Pumpkin Carving as a model for Genome Assembly

So - we have this pumpkin carving contest every year in the UC Davis Genome Center.  And people from my lab have done some excellent pumpkins in the past.

See for example some details on their 2014 pumpkin:






And I have on and off carved pumpkins on sciency themes every once in a while.




So this year, when the Genome Center admins sent around an email saying they had bought pumpkins for people to use, I decided it would be fun to do something this year.  But then 10/30 came and we had still not done anything.

So I came up with a crazy idea.  Cut up pumpkins in different ways as an example of genome sequencing strategies.  And, with the help of a few people in my lab and some of the people in neighboring labs, this is what we did.

So - first - we took three pumpkins.

And we decided to make one of them a representation of long read sequencing and another a representative of short read sequencing.  So - using a saw provided by people in Justin Siegel's lab, I cut one pumpkin into horizontal slices and remove the innards and made that the "long read sequencing" example.  And then I took pumpkin #2 and again cut into horizontal slices but this time I  then cut those slices up into chunks.  And we then stored the pumpkin pieces overnight and Katie Dahlhausen in my lab made some nice signs to add to the display. In addition, the decorated pumpkin #3 with some "Shotgun sequencing" motifs.  And voila, we had our pumpkins ready for the contest for 10/31.

So I headed in to work early, and set up our display.





And I posted about it to Twitter.


But something seemed lacking.  So I went and got another pumpkin


And now it felt complete.

And then, after the symposium I decided - hey - we should try to reassemble these.  I took some pics of this and made them into videos / gifs.
Long piece assembly. 

Assembling the long piece pumpkin shotgun was easy.



Linking assembly.

Assembling from the linking pieces was harder.  And in the end we did not quite get it back together.




We did not even try to assemble the small pieces. But the next day I did ponder recovering them and the other pieces and doing a meta pumpkin assembly.


Anyway - this ended up being pretty fun.  Lots of ideas about how to do it better (e.g., we should have barcoded / labelled the pieces so that we could guide the assembly if we failed to do it without guidance).   And thanks to all the discussions with people out there and to the people in my lab who helped put this all together.

Also I made a Wakelet of some of the Twitter discussion

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DEB 2016 Summer Meetings Schedule

Meeting season is upon us. Here’s a quick overview of the where, when, and who for finding your DEB representatives at annual meetings this summer. Note: Lists of expected attendees are tentative and subject to change. Check back for updates and additional details of scheduled sessions and other outreach activities as they become available.

 

Society of Wetland Scientists’ 2016 Annual Meeting

http://swsannualmeeting.org/

31 May – 4 June 2016; Corpus Christi, Texas

Liz Blood (Ecosystems)

 

EEID (Ecology and Evolution of Infectious Disease)

http://eeid.cornell.edu/eeid-2016/

3 – 5 June 2016; Ithaca, New York

Sam Scheiner (Evolutionary Processes); Karen Alroy (Science Associate); Diana Weber (AAAS S&T Policy Fellow)

 

ASLO Summer Meeting

https://www.sgmeet.com/aslo/santafe2016/default.asp

5 – 10 June 2016; Santa Fe, New Mexico

Alan Tessier (DDD); Lou Kaplan (Ecosystems); Maria Gonzalez (Population and Community Ecology); Tim Kratz (Macrosystems & NEON Science); Mike Vanni (Postdoctoral Fellows program in DBI)

Event: NSF Funding Opportunities in Aquatic Sciences; Date: Tuesday, 7 June; Time: 12:00 – 13:30

 

ASM Microbe 2016

http://www.asmmicrobe.org/

16 – 20 June 2016; Boston, MA

Matt Kane (Ecosystems); Leslie Rissler (Evolutionary Processes)

 

Evolution 2016 (ASN/SSE/SSB)

http://www.evolutionmeetings.org/evolution-2016—austin-texas.html

17 – 21 June 2016; Austin, Texas

Paula Mabee (DD); George Gilchrist, Paco Moore, Leslie Rissler, Sam Scheiner (Evolutionary Processes); Gordon Burleigh (Systematics and Biodiversity Science)

Event: NSF information session; Date: Monday, 20 June; Time: 12:00 – 13:00

 

