Visualizing Tweeter biodiversity observations

At Ebiosphere09, there was an Informatics Challenge that Rod Page won, congratulations!

Vizzuality wanted to participate but we did not find the time to work on it. During the conference we found people like @IvyMan twittering observations on biodiversity. This was part of the "The eBiosphere Real-Time Citizen Science Challenge!" which published the rules on how to tweet.

We were far too late to participate on it, but we thought it could be cool to give it a try using the new Flex 4 "Gumbo". @xavijam from Vizzuality was starting to learn Flex 4 so he took this challenge.

We make use of the Twitter API to query for the patterns explained on the challenge rules. Once we get the tweets, parse the latitude and longitude, get the scientific name of the observation and finally present it in a map together with images taken from Flickr.

If you want to make an observation appear on the app just tweet something like:

#eBio observation: #Puma_concolor /-50.412673039931825, -100.713207244873047/ method:iPhonePhotoFlying Puma Concolor

The idea is to mashup the data from Twitter together with the data from Flickr using the Darwin core machine tags. The reason for the second is that we are great supporters of people providing those tags and we created even some stickers to support them.

This is just an exercise to learn Flex 4 and promote the use of microformats and machine tags. But we hope you find it cool.

Some comments. Magically the tweets from @IvyMan on this disappeared while we were developing. Additionally there is not many machine tags in Flickr for the moment on darwin core terms, so there is some fakes over there too.

All the credit goes to @xavijam for working on it! And from his experiments we are learning that is not going to be that easy to migrate to Flex 4.

Open application

World Database on Marine Protected Areas new website

The UNEP-World Conservation Monitoring Centre (UNEP-WCMC) today unveiled  The World Database on Marine Protected Areas - a site designed to provide the most comprehensive set of Marine Protected Areas (MPAs) available.

http://www.wdpa-marine.org

"With less than one percent of the oceans under legal protection, i

t is essential to maintain a dataset that focuses on MPAs and representation of the diverse species and habitats found in the marine environment." is read on the website.

Vizzuality has developed the User Interface and general design of the website, including the logo. Working together with UNEP-WCMC, and specially Craig Mills, we have developed innovative solutions to display this huge amount of data in a hopefully engaging website to invite people explore our oceans. 

But enough of "official words", here at biodivertido we would like to explain what are the technologies behind it and how things work under the hood. 

Technologies:

The website is a mix between HTML and Flash. The Flash application in the front has been developed using the Flex framework plus some Flash little things. On the ser

ver s

ide there is ASP.NET and WebORB to do AMF remoting. 

GIS:

The GIS engine behind the scenes is ESRI ArcGIS Server. WCMC pr

epared the different tiles

 and caches for all layers. There is some places where we have used the new ArGIS Server REST API.

On the client side the whole project is very much based on the great Google Maps API for Flash. We want to thank Pamela Fox from Google for her great support of the community. There is several techniques that we have introduced while working on this project like:

• Tile Mouse Over: To change the cursor when hovering over features on tiles.
• WMS overlays: Dynamically changing the Tile Overlays based on zoom levels for cached and not cached tiles.
• Panoramio and Wikipedia markers without proxies.
• Encoded Polilynes for multipolygons with inner rings.

Database:

WCMC is using Microsoft SQL Server 2008 Spatial Database and we worked with them to generated Google Encoded Polylines out of the database. 

There are also some things coming from the ESRI spatial database and some stats where dones using it, but I think the general idea is to mo

ve everything to SQL Server.

Deployment:

The whole website is being served from an Amazon EC2 instance. The idea is also to make use of the Amazon Cloud Front CDN to distribute tiles and other static files, but for the moment everything is in EC2. 

We will probably post more specific details on different parts of this project in the next weeks, but we wanted to give you a broad overview of how the project works and the different technologies being used.

One more thing...

One great thing of working with UNEP-WCMC is that all the source code that we have developed is Open Source! We are still working on specific details on what license the source will get, but for those curious, starting from today you can checkout all source code from Vizzuality SVN repository. Please let us know if you find it interesting!

We are still under Beta phase of the project, so it might be that you find some bugs, please report them!.

Thanks again to UNEP-WCMC to let us work on this great project and look forward to make it better!

Using Google Spreadsheets with Google Maps for Flash

I have recently been working on a little project that had a very simple purpose: Put in a map around 200 markers about where to find dog waste bags disposals in a town. This might have little intersection with biodiversity, but I think some of the ideas might be useful for other people.

The idea was to create a simple map/widget that could be managed by a non technical person and did not require setting up databases and hosting services. The kind of project you want to set up and forget more or less about it.

Well, the simplest thing to manage the location of the disposal is something like and spreadsheet and the internet version for that is Google Spreadsheets. I started thinking on using the Spreadsheet mapper, but it has far too much options, and we did not really need to share a KML file. So I thought creating something simpler. Just my required columns on the document and connect from Google Maps for Flash. So we wo

uld be able to just distribute the Flash SWF file and it will take 

care of connecting to Google Spreasheets, download the data and display it on the map.

