Encyclopedia of Life Blog

Thanks to amazing efforts by many of the biodiversity informatics group staff (especially Pam who’s basically not slept since we went live very early Tuesday morning), we’re back up and running again. We’ve been stable since yesterday afternoon, but we’re still dealing with many more hits than we ever expected - we’re now listed on over 400 press websites in 10 different languages!  So please bear with us if things are a bit slow or we need to take the site down to try to make additional upgrades to improve the performance. We’re currently working on ways to address this going forward so everyone can experience the Encyclopedia of Life. Thanks for your patience!

Many impatient visitors to The Encyclopedia of Life are no doubt clamoring for a look inside. So you can at least have a glimpse, here are two videos we just posted to YouTube:

Homepage:

Species Pages:

You may have noticed that the EOL site has been flaky at best since approximately 12 EST this afternoon. Although we are serving the site from a load balanced cluster of several machines, we are experiencing phenomenal loads.

I just churned through the web logs from web machines in this cluster and there were 5.8M hits in the span of 3 hours. Most of these happened within 1 hour. We were down (and continue to experience intermittent access) for a few hours, then flipped the machines back on. Since then, there were an additional 5.7M hits, totaling 11.5M hits since 9AM this morning and it is now 2:45PM here. Wow!

We are working hard to resolve the issue so stay tuned and please have patience! I’ll post updates here as the day progresses.

Update Feb 27 @ 11:45AM EST:

In the first 24 hours (minus the approx. 3-4 hours we were completely down) there were:
18.5M hits, 13.3M page views, and 940GB of data transferred.

The Encyclopedia of Life was officially launched and we are tracking progress and responses. Please be sure to complete the survey accessible on the homepage and to also participate in our forum. We haven’t said much yet about what’s going on behind the scenes, so here’s a quick glimpse into the gadgetry whirring away and the people keeping it all working well at the Marine Biological Laboratory in Woods Hole, MA:

The EOL Biodiversity Informatics Launch Team

Pam Fournier, keeps the rack-mounted servers (one of three cabinets shown) working well

We’ll have plenty more to write about the infrastructure and informatics behind EOL. That is, when we stop to take a breath.

February is coming to a chilly end in the heartland. Besides sitting around in long underwear and rhapsodizing about how warm and lucky all the people going to the upcoming TED conference next week in Monterrey, California (Feb. 28th) are going to be, the BioSynC has been active in several areas. We have been hosting visitors, working on outreach and planning future meetings, here is the latest:

Construction of the center is buzzing along, with lights, ceiling, and doors installed recently, and we are excited to see that the colored accent walls have been painted-heralding the final push to finish by the end of March. Here are some pictures of the unfinished (but getting close) space:

On February 5, we were happy to have a visit from Jamee Field, new member of the Board of Trustees at the Field Museum (and daughter of Marshall Field) in order to see the progress of the new center facilities.

On February 7th Audrey Aronowsky, Rick Ree and Mark Westneat had a conference call with the team at Adobe Systems and got an update on the progress of new phylogenetic tree visualization that they are creating as a portal to the EOL. Visualization tools for evolution and biogeography are a central goal of BioSynC, and we are looking forward to having our collaborative visualization tool demonstrated by Adobe at TED.

On Feb. 8, Mark Westneat presented a seminar to the High School Transformation Project of the Education Department, entitled “Coral Reef Fishes: Biodiversity, Evolution and Bioinformatics”, highlighting potential uses of the Encyclopedia of Life for teachers and students.

On February 11th Audrey Aronowsky attended a meeting at the MacArthur Foundation along with Field Museum’s Elizabeth Babcock (Education) and Steve Strohmeier (Institutional Advancement) to discuss a digital learning initiative that MacArthur is interested in funding that will involve both the Field Museum and the EOL.

BioSynC is participating in and hosting two upcoming synthesis meetings. The first one, “IEDG 2008: Integrating Evolution, Development and Genomics” will take place May 28th-30th at UC Berkeley and will be hosted by Berkeley graduate students led by Jan Vendetti. The second one, “Mega-phylogeny Assembly by Literature-mining and Grafting” will take place April 18th-20th, and will be the first meeting to take place in the completed center. It will be led by Assistant Director Rick Ree and will focus on assembling a phylogeny of North American vascular plants. The main purpose of the meeting will be to train students how to use numerous computer applications to assemble and graft together phylogenetic trees.

