Tag: UC Davis

Registration is Open for December Bioinformatics Bootcamps at #UCDavis

Forwarding this …

“Registration is now open for Bioinformatics Bootcamps in December!

We’re excited to announce our next offering of Bioinformatics Bootcamps, which will be held on the UC Davis campus December 10-13.

These focused one-day courses are perfect for the student, postdoc, faculty, or industry professional looking to get up to speed quickly on the latest technologies and techniques in bioinformatics. Students will work on their own laptops and have continued access to software and example data used in the exercises through our public Amazon Web Services virtual machine (details here). The first three bootcamps will use the Galaxy platform, and the final bootcamp will use both Galaxy and the command-line. The Alignment and Assembly bootcamps (Dec. 11th & 12th) require you to know Galaxy, so if you are unfamiliar with Galaxy, you should also take the Introduction bootcamp on Dec. 10th.

Tuesday, December 10:

Introduction to Next-Generation Sequence Analysis with Galaxy

Wednesday, December 11:

Next-Generation Sequence Alignment and Variant Discovery

Thursday, December 12:

Genome Assembly using Next-Generation Sequence Data

Friday, December 13:

Introduction to the Amazon Cloud for Galaxy and the Command-Line

Daily instruction will run from 9am until 5pm. Lunch, light breakfast, and snacks will be provided. Enrollment for each bootcamp will be capped at 24 students. Please enroll early to be assured of a seat, as these bootcamps usually fill up quickly!

More information, including full descriptions of each bootcamp can be found at https://training.bioinformatics.ucdavis.edu/bootcamps/

Pricing and Payment

The cost for each bootcamp is $200 (academic/government) or $250 (non-academic/industry). We now accept credit cards. UC Davis attendees can also charge their registration directly to a DaFis account.

Questions

If you have any questions, please don’t hesitate to contact us:

· Training email: training.ucdbio@gmail.com

· Core email: ucdbio@gmail.com

· Core main telephone line: 530-752-2698

We hope to see you in December!

– The UC Davis Bioinformatics Core Team

http://training.bioinformatics.ucdavis.edu

http://bioinformatics.ucdavis.edu/

#UCDavis Phaff Yeast Collection & Kyria Boundy-Mills featured on Radio New Zealand

Cool story on Radio New Zealand featuring one of my favorite microbiologists (Kyria Boundy-Mills) and one of my favorite microbiology related things at UC Davis (the Phaff Yeast Collection).
  http://www.radionz.co.nz/audio/remote-player?id=2570012

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

A message from UC President Napolitano

Figured this was worth posting:

 

Figured this was worth posting:

———- Forwarded message ———-
From: Office of the President – Strategic Communications <communications@ucop.edu>
Date: Mon, Sep 30, 2013 at 10:40 AM
Subject: A message from UC President Napolitano
To: “UC Davis Faculty, Staff and Students”

September 30, 2013

UC COMMUNITY OF LEARNING

Dear Friends:

It is a privilege and an honor to write to you today, my first day as the twentieth President of the University of California. I am both excited and humbled by the challenges and opportunities that lie ahead. I look forward to working with you.

I bring many things with me to California, beginning with an unshakeable belief in the transformative power of education. I also bring a deep appreciation for the greatness of this university, and for what that has meant, and will mean, for the past, present, and future of the state, the nation, and the world.

It is my intent, beginning today, to serve as the strongest advocate possible for the University of California, ready to stand up at every opportunity on its behalf, in any venue that will have me. Together, let us strive not only to maintain UC’s position as the world’s premier public university, but also to push the University forward to ever new heights. The University of California, and California itself, expect and deserve nothing less from all of us.

Very truly yours,

Janet Napolitano
President

Women in Leadership film series and panel discussion

Just heard about this film series (and ending panel discussion) to take place in the GBSF auditorium this fall – sign up via EventBrite links in this PDF link:

Women in Leadership flyer RSVP

The Women in Leadership Seminar Series will showcase 3 films highlighting gender imbalances around the world—Girl Rising and Half the Sky examined issues like education access for girls and sexual trafficking. To frame the current dialogue about women’s rights in the US, the documentary Makers: Women Who Make America chronicled the past 70 years of women’s pursuit of equality and justice. Inspired to illuminate these issues in the UC Davis community, graduate students Nicole Chaffee and Jeni Lee, with support from Dr. Judith Kjelstrom, designed the Seminar Series to educate, advocate, and inspire our peers to strive toward leadership roles and encourage women in the workplace. The Women in Leadership Seminar Series and Panel could not have been successful without the support of: the UC Davis Biotechnology Program, the Chancellor’s Office, the UC Davis ADVANCE Program, the UC Davis Women’s Resource and Research Center, the UC Davis Office of Campus Community Relations, and the Sacramento Valley Chapter of the Association for Women in Science.

