An Introduction to Bloom Filters (computation) and Biology

If you don't know anything about Bloom Filters, please attend, listen, and contribute to the discussion after my quick ramp-up talk (15-20 minutes).


The discussion (45 minutes to 1:30 depending on what comes up) after my talk about how people in the group are already using this or might have thought of uses based on the talk.


You can find out about Bloom Filters by looking at the Wikipedia article.

Hopefully I'll learn about biological computation applications from the group.  :-)

-Todd

--
Todd Bezenek, E.I.T.

Computer Scientist and Principle [sic] Engineer The Omnifid.us Project
Email: [masked]
When you're in space, all you really want is air.

 

 

Shabnam is also giving a short introduction on an application in DNA sequencing, so that we have the biological angle covered.

 

 

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  • Todd B.

    You can find the "slides" for the talk here: http://bezenek.blogspot.com/2012/11/computational-biology-talk-at-hacker.html

    The links are not obvious. The blogger.com editor is not very good.

    @Rahul: You will get most of what you need by following the links in the notes. There are lots of good things there.

    For more information about lossless compression, look at Ross Williams' book. His Web site is: www.ross.net

    -Todd

    November 14, 2012

    • A former member
      A former member

      Thanks, Todd, for pulling this together.

      November 14, 2012

  • Shabnam T.

    Hi Gabriele and Todd

    Am I presenting on November 13th as well about the Bruijn graphs? :)
    .... I can prepare something small but I initially thought that we will have one topic per session.

    Let me know please.

    Best,
    Shabnam

    November 8, 2012

    • Todd B.

      Shabnam: The Bruijn graphs fit right in with this. If you can prepare two or three slides to describe how they work, that will be a good addition.

      November 8, 2012

    • Shabnam T.

      I will prepare few slides ... Thanks Todd

      November 9, 2012

  • Todd B.

    I'll probably segue into the Smith-Waterman algorithm (http://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm) as that appears to be more applicable for DNA sequence matching.

    I can also spend 10 minuts summarizing the work done at the Berkeley Par Lab over the last few years to make an important set of problems (dense- and sparse-matrix operations) scale better on supercomputers. We can even fix up the definition here for fun: http://mathworld.wolfram.com/SparseMatrix.html

    November 5, 2012

  • Gabriele S.

    I'd have two suggestions on this topic: 1) how much do we need to care about computational complexity in biological computations,
    and 2) do biological systems use techniques to reduce their own computational complexity, which?

    November 4, 2012

    • joschka-joseph a.

      Gabriele: Uh..somewhat confused. These are suggested topics or "raison d'etre"? As for your question 1. I'd read http://en.wikipedia.o...­ as for question #2 Degenerecy & Complexity in Biological Systems. http://www.pnas.org/c...­

      1 · November 4, 2012

    • Todd B.

      I suggest jumping up a level. Which of the items mentioned in the Wikipedia "Computational Biology" entry (biomodeling, genomics, neuroscience, etc.) are we discussing? The answers to these questions may be different for each area.

      November 5, 2012

  • joschka-joseph a.

    The Wikipedia article is VERY GOOD. I'm trying to see if I can develop a program for it out of my newly found python skills.

    November 4, 2012

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Rafaël

We just grab a coffee and speak French. Some people have been coming every week for months... it creates a kind of warmth to the group.

Rafaël, started French Conversation Group

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