I have written about the Word add-in for Ontology Recognition (the focus of the BioLit project) in the past. The project was also mentioned in my contribution to the Fourth Paradigm book and our “A ‘smart’ cyberinfrastructure for Research” article. It was one of the projects in which I was actively involved while in Microsoft Research, together with Lee Dirks, Alex Wade, and Pablo Fernicola (who took over on the technical side and did a remarkable job).

I think the project was a great success. It was lead by Phil Bourne and Lynn Fink. Lynn did an absolutely amazing job at shaping and managing the project and it was a pleasure working with her.

The work is now reported at the BMC Bioinformatics journal: “Word add-in for ontology recognition: semantic enrichment of scientific literature”. The paper is already marked as “highly accessed”, which is great to see.

Great work everyone!

Next time you get that steering wheel in your hands, think of us bikers...

Great British commercial. Check out the “making of” as well for some of the thinking...

The Zentity folks at MSR’s External Research group (Lee Dirks, Alex Wade, and Oscar Naim) and the wonderful guys at the University of Southampton, School of Engineer Sciences (Steven Johnston, Mark Scott, Kenji Takeda, Simon Cox, and Less Carr) organized a Dojo event at Dev8D around Zentity. It was great seeing the reports and the interest.

The winner of the challenge, Martin Evans, created a Web API on top of Zentity to expose JSON-formatted representations of the entities in the Zentity graph store. Cool stuff.

Well done to everyone involved, especially to Kenji, Steven, Mark, and Oscar!

Remember the “No pants light rail ride”? This time we did a “Choo Choo train” in downtown Seattle :-) Like before, it was organized by the “Emerald City Improv”. That was last Sunday and it was soooo much fun. There were so many surprised and/or laughing faces of people as the train was going around. It was great! :-)

A funny moment (at least I thought it was funny at the time), when Gina and Eric were running around the streets to catch the train :-) They were late and the Choo Choo train had already departed so I was texting them with the location and they were trying to come find it. But then our “driver” would take a sudden turns... :-)

Yes, we even had our own live “rail-cross bar” doing “din din din” noises :-)

Here’s an article and photos about the event from Seattle’s PI: “Did you catch the ‘choo-choo train’ in downtown Seattle?”

  
(source: Seattle PI blogs)

It’s been some time since my last “travel” blog entry. I still plan to write about the fun/skiing week in Italy but I am not finding the free time to finish the video I am editing :-(

Last weekend, I rode my motorbike to Vancouver to experience some of the Olympic Games vide, hang out with my friends there, and attend one of the events. It was a fantastic experience.

The weather throughout the weekend was amazing. I took the scenic way up to Vancouver, enjoying the sun, the wind on the motorbike, and the landscape. Highway 11 in particular, along the Pacific Ocean coast and just before Bellingham was gorgeous.

 

After a long wait at the border, I went straight to a small park to meet my friend Colette, who was there proof-reading her PhD thesis. Since my visit, she’s submitted it!!!!!! I am sooooo happy for her. Such a huge milestone in her life. Well done my Coco!

Then, out and about in Vancouver, absorbing the vibe. Soooooooooo many people!

I met my friends Theoni and Simran. A great surprise was that Angela (Theoni’s and Dennis’ mom) was there too. It was soooo nice to see her again. More people joined and we ended up at an Irish bar for drinks, live music, and Olympic games on large screens :-)

 

After sleeping for 4 hours or so, we woke up early to get the buses to Cypress mountain. I was very lucky to have found a ticket for the same event as Theoni and Simran, even though we had to take different buses, at 5-6am. The stand for the spectators they had built was a really impressive structure.

The sun came out and the fun begun!

 

The event was ski cross, a first time for the Winter Olympic games. It was very very exciting to watch.

If you watched the coverage, you might have spotted me taking a photograph of the camera looking straight at me :-)

 

I was really impressed with Chris Del Bosco, the skier competing for Canada. Unfortunately, he came forth overall, after crashing from 3rd position at the final corner jump. I only found out about his story afterwards. It’s amazing how he turned his life around.

At the end, he came up to the stand. Everyone was hugging me and congratulating for his efforts. He was pleasant and was talking to everyone, giving autographs. I really like personalities like his. He’s definitely a winner in my eyes!

Since Theoni and Simran were very shy, I went and talked to him, congratulated him, and asked for the photograph :-)

 

On the way back, I decided to get Highway 11 again. It was getting dark so I thought it’d be an excellent opportunity for some sunset shots. I was not disappointed. The ride was great and the scenery was amazing.

 

Great weekend!