Although we are a small team and are in the midst of filling positions, we are working very hard to ensure the public launch is a success. The Biodiversity Informatics component of the Encyclopedia of Life is stationed in Woods Hole, MA at the Marine Biological Laboratory. Some of us are long-time Cape Cod residents, but others have travelled great distances to help fulfill the dream.

David J (Paddy) Patterson
Biodiversity Informatics Leader

As a taxonomist responsible wholly or in part for the discovery of about 250 taxa, my view is that taxonomists are the information managers of biology, and that bioinformatics is a domain within taxonomy. I am a member of the International Commission of Zoological Nomenclature. I am also a Senior Scientist at the Marine Biological Laboratory in Woods Hole Massachusetts and holds professorial positions at Brown University (Rhode Island) and at the University of Sydney (Australia).

Jennifer Schopf
System Architect

I’m the System Architect for the informatics group of EoL, which means I’m responsible for the overall management of this portion of the project, including working with end users to define requirements, working with the development team to come up with specifications, architectures and plans, and overseeing the day-to-day deliverables and progress. For the previous 6 years I was part of a large distributed software group called Globus, which also took a research project and made it into production-quality code for a large set of users. I came to EoL in part because it’s such a fascinating idea - a Web page for every species! - and I wanted to be part of a team that worked closely with scientists to change how they do their research.

Patrick Leary
Portal & Aggregation Project Leader

I have been working at the Marine Biological Laboratory on biodiversity informatics projects since 2001. I received a BA in Computer Science and Mathematics from Skidmore College in 2005 and have been working full-time at the MBL since then. Before working for EOL I was the lead developer and database administrator for the uBio project. Some of my recent developments have included natural language processing tools for identifying scientific names, applications which index and aggregate recent biodiversity literature, and tools which automatically mark-up documents with semantic annotations. For EOL, I develop and maintain our central data indices and repositories, as well as create the web services used to interact with these data bases. I see the Encyclopedia of Life as a communal resource which can help connect those interested in learning about biodiversity directly to the most compelling resources available. I hope EOL can promote awareness in biodiversity, and engage a n ew generation of future biologists.

Peter Mangiafico
Research & Development Project Leader

I have an undergraduate degree in Physics, an MS education and an ME Engineering Physics. I’ve worked for NASA as a data analyst, as a researcher on digital medical imaging, and in technology companies in every role from sales to marketing to technical project management, web software development and as director of web application development. For the EOL, I have worked on the presentation layer of the preliminary version of the EOL.org species pages to be released at Ted 2008 and in the future will be working with new technologies and investigating partnerships, as well as creating prototypes and assisting in the integration of these technologies into the core EOL infrastructure. What I like best about the EOL is working with the enthusiastic and talented group of individuals that are undertaking this most incredible project.

David P. Shorthouse
WorkBench Project Leader

I have an undergraduate and Master’s of Science degree from Laurentian University in Sudbury, Ontario where I focused my interests on ecological questions using spiders as a focal taxon. I have done the same for my Ph.D. thesis at the University of Alberta where I used ground-dwelling spiders as indicators of whole-forest biodiversity. I am leading development of what we are internally calling the “WorkBench” environment. This will be where users create, mix, mash, and reuse materials. There are lots of exciting ideas for how this will work and I am dilligently putting the pieces together. What excites me most about the Encyclopedia of Life is the unbounded enthusiasm people have, especially those who may not have formal training in biology but are just as empassioned about biodiversity as are taxonomists and ecologists.

Pam Fournier
Information Technology

I am in charge of the Information Technology area for the Encyclopedia of Life. I am responsible for all aspects of server system design, implementation, and support. The servers include infrastructure, domain, and site servers run on various operating systems. My background includes degrees in Computer Science and Accounting with certifications and experience in software development, project management, networking, and systems administration. I joined the EOL because I looked forward to the challenges offered by such an extreme project. What I like best about the EOL is the working with such a dedicated group of people and the “can do” attitude which abounds here.

Alexey Shipunov
Cybertaxonomist

I am botanist, taxonomist, and a developer, all in one. My Ph.D. in Moscow State University was on the taxonomy of Russian plantains. My recent academic pursuits focused on molecular taxonomy and diversity of orchids and endophytic fungi. I like diversity of any kind, but am especially intrigued by the global diversity of species. The vast majority of species are still undescribed, but at the same time, many species have been described several times over and consequently, have different names. To deal with this issue, I am leading what we are calling Union — a system that will intelligently inform an end-user of currently recognized names but will also inform him/her of other names including homonyms, synonyms, vernaculars, misspellings, and surrogates.

