Genome Blog [Category - Bioinformatics] Blog Description [Category - Bioinformatics] en-us Sun, 01 Aug 10 21:59:54 UT Sun, 01 Aug 10 21:59:54 UT http://blogs.law.harvard.edu/tech/rss Marqui 6.0 System Administrator System Administrator Interview with Paul Gordon on Semantic Web Technologieshttp://www.genomealberta.ca/blogs/interview-with-paul-gordon-on-semantic-web-technologies.aspx guest post from Susanne Cardwell
Administrative Coordinator 
Bioinformatics Platform Applied Computational Genomics Course

  Paul Gordon, the Bionformatics specialist for the Sun Center of Excellence for Visual Genomics, gave the following description of Semantic Web Technologies and how they relate to the programs he is developing called Daggoo and Seahawk:

  “In a nutshell,” says Paul Gordon, “Semantic Web technologies are about using URLs instead of words to refer to concepts.” He says that the advantage is that URLs (i.e., Web addresses like http://...) are unambiguous – it’s easier for computers to use URLs as computers have historically had problems with interpreting natural language. He states that the reason you want to use URLs in this capacity is so that the computer can surf the web for you instead of you manually trying to find answers on the web. “In short, it is about having a web of data instead of a web of documents,” says Gordon. One major problem is how to shoehorn the current Web into this Semantic model, and this is his primary focus. 
]]>Tue, 16 Mar 10 16:15:00 UTGenomics at BioHackathon 2010http://www.genomealberta.ca/blogs/genomics-at-biohackathon-2010.aspxguest post from Susanne Cardwell
Administrative Coordinator
Bioinformatics Platform Applied Computational Genomics Course


Paul Gordon, bioinformatics specialist with the Sun Center of Excellence for Visual Genomics, recently attended the Hackathon 2010, at the University of Tokyo. The objective of the Hackathon 2010 was to define technologies and standards for the global life sciences community for the next generation of web technologies often call the Semantic Web.

There were approximately 40-50 participants, and Paul was representing the Genome Canada Bioinformatics Platform. Several Canadians in attendance were some of the pioneers in Semantic Web Technologies for the Life Sciences. 

Bio Hackathon 2010 was about creating a critical mass of data providers providing the same format of information for the purpose of standardization. Standardization allows for people to ask queries or questions that require information from multiple databases. A major aim of the meeting was to educate the developers on some of the semantic web technologies, which include RDF, Sparql, and Semantic Web Services. Paul Gordon and others enlightened the participants about these technologies, how to create queries using these technologies, and use case development.

Another major aim of the meeting was the writing of computer code. Gordon focused on making it easier to use these technologies over existing databases.



BioHackathon Group Photo]]>Mon, 01 Mar 10 03:45:00 UTA New Species: Virtual Organismshttp://www.genomealberta.ca/blogs/main_01081001.aspxGuest post by Susanne Cardwell,
Administrative Coordinator,
Applied Computational Genomics Course 

Artificial intelligence is developing an impact in the science realm, and especially in computer science and biology. With the advent of artificial intelligence, the idea of giving computer programs life has become popularized.

Why is this important? The wave of the future includes the evolution of virtual organisms. These are programs that have intelligence and that are able to operate in a virtual environment that humans can interact with (Terra Nova). Terra Nova blog writer Bob McGinley on June 01, 2007 said that “we can use virtual organisms to optimize all kinds of things like traffic systems, manufacturing, medical procedures, or even non-player characters (NPC's) in virtual worlds”.

Furthermore, for Mark Ward's book called “Virtual Organisms: The Startling World of Artificial Life”, the editorial review explains how programs that “mimic the sexual reproduction... may someday run telephone networks and other large electronic systems” (amazon.com, 2009).]]>Fri, 08 Jan 10 15:15:00 UTOn Perl Programshttp://www.genomealberta.ca/blogs/main_12210901.aspxguest 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.

]]>Mon, 21 Dec 09 15:30:00 UTWhat is Bioinformatics?http://www.genomealberta.ca/blogs/main_12140901.aspxguest 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).

 

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