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At the interface of biotech and infotech

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    Hundred nanoseconds a day started by mndoci
    The big machines started by mndoci
    The big machines started by mndoci
    Image via Wikipedia



    So the latest Top 500 list is out, so why doesn’t it excite me as much as it used to. Well partly cause many of those machines are not easily accessible, while other computing resources are within reach. Perhaps partly because for a lot of
    Freerisk – An open platform for risk modeling started by mndoci
    Freerisk – An open platform for risk modeling started by mndoci
    Image by ynse via Flickr



    I’ve been meaning to write about Freerisk.org for a while now, but only got reminded yesterday as I read the Wired article about Toby Segaran’s (and Jesper Anderson’s) new project.
    Freerisk.org sucks in finan
    Hundred nanoseconds a day started by mndoci
    Image by vitroids via Flickr



    100 nanoseconds a day. 100 nanoseconds a day. 100 nanoseconds a day
    That is amazing. I used to get supercomputing time to do 100 ns simulations during my PhD and those used to last days, but that’s exactly what NAMD has achieved
    Write heavy file system workloads started by mndoci
    In a blog post last year James Hamilton wrote about workloads in large scale network file systems. In his summary about of study on the subject he writes

    Some of the important points that spring out for me: the percentage of random access is increasing; for those accesses that are seque
    Supercomputing Masterclass – A request for information started by mndoci
    I have been invited to give a Masterworks talk on Data Challenges in Genomics for Supercomputing 09. I would like to dive into the details about the technical and scientific challenges of high throughput genomics, from microarrays to next gen sequencing and beyond and how we need to be manage the
    Web as platform: Linking data. RDF stores and augmentation started by mndoci
    Mashing up RDF data. See how you can use the Talis Platform to augment one data set with another.
    TrendingTopics.org: A reference site for data analytics in Hadoop and Hive started by mndoci
    In episode 21 of Coast to Coast Bio (not yet released) I talk about Hive. For those who may not know, Hive is a data warehouse infrastructure built on top of Hadoop.
    One of the most recent Amazon Public Data Sets is a sample of Wikipedia page stat statistics by Peter Skomoroch. The full dat
    High scale design patterns in the life sciences started by mndoci
    Image via Wikipedia



    I’ve written about software failures in the past. As I get a better understanding of scale and architectures and talk to others about some of the core design principles of systems at scale, e.g. Recover Oriented Computing (also see this talk
    Our publishing model encourages bad behavior started by mndoci
    My lack of enthusiasm for the current publish or perish model is well documented. This thread from Friendfeed highlights one of the many problems with the current state of peer review and the publishing model and implications for tenure etc. Everything is interconnected, and ends up leading to
    Almost back : business|bytes|genes|molecules started by mndoci
    When Whole Genome Sequencing becomes passe started by mndoci
    In a recent blog post at MassGenomics talking about the recently published sequence of a Korean individual, Dan Koboldt makes an interesting observation. He notes

    This week’s publication of the genome of a Korean individual in Genome Research marks the fifth individual whole genom
    test post started by mndoci
    ignore
    bbgm is on temporary hiatus started by mndoci
    Image by Gojca via Flickr
    This is the longest hiatus I have taken in a long time. Part of it is work related, but mostly, this is about moving domain registrars, hosts, etc, all at the same time.
    Will resurface soon. In the meantime, I am active on Twitter and Friendfeed%0
    When software embraces failure started by mndoci
    I recently heard someone talk about software as being operational. The context was large scale systems and how it is important not just to run hardware systems that operate at scale but also software that operates at scale. And having spent a lot of time lately in a world where operational excelle
    Some early Wolfram|Alpha driven thoughts started by mndoci
    Image via Wikipedia
    So Wolfram|Alpha is finally live. People have had mixed luck with it, as have I. Some items, especially related to mathematics and the physical sciences are really well represented. Others, not so much. When it works, it works brilliantly. Take a search for somet
    HPC and abstractions started by mndoci
    Image via Wikipedia
    Dan Reed has a great essay up on the Blog@CACM site about High Performance Computing and abstractions.
    He writes

    I am confident that high-performance computing can and should learn a few tricks from the world of web services. We need a Ruby on Rails External Link
    Web as platform: Chemvendor grows up and becomes Chemcaster started by mndoci
    Rich Apodaca is one of my favorite bloggers out there. His blog covers topics of interest at a number of levels, from cheminformatics to Ruby on Rails to we services. He also happens to be the found of Metamolecular which develops software and services that, in the words of the site, brings
    Benevolent dicators and scientific collaboration started by mndoci
    On the drive in to work today I was listening to The Semantic Web Gang where the folks were discussing VoCamp, where a bunch of folks got together to discussion and build ontologies (more build than discuss). A couple of things struck me as I listened. If you want to develop standards and %5
    Digital library quick hits started by mndoci
    Image via Wikipedia
    Just got back from the DLF Spring Forum, where I gave a keynote talk that talked primarily about the need for libraries to live in a world that is very different from the one they have historically functioned in and how a model based on loosely coupled services can play a rol
    Computational Thinking started by mndoci
    Been listening and reading to Jon Udell talk about Computational Thinking. Still need to wrap my head around the whole concept, but wanted to introduce the topic and hope that others would also find this topic interesting.
    In a talk earlier this year, Jon defined Computational Thinking as fol
    Innovation or Committee started by mndoci
    Yehuda Katz has an interesting blog post about innovation and best practices. In it he writes (emphasis mine)
    As Rubyists, we need to discourage artificial attempts to encourage conformance and discourage innovation. Rails shops should find other ways to advertise the quality of their pract
    Data data everywhere started by mndoci
    This is an exciting time to be a data geek. Today, there was a webcast (which I missed) for Wolfram|Alpha, which I am super excited about and hope that it is as good as it could be. Google just launched a new feature that makes it easy to find and compare public data [...]
    Entity extraction using Reflect started by mndoci
    Reflect comes to us from some familiar names, including Lars Juhl Jensen and Michael Kuhn and was the winner of the Elsevier Grand Challenge.
    What is Reflect? From the About page

    Reflect is a new service able to recognise proteins and small molecules mentioned in a web page, and link t
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