Update on Curtobacterium and Other Musings

In my first year in the Eisen lab, I was lucky to be able to participate on the Undergraduate Genome Sequencing Project in which I published the draft genome of Curtobacterium flaccumfaciens, the first of it’s genus. An important aspect of this project was blogging about what we were doing: All the successes, the failures, and everything in between, something that I was terrible at evidenced by my one maybe two blog posts. However, the longer I have been in this lab, I find the significance of social media in science, both to myself and the world, grows.

After almost a year since the paper was published, the Eisen lab received an email inquiring about my blog post on Curtobacterium and the difficulties we had with getting enough active DNA and continuing with sequencing. They wanted to know if we were having trouble with DNA extractions on the bacteria, especially since they were interested in sequencing other species of Curtobacterium and were worried if the genus was finicky. We had later found that the viability of our ligase decreased with each successive freeze-thaw causing the huge issue in DNA library prep and were able to inform them that extracting DNA and sequencing Curtobacterium should be a relatively painless process.

There were two things that stuck me as interesting when David, my supervisor on the project, informed me about the email exchange. First, that it was awesome that a blog post that I, an insignificant undergraduate, wrote was seen by other researchers and contained information (as small as it was) that could help them in their research. Second, and more abstract, that science has increasingly become more of a collaborative effort. When I originally thought about sharing in science, the infamous Koch-Pasteur rivalry quickly came to mind. Information simply wasn’t shared as readily at that time. I like to think idealistically that the idea of hoarding information to get ahead of contemporaries has become less common and science will become even more collaborative than it is now. Or the idea of charging to view more than just the Abstract will cease to exist and the number of open-access articles will continue to grow because at the root of researchers (at least originally) is the pursuit of knowledge and dissemination of information. Just some musings I had and who am I to talk? I haven’t even graduated undergrad yet and haven’t joined the race to find the richly rewarding cure to cancer.

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Sheffrin Lecture – Sendhil Mullainathan – 4/17 5:30 PM “Scarcity: A Talk for People Too Busy to Attend Talks”

From an email I recieved:

The annual Sheffrin Lecture in Public Policy (an annual Division of Social Sciences Event) will take place this Thursday, April 17th, 5:30 pm in the Alumni Center (AGR Room) and will feature Professor Sendhil Mullainathan from Harvard, talking about his recent book, Scarcity (co-authored with Princeton Psychologist Eldar Shafir).

Some more detail is below:


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Special Seminar: Single Cell Genomics – 4/25 at #UCDavis

Sharing …

**Please share this special seminar announcement with others who may be interested

Luke Stewart

Senior Field Application Specialist

Fluidigm Corporation

Noriko Satake, MD

Assistant Professor, UC Davis

Single Cell Genomics – cutting edge microfluidic tools defy the law of averages by enabling resolution at the single cell level

Friday, April 25, 12:10 – 1:00 pm

Education Building, Lecture Hall 1222

4610 X Street, Sacramento 95817

UC Davis Health System campus

Light lunch will be provided for those who

RSVP by April 22 to ocr@ucdavis.edu

Co-hosted by:

BGI@UC Davis, the UCDCCC Genomics Shared Resource and the Department of Pathology & Laboratory Medicine

BGI@UC Davis will be presenting a seminar series to be held once per quarter during the academic year. If you have questions or need additional information, please email bgi-ucdavis@ucdavis.edu.
BGI UC Davis seminar Stewart 4-2014.pdf

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CSIS/UCHRI Event: “Authorship Between Literature & Science” 4/15


A workshop of the “The Material Cultures of Knowledge” Multi-campus Research Group, sponsored by UCHRI

When: Tuesday, April 15, 3:00-6:00PM
Where: CSIS/STS Room, SSH 1246 (Map: http://tinyurl.com/1246ssh)

*Please RSVP if you plan to attend: http://tinyurl.com/AuthorshipDavis2014

Speakers will include:




With Comments From:



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4/10 1 PM: John Wingfield “Vision for Biology at the National Science Foundation”

University of California, Davis College of Biological Sciences

Special Seminar

Dr. John Wingfield

Assistant Director for the Biological Sciences National Science Foundation USA

“Vision for Biology at the National Science Foundation”

Thursday, April 10, 2014 1:10 PM
1022 Life Sciences
John Wingfield seminar.pdf

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Workshop by @hollybik Using Social Media to Promote Your Research April 10th

Using Social Media
to Promote Your Research

Thursday, April 10, 2014
Memorial Union, Garrison Room

Many view social media as either a fun distraction, a waste of time – or both! But social media tools can be a tremendous resource for academics seeking to share their research, find new collaborations, and ultimately advance their careers.

Attend this workshop to learn how to:

· Use social media to share and promote your research

· Identify appropriate audiences and avoid pitfalls

· Choose the right platforms to help you achieve your goals

Please pre-register using this online form: http://bit.ly/1ajX6Pc (Pre-registration will help to guide the format of the workshop and the type of social media tools covered)

Workshop Leader: Holly Bik, Ph.D., Holly Bik is a postdoctoral scholar in marine genomics, working in Jonathan Eisen’s lab at the University of California Davis. Dr. Bik is extensively involved in the use and promotion of social media in academic settings. She has several social media sites dedicated to the dissemination of science including: Dr. Holly Bik | Deep Sea News; @hollybik – Twitter; Holly’s personal Homepage; Holly Bik – Google Profile

Sponsored by

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A Viromics Workshop: Tools & Tricks to See the ‘Virus’ in Diverse Sequence Datasets

Just got this and thought it would be of interest:

Dear colleagues,

We would like to call your attention to a full-day Viromics Workshop being held in advance of the American Society of Microbiology on Saturday May 17, 2014 at the Boston Convention Center. Discounted registration ends April 7th.