Botany 2016

http://www.botanyconference.org/

30 July – 3 August 2016; Savannah, Georgia

Gordon Burleigh, Joe Miller & Simon Malcomber (Systematics and Biodiversity Science)

ESA Ecology 2016

http://esa.org/ftlauderdale/

7 – 12 August 2016; Ft Lauderdale, Florida

Alan Tessier (DDD); Doug Levey & Betsy Von Holle (Population and Community Ecology); Liz Blood, Henry Gholz & Karina Schäfer (Ecosystems); Janice Bossart (Evolutionary Processes); Cheryl Dybas (Public Affairs); John Adamec (Staff)

Booth: #333

Event: Funding Agency Information Session; Date: Monday, 8 August; Time: 11:30-13:15

 

North American Ornithological Conference 2016

http://americanornithology.org/content/north-american-ornithological-conference-2016

16 – 20 August 2016; Washington, DC

Doug Levey (Population and Community Ecology)

 

ecoSummit 2016

http://www.ecosummit2016.org/

29 August – 1 September 2016; Le Corum, Montpellier, France

Karina Schäfer (Ecosystems)

 

Entomology 2016 (XXV International Congress of Entomology)

http://ice2016orlando.org/

25 – 30 September 2016; Orlando, Florida

Janice Bossart (Evolutionary Processes)


DEB Summer 2015: Where to find us at Professional Meetings

We’ve got a busy summer meeting schedule and are offering numerous opportunities to hear the latest NSF updates, meet your Program Officers, and learn about funding opportunities in-person. Since it is so close this year, there will be a fairly large contingent of us heading up to Baltimore for the ESA meeting. But, we’re not forgetting the other side of the house; we’ll have representatives at both of the big, international evolution conferences. We’ll also be at the IALE Congress and the joint Botany meeting, and we were already at ASM earlier this season.

And remember, if you can’t make it to our lunchtime brown-bag sessions to hear the latest from DEB, you can always email one of the attending Program Officers to set up another meeting time, catch us in the poster hall, or drop by our information tables (where available).

 

26 – 30 June, 2015: Guarujá, Brazil. Evolution 2015

Featuring: Simon Malcomber, David Mindell, Sam Scheiner, Kelly Zamudio

Presentation Followed by Q & A (NSF Update)
Sunday 28 June, 12:00 – 13:30 (during lunch break), Meeting Room Diamantina

 

6 – 9 July, 2015: Portland, OR. 9th International Assoc for Landscape Ecology World Congress

Featuring: George Malanson

Panel Discussion: Funding Opportunities for Landscape Ecology at the US National Science Foundation
Monday 6 July, 5:30 PM – 6:30 PM, See Final Schedule for Location

Additional Notes: Tuesday eve poster session is a good time to meet up with George.

 

25 – 29 July, Edmonton, Alberta. Botany 2015

Featuring: Joe Miller

With Special Appearances: Roland Roberts, Judy Skog

NSF Information Booth (Exhibitor #114)
All Days, Staffed during poster sessions, by appointment and whenever we can be there, Hall D.

NSF Outreach Presentation and Discussion
Wednesday 29 July, noon, location TBA (check final program).

 

9 – 14 August, 2015: Baltimore, MD. Ecological Society of America 2015

Featuring: Henry Gholz, Doug Levey, Sam Scheiner, Alan Tessier, Alan Wilson, George Malanson, Diane Pataki, John Adamec, Shannon Jewell

With Special Appearances by: Matt Kane (TBD), Betsy Von Holle (W, Th, F), Emily Leichtman (Su, M)

NSF Information Booth (Exhibitor #438)
Monday 10 – Thursday 14 August, All-day, Baltimore Convention Center Poster/Exhibit Hall.

Special Session (SS 2): Ecology on the Runway: An Eco-Fashion Show and Other Non-Traditional Public Engagement Approaches
Monday 10 August, 11:30 AM-1:15 PM, Baltimore Convention Center 310.

Special Session (SS 10): New Frontiers: Bridging the Gaps Between Continental and Global-Scale Research Networks, A Special AGU-ESA Event and Evening Social
Monday 10 August, 8:00 PM-10:00 PM, Baltimore Convention Center 309.

