Yesterday the five recipients of the Microsoft Research New Faculty Fellowship Program were announced. Congrats to Wei Wang from UNC who is also a MSR eScience RFP recipient for the A Comprehensive Protein Database Indexed by Spatial Motifs “MotifSpace” project.
I do look forward to seeing the daily image Bing has as background on the search page – and was really excited to see “Bing’s Best” as a Win7 theme, I’ve been enjoying some great photos rotating on my desktop…
[Update] You can also add this functionality to WindowsXP
Wallpaper Rotator, from Microsoft's CodePlex, allows to dynamically change the desktop background (similar to Windows 7). (Thanks to Blake from The Road to Know Where)
Personalization Gallery - Windows 7 themes, wallpapers, and gadgets - Microsoft Windows
Back from vacation to lovely Sunriver, OR
Slides and webcasts from all the 2005 MSR Faculty Summit sessions are available at:
Valerie Daggett and her team at UW have put up a site with their simulations of over 300 proteins for a combined simulation time of more than 35 microseconds. This site contains information for their top 30 targets. The other interesting part is that they have built this using SQL Server and use SQL Server Analysis Services to create cubes of the molecule locations.
Dynameomics Dynameomics is a continuing project in the Daggett group to characterize the native state dynamics and the folding / unfolding pathway of representatives from all known protein folds by molecular dynamics simulation. This effort began with the creation of a consensus fold list. This was done by cross-referencing the fold definitions used in SCOP, CATH, and the Dali Domain Dictionary as described in the Origin of the Fold List page. Next, targets were selected from the consensus fold list. A target refers to a specific protein structure from the PDB that has been chosen to represent a given fold (see the example on the left). The specifics of this choice are give on the Target Selection page. The complete list of consensus folds, their populations and targets are provided in the fold and target pages. At this time, we are continuing to simulate targets from the fold list, generally in order of decreasing fold population. The simulation protocols, software, and analyses are described on the methods page.
Dynameomics is a continuing project in the Daggett group to characterize the native state dynamics and the folding / unfolding pathway of representatives from all known protein folds by molecular dynamics simulation.
This effort began with the creation of a consensus fold list. This was done by cross-referencing the fold definitions used in SCOP, CATH, and the Dali Domain Dictionary as described in the Origin of the Fold List page. Next, targets were selected from the consensus fold list. A target refers to a specific protein structure from the PDB that has been chosen to represent a given fold (see the example on the left). The specifics of this choice are give on the Target Selection page. The complete list of consensus folds, their populations and targets are provided in the fold and target pages.
At this time, we are continuing to simulate targets from the fold list, generally in order of decreasing fold population. The simulation protocols, software, and analyses are described on the methods page.
Source: Dynameomics - Home Page
I realized I forgot to post about Craig Mundie's article in the March/April Technology Review -
Science as a Web Service XML can supercharge research. <...> XML is also one of the enabling technologies for grid computing and Web services, which will revolutionize the scientific community in the coming decade by enabling the free exchange of information across distributed systems. Remote computation will be directly accessible from any desktop, and sensors and instruments will have their own Internet addresses. The immediate challenge for the scientific and engineering community is to take advantage of available data management and data analysis tools. The larger and longer-term challenge is for the leaders in academic research to leverage software and Web services technologies to standardize the way they present and track their data.
XML can supercharge research.
<...>
XML is also one of the enabling technologies for grid computing and Web services, which will revolutionize the scientific community in the coming decade by enabling the free exchange of information across distributed systems. Remote computation will be directly accessible from any desktop, and sensors and instruments will have their own Internet addresses.
The immediate challenge for the scientific and engineering community is to take advantage of available data management and data analysis tools. The larger and longer-term challenge is for the leaders in academic research to leverage software and Web services technologies to standardize the way they present and track their data.
Yesterday I had a really good discussion with Jamie Cromack on her efforts around putting together a Learning Assessment Toolkit. This toolkit is are valuable asset for professors teaching both in CS and STEM.
