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
All species like some gadgets
While movie hero James Bond gets his spy gadgets from his loyal developer Q, almost every other species on Earth has to put a little more effort in armoring themselves. But that does not mean they cannot rely on some good ol’ friends to do so. In fact, the acquisition of genes from two or more species through lateral gene transfer can lead to innovations that at times can be painful—sometimes even deadly—to others.
One of those evolutionary novelties is noticeable for certain types of jellyfish that developed the ability to sting after their ancestors acquired a gene from a bacterium and incorporated that material in their own DNA. This gene transmission helped jellyfish to create an innovative defense tool to fend off other species that could endanger them. The result is quite frightening: more humans get killed by jellyfish than sharks. (more…)
January 21, 2013 | Categories: Building Open Tree | Tags: #opentree, Archaea, Bacteria, biology, Darwin, DNA, DNA sequencing, domains of life, Eukaryotes, evolution, evolutionary biology, evolutionary trees, frankenstein, horizontal gene transfer, James Bond, jellyfish, lateral gene transfer, lineages, national science foundation, network, open tree of life, phylogeny, research, science, sequencing, species, spider, sushi, tree of life, web | 1 Comment
‘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