Health NewsThe Omics of Avatar
The science in the science fiction movie Avatar is in my opinion – excellent! Let me tell you what I’m thinking. Science fiction can be so off the wall that many of the basic laws of science must be broken for the plot to work. This is not the case in Avatar. Avatar is one of those science fiction movies in which the science seems to be very probable because it is either currently real science, or certainly technologies which are predictable based on current science. I personally find it much easier to have suspended disbelief in science fiction movies if the science is believable.
After a few brief trailers, a sign came on the screen saying put your 3-D glasses on now.
On Perl Programs
guest post from Susanne Cardwell,
Administrative Coordinator for the Applied Computational Genomics Course
Perl is a dynamic programming language used in many areas - especially in bioinformatics. It is a freely downloadable and commonly used with Unix systems, although some variants are available for Microsoft Windows.
On perusing notes made for one of the lecture days of the 2009 Applied Computational Genomics Course , I located some interesting information on Perl in bioinformatics. Perl, as used in bioinformatics, allows for a number of operations, including:
- translation of DNA sequences in a single frame
- transcription of DNA to RNA
- production of reverse complements of DNA sequence nomenclature
- coding for aiding RNA splicing
- generation of Blast output
- prediction and evaluation of genes
- annotation of a small genome (such as E. coli) or a collection of EST’s (Wishart, 2009)
MedicineNet, Inc. (2009) defined genome annotation as “the process for identifying the location of genes and all of the coding regions in a genome and determining what those genes do.” For instance, DNA Forensics allows for the identification of organ donor matches and the identification of individuals suspect in a crime through DNA profiling through scans of 13 DNA regions (Human Genome Project Information, 2009). A more specific example of genome annotation is when you determine the function of the gene (such as protein excretion, protein family and transcription identification, and transcription determination (Abdellateef, 2009, December 17, personal communications) and the regions of the gene that would eventually translate into protein. Perl helps allow for complex annotation to take place – annotation that would not otherwise have been possible through traditional means.
Giant Viruses, borrowed Cat Genes and Jingjing’s Genome
This past week’s science readings on the web look like they might well have come from the tabloid magazines. Besides all the jokes about changing a tiger into a lion or a cheetah, we have stories of giant viruses driving the evolution of microorganisms. We note that cat DNA has been found in the HIV/AIDS virus and pandas are genetically like dogs.
What is Bioinformatics?
guest post from Susanne Cardwell,
Administrative Coordinator for the Applied Computational Genomics Course
Bioinformatics, using mathematical modeling, statistics, graphical interfaces, and other devices, makes efficient computing tasks in biology and genetics that would otherwise require terabytes of computing power in order to interpret ( innovation.org, 2009). Some of the functions of bioinformatics include:
- Analytics on three dimensional protein structures (innovation.org, 2009)
- Computer-aided design of new drugs (innovation.org, 2009) Determination of gene and drug interaction (innovation.org, 2009)
- Provision of visualization tools (The MathWorks, 2009)
- Supplication of analytics on genetic sequences
- Comparison of nucleotides or amino acids (The MathWorks, 2009)
- Performance of statistical analysis on genetic data
- Comparison of a wealth of information from various databases of genetic sequences
- Integration of data for gene-based drug development (Ajith, 2003).
3 Dimensional Annotation
guest post
Susanne Marie Cardwell,
Administrative Coordinator for Genome Alberta
While flipping through notes on the recent Applied Computational Genomics Course I stumbled upon an interesting concept that as a Communications graduate student found quite remarkable: the coming advent of 3- and 4-dimensional annotation. As I started out at the University of Calgary as an Honours Mathematics major, I found some interesting parallels with the multi-dimensional annotation and the concept of multiple (spatial) dimensions in mathematics.
1-dimensional and 2-dimensional genome annotation have been areas researched and studied for quite some time, and will continue to have a formative role in genetics research, as they provide unique information, becoming more complex with each layer of dimensionality.
Like a point on a line, one dimensional annotation provides information on location, but does not give information about spatial or evolutionary organization that can be found in higher dimensional annotations. In mathematics, the one-dimensionality can be likened to investigating a point on a line, which demonstrates position; the two-dimensionality provides information on a region in a graph, which allows for organization of gene structures, positioning, and relationships to become more apparent. Three-dimensionality, allows for information on more than a surface, but an object within a x, y, z plane system, which enables the concept of derivatives and integrals, from a mathematical sense, to perform operations and to include more complex functions such as motion and transformation from one dimensionality to another.
David and Goliath Stay Away from the Slingshots
It was one of those moments when you realise that you have to put to the test everything you've been saying about public relations, communications, and how wonderful social media is for building relationships.
It started on Monday when I clicked on a Twitter link from @sciencebase which took me to a new Facebook application from Sigma-Aldrich called Your Favourite Gene . Among the app's many features is the option to send your favourite gene to your friends. That was the 'uh-oh' moment because our GenOmics application includes the same option and it was that feature that really gave us a social media boost in April of 2008.
My first reaction to what I saw was that 'how dare they copy our work' but that quickly passed because that was certainly not what had happened and was no way to deal with the situation anyway. No, the real problem was that even though Facebook had just announced they have hit the 350 million active user mark, there are only so many people who will want to send a gene to their friends.
Sigma-Aldrich is the Goliath with a huge conglomeration of life science divisions and products, with offices and staff around the world. Genome Alberta is the David in the equation with our Calgary office of 8 people plus a few project managers scattered around the province. We are a not-for-profit research funding organization, Sigma probably has a social media budget bigger than our entire core budget for the year. Our GenOmics application was about to be crushed because I never really believed that whole David parble anyway.
We just didn't have a big enough slingshot.
Genomics: Zoom Zoom
The Knights of the Round Table, an organization that has served Calgarians for more than 80 years, invited me to enlighten them about genomics. I was joining an impressive list of previous speakers and I wanted to make sure I did a good job. I indicated to them at the beginning of my presentation that I was covering at least 150 years of knowledge in a mere 20 minutes. I called the talk Genomics: Zoom Zoom. With apologies to Mazda, I told the audience that it was going to be like them driving in a sports car rally around the Roman ruins of Verona with me sitting in the back seat and telling them what I was seeing out the window.