Sarah Bordenstein
Content Manager

I serve as Content Manager for the EOL Informatics Group. With an undergraduate and Master’s of Science degree in Biology, I have worked at the Marine Biological Laboratory for four years in the areas of Education and Outreach. Prior to joining the EOL team, I led development of Microbial Life, a digital library dedicated to the ecology, evolution and diversity of microbes. I also coordinated the collection of legacy data for the International Census of Marine Microbes and served as education liaison for the local community. I am particularly interested in empowering teachers and students to participate in the scientific discovery process by making learning resources, tools and datasets freely available online. I feel extremely lucky to be part of EOL as I believe this resource will greatly enhance our awareness of biodiversity and facilitate the collection and distribution of biological information.

Jon Ferguson
Scientific Informatics Analyst

I’m moving to Woods Hole to be part of the Biodiversity Informatics group. Having lived in Scotland with large a family for a number of years it’s a big move. The kind of thing you do only when an opportunity to be part of something big comes along. What captures my imagination about EOL is both the beauty of the subject and the scale of the undertaking. To make this work we’ll need strong collaboration from biologists and semantic researchers around the globe. Meeting and working with these people will surely be the most exciting part of all.

Kristen Lans
Project Administrator

I bring a background in Environmental Education and Administration to the Encyclopedia of Life’s Biodiversity Informatics Group. I earned a MA in Education at Portland State University in Oregon, where my thesis focused on creating participatory, web-based sustainable design tools for K-12 students and teachers. In 2005 and 2006, I was awarded the US Environmental Protection Agencys’s P3 (People, Prosperity, and the Planet) Award for this work. I am hopeful about EOL’s potential as a medium to engage students with the natural world and to empower them to participate in designing creative solutions to stop environmental degradation where they live. I also hope that EOL will play a role in preserving and cataloguing biodiversity in the developing world, particularly by allowing underrepresented populations to contribute knowledge about culturally-specific species names, uses, and social and ecological functions.

One reason the Education and Outreach component is so exciting is because the EOL is an incredible platform for creating interest and awareness about the world around us.  It can be leveraged for inspirational, in-depth awareness building and educational experiences as well as be used for practical applications, such as environmental management.  The opportunities for learning, teaching and exploration are vast and limited only by one’s imagination!   

Discussions with teachers in formal and informal education settings so far indicate interest to use EOL as a tool to learn fundamental concepts, such as the scientific method and to enhance the learning related to topics such as evolution, taxonomy, systematics, ecology and extinction.  But that is just the beginning.

There are also more complex or integrated concepts and applications that the EOL will be able to support as it develops over time and accumulates more information on each species page.  Some of these examples include teaching and learning about ecosystem function and the services they provide such as climate regulation and water purification.   Eventually, we hope to develop virtual ecosystems that can be manipulated in a variety of ways so students can test the effects of changes of different types and magnitudes.

Beyond learning possibilities, the EOL will be an important information resource for conservation professionals or environmental managers in governments, corporations or other settings who need to develop management plans or monitor the status of selected species.  Media specialists could use the EOL to fact check their stories, as well as provide links from EOL pages to their stories that will put those species in context of current day issues and news.  The EOL will provide a convenient “one-stop shopping” website of current, authoritative information that can be trusted. 

 Another reason this job is rewarding is due to the partnerships that will grow as EOL starts to grow.  EOL is predicated on collaboration and partnerships.  We understand that EOL content will be richer and a greater diversity of learning and teaching models will be generated through conversations and collaborations with partners and interested members of the public.   Initial audiences Education and Outreach wishes to involve in the development and use of EOL include citizen scientists and hobbyists, educators and learners in formal education institutions (Kindergarten through 12^th grade and college level courses) and informal science education settings (e.g., natural history museums, nature centers, National Parks). 

In addition, Education and Outreach will develop mechanisms to support capacity building of scientists and institutions working on biodiversity and environmental issues in developed and developing countries.  It is expected that all of these audiences will also provide information back into the EOL.  This information could be in the form of observations about a particular species, photographs or sound recordings.  We hope that many of the scientists will volunteer to become curators of species pages and share their knowledge about selected species in their country with the rest of the world. 

If you have specific ideas about how you would use and/or contribute to the EOL, please post them for me and others to see.   I look forward to working with individuals and institutions that bring tremendous skills, interest and innovation to the biodiversity learning space!    

