Dan on eScience & Technical Computing @ Microsoft

eScience & Technical Computing - Web Services and Scientific Research

  • Dan on eScience & Technical Computing @ Microsoft

    Silverlight-based cycle stealing


    Savas and I had talked about this idea of using Silverlight-based cycle stealing and wondered how well it would work.  It's good to see this article Logoon CodeProject about Legion: Build your own virtual super computer with Silverlight by Daniel Vaughan

    Legion is a Grid Computing framework that uses the Silverlight CLR to execute user definable tasks. Legion uses an ASP.NET application and web services to download tasks, upload result data, and provide grid-wide thread-safe operations for web clients or agents. Multiple tasks can be hosted at once, with Legion managing the delegation of tasks to agents. Client performance metrics, such as bandwidth and processor speed, may be used to tailor jobs for clients. Legion provides a management service and WPF application that is used to monitor the Legion grid.

    I have deployed Legion to a demonstration server here so you can see it in action.

    I wonder if Daniel is aware of the previous Legion grid system by Andrew Grimshaw that turned into Avaki (now part of Sybase)

  • Dan on eScience & Technical Computing @ Microsoft

    PubMed Central Article Authoring Add-in


    Scientists should find this Word 2007 add-in very useful, especially when submitting to PubMed central.  It also shows how this could be utilized with other systems need to capture Metadata at the time of authoring.

    This Technology Preview release of the Article Authoring Add-in for Microsoft Word 2007 provides authors of scientific articles with the ability to read and write files from Word 2007 into the XML format used by the National Library of Medicine for archiving articles in the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature, PubMed Central.

    Download details: Article Authoring Add-in

    More details on the add-in at Savas' blog

  • Dan on eScience & Technical Computing @ Microsoft

    [Paper] Statistical Resolution of Ambiguous HLA Typing Data


    A MSR Tech Report is now available on Statistical Resolution of Ambiguous HLA Typing Data - Here's the non-technical summary of the paper:

    At the core of the human adaptive immune response is the train-to-kill mechanism in which specialized immune cells are sensitized to recognize small peptides from foreign sources (e.g., from HIV virus or bacteria). Following this sensitization, these immune cells are then activated to kill other cells which display this same peptide (and which contain this same foreign peptide). However, in order for sensitization and killing to occur, the foreign peptide must be ‗paired up‘ with one of the infected person‘s other specialized immune molecules—an HLA molecule. The way in which peptides interact with these HLA molecules defines if and how an immune response will be generated. There is a huge repertoire of such HLA molecules, with almost no two people having the same set. Furthermore, a person‘s HLA type can determine their susceptibility to disease, or the success of a transplant, for example. However, obtaining high quality HLA data for patients is often difficult because of the great cost and specialized laboratories required, or because the data are historical and cannot be retyped with modern methods. Therefore, we introduce a statistical model which can make use of existing high-quality HLA data, to infer higher-quality HLA data from lower-quality data.

    Statistical Resolution of Ambiguous HLA Typing Data

  • Dan on eScience & Technical Computing @ Microsoft

    MS eScience & Berkeley Water Center


    Here's a really good article from the Berkeley Lab View on the work that Catharine Van Ingen and Stuart Ozer from MSR have been involved with w/ LBL and the Berkeley Water Center.  The use of SQL Server Analysis Services and Reporting Services have made a real difference in how scientists can explore AmeriFlux and water sensor data.   You can see the datasets for the AmeriFlux and the Russian River at http://bwc.berkeley.edu/ Also Deb Agarwal and team have done a real good job w/ their User Manual outlying how to access the data via the web and Excel

    Lab Team Helping Smooth Flow of Water Data

    By Jon Bashor

    A collaboration among Microsoft, Berkeley Lab and UC Berkeley is underway to make it easier for researchers to access and analyze collected data on water, with the goal of accelerating research in the increasingly important areas of water supply and climate change.

    Called Microsoft e-Science, the project is part of the Berkeley Water Center’s effort to marshal expertise from public institutions and the private sector to enable researchers to easily access and work with water data. The year-old center is the brainchild of Berkeley Lab’s Computational Research Division (CRD), UC Berkeley’s College of Engineering and UC Berkeley’s College of Natural Resources.

    Source: [Read More] Berkeley Lab View -- March 16, 2007

  • Dan on eScience & Technical Computing @ Microsoft

    Microsoft SharedView Beta


    Very cool - a light weight way to share applications...brings me back to the NetMeeting days..

    There is even integration with Word - could this be the way for academic papers to be written, such that they aren't being emailed back and forth all the time.

    If a Microsoft Office Word document is being edited during a SharedView session, the Track Changes feature in Word is automatically enabled, and each change is highlighted with a text identifier indicating which user made the change.

  • Hold more effective meetings and conference calls

    Connect with up to 15 people in different locations and get your point across by showing them what's on your screen.

  • Work together in real time

    Share, review, and update documents with multiple people in real time.

  • Use when and where you want

    SharedView is easy to use, from anywhere, at a moment's notice.

