Seminar 12-12 #UCDavis – Nick Anderson “System design & data provenance in prospective biospecimen collection & management”

Department of Computer Science Colloquium

System design and data provenance in prospective biospecimen collection and management
Nicholas Anderson
Director of Informatics Research, UCDMC

WHEN:Thu Dec 12, 2013 15:10, 50 minutes
WHERE: 1131 Kemper Hall
HOST: Nina Amenta

Access to high quality biospecimens collected from patients requires interaction with a range of clinical and operational systems and roles. The NWBiotrust system implements a modular architecture that encapsulates requirements for security and data use, and tracks the lifecycle of individual patient-acquired biospecimens from collection through processing, clinical annotation and distribution. This system is built to maintain both module and overall workflow auditability of all stages of an implemented study collection protocol. I will discuss the design requirements for this system, and the challenges involved in implementing systems which cross institutional legal privacy boundaries.

PacBio Sequence Assembly Workshop

PacBio is hosting an evening symposium next week as part of another workshop I’m organizing on campus. All are encouraged to attend! Plenty of food available afterwards.

PacBio Sequence Assembly Workshop

Tuesday, December 17th 2013, 4 pm – 7 pm

The Auditorium, 1005 GBSF

4:00 pm                     Welcome & Introductions

4:00 – 4:30 pm        Shane Brubaker, Solazymes

“Assembly, haplotyping, and annotation of a high GC algal genome.”

4:30 – 5:00 pm         Jason Chin, PacBio

“String graph assembly for diploid genomes with long reads.”

5:00 – 5:30 pm         Lex Nederbragt, University of Oslo

“Using PacBio reads to improve and validate the assembly of the complex Atlantic cod genome.”

5:30 – 6:00 pm         Lawrence Hon, PacBio

“Larger genome hybrid assembly with PacBio.”

6 pm – 7:00 pm        Reception & Discussions

Light Refreshments Will Be Served in GBSF Lobby

Seminar at #UCDavis 12/9 – Kimberly Seed on host/phage evolution

Department of Microbiology & Molecular Genetics Recruitment Seminar

Kimberley Seed, Ph.D.

(Tufts University School of Medicine)

"Microbial warfare: Evolutionary dynamics between epidemic Vibrio cholerae and a predatory phage"

Monday, December 9, 2013

10:00 am
1022 Life Sciences

Host: Prof. Rebecca Parales, Dept. of Microbiology & Molecular Genetics


Seed 12-9-13.doc

Leonardo Art Science Rendezvous at #UCDavis 12/2 w/ Amy Franceschini, Art Shapiro, Justin Schuetz, Mary Anne Kluth


Leonardo Art Science Evening Rendezvous

Monday, December 2, 2013

Location: 3001 PES (Plant and Environmental Sciences)

UC Davis Campus


Speaker Schedule:

Monday December 2, 2013

6:30-7:00 Socializing/networking

7:00-7:25: Amy Franceschini

7:25-7:50 Arthur Shapiro

7:50-8:10 BREAK. (During the break anyone in the audience currently working within the intersections of art and science will have 30 seconds to share their work).

8:10-8:35 Justin Schuetz

8:35-9:00 Mary Anne Kluth

9:00-9:30 Discussion/Networking

Speaker Bios/Information:

7:00-7:25. Amy Franceschini. Title: “Excursions through Domains of Familiarity and Surprise.”

Bio: Amy Franceschini is an artist and founder of the San Francisco-based art and design collective, Futurefarmers. Her work is highly collaborative and usually involves a diverse group of practitioners who come together to make work that responds to a particular time and space. Amy creates tactile frameworks for exchange where the logic of a situation can disappear – where moments of surprise and wonder open the possibility for unexpected encounters and new perspectives on a particular situation. This situational approach emerges as temporary architectural interventions, public programs, choreography, radical journalism and museum exhibitions. Amy received her MFA from Stanford University. She is a Guggenheim Fellow and has exhibited at the New York Museum of Modern Art, New York Hall of Sciences and the Solomon R. Guggenheim Museum.

7:25-7:50. Arthur Shapiro. Title: “Butterflies in Illuminated Manuscripts and Renaissance Art–Homage to Vladimir Nabokov."

Bio: B.A. University of Pennsylvania 1966 (Biology), Ph.D. Cornell 1970 (Entomology); at UC Davis since 1971; current title Distinguished Professor of Evolution and Ecology; Fellow, American Assoc. for Advancement of Science, California Academy of Sciences, Royal Entomological Society (U.K.) and Explorers Club; 300 scientific publications (one book, Field Guide to Butterflies of the San Francisco Bay and Sacramento Valley Regions, U.Calif. Press, 2007), 16 completed doctoral and 15 masters students under his direction; Once a Fellow of the Davis Humanities Institute; He does a lot of stuff in Argentina; He works on butterfly biogeography, evolution, and ecology; and drinks Pabst Blue Ribbon by the gallon.

