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Hadoop in Biotech

UPDATE - We are looking at a place at Dundas & Ossington. Thanks Wally!

At a high level I will cover the various toolsets in use by Cloudera and biotech users.

Open to specific use case discussions. Please bring your Bioinformatic data challenges. I only intend to speak for part of this User Group to allow for members of the Biotech research community get their questions answered, connect with colleagues, and hopefully learn how others have solved problems with Hadoop in biotech.

As my comment noted below, this intended for those individuals who work with Bioinformatics data or intend to in the future. This is one of those of those sessions where 5-10 people exchanging ideas and challenges is more productive than 30 people asking us what we mean by Short-Read Aligners or Single Nucleotide Polymorphisms.

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  • Adam M.

    September 19, 2012

  • Ram V.

    Very good. I learnt a lot, particularly about implementing Hadoop infrastucture keeping existing programs/software.

    September 19, 2012

  • Tom K.

    My interest in this session is purely driven by my wife who currently utilises the MaRS lab for analysis on datasets for her PhD research, which is why I was excited when this session came up. Would it be any help to bring in some data to use?
    I am also in the same group as Tri, please feel free to move me to bottom priority. Thanks!

    September 10, 2012

    • Adam M.

      Hello Tom. Why not bring your wife and her data? :) She could probably help to provide some context for the workflow I'll go through. What I'm professionally curious about is what the data is (DNA, mRNA, amino-acid chains, GEO microarrays, etc) and what her scientific workflow looks like. I'm going to be a covering toolsets that were used in an actual chain of work. Some of her work may overlap on that workflow and some may not.

      Also, if you have to bring it then I assume it's new experimental data and not something she may have already published to one of the many Bioinformatic databases.

      September 10, 2012

  • Tri N.

    Hi Adam,

    No pb. Actually I don't work in Biotech. I am just a DB guy who happens to be interested in sciences in general. My knowledge in biology and genetics are basic, I am just curious as how big data is used in this area. I hope this session would give me some elements to understand how the genome sequencing was achieved. I can learn Hadoop in a book. But hearing people talking about Hadoop AND biotech is valuable for me personally. However, I cannot really contribute to the discussion as I am not professional in the biotech area. If you need to make room for other attendants, please feel free to move me in the bottom priority.

    September 5, 2012

    • Adam M.

      Hello Tri, I've made room for other attendants so please come if you wish. This session will cover how certain tools on Hadoop are employed in bioinformatic workflows. If we're lucky, Brian O'Conner will be there too and tell us about Seqware.

      September 5, 2012

  • Adam M.

    if you got burned in my RSVP purge I'm sorry. Don't take it personally, I just went down the list and removed people who looked very new to Hadoop and were not involved in Biotech (based on what they did or did not state in their introduction). It's not exactly the most scientific way to purge. :)

    September 4, 2012

  • A former member
    A former member

    I have an account at Bento Miso. They can seat 50 - they've been a location for the Ruby Talk nights a few times. Let me know if you need a hookup [masked]

    September 3, 2012

  • Wally T.

    My company has a photography/recording studio (at Dundas and Ossington) that has 50 chairs and a presentation setup in a room about 700 sqft. It isn't roomy for 50 people, but it can handle it. Please let me know if you are interested in holding it there. We don't work in Biotech, but are very interested in Hadoop in general. And promise to keep our lack of bio-knowledge under wraps while we observe the session.

    September 2, 2012

    • Adam M.

      that sounds like a solid option. can we get in touch Wally? [masked] or[masked]-4037. thanks!

      September 2, 2012

    • Wally T.

      Hi Adam, you can reach me at[masked], or I'll try you on Tuesday morning. Cheers!

      September 2, 2012

  • Adam M.

    Folks, I am aiming for this to be an interactive discussion of tools and Hadoop in Biotech. There is a a cap of 50 people for this event to due the room I am booking. Please RSVP Yes only if you are already or intend to work with Bioinformatics data. We cannot have a productive discussion if half the audience is just there to try and pick up more Hadoop exposure, knows nothing about the subject matter, and prevents us from discussing actual Hadoop problems.

    I appreciate that there are a lot of people wanting to learn about Hadoop and we will have more meetups focused on the technology in general. At some point, we want most of the meetups to focus on the actual users of the technology. I love introducing this technology, but most of the work I put into this group will eventually go to those that actually intend to use Hadoop. Please remember that there is always Hadoop training and certification and none of our sessions will ever amount to that.

    August 26, 2012

  • Adam M.

    We will be booking MaRs shortly. No, there isn't much on Machine Learning in common Biotech use cases. I will propose two new meetups: the Pig-Fest and a Machine Learning meetup.

    August 24, 2012

  • Hardik

    Just to benefit everyone : Here's the intro to data science http://datascience101.wordpress.com/2012/08/24/nice-intro-to-data-science-slides/

    August 24, 2012

  • Masoud C.

    Will there be much material in this session for the machine learning/data sciences practitioner?

    August 24, 2012

  • Hardik

    August 24, 2012

  • Hardik

    As we gonna have a lot of talk about human genome sequencing and analysis - thought having 101 on genes would make this meetup more interactive and interesting - throwing some balls 1) Genome Basics http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp1_1_1.shtml#genome1 2) Hadoop in BioInformatics http://www.slideshare.net/mndoci

    3) 101 on Genes /hadoop-for-bioinformatics
    https://www.23andme.com/gen101/genes/

    from #3 - the human genome searchable is now becoming reality and role of Hadoop is going to be interesting

    August 24, 2012

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