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.

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”

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:

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

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.

Workshop at #UCDavis: Overcoming Imposter Syndrome with Valerie Young #UCDAdvance

Please forward to graduate students and postdocs (flyer):

How to Feel As Bright and Capable As They “Think” You Are

Why Smart People (including Graduate Students and Postdocs!) Suffer from the Impostor Syndrome
and How You Can Thrive In Spite of It

Thursday, October 9, 2014
2:00-4:00pm | Conference Center, Ballroom A&B
Please Register:

· Do you secretly worry that others will find out you’re not as intelligent and competent as they seem to think you are?

· Do you often dismiss your accomplishments as a “fluke” or “no big deal?”

· Do you think, “If I can do it, anyone can”?

· Do you sometimes shy away from taking on even greater challenges because of nagging self-doubt?

· Are you crushed by even constructive criticism, taking it as evidence of your ineptness? If so, join the club!

Key Take Aways

§ Why the impostor syndrome is not “just low self-esteem”

§ Creative ways “impostors” discount or minimize their success

§ Perfectly good reasons why smart people feel like frauds

§ How your personal Competence Type may be setting you (or your students) up to fall short

§ Procrastination, holding back and other unconscious coping strategies “impostors” use to avoid being found out

§ The role of academic culture in fueling self-doubt

§ Why women are both more susceptible to and held back by impostor feelings

§ Practical steps to help yourself, your students, or high achieving children to interrupt the impostor syndrome and end needless self-doubt

You’ll walk away with practical strategies for interrupting the Impostor Syndrome that you can start using immediately. By applying these simple but powerful techniques you’ll finally be able to begin to see yourself as the bright, competent person you really are!

Dr. Valerie Young is an internationally known speaker and the author of the award-winning book The Secret Thoughts of Successful Women: Why Capable People Suffer from the Impostor Syndrome and How to Thrive in Spite of It (Crown/Random House) now available in five languages including Russian. Valerie has addressed such diverse audiences as Chrysler, Intel, IBM, P&G, Boeing, Merck, McDonalds (Europe), Society of Women Engineers, American Women in Radio and Television, and faculty and students at over 60 other colleges and universities including Harvard, Stanford, Cornell, MIT, and Princeton. Her work has been cited in such publications as The Wall Street Journal, USA Today Weekend, O magazine, Entrepreneur, Kiplinger’s, Inc., The Chicago Tribune, Sydney Morning Herald, More, The Globe & Mail, Woman’s Day, Redbook, and the Irish Independent.

Rob Pringle – EVE seminar speaker at #UCDavis today 4 PM –3 Kleiber Hall

Got this in email and thought it would be of interest to many .. should be worth going to.

Rob Pringle from Princeton is the first seminar speaker of the Ecology and Evolution seminar series. Rob is a very versatile ecologist with many interests and passions. (
His interests in his own words:

I seek to understand how direct and indirect species interactions (predation, herbivory, competition, mutualism) combine with abiotic factors (climate, habitat heterogeneity) to determine the diversity and abundance of species at multiple scales. My method is rooted in natural history and manipulative field experiments and supplemented by whatever computational, isotopic, molecular, remote-sensing, and social-scientific approaches are necessary to understand the mechanisms underlying phenomena in nature. Most of this work is done in the savannas of eastern and southern Africa.

My current work focuses on three interrelated sets of questions. First, what are the functional roles of large mammals in savanna systems, how are these functional roles contingent upon climate, and what are the ecological consequences of large-mammal extinction? My lab is working on these questions in central Kenya (where since 2008 we have been excluding different large-herbivore species from a series of 1-ha plots replicated across a rainfall gradient) and Mozambique’s Gorongosa National Park, where large-mammal populations are recovering following near-extinction of many species from 1977-1994.

Second, how does self-organized spatial pattern arise in landscapes, and what are the consequences of this patterning for animal behavior and ecosystem functioning? Throughout much of Africa, termite mounds occur in strikinglyoverdispersed spatial patterns. We know that these patterns are ubiquitous and ecologically important, yet we have limited understanding of how they arise and what emergent effects they have at the ecosystem scale. Work here is also concentrated in Kenya and Mozambique.

Finally, I am using small experimental islands in the Bahamas to extend classic work about how invasive predators and competitors affect the behavior, population dynamics, and coexistence of Anolis lizards, and how interactions among lizards propagate to influence island food webs more generally.

Valentine’s Day Seminar at #UCDavis: Herbert M Sauro: Reproducibility in Systems and Synthetic Biology: Issues at the bench and the computer.

The Genome Center Biological Networks Seminars Series present:

Reproducibility in Systems and Synthetic Biology: Issues at the bench and the computer.

Speaker: Herbert M Sauro
Associate Professor
Department of Bioengineering

University of Washington
Date: Friday, February 14th, 2014, 10am – 11pm
Location:  1005 GBSF

Reproducibility has been and is becoming more of an issue as the research we do becomes more complex. In the work I do there are two areas that warrant concern. The first is that the computational experiments we publish as a community are rarely if ever reproducible. Secondly, in synthetic biology where we design new organisms which are are also published we again are confronted with the fact that the bulk of published synthetic biology designs can not be recreated without recourse to the original constructs themselves. Sometimes even then the reported experiments cannot be reproduced. Reproducibility is at the heart of the scientific method and it damages science, particularly in the eyes of the general public, if the work we do cannot be easily reproduced. In addition, there are cost concerns when it can take months of labor to recreate work already done. The good news is that, at least in computational science, the reason for the lack of reproducibility is due almost entirely to human error. This is likely to true in experimental science as well. Human error can in theory be easily corrected. In this talk I will discuss some of the efforts going in my lab and others in relation to reproducibility in computational modeling and the design and implementing of synthetic organisms.

At #UCDavis 1/23 – Mercedes Pascual “Climate forcing and the population dynamics of infectious diseases in changing human landscapes”




Mercedes Pascual

Rosemary Grant Collegiate Professor of Ecology and Evolutionary Biology Research Professor, Center for Computational Medicine and Bioinformatics, University of Michigan


Climate forcing and the population dynamics of infectious diseases in changing human landscapes

Dr. Pascual is an internationally recognized theoretical ecologist interested in the population dynamics of infectious diseases, their response to changing environments, and their interplay with pathogen diversity. Her cutting edge research on responses to climate forcing considers in particular water-borne and vector-borne infections. She is also interested in the structure and dynamics of large ecological networks of consumer- resource interactions known as food webs.

Dr. Pascual received her Ph.D. degree from the joint program of the Woods Hole Oceanographic Institution and the Massachusetts Institute of Technology. She was awarded a U.S. Department of Energy Alexander Hollaender Distinguished Postdoctoral Fellowship for studies at Princeton University, and a Centennial Fellowship in the area of Global and Complex Systems awarded by the James S. McDonnell Foundation for her research at UM. She is a fellow of the American Association for the Advancement of Science, an external faculty member of the Santa Fe Institute, and is a Howard Hughes Medical Institute Investigator.

Sponsored by Department of Evolution and Ecology College of Biological Sciences Storer Life Sciences Endowment University of California, Davis

Thursday January 23, 2014 4:10 P.M.

100 Hunt Hall

Storer_Mercedes Pascula flyer.doc.pdf