Tuesday, October 28, 2008

Internet Archive's new book viewer

Here's a sample that apparently only works in Firefox and Safari:

This is great! I love that IA has integrated a really usable book viewer into their offerings, and I'm intrigued by the fact that it's open source. Since BHL content is being scanned and served through Internet Archive, I could envision building the following enhancements into this viewer:

Friday, October 24, 2008

Storage requirements for a Biblioburro: TIF vs. JPEG2000

Biblioburros, originally uploaded by chrisfreeland2002.

I gave a presentation recently and bemoaned the fact that I didn't have a metric for describing the number of open access books that had been scanned by the Biodiversity Heritage Library (22,000 at the time of the presentation). Is that the size of a book mobile? A small public library? A rare book reading room?? No one can give me a good metric for visualization.

Lo and behold, that very day (no joke) the NYTimes ran a story about Luis Soriano, a Columbian who loads up his "Biblioburro" - two burros carrying books - and takes them from village to village. A 10-legged bookmobile (8 on the burros, 2 on Luis), if you will. Luis has 4,800 books. So, finally, I had a metric for BHL...if 2 Biblioburros can carry 4,800 books, then for the sake of visualization I'll say that 1 Biblioburro can carry 2,400 books. BHL, to date, has scanned 9 Biblioburros of content! Woo hoo!

I gave another talk at the Biodiversity Informatics Standards (dubbed TDWG; don't ask) annual conference in Fremantle, Australia, on the advantages of JPEG2000 for use in natural history museums and libraries, given its superior compression technology over traditional JPEG. I took the Biblioburro concept a step further, and using metrics & averages from our scanning efforts, determined that 1 Biblioburro is carrying an average of 1,000,000 pages of literature, which equates to 24TB of RAW or TIF images, and only 2TB of JPEG2000 images, demonstrated here:

If you want to know which of these is easier to manage & maintain, just ask the donkey.

Here's the presentation, along with some other information about JPEG2000, including a plug for the supercool new open source JPEG2000 server, djatoka:

Monday, October 20, 2008

Nomina III workshop group

Nomina III workshop group, originally uploaded by dremsen.

Yeah, life is rough for a bioinformatician.

Thursday, October 16, 2008

Sydney, my new favorite city

Sydney Opera House, originally uploaded by chrisfreeland2002.

Note: the links should open in a new window.

My partner Chris and I have spent the past 9 days (give or take with time differences) in Sydney and its environs. I've found it to be a fantastic, cosmopolitan city. Though all large international cities are alike these days, what with our global economy, Sydney certainly does have some unique aspects that make it stand out. Some highlights:

The Sydney Opera House and the Harbour Bridge on Sydney Harbour are certainly the images everyone has of the city. And for good reason - they are beautiful structures in a beautiful setting. The Opera House is more lovely up close than I expected; it's made of beige and ivory tiles in various patterns, not a flat white shell. We walked across a bit of the Bridge to get a spectacular view of the Harbour and Opera House. We most definitely DID NOT do the BridgeClimb, which straps you to the bridge and lets you climb to the top. No, we saved the daring for another day. Lastly, we took in opening night of Puccini's La Bohรจme at the Opera House. It was a contemporary staging, which made the already-nearly-unavoidable comparisons to Rent altogether unavoidable. We enjoyed it, for sure, but probably would have liked it more with a traditional staging - corsets and the like. I just kept waiting for Mimi to pole dance and howl at the moon...and apparently she doesn't do that in the original opera. Now we know.

We spent a day at Taronga Zoo, which was fabulous. You take a ferry across the harbour to get there, which made me a bit nervous because I get seasick (I was fine). Once on dry land we made our way to the top and saw some amazing views of Sydney. We also saw some of Australia's native critters, like dingoes, wallabys, kangaroos, a lonely cane toad (not a native, I know), and of course koalas. But for some odd reason my favorite was the Tasmanian devil. He just looked so darn cute, until he opened his mouth and you saw these giant fangs! He didn't spin around or anything...