On December 2nd, the series culminates in a Panel Session of extraordinary female leaders from academia, industry, and government, who will discuss the challenges and rewards of being a successful female leader. Our six exceptional panelists are: Linda Katehi, Chancellor, UC Davis; Maureen Stanton, Vice Provost Academic Affairs, UC Davis; Meg Arnold, CEO, Sacramento Area Regional Technology Alliance (SARTA); Constance McKee, CEO, Manzanita Pharmaceuticals; Lois Wolk, Senator, California State Senate; and Michele Wong, CEO, Synergex and CleanWorld.

The overall objective of the Series is to educate, advocate, and inspire women by setting the stage for in-depth discussions regarding issues of equity. Both women and men are encouraged to join in this dialogue about women’s rights, as facilitating meaningful discourse will not only encourage men to embrace their female counterparts as fellow leaders, but importantly, will empower young, bright females to pursue leadership roles. Increasing the number of women in leadership positions will ensure the presence of a female voice and will set positive examples for future generations.

Stunningly bad news-like report on UC Davis neurosurgeons – bacteria in brain story

Well, if you are not keeping up the saga of the UC Davis neurosurgeons who injected bacteria into patients brains continues.

This week it was reported that the surgeons have (finally) stepped down from UC Davis Medical School: See the SacBee story for more detail.

Also I have been compiling information on the case here: #UCDavis neurosurgeons conducted experimental surgery w/o IRB approval.

And personally I am glad to see them go. That being said, it would be nice if news stories about the case were not too outrageous. This one from “NerdAlert” is particularly bad:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Graduate Student Opportunity in Marine Biology /Environmental Sequencing of micro eukaryotes

Posting a grad student opportunity for a new project I’m involved in – The project will be using high-throughput sequencing techniques to study microbial eukaryotes in Arctic sediments.

Graduate Student Opportunity in Marine Biology / Biological Oceanography
UAF School of Fisheries and Ocean Sciences, Fairbanks, Alaska USA

We are seeking a graduate student research assistant for a project applying high-throughput DNA sequencing techniques in the study of meiofaunal communities in the Arctic. The student will take a lead role in sample processing and data analysis, including both standard microscopic analysis and morphological taxonomy and high-throughput sequencing approaches. Data will be used to assess meiofaunal community structure and diversity in the US Arctic, and identify possible environmental drivers of community structure. Skills developed will include DNA extraction, purification, and next-generation sequencing methods, and analysis of sequence data. Prior experience in molecular methods is desirable, but not essential. The student may also have the opportunity to participate in research cruises in the Arctic.

Prospective students are encouraged to apply at either the MS or PhD level (PhD candidates would be expected to develop additional research objectives that complement the project, and to work with the advisor in pursuing additional funding sources). The position will be based at the University of Alaska, Fairbanks, but the student will be expected to travel for extended periods to University of California, Davis to receive training in sequencing methods and data analysis. Funding is available for 2.5 years, including tuition, stipend (starting at ~$21,000 / year for MS students), and basic health insurance. The successful candidate will be expected to enroll in the graduate program in Spring 2014, but may be hired as a staff research technician as early as Oct. 1, 2013 if available.

To apply:
Application materials and general information about the graduate program are available at http://www.sfos.uaf.edu/prospective/graduate/. Application deadline for spring enrollment is October 15, 2013. Required materials include three letters of recommendation, general GRE scores, and transcripts from all institutions attended. If interested, or for additional information about the project or the position, contact Sarah Hardy (smhardy@alaska.edu) or Holly Bik (hbik@ucdavis.edu).

