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Microsoft Research Connections Blog

The Microsoft Research Connections blog shares stories of collaborations with computer scientists at academic and scientific institutions to advance technical innovations in computing, as well as related events, scholarships, and fellowships.

  • Microsoft Research Connections Blog

    Interactive genomics: querying genomes across the cloud


    Big data: you can hardly pick up a newspaper without reading about some new scientific or business acumen derived from mining some heretofore-untouched volumes of digital information. Well, I’m happy to say that genome sequence data—which certainly qualifies as big, both in volume and velocity—is joining the party, and in a most meaningful way. When combined with information from medical records, genome data can be mined for new insights into treating disease.

    Currently, however, genomics analyses are dominated by batch processing, which means that simple analytical questions can take days to answer. A more efficient way to exploit genomics data would be to run queries against a large genome database in the cloud, by using a platform like Windows Azure. In this scenario, the queries are answered across the network in seconds.

    Towards this vision, I have been working with researchers at University of California San Diego (UCSD) and have invented the Genome Query Language (GQL), which features three operators that allow error-resilient manipulation of genome intervals. This, in turn, abstracts a variety of existing genomic software tasks, such as variant calling (determining whether a person has a different gene from the reference) and haplotyping (ascribing genomic variation as being inherited from the mother or the father). GQL is inspired by the classic database query language SQL and has similar operators; however, GQL introduces a major new operator: the fault-tolerant union of genomic intervals.
    To understand how GQL could be used on the Windows Azure platform in the cloud, imagine that a biologist is working on the ApoE gene, which is responsible for forming lipoproteins in the body. Wondering how ApoE gene variations affect cardiovascular disease (CV), the biologist types in a query with the parameters “ApoE, CV” on a tablet computer, just as you might enter a search-engine query. The query is sent to the GQL implementation in the cloud, which returns the ApoE region of the genome in patients with cardiovascular disease. Since the ApoE gene is quite small, the data is processed quickly in the cloud and returned in seconds to the biologist’s tablet. The biologist can then use customized bioinformatics software to mine the data to identify variations.
    We have implemented GQL on Windows Azure and used it to query genomic data expeditiously. We have shown, for example, how GQL can be used to query The Cancer Genome Atlas for large structural variations by using only 5 to 10 lines of high-level code. The code took approximately 60 seconds to execute on the Windows Azure application in the cloud when run on an input human genome file of 83 gigabytes. GQL can improve existing software as well by refactoring queries, significantly speeding up results. It could also be used to facilitate browsing by queries and not just location within the UCSC genome browser.
    To make the GQL implementation provide interactive speeds, two optimizations were crucial: cached parsing and lazy joins. Combined, they sped up query processing by a factor of 100. I encourage interested readers to explore the details of our research—the GQL queries we used, the optimizations we implemented, and the experimental results we achieved—in the Microsoft Research Technical Report: Interactive Genomics: Rapidly Querying Genomes in the Cloud.
    —George Varghese, Principal Researcher, Microsoft Research

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  • Microsoft Research Connections Blog

    ChronoZoom offers new tools for history teachers


    Make your mark in history with ChronoZoom

    Last week, from November 22 to 24, I was in St. Louis, Missouri, at the annual conference of the National Council for the Social Studies (NCSS), helping to promote the terrific work of our international partners in creating open-source technologies and free curricula to support history education. I spent two days in the NCSS exhibit hall demoing ChronoZoom, an interactive, multimedia timeline of the history of everything, which won the SXSW Interactive Award for Best Educational Resource last year.

    I wasn’t the only ChronoZoom fan in St. Louis. Three of our collaborators presented at the conference, which draws 3,000 to 4,000 social studies educators each year. One of our pilot projects is actually in St. Louis, and its presentation was given by 13 high schoolers, all advanced-placement history students, who shared their collaborative timeline of world religions—and the power of ChronoZoom.

    The pedagogical value of ChronoZoom was apparent in their comments, such as this from Dimitri Rucker, one of the all advanced-placement high schoolers:

    “ChronoZoom changed the way I thought about history because of the format it’s displayed in. With the zooming capabilities, you can quickly and visually learn about history all the way from cosmos to humanity now and I think that’s very interesting about this educational tool. With ChronoZoom, we incorporated the timeline of religion and philosophy and how they have affected history throughout time. And by using ChronoZoom, it is easier to show the large timeline of events to help explain how religion has affected the world.”