8:10-8:35. Justin Schuetz . Title: ”Approximating equations: visual and statistical explorations of truth.”

Bio: A.B. Bowdoin College (Biology, Studio Art), Ph.D. Cornell University (Ecology and Evolutionary Biology), MFA San Francisco Art Institute (Photography). As Director of Conservation Science for National Audubon Society I lead a team that aims to describe relationships between birds, people, and places so that we can better shape conservation outcomes. Much of our recent work has focused on reconstructing responses of birds to historical climate change and forecasting responses to future climate change. As a visiting faculty at San Francisco Art Institute I co-teach a class on scientific and artistic exploration of biological systems. Recently I have been using images and text to explore the ideas of a Japanese mathematician whose work has changed how biologists construct statistical models of the world.

8:35-9:00. Mary Anne Kluth. Title: "Narratives of Inquiry in a Contemporary Art Practice."

Bio: Mary Anne Kluth is an interdisciplinary artist and received an MFA from the San Francisco Art Institute in 2008 and a BFA from California College of Arts in 2005. Her work explores the nexus of landscape imagery, narrative, and information, and her most recent body of work deals with descriptions of landscape from the 1860s, and contemporary theme park simulations. She recently completed a residence at the Kala Art Institute and had museum exhibitions at the Museum of Art and History, Santa Cruz, and the Contemporary Art Center, Las Vegas. Her work has been featured in ARTnews, Beautiful Decay, and Harper’s, amongst other publications. Kluth has written catalog essays, reviews and contributed to various publications, including Art Practical, Artweek, Art Ltd. and Stretcher. She is represented by Gallery Wendi Norris in San Francisco.


Anna Davidson is currently a Ph.D. candidate in the Department of Plant Sciences at the University of California, Davis studying ecophysiology of fruit trees. She also makes bioart using fungus and other living materials as a medium. As a teacher for the UC Davis Art Science Fusion Program, she leads the found object and sculpture studio section of the class titled Entomology 1, Art, Science, and the World of Insects. She is very interested creative curriculum development in science.

For more information:

Location: 3001 PES (Plant and Environmental Sciences)

UC Davis Campus


Upcoming LASERS:

Thursday February 6th, 2013

Phillip Benn-Artist-Digital Artist-Oakland

Terry Nathan-Atmospheric Sciences and the Art Science Fusion Program UC Davis

Genevieve Quick-Artist-Bay Area

Maciej Zwieniecki-Professor of Plant Sciences, UC Davis

Monday, April 7th, 2014

Christina Cogdell-Professor of Design and Art History, UC Davis

Jesse Drew-Professor of Technoculutural Studies- UC Davis

Michael Neff-Professor of Computer Science and Program of Cinema and Technocultural Studies at UC Davis

Wendy Silk-Professor of Land, Air and Water Resources and the Art Science Fusion Program-UC Davis

Leonardo Art Science Evening Rendezvous Dec. 2.pdf

Manual Kleiner talk 12/4 at #UCDavis Functional genomics and ecophysiological studies of the bacterial symbionts in a gutless marine worm

Department of Microbiology & Molecular Genetics Recruitment Seminar

Manuel Kleiner, Ph.D.

(Max Planck Institute for Marine Microbiology)

"Functional genomics and ecophysiological studies of the bacterial symbionts in a gutless marine worm"

Wednesday, December 4, 2013

10:00 am

1022 Life Sciences

Host: Prof. Douglas Nelson, Dept. of Microbiology & Molecular Genetics


Kleiner 12-4-13.doc

12/2 at #UCDavis: Provost’s Forum: Dr. Caroline Hoxby: Opportunity, Meritocracy, and Access to Higher Education

-Please distribute widely to faculty, staff and students

Dr. Caroline Hoxby, Professor of Economics at Stanford University, will speak about “Opportunity, Meritocracy, and Access to Higher Education” on Monday, December 2, at 3 p.m. in the Multi-Purpose Room of the Student Community Center; a flyer is attached. For details and supplementary materials, visit

The Provost’s Forums lecture series was established in 2012 to make a significant contribution to our campus dialogue on a vital issue: what public universities should and can be in the 21st century. The presentations by our 2012–13 distinguished lecturers were of a very high quality, and I expect the same to be true of this year’s events.