Postdoc position in innovating scholarly communication at #UCDavis w/ me, Mario Biagioli & Mackenzie Smith

7/26/13

Postdoc Position in Innovating Scholarly Communication

A new UC Davis initiative on “Innovating the Communication of Scholarship” is hiring a 3-year postdoctoral fellow, starting September 1, 2013. This is a cross-disciplinary project to study the future of academic publishing, involving faculty from the Center for Science and Innovation Studies, the Library, the Genome Center, and the School of Law (with additional collaborators in Computer Science, English, Philosophy, and the Graduate School of Management). Research topics include open access models, peer review, new forms of quality metrics, data publication, use of social media, and new forms of misconduct.
The successful candidate will conduct research, collaborate on or lead organization of conferences, workshops, pedagogical activities, and grant writing. A Ph.D. is required in a relevant field such as Science and Technology Studies, Library and Information Sciences, Communication, Law, Science, or English. Other disciplines will be considered depending on the specific focus of the candidate?s research and other experience. Qualified applicants will have experience working successfully in teams and managing multi-year projects. He or she will possess excellent written and oral communication and administrative skills.
Salary is based on experience and qualifications according to UC Davis guidelines.
To apply: E-mail a PDF file containing your CV, short description of your research experience relevant to this position, and contact details for three references to Mario Biagioli, MacKenzie Smith, Jonathan Eisen.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Expansion of Academic Freedom at the University of California

Just got pointed to this revision of the UC Faculty Code of Conduct which was recently approved by the UC Regents: http://regents.universityofcalifornia.edu/aar/jule.pdf

I was pointed to it by Greg Pasternack from UC Davis who has been a major force in trying to guarantee academic freedoms at UC Davis.

Colleagues, 

  Four years and one month after the UCD Committee on Academic Freedom and Responsibility first raise the alarm about the danger of unjust discipline faculty in the UC system may face (and certainty have faced) for speech and actions regarding institutional matters, I am very happy to report to you all that on July 18 the UC Regents approved our proposed amendment to APM-015 that guarantees faculty academic freedom to speak out about institutional matters.  Given the number of judges that have ruled that faculty speech on institutional matters is *not* protected by the First Amendment, even in public universities, getting this freedom inscribed into APM-015 provides a policy-based guarantee no longer reliant on external interpretation. 

  See attached, notably the underlines in attachment 2.  You can also download it from http://regents.universityofcalifornia.edu/aar/aar.html under “committee on educational policy” 

  This is the greatest expansion in academic freedom in the history of the UC system, because all previous notions of academic freedom limited the application of the idea to just one’s area of scholarship.  Prior to this, the biggest change was to no longer require “dispassionate” scholarship.  However, academic freedom is no longer shackled to scholarship.  We are free to speak on all institutional matters, whether they are within our sphere of scholarship or not.  We may do so using any forum or medium. 

  Now go out and use your freedom to stir up brilliant controversies 😉 

Best wishes, 

-Prof. Greg Pasternack

The section he called particular attention to is in line 4 in the part on “Professional Rights of Faculty” which reads “freedom to address any matter of institutional policy or action when acting as a member of the faculty whether or not as a member of an agency of institutional governance.” This clearly relates to some real and perceived challenges to academic freedom at various UCs and it is good to have a formal policy that says such a freedom is a right of the faculty.

You go Greg …

Related posts:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Fall 2013 Graduate Course in Applied Ecological Genetics: ECL242 / PHR242

Thought this might be of interest

 

Dynamic graduate level course in ecological genetics offered Fall 2013 at UC Davis.

Applied Ecological Genetics:
Genetics and Genomics for Ecology, Health, and Conservation of Natural Populations

Making genetics friendly and accessible.
This course is an introductory course to the topic for graduate students…and yet packed with great information.

REGISTRATION INFO:
Ecology and Pop Bio grad students sign up for ECL242 CRN 29983
Grad students in all other grad groups sign up for PHR242 CRN 46002 

3 units
10:00-11:50 Wed and Fridays Fall quarter 2013
Instructor: Holly Ernest

For graduate students in any graduate group interested in applications of genetics/genomics for ecology, conservation biology, and natural systems management.  Space as available for post-docs, project scientists, and others.

More info:  http://www.vetmed.ucdavis.edu/vgl/wildlife/Ecological_Genetics_Course.html

Great course for students interested in:
• building skills and knowledge to develop the best questions and approaches for ecological genetic and genomics projects
• gaining knowledge in ecological and conservation genetics/genomics for a career in wildlife and natural resource agencies, nonprofit organizations, and academic institutions.  Genetics and genomics is increasingly a key conservation tool.
• evaluating published genetic analyses for ecological questions and management applications.
• applicable to fields including, but not limited to, conservation ecology, population biology, wildlife health, disease ecology, avian science, plant biology, anthropology, entomology, veterinary medicine, and others.

