Assembling, Visualizing, and Analyzing the Tree of Life

Posts tagged “open tree of life

Online publication to follow the three AVAToL projects

PLOS Currents: Tree of Life

PLOSPeer-reviewed articles about the Open Tree of Life as well as two related projects, Arbor and Phenomics, will be available on PLOS Currents: Tree of Life. The online publication allows the researchers to document their progress in developing software and other tools.

The three research endeavors were developed during an Ideas Lab last year as part of the National Science Foundation’s (NSF) Assembling, Visualizing, and Analyzing the Tree of Life (AVAToL) program. The Open Tree of Life project strives to produce the first draft of a comprehensive tree of life and provides tools for community enhancement and annotation. The Arbor project is developing comparative methods with utility across large sections and the entire tree of life. Finally, the Phenomics project is developing approaches for exploring and documenting phenotypic diversity across the tree of life.

“It’s meant to be a quick outlet for solid phylogenetic studies”

PLOS Currents websites encourage researchers to share their findings with a minimal delay to their peers. The Tree of Life section is focused on rapid publication of phylogenetic and systematic studies with novel data and/or analyses. According to Keith Crandall, one of the three editors of the journal and an investigator of the Open Tree of Life, “it’s meant to be a quick outlet for solid phylogenetic studies to get them and their data into the public domain.” (more…)


Presentation slides from Evolution 2013 available

Open Tree of Life at meetings

The Open Tree of Life project is one of the many phylogeny projects that are featured during the Evolution 2013 meeting that currently takes place in Snowbird (UT). The presentation slides from Karen Cranston, the principal investigator of Open Tree of Life, are available online (LINK). Presentation slides from other investigators are added here in the upcoming days.

Evolution 2013 is the joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN). The conference meets jointly with the iEvoBio conference. Open Tree of Life is represented at both events. About 1400 participants are expected to share their research in evolution, systematics, biodiversity, software, and mathematics.


Free webinar: Putting all species in a graph database

Biology + Technology = OTOL

Neo4j screenshotOne 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


Karen Cranston talks about open licensing and Dryad

Making scientific data available

 

In case you haven’t seen the video yet, Open Tree of Life investigator Karen Cranston talked about sharing research data in open access data repositories during the Creative Commons 10-year celebration in Raleigh, North Carolina, last December. She mainly focused on the use of CC0 for Dryad, which is a curated general-purpose repository that makes the data underlying scientific publications discoverable and freely reusable. Cranston also mentioned that data availability leads to more citations, which is highly valued in the academic community. You can access the presentation slides as well (link).


Interview with Open Tree of Life investigator

Crandall featured on PeerJ blog

Keith Crandall for bio low resOpen Tree of Life investigator Keith Crandall is featured on the blog of PeerJ, which is a peer-reviewed, open access journal on the Internet. Crandall is an Academic Editor for PeerJ and is the director of the Computational Biology Institute at George Washington University. He was the editor for the “living fossil” manuscript that got much news media attention last week. Here’s the link to the interview.


Building an API for the Open Tree of Life database

Do you want an app for this?

Screen Shot 2012-08-29 at 9.22.20 PMThe developers of the Open Tree of Life would like to know from the phylogenetic community what kind of information they want to extract from its database when the first draft is released later this year. With those preferences, it is possible to develop an API that gives scientists the opportunity to build their own websites or software packages that use the data.

An API (application programming interface) is a digital tool that allows one website or software program to “talk” to another website to dig up certain pieces of data. For instance, a lot of people use Tweetdeck to navigate the ongoing bombardment of messages in the Twittersphere. In that case, Tweetdeck is connecting to Twitter, through its API, to receive and order the messages according to the preferences of the user.

In case of the Open Tree of Life, an API gives researchers advanced access to the data of about two million species, the phylogenies that have been created to illustrate possible relationships between them, and the underlying data and methods of synthesis. “For example, it will be possible to select smaller trees for specific species or find out how many studies there are for a particular node within the database,” says Karen Cranston, the lead investigator of the project. (more…)


Connecting millions of data points in a graph database

Creating ‘Facebook’ for species

Neo4j screenshotThe 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…)


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