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  • samanta
    replied
    Effectiveness of which one are you asking about - cloud computing in general or hadoop?

    Cloud computing basically allows you to rent computer time from some company managing the hardware. To an user, it is nothing different from using a local supercomputing facility at the university or other place.

    Hadoop is a different paradigm and has been useful for large data. You can even set it locally and do not need cloud computing for it. I have few posts on hadoop for bioinformatics.

    Leave a comment:


  • johawashin49
    replied
    Such an amazing post! This is an interesting thread. I wonder how effective this cloud computing is.






    _____________________________________________________________________________________________________
    "Defect-free software does not exist."
    ~ Wietse Venema ~
    Hosting Dallas

    Leave a comment:


  • samanta
    replied
    Hi all,

    I managed to get contrail up and running.

    Here is how to run the program on the test case provided by Schatz.

    Leave a comment:


  • FractalExpression
    replied
    has anyone gotten this up and running? does it read raw sequence files? so many questions!

    Leave a comment:


  • seb567
    replied
    Originally posted by jjv5 View Post
    The source code has been released but it does not look like one could just run it. No documentation, no hints. Any word on when a usable version might be available?
    Meanwhile ->

    Michael Schatz (Cold Spring Harbor Laboratory)
    "Cloud Computing and the DNA Data Race: Theory and Practice."

    Leave a comment:


  • jjv5
    replied
    The source code has been released but it does not look like one could just run it. No documentation, no hints. Any word on when a usable version might be available?

    Leave a comment:


  • Gangcai
    replied
    I am also looking forward to the first release of Contrail....

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  • Zigster
    replied
    I am also wondering if this assembler is written in entirely in Java. Isn't that a Hadoop requirement?

    Leave a comment:


  • Zigster
    replied
    does anyone know when the first release of Contrail is scheduled?

    The quality of software coming from the Salzberg and Pop labs has been very high. Despite the inelegant name, I am really looking forward to seeing how Contrail compares with Velvet, Abyss, SOAPdenovo, etc..
    Last edited by Zigster; 01-11-2010, 10:34 AM.

    Leave a comment:


  • Assembly of Large Genomes using Cloud Computing by Contrail

    I have found a new software (the code source is not available yet) for large genomes assembly(http://sourceforge.net/projects/contrail-bio/). It relies on Hadoop to iteratively transform an on-disk representation of the assembly graph, allowing an in depth analysis even for large genomes, which can reduce the memory requirement. Contrails also use de Brujin graph strategy to do the short reads assembly.
    for more see the wiki: http://sourceforge.net/apps/mediawik...title=Contrail

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  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

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