The Microsoft Research Assessment Toolkit was conceived to provide higher education faculty members with user-friendly, focused resources to assist in developing and conducting rigorous educational assessment. The Toolkit includes a variety of items to facilitate the planning and implementation process, including: An overview of assessment and assessment planning guide. User self-assessment tool to help faculty determine their level of assessment experience. The components of the kit are coded to allow users to find tools and strategies appropriate for their needs. Frequently Asked Questions (FAQ) that explain assessment issues with minimal use of jargon. Case studies of effective assessment that provide a snapshot of faculty in various computational science or STEM disciplines. A guide to selecting assessment tools. Annotated resources primarily focused on computational science and STEM disciplines and organized by topical categories. Web links to various assessment-related sites or organizations. Development of the Toolkit will be an ongoing effort; Toolkit materials are available online at http://research.microsoft.com/erp/AssessmentToolkit.
The Microsoft Research Assessment Toolkit was conceived to provide higher education faculty members with user-friendly, focused resources to assist in developing and conducting rigorous educational assessment. The Toolkit includes a variety of items to facilitate the planning and implementation process, including:
Development of the Toolkit will be an ongoing effort; Toolkit materials are available online at http://research.microsoft.com/erp/AssessmentToolkit.
Michael Kordahi created a way to see how Bing search results compare to the other big search players - it gives you 3 columns of results and you can vote which one has the best results. If you’re using IE you can also add BlindSearch as a IE search provider.
The “Search Taste Test” – do you really know the difference? So there is plenty of talk about Google being the best search engine out there, but with some pretty amazing improvements recently made to Live Search, and now particularly the launch of Bing, our new “decision” engine, it’s really time to see if Google really is the best – for you personally. One fun way of doing this is to use this fun little utility that Michael Kordahi wrote (a teammate of mine) called Blind Search. Basically, you head over to http://blindsearch.fejus.com, enter your search term, and click the search button. The tool goes off and searches for your terms at Google, Bing and Yahoo. You get the three sets of results back – all formatted anonymously so you don’t know which column of results was returned by which search engine. Then you can either “vote” for the search engine that gives you the best, most appropriate results for you personally, or you can simply click on one of the results themselves and head off on your way like you would if you were using the actual search engine. One really cool thing is that if you’ve been using Google and want to try out Bing, but aren’t quite ready to make the switch (personally I now use Bing as my favoured search provider but hey, you never know), you can actually use Blind Search as your default search provider.
So there is plenty of talk about Google being the best search engine out there, but with some pretty amazing improvements recently made to Live Search, and now particularly the launch of Bing, our new “decision” engine, it’s really time to see if Google really is the best – for you personally. One fun way of doing this is to use this fun little utility that Michael Kordahi wrote (a teammate of mine) called Blind Search.
Basically, you head over to http://blindsearch.fejus.com, enter your search term, and click the search button. The tool goes off and searches for your terms at Google, Bing and Yahoo. You get the three sets of results back – all formatted anonymously so you don’t know which column of results was returned by which search engine. Then you can either “vote” for the search engine that gives you the best, most appropriate results for you personally, or you can simply click on one of the results themselves and head off on your way like you would if you were using the actual search engine.
One really cool thing is that if you’ve been using Google and want to try out Bing, but aren’t quite ready to make the switch (personally I now use Bing as my favoured search provider but hey, you never know), you can actually use Blind Search as your default search provider.
The odd ramblings of a geek pretending to not be "all grown up" : The “Search Taste Test” – do you really know the difference?
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 on 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.
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)
Here's a very helpful post I ran across from Volker's blog on debugint MPI application on Windows....
VolkerW's WebLog : Debugging MPI on Windows This week our team hosts an event for Microsoft partners working on HPC migration projects. Developing requires debugging. The Microsoft toolset, namely Visual Studio, supports remote debugging of MS-MPI based applications. Christian is helping out in the lab and started a 2 part blog post about How to Debug MPI Applications in Visual Studio 2005. More details about debugging of parallel applications can also be found on MSDN and here. Virtually Yours
This week our team hosts an event for Microsoft partners working on HPC migration projects. Developing requires debugging. The Microsoft toolset, namely Visual Studio, supports remote debugging of MS-MPI based applications. Christian is helping out in the lab and started a 2 part blog post about How to Debug MPI Applications in Visual Studio 2005. More details about debugging of parallel applications can also be found on MSDN and here.
Virtually Yours
VolkerW's WebLog : Debugging MPI on Windows
World Wind lets you zoom from satellite altitude into any place on Earth. Leveraging Landsat satellite imagery and Shuttle Radar Topography Mission data, World Wind lets you experience Earth terrain in visually rich 3D, just as if you were really there.
