The Genome Center Biological Networks Seminars present:
Date: Friday, March 01st , 2013, 11am – 12pm
Location: 4202 GBSF”Gene Regulatory Networks in Archea”
Speaker: Marc Facciotti, PhD
Assistant Professor, University of California, Davis
http://www.bme.ucdavis.edu/facciotti/
For more information regarding the seminar series, upcoming talks and how to subscribe in our mailing list, please visit http://www.bionets.ucdavis.edu/
UC Davis will be hosting a 2.5 day QIIME workshop following the SMBE Satellite Meeting on Eukaryotic -Omics, running Thursday afternoon May 2nd through Saturday May 4th. Meeting participants and local Bay Area researchers are encouraged to attend.
Due to space constraints, this workshop will be strictly limited to 32 participants.
Click here to complete the application form (form closes March 22, 2013, and this deadline will not be extended)
From CPB Postdoc Luke Mahler:
Dear Davis Ecologists and Evolutionary Biologists,
This Spring Quarter, I’ll be delivering my CPB Postdoctoral Fellowship Workshop, which will be entitled:
“Phylogenetically correct analysis of species data in ecology and evolution”.
This workshop will consist of 3 sessions, to take place over three days:
April 2: 4:10PM-5:30PM (lecture; note this will be the CPB seminar for this week)
April 3: 11:00AM-1:00PM (tutorial 1 – feel free to bring your lunch)
April 4: 1:00PM-3:00PM (tutorial 2)
The format of this workshop will be an introductory lecture followed by two hands-on R tutorials.
In the lecture, which will take place during that week’s CPB seminar slot, my goal is to (1) review why it’s important to account for phylogeny during data analysis, (2) briefly introduce a suite of current methods for doing so, and (3) critically discuss the inherent assumptions and limitations of phylogenetic comparative methods, outlining best practices for conducting basic analyses.
In tutorials, I will lead participants in a series of computer exercises (all in R) designed to provide hands-on experience implementing the most commonly used phylogenetic statistical analyses. In the first tutorial, participants will learn how to prepare and import phylogenetic trees and species data set for analysis, how to visually explore these data, and how to measure phylogenetic signal and select an appropriate model of trait evolution. In the second tutorial, we’ll conduct a number of phylogenetic statistical analyses with a focus on linear models and principal component analysis. We’ll discuss parameter estimation and interpretation under these models, and will cover techniques for assessing sensitivity of results to phylogenetic uncertainty.
The target audience for this workshop are scientists at any stage who are familiar with phylogenetic trees but don’t necessarily have specialized knowledge about how to work with trees when analyzing ecological or other comparative data. No prior experience using R is necessary, although attendees will need to bring their own laptops, and will need to install R in advance of the workshop (it’s free). Attendees do not need to bring data files – we’ll analyze example data sets which I will provide. Faculty, postdocs, and students are all welcome to attend.
If you are interested in attending this workshop, PLEASE CONTACT ME BY EMAILING lmahler@ucdavis.edu. We haven’t decided yet where to hold the workshop – this decision will be based on anticipated attendance. We’ll do our best to secure a room that can accommodate everyone who interested in attending, but can’t guarantee there will be room for you if you don’t let me know in advance.
Thanks, and I hope you can make it.
Best,
Luke Mahler
Center for Population Biology Postdoctoral Fellow
2320 Storer Hall
University of California, Davis
One Shields Avenue
Davis, CA 95616, USA
Forwarding this:
Dear colleague,
You are cordially invited to participate and submit an abstract to the 10th international congress on halophilic microorganisms – Halophiles 2013, which will be held on the campus of the University of Connecticut, Storrs from June 23rd – 27th 2013.
This conference will bring together an exciting cohort of scientists from many fields of halophile research including but not limited to biodiversity, evolution, ecology, astrobiology, biogeochemistry, biochemistry, physiology, protein structure/function, genetics, genomics, metagenomics, and biotechnology.
Please visit our website for more details. www.regonline.com/halophiles2013
Key Dates:
Deadline for Abstract Submission – April 30th
Deadline for canceling with full refund – May 24th
Deadline for canceling 50% refund – June 7th
Please, kindly forward this invitation to your colleagues.
Sincerely,
Thane Papke, Organizing Chairpeson
Below is a guest post from my friend and colleague Kimmen Sjölander, Prof. at UC Berkeley and phylogenomics guru.
Announcing the FAT-CAT phylogenomic annotation webserver.
FAT-CAT is a new web server for phylogenomic prediction of function and ortholog identification and for taxonomic origin prediction of metagenome sequences based on HMM-based classification of protein sequences to >93K pre-calculated phylogenetic trees in the PhyloFacts database. PhyloFacts is unique among phylogenomic databases in having both broad taxonomic coverage – more than 7.3M proteins from >99K unique taxa across the Tree of Life, including targeted coverage of genomes from Eukaryotes, Bacteria and Archaea — and integrating functional data on trees for Pfam domains and multi-domain architectures. PhyloFacts trees include functional and annotation data from UniProt (SwissProt and TrEMBL), GO, BioCyc, Pfam, Enzyme Commission and other sources. The FAT-CAT pipeline uses HMMs at all nodes in PhyloFacts trees to classify user sequences to different levels of functional hierarchies, based on the subtree HMM giving the sequence the strongest score. Phylogenetic placements within orthology groups defined on PhyloFacts trees are used to to predict function and to predict orthologs. Sequences from metagenome projects can be classified taxonomically based on the MRCA of the sequences descending from the top-scoring subtree node. Because of the broad taxonomic and functional coverage, FAT-CAT can identify orthologs and predict function for most sequence inputs. We’re working to make FAT-CAT less computationally intensive so that users will be able to upload entire genomes for analysis; in the interim, we limit users to 20 sequence inputs per day. Registered users are given a higher quota (see details online). We’d love to hear from you if you have feature requests or bug reports; please send any to Kimmen Sjölander – kimmen at berkeley dot edu (parse appropriately). Interesting paper came up in my automated google searches for “phylogenomics”: Transitioning Toward a Universal Species Concept for the Classification of all Organisms | InTechOpen. It is by Jim Staley who has been writing a lot about microbial species concepts in the last few years. In addition to trying to bridge the gap between bacteria/archaea and eukaryotes in terms of species concepts. Not sure how I feel about everything in the paper but it has a really nice history of how species have been defined for bacteria. He breaks down this history into four periods
The DHS lockdown has been lifted. I want to thank the students, staff and the Davis Police Department for their immediate and professional response during this time. Again, all of our students are safe.
Winfred Roberson
Superintendent
Just got this email and thought I would post
Your students are safe. The district received reports that someone was armed in the vicinity of Oak Avenue and B Streets. The police were summoned and the suspects have been detained. We want to assure parents/guardians all safety protocols are in place and all precautions were taken. DHS, North Davis, King High and DSIS schools were on lockdown and have been released. DHS remains on lockdown pending further investigation. Additional information will be forthcoming as it becomes available.
Winfred Roberson
Superintendent
Jonathan Eisen's Lab 