  • Source: Microsoft SharedView Beta

  • Dan on eScience & Technical Computing @ Microsoft

    Paint.NET - cool student project


    Sat through a presentation on Paint.NET – really cool paint app built on .NET from students from WSU.  They are coming out with a 2.0 version on Dec 17th. 

  • Dan on eScience & Technical Computing @ Microsoft

    Math and equations in Office



    One of the most hidden features in Word 2007 is the equation editor – it allows you to input equations using the linear format and the equations that are generated are truly visualizing appealing. 

    There are some videos showing the use of equation editor, but I just see that Murray Sargent is the “star” in a new video walking through some complex equations and showing some of the other formatting/alignment features that are included. 

    Silverlight version of Video 

    Word 2007 Math Overview
    Murray Sargent: Math in Office
  • Dan on eScience & Technical Computing @ Microsoft

    Cloud Design Patterns now available


    Great news for folks looking for guidance on developing apps for the Azure Cloud – take a look at the Cloud Design Patters – it includes the following

    • Twenty four design patterns that are useful in cloud-hosted applications. Each pattern is provided in a common format that describes the context and problem, the solution, issues and considerations for applying the pattern, and an example based on Windows Azure. Each pattern also includes links to other related patterns.
    • Two primers and eight guidance topics that provide basic knowledge and describe good practice techniques for developing cloud-hosted applications. The format of each primer and guidance topic is designed to present this information in a relevant and informative way.
    • Ten sample applications that demonstrate the usage of the design patterns described in this guide. You can use and adapt the source code to suit your own specific requirements.

    Cloud Design Patterns

    This guide from the Microsoft patterns & practices group, produced with the help of many people within the developer community, provides solutions for common problems encountered when developing cloud-hosted applications.

        The guide:
    • Articulates the benefit of applying patterns when implementing cloud applications, especially when they will be hosted in Windows Azure.
    • Discusses the problems that the patterns address, and how these relate to Windows Azure applications.
    • Shows how to implement the patterns using the features of Windows Azure, emphasizing benefits and considerations.
    • Depicts the big picture by showing how these patterns fit into cloud application architectures, and how they relate to other patterns.
    • Dn568099.A345734E1F4CCB94342231F94DC62190(en-us,PandP.10).png

    Cloud Design Patterns

  • Dan on eScience & Technical Computing @ Microsoft

    Develop with Python in Visual Studio, connect with Kinect and Excel


    There is a new release of the Python Tools for Visual Studio and it includes Pyvot: a connector to Excel that allow data transfer and manipulation – check out the tutorial.  It also has a PyKinect, to leverage Kinect for new natural user interactions (NUIs)… 

    An integrated environment for developing Python in VS2010 PTVS 1.1 Alpha is Live!

    • Supports CPython and IronPython
    • Python editor with advanced member and signature intellisense
    • Code navigation “Find all refs”, goto definition, and object browser
    • Local and remote debugging
    • Profiling with multiple views
    • Integrated REPL window with inline matplotlib graphics
    • Support for HPC clusters and MPI, including debugging & Profiling
    • Interactive parallel computing via integrated IPython REPL


    Python Tools for Visual Studio

  • Dan on eScience & Technical Computing @ Microsoft

    Rename file extension with PowerShell


    Last week I ended up finding that one of my directories of pictures lost their file extensions – so I thought I’d spin up PowerShell in Win8 and see if I could remember how to do. Smile 

    After a little trial and error I ended up with the following PowerShell Script – reminded me how powerful and easy PowerShell is for scripting all of Windows.

    1. $proj_files = Get-ChildItem | Where-Object {$_.Extension -ne ".jpg"}
    2. ForEach ($file in $proj_files) {
    3. $filenew = $file.Name + ".jpg"
    4. Rename-Item $file $filenew
    5. }
  • Dan on eScience & Technical Computing @ Microsoft

    Data needs to be Discoverable, Accessible, and Consumable


    While the Data Deluge is upon on the scientific communities, how to manage and share the scientific data is still a challenge.  To really allow data to be useful for scientists and general consumers data needs to be Discoverable, Accessible, and Consumable.

    Discoverable – How do you find the data?  Searching for data via search engines is not the right way to find the information.  Sites like data.gov is a good start for getting to scientific data, but how to find the smaller pots of data.

    Accessible – To do anything useful with the information/data – it needs to be made available – that means the data needs to be easily downloaded, not hidden behind many web pages and locked up behind passwords. 

    Consumable – it needs to be straight forward (one-click) to bring the data into applications for analysis (ie. Excel, MatLab, etc).  Put it into the hands of the users.

  • Dan on eScience & Technical Computing @ Microsoft

    Happy 2nd Birthday WorldWide Telescope



    Today is the 2nd anniversary of the launch of WWT – congrats to Jonathan, Curtis, and the rest of the small team.  Besides the initial windows client (that lead to Scoble’s post - Microsoft researchers make me cry) there is the web client (silverlight), a web control, and the Bing Map WWT addin.

    There is still more to come…

    WorldWide Telescope

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