\neScience Workshop 2006<\/a>
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Microsoft Research\u2014in partnership with the Berkeley Water Center, the Colleges of Engineering and Natural Resources at UC Berkeley, and the Lawrence Berkeley National Laboratory\u2014held the 2010 Microsoft Research eScience Workshop on\u00a0October 11\u201313 in Berkeley, California.<\/p>\n
Scaling the Science<\/h2>\n
Curre![\"exterior\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/exterior.jpg\")
nt opportunities in the physical and biological sciences and their technological applications require the means to fundamentally understand processes at the molecular level and to extend those processes to predict performance at larger scales. eScience is developing approaches for conducting this scaling and has been essential in addressing fundamental questions in biology and astronomy. While additional applications remain in the basic sciences, these fields have demonstrated pathways for advances in the applied environmental and social sciences where the linkages between scales and disciplines require focused contributions from the eScience community.<\/p>\n
This \u201cScaling the Science\u201d workshop provided opportunities to observe how eScience has provided scaling across various fields and to explore some of the challenges that remain for realizing the ambitions of the fourth paradigm.<\/p>\n
About the Workshop<\/h2>\n
The goal of this se![\"claremontatsunset\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/claremontatsunset.jpg\")
venth annual cross-disciplinary workshop was to bring together scientists from diverse research disciplines to share their research and discuss how computing is transforming their work. The event also included the presentation of the third annual Jim Gray eScience Award to a researcher who has made an especially significant contribution to the field of data-intensive computing.<\/p>\n
<\/p>\n Each year, Microsoft Research presents the Jim Gray eScience Award to a researcher who has made an outstanding contribution to the field of data-intensive computing. Find out who the recipient of this year’s award is.<\/p>\n \t From 2007 to 2014, The Jim Gray eScience Award recognized eight researchers for their outstanding work in the field of eScience. Recognizing these pioneers in data-intensive science has helped advance the prestige of the field and strengthen the community. <\/em><\/p>\n Dr. Paul Watson is professor of Computer Science and director of the Digital Institute at Newcastle University UK, where he also directs the $20M RCUK Digital Economy Hub on Social Inclusion through the Digital Economy. As a Lecturer at Manchester University, he was a designer of the Alvey Flagship and Esprit EDS systems. From 1990 to 1995, he worked in industry for ICL as a designer of the Goldrush MegaServer parallel database server. In August 1995, he moved to Newcastle University, where he has been an investigator on wide range of eScience projects. His research interest is in scalable information management with a current focus on cloud computing. Professor Watson is a Chartered Engineer and a Fellow of the British Computer Society. Learn more\u2026 (opens in new tab)<\/span><\/a><\/p>\n Dr. David Lipman (opens in new tab)<\/span><\/a>, M.D., is director of the National Center for Biotechnology Information (NCBI). Under his leadership, NCBI has become one of the world\u2019s premier repositories of biomedical and molecular biology data, providing invaluable information to both the research community and the public. Every day, more than 3 million users access NCBI\u2019s more than 40 databases. Learn more… (opens in new tab)<\/span><\/a><\/p>\n Antony John Williams (opens in new tab)<\/span><\/a> is vice president of strategic development and head of Chemoinformatics for the Royal Society of Chemistry. He has pursued a career built on rich experience in experimental techniques, implementation of new nuclear magnetic resonance (NMR) technologies, research and development, and teaching, as well as analytical laboratory management. He has been a leader in making chemistry publically available through collective action: his work on ChemSpider helps provide fast text and structure search access to data and links on more than 28 million chemicals, and this resource is freely available to the scientific community and the general public.