News from the Fraser Lab

On being quoted in the NYT, Preprints, and Beer (and Tacos)

James Fraser
16 March 2016

At the ASAPbio meeting, I talked about the importance of building a lab culture as a junior faculty member. Two of the most important things about the culture we are trying to build in the Fraser lab are: 1) we have high scientific standards and 2) we enjoy communicating our results. Preprints help us with both. We set a high standard by showing the world our results when we are ready by posting a preprint, not after weeks or months in review. We also do this because we hope that other scientists will give us feedback and build on our work. We celebrate posting the preprint (which we do simultaneously upon submitting to a journal, but more on that later) because we want to congratulate each other on the hard work that went into the paper. Preprints return the control over both of these important aspects of culture to us, the scientists.

In articulating these aspects of our lab culture, I also mentioned our lab motto: Beer and Tacos. Now that this phrase has made the New York Times, I thought I might explain the history of “Beer and Tacos”. My attraction to this phrase has its origin, like many of my scientific interests, in baseball statistics. In 2003 (when I was an undergraduate at McGill), Dayn Perry used the “Beer and Tacos” analogy in describing the false dichotomy between data driven analytics (sabermetrics/statistical analysis) and observational scouting (which is more qualitative). Perry’s story was in part motivated by a grumpy article written by my hometown baseball writer Richard Griffin. Although I’ve never actually confronted Griffin about it, I think I may have played a small part in Griffin’s motivation for writing the article. A few days before his article appeared, I was on the field at the SkyDome prior to a Blue Jays game filming a brief segment for the Discovery Channel Canada on baseball statistics (unfortunately, I can’t find the video online!). Griffin walked by, shook his head, and continued on his way. Griffin hated analytics and loved scouting.

At the time this was a bit of a holy war. It is dramatized in the movie Moneyball, based on the excellent book by Michael Lewis. In recent years, the value of analytics has been proven time and time again not only in baseball, but also in other sports and even in finance, marketing, etc. However, part of the reason that analytics keeps permeating more and more areas is that there is an intense drive to capture the qualitative aspects and turn them into something quantitative. It is no longer sufficient for a scout to say that an outfielder “tracks the ball well”. This skill wasn’t captured that well in 2003 by simple counting statistics like range factor, but now we can plot the actual path the player takes to determine whether he takes the most efficient route to the ball. What does “beer and tacos” mean? Dayn Perry said it best. In responding to Richard Griffin and others who argued that organizations such as the Boston Red Sox, run at the time by Theo Epstein, should focus less on stats and more on scouting, Perry wrote:

“Grumps like Griffin don’t understand the concept of synergy. A question that’s sometimes posed goes something like this: “Should you run an organization with scouts or statistics?” My answer is the same it would be if someone asked me: “Beer or tacos?” Both, you fool. Why construct an either-or scenario where none need exist? Heady organizations know they need as much good information as possible before they make critical decisions. Boston under Epstein, for example, is a veritable clearinghouse for disparate ideas and perspectives, and so far it’s working just fine.”

From 2005-2010, I was in graduate school at UC Berkeley. When my graduate advisor, Tom Alber, would suggest multiple experiments during group meeting, I would often yell out “Beer and Tacos” from the back of the room. The idea being that we shouldn’t prioritize only experiment A or experiment B, but that we should probably consider doing both. In 2011, when I started my lab, I continued shouting “Beer and Tacos” in my own group meetings at UCSF. We want to create “a veritable clearinghouse for disparate ideas and perspectives”.

Now we come to publishing. People like Mike Eisen argue for BEER (only immediate publication/preprints and post publication peer review/PPPR) and people like Emilie Marcus argue for TACOS (only traditional journals, unless you have a special “wink wink” agreement). The system is evolving. It’s clear that “journals only” is not going to be the future. The delays and politics around “formal peer review” can be detrimental to our goals as scholars. However, many of the trends on how journals are coordinating peer review are all about openness, speed, and scholarship. It’s also clear that journals can add value, even beyond the obvious benefits in coordinating peer review: reading the table of contents is (surprisingly) the nearly exclusive way that many scientists become aware of work outside their lab. Becoming aware of papers in this manner is not the ideal system in the long term, but it does add value today. The exact pairing of preprints and journals is in flux - but there is wide agreement that we value scholarship and rapid communication of results.

As we debate exactly what type of beer we will be drinking in the future and what filling should go in the taco, my lab cares about getting our work out there as quickly as possible and ensuring that it reaches the widest audience possible. So we ignore shouts for “Beer OR Tacos” and choose “Beer AND Tacos”. When we post preprints, we are happy about getting our work out there immediately, we are eager to improve the work through peer review in any form, and we are hopeful that eventually publishing in a traditional journal will help it find an audience. And so we go to celebrate, as a lab, by ordering “Beer and Tacos”.