Workshop (WK 53): Federal Agency Networking Session (Come and meet your Program Officers from NSF and beyond!)
Thursday 13 August, 11:30 AM-1:15 PM, Baltimore Convention Center 316.

 

9 – 15 August, 2015: Lausanne, Switzerland. European Society for Evolutionary Biology

Featuring: George Gilchrist and Leslie Rissler

Presentation followed by Q & A (NSF Update)
Thursday 13 August, noon, location TBA.

Additional Notes: This will be the same program as presented at Evolution 2015 (if you’re like us and had to choose one or the other, we’ve got you covered!)


DEB Summer 2015: Where to find us at Professional Meetings

We’ve got a busy summer meeting schedule and are offering numerous opportunities to hear the latest NSF updates, meet your Program Officers, and learn about funding opportunities in-person. Since it is so close this year, there will be a fairly large contingent of us heading up to Baltimore for the ESA meeting. But, we’re not forgetting the other side of the house; we’ll have representatives at both of the big, international evolution conferences. We’ll also be at the IALE Congress and the joint Botany meeting, and we were already at ASM earlier this season.

And remember, if you can’t make it to our lunchtime brown-bag sessions to hear the latest from DEB, you can always email one of the attending Program Officers to set up another meeting time, catch us in the poster hall, or drop by our information tables (where available).

 

26 – 30 June, 2015: Guarujá, Brazil. Evolution 2015

Featuring: Simon Malcomber, David Mindell, Sam Scheiner, Kelly Zamudio

Presentation Followed by Q & A (NSF Update)
Sunday 28 June, 12:00 – 13:30 (during lunch break), Meeting Room Diamantina

 

6 – 9 July, 2015: Portland, OR. 9th International Assoc for Landscape Ecology World Congress

Featuring: George Malanson

Panel Discussion: Funding Opportunities for Landscape Ecology at the US National Science Foundation
Monday 6 July, 5:30 PM – 6:30 PM, See Final Schedule for Location

Additional Notes: Tuesday eve poster session is a good time to meet up with George.

 

25 – 29 July, Edmonton, Alberta. Botany 2015

Featuring: Joe Miller

With Special Appearances: Roland Roberts, Judy Skog

NSF Information Booth (Exhibitor #114)
All Days, Staffed during poster sessions, by appointment and whenever we can be there, Hall D.

NSF Outreach Presentation and Discussion
Wednesday 29 July, noon, location TBA (check final program).

 

9 – 14 August, 2015: Baltimore, MD. Ecological Society of America 2015

Featuring: Henry Gholz, Doug Levey, Sam Scheiner, Alan Tessier, Alan Wilson, George Malanson, Diane Pataki, John Adamec, Shannon Jewell

With Special Appearances by: Matt Kane (TBD), Betsy Von Holle (W, Th, F), Emily Leichtman (Su, M)

NSF Information Booth (Exhibitor #438)
Monday 10 – Thursday 14 August, All-day, Baltimore Convention Center Poster/Exhibit Hall.

Special Session (SS 2): Ecology on the Runway: An Eco-Fashion Show and Other Non-Traditional Public Engagement Approaches
Monday 10 August, 11:30 AM-1:15 PM, Baltimore Convention Center 310.

Special Session (SS 10): New Frontiers: Bridging the Gaps Between Continental and Global-Scale Research Networks, A Special AGU-ESA Event and Evening Social
Monday 10 August, 8:00 PM-10:00 PM, Baltimore Convention Center 309.

Workshop (WK 53): Federal Agency Networking Session (Come and meet your Program Officers from NSF and beyond!)
Thursday 13 August, 11:30 AM-1:15 PM, Baltimore Convention Center 316.

 

9 – 15 August, 2015: Lausanne, Switzerland. European Society for Evolutionary Biology

Featuring: George Gilchrist and Leslie Rissler

Presentation followed by Q & A (NSF Update)
Thursday 13 August, noon, location TBA.

Additional Notes: This will be the same program as presented at Evolution 2015 (if you’re like us and had to choose one or the other, we’ve got you covered!)