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Could a semantic, chemical authoring tool be developed for Microsoft Word? The paper and PDF formats that are the standard vehicles for scholarly communication are great at presenting natural language for people to read, but are not as good at carrying the machine-interpretable semantic data that is becoming an increasingly important aspect of making sense of today's "data deluge." Tony Hey, Savas Parastatidis, and Lee Dirks from Microsoft Research initially discussed this possibility with Dr. Peter Murray-Rust of the Unilever Centre at Cambridge University back in 2007. Peter is considered the "father" of Chemical Markup Language (CML is a semantic XML representation of chemical entities) and explained that a large percentage of chemists use Microsoft Word to write their research papers. He hoped that by incorporating CML into Word, he could expedite his idea of developing a semantic, chemical authoring tool. We wondered if Peter would partner with us in this endeavor. Suffice it to say that when he agreed to sign on, a project was soon underway.
I first met Peter and Joe Townsend in early 2008, just after I joined the Microsoft External Research team. Peter, Joe, and Jim Downing were all visiting Redmond to discuss making this idea a reality through a joint development project between our team in Redmond and Peter and his team in Cambridge. I was asked to serve as the program manager for this adventure.
We all had a common vision for what we wanted to achieve, but we faced many obstacles. Multiple time zones, varying degrees of programming language familiarity, different project management styles, and a total lack of chemistry knowledge on my part made the first six months a little slow going.
Still, we made progress: Embedding the CML files for each molecule referenced in the document was fairly straightforward. One of the nice features of the new DOCX format is that each file is basically a ZIP file—a container into which we could park each bit of chemistry as its own XML file. And we could also anchor these to bits of text in the document itself (in other words, the document.xml file).
So far, so good—as long as the thing in the document was text. Or an image. In fact, we got by for a while by having a handy PNG graphic for each of the molecules that we had in CML, so that when we imported a CML file we could also slip the pre-fabricated graphic into the document. It couldn't be edited, but it made the point to the casual observer that a human could see a two-dimensional (2-D) representation of the molecule, or the label in the document. More importantly, it demonstrated that a machine can understand the underlying semantics of the chemistry by reading the CML representation.
But what about all the fancy subscripts and superscripts, and pre-sub, and pre-super, and sub-super, or super-super scripts required of charges, electrons, isotopes, hydrogen dots, labels, and so forth? For this, we looked to Murray Sargent, the guru of all things mathematical and the driving force behind the great equation editing features in recent releases of Word. After reviewing our options, we decided to build upon Word's math zone features. This would allow us to take advantage of the work already done to support the complex and flexible layout required of mathematical equations.
Meanwhile, our team was spending a good deal of time reviewing options for our 2-D chemical editor. We ended up launching a separate Windows Presentation Foundation (WPF) pane from within Word, which reads in the CML, renders it, and allows the user to perform various editing functions, all while preserving a certain amount of "chemical intelligence."
This was not just characters and lines on a drawing board. When you select a particular atom, the options that you get for editing are dependent on the sorts of things that are chemically viable in that particular structure. And when you save an edited structure, the Chemistry Add-in for Word (Chem4Word) writes the modified CML back into the DOCX package, creates a PNG (for viewing in the document), updates the chemical formula, and prompts the user to update any of the other labels from the CML file.
Once this initial work was established, we brought the chemical intelligence developers and the WPF developers closer together—in the U.K.—so they could meet in person more frequently. This helped move the project along at a good pace, culminating in our beta release at the American Chemical Society Annual Meeting in March 2010.
Since the beta release, most of the work has been on Joe's shoulders. He has done significant clean-up, fixing bugs and taking in a lot of usability feedback (especially from his students). Most importantly, he has added the ability to look up existing molecular structures via existing web services at the NCBI's PubChem and the Unilever Centre's OPSIN databases. These can be used in the Chem4Word version 1.0 ribbon via load from PubChem.
I am extremely proud of this project and I am thrilled to finally see version 1.0 released to the world. We have so much more to do, however. A colleague in the U.K. recently helped explain the potential directions:
"The future of research will be powered not only by ever more rapid dissemination of ever large quantities of data, but also by software tools that 'understand' something about science. These tools will behave intelligently with respect to the information they process, and will free their human users to spend more time doing the things that humans do best: generating ideas, designing experiments, and making discoveries," said Timo Hannay, Managing Director for Digital Science at MacMillan Publishers Ltd. "Chem4Word is one of the best examples so far of this important new development at the interface between science and technology."
The Chem4Word project was one of our team's first open source releases. Just after the beta release last March, we launched the source code project on CodePlex under an Apache 2.0 license. And today, we are announcing that the project has joined the Research Accelerators gallery as a part of the Outercurve Foundation.
Here's to a long and happy future for the Chem4Word project—we hope it will offer the community a method for better facilitating and enabling semantic chemistry.
