Advice needed from a future reviewer…

I found myself writing this email to some collaborators, but halfway through realized that it’d be nice to get EVERYBODY’s input. Probably, one of you is going to review my next paper, so how awesome would it be for you to just tell me what you think now, and make both of our lives easier later.

To test whether taxa vary significantly across groups of samples, we first need to filter the OTU table to get rid of OTUs that are not present in most of the samples and/or that do not vary across samples. This must happen for statistical reasons.

As far as I know, there are two ways to do this. One, is to remove OTUs that occur in fewer than 25% of the samples (25% is suggested by the QIIME folks). The other is to calculate the variance of the OTUs across samples and remove the OTUs that have a variance less than 0.00001 (0.00001 is an arbitrary number thrown out there by the phyloseq developer.)

A third option would be to apply both criteria.

My inclination would be to go with the third option, but mostly because I want to limit as much as possible the number of hypothesis tests that we do in order to avoid draconian p-value corrections.

I’m not a big fan of arbitrary thresholds, but they are so frequently required that I’ve made my peace with them. However, if someone can suggest a non-arbitrary threshold, that’d be great.

But mostly, I want to make sure that everyone agrees now on the method that we use so that I only have to do this once. Thoughts?

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Talk at #UCDavis: Standardizing Species: Listening to, representing, and universalizing bird sounds in the 20th Century

Talk: Standardizing Species: Listening to, representing, and universalizing bird sounds in the 20th Century


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At #UCDavis: the UC #OpenAccess Policy & what it means for you (10/22, 1:30-3 pm)

The UC Open Access Policy and what it means for you (10/22 from 1:30-3pm)

A Discussion with Catherine Mitchell and Dr. Robert Powell on the UC OA policy
Date & Time: Wednesday, October 22, 2014 from 1:30-3:00pm
Location: Shields Library, Nelle Branch Room, 2nd floor (at the far end of the main reading room)

The UC Open Access Policy ( or was passed by the UC Academic Senate on July 24, 2013, and is going into effect for all UC campuses, including UC Davis, on November 1, 2014. The policy grants UC faculty the right to make their articles freely available to the public by depositing a pre-publication copy in an open access repository. What does this policy mean for faculty at UC Davis?

Come to this talk by Catherine Mitchell of the California Digital Library (CDL), who will describe the tools and services that CDL is developing to support the policy, and Dr. Robert Powell of Chemical Engineering, who will give background on the policy and its passage through the UC Senate. Afterwards a Q&A panel will be held with the speakers, UC Davis librarians and open access researchers to answer questions and discuss the implications of the policy and open access.

This talk is being held during Open Access Week 2014, an annual international event to raise awareness about open access issues.

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UC #OpenAccess policy comments wanted from Academic Senate members by 1/7/15

The University invites comments on the proposed draft Presidential Policy on Open Access, which is based on the Academic Senate Open Access Policy for all Academic Senate members adopted on July 24, 2013.

The proposed new policy extends open access rights and responsibilities to all non-Senate members of the UC community who are authors of scholarly articles, including faculty, other academic personnel, students, administrators, and staff. The policy allows non-Senate authors of scholarly articles to maintain legal control over their research articles while making their work freely available to the public. In addition, the proposed policy outlines procedures for implementing the policy for all UC authors, both Senate and non-Senate. Although the policy assumes all authors will make their scholarly articles available to the public, there is a procedure, which authors must undertake proactively, to opt out of the open access process.

The proposal is located on the UCOP Academic Personnel and Programs website, “Policies under review,” under the “Systemwide Review” tab at If you prefer these documents as attachments, please let me know.

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Today at #UCDavis: Phillip Romero from UCSF: Data-Driven Exploration of Sequence and Function

Dr. Phillip Romero, UCSF
4:10 p.m. Chemistry in Rm 179
Seminar Title: “Data-Driven Protein Engineering: Learning the Sequence-Function Mapping from Experimental Data”

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Seminar at #UCDavis 10/30 – Scott Edmunds on “Open Publishing for the Big-Data Era”

Seminar of possible interest

Thursday, Oct 30th
12:10 PM to 01:30 PM
SS&H 1246

Scott Edmunds
from Gigascience / BGI

"Open Publishing for the Big-Data Era"

For more information see:

Additional information below:

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Diana Wall at #UCDavis 10/23 4 PM: Lessons from an antarctic desert …

Diana Wall flyer 1.pdf

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Biomedical Ph.D. Career Development Trends, Wed 10/22 @ 3 pm at #UCDavis

well, this could be intersting :

