Biology + Technology = OTOL
One of the developers of the Open Tree of Life demonstrates Thursday, during a free webinar, how graph databases are used to construct a tree of life. The lecture is organized by Neo Technology, which is the maker of Neo4j, an open-source database that is used for OTOL.
Stephen Smith, an ecology and evolutionary biology professor at the University of Michigan, is going to explain how Neo4j and other digital technologies are assisting in constructing the tree of life. Starting at 10:00 PDT (19:00 CEST), he will also discuss other aspects of the interface of biology with next generation technologies.
“Our project is building the tools with which scientists in the community can continually improve the tree of life as we gather new information. Neo4j allows us to not only store trees in their native graph form, but also allows us to map trees to the same structure, the graph. So in fact, we are facilitating the construction of the graph of life,” says Smith.
Neo4j approached the Open Tree of Life team to present a webinar because it is a project that utilizes the Neo4j graph database to represent the interconnectedness of biological data. The company considers the project a great example of how a graph database can better model the natural world.
The online lecture is intended for a broad audience including beginner computer programmers, advanced hackers, data scientists, natural scientists, and anyone interested in the cross-section of science and technology, especially data modeling. Over 150 people have already registered online.
The registration form: LINK
Update: The video from this webinar is available on vimeo: http://vimeo.com/67870035
June 3, 2013 | Categories: Building Open Tree, Open data, Press releases, Webinar | Tags: #opentree, biology, community, database, digital data, evolutionary biology, graph, graph database, Neo Technologies, neo4j, open tree of life, phylogeny, software, webinar | 2 Comments
Creating ‘Facebook’ for species
The Open Tree of Life database is not just a list with about two million species. Information is added about their special characteristics and possible relationships with others as well. “It may become tens or hundreds of million pieces of data when we are all done.”
Stephen Smith, an evolutionary biology professor at the University of Michigan, is working together with the other researchers of the Open Tree of Life project to develop the programs and tools that will be used to construct the full tree of life. Scientists from all over the world can then synthesize all the information in the database.
“We are currently building the back-end of the Open Tree of Life. We need to create software that allows us to put all our information in a graph network, so that we can easily retrieve the information that researchers are specifically looking for.” (more…)
February 26, 2013 | Categories: Building Open Tree, We need your help! | Tags: #opentree, community, database, digital data, evolutionary biology, evolutionary trees, Facebook, graph, graph database, graph search, neo4j, network, open data, open science, open tree, open tree of life, phylogeny, social media, social network, species, synthesis, tree of evolution, tree of life species, Twitter, What is the Tree of Life | 3 Comments
‘Let the computer do the work’
Creating a phylogenetic tree is no easy task. It usually involves a complex synthesis of multiple datasets, but it leads to much satisfaction when all work is done—until new data come in.
Then, the process typically starts all over again: building a new tree from scratch.
Mark Holder, a professor of statistical phylogenetics at Kansas University and one of the investigators of the Open Tree of Life project, maintains that there is a real need for scientists to have access to digital tools that save them from doing quite a few labor-intensive procedures.
“In the past, researchers combined information from different trees and then analyzed the data. But they never made good computer systems that allowed for continuous updating. They would not be able to see how an entire tree would look like when they added more data or another individual tree. In that case, they had to start over.”
October 22, 2012 | Categories: Building Open Tree | Tags: #opentree, database, digital data, evolutionary trees, graph, graph database, network, open tree of life, phylogeny, research, science, social media, software, species | 2 Comments