It is my hope that a great many members of our community, broadly representing our schools, colleges, and departments, will turn out for the 2013–14 forums. The information and ideas to be presented there deserve to be disseminated and discussed widely throughout our community.

For more information on The Provost’s Forums on the Public University and the Social Good, including a calendar of all of this year’s events, visit

For details and supplementary materials for upcoming Provost’s Forums, visit

To view videos of past Provost’s Forums, visit

Thank you for your help.


Ralph J. Hexter

Provost & Executive Vice Chancellor

Distinguished Professor of Classics & Comparative Literature

University of California, Davis

One Shields Avenue

Davis CA 95616

Provost’s Forums-Hoxby 2013.pdf

Exit Seminar today at 2 PM at #UCDavis Determinants of tropical vertebrate community composition – Lydia Beaudrot

Exit seminar today at 2:10pm in Wickson 2124.

Title: Determinants of tropical vertebrate community composition

Lydia Beaudrot

Seminar at #UCDavis 11/20 Bacterial sensing and degradation of aromatic compounds – Prof. Rebecca Parales

MIC 291: Selected Topics in Microbiology

Work-in-Progress Seminars

Prof. Rebecca Parales
(Department of Microbiology & Molecular Genetics)

"Bacterial sensing and degradation of aromatic compounds"

Wednesday, November 20, 2013

4:10 pm

1022 Life Sciences

Parales 11-20-13.doc

BioAgFR 2013 NCBI Discovery Workshops @ UC Davis Library Webinar Edition

>A Fall 2013 Hello to our Library Faculty Representatives to the Shields
>Library Biological & Agricultural Sciences Reference Department.
>Would you please distribute the following email notice to your
>respective departmental email lists, especially those for your graduate
>Thank you!
>The UC Davis Library is pleased to announce:
>2013 NCBI Discovery Workshops @ UC Davis Library [Webinar Edition]
>The workshops will focus on the following areas:
>1. Sequences, Genomes, and Maps: December 17, 2013 from 12:30-2:30pm PT
>2. Proteins, Domains, and Structures: December 18, 2013 from
>12:30-2:30pm PT
>3. NCBI BLAST Services: December 19, 2013 from 12:30-2:30pm PT
>4. Human Variation and Disease Genes: December 20, 2013 from
>12:30-2:30pm PT
>To register:
>You are welcome to register for one or more workshops, each emphasizing
>different sets of NCBI resources. Specific examples will be used to
>highlight important features of the resources and tools under study and
>to demonstrate how to accomplish common tasks.
>Electronic copies of detailed handouts for each session will provide
>step-by-step instructions and additional information about each example.
>All workshops are taught by NCBI staff and will consist of 1.5 hours of
>instruction followed by a Q & A period.
>Due to the US Government sequester, the workshop instructors will not
>be able to present in person at UC Davis, as in previous years.
>Instead, you are invited to attend all sessions via webinar, using your
>own computer or perhaps collaborating with your department or research
>group to view together.
>NCBI Discovery Workshops Website:
>Questions? Contact bioagquestions or

Provost’s Forum 12/2- Dr. Caroline Hoxby – Opportunity, Meritocracy, and Access to Higher Education

Posting this via an email I received:

Dear Faculty, Staff, Students and Community Members,

In cooperation with the Center for Poverty Research, we are pleased to announce that the next event in the Provost’s Forums on the Public University and the Social Good will be held on Monday, December 2nd.

Dr. Caroline Hoxby, Professor of Economics at Stanford University, will speak about “Opportunity, Meritocracy, and Access to Higher Education.”

Caroline Hoxby is the Scott and Donya Bommer Professor of Economics at Stanford University, the Director of the Economics of Education Program at the National Bureau of Economic Research, and a Senior Fellow of the Hoover Institution and the Stanford Institute for Economic Policy Research. A public and labor economist, Hoxby is one of the world’s leading scholars in the Economics of Education. She is the Principal Investigator of the Expanding College Opportunities project, which has had dramatic effects on low-income, high-achievers’ college-going. Some of the other research for which she is best known includes explaining the rising cost of higher education, the effects of school choice and charter schools on student achievement, and the effects of teacher unionization. We hope you can attend this exciting event: Monday, December 2, 2013 – 3 p.m., Multi-Purpose Room, Student Community Center.

For more information please see the attached flyer, visit our website: The Provost’s Forums on the Public University and the Social Good, or contact Alycia Thompson. In addition, please forward to any interested parties, as events are open to the public.

Provost’s Forums-Hoxby 2013.pdf