Link to article...
This will be very useful to the scientific apps that had been trying to use BizTalk to handle some of the scientific computing workflows. I'm quite interested in seeing apps that try it out - I'm sure Paul Roe from QUT will be moving their Bioinformatics project over to it. http://msdn.microsoft.com/workflow has all the info - including hands on labs and Try out Windows Workflow Foundation online at MSDN VirtualLab.
Here's an quick way to help build WPF applications....
Welcome to the home of code name "Acropolis" The Microsoft code name “Acropolis” Community Technology Preview 1 is a set of components and tools that make it easier for developers to build and manage modular, business focused, client .NET applications. Acropolis is part of the “.NET Client Futures” wave of releases, our preview of upcoming technologies for Windows client development. Acropolis builds on the rich capabilities of Microsoft Windows and the .NET Framework, including Windows Presentation Foundation (WPF), by providing tools and pre-built components that help developers quickly assemble applications from loosely-coupled parts and services. With Acropolis you will be able to: Quickly create WPF enabled user experiences for your client applications. Build client applications from reusable, connectable, modules that allow you to easily create complex, business-focused applications in less time. Integrate and host your modules in applications such as Microsoft Office, or quickly build stand-alone client interfaces. Change the look and feel of your application quickly using built-in themes, or custom designs using XAML. Add features such as workflow navigation and user-specific views with minimal coding. Manage, update, and deploy your application modules quickly and easily.
The Microsoft code name “Acropolis” Community Technology Preview 1 is a set of components and tools that make it easier for developers to build and manage modular, business focused, client .NET applications. Acropolis is part of the “.NET Client Futures” wave of releases, our preview of upcoming technologies for Windows client development.
Acropolis builds on the rich capabilities of Microsoft Windows and the .NET Framework, including Windows Presentation Foundation (WPF), by providing tools and pre-built components that help developers quickly assemble applications from loosely-coupled parts and services. With Acropolis you will be able to:
Source: Microsoft code name "Acropolis" - WindowsClient.net
So glad to see the CTP of Data Mining Add-ins available - I see this is as Data Mining for the rest of us...
Microsoft SQL Server 2005 Data Mining Add-ins for Office 2007 (Data Mining Add-ins) allow you take advantage of SQL Server 2005 predictive analytics in Office Excel 2007 and Office Visio 2007. The download includes the following components: Table Analysis Tools for Excel: This add-in provides you with easy-to-use tasks that leverage SQL Server 2005 Data Mining under the covers to perform powerful analytics on your spreadsheet data. Data Mining Client for Excel: This add-in allows you to go through the full data mining model development lifecycle within Excel 2007 using either your spreadsheet data or external data accessible through your SQL Server 2005 Analysis Services instance. Data Mining Templates for Visio: This add-in allows you to render and share your mining models as annotatable Visio 2007 drawings.
Microsoft SQL Server 2005 Data Mining Add-ins for Office 2007 (Data Mining Add-ins) allow you take advantage of SQL Server 2005 predictive analytics in Office Excel 2007 and Office Visio 2007. The download includes the following components:
Source: Download details: SQL Server Data Mining Add-ins for Office 2007 CTP
This week I’m on the road – yesterday attended the opening of the SDSC/CAL-IT2 Synthesis Center – a collaboration space for computational science and visualization. The SDSC Notebook Project which MSR sponsors as part of the eScience Program is now part of the Synthesis Center.
Today I’m at the International Conference on Computational Science 2005 (ICCS 2005): "Advancing Science through Computation" at Emory University in Atlanta. I’m here to give a short industry talk on “eScience with Databases and Web Services” and will highlight some of the eScience projects I support as well as push the use of databases exposed as web services and consumed by smart clients to help solve scientific research problems.
Had breakfast with Marty – who was at ICCS to present the paper Toward GT3 and OGSI.NET Interoperability: GRAM Support on OGSI.NET [pdf] and chair the Parallel and Distributed Computing session
Blair Jennings, lead developer for the Collaboration Notebook Project was interviewed for .NET Rocks while they were in San Diego.
Great opportunity to get a special academic discount on Windows HPC Server 2008.
Windows® HPC Server 2008 Experience Counts Academic Program You know the value of high-performance computing (HPC). No matter the topic - the inner workings of the universe or the economy; the spawning of a hurricane or urban development - HPC has become a key driver of the type of research that leads to groundbreaking insights.