The Zentity team is soliciting your feedback. They just broadcasted a message that I thought might be good to redistribute through this blog as well. Please note that the deadline for paper submission is FAST approaching. I’m looking forward to seeing all the things that the Zentity community is doing with the platform.

Furthermore, if Oscar Naim (Zentity’s great Program Manager) manages to pull things off, I will be staying up all night Thu->Fri in order to virtually participate, through videoconferencing, at the DEV8D conference and answer any Zentity-related questions that developers might have.

We are very excited about the fact that you have deployed or are evaluating Zentity, and we would very much like to hear from you in order to keep improving our product.

We are particularly interested in the following information (although all feedback is welcome):

1. Installation/deployment experience
2. Zentity as a platform
3. Available documentation
4. Tools to help you get started
5. Intended and actual use
6. Performance
7. Dataset size currently in use
8. Pain points

This is a great opportunity for you to help influence the direction that Zentity will follow in future releases, so we hope you will share your experience!

As you may know, the annual Open Repositories 2010 conference will be held in Madrid, Spain this July.  This would be an excellent opportunity for you to come and present your experiences with Zentity and to learn more about what’s coming in our next version of Zentity. Hundreds of people in the repository space will attend, discussing the latest innovations in repository technologies and implementations. The Microsoft Research team is planning to have a Zentity community presence at the Open Repositories conference.  We wanted to raise this point because we wanted to suggest that you might consider putting forth a proposal to speak at the conference.  We have registered a good deal of interest in Zentity, but we’d very much like to see papers/sessions at the conference where you would be able to share your experiences (good and bad) with the platform with the wider community.  Please note that the deadline for submissions is March 1st.

On a related note, Microsoft is hoping to convene a Zentity half-day workshop/tutorial in conjunction with this conference in Madrid.  This will hopefully be another opportunity for our nascent community to learn what's new with the platform, as well as to discuss practical implementation issues, suggest new features, etc.  Assuming you are able to attend, we would be very pleased if you would consider participating in this event as well.  Please, let us know if you are interested and we can provide additional details.

(For those of you in the UK, we also wanted to point out that there will be a Zentity Lab NEXT WEEK as part of the DEV8D conference in London, UK on February 24-27th, and you are welcome to join us.  Hope to see some of you there!)

Thanks again for using and evaluating Zentity and we looking forward to hearing your feedback and comments!

Today at yoga (yes, I woke up at 5.15am again for a 6.30 class ), our lovely instructor Jen shared a poem with us that I really liked:

“To laugh is to risk appearing a fool,

To weep is to risk appearing sentimental.

To reach out to another is to risk involvement,

To expose feelings is to risk exposing your true self.

To place your ideas and dreams before a crowd is to risk their loss.

To love is to risk not being loved in return,

To live is to risk dying,

To hope is to risk despair,

To try is to risk failure.

But risks must be taken because the greatest hazard in life is to risk nothing.

The person who risks nothing, does nothing, has nothing, is nothing.

He may avoid suffering and sorrow,

But he cannot learn, feel, change, grow or live.

Chained by his servitude he is a slave who has forfeited all freedom.

Only a person who risks is free.

The pessimist complains about the wind;

The optimist expects it to change;

And the realist adjusts the sails."

UPDATE: I changed the title of the post to the correct title for the poem and the poet’s name. Thanks to Mike Amundsen for letting me know.

I use my social streams and digital recordings of what I do in real life as part of a personal mutli-year investigation into semantics and digital memory. For some time now, my Twitter steam was mirrored to my Facebook one and archived on my blog, as part of “life as it happens”. I am seriously considering separating the coupling and maintaining two streams with different roles.

The Twitter one would act as a broadcast stream of work, technical, interesting stuff while the Facebook one as a recording of my personal adventures, whereabouts, and mishaps. Links to my blog entries will continue to appear in both and everything will be archived on this web site. I still have some infrastructure to take care of. As soon as the “divorce” is official, I’ll let everyone know.

Both streams are open to everyone of course.

I just remembered that the Science Commons Symposium is taking place this coming Saturday. It’s promising to be a very cool event, organized by my friends over at External Research in Microsoft Research. I am really looking forward to it. The list of speakers is impressive! If you are around and haven’t joined, I encourage you to do so!

Science Commons Symposium - Pacific Northwest

Please join us on Saturday February 20^th for an all-day symposium on accelerating scientific discoveries.

9:30am to 5:30pm Microsoft – Building 99

The conference is international in scope and features several of the most important figures in the areas of online science and Open Access.  We are expecting a strong turnout by a broad variety of academic researchers, librarians, as well as other roles who are interested in developing alliances with scientists and technologists who are creating new modes of scientific communication.

