Jul 11

Progress of Colin’s 2013 Rubenstein Project (Ⅰ)

Project Description

As a 2013 EOL Rubenstein Fellow, my project is “Using the multiple classifications harvested by EOL for analysis to obtain the degree of coverage and congruence among hierarchies and nomenclatures.” As we know, many taxonomic hierarchies have been created due to:

a.       Taxonomists have different views on biological classification

b.       New technologies like phylogenetics create new perspectives on taxa relationships.

c.       Biological classification is a job proceeding with time, and the old classification should be updated when new groups of species or specimens are found.

d.       The scopes and coverage of different classifications are usually geographically restricted.

Analysis on these hierarchies (or taxonomic trees) to find out the congruence and incongruence is interesting, and required both by researchers on biodiversity informatics and taxonomy according to our first stage requirement analysis. Considering the long term usage and the requirement of potential users, we plan to implement a mature tool Taxonomic Hierarchy Comparator (THC) for managing and comparing different taxonomic hierarchies.

 

Potential Users of THC:

1.       Researchers on Biodiversity Informatics who want to know where the differences are among the hierarchies, what biological group is hot, and where the gap to be filled is.

2.       Taxonomists who want to find out the incongruence between their taxonomic views and others’. They can analysis their own hierarchies against with EOL hierarchies.

 

Main Functional Requirement

1.       User management

User should have an account before using THC. That will help them to create and manage their own taxonomic hierarchies and keep analysis experiment result permanently for reuse. User management is required to manage user account including registration, authorization, log in/out, and account update.

2.       Hierarchy management

a.       Create hierarchy: hierarchy can be created from different methods. User can upload an Xml in BSBC format or DWCA file, or copy a hierarchy from shared hierarchies’ pool. EOL hierarchies will be imported to THC by web API provided by EOL.

b.       Edit hierarchy: a simple editor for user to modify the hierarchies. It will help user to edit scientific names, change position of taxon, insert new taxon, and delete taxon.

c.       Share hierarchy: user can share his own hierarchies to others for analysis, but others cannot modify the shared hierarchies.

d.       Export hierarchy: help users to save their hierarchy as standard DWCA file or BSBC xml.

3.       Analysis experiment

a.       Create experiment: give an identifier and some descriptions for the experiment; select which hierarchies for analysis. THC will keep the analysis result.

b.       Share experiment: result of analysis can be shared with other users

c.       Implementation: submit the analysis task to server, and waiting for response message. It is a time consuming process, so task queue is required to deal with multiple analysis tasks. Analysis is based on algorithm proposed by us.

d.       Visualization: it is an important function for expressing analysis result. It should show where the congruence and incongruence explicitly is.

e.       Computation: base on the result, “intersection” computation between two hierarchies is to extract the common part and “difference” is to produce the incongruence part.

 

Use Case

Some use cases have been designed to show how users or manager engage THC and how the requirements are realized in the context of software. Fig1 is the use case of experiment.

Fig1 Use Case of Experiment

Fig1 Use Case of Experiment

Another progress is a paper about the method and algorithm is being written, and we hope it can be published in a relative journal in next stage.

More progresses are about database design and interface design and will be posted at the end of July.

 

This article is excerpted from “requirement analysis of THC”

Author: Colin, 2013 EOL Rubenstein Fellow

Jul 10

New One Species at a Time Podcast: Saltwater Crocodile

The city of Darwin in Australia’s Northern Territory lies in the heart of crocodile country. In the 1950s, saltwater crocodiles were shot, skinned, and turned into shoes and handbags. After hunting was banned in the 1970s, crocodile numbers climbed. Now there’s a croc for every man, woman, and child in Darwin. Can the human citizens learn to live alongside their toothy neighbors?

Listen to the Podcast   

Meet the Scientist   

Learn more about the Saltwater Crocodile on EOL  

Image Credit: Gerald and Buff Corsi. CalPhotos. CC BY-NC-SA. http://eol.org/data_objects/12512171

Request for feedback regarding “Add to Reddit” button on EOL

The EOL development team is considering adding a “share with Reddit” button to EOL pages everywhere similar buttons to “Tweet” and “Like on Facebook” are found.

The debate comes down to the tension between supporting Reddit users who want to share EOL content with their various communities vs concerns about Reddit in general, especially in light of some of the content found on the site.

Do you have an opinion?  Please share it with me by email at bcorrigan@eol.org or tweeting a message to @eol or @eolpm - and thank you.

Image Credit: National Park Service, US Department of Interior, Public Domain.

In our latest podcast we venture to Santa Cruz Island, off the coast of California, to look into the mystery of the island’s tiny foxes, descendants of gray foxes who rafted over from the mainland more than ten thousand years ago and branched off to form a new, smaller species. 

Despite weighing a mere three pounds, these diminutive grey foxes thrived and for millennia they reigned as the island’s top predator. But twenty years ago, their numbers began to plummet, from three thousand in the early 1990s to fewer than one hundred by 2000. Learn how conservationists solved the puzzle of the vanishing foxes and helped them stage a comeback.