You know the value of high-performance computing (HPC). No matter the topic - the inner workings of the universe or the economy; the spawning of a hurricane or urban development - HPC has become a key driver of the type of research that leads to groundbreaking insights.
Microsoft Higher Education - Experience Counts
I stopped by Georgia Tech today and visited with May Wang in the dept of BioMedical Engineering. May is one of the eScience RFP receiptants for the Advanced Biomedical Computing Systems for Cancer Research project and the folks in her Medical Informatics and BioImaging Lab are doing some really good work applying computing technologies to help solve cancer related research problems.
Saw this post by Qixing on the uses of Silverlight in different sites - I'd like to start compiling a list of eScience sites/applications using Silverlight...let me know if you are using it...
It's great to see the MSR SenseWeb project picked as one of 2006 most significant advances in information technology by Technology Review. Check out the SensorMap and you can see the JHU Life Under Your Feet Project sensors on the map.
Geotagging. GPS is becoming a more common feature in mobile phones, cameras, and cars. The result is a world of people, pictures, cars, and data trails on maps. A Microsoft research project aggregates disparate sensor data to map the world in real time.
Source: Technology Review: The Year in Infotech
I finally had sometime to check out Books.live.com and it is wild - there are tons texts to look at...very interesting....
A couple of books I found - The Life of Columbus in Pictures and I especially like this inscription from the "Orators of the American Revolution"
To Students who are not Drones, Christians who are not Bigots, and Citizens who are not Demagoues,
To
Students who are not Drones,
Christians who are not Bigots,
and
Citizens who are not Demagoues,
Link to Live Search Books: Orators of the American Revolution
This is great news for the Bio researchers...info at iNquiry Bioinformatics Portal for Microsoft Compute Cluster Server - they also mention the "The Scientific Desktop"
"The scientific desktop" aims to build a bridge between common computing tools and everyday scientific computing tasks. One example is an Excel add-in that enables researchers to launch Blast queries directly from Excel and then get results back into their spreadsheet application.
HPCWire: The BioTeam Delivers Informatics Solution on Microsoft CCS The BioTeam, a consulting collective that delivers informatics solutions to the life science industry, has announced that it is releasing their iNquiry software on the Microsoft's new Windows Compute Cluster Server 2003. The challenge is many informatics problems are data-intensive and require high computational power to solve. However, the individuals who work on these problems are not always experts in scalable computing. Science departments and other groups that are getting into high performance computing for the first time need a platform that is powerful but easy to use, and cost effective. The installation, customization and ongoing support of a scalable commodity cluster have traditionally presented a formidable challenge to busy scientists, and limited budgets. BioTeam's iNquiry software platform enables the rapid deployment of a ready-to-use cluster and web portal for use in life science informatics settings. It comes preconfigured with many open source scientific applications and can be extended to support additional commercial, open-source or internally developed applications. Microsoft Windows Compute Cluster Server (CCS) 2003 is a new HPC operating system specifically designed for group and departmental-level deployment. "Windows Computer Cluster Server 2003 has everything needed to quickly deploy a Windows-based cluster," said Michael Athanas, founding partner of The BioTeam. "The combination of Microsoft's product and iNquiry will be a solid and compelling compute solution platform for researchers and scientists."
The BioTeam, a consulting collective that delivers informatics solutions to the life science industry, has announced that it is releasing their iNquiry software on the Microsoft's new Windows Compute Cluster Server 2003.
The challenge is many informatics problems are data-intensive and require high computational power to solve. However, the individuals who work on these problems are not always experts in scalable computing. Science departments and other groups that are getting into high performance computing for the first time need a platform that is powerful but easy to use, and cost effective. The installation, customization and ongoing support of a scalable commodity cluster have traditionally presented a formidable challenge to busy scientists, and limited budgets.
BioTeam's iNquiry software platform enables the rapid deployment of a ready-to-use cluster and web portal for use in life science informatics settings. It comes preconfigured with many open source scientific applications and can be extended to support additional commercial, open-source or internally developed applications.
Microsoft Windows Compute Cluster Server (CCS) 2003 is a new HPC operating system specifically designed for group and departmental-level deployment.