We have an exciting lineup of speakers including:

• John Wilbanks is the VP of Science Commons.  John and the Science Commons team help people and organizations from every part of the scientific ecosystem lift legal and technical barriers to research and discovery.
• Heather Joseph is the Executive Director at SPARC, the Scholarly Publishing and Academic Resources Coalition. She leads SPARC's advocacy efforts to support widespread adoption of open access to scholarly research.
• Anthony Williams is a leader in the domain of free access chemistry. He is the VP of Strategic Development for the Royal Society of Chemistry, the president of ChemConnector and the founder of ChemZoo Inc.
• Jean-Claude Bradley  is an Associate Professor of Chemistry and the E-Learning Coordinator at Drexel University.
• Cameron Neylon is a biophysicist who has always worked in interdisciplinary areas and is a leading advocate of data availability.
• Stephen Friend is the founder and president of Sage, a not-for-profit medical research organization designed to revolutionize how researchers approach the complexity of human biological information and the treatment of disease.
• Peter Binfield is the publisher of the online journal PLoS ONE, one of the journal offerings of the Public Library of Science, and is a respected innovator and analyst in the fields of online science, scholarly publishing (both Open Access and mainstream/commercial), and scientific communication.
• Peter Murray-Rust is an accomplished chemist, a faculty member of Churchill College at the University of Cambridge, a leader in the Open Data movement, a founding member of the Blue Obelisk organization.

The symposium will be held on the Microsoft campus (Building 99) in Redmond, Washington. Breakfast pastries, coffee breaks, lunch and an evening reception will be provided thanks to the generous support of Microsoft. 

Registration and more details can be found at: http://scs.eventbrite.com/ and http://sciencecommons.org/

When Blaise first presented Photosynth at TED few years ago, everyone was amazed. Well, the work that he’s been doing over at Bing Maps is starting to show off and it’s absolutely wonderful. I just watched his recent presentation on “augmented-realy maps”. Blaise and his team continue to innovate big time!

(source: Augmented-reality maps: Blaise Aguera y Arcas on TED.com)

I am really enjoying the work that my new team does. We are a Cloud-focused team. I am really looking forward to when we are going to be in a position to talk in public about what we are building. I am learning a lot and the people in the team are fantastic!

 

The following observation is by no means unique or original. Many many out there have been doing similar and even more complicated calculations, illustrating the value of Cloud Computing. Many use similar insights already for their day-to-day operations. Cloud Computing infrastructures have enabled so many businesses to take off and scale, at a fraction of the typical infrastructure costs. So, nothing new here :-)

I am recording it because it led me to the realization that us developers/architects/philosophers*, not just CIOs and CTOs, have to also start embracing the new platforms out there and incorporate economics-related thinking in the way we develop, not just deploy and operate, software and services. Again, the following observations are very simple and obvious, so don’t expect to find anything profound. You’ve been warned :-)

 

The Cloud is not just a platform for deploying applications and services. It’s a great tool for our day-to-day lives as developers as well.

Recently, we had to transfer 2TB of data as a test for one of the components we are developing. As part of the transfer process, we wanted to calculate the MD5s of thousands of files. We used Azure storage as the destination for our files. We effectively used it as a data repository, as a disk, directly from our locally-running software component. Our intake process was running on a local computer, getting the data from the Internet and placing it on Azure. Then, another computer was reading the data from the “disk”, calculating the MD5s, and storing the results back into the Cloud. That was our mistake. Some simple calculations illustrate why.

 

An Azure (or Amazon Web Services customer for that matter), pays for the data it transfers into the Cloud storage and for the data it transfers out. Any transfers inside the Cloud are free.

For Azure (and assuming that the transfers happen in the US), the cost is $0.10/GB in and $0.15/GB out. In other words, we had to pay (I am not adding the per-10k-transactions cost here):

• $0.10 x 2 x 1,024 GB ~= $205 to bring the data into Azure
• $0.15 x 2 x 1,024 GB ~= $307 to get the data out of Azure in order to perform the MD5 calculations

Now, had we used an Azure compute instance to do the calculation of MD5s, we would have dramatically reduced the cost of our task. Assuming we can get 100Mbits from Azure storage to an Azure worker role, we can process ~12.5MB/s. Let’s assume for the moment that we can calculate the MD5 almost instantly and that we are bounded by the bandwidth. We will need ~46.5 hours to calculate all the MD5s. We cannot get 100Mbits out of Azure to a local machine, so it would have been much much more time consuming to do the calculation outside of Azure.

