Compiling a list of REU opportunities for my students

3 Dec

I started looking into opportunities for undergrad students who are interested in biology and bioinformatics / computer science. The list is far from complete. I will add when I have more time!

What is an REU? 

NSF funds a large number of research opportunities for undergraduate students through its REU Sites program. An REU Site consists of a group of ten or so undergraduates who work in the research programs of the host institution.

Auburn University NSF REU Site in Computational Biology

http://www.auburn.edu/cosam/bioinformatics/nsf_reu.htm

Deadline: March 1st, 2017

Integrated Science For Society Boston College

http://reu.bc.edu/

February 1st, 2017

BRITE REU Boston University

HTTP://SITES.BU.EDU/BRITEREU/

Feb 17th, 2017

Cornell

http://bti.cornell.edu/education/internships/

Unclear if open this year (2017)

City College New York

https://www.ccny.cuny.edu/biology/nsf-reu-summer-program

Unclear if open this year (2017)

National Science Foundation logoFrom Genomes to Phenomes — Exploring Function Across Scales

http://www.clemson.edu/centers-institutes/culsoc/research-experience.html

February 5, 2017

NSF REU in Bioinformatics and Computational Neuroscience, Cold Spring Harbor

http://www.cshl.edu/Education/NSF-REU-in-Bioinformatics-and-Computational-Neuroscience.html

Unclear if open this year (2017)

Computational Genomics Undergraduate Research Experience, Charleston

http://omics.cofc.edu/

February 15, 2017

Research Experience for Undergraduates (REU) at the Intersection of Mathematics and Biology, Florida

http://research.fit.edu/reu-biomath/

Unclear if open this year (2017)

Undergraduate Research Experience in Genomics, Proteomics and Bioinformatics” award to Florida A&M University located in Tallahassee FL

http://www.famu.edu/index.cfm?REU&Introduction

Please submit Application Forms before March 21, 2016.

A program designed for students who want to immerse themselves in genetics and genomics research, Jackson Labs

https://www.jax.org/education-and-learning/high-school-students-and-undergraduates/learn-earn-and-explore

Thursday, February 2 – Application deadline

Note to self: Continue searching here:

https://www.nsf.gov/crssprgm/reu/list_result.jsp?unitid=5047&d-49653-p=3

Love Trumps Hate

9 Nov
Today in the biology department at SF State.

Today in the biology department at SF State, our students and my colleagues reminded me that Love Trumps Hate. 

Canvassing in Nevada

24 Oct

Last weekend I went to Reno, Nevada, to canvass for the Democrats.

Ready to canvass in Reno, Nevada!

Ready to canvass in Reno, Nevada!

We drove to Reno on Saturday morning, then spent the afternoon knocking on doors and talking to people, went out for a simple dinner and checked into our hotel. On Sunday morning, we drove back and made a little detour to drink coffee on the shore of Lake Tahoe. It was a fun road trip!

How does canvassing work?

As expected, we found the campaign to be well organized. After we arrived at one of the campaign headquarters in Reno, they explained to us what we were going to do. They gave us a list of addresses with names of people who lived there. Our list contained 87 addresses. It took us almost four hours to knock on all the doors! To everyone who wanted to talk to us, we asked then whether they were planning to vote for Clinton, for Catherine Cortez Masto (she could become the first Latina in the Senate) and Chip Evans (Congress). We then asked if they knew when and where they planned to vote and we explained how easy it is to do early voting in Nevada. In Reno (Washoe County), you have from Oct 22 to Nov 4th to go to any early voting location in the county, and there are many such polling stations, for example, in the library or the supermarket. Finally, if people were supportive of the Democratic candidates, we’d ask them whether they’d be interested to volunteer.

Who did we talk to?

I had never really thought of how canvassing is done, but I somehow assumed that it would consist of convincing people to vote for Clinton and not Trump. However, I had only one conversation on Saturday where I explained why I support Hillary, and Trump was hardly mentioned at all (what a relief!) Instead, we were mostly talking to people who were known to be supportive of Democrats, but who may or may not actually vote. Our main goal was therefore to encourage people to go and vote and to use the opportunity of early voting in Nevada. That’s why it was probably most important for us to be able to say: “Do you know that you can vote today in the supermarket down the road until 6PM? And tomorrow they’re open from 11 till 4.”

Would I do it again?

Yes, absolutely. It was fun (and tiring). Most people were happy to talk to us. I may have convinced a few people to go and vote and I may have encouraged someone to volunteer for the campaign. Plus, the weather was nice and I walked 5 miles. Highly recommended!

