April, 2010

Dan on eScience & Technical Computing @ Microsoft

eScience & Technical Computing - Web Services and Scientific Research

April, 2010

  • Dan on eScience & Technical Computing @ Microsoft

    Is Open Data Protocol (OData) the way to expose Scientific Data?

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    Lately I’ve been looking at OData – the Open Data Protocol and have been wondering if this is the universal way to make Data Discoverable, Accessible, and Consumable – and as Roy pointed out “Shareable”.  It seems to have many of the characteristics that are needed to expose and share science data: Simple, Lightweight, cross platform, built on Web Protocols, keeps track of Provenance, etc.

    It builds off AtomPub and can be viewed in human readable form – you can test out the services – see http://services.odata.org/OData/OData.svc/ or if you want real data, you can test out services from Netflix, City of Edmonton, or even some Climate Change data sets from DOE via the Open Science Data Initiative.

    There is a SDK and there are a number of OData Producers and Consumers you can get started with.

    Best of all – they have a logo :-) odata

    The Open Data Protocol (OData) is a Web protocol for querying and updating data that provides a way to unlock your data and free it from silos that exist in applications today. OData does this by applying and building upon Web technologies such as HTTP, Atom Publishing Protocol (AtomPub) and JSON to provide access to information from a variety of applications, services, and stores. The protocol emerged from experiences implementing AtomPub clients and servers in a variety of products over the past several years.  OData is being used to expose and access information from a variety of sources including, but not limited to, relational databases, file systems, content management systems and traditional Web sites.

    OData is consistent with the way the Web works - it makes a deep commitment to URIs for resource identification and commits to an HTTP-based, uniform interface for interacting with those resources (just like the Web).   This commitment to core Web principles allows OData to enable a new level of data integration and interoperability across a broad range of clients, servers, services, and tools

    Open Data Protocol (OData)

  • Dan on eScience & Technical Computing @ Microsoft

    Folding@Home on Azure – Distributed Computing

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    Here’s a good way to get up to speed on WindowsAzure and contribute to a worldwide distributed computing project (Folding@Home) – by participating in the webcast you’ll also receive a temporary, self-expiring full-access account to work with Azure for a period of 2-weeks at no cost – that’s worth the webcast investment time. 

    Feeling @Home with Windows Azure, at Home

    @Home with Windows Azure I’ve spent a lot of time over the past few months working with and talking about Windows Azure to a variety of audiences, but if you’re anything like me, it can be hard to truly ‘get it’ until you touch it.  So to bring it all home (pun intended), my colleagues Brian Hitney, John McClelland, and I have been working on a pretty cool virtual event.

    @Home with Windows Azure, is a two-hour webcast, which we’ll be repeating over the next couple of months, through which we’ll cover many of the core components of Windows Azure in a rather unique context; this is not your father’s “Hello World” experience!

    The application we’ll be building leverages Stanford University’s Folding@home project.  Folding@home is a distributed computing application, where participants donate spare cycles of their own machines (at home, get it?) to running simulations of protein folding.

    Protein folding refers the process by which proteins assemble themselves to perform specific functions, like acting as enzymes or antigens.  When things go wrong, diseases and conditions such as Alzheimer’s and cystic fibrosis can result, so understanding why things go wrong is critical to advancing treatment and finding cures.   Protein folding though is a very compute-intensive operation, and simulating just a nanosecond of folding activity can take as much as a day of CPU time!

    That’s where Windows Azure comes in.  During these sessions we’ll walk through the steps to build a cloud application that will use Azure compute instances to contribute to the Folding@home project.   Registrants will get a no-strings-attached, two-week Azure account as part of the deal, so you’ll have a chance to build your own Azure application and contribute to medical science – how cool is that!

    Jim O'Neil | Supporting Developers Across the Northeast

  • Dan on eScience & Technical Computing @ Microsoft

    WWT Fisheye and spherical mirror projection

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    In the latest WWT release put out on Tax Day (April 15th) – one of the features that was included was the ability to utilize WWT in different projections – so you can use WWT in Planetariums. Below Paul Bourke tested those features out on his iDome (btw – I’d love to get my hands on that :-)) - see his review and photos

    Docs on using the WWT in the projection/planetarium mode – are available at WorldWide Telescope Planetarium 

    World Wide Telescope: Fisheye and spherical mirror projection05[1]

    Written by Paul Bourke
    April 2010

    The following is a discussion from tests of the WWT (World Wide Telescope) software and in particular its handling of projection using a fisheye lens or spherical mirror and the warp maps that describe how to distort fisheye images for this projection technique. This is not an endorsement of the product for its intended users but simply a test/evaluation of the fisheye generation and optional warping. Check out more of the review at World Wide Telescope: fisheye and spherical mirror projection

  • Dan on eScience & Technical Computing @ Microsoft

    Chem4Word : Introducing Chemistry Add-in for Word

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    For those interested in adding chemical symbols to documents – checkout the Chem4Word project, you can install the Chem4Word add-in which utilizes the Chemical Markup Language and makes it easier for students, chemists and researchers to insert and modify chemical information, such as labels, formulas and 2-D depictions.

