Postdoc opportunity in clade definitions for the Tree of Life

October 12th, 2016
By Cellinese,Nico

We are seeking a second postdoctoral fellow to support the Phyloreferencing project. Our ideal candidate is a biologist by training, and has strong expertise in systematic biology. The focus of your work would be on working with select NSF GoLife projects to develop meaningful phyloreferences and to use these in proof-of-concept applications for aggregating trait and other domain-relevant data. In addition, you would work with the ARBOR project to research integrating phyloreferences into trait-based analysis and visualization workflows.

The Phyloreferencing project is a collaboration between Dr. Nico Cellinese (Florida Museum of Natural History, University of Florida) and Hilmar Lapp (Center for Genomic and Computational Biology, Duke University) newly funded by the National Science Foundation. The postdoc will be based in the lab of Dr. Cellinese, but will work closely with both PIs. Starting date is negotiable. Salary is $50,000.

Why phyloreferencing?

The ability to freely and precisely communicate organism-linked data suffers serious limitations from the traditionally used taxon names based in Linnaean nomenclature. The semantics of such names are too often ambiguous, subject to divergent interpretation, and unavailable to computation. And with the advent of next-generation sequencing, metagenomics, and other modern biological data collection technologies, many groups of organisms for which we have interesting data do not yet, and may never have a Linnaean name.

Our project aims to overcome these limitations by defining ontology-based references (phyloreferences) to elements on the Tree of Life that are unambiguous and the semantics of which are amenable to powerful machine reasoning. One of the foundations of phyloreferencing is formed by the decades of theoretical and applied work on phylogenetic taxonomy. Ongoing computational work involves researching and developing OWL models and ontologies, tools for converting existing data into OWL format, and online proof-of-concept applications for using machine reasoning to navigate biodiversity data by clade semantics.

You can read the full grant proposal here.

Postdoctoral project responsibilities

You will work closely with the project PIs, existing postdoc and graduate students to generate the major project deliverables, focus on extending proof-of-concept tools to data integration use-cases beyond the Open Tree of Life project as the main phylogeny provider. Specifically, you will work with other projects funded by NSF’s GoLife program to obtain large phylogenies, gather sources for meaningful phyloreferences, and develop phyloreferencing proof-of-concept applications for these. These applications will include aggregating trait and other domain-relevant data. You will also work with the ARBOR Evolutionary Workflows project to prototype ways for integrating phyloreferences into trait-based analysis and visualization workflows that can be executed within the ARBOR framework.

While working with us on this project, you will gain familiarity with ontology development and ontology-enabled applications, including generating phyloreferences at a Tree-of-Life scale. You will also have the opportunity to explore, develop and test alternative approaches to clade definitions at every taxonomic level and at the broadest possible scales. You will have opportunities to publish both empirical and theoretical work.

Qualifications:

  • PhD in Biology or a related field.
  • Strong background in Systematic Biology required. You should be well versed in all aspects of theoretical phylogenetics and related topics.
  • Programming experience in languages frequently used in scientific computing and for managing or converting scientific data (e.g., Python) is useful (and thus preferred) but not required.
  • Excellent communication and writing skills, and ability to interact productively with other projects’ PIs and personnel.
    How to apply:

Please submit a letter of interest and CV, together with the names and contact information of three academic references, to Dr. Nico Cellinese (ncellinese@flmnh.ufl.edu). All other inquiries should also be directed to Dr. Cellinese. The position will remain open until filled.

Seeking graduate students to work on Mediterranean Campanulaceae

October 15th, 2015
By Cellinese,Nico

I am looking for a graduate student interested in studying evolutionary patterns and processes in the Mediterranean Basin using Campanula as a model. Field work is tough as you will be traveling throughout the beautiful Aegean archipelago, visiting many uninhabited islets in addition to some of the most amazing Mediterranean spots. You will also be forced to explore the striking Peloponnesos, Turkey, Cyprus, and the western Mediterranean islands. If you apply and are accepted by the Department, you can start fieldwork in May 2016 and travel with me during your very first field season 🙂

To apply contact me and visit the Biology Department graduate program. Deadline is set to December 1, 2015.

Rebecca’s NSF-EAPSI Fellowship

September 10th, 2015
By Cellinese,Nico

Rebecca was awarded a NSF-EAPSI Fellowship and spent the summer in China collecting Micranthes. Her story is featured by NSF! Awesome job! http://nationalsciencefoundation.tumblr.com/post/128787935708/collecting-micranthes

 

Postdoctoral fellow in Computable Semantics for the Tree of Life

May 3rd, 2015
By Cellinese,Nico

The Phyloreferencing project seeks a postdoctoral fellow for researching and developing computational semantics approaches to large-scale biodiversity data integration problems. The project aims to enable addressing elements in the Tree of Life by unambiguous, transparent, and fully computable semantics of their patterns of evolutionary descent. The work involves researching and developing OWL models and ontologies, tools for converting existing data into OWL format, and online proof-of-concept applications for using machine reasoning to navigate biodiversity data by Tree of Life-semantics.