Ready to canvass in Reno, Nevada.

Ready to canvass in Reno, Nevada.

 

 

 

 

How you can help the Clinton campaign from California and why you should

15 Oct

hillary

I would like to convince you to join me in helping the Clinton campaign.

Why help the campaign?

First of all: does the campaign still need help? It seems like a sure win at this point!

1. Things can change quickly. Chances of Trump winning are small, but if it does happen it would be a major disaster for the country and the world, so I want to do my part to prevent it.

2. The senate is not a sure win, and right next door, in Nevada, is one of the tightest races for a senate seat. A democratic majority in the senate is within reach and would make a huge difference.

What to do?

For the longest time, I didn’t realize how I could help the Clinton campaign. Now I do, and I thought I share it with you!

1. Send money.

2. Volunteer for a two hour shift at one of the SF phone banks.

3. Drive or fly to Nevada (Reno or Las Vegas) in one of the next weekends to get out the vote right where it matters most.

To sign up for a phone bank or to go to Nevada, go to:

https://www.hillaryclinton.com/events/

Is it hard?

I did a two-hour shift at the phone bank last week and it was easy. I was calling people who were known Hillary supporters to ask if they wanted to go to Nevada to get out the vote. It was a simple question with a simple yes/no answer. I was not supposed to try and convince people of something they didn’t want.

The ridiculous order of the streets in the Excelsior (SF)

26 Sep

I live in the Excelsior neighborhood in San Francisco. My street is Athens Street. If I walk westwards from my home, I come to Vienna Street and then Naples, Edinburgh and Madrid. If you have any knowledge of map of Europe, you realize that the order makes no sense!

(Also, why is there Naples, but not Rome, and why Munich, but not Berlin? And why oh why, is there no Amsterdam Street? So many questions!)

Last week, I asked the students in the CoDE lab to create a map to show the ridiculous order of the streets in the Excelsior. They had fun figuring out how to make a map in R, so I thought I share their work here. Several students were involved, but my graduate student Olivia Pham did most of the work.

The code is here: http://rpubs.com/pleunipennings/212840

europe_excelsiormap

The surprising order of street names in the Excelsior neighborhood in San Francisco. We connected the cities in the order of the streets. London Street is the first city-name street if you enter the neighborhood from Mission Street, just east of London Street is Paris Street, then Lisbon Street etc. The last city-name street is Dublin Street which is closest to McLaren Park.

excelsiormap

A map of part of the Excelsior neighborhood showing the order of the city-name streets.

Successful experiment helps me sleep

5 Sep

A couple of weeks ago, I read about an experiment that showed that 100% of breastfed babies could learn to sleep through the night by eight weeks. I was skeptical, but also intrigued. My baby was eight weeks old then, and definitely not sleeping through the night. In case you are not familiar with baby sleep jargon: “sleeping through the night” usually means that a baby sleeps from before midnight till after 5AM. I think that midnight till 5AM is a very short night, but, hey, for a two-month old this is still pretty cool!

I decided to look up the original paper that described the experiment. Here is the link to the paper in case you want to read it too. The experiment was quite simple. The researchers recruited 26 first-time parents to participate in a baby sleep study. All of them were planning to exclusively breastfeed the baby until at least eight weeks. 13 families were put (at random) in the control group and 13 were put in the experimental group.

Simple instructions for the experimental group

Both groups of parents were asked to keep detailed 72 hour diaries once a week for eight weeks, in which they recorded when their baby slept, when it nursed and how much milk it consumed at each feed*.

In addition, the parents in the experimental group were told to do the following:

1. Always feed the baby between 10PM and midnight (focal feed).
2. Try not to hold, rock or nurse the baby to sleep.
3. Accentuate the difference between day and night.
4. Make sure the baby is really crying before picking them up (and do not pick them up when they only whimper).

At three weeks, if the baby was growing well, the following instruction was added:
5. If the baby wakes up and cries between midnight and 5AM, try reswaddling, patting, diapering and walking. Only if after trying these things the baby is still crying, offer a feed.

It worked for the babies in the study!

The results were very clear. The babies in the experimental group learned to sleep through the night. When they were eight weeks old, all 13 babies in the experimental group (100%) slept through the night at least two nights of the three nights that the sleep diaries covered. This was true for only three out of 13 babies in the control group (23%). The researchers found no differences in total milk intake or weight gain between the two groups.

Pinilla_LongestSleepBout.jpg

What I did

I was inspired by the clear results and the simple protocol that was used in the study. Other sleep-through-the-night plans I had previously read about included very strict day-time routines, which I didn’t want to stick to. So I decided to try to follow the protocol for a few weeks. I already didn’t hold or nurse the baby to sleep and the day-night difference was clear – so I made no changes there. I now added the focal feed between 10PM and midnight and if the baby woke up, I tried reswaddling, a new diaper and a bit of walking before I offered the little one a feed. I also tried to wait until the baby was really crying before picking her up, but I found this very hard, and I wasn’t very consistent with it. Also, some nights I was very tired, and I gave in quickly, and simply nursed the baby so that I could get back to sleep**.

And it worked for my baby too!

I started just before our baby was eight weeks old. After a week, I noticed that she was sleeping longer stretches and after three weeks, she started sleeping through the night consistently. She has done several nights of eight hours already (she gets her night feed at 10PM and sleeps till 6AM). I am stoked! I had no idea that this was possible, and it wasn’t even hard!
Thank you Dr Teresa Pinilla and Dr Leann L. Birch for writing that paper 23 years ago! If I manage to write a paper this semester, it will be thanks to you!

*To find out how much milk a breastfed baby drinks, the baby can be weighed before and after the feeding.
** This may sound like I was doing everything by myself, and that was only true at night. During the day my husband did the laundry, the cooking, the grocery shopping and most of the care for our toddler.

 

The acknowledgement section of our NSF proposal

25 Aug

A few weeks ago two colleagues and I submitted an NSF proposal. We submitted on a Friday afternoon even though the deadline wasn’t until Tuesday! I am proud that we managed this almost without any deadline stress!

I had fun and we wrote a great proposal

I know that we may not end up getting funded by NSF, but until we get that message, I plan to be very optimistic. We wrote a really neat proposal for a great project. I can’t wait to get started! The ambitious goal of the project is to determine the fitness cost of every possible point mutation in the HIV genome in vivo.

I think nobody likes to write proposals when the success rate is only 5%, but I actually enjoyed working on this proposal and I learned a lot while writing it: both about the biology of our project and about the art of proposal writing. It’s important for me to commit that to paper (OK, screen) so that if NSF decides not to fund us, I will remember that writing the proposal was actually a good experience.

Writing with a newborn

In addition the many scientists and administrators who contributed to the proposal, I also want to mention how I could write a proposal with a newborn. We started working on the proposal two weeks before I gave birth and we submitted the proposal when our baby was just shy of seven weeks old. The hours that I spent on the proposal were made possible by my mom who flew in to help and by the fact that Facebook gives new parents four months paid paternity leave so that my husband was also at home during my maternity leave. It was fun to be home together with my husband and we took shifts working and taking care of Maya. Most days I worked on the proposal just two or three hours, so a large part of the work was done by others.

HomeOfficePleuni

Me in my home office with baby, changing table, a laptop and a grant writing handbook.

It was a huge team effort

Many people were involved in writing the proposal. Many more than I ever expected to be. I want to list them here so that I remember who helped out and also to show that being a researcher doesn’t have to be a lonely affair.

Note that these people are only the people I am aware off. Others certainly helped my co-PI Adi Stern.

The main team that wrote the proposal consisted of four people:

  • co-PI Adi Stern (Tel Aviv)
  • postdoc Marion Hartl (SFSU)
  • professional grant writer Kristin Harper
  • myself

At SFSU, people from the Office for Research and Sponsored Programs helped:

  • Rowena Manalo
  • Raman Paul
  • Michael Scott
  • Jessica Mankus
  • Uschi Simonis (vice-dean for Research)

At Stanford there were

  • co-PI Bob Shafer
  • collaborator David Katzenstein
  • Elizabeth White (Katzenstein lab)
  • Holly Osborne (Office for Sponsored Research)

In Tel Aviv

  • Office for Sponsored Research
  • Adi Stern’s lab members brainstormed ideas
  • Maoz Gelbart help with ideas and figures

Colleagues who read earlier versions of the proposal

  • Sarah Cobey (U Chicago)
  • Sarah Cohen (SFSU)
  • Alison Feder (Stanford)
  • Nandita Garud (UCSF)
  • Arbel Harpak (Stanford)
  • Joachim Hermisson (U Vienna)
  • Claus Wilke (U Texas Austin)

A huge thank you to all these amazing people! I am lucky to be part of such a supportive community.

team-451372_960_720