Objectives: 
1. Students will gain understanding of the scope and breadth of genetic/genomic applications for research and applications in ecology, conservation management, and wildlife population health.
2. Students will become familiar with concepts of laboratory and computational techniques commonly used for ecological genetics research.
3. Students will become familiar with key theory underlying genetic data analysis for ecology.
4. Students will gain knowledge and skills in development of well-designed questions, hypotheses and research projects, basic data analysis techniques, and problem-solving in the field of ecological genetics.

Topics
• Sampling techniques and strategies
• Molecular markers and lab techniques: including next generation sequencing, whole genome, microsatellites, mitochondrial DNA, etc
• Data analysis
• Study design
• Genetics of endangered species; invasive species
• Introductory material for Ecological genomics – future courses will be offered by Ecology faculty in this area.  ECL242 will help set the foundation for the more advanced genomics courses.
…and much more! … covered in lecture, computer lab, and discussion

Special Guest speakers and sessions tentatively on schedule
• Computer lab sessions: intro to computational aspects of work with genetic data, genotypic data, sequence data;
• Genome research specialists lined up to tell us about: genomics of wild ancestors of crop plants, insects that are key disease vectors, polyploid fish, birds of conservation concern, endangered mammals, genomics and ecotoxicology, etc
• UCD Genome Center talk and tour

Note that this course will likely be one of the core courses for Ecology Grad Group’s proposed new Area of Emphasis (AOE) in Ecological Genetics and Genomics

6/12 at #UCDavis: Stephen Scherer on “Detection of Clinically Relevant Genetic Variants in Autism Spectrum”

UC Davis MIND Institute’s 2012-2013 Distinguished Lecturer Series

SPEAKER: Stephen Scherer, PhD, DSc
TOPIC: Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder
DATE: Wednesday, June 12, 2013
TIME: 4:30 pm – 6:00 pm
LOCATION: MIND Institute Auditorium (2825 50th Street, Sacramento)

Background Information ( see attached and below)

Bio Info: Stephen Scherer, PhD, DSc, FRSC, holds the GlaxoSmithKline-Canadian Institutes of Health Research Endowed Chair in Genome Sciences at The Hospital for Sick Children and University of Toronto. Dr. Scherer is director of the University of Toronto’s McLaughlin Centre and The Centre for Applied Genomics. He has made numerous contributions to medical genetics including mapping, sequencing and disease gene studies of human chromosome 7. In 2004, his team co-discovered global gene copy number variation (CNV) and has since shown that CNV is the most abundant type of genetic variation of human DNA. His group then identified CNV that contribute to the etiology of autism and many other disorders. The Database of Genomic Variants that he founded facilitates hundreds of thousands of clinical diagnoses each year. His work is documented in over 300 publications and patents and cited more than 20,000 times, ranking him as one of the top cited scientists over the past decade worldwide. Dr. Scherer has won numerous honors such as the 2004 Steacie Prize, an International Howard Hughes Medical Institute Scholarship, and the Premiers Summit Award for Medical Research. He is a distinguished Fellow of the Canadian Institute for Advanced Research, the American Association for the Advancement of Science, and the Royal Society of Canada.

Presentation: (Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder )
Autism Spectrum Disorder (ASD) demonstrates high heritability, familial clustering and ~4:1 male to female bias, yet the causes are only partially understood, due to extensive clinical and genetic heterogeneity. Whole genome sequencing (WGS) promises added value to identify novel ASD risk genes, as well as new mutations in known loci, but an assessment of its full utility in an ASD group has not been performed. In a pilot study, we used WGS to examine 32 families with ASD to detect de novo or rare inherited genetic variants predicted to be deleterious (loss-of-function and damaging missense mutations). Among ASD probands, we identified deleterious de novo mutations in 6 of 32 (19%) and X-linked or autosomal inherited alterations in 10 of 32 (31%) families (some had combinations of mutations). The proportion of families identified with such mutations was larger than has been previously reported, a yield that is in part due to the more comprehensive coverage afforded by WGS. Deleterious mutations were found in four novel, 9 known, and 8 candidate ASD risk genes. Examples include CAPRIN1 and AFF2 (both linked to the FMR1 gene that is involved in fragile X syndrome), VIP (involved in social-cognitive deficits), and other genes such as SCN2A and KCNQ2 (also linked to epilepsy), NRXN1, and CHD7, which causes ASD-associated CHARGE syndrome. Taken together, these results suggest that WGS and thorough informatic analyses may improve the detection of genetic variants likely associated with ASD or its associated clinical symptoms

Scherer_ Bioabstract_05282013.pdf