    Introducing Chemistry Add-in for Word

    Every discipline has its own language. The ability to communicate and collaborate in a discipline-specific language is essential to scientific research, especially in an environment characterized by staggering volumes of data.

    In chemistry, not only is there a specific language, but also specific symbols. Empowering those symbols by enabling them to communicate across technologies and formats, as well as simplifying authoring and semantic annotation, is at the heart of the Chemistry Add-in for Word. Informally called Chem4Word, this free tool is being unveiled today during the American Chemical Society’s Spring 2010 National Meeting & Exposition.

    Chem4Word makes it easier for students, chemists and researchers to insert and modify chemical information, such as labels, formulas and 2-D depictions, from within Microsoft Office Word. Designed for and tested on both Word 2007 and Word 2010, it harnesses the power of Chemical Markup Language (XML for chemistry), making it possible not only to author chemical content in Word, but also to include the data behind those structures. Chem4Word and Chemical Markup Language make chemistry documents open, readable and easily accessible, not just to other humans, but also to other technologies.

    In the image below, the name and 2D views of the same chemical are shown in the document, along with the Chemistry Navigator, which displays all of the chemistry zones within the current document.

    In addition to authoring functionality, Chem4Word enables user denotation of inline “chemical zones,” the rendering of high-quality and print-ready visual depictions of chemical structures and the ability to store and expose semantic-rich chemical information across the global chemistry community.

    The product of an ongoing collaboration between Microsoft Research and Dr. Peter Murray-Rust, Dr. Joe Townsend, and Jim Downing from the Unilever Centre for Molecular Science Informatics at the University of Cambridge, the Chem4Word project took inspiration from the mathematic-equation authoring capabilities in Word 2007. We also have taken advantage of user-interface extensibility and XML features already included in Office 2007 and Office 2010, and we hope this provides a demonstration of the power of Microsoft Office as a platform. Microsoft Research worked closely with key individuals in the field of chemistry to develop this tool, but Microsoft Office provides the tools and resources to enable other domains to develop on top of Office applications.

    Further guiding the development of the Chem4Word project was the Microsoft External Research team’s commitment to supporting the scholarly communications lifecycle, which calls for software and related services that enable the coordinated, seamless exchange of data and information, from authoring through publication to long-term preservation.

    The beta release of the Chemistry Add-in for Word is available for free download. Later this year, it will be released as an open-source project under an Apache license via CodePlex.

    External Research Team Blog : Introducing Chemistry Add-in for Word

  • Dan on eScience & Technical Computing @ Microsoft

    TechNet Creates Silverlight Application as Clearinghouse for Technology Resources

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    I’m a sucker for good technology and really useful  interfaces and applications – I just saw this post from the MSPress about the TechNet Desktop Player – not only will it be really useful for finding tech resources based on your role, but also if you set your zipcode in the setting it gets you access to local events that are happening.  They also have it enabled to allow you to download the Silverlight app and run it locally on your desktop…very cool.  I could also see it being an interface to the Zentity platform for viewing organization’s digital library ecosystem.

    TechNet Creates Silverlight Application as Clearinghouse for Technology Resources

    Ever wish that you could find information about a technology in just one place? TechNet is trying to grant that wish.

    A beta version of the Microsoft Desktop Player is available now at www.microsoft.com/click/desktopplayer . With this application, you can search for resources specific to your role and technology. It’s still in beta, so I noticed that some of the Webcasts were a little fuzzy. However, it’s a great start at compiling resources from all over Microsoft to help you find information and instruction. To test it, I queried using the following criteria:

    TechNet Desktop Player

    Microsoft Press : TechNet Creates Silverlight Application as Clearinghouse for Technology Resources

  • Dan on eScience & Technical Computing @ Microsoft

    More Goodies into Windows HPC – cycle stealing, VS2010, Excel 2010, Linux Interop

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    The article from HPCwire on  Microsoft Injects More Goodies into Windows HPC highlights some of the new features in beta2.  I’m especially happy to see the support for Win7 desktops as computational nodes – desktop cycle stealing, something that always gets asked about.  The other key additions being:

    • VS2010 integration
    • Parallel Nsight, NVIDIA's software development toolset for GPU computing that is offered as a Visual Studio plugin
    • New services for Excel 2010
    • Adds compatibility with mixed-OS cluster management platforms from Adaptive Computing, Clustercorp and Platform Computing.

    HPCwire: Microsoft Injects More Goodies into Windows HPC

    <…>

    For example, Microsoft has added the ability to aggregate Windows 7 workstations into an HPC cluster. Essentially, each workstation is monitored and managed as an ad-hoc compute node within a traditional cluster. Capabilities like time-of-day scheduling and shutting down of preemptive jobs are included so that the machine can be made available to a real live person when required. The common scenario is one where an organization has a small cluster made up of say dozens of servers, along with perhaps hundreds of Windows 7 PCs sitting idle at night.