\u00a0Learn more… (opens in new tab)<\/span><\/a><\/p>\n Mark Abbott (opens in new tab)<\/span><\/a> is dean and professor in the College of Oceanic and Atmospheric Sciences at Oregon State University. He is also serving a six-year term on the National Science Board, which oversees the National Science Foundation and provides scientific advice to the White House and to Congress. Throughout his career, Mark has contributed to integrating biological and physical science, made early innovations in data-intensive science, and provided educational leadership. Learn more… (opens in new tab)<\/span><\/a><\/p>\n Phil Bourne (opens in new tab)<\/span><\/a>, the recipient of the third-annual Jim Gray eScience Award, is a professor in the Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California at San Diego. Phil is also the Associate Director of the RCSB Protein Data Bank, an Adjunct Professor at the Burnham Institute, and a past president of the International Society for Computational Biology. \u201cPhil\u2019s contributions to open access in bioinformatics and computational biology are legion, and are exactly the sort of groundbreaking accomplishments in data-intensive science that we celebrate with the Jim Gray Award,\u201d notes Tony Hey, Corporate Vice President of External Research.\u00a0 Learn more… (opens in new tab)<\/span><\/a><\/p>\n Jeff Dozier (opens in new tab)<\/span><\/a> was presented the 2009 award<\/a> in recognition of his achievements in advancing environmental science through leading multi-disciplinary research and collaboration. While presenting the award, Tony Hey stated, \u201cJeff Dozier’s work epitomizes what the Jim Gray eScience Award is all about \u2026 using data-intensive computing to accelerate scientific discovery and, ultimately, to help solve some of society’s greatest challenges. By combining environmental science with computer science technologies, Jeff brings a new level of understanding to climate change and its impact on our planet.” Learn about Dozier\u2019s thoughts about environmental science in The Fourth Paradigm: Data Intensive Scientific Discovery<\/em>, pages 13\u201319.<\/p>\n At the 2008 Microsoft eScience Workshop<\/a>, the Jim Gray eScience Award was presented to Carole Goble (opens in new tab)<\/span><\/a> in recognition of her contributions to the development of workflow tools to advance data-centric research. To learn about her work and the role of workflow tools in scientific research, see my experiment (opens in new tab)<\/span><\/a> and The Fourth Paradigm: Data Intensive Scientific Discovery<\/em>, pages 137\u2013145.<\/p>\n The winner of the first Jim Gray eScience Award was Alex Szalay (opens in new tab)<\/span><\/a>, professor in the Department of Physics and Astronomy at\u00a0The Johns\u00a0Hopkins University. Alex was recognized for his foundational contributions to interdisciplinary advances in the field of astronomy and groundbreaking work with Jim Gray.<\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t<\/div>\n\t<\/p>\n Johnson & Johnson Pharmaceutical R&D is using Microsoft Research\u2019s Microsoft Biology Foundation to design new chemical compounds that could improve the health and quality of life of patients around the world.<\/p>\n \t By Rob Knies<\/p>\n October 12, 2010 6:00 AM PT<\/p>\n Researchers at Johnson & Johnson Pharmaceutical Research and Development (opens in new tab)<\/span><\/a> (J&J PRD) faced a challenge. Over the years, they have built a state-of-the-art platform to enable discovery of small-molecule drugs, but the expanding role of biologics in pharmaceutical research required a new set of tools to handle large-molecule compounds.<\/p>\n Developing such functionality from scratch was a daunting proposition. It would take time and resources while delaying development of novel treatments for debilitating diseases and disorders.<\/p>\n Researchers at Microsoft Research had a solution. Their new, open-source library of bioinformatics functions, the Microsoft Biology Foundation (MBF), part of the Microsoft Biology Initiative, was designed to address just such a challenge. When the J&J PRD researchers learned about this, they immediately became intrigued.<\/p>\n This confluence of need and opportunity occurred in late November 2009. Now, less than a year later, the benefit has become manifestly apparent. Instead of spending costly time building a foundation for the new biological infrastructure, J&J PRD was able to focus on delivering value-added functionality needed to facilitate development of innovative treatments that have the potential of improving the health and quality of life of patients around the world.<\/p>\n \u201cBy using MBF, we were able to provide our users with a greater level of functionality in less time to our users for our initial development phase in the large-molecule space.\u201d says Jeremy Kolpak, J&J PRD senior analyst, who will be discussing his team\u2019s MBF deployment during the 2010 eScience Workshop, being held in Berkeley, Calif., from Oct. 11-13, \u201cIt allowed us to focus on value-added functionality for our scientists and has helped us adapt to new requests quite easily.\u201d<\/p>\n Such testimony brings a smile to the face of Simon Mercer, director of Health and Wellbeing for External Research, a division of Microsoft Research.<\/p>\n \u201cThe principal advantage of MBF,\u201d Mercer says, \u201cis that, because it\u2019s free and open-source, as a programmer, you get a certain amount of prewritten functionality that you can just build on top of. It gives you more time to do the real science, because we\u2019ve already supplied the basics.