The cost of using an Azure worker role for 46.5h:

• 46.5h x $0.12/h = $5.58

Wow. Compare $307 against $5.58! That’s a huge saving and I still haven’t included the cost of owning, managing, maintaining the infrastructure in order to perform the calculation locally (hardware, software, networking, power, human resources). All we have to do is deploy our app on an Azure compute node and finish our task for $6. More importantly, given that our task at hand is highly parallelizable, we could just use 10 or 20 or 40 Azure instances and finish in a fraction of the time for the same cost. Installing a cluster to scale out an one-time task would have dramatically increased the total cost for that operation.

Our job as developers is to come up with great designs and build good quality software that meets customer requirements. We should also be thinking about the cost of delivering the software. Cloud computing infrastructures are here to help.

 

* :-) “why a philosopher”

Last Sunday, Michele, Dave, and I participated in the “No Pants Light Rail Ride” event. Similar events take place in major US cities every year. This one was the first one in Seattle.

It was an absolute blast. We had such a good time! Just looking at the expressions of unexpected passengers was great :-) Michele and Dave... you were both such a good company. Many thanks!

Videos and photographs of the event are all over the place. Here are some representative ones.

• The Komo News report is fun. The reporter took his pants off at the end :-)
• The Highline Times post has some nice photos (just click on the first one).
• The Seattle PI has some video shots. David is the one talking at the start. I can be seen in two of the shots in the first few seconds, albeit very very briefly. At the end of the video, the shot of the pants on the conveyor belt at the airport is great :-)
• King 5 news: Michele and Dave can be seen. The “happy faces” guy is blocking me :-(

A random YouTube video.

 

And here are some of Dave’s excellent photographs (I can’t believe I am posting photos of myself without pants :-)

  
  

It’s been long time in the making but, finally, Tony is blogging :-) In fact, it seems that the entire External Research team might be posting through the same blog. Definitely worth following! And no, I am not just saying this because it’s my previous team and I really like everyone over there :-)

External Research blog

The inspiration behind this blog is a strong desire to foster connections that lead to meaningful breakthroughs; to engage in ongoing dialog in an open forum; to discuss and debate the information and ideas critical to harnessing the power of science and technology to address the most urgent global challenges.

Every day, I have the privilege of witnessing the wonder of discovery, regardless of where it takes place, or whether it’s undertaken by academic researchers and scientists around the world or within Microsoft External Research. For those of us at Microsoft External Research, the opportunity to collaborate with the finest and researchers and scientists working across the globe today is the core of everything we do.

This blog is being launched at a critical juncture in the research field. Over the next decade, it’s predicted that more scientific data will be accumulated than has been collected thus far in all of human history. For every member of the global research community, that fact represents a serious responsibility. Given the richness of available resources, it’s important to make the most of that data by sharing not only ideas but inspiration as well, and to challenge one another to contribute the best work possible to the global, virtual collective of dedicated research and technology professionals. The work being undertaken by the global research community is significant: the impact of the research being done throughout the community extends far beyond today. And, by collaborating in order to share the best work, the pursuits will benefit generations to come.

Please, let us know what’s on your mind. Let us know what’s important to you and how the research community can make a meaningful contribution to your work. On behalf of all of us at Microsoft External Research, we look forward to the conversation.

Tony Hey, Corporate Vice President

Microsoft External Research

(source: Welcome to the Microsoft External Research blog)

Last February, I linked to a video, which I thought was very powerful, from Konstantinos Pilavios. Here’s another one called “Small Pleasures” (make sure you watch it all the way to the end).

(thanks to Ioannis Kavouras for the link)

Our upcoming book (tentative title: “REST in Practice”) has a Facebook page, so go become a fan. We are going to start posting news/updates about the book soon. You’ll also be able to ask questions, monitor our progress, and give us feedback. However, if you are not a Facebook fan, you can always contact us directly:

Savas Parastatidis: Web, Facebook, Twitter, email

Jim Webber: Web, Facebook, Twitter, email

Ian Robinson: Web, Twitter

We are also considering launching the “restbucks.com” Web site.* “Restbucks” is a coffee shop. It is used throughout the book as an example of how Web technologies could be used to build Web-based services solutions (inside and outside of an organization), apply hypermedia in the implementation of business processes and documents, address scalability and fault tolerance issues through caching, utilize Atom and Atom Pub, etc.

We are very excited about the book and we are making our best to bring it to your hands as soon as possible. We are also thrilled to see our work already influencing the thinking behind efforts like Restfulie.

 

* We need to check with a lawyer first for obvious reasons :-)