    My goal at the conference was to increase awareness of ChronoZoom and to encourage teachers to try it and provide feedback. In particular, we are interested in sharing the new authoring tools that provide a simple, intuitive means of creating timelines and then creating presentations around those timelines in a fashion similar to PowerPoint or Prezi. Our engineering teams will be prioritizing their work according to teacher requests, so this is an excellent opportunity for teachers to shape a piece of technology designed specifically for educational use.

    Free resources for teaching history with ChronoZoom

    I gave a lot of demos to share our technical work around ChronoZoom, but our big news was the non-digital, standards-aligned curriculum we released in partnership with the NCSS, the American Historical Association, the University of North Carolina at Chapel Hill, and a team of amazing curriculum developers and subject matters experts. As I said repeatedly at the conference, the easiest thing about creating educational technology is creating the educational technology. Once that is done, the hard work begins: creating the pedagogical support necessary to make the technology comprehensible and easy for educators and students to use.

    The curriculum consists of three core units that cover different approaches to teaching historical thinking: (1) The Causes of World War I, which teaches about causality and multiple perspectives; (2) Atlantic Encounters, which presents a more abstract introduction to historical thinking by studying the moments when two cultures meet and how the meeting changes both cultures; and (3) The ChronoZoomers Guild, which provides lesson templates and associated materials to create an immersive experience involving time travel and the alteration of pivotal events in world history. Read more about these three units.

    Middle-school history teacher Samantha Shires helped develop the World War I curriculum and piloted it with her class of seventh and eighth graders in Greensboro, NC. What stood out for her was ChronoZoom’s usefulness as a presentation and assessment tool. “There’s a certain amount of messiness to history that can make it a challenge to fully understand,” she said. “ChronoZoom provides a visual representation that helps my students make sense of the messiness and act as an operator of history, rather than merely a bystander.”

    ChronoZoom Curriculum and Technology

    Each of the lesson plans is designed to be open-ended with enough room for individual educators to flex their creative muscles. In each lesson, teachers guide the students to answer basic research questions by using authoritative primary sources that are curated by subject matter experts. Then, students are invited to use ChronoZoom to build timelines and presentations based on their research. This allows students to demonstrate their understanding of the subject matter as well as their mastery of historical thinking principles outlined in the C3 social studies standards and the upcoming Common Core standards.

    We encourage history teachers to download the curriculum, experiment with ChronoZoom, and join our community. If you like the ChronoZoom curriculum, let us know through the website forums. If you don’t like it, definitely let us know. Your feedback is essential to help ensure that we provide a curriculum that suits your needs.

    So again, please try ChronoZoom and let us know what you think. I look forward to possibly working with you as we continue to evolve ChronoZoom, striving to make it a great example of what the future of education might be.

    Donald Brinkman, Program Manager for Digital Humanities, Microsoft Research Connections

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    The curriculum for teaching historical thinking with ChronoZoom

    Lesson 1:  Causes of World War I
    This unit focuses on the events of 1874 to 1914 that led up to the onset of World War I.  The focus of this unit is causality and multiple perspectives.  The material is taught by using non-digital techniques in the classroom.  Students can subsequently use ChronoZoom to create timelines based on what they have learned, and present these learnings to their classmates and teacher.

    Lesson 2: Atlantic Encounters
    This unit explores the difference between encounters and contacts. It poses such questions as “Do cultures have a moment when they collide, when the world is changed forever and seemingly inevitably? Or do cultures interact and mingle over longer periods of time?” It challenges students to show causation, contingency, and consequences, and introduces them to historical thinking by studying encounters among cultures from across the Atlantic and the outcomes of these interactions. By exploring the question "How did Atlantic encounters shape North America?", students will understand that these encounters among indigenous Americans, Africans, and Europeans were major turning points in the history of the world. Drawing upon primary and secondary sources, students create and analyze exhibits collaboratively on ChronoZoom timelines.