\u201d<\/p>\n It didn\u2019t take long for J&J PRD to grasp the implications of MBF.<\/p>\n \u201cWe were in the process of developing our own infrastructure to work with sequences,\u201d Kolpak explains. \u201cThis was part of a larger move in our organization to improve how R&D with large molecules was performed and integrate that process with an existing and mature framework for working with small molecules.<\/p>\n \u201cWe have been using MBF from the day we heard of it.\u201d<\/p>\n That is precisely the focus of the Health and Wellbeing effort within External Research: to collaborate openly with the bioinformatics community by applying advanced computing technologies to provide unprecedented insight into disease and human healthcare.<\/p>\n MBF, built on the Microsoft .NET Framework<\/a> and aimed at making it easier to implement biological applications on the Windows platform, was launched in Boston on July 9 during the 11th annual Bioinformatics Open Source Conference. Since then, thousands of bioinformaticians have downloaded<\/a> the tool kit.<\/p>\n \u201cThere are a lot of biologists who start as post-docs but don\u2019t end up going into biological research themselves,\u201d Mercer says. \u201cThey end up managing the data and writing the scientific applications that the biologists need to do research. They can be anywhere on the continuum between full biologists with no computing background to full computer scientists with little or no biological background.<\/p>\n \u201cThey work alongside the biological scientists, but they won\u2019t necessarily be<\/em> those scientists. They\u2019ll write scripts and write programs to help the lab run, and they\u2019ll also probably do some data analysis.\u201d<\/p>\n Companies and academics that pursue such work, naturally, are more concerned with the value they can derive from using software tools than with building the tools themselves.<\/p>\n \u201cI\u2019ve heard it over and over again from executives of different pharmaceutical companies,\u201d Mercer says. \u201cPossibly 90 percent of their software stack has been developed in house but offers them no competitive advantage. The real crown jewels in bioinformatics are relatively small compared with the huge bulk of software they have to maintain.<\/p>\n \u201cThey\u2019re often in a situation where they want to exchange data with other pharmaceutical companies on a pre-compete level, and they find that hard, because their processing pipelines are uniquely their own. A lot of commercial companies are looking for things like MBF to adopt as a common platform, so they are using the same tools, analyzing the data in the same way, and they are able to share data sets and cut costs.\u201d<\/p>\n In other words, MBF helps make bioinformaticians\u2019 work a bit simpler. That certainly appears to be the case at J&J PRD.<\/p>\n \u201cWe have integrated it into our data-analysis and -visualization platform, Third Dimension Explorer, which has been developed in house,\u201d Kolpak says. \u201cThis platform is used in a multitude of different contexts.\u201d<\/p>\n With regard to J&J PRD\u2019s large-molecule exploration, he lists the ability to achieve five distinct tasks:<\/p>\n \u201cThe goal,\u201d Kolpak says, \u201cis to capture operations that are performed routinely and make it extremely efficient to execute in one place. But at the same time, we are not trying to replace existing sequence-analysis tools for the more complex and less used operations.\u201d<\/p>\n At Johnson & Johnson Pharmaceutical R&D, there are hundreds of users of the Third Dimension Explorer tool. The MBF-related development is still being completed and rolled out, but 40 people already are using the enhanced data-analysis platform\u2014and deriving significant benefits.<\/p>\n \u201cIt\u2019s hard to quantify the amount of time it has saved us,\u201d Kolpak says, \u201cdue to the fact we work with an agile development methodology and, for each iteration, we are finding new functionality in MBF that we can utilize. I would say that, for our initial rollout, which required a large amount of framework implementation, it saved us around three months during a six-month initial development cycle.\u201d<\/p>\n Biological work might not be the first thing that comes to mind when people think about Microsoft, but it supports such scientists nevertheless.<\/p>\n \u201cInside Microsoft Research, we\u2019ve done lots of biology,\u201d Mercer says. \u201cIt\u2019s not what everybody would expect, but a lot of researchers apply their computer-science research in the biological domain for healthcare. How can you apply Microsoft technologies to scientific research? We often do that through collaborations with academics, where the academic brings the biology, in this case, and Microsoft brings the computer science. Together, hopefully, we advance further than either side would have done independently.