Sounds very easy no? Just publish the spreadsheet, setting automatically republish on changes, select the CSV format, and you get a perfect API to your data. Look at ours for example.

Then on the Flex app is as simple as parsing a CSV and dynamically create the needed markers.

The only problem is... Google does not like crossdomain.xml f

iles like everybody else in the 2.0 internet. 

Therefore we were gonna have to create a proxy server to bypass the security restrictions, but we really did not like the idea of havi

ng to set up one just for this small thing and maintaining it. 

So I decided to take a look at Yahoo Pipes to bypass the crossdomain issue. You just need to create a simple Pipe that consumes the CSV from spreadhseets and output it as JSON. Yahoo pipes has an open crossdomain file, so no problems. Here is my pipe for example. Very simple and effective.

You can see the final result in here. And of course you can always grab the code from Vizzuality Google Code repository. 

The project had to deal also with transforming UTMs into Latitude/Longitudes and some other issues, but I think this overview is enough. The source code is so simple that I dont think its needs more explanations.

We would like to start using the Google Data API much more in the future, specially the shiny new Google Maps Data API, but I think this makes for a very simple solutions for lot of small projects like this one.

And finally, Google, please start setting up crossdomain files on your APIs, or at least, explain us why you dont do so... the actual situation is very frustrating.

Greenpeace BlackPixel | Beautiful Idea

Today we've discovered BlackPixel. A beautiful initiative by greenpeace to save energy.

The application draws a black square in your screen that not disturb your visualization.

If you over the square, you can view how many energy is being saved.

A little effort for you, a big benefit for all.

You can know more about it here

We are going to E-biosphere 09

E-Biosphere 09 starts next Monday 1st of June on London. Today we want to announce that most of us, Tim Robertson, Sergio Alvarez, Dave Martin and Javier de la Torre, will be there.

Even more, we have a booth! GBIF & Vizzuality are joining efforts to showcase the recent projects we have been working on and some of the future ones. We are all very excited to showcase what kind of things can be done with biodiversity data and visualizations.

Tim, Sergio and Javier will be present at the booth, but we would like to be present online at the same time. Our idea is to use this blog as the online platform to present the different ideas, prototypes, wireframes, etc that we will showcase at E-biosphere 09. Especially as Andrew could not join us for London. So the blog is our online booth!

In the next few days we will be working hard on different topics, including species distribution, analyses, data integration, indexing, visualisations, taxonomy, data publishing, computing on the cloud, migration paths etc. So stay tuned to know what is going on in multiple posts that we will publish here.

Aditionally you can follow some of us on Twitter:

@jatorre

@saleiva

@andrewxhill

@timrobertson100

If you happen to attend e-biosphere please come and join us at the booth, if not we look forward to get your comments on the blog.

See you all in London!

Javier, Tim, Sergio, Dave, Andrew.

A new contributor to Biodivertido

So, I’ve decided to become a blogger. But Javier said that on my quest to riches, I needed to first give a quick introduction. Here you go.

My name is Andrew Hill. I am working on my PhD in Rob Guralnick’s lab in the Ecology and Evolutionary Biology department at the University of Colorado. I began working here almost 3 years ago on a project to reconstruct the evolution and spread of influenza through time and over geography (see here or here). Like the influenza itself, my interests have mutated rapidly. Most of my work now involves at least one of three informatics subtypes; biodiversity informatics, phyloinformatics, or (I’m not sure people say this) visual informatics. I have ongoing research on the evolution of influenza, as well as a handful of smaller genomics and bioinformatics projects, and am just now starting work for the OBIS-USA project.

As for my role at Biodivertido, I don’t know yet. Rob, Walter Jetz, and EOL just put on an excellent workshop in Chicago that gave me, Tim, and Javier the opportunity to talk about our interests and coordinate some of our efforts on a couple of new projects. We will likely be giving you more details about some of those in a few hours. So don’t go far from your RSS feed.

For now, all I can say is that I’m extremely excited to be working with these guys and will hopefully be contributing cool things very soon.

GBIF-World Database on Protected Areas project

The GBIF-WDPA project intersects together the data from GBIF and the World Database on Protected Areas. It was developed by Vizzuality for GBIF and IUCN. I have talked about this project in different posts already, but I thought it could be interesting to share an screencast I created some time ago about it.

The video has a little introduction on what was the project about, what technologies were used and finally a demo of the application itself.

Ah! If you want to try the tool for yourself it is finally published. Try it for:

Australia

United States

Spain

Germany

Great Barrier Reef

Yosemite

Posets Maldeta (Pyrenees)

We are working right now on some more advanced visualizations, but this will come hopefully soon. I hope you enjoy it.