The project is a collaboration between Dr. Nico Cellinese (Florida Museum of Natural History, University of Florida) and Hilmar Lapp (Center for Genomic and Computational Biology, Duke University) newly funded by the National Science Foundation for 3 years. The incumbent will be based in the lab of Dr. Cellinese, but will work closely with both PIs and will periodically travel to Lapp’s lab at Duke University. Starting date is negotiable but the sooner the better. Salary is $50,000 with a 3% annual increase.

Why phyloreferencing?
Integrating and querying biological data across organisms, whether on small or large scales, to this day relies on traditional names for organisms and groups of organisms based on Linnaean nomenclature. However, when it comes to integrating and communicating data, these suffer from two major limitations. Firstly, because they are simple text-strings, machines cannot access the meaning intended by those who coin a name and those who apply it, resulting in rampant ambiguity and inconsistency in what organism names are interpreted to mean. Secondly, there are many groups of organisms for which a Linnaean name does not and may never exist, but for which valuable biological knowledge needs to be communicated. The Phyloreferencing project aims to address these challenges by defining ontology-based references (“phyloreferences”) to elements on the Tree of Life that are unambiguous have fully computable semantics. To accomplish this, we are using OWL, OWL ontologies, and machine reasoning. Phyloreferences build on a large body of theoretical and applied work on phylogenetic taxonomy.

The overall deliverables of the project include a formal specification for phyloreference encoding and reasoning in OWL; ascertaining correctness of the specification using small-scale tests verifiable by domain experts; and a large-scale proof-of-concept application for using phyloreferences to navigate biodiversity data resources.

The full grant proposal is available at http://dx.doi.org/10.6084/m9.figshare.1401984.

Postdoctoral project responsibilities
The postdoc will work closely with the project PIs and graduate students to generate the major project deliverables, which include the following:

  • As part of creating a specification for encoding phyloreferences and phylogenies in OWL, the postdoc will participate in OWL model and ontology development for phylogenies and phyloreferences; develop templates for constructing phyloreferences in OWL; and develop tools to convert published phylogenies and phyloreferences to OWL ontologies.
  • The postdoc will create an online proof-of-concept application that uses OWL reasoning to allow users to query biodiversity data resources using phyloreferences and Tree of Life-scale phylogenies.

All software source code, ontologies, and related products will be developed collaboratively on Github and be made available under open-source licenses.

Qualifications:

  • PhD in Computer Science, Computational Biology, Bioinformatics or a related field.
  • Domain knowledge in biology, biodiversity, or evolution is helpful, but not required.
  • Strong knowledge of Description Logic semantics, ontologies and modeling (ideally OWL ontologies).
  • Experience with logic machine reasoning (ideally OWL DL reasoners and entailments).
  • Strong programming experience in languages frequently used in scientific computing, and especially for computing with ontologies (Java, Scala, functional languages) and for managing or converting scientific data (e.g., Python).
  • Experience programming with OWL API or other APIs to working with machine reasoners.
  • Experience with web-application development (in particular using JavaScript, or microframeworks).

How to apply: To apply please submit a letter of interest and CV, together with the names and contact information of three academic references, to Dr. Nico Cellinese ncellinese@flmnh.ufl.edu (to whom inquiries should be directed). The position will remain open until filled. The University of Florida is an Equal Opportunity Employer.

Congratulations to Andy Crowl!!

February 18th, 2015
By Cellinese,Nico

Andy was awarded a dissertation improvement grant (NSF-DDIG) to work on a project titled “Integrating Biogeography, Cytology, Niche Modeling and Phylogenetics to Understand the Evolutionary History of Endemic Campanula Species in the Mediterranean”. Way to go, Andy!!

She’s A Scientist

November 14th, 2014
By Stubbs,Rebecca L

The Cellinese and Soltis Labs represented botanists at the Florida Museum of Natural History’s annual She’s a Scientist program last weekend!

image3

We’re working on the website…

September 24th, 2014
By Miles,Nicholas Wm

It’s Wednesday afternoon and we’re updating the website. Content here we come!

lab

Memories from the 2014 Annual Botany Meeting in Boise, ID

August 26th, 2014
By Cellinese,Nico

1506190_10204324810229965_84047260466500705_o-2

Andy received the BSA Graduate Student Research Award

10460617_10204331570718973_5876790173477254169_o-2-2

Rebecca received the ASPT Graduate Student Research Award

10501763_10152284300892634_7110879547916940023_n-2

Fun times with the Cellinese, Manchester, Moore, Soltis, Wolf labs

New data on Legousia and Triodanis

March 27th, 2014
By Cellinese,Nico

Linda Nhon and Andy Crowl showcased our preliminary results on the work on Legousia and Triodanis (Campanulaceae) at the UF Undergraduate Scholar Program event.  We are getting interesting results!  The poster is only showing our preliminary chloroplast tree but we have very interesting nuclear trees too, based on PPR alleles.  For example, Legousia is back to be consistently monophyletic. We will show a more detailed poster at the next Annual Botany Meeting in Idaho. This work is also co-authored with Romey Haberle (Pacific Lutheran University, WA) and Guilhem Mansion (Berlin Botanic Garden, Germany).  More to come!Slide1