<\/p>\n \u201cEventually, you have to ask yourself the question, \u2018Why don\u2019t we just build a platform so that all of the common elements are written once and don\u2019t need to be written again for every single project?\u2019 And once that platform exists, and it\u2019s open-source and free, why not give it away to the community so it can benefit?\u201d<\/p>\n There are specific ways in which MBF can assist in the biological domain, such as with modularity, extensibility, and code maintenance.<\/p>\n \u201cThose sorts of things that professional programmers think of aren\u2019t necessarily the first things in the minds of those who are writing scripts to support a lab,\u201d Mercer continues. \u201cMBF sits in the middle, with prewritten functionality in nice, digestible chunks, very standardized.\u201d<\/p>\n There are quite a few other biological libraries akin to MBF already in use, some of them for a decade or more. But over time, they have grown unwieldy, making it hard to extend them. And they tend to be written in script-based languages that have no type checking. MBF, on the other hand, offers type checking and guarantees, and it\u2019s built atop the common-language runtime, providing the flexibility to handle any of the more than 70 languages that work with .NET, thereby making easy for a heterogeneous community to use without having to conform to a single language.<\/p>\n \u201cWe\u2019ve also wrapped the individual bits of MBF as workflow activities for our Trident<\/a> workflow workbench,\u201d Mercer adds, \u201cwhich is also free and downloadable. \u201cYou don\u2019t even have to be a programmer to use MBF. You can just drag and drop and connect the building blocks together to build workflow pipelines.\u201d<\/p>\n External Research attempts to understand the precise scientific challenge encountered by its MBF partners, a methodology termed scenario-based development that identifies areas where MBF can be made more useful. That methodology will be a key component of the next wave of the tool\u2019s enhancement.<\/p>\n \u201cWe\u2019re approaching our partners in the academic community and the commercial world to define those scenarios,\u201d Mercer says, \u201cand that\u2019s what\u2019s driving the direction in MBF v2. We encourage the wider community\u2014people who download the source code, understand it, and start developing their own extensions to support their own science\u2014to participate, because the more of those we get, the more broadly we can develop MBF. It will grow by the actions of the community, to support the science that the community wants to support.\u201d<\/p>\n That, in the example of J&J PRD, is exactly what is happening.<\/p>\n \u201cA lot of what is on our wish list we have been developing in stride,\u201d Kolpak says, \u201cmainly a visualization tool for viewing sequences, in addition to some other sequence file-format supports that contain more than just sequence data. These are all things we plan to contribute back to the MBF development.\u201d<\/p>\n And the community at which MBF is focused expects to use open-source code.<\/p>\n \u201cIf we want to run a project that would be recognizable and familiar in form to the academic community,\u201d Mercer says, \u201cthen that would be a software-development project that is open-source, because open-source is a very common model there. We want to get contributions from as broad a set of people as possible.<\/p>\n \u201cWe want scientists to get a value out of using Windows,\u201d he concludes. \u201cWe want scientists to pick up different tools that we have and understand that they can help them do their research more effectively and reach insights more quickly than they would otherwise manage to do. We\u2019ve got a lot of value to offer in that area.\u201d<\/p>\n The folks at Johnson & Johnson Pharmaceutical Research and Development couldn\u2019t agree more.<\/p>\n \u201cI am a software developer by trade,\u201d Kolpak says, \u201cand by using MBF, I have the confidence that what I am providing our users is not just solid code, but also that the science behind it is accurate.\u201d<\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t<\/div>\n\t<\/p>\n Researchers at University of California, Berkeley, work with Microsoft Research to analyze vast amounts of data without supercomputers.Opens in a new tab<\/span><\/p>\n \t Malcolm Atkinson, e-Science Institute<\/p>\n The global digital revolution provides a fertile and turbulent ecological environment in which e-Science is a small but vital element. There is a deep history of e-Science, but coining the term and injecting leadership and modest funds had a huge impact. A veritable explosion of activity has led to a global burst of new e-Science species. Our challenge is to understand what will enable them to thrive and yield maximum benefit as the digital revolution continues to be driven by commerce and media.