    Lesson 3: ChronoZoomers Guild
    The third unit is a foundation to support historical thinking and is truly content-agnostic.  The material from the World War I unit is used to demonstrate the principles, but the unit is intended to be “plug and play” for any history content, allowing students to populate the templates with whatever historical information the class is studying.  This unit provides lesson templates and associated materials to immerse students in an epic narrative that revolves around the class being contacted by a secretive organization from the future that uses time travel to alter pivotal events in world history.  Students must master fundamental historical thinking concepts and meet Common Core historical literacy standards. They are then invited to create a timeline in ChronoZoom and present it as a proposal to change past events in order to create a better future.

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  • Microsoft Research Connections Blog

    Computer Science Education Week: "touching" on the Hour of Code


    It’s time to revise the traditional “three Rs” of education in the United States. In addition to “reading, ‘riting, and ‘rithmetic,” we need to add computer science. Yeah, I know it doesn’t even contain an “r,” but computer science is just as important as those fundamental “r” skills. And that brings me to the topic of this blog: Computer Science Education Week (CSEdWeek), an annual US event that stresses the need to teach computer science basics to every student. This year, CSEdWeek runs from December 9 to 15.

    "Touching" on the Hour of Code

    I am especially excited to work in partnership with, a new non-profit organization that initiated one of CSEdWeek’s prime events: the “Hour of Code.” The event aims to introduce 10 million students of all ages to computer science ideas and tools—and to let them try coding for one hour—while also demonstrating to parents, teachers, and policymakers how accessible coding can be. And at a deeper level, we hope it will drive demand for expanded computer science courses and activities in secondary schools.

    As part of CSEdWeek, I am in central Oregon at the Culver Middle School and Culver High School, introducing students to programming through an hour of coding by using TouchDevelop, a free Microsoft Research mobile application development tool. I’ll also host an all-school assembly on “How Computer Science Can Solve the World’s Greatest Challenges.”
    In addition, I get to spend a day devoted to my greatest passion: sparking young girls’ interest in computer science. I will meet with 93 Culver Middle School girls, introducing them to computer science research and the importance of user experience design. Too many young people only hear about the difficulty of programming; I strive to show them the art, creativity, and satisfaction involved in making an application that meets the end user’s needs. They’ll learn about the storyboarding process and how to design an application, and then they’ll help create the user interface for Games Learning Society, a research project I’m working on with Constance Steinkuehler at the University of Wisconsin. I will also give them a preview of a program we will announce this week—so stay tuned to learn about great partnerships and an event that will entice even more young women to pursue computer science careers.

    Kent Middle School students learn coding with help from Rane Johnson-Stempson during Computer Science Education Week.
    Middle school students learn coding with help from Rane Johnson-Stempson during Computer Science Education Week.

    Despite the excitement of CSEdWeek, my commitment to and passion for what it represents doesn’t begin and end during this week. Early last week, I met with 75 high school students from the Auburn (WA) Mountainview High School IT Academy Program and shared Kodu, .NET Gadgeteer, WorldWide Telescope, and other Microsoft Research technologies with them. They also learned about the exciting future of computing from bright young Microsoft employees who are in an accelerated career development program.

    Later in the month, I will head to Redmond (OR) Middle School to conduct a TouchDevelop programming event with all of the students and to introduce middle school girls to user experience design. And I’m not alone in this outreach effort; several of my Microsoft Research colleagues are also volunteering at elementary, middle, and high schools to excite students about computer science. Judith Bishop is in South Africa to expose students to TouchDevelop, and Arul Menezes, Krysta Svore, and Peli de Halleux are visiting Seattle-area middle and high schools to help students experience an hour of coding.

    Why is coding so important? The digital age has transformed how we work and live, making computer science and the technologies it enables central to our daily lives. By 2020, an estimated 4.6 million computer-related jobs will be available for those with skills in computer science—jobs that will address such issues as climate change, healthcare provision, and economic development. Unfortunately, many educational institutions in the United States have not been able to keep pace with technological advances, leaving students without fundamental computer science skills: of the more than 42,000 high schools in the United States, fewer than 3,250 were certified to teach advanced-placement computer science courses in 2013. Only 14 states count computer science courses toward a student’s graduation requirements in math and science, and no states require a computer science course as a condition of graduation. This must change if we want students from the United States to have future career opportunities in global computer science fields.

    By the way, you don’t have to work at Microsoft Research to be part of this effort: to learn about more free tools you can share with students to interest them in computing, visit Research tools.

    Rane Johnson-Stempson, Director, Education and Scholarly Communication, Microsoft Research Connections

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