    Since these workstations are likely to be hooked up to the LAN via a high-latency Ethernet connection, the type of HPC workloads that can be run on them is somewhat more limited than that of a typical InfiniBand-connected cluster. In theory, any highly parallel but loosely coupled application would be suitable. If you have such a setup, you can essentially add a night-time cluster for free (well, at least for the cost of the power to run it).

    The next big enhancement is the integration with Visual Studio 2010, which is due to be launched next week. This new version of Visual Studio contains lots of support for creating, testing and deploying parallel apps. It includes the hooks for Microsoft's MPI, SOA-type execution, and new services for Excel 2010. Mendillo characterized the integration between Visual Studio and Windows HPC Server as a "big breakthrough moment." He may be right. Visual Studio has over 7.5 million users today, which is the largest user base for any software development suite. Given that, the ability to program from the client across the cluster is a big deal.

    The Excel tool has received special attention since it has become a fairly widespread tool for HPC-types -- scientists, engineers, financial quants, and the like. Basically, Microsoft has layered HPC services on top of vanilla Excel so that users can distribute computations across a cluster. Mendillo says there are a lot of Excel applications that are suited to this type of parallelization. One example is a life insurance actuarial calculation. On a workstation, a typical such calculation could take 14 hours. Mendillo claims distributing that work across a small  cluster -- say 16 to 32-nodes -- cuts that time down to two and a half minutes. Microsoft is partnering with integrators Wipro, Infusion and Grid Dynamics to help customers migrate their Excel workbooks and develop new parallelized apps.

    Along these same lines comes Parallel Nsight, NVIDIA's software development toolset for GPU computing that is offered as a Visual Studio plugin. Microsoft has been working with NVIDIA on this for a while, but the software maker's big contribution is low-level GPU support on the server side so that everything works seamlessly end-to-end. The whole package allows programmers to develop, test, and run GPU-accelerated applications, all with the Windows universe. This has the makings of a nice synergy for both vendors as it allows NVIDIA to piggy-back on the ubiquity of Visual Studio and gives Microsoft a GPU development capability alongside its CPU toolset.

    The last piece of the puzzle for Windows in HPC is Linux interoperability. Although some dual-boot operating system capability has been there in the past, the beta release adds compatibility with mixed-OS cluster management platforms from Adaptive Computing, Clustercorp and Platform Computing. This allows the system admin to statically boot specific nodes with Linux or Windows. In the case of Platform Computing, dynamic OS provisioning can be supported via the company's ISF Adaptive Cluster platform. The whole idea here is to be able to serve Windows and Linux HPC apps on the same hardware, and to do so as transparently as possible. This is a must-have feature for Microsoft, inasmuch as HPC customers have come to expect Linux as the default OS.

    If any of this arouses your interest, Microsoft is making the beta available for downloading on its Windows HPC Server trial site. There could be another beta round says Mendillo, or they may go straight to the final release. In either case, he expects the Windows HPC Server 2008 R2 product to be shipping later in the fall.

    HPCwire: Microsoft Injects More Goodies into Windows HPC

  • Dan on eScience & Technical Computing @ Microsoft

    Memories for life – SenseCam available

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    It’s great to see that the technology behind the SenseCam work out of MSR Cambridge is now available for anyone to utilize.  It’s had some real success as an aid for people with memory loss – check out the papers – but it could also be used as a data collection device, I see it being used in environmental projects – long battery life – proximity sensor, etc…

     

    Vicon Revue Product
    Revue. Memories for life.

    Welcome to Revue. The wearable digital camera designed to take photos passively without intervention whilst being worn by the user.

    Based on Microsoft SenseCam technology, Revue is a research tool aimed at medical researchers as an aid for people with memory loss.

    Vicon Revue | Memories for life

  • Dan on eScience & Technical Computing @ Microsoft

    Bing Earth Day Photo Contest for US Students due April 11th

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    I hadn’t seen the Bing Earth Day Photo Contest till today…there are some really good prizes for both the students and their schools.  I was looking at some of the photos – since you can submit ratings and there are some really good ones that have been submitted.

    Bing Earth Day Photo Contest for US Students

    Bing has kicked off a homepage photo contest for students in the United States to submit photoshomepage_web to help celebrate the 40th anniversary of Earth Day. The winning photo will be displayed on the Bing homepage on April 22 - Earth Day.

    In addition to the grand prize winner seeing their photo on Bing.com, there are some great prizes for both students and their schools. Winners across the four age groups (ages 5-10, 11-13, 14-17 and 18+) will win a trip for two to the Microsoft Campus in Redmond, Washington. Additionally, each winner will receive equipment from HP and Canon to help build digital photo resources at their school.

    Software Enabled Earth : Bing Earth Day Photo Contest for US Students

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