<\/p>\n Webcast<\/a><\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t <\/span><\/b><\/p>\n This year, Microsoft Research presents the Jim Gray eScience Award to a researcher who has made an outstanding contribution to the field of data-intensive computing. The award\u2014named for Jim Gray, a Technical Fellow for Microsoft Research and a Turing Award winner who disappeared at sea in 2007\u2014recognizes innovators whose work truly makes science easier for scientists. <\/span><\/p>\n Webcast<\/a><\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t Adam Bly, Seed<\/p>\n The future of science is open, not because it ought to be but because it needs to be. Today, science’s potential is hindered by the disconnected nature of the world’s scientific information and the closed architecture of science itself. So how do we get from here to there? How can technology make open science real?<\/p>\n Webcast<\/a><\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t<\/div>\n\t<\/p>\n \t Microsoft Biology Foundation: An Open-Source Library of Re-usable Bioinformatics Functions and Algorithms Built on the .NET Platform<\/strong><\/p>\n Webcast<\/a><\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t Scientific Data Visualization using WorldWide Telescope<\/strong><\/p>\n Webcast<\/a><\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t Data-Intensive Research: Dataset Lifecycle Management for Scientific Workflow, Collaboration, Sharing, and Archiving<\/strong><\/p>\n Webcast<\/a><\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t Parallel Computing with Visual Studio 2010 and the .NET Framework 4<\/strong><\/p>\n Webcast<\/a><\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t<\/div>\n\t<\/p>\n \t Webcast<\/a><\/p>\n Exploration of Real-Time Provenance-Aware Virtual Sensors Across Scales for Studying Complex Environmental Systems<\/strong><\/p>\n Yong Liu, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign<\/p>\n Development and Application of Network of Geosensors for Environmental Monitoring<\/strong><\/p>\n Rafael Santos, INPE\u00a0\u2013 Brazilian National Institute for Space Research<\/p>\n Opens in a new tab<\/span><\/p>\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/li>\n\t\t![\"tonyhey_2009_closesquare_72x72\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/tonyhey_2009_closesquare_72x72.jpg\")
Primary support for the workshop was provided by Microsoft External Research, headed by Corporate Vice President Tony Hey<\/a>.<\/p>\nHighlights<\/h2>\n
![\"bourne_tony_award_sm\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/bourne_tony_award_sm.jpg\")
Jim Gray eScience Award 2010<\/strong><\/p>\n\n\t\t\t\t\t\t\t\t
Past award recipients<\/h2>\n
2014 award<\/h3>\n
![\"paulwatson-2014_102x140\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/paulwatson-2014_102x140.jpg\")
Paul Watson was awarded the 2014 Jim Gray eScience Award<\/p>\n2013 award<\/h3>\n
![\"jga2013-hey-lipman210x140\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/jga2013-hey-lipman210x140.jpg\")
Tony Hey presents David Lipman with the 2013 Jim Gray eScience Award<\/p>\n2012 award<\/h3>\n
![\"escience2012_jimgrayaward-winner\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/escience2012_jimgrayaward-winner.jpg\")
Antony John Williams receives the Jim Gray eScience Award from Tony Hey at the 2012 Microsoft Research eScience Workshop<\/p>\n2011 award<\/h3>\n
![\"jga2011_hey_abbott\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/jga2011_hey_abbott.jpg\")
Tony Hey presents Mark Abbott with the Jim Gray eScience Award at the 2011 Microsoft Research eScience Workshop<\/p>\n2010 award<\/h3>\n
![\"bourne_tony_award\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/bourne_tony_award.jpg\")
Phil Bourne accepts the Jim Gray eScience Award from Tony Hey at the 2010 eScience Workshop<\/p>\n2009 award<\/h3>\n
![\"hey_dozier\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/hey_dozier.png\")
Jeff Dozier accepts the Jim Gray eScience Award from Tony Hey at the 2009 eScience Workshop<\/p>\n2008 award<\/h3>\n
![\"carole_goble\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/carole_goble.png\")
Tony Hey presents Carole Goble with the 2008 Jim Gray eScience Award<\/p>\n2007 award<\/h3>\n
![\"jga2011_hey_szalay\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/jga2011_hey_szalay.jpg\")
Tony Hey presents Alex Szalay with the 2007 Jim Gray eScience Award<\/p>\n![\"mbf_thumb\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/mbf_thumb.jpg\")
Using Software to Enhance Healthcare<\/strong><\/p>\n\n\t\t\t\t\t\t\t\t
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![\"cloudcomputing_72x72\"](\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/09\/cloudcomputing_72x72.jpg\")
Studying the Breathing of the Biosphere<\/strong><\/p>\nMonday, October 11<\/h2>\n
Keynote Presentations<\/h3>\n
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Tutorials<\/h3>\n
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Sessions<\/h3>\n
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