Listen to the podcast

Meet the Scientist

Learn more about the Island Fox on EOL

May 20

As they wing their way across North America, millions of migrating monarch butterflies form a living river of orange. In this episode, the second of two podcasts on monarchs, we’ll meet citizens young and old who are dipping a toe in that river in the name of science and of beauty.
Listen to the podcast
Watch the Monarch Butterflies Eastern Migration Google Earth Tour Video
También puede ver este vídeo con subtítulos en español aquí.
Photo: © Ted Kropiewnicki
CC-BY-NC-SA
Supplier: Tree of Life web project
Location Created: Bear, Delaware, USA
View source 

As they wing their way across North America, millions of migrating monarch butterflies form a living river of orange. In this episode, the second of two podcasts on monarchs, we’ll meet citizens young and old who are dipping a toe in that river in the name of science and of beauty.

Listen to the podcast

Watch the Monarch Butterflies Eastern Migration Google Earth Tour Video

También puede ver este vídeo con subtítulos en español aquí.


Photo: © Ted Kropiewnicki

CC-BY-NC-SA

Supplier: Tree of Life web project

Location Created: Bear, Delaware, USA

View source 

May 07

EOL/Google Earth Monarch Butterfly Tour Now Available

Every year eastern monarch butterflies begin a journey north from their overwintering grounds in Mexican forests. The epic migration spans generations and the better part of a continent.

EOL is pleased to announce a new Google Earth tour video showcasing the migration of monarch butterflies (Danaus plexippus) in North America, and the people that help them out along the way.

This Google Earth tour is accompanied by two companion podcasts, the first of which can be found here.

This Google Earth Tour was produced by Atlantic Public Media in cooperation with the Encyclopedia of Life Learning + Education group located at the Harvard Museum of Comparative Zoology.

Apr 18

More on Garlic Mustard (Alliaria petiolata) on EOL
(photo by Ondřej Zicha [CC BY-NC] via Biolib.cz)

More on Garlic Mustard (Alliaria petiolata) on EOL

(photo by Ondřej Zicha [CC BY-NC] via Biolib.cz)

Rodents of Unusual Size Do Exist | Around The Mallsmithsonianmag.com
But­ter­cup and West­ley may have doubt­ed the ROUS’ exis­tence in 1987′s The Princess Bride, but the love-stricken pair quick­ly caught on when the “Rodents of Unusu­al Size” attacked.A team of sci­en …

R.O.U.S. exist?  Inconceivable! (see esp. http://flip.it/H1eS8)

Rodents of Unusual Size Do Exist | Around The Mall
smithsonianmag.com

But­ter­cup and West­ley may have doubt­ed the ROUS’ exis­tence in 1987′s The Princess Bride, but the love-stricken pair quick­ly caught on when the “Rodents of Unusu­al Size” attacked.

A team of sci­en …

R.O.U.S. exist? Inconceivable! (see esp. http://flip.it/H1eS8)

Plantingthehighline.org
The Chelsea Grass­lands in bloom.The High Line’s plant­i­ng design is inspired by the self-seeded land­scape that grew on the out-of-use ele­vat­ed rail tracks dur­ing the 25 years after trains stoppe …

Following up on my flip re: the High Line in NYC, this is an index of the plants you can expect to see blooming there, by month.  Very well done, which should not surprise anyone.

Planting
thehighline.org

The Chelsea Grass­lands in bloom.

The High Line’s plant­i­ng design is inspired by the self-seeded land­scape that grew on the out-of-use ele­vat­ed rail tracks dur­ing the 25 years after trains stoppe …

Following up on my flip re: the High Line in NYC, this is an index of the plants you can expect to see blooming there, by month. Very well done, which should not surprise anyone.

Beetles and Moths - A One Species at a Time Podcast from EOL
How much trouble can an unassuming black beetle no bigger than your fingernail be? Plenty, as we learn in this episode of One Species at a Time. Tiny stowaways like the European Gazelle beetle are arriving on container ships and wreaking havoc with native ecosystems. Long-standing pests like the gypsy moth have been joined by new exotic species that are crowding out North American fauna. Ari Daniel Shapiro journeys to the forests of Oregon to meet the beetles.
Listen to Podcast
Explore Extras
Subscribe to the One Species at a Time Podcast on Apple iTunes
To learn more about how to use EOL’s One Species at a Time podcasts in the classroom and in broadcast media, please see our Podcast Guide for Educatorsor contact the EOL Learning & Education group.
(photo of Delta Flower Beetle Trigonopeltastes delta by Lynette Schimming, CC BY-NC, contributed to EOL via the EOL Group on Flickr)

Beetles and Moths - A One Species at a Time Podcast from EOL

How much trouble can an unassuming black beetle no bigger than your fingernail be? Plenty, as we learn in this episode of One Species at a Time. Tiny stowaways like the European Gazelle beetle are arriving on container ships and wreaking havoc with native ecosystems. Long-standing pests like the gypsy moth have been joined by new exotic species that are crowding out North American fauna. Ari Daniel Shapiro journeys to the forests of Oregon to meet the beetles.

Listen to Podcast

Explore Extras

Subscribe to the One Species at a Time Podcast on Apple iTunes

To learn more about how to use EOL’s One Species at a Time podcasts in the classroom and in broadcast media, please see our Podcast Guide for Educatorsor contact the EOL Learning & Education group.

(photo of Delta Flower Beetle Trigonopeltastes delta by Lynette Schimming, CC BY-NC, contributed to EOL via the EOL Group on Flickr)