’ principal investigator, Dr Steve Squyres, of Cornell University, concludes that the sedimentary rocks found by Opportunity preserve a record of environmental conditions different from any on Mars today.

“Liquid water was once present intermittently at the Martian surface at Meridiani, and at times it saturated the subsurface,” the team concludes. “Because liquid water is a prerequisite for life, we infer that conditions at Meridiani may have been habitable for some period of time in Martian history.”

Opportunity has explored two craters, Eagle and Endurance, near its landing site. In both areas, layers in the bedrock showed that it had been laid down as sediments, implying past oceans and voids in the rock were probably caused by the dissolution of salt.

Opportunity also found quantities of small spheres, named “blueberries” — even though they are grey, not blue. These marbles consist of the iron-rich mineral haematite. Similar spheres have been found in the deserts of southern Utah, formed as iron-rich water seeped through sandstone.

The first idea that Mars might contain life came from the astronomer Giovanni Schiaparelli, who thought that he saw canals when he looked at Mars through a telescope at the end of the 19th century. H.G.Wells popularised the idea in The War of the Worlds, published in 1898.


* Named after the Roman god of war for its angry red appearance, Mars is about half the size of the Earth and is one and a half times further from the Sun

* Mars has clouds, weather and winds. Its atmosphere is thin, consisting mainly of carbon dioxide

* The surface of Mars is a frozen, rock-strewn desert, with sweeping dunes and huge craters. Its craters and volcanoes are far larger than any found on Earth. The largest volcano, Olympus Mons, is 78,000 feet high

* In 1976, two Viking landers arrived on the surface of Mars looking for life. They found none

* A meteorite from Mars found in the Antarctic seemed to contain structures suggestive of life and reignited the possibility that Mars had once been home to life in a microscopic form

* A belief that Mars once contained water — and may still — was confirmed this year by the Opportunity and Spirit rovers. But Beagle 2, the British probe designed to search for life, disappeared without trace and is presumed to have crashed into the Martian surface

* Some time in the next decade Nasa plans to bring back samples from Mars that may answer questions about Martian life

November 22, 2004

How Perl Saved the Human Genome Project

An oldie but a goodie

How Perl Saved the Human Genome Project

November 21, 2004

Of mice, men and in-between

Of mice, men and in-between
Scientists debate blending of human, animal forms

November 18, 2004

The CSI effect

A recent article talked about the "CSI effect" and how it has had a negative effect on some jury members, because many people feel that the technology used on CSI already exists.

Today I play devils advocate :)

In relation to some of the "tests" they do, do you feel that this fictional or nearly fictional display of technology is good for the innovation in the areas of DNA analysis, testing, etc?

What are your other thoughts on the topic in general?


I created this blog to allow people to discuss many of the broader issues in the Biotechnology field. Whether your cup of tea is DNA, bio informatics, biology or just a jack of all trades feel free to contribute anything you think the group would find interesting. Send any story submission ideas or links to kevin @ .