This announcement is sent on behalf of Associate Dean John Harada

Biomedical Ph.D. Career Development Trends: Implications for Workforce Development & Diversity

· Wednesday, October 22, 2014 at 3:00 – 4:00 PM

· Location: Memorial Union, MUII room (2nd floor)

· Target Audience: STEM faculty, postdocs, and students

· Recent biomedical workforce policy efforts have centered on the twin challenges of enhancing career preparation for graduate students and postdocs, and increasing diversity in the research workforce & professoriate. Dr. Gibbs will discuss results of his work that has focused on the graduate and postdoctoral training experiences and career-decision making of recent Ph.D. graduates, and whether/how these differ across lines of race/ethnicity and gender. Specifically, Dr. Gibbs will share from a focus group study, and national survey of 1500, recent biomedical PhD graduates (including 276 from URM backgrounds).

· Speaker: Kenneth Gibbs, Jr., PhD, is a Cancer Prevention Fellow at the National Cancer Institute (NCI). Dr. Gibbs conducts policy-relevant research aimed at strengthening the research enterprise.

· For more info and to RSVP:

flyer – Biomedical PhD Career Pathways.pdf

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Aspen Center for Biophysics: Workshop on Microscale Ocean Biophysics

Just got this from the Moore Foundation ..

Dear colleague,

The MMI team would like to apprise you of the following meeting on microscale ocean processes. Please share with potentially interested colleagues; the application deadline is quickly approaching — October 15, 2014. Further information can be found at and

Workshop on Microscale Ocean Biophysics

At Aspen center for physics

11-16 January 2015

Application deadline: 15 October

This highly interdisciplinary meeting will focus on how physical processes affect aquatic organisms at small scales, and thereby the global processes in oceans and lakes that microorganisms overwhelmingly govern. Over the past two decades, there has been a growing realization that the ecology of these organisms depends not only on the bulk environmental conditions, but also crucially on small-scale biophysical interactions and microscale heterogeneity in the physical and chemical conditions. It is becoming clear that physical processes play a fundamental role in shaping the microscale landscapes that form the arena in which these organisms forage, reproduce and encounter each other. A key goal of this meeting is to help advance our understanding of aquatic ecosystems by replacing current statistical and heuristic descriptions with a mechanistic understanding of the component processes. This cannot be achieved without a strong appeal to small-scale fluid physics, mass transport, active suspensions, turbulence, and mechanics in general. The result is a rich landscape of opportunities for physicists, mathematicians, chemists and engineers to be involved in oceanographic and environmental problems, and for oceanographers, biologists and ecologists to inspire and utilize physical concepts and approaches more pervasively. The vision underpinning this meeting is that the interdisciplinary application and advancement of these topics in the context of oceanographic processes will greatly improve our understanding of how organism life is constrained and has evolved to exploit the fundamental laws of physics.

Deadline to apply is October 15, 2014

Apply here:

Roman Stocker (MIT)
Stuart Humphries (University of Hull)
Thomas Kiørboe (Technical University of Denmark)
Lee Karp-Boss (University of Maine)
Justin Seymour (University of Technology, Sydney)

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At #UCDavis Leonid Chindelevitch, 10/09/14 “Probing Networks to Understand Nature”

Department of Computer Science Colloquium Seminar Series

Speaker: Leonid Chindelevitch

Harvard, MIT

Host: Dan Gusfield

WHEN: Thurs. Oct 9, 2014 3:10pm

WHERE: 1131 Kemper Hall

Title: Probing Networks to Understand Nature

Abstract: Networks are a fundamental tool for understanding the intricate interconnections that govern biological systems. This talk will describe two ways in which networks, in combination with mathematical models and algorithmic techniques, can yield valuable biological insights.

Causal regulatory networks help reveal the hidden regulators of gene expression patterns. To facilitate their analysis we established an efficient method for evaluating the significance of the overlap of ternary signals, which generalizes Fisher’s exact test. We used this method to analyze a large-scale causal regulatory network and uncovered new regulators of cardiac hypertrophy.

Metabolic networks help identify novel drug targets. We uncovered structural features of these networks that had been missed by previous researchers, and developed a theoretical framework based on duality for analyzing them in a consistent fashion. We used this theoretical framework to create a new metabolic network for Mycobacterium tuberculosis by algorithmically merging two existing networks, and identified several putative drug targets.

Bio: My research interests lie primarily in the modeling of infectious diseases, both on the molecular level (using approaches from computational and systems biology) as well as on the population level (using approaches from epidemiology and biostatistics). I am particularlly interested in the interactions between science, medicine and policy as they relate to improving patient outcomes, especially in low-income, low-resource settings.

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