Today is the Chinese new year! Despite an intense cold-snap stranding millions, China celebrated The Year of The Rat with traditional fireworks and fanfare. We will celebrate by examining some of the wonders of a very controversial mammal who, according the an ancient Chinese tale, beat all the other animals in a race to be the first in the zodiac, it managed to especially irritate the cat by betraying its trust, accounting for their uneasy relationship to this day. People born in this year are expected to possess qualities associated with rats, including creativity, honesty, generosity, ambition, loyalty, a quick temper and wastefulness.

There are approximately 56 species of rat, the two that we are familiar with, many of us on a daily basis, are: the Norwegian Rat, Rattus norvegicus, found in both the sewers of our cities, and your local pet store, and the black rat, rattus rattus, also found in the sewers but preferring the warmer cities and generally kept out of pet stores.

Assuming everyone already knows a bit about rats, for example the fact that they live 2-3 years, are social, intelligent, and are important prey for many predators, as well as that they play an important role in scientific research, I would like to highlight some of the lesser known things about them. (For a more practical and informative bit of info on rats, check out what rat expert Robert M. Corrigan had to say in response to people’s questions about them in a recent blog session. Part I, Part II, Part III.)

One thing I learned today, is that rats are ticklish, and they laugh when you tickle them, check out this video of an odd scientist tickling a rat.

People have very intense positive and negative relationships with rats. For one, there was the bubonic plague, which was transmitted by them, like the cat incident, many people still have not forgiven the rat for its involvement in the plague. Some people, however are not bothered by rats per se, they even keep them as pets. Some of those people take it to the next level by showing their rats in rat shows, for a “Best in Show”-esque view of what that scene is like check out this 25 minute spot on Fancy Rats in Australia, it’s actually amazing and worth your time.

In India, there is a temple where people worship rats. They feed them and touch them and feel especially blessed if they can eat the food that the rats have touched:

Other human-rat affection can be found in the recent movie “Ratatouille”, which manages to tackle our greatest phobia of rats, by associating them positively with our food. Also, my personal favorite the character Master Splinter from teenage mutant ninja turtles. Here he is “making a funny”.

Hello and welcome to the Encyclopedia of Life (EOL) Education and Outreach component!  It is one of the five principal components of the EOL initiative and it is housed at Harvard University’s Museum of Comparative Zoology, located in Cambridge, Massachusetts, USA.    

The purpose of the Education and Outreach component is to make EOL relevant, useable and interesting to a broad range of international audiences.  In addition to EOL being a useful resource about biodiversity for educators, citizen scientists, media providers and others, Education and Outreach also wants people to participate in EOL by providing their own observations, photos, videos, sound recordings and data about species they study.   

Furthermore, models for how to use the EOL as a teaching and learning resource will emerge and be shared on the EOL website.  These will provide examples for others to use and build upon.  Some of these applications can be anticipated now; others will emerge only with increased use over time and with advances in technology and content available through the EOL.  Together, EOL and users will explore and promote new and exciting uses of this extraordinary resource in diverse global settings.   

Over the next 12-18 months the Education and Outreach component will be dedicated to identifying the current and future needs of a number of target audiences.  As we get feedback from people and start dialogues, we hope interest and excitement for EOL will build.  Through discussions, partnerships and input from interested users we expect to develop the resources and support to enable different audiences to use the EOL effectively.  Ongoing evaluation will provide a foundation for future products, activities and outreach.     

This is no small feat and I will need your help!  In fact, if you want to help me right now, please take the User Survey that can be found on the main site.   Your input on this survey will allow us to understand who is currently coming to the EOL website and what they are hoping to get from their visit.  There are only a handful of questions and it should take about 5 – 10 minutes to complete – thanks in advance for your participation! 

A bit about me.  I started in November 2007 as the Education and Outreach Director and am currently the only Education and Outreach staff member.  While I’m the only Education and Outreach staff member, I don’t operate in isolation!  I work regularly with other EOL staff in all the component groups (i.e., Informatics, Biosynthesis Center, Biodiversity Heritage Library and the Species Pages).  And I also work with Steering Committee members and many Institutional Council Members, who are located around the world.   

Prior to joining EOL, I worked at Earthwatch Institute for 10 years as the Chief Scientist of the United States office.  In that role I oversaw and lead the science, education and conversation departments.  I have a doctorate in environmental sciences and have always been interested and dedicated to making science accessible for broad public purposes and to have people share in the joy of scientific discovery. 

