Archive for September, 2012

“ENCODE Decoded” Fri. Oct. 12th 4-6pm GBSF Auditorium

September 26, 2012 Leave a comment

Hello All,

Have you been curious about the huge 30 paper release by the ENCODE Consortium?  We are proud to present “ENCODE Decoded” on Friday October 12th from 4:00-6:00p in the Genome Center’s Main Auditorium (Rm 1005).  This will be a series of brief presentations followed by substantial discussions which will cover a portion of the recent and massive ENCODE release.  This will involve both faculty & students and there will be refreshments and snacks served.  Below is a schedule, with a list of the presenters and the ENCODE “Thread” they will cover.

For more info about these threads and a comprehensive list of the ENCODE Consortium papers please visit   and for general ENCODE info

We strongly encourage both faculty and students to attend as we are hoping to have a lively discussion, not merely a presentation of these papers’ contents. Lest you be concerned about the level of participation, we have commitments from Dr. Janine LaSalle, Dr. Frederic Chedin and Dr. Dave Segal to attend.  Try to arrive early to get your drinks and snacks as we plan to start promptly at 4:00pm, however late arrivals are welcome.

ENCODE Decoded Agenda:

Intro to ENCODE, Background and Basics“:  Keith Dunaway

RNA and Chromatin Modification Patterns Around Promoters“:  Erick Loomis   –>

Non-coding RNA Characterization“:   Johnathon Anderson   –>

Three-Dimensional Connections Across the Genome”   Keith Dunaway  –>

Please email Johnathon Anderson ( or Keith Dunaway ( if you have any questions or input.


BMCDB Colloquium 2012 Schedule

September 24, 2012 Leave a comment

Categories: Uncategorized

Free Metabolomics Workshop in SF October 5th

September 23, 2012 Leave a comment

Free Regional workshop:

Practical Applications of Metabolomics

Friday, October 5, 2012

9:00 a.m. – 1:00 p.m.

San Francisco Airport Marriott in Burlingame, CA

Workshop Banner

Practical Applications of Metabolomics

Metabolomics, the global profiling of biochemicals and metabolites, has broad applications in understanding complex biological systems. As metabolomics platforms have become more robust, applications of the technology have moved from basic research in university labs to solving practical problems in the pharmaceutical, biotechnology and consumer products industries.

The half-day workshop provides an overview of the current state of metabolomics and how the technology has been applied to solve a variety of problems including:

  • Understanding disease mechanism and identifying biomarkers

  • Elucidating mechanism-of-action of a drug/ingredient

  • Unraveling off-target effects of a drug/ingredient

  • Profiling biochemical changes for bioprocess/fermentation optimization

  • Establish/support claims


  • John Ryals, Ph.D., Chief Executive Officer,
    Metabolon, Inc.
  • Kristin Eckel-Mahan, Ph.D.
    University of California at Irvine
  • Steve Watkins, Ph.D.
  • Bradford Hill, Ph.D.
    University of Louisville
  • Peter Jackson, Ph.D.
  • Esmerina Tili, Ph.D.
    Ohio State University
  • Kirk Beebe, Ph.D.
    Metabolon, Inc.

San Francisco Airport Marriott
1800 Old Bayshore Highway
Burlingame, CA 94010
(650) 692-9100

Seating is limited – Please RSVP as soon as possible.

I will be driving down to attend this, if you are interested in coming along let me know.

Top 10 Best Things To Know As An Incoming Graduate Student

September 21, 2012 1 comment

Top 10 Best Things To Know As An Incoming Graduate Student
1. Cite EVERYTHING, especially if it was written by your PI.  And make sure you read all those papers as well.
2. Remember that it’s better to be called “roton” than rotten.
3. Establish study groups early, and ask questions if you’re confused.
4. Don’t forget to eat, sleep, and occasionally have some fun (outside of lab)
5. Become friends with the lab technician- they know where everything is and how to operate it.
6. Liquid nitrogen is cold, very cold.  Likewise, Bunsen burners are hot, very hot.
7. Go out to lunch with your fellow first years- they understand best what you are going through, and 20 years from now they might be reviewing your papers.
8. Don’t be afraid of cockroaches, dead mice, or Drosophila.  They’ll turn up in the most unlikely places.
9. If you don’t like a lab after 5 weeks, you are definitely not going to like it after 5 years.
10. Get organized- keep a calendar and a list of things to do.  5 years feels like all the time in the world, but goes by incredibly fast.

Good luck first years

-BMCDB Bloggers


BMCDB Annual Colloquium. Monday Sep 24, 2012

September 20, 2012 1 comment

Tips for riding your bike around UC Davis

September 19, 2012 2 comments

This first week of all the students being back in Davis is an exciting time but, also a hazardous time. The main danger being, riding your bike in a sea of inexperienced freshmen who are unfamiliar with the rules of the road and the responsibilities of riding a bike in Davis. Here are some tips to help avoid an embarrassing, costly and potentially harmful situation on your bike.

First tip: Get familiar with the laws/rules for riding a bike. Cops in Davis will pull you over and ticket you on your bike for: running a stop sign or red light, not using your hand to signal, riding with both headphones in (one is alright), riding inebriated (can lead to losing your drivers license) or otherwise irresponsibly/dangerously, and I think most importantly – for not having a bike light at night. A strong front light, back light, and ideally white or reflective clothing are strongly recommended while biking at night. Also, be familiar with the signs and be careful not to ride your bike in certain areas where it is forbidden (the MU and in certain sections of the Arboretum).

Second Tip: Pay attention while entering/exiting rotaries on campus! Most sensible people are familiar with the rotaries, but unfortunately most freshman are not very sensible. Technically the riders in the rotary have the right of way. Bikes entering the rotary must yield to bikes already in the rotary however, do not count on other riders to adhere to this rule. Many people will just bike right into a rotary without looking, so just be aware of this. When exiting the rotary it is never a bad idea to signal, and check over your shoulder that you will not hit another rider as you turn out of the rotary. Also be wary of actual traffic in the rotaries, buses, trucks, and cops can cause mass confusion when a high volume of bike traffic is present. Rotaries mishaps account for the majority of collisions and injuries on campus, so just be careful!

Third tip: Don’t be afraid to speak up! While riding around campus, especially around lunch of in between classes you will run into groups of slow moving bikes or people walking in the bike lane. Occasionally you can easily pass them by, but it is often necessary to alert those blocking the way of your presence. Just a quick “On your left/right” can save you from getting nailed by a swerving bike or errant pedestrian. Also very helpful with riders who are unable to ride in a straight line or are completely unaware of their surroundings (be especially aware of Cruiser bikes as they tend to be harder to control).

Davis is a great place to ride a bike, just make sure you do it safely and responsibly. If anyone has any other recommendations or stories please feel free to chime in!

Updates: When walking in a bike lane, remember to walk on the left side so you can see oncoming traffic. It is also a good idea to buy a U-lock, almost any other kind of lock can be easily cut (and there is nothing worse than finishing a long day in lab, and finding out that your bike has been stolen). Also a good idea to register your bike with the campus police for a variety of reasons.

Pro tip: As we transition from Summer/Fall into winter remember that the weather changes dramatically. Equipping yourself with splash guards on your front and rear bike tires can save you from getting an impromtu mud facial next time it rains. Riding your bike in the rain is not that bad, as long as you have the right equipment. Getting a solid rain jacket, rain pants, and a pair of water resistant gloves will make you much happier when you arrive at your destination.

Happy Riding!


How to explain the Scientific Method to students these days

September 19, 2012 1 comment

Not sure who is the source of this, but I am working to find out.

Categories: Funny Links/Comics