—Alex Wade, Director of Scholarly Communication, Microsoft Research
For more information, check out the Chemistry Add-in for Word press release.
Human memory is all too fallible. We all misplace items or forget to run an errand occasionally; our memories of specific events can fade with time as well. But severe memory issues can have a devastating impact on quality of life for individuals with clinically diagnosed memory disorders that are related to acquired brain injury (for example, an accident) or neurodegenerative diseases (for example, Alzheimer's disease).
There is no cure for memory loss. In the past, neuropsychologists had to rely on fairly primitive devices (such as photo albums, diaries, and electronic reminders) to help patients cope with memory conditions. Technology is rapidly evolving, however, and providing new opportunities to help patients.
A notable development in the field is the SenseCam, a memory-enhancing camera developed by Microsoft Researchers at the Cambridge campus and subsequently licensed to Vicon. Vicon sells the SenseCam as a medical device, the Vicon Revue, which has been named one of the 100 best innovations of 2010 by Popular Science. The SenseCam uses a wide-angle lens to document the patient's day—including places visited and people seen—creating visual "memories" through pictures. The camera, which is worn around the neck, takes a photograph:
At the end of the day, the patient downloads the images to a computer. These images create visual reminders of events from throughout the day—essentially, they are digital memories. These SenseCam images appear to stimulate the episodic memory of patients who view them. Unlike staged (or posed) photographs, which tend to change the nature of the very moment being captured, SenseCam images are recorded passively, with no conscious effort or intervention. Combined with the relatively large number of images, this seems to have a powerful effect on recall. Numerous patients have benefitted from true autobiographical recall through this technology; typically, a handful of images stimulates the same feelings and emotions the wearer had when they occurred.
Ultimately, we hope that SenseCam will have the potential to alleviate the onset of Alzheimer's disease in at-risk patients. Multiple studies around the globe, funded by Microsoft External Research, have helped us understand how SenseCam can help patients with a variety of memory-loss conditions. These studies include:
The SenseCam was recently featured in TIME magazine and is currently on display at the Science Museum in London. For more information, see the Introduction to SenseCam.
—Steve Hodges, Principal Hardware Engineer, Microsoft Research, and Kristin Tolle, Director, Natural User Interfaces Team, External Research division of Microsoft Research
On a chilly autumn day, robots descended on Altamont Elementary School in Altamont, New York. Were the students terrified? Far from it: they were enchanted and energized, as they explored the realm of social robotics under the guidance of Jennifer Goodall and Katy DeCorah of the University at Albany-State University of New York (UAlbany). Goodall and DeCorah presented UAlbany's Social Robotics Workshop, an innovative program designed to introduce K-12 students to the roles that robots might play in the future and to excite young people about technology in general.
The brainchild of Goodall, assistant dean of the Department of Informatics, and Nick Webb, senior research scientist at the university's Institute for Informatics, Logics Security Studies, the Social Robotics Workshop introduces students to the core concepts of robotics and enables them to experiment with robots and to program simple interactive behaviors. Built around the "sense, plan, act" paradigm-an approach that dates from the earliest days of robotics-the workshop challenges the students to program robots with personalities. For example, students might program their robots to politely say "Excuse me!" when they bump into someone, or they might have their robots convey annoyance through an angry expression on the "face" screen.
"Exercises using these software platforms allow students ... to try simple social robotic experiments, such as talking, indicating primitive emotions and simple vision exercises," said Goodall. The program clicks with students in large part because they can see a real connection between their simple experiments and future robotics applications. Moreover, working with the robots inspires the students to learn more about computer science and engineering, which is the key goal of the workshop.
Funding for the Social Robotics Workshop comes from the National Center for Women & Information Technology Academic Alliance Seed Fund, which is sponsored by Microsoft Research Connections, the division of Microsoft Research that collaborates with academia to help shape the future of computing. The Seed Fund provides grants "to develop and implement initiatives for recruiting and retaining women in computer science and information technology fields of study."
The Social Robotics Workshop is one of 19 projects that have received grants since the inception of the Seed Fund in 2007. To date, grants totaling more than $315,000 have been awarded. The UAlbany initiative was one of three to receive grants in round six of the Seed Fund. In the recently completed round seven of the competition, five projects won grants of $10,000 each. The winning initiatives range from programs to encourage women undergrads to major in computer science to a two-week summer outreach program aimed at high schoolers.
Back at Altamont, the success of the Social Robotics Workshop is confirmed in the thank-you notes from the students. "Dear Jen," wrote one of the young experimenters, "Thank you for helping us program our robots. It was much easier with your help. I like the way you broke it down into steps. It made it much easier. It was exciting to work with robots. It felt like we were real scientists! When I go to collage [sic] I want to do robots. THANK YOU!"
—Jane Prey, Senior Program Manager, Microsoft Research Connections