Summer's Gone

James Fraser
23 August 2015

almost… it’s been a bit too long since we updated the website:

  • Erin joined the lab!
  • Lin came back from parental leave!
  • Andrew completed the Insight Data Science program!
  • Alex and Pooja rotated!
  • Saul was a great SEP student!
  • Jennifer did great lab work and updated the lab cartoon!
  • We published a bunch of papers!
  • Joslyn got promoted and Eleanor took over our admin responsibilities!
  • and we started planning for this year’s version of PUBS

Welcome new UCSF Faculty Fellow Joe Bondy-Denomy

James Fraser
12 May 2015

A warm welcome to new UCSF Faculty Fellow Joe Bondy-Denomy. Joe was a graduate student with Alan Davidson at University of Toronto, which is also the lab that gave me a start in science as an undergraduate. The Bondy-Denomy Lab builds on his groundbreaking discovery of naturally occurring anti-CRISPR proteins that antagonize the CRISPR systems that are all the rage in genomics. Welcome Joe!

Welcome Joe Bondy-Denomy

Spring quarter has sprung

James Fraser
22 April 2015

A belated welcome to our new rotation student Eugene!


And farewell to Erin and Evan who have moved on to their final rotations in the Gestwicki and Frost labs, respectively…

We are apparently on a roll of rotation students with first names that start with the letter “E”…

EMRinger: a side-chain-directed approach to study model-to-map agreement in cryo-EM

Ben Barad
18 February 2015

For the past year, I have been working in the Fraser Lab on developing an analysis framework, which we call EMRinger, for doing model-to-map validation in the burgeoning field of near-atomic-resolution single particle electron cryomicroscopy (cryo-EM). We recently submitted our paper for review; at the same time, we preprinted it in bioRxiv and open sourced the code. We hope that even as the article undergoes the peer review process, the tool will be available for scientists hoping to get an independent metric for progress in their refinement. We also hope people will be able to start including it as a “Table 1” metric now that the code and the manuscript are available. We have already been using EMRinger with our collaborators for a few months, and we are excited to see how it gets used now that it is out in the wild!

The manuscript is the best place to get scientific details about the work, but I am writing this post to talk informally about the method, as well as the process of developing it and the preprinting experience.

The background: ab initio modeling in cryo-EM

In the past two years, electron cryomicroscopy has been able to achieve resolutions at which atomic models can begin to be inferred without any sort of crystallographic reference structure, as a result of major developments both in camera technology and computational analysis. Electron microscopy holds tremendous promise for structural biology because of its ability to solve structures with minimal amounts of protein and without needing to find conditions for crystallization. Already, it has become one of the preferred methods for solving structures of large membrane proteins and biological complexes. However, the tools for validation of structures from cryo-EM are in their infancy relative to diffraction methods, and there are different requirements for validation compared to diffraction. Our tool takes advantage of the density around side chains, the highest resolution information available, to sensitively report on backbone positioning in the map.

EMRinger - using side chain information to sensitively report on backbone position.

EMRinger Process EMRinger is named after its progenitor, Ringer, from the Alber lab at Berkeley. Like Ringer, it rotates the Cγ atom around the χ1 angle of a side chain, interpolating the density value in the map as it rotates. The angle of peak density is interpreted as the correct position of the side chain in dihedral space. Based on knowledge from performing Ringer on structures in the PDB, as well as from basic steric considerations, we know that properly modeled side chains should have χ1 density peaks at or near rotameric positions (60º, 180º, and 300º). There are two major reasons that the peak may not be rotameric: first, if there is no signal above noise from the side chain, the peak will be chosen randomly from the noise and may be rotameric, and second, if the backbone and Cβ positions are incorrect, the measured angle relative to that backbone may be reported as nonrotameric when the Cγ samples its true position. We take advantage of this second expected behavior to quantify the quality of model-to-map fit of models from cryo-EM.

Generating the EMRinger score

In order to separate the effects of noise from the effects of mispositioned backbone atoms, we implement a signal cutoff threshold for peaks, with the assumption that any side chain with a peak map value below that threshold may be sampling noise and should not be used for analysis. For the remaining side chains, we use the fraction of side chains with rotameric peaks from EMRinger as a metric for the quality of model-to-map fit.

Choosing the right threshold is a challenging question; at too low of a cutoff, peaks are coming from noise as often as