"Windows Computer Cluster Server 2003 has everything needed to quickly deploy a Windows-based cluster," said Michael Athanas, founding partner of The BioTeam. "The combination of Microsoft's product and iNquiry will be a solid and compelling compute solution platform for researchers and scientists."
Source: The BioTeam Delivers Informatics Solution on Microsoft CCS
The latest version of TechNet Flash has some good pointers to details on SQL Server 2008 and the CTP available for download. Some of the things scientists might find interesting are:
Organizations today thrive on data. Understanding data trends and having a vision of the requirements of your data-driven applications is crucial in meeting the needs of these applications going forward. For a view of the Microsoft data platform vision, and to see how Microsoft SQL Server 2008 will deliver on that vision, the Microsoft SQL Server 2008 Product Overview white paper is a great place to start. And Microsoft recently released a Community Technology Preview (CTP) version of SQL Server 2008 for you to download and provide your feedback to the SQL Server development team. For a quick look at the key improvement pillars in the SQL Server 2008 CTP, click over to the SQL Server 2008 June CTP Highlights. Over the next month, we are also featuring a series of SQL Server 2008 TechNet Webcasts including the SQL Server 2008 Data Management Overview on July 26. Check out the Webcasts section below for the entire series.
Source: http://www.microsoft.com/technet/abouttn/subscriptions/flash/archive/07-25-07.htm
Don Syme annouced a new drop of F# - I especially like these samples:
F# 1.1.13 now available! I’m pleased to announce that F# 1.1.13 is now available! You can download this release from http://research.microsoft.com/fsharp/release.aspx . This is an exciting release, containing many important enhancements to the language that make F# programming simpler, more powerful and easier to explain and understand. We’re particularly pleased with comprehensions, which, although found in other languages, works beautifully in conjunction with other F# language features such as pattern matching. These also simplify the use of many .NET APIs and collection types. We've also included named arguments, C# 3.0-style property setters and a host of improvements to the F# library, as well as a good number of bug fixes based on feedback from our rapidly expanding user base.
I’m pleased to announce that F# 1.1.13 is now available! You can download this release from http://research.microsoft.com/fsharp/release.aspx .
This is an exciting release, containing many important enhancements to the language that make F# programming simpler, more powerful and easier to explain and understand. We’re particularly pleased with comprehensions, which, although found in other languages, works beautifully in conjunction with other F# language features such as pattern matching. These also simplify the use of many .NET APIs and collection types. We've also included named arguments, C# 3.0-style property setters and a host of improvements to the F# library, as well as a good number of bug fixes based on feedback from our rapidly expanding user base.
Source: Don Syme's WebLog on F# and Other Research Projects : F# 1.1.13 now available!
Designing for Usability in e-Science An International Workshop on Interrogating usability issues in new scientific practice, within the Lab and within Society A workshop to explore both the design needs for EScience, and the implications of designing for eScience The National EScience Center Edinburgh, Scotland January 26-27 (Thurs-Friday) 2006
Designing for Usability in e-Science
An International Workshop on Interrogating usability issues in new scientific practice, within the Lab and within Society
A workshop to explore both the design needs for EScience, and the implications of designing for eScience
The National EScience Center Edinburgh, Scotland January 26-27 (Thurs-Friday) 2006
Link to source...
Just saw VolkerW post info on the whitepaper to help understand how to setup a cluster to dual boot between WinCCS and Linux...very helpful.
Dual Boot CCS and Linux Hot off the (virtual) press: "Windows® Compute Cluster Server 2003 and Linux." Many partners, especially in academia, have asked about and experimented with getting a system to dual boot a Linux distro and Windows Compute Cluster Server (CCS). Microsoft has published a whitepaper describing the installation and configuration of a High-Performance Computing (HPC) cluster for a dual boot of Microsoft Windows CCS and the Linux OpenSuSE Operating System (OS). Download the doc here. Virtually Yours
Hot off the (virtual) press: "Windows® Compute Cluster Server 2003 and Linux." Many partners, especially in academia, have asked about and experimented with getting a system to dual boot a Linux distro and Windows Compute Cluster Server (CCS). Microsoft has published a whitepaper describing the installation and configuration of a High-Performance Computing (HPC) cluster for a dual boot of Microsoft Windows CCS and the Linux OpenSuSE Operating System (OS).
Download the doc here.
VolkerW's WebLog : Dual Boot CCS and Linux