WS21 A Viromics Workshop: Tools and Tricks to See the ‘Virus’ in Diverse Sequence Datasets

Viruses are fundamental to ecosystems ranging from oceans and sediments to plants and humans with impacts ranging from mortality and horizontal gene transfer to metabolic reprogramming. However, our ability to study them has been bottlenecked by the lack of (i) ecologically relevant isolates resulting in ‘unknowns’ dominating culture-independent surveys and (ii) rigorously evaluated
sample-to-sequence pipelines coupled to community-available informatic tools to generate and make sense of complex viral metagenomic datasets. Fortunately this is changing, and rapidly. New tools are emerging that will democratize the tremendous discovery potential of viral metagenomics. This all-day ASM workshop will introduce these emerging tools and empower a new generation of microbiologists to “see” hidden viruses in datasets ranging from viral metagenomes in diverse environments to microbial datasets from single cell and community genomics projects.

Details here:

Matt Sullivan, Ph.D.
University of Arizona

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Storer Lectureship in Life Sciences – Dr. Jerry Coyne – 4/9& 4/10 at #UCDavis

Well, this should be interesting …

Public Lecture:

Wednesday April 9, 2014

Faith is not a virtue: the incompatibility of science and religion.”

4:10 PM ARC Ballroom A


Scientific Lecture:

Thursday April 10, 2014

Two flies on an island; Speciation in Drosophila on São Tomé

4:10 PM 176 Everson Hall

Storer Lectureship – Dr. Jerry Coyne.pdf

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June R Workshop from Pat Schloss

From Pat Schloss/ the Mothur-announce mailing list

Hi mothur fans,
I’ll be hosting another Crashcourse in R Workshop for Microbial Ecologists this June. The workshop will run from June 23rd to 25th near the Detroit airport. The workshop is being filled on a first come, first served basis. The workshop is geared towards people with interests in microbial ecology that would like to learn R or to learn it better so you shouldn’t feel like this isn’t for you if you are a beginner. I assume no previous computer programming experience. The workshop is an even blend of lecture/discussion and hands on use of R with real data and typically uses mothur output files as a starting point. This is a new workshop that I am offering, so here is a rough outline of what the workshop schedule will look like (it is subject to some minor changes)…

AM Introduction to R – operations, variable types
PM R basics – getting data in and out, packages


AM Plotting: Core functions
PM Plotting: Lattice / RGL


AM Programming in R – Functions, loops
PM Programming in R – Controlling flow

Each day there will be a lecture and discussion interspersed with hands-on activities and it will run from 9 to 5. If you would like to meet with me one-on-one to discuss your project, I can do that in the evening and during breaks. Please email me for more details. Thanks,
Pat Schloss

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UC Davis Summer Bioinformatics Workshops — Registration is Open!

Registration is open for the 2014 Bioinformatics Summer Workshops!

Now in it’s 7th year, the UC Davis Bioinformatics Training Program will be holding two week-long workshops this summer:

June 16-20, 2014: Using Galaxy for Analysis of High Throughput Sequence Data

Sept. 15-19, 2014: Using Command Line for Analysis of High Throughput Sequence Data

These workshops will be held on the UC Davis campus and will run from 9am to 5pm on the dates indicated.


Both workshops will cover modern high throughput sequencing
technologies, applications, and ancillary topics, including:

· Illumina HiSeq / MiSeq, and PacBio RS technologies

· Read Quality Assessment & Improvement

· Genome assembly

· SNP and indel discovery

· RNA-Seq differential expression analysis

· Experimental design

· Hardware and software considerations

· Cloud Computing

Each workshop will include a rich collection of lectures and hands-on sessions, covering both theory and tools. We will cover the basics of several high throughput sequencing technologies, but will focus on Illumina and PacBio data for hands-on exercises. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data.

In June, workshop exercises will be performed using the popular Galaxy platform (http://usegalaxy.org) on the Amazon Cloud
(http://aws.amazon.com/) which allows for powerful web-based data analyses. There are no prerequisites other than basic familiarity with genomic concepts.

In September, exercises will be performed using the Linux command line. Therefore, for this workshop, it is strongly recommended that participants should also have basic familiarity with the Linux/Unix (or Mac) command line.

Who Should Attend

Prior course participants have included faculty, post docs, grad students, staff, and industry researchers. Anyone with an interest in sequence analysis is welcome!

Registration Info

Attendance is limited to 35 participants per workshop in order to foster an effective learning environment and ensure sufficient one-on-one attention. Course tuition is $1,500 for academic or non-profit participants and $1,800 for other participants. Amazon has kindly provided grants of $100 per participant for Amazon Web Services accounts. This will allow you to perform analysis during and after the course using Amazon’s resources, without purchasing your own high performance computing servers!

To register, click on the links above or go to
training.bioinformatics.ucdavis.edu/. We now accept credit cards, as well as UC recharge accounts, for payment. Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.


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

· Core main telephone line: 530-752-2698

· Core email: bioinformatics.core@ucdavis.edu

See you this summer!

The UC Davis Bioinformatics Core Team



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