Another animal encounter took us by surprise. We were strolling through the Royal Botanic Gardens and came upon a colony of Grey-headed flying-foxes (fruit bats). One, they were huge (I swear they were bigger than my little dog) and two, there were so many of them! We sat on a bench and watched them for at least a half an hour, flying from tree to tree and getting into fights with one another. It was just so unexpected. And again, they were HUGE!

We did an excursion to the Blue Mountains, about 2 hours by train outside of Sydney. When we arrived it was very chilly and there was a significant amount of fog that obscured the views. We spent the morning walking through trails down in the valley until the mist cleared, and once it did - WOW! The views were spectacular! We spent the rest of the day hiking up and down the trails, crossing dangerous little bridges, and otherwise trying to avoid falling to our deaths. By far, though, the best view was of Bridal Veil Falls, which was just absolutely beautiful. The highlight of the trip for both of us, I think, and something that will stay with me forever. Just stunning.

It's spring now in Sydney and the weather has been gorgeous. There was one rainy day, so we spent it inside at the Sydney Aquarium. Chris Cozzoni is a fan of aquariums, and this one is a good one. We saw platypus swimming around, walked under a tunnel with sharks overhead, and I snapped the funniest "Stick Figure in Peril" I've ever seen at a crocodile exhibit. Aussies & Sydneysiders have a great sense of humor...one I very much appreciate.

I was surprised, though, by a language barrier I hadn't expected. Aussie slang is quite different. In all honesty, I had an easier time ordering coffee in Bratislava, Slovakia, than on our first day here. Granted, I was a bit jet lagged, but I nearly had an epileptic fit trying to order a coffee for Chris and a coffee with cream for me from a stand. A sign would have helped. Turns out I needed to order a 'long black' for him and a 'flat white' for me. None of the guidebooks mentioned this little difference. Coffee is very, very important, so they should get the word out. Like, Qantas should brief you in the landing video before arriving in the country or something. Other differences that amused me were fairy floss (instead of cotton candy) and cinnamon snails (instead of cinnamon rolls). In general I was quite inspired by the food, and plan to incorporate some ideas into my cooking blog.

All said, it's been a wonderful trip. After 10 years together Chris and I have learned how to travel together very well and it's been great to experience this unique and vibrant city together. We've kept up on all the financial issues at home (naturally, given Chris' job) and the presidential election (everyone's for Obama; folks have dubbed Palin 'half-baked Alaskan'...which may well become a new recipe!).

We're off tomorrow - Chris back to the States and me on to Perth/Fremantle for another week to attend the Taxonomic Databases Working Group annual conference, where I'm giving two presentations (one on BHL, one on the JPEG2000 image format) and exhibiting a poster about my recent work.

Cheers, and carry on,


Wednesday, October 08, 2008

Status of biodiversity services

The brilliant Rod Page has created a monitoring service for bioinformatics web sites & services (like DiGIR) after he ran into uptime issues with databases at Smithsonian & other large institutions. Check it out at:

His rationale, posted to the Taxacom listserv:

Additional information about Rod's thoughts here, on Twitter:
(Tweets as documentation. A first!)

I applaud this idea. As I Twittered (Tweeted?) back to Rod, he has "created an incentive chart for bioinformatics services, like in sales." A little competition is good among peers, and this is the first time I've seen a visual overview of how my servers & sites are doing compared with others in my field. I'm sure this was Rod's goal and he nailed it.

Now, how do we ensure that the service monitor is up?

Tuesday, October 07, 2008

Riley, In Memoriam

Riley 2, originally uploaded by chrisfreeland2002.

Monday, October 06, 2008

The Right Rev. Chris Freeland

So in addition to running technology projects and writing a cooking blog I also marry people. Chris and Emily are neighbors of ours, and great friends. I offered my services in jest at a dinner party more than a year ago and they took me up on the spot. They held the wedding at my place of employment (Missouri Botanical Garden), which was very cool for me, and absolutely beautiful. The whole event, from processional to last dance, was traditional, yet unconventional, and totally unique - just like Chris & Emily. I was honored & thrilled to play a part in their day.

And maybe someday my partner of more than 10 years and I will be able to do the same. Sure, we can go to California or Massachusetts and other East Coast cities, or Iowa, but that would carry no legal benefit as we live in Missouri. Someday.