I am delighted to hold this exciting post at EOL!  I’m learning a lot about what it takes to create a truly global initiative and how to support and involve people from around the world to teach and learn about biodiversity and all it relates to. 

In my next entry I’ll talk more about the audiences EOL wishes to work with in the near future.

In last week’s issue of Science News there was a wonderful article about us by Susan Milius:

“Biological Moon Shot–Realizing the dream of a Web page for every living thing”

(Week of Feb. 2, 2008; Vol. 173, No. 5 , p. 72)

The article covers much of what is currently going on in the EOL in these last few pre-launch weeks, it does an especially good job of conveying how accessible and useful the EOL will be in the future while at the same time explaining some of the reasons why it will take some time for it to realize it’s full potential.

I highly encourage anyone interested to read the whole article for themselves, but here is a nice tidbit from it that I added some links to:

“Sample encyclopedia Web pages show flashy images and videos plus links to the latest genetic sequences and a scan of the page of the book in which the first published description of a species appeared. Cool, yes, but time-consuming. Developing entries of that quality for millions of species will take years, and Edwards doesn’t want the world to lose interest in the meantime.

So, the encyclopedia will release something fast, but just a small something: a portal to basic info on fish. The creators will present the pages as a work in progress, soliciting user comments.

Visitors will be able to admire a portrait of the zebra turkeyfish and a map of its range in the Pacific, for example, or learn that the white-spotted boxfish typically frequents tropical waters 1 meter to 30 m deep. The modern Latin names will be paired with tables of common names in dozens of languages.

The fish information itself won’t be an encyclopedia creation. Instead, the informatics specialists are building a new portal to an existing site, called FishBase. This strategy illustrates how such a grand undertaking as the compendium of all living things might just be possible. The project won’t start from scratch with 10,000 taxonomists typing until they create an encyclopedia. Specialists have already made databases with reliable information, and the encyclopedia will provide a central entryway for using these trusted sources.

“Everybody wants his or her favorite organism there first,” says Edwards. “If you’re a leech lover, you want leeches. If you’re a spider lover, you want spiders.” What the encyclopedia crew is actually going to present next, with or just after the fish, are plants in the Solanaceae family—including tomatoes, peppers, petunias, tobaccos, and potatoes. “It’s timely, because 2008 is the International Year of the Potato,” says Edwards. (Not a joke. See “It’s Spud Time”.)

As the Encyclopedia of Life grows, its tools will capture the latest research to enrich those sources. Google-like aggregation technology will register new publications or gene sequences, for example, that appear on the Web.

“The most exciting thing about this project to me is that we have a blizzard of information coming at us all the time—and it’s not just in science, it’s everywhere,” says Mark Westneat of the encyclopedia group based at the Field Museum of Natural History in Chicago. Financiers monitoring markets and even travelers wondering whether to pack boots have some fine systems for sifting out the desired snowflakes from all the rest of the information. “Biologists are a little bit behind in informatics tools,” he says.

The fish segment illustrates another feature of the encyclopedia plan: the quality of sources. Westneat, who studies reef fishes, encountered FishBase in its larval stage at a biologists’ gathering in the Philippines in 1995. One of its originators, fish biologist Rainer Froese, brought an early version of this database and appealed to his colleagues to groom glitches out of it and supply photographs. “We grudgingly did so,” says Westneat. “We thought, ‘Oh, this will be nice for school kids and stuff, but I’ll never use it.’” Then heroic efforts by William Eschmeyer of the California Academy of Sciences in San Francisco standardized the taxonomy with up-to-date forms and lists of synonymous names. “All of a sudden, FishBase became this incredibly valuable resource,” Westneat says. “I use it every day.”

Such trustworthy information isn’t just swimming free in the seas. “A significant challenge facing the Encyclopedia of Life is engaging the scientific community to provide content,” says botanist Richard Ree of the Field Museum. “Similar initiatives have been tried in the past, and I think it’s safe to say that none met with resounding success.”

Ree does add that the project has advantages over previous proposals. The star power of E.O. Wilson and the TED conference attendees could catalyze interest from the corporate sector and allow access to its considerable experience in developing tools for managing computer information.

The encyclopedia planners are well aware of the need for active support from scientists, says Westneat. He leads a team focusing on how to make the encyclopedia so useful that scientists will decide that providing top-quality information is worth their time. “The scientific community is going to make the Encyclopedia of Life rich, and it’s going to make it correct,” he says. In turn, that gold standard information should enrich the specialists’ pursuits.”