In defense of science

28 Jan

I (Pleuni Pennings) endorse the following, which was drafted by Graham Coop (UC Davis), Michael Eisen (UC Berkeley) and Molly Przeworski (Columbia):

We are deeply concerned by the Trump administration’s move to gag scientists working at various governmental agencies. The US government employs scientists working on medicine, public health, agriculture, energy, space, clean water and air, weather, the climate and many other important areas. Their job is to produce data to inform decisions by policymakers, businesses and individuals. We are all best served by allowing these scientists to discuss their findings openly and without the intrusion of politics. Any attack on their ability to do so is an attack on our ability to make informed decisions as individuals, as communities and as a nation.

If you are a government scientist who is blocked from discussing their work, we will share it on your behalf, publicly or with the appropriate recipients. You can email us at

If you use this email address, here is a PGP public key for PGP encryption:



Correction to eLife paper published

24 Jan

We just published a correction to our 2016 eLife paper.

While we were preparing the code to share it on Github, we discovered an error in calling drug resistance mutations (DRMs) in the protease gene in 140 sequences in our dataset (out of 6,717 sequences). The mistake was related to how R reads in data using read.table(). Even though the error only affected 2% of the sequences, it affected all downstream analysis and multiple figures had to be updated to reflect this correction. The resulting changes are minor and do not substantially change the conclusions and in some cases make them stronger.

When the analysis is updated with new numbers for these 140 sequences, all of our conclusions hold qualitatively, although the points in some figures shift slightly quantitatively. In fact, updating to the correct DRM calling for these sequences results in estimates for two treatments that are more in line with the expectations laid out in our paper.

As an illustration of this effect, we show here a version of Figure 4, which appeared in the paper (although has been slightly altered here for readability), and the shift of the model coefficients after correcting the 140 sequences of DRM calling. As you can see, the shifts are minor in most cases, and only serve to strengthen our conclusions for two of the PI treatments (points in the middle of the figure in light blue).


Figure 4, from the paper (slightly altered here for readability) shows the shift of the model coefficients after correcting the 140 sequences of DRM calling. The shifts are minor in most cases, and only serve to strengthen our conclusions for two of the PI treatments (points in the middle of the figure in light blue).

After finding the original mistake, we spent a lot of time going through all of the code for the paper and found a few other small mistakes in the description of the analysis. In all cases, the mistakes were minor.

The eLife editors and staff were very helpful in the entire process.


Feder, Alison F., et al. “More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.” Elife 5 (2016): e10670. Link.



Happy holidays from the CoDE lab!

20 Dec


PINC students teach coding to middle school girls

28 Nov

Promoting Inclusivity in Computing (PINC)

Three PINC students (Kimmie Richardson-Kubitsky-Tsui, Darleen Franklin and Olivia Pham) and Kadie Williams from the CoDE Lab taught a coding workshop for middle school girls as part of the  Expanding Your Horizons day at SFSU. 

The girls learned to make an app for an Android phone.


View original post

Lab member Dwayne Evans wins ARCS scholarship

18 Nov

Dwayne joined the lab in 2015 and works on drug resistance and Prep (a drug that prevents HIV infection). He is now an ARCS scholar! Congrats, Dwayne!

The ARCS website writes about Dwayne: An MBRS-RISE (Research Initiative for Scientific Enhancement) and Genentech Dissertation Scholar, Dwayne’s research interests include the evolution of drug resistance in the Human Immunodeficiency Virus type-1 when exposed to Pre Exposure Prophylaxis (PrEP). At SFSU, his research is focused on determining whether PrEP increases the number of patients with drug resistance. Dwayne plans on pursuing a Ph.D. in bioinformatics and continuing to study the relationship between HIV drug resistance and patient infection rates. Aside from research, Dwayne enjoys mentoring undergraduates, learning R programming language and teaching locking choreography in dance classes.


Dwayne Evans, Code Lab member since 2015, at the ARCS scholarship dinner. 


Code Lab walks to Fort Funston

23 Oct

Our campus is close to the ocean, but we are usually too busy to take advantage of that.

Last week we took the afternoon off to walk to Fort Funston.


Members of the Code Lab at Fort Funston. 

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

15 Oct

Being A Better Scientist


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…

View original post 116 more words

%d bloggers like this: