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.

WMS Tiling Clients

For projects relying on open source software and using WMS services for their map applications perhaps the most obvious choice for a client application is to write something using the OpenLayers API. This is a very extensive javascript API and is used to demonstrate the open source OGC compliant servers MapServer and GeoServer. Its straight forward to construct a map and then to overlay multiple layers using WMS services.

The screenshot above shows a layer of 0.1 degree cell densities representing data from Australian National Herbarium rendered using GeoServer layered on top of the Google satellite base layer, all pulled together using OpenLayers.

Running this locally the map was rendered by OpenLayers rather quickly. Running this on an externally hosted server I began to notice curious loading of tiles by OpenLayers. So I did a stripped down comparison of the same functionality using the Google maps API. Rendering the cell density tiles from a WMS service in Google maps was done using a javascript function written by John Deck - available here.

The performance improvement with Google maps was immediately obvious. Using the Firefox YSlow plugin we see:

OpenLayers	Google Maps API

So the main thing of interest here is the number of tiles loaded by OpenLayers compared to Google maps (91 vs 50 - although oddly the total size of the images loaded is roughly equivalent, and the tile size for both seems to be 256x256 pixels). Increasing the size of the tile for OpenLayers does reduce the number of tiles requested (I tested with 512x512 and 1024x1024) but this has little effect on performance in openlayers.

So the performance difference between Google Maps and OpenLayers could be accounted for by any combination of the following:

• Incorrect use of the API (test for OpenLayers is here) and we are missing configuration to reduce tile loading in openlayers
  
• The tile loading algorithm for Google maps is more efficient in only loading the required tiles for selected view areas
• Openlayers is preloading more images to speed up panning. This would be good, but OpenLayers doesnt seem to prioritise the loading of currently viewed tiles.
  

The source for the test for OpenLayers is here, and for Google maps here.

The Taxonomy browser visualization #1 - Tree Lists

Hi, my name is Sergio Alvarez Leiva and this is my first pos at biodivertido, Finally. I'm part of Vizzuality and work as Interaction Designer for GBIF among others. I will mainly be posting about Interaction Design, UX and Design in general, althought I'll try to post about Front.end developing a little. I hope you find it interesting.

Since I began designing for Biodiversity data, I've encountered lot of interesting challenges related to the size of the datasets .

Maybe, one of the hardest challenges is designing a taxonomy browser visualization. The taxonomy browser can represent up to 1.7M names, with nodes with more than 200 childs. That makes it complicate in terms of interaction design and performance.

I will write in a series of post my impressions on different techniques we have been experimenting:

In this first post I'm going to talk about tree list visualizations, but before I get into details, I'd like to talk a little about generic concepts that might be applied to all the visualizations. There is a lot of bibliography about trees out there, but let me introduce here my own "easy" concepts.

When browsing a tree you need to know where you are and what is around you, thats parent and brothers and in general this is called Contextualization. Then you need to be able to find the childs, thats Discovering. All this needs to be easy to do, Usability and UX, and finally must be easy to integrate with the application, Easy integration.

On those terms, the tree list visualization presents some advantages and disadvantages.

- Contextualization: Maybe the list visualization is the most standard way to solve this problem. The tree lists lets the user discover the whole tree by clicking in the different nodes. But the problem is the vertical size that the tree gets when the user deployes a node (This is an integration problem too). When the user will have deployed more than 3 levels, he will have to use the vertical scroll, and probably, this action will make the contextual information (parent nodes and "brothers") out of the visible screen area.

This problem could be solved implementing some variations in the Tree list; We could hide all the nodes not related to the selected child and get more space for view only the important nodes.

-Poor UX : "Discovering biodiversity". We have to involve the users in our play and invite they to discover more and more. I think the Tree Lists are a little boring...we need more action!

- Usability: This visualization is pretty used and the users will understand how it works quickly. On the other hand, I think that in a Tree list is not so easy to find the desired node - the users would have to deploy a lot of nodes, and scroll a lot too, before find their objective. Maybe would be positive for this point to implement a search box. It might depend of the data size.

Conclusion; We've a standard visualization that lets us to implement a Taxonomic browser in a lot of different situations. I think this is not the best solution that we could implement, but its true that we could use this always. 

 

SpatialKey and biodiversity primary data analysis

Some days ago the good people from Universal Mind open the beta program for their new product called SpatialKey. For those who are not in the Flex community, Universal Mind is a very recognized company developing Rich Internet Applications. So it was a great pleasure when I saw months ago that they were working on a new geospatial product for data analysis.

I was lucky to get an invitation to the beta program and be able to take a look. They are promising some great things, but for the moment the beta is limited in certain ways I will describe later. The best to get an overview of it is to watch some of their ubercool videos (maybe too much for my taste).

I wanted to give it a try as soon as possible, and coincidentally I just finished working on the new WDPA-GBIF widget. The widget allows you to visualize biodiversity primary data, from GBIF, for all protected areas in the world. Check out for example the protected areas in Australia. Then select for example an area like the Great Barrier Reef. You will be able to download the data in multiple formats.

With this I downloaded the data for the Canadian Rocky Mountains and imported it in SpatialKey. The import now is limited to 10.000 records and 25 columns, so I had to delete multiple columns and records. I think SpatialKey should allow the discard of the data visually when it is already uploaded.

With SpatialKey you manage separately your datasets and the reports you create based on them. The reports right now are not exportable to the outside. I mean, you can not print or distribute as a widget the report you have created. I know they are working on it, but for the time being I only have 2 possibilities to show you how it looks like: share my report with everybody that gives me his email, or just do a little screencast for everybody to watch here. For the first one if someone is really interested to get into the system to take a look, send me an email. the screencast is following:

So here goes the things that I like a lot:

• The heatmaps are just gorgeous. I would love to know how they do it.
• The timeline filter is great. Has some usability issues but is great.
• The way grids are displayed for summaries. The hover effect is very good and the tooltip very clear.
• The filter "pods" are nice, but I wonder what would happen when you have thousands of hundreds records to search or select on. I suppose that when there is lot of data only the search would be enabled and not the selection.
• Great look and feel.

Other comments following:

• Is it necessary to refresh on every map movement? I understand it is on the zoom and if you have the filter by visible area disabled.
• Not having the possibility right now to share the reports as widgets to embed on the blog.
• It would be nice to also let the user provide a polygon or geometry to define the boundaries of the analysis. In this case for example would help a lot to visualize the borders of the protected area.

And finally, the things I really wonder how they work internally:

• The heatmaps!
• The data structures they use for dynamically regrouping the data on the client.
• If it is true that they can handle millions of records, how does the server infrastructure looks like. I know it is Java, but what about the data store, how can they handle the creation of dynamic indexes or how do they do it? Would it work with GBIF data?

My general impression of the tool is great. It looks awesome and works really well. It looks very similar to some of the ideas we have for developing analytical tools for biodiversity data with GBIF. Tim give your impressions please!

I would love to see more and more such analytical tools for biodiversity. How they call them? Something like Bussiness Intelligence, I think we need some of this in our community. For the time being I will try to get into talks with Universal Mind on the applicability of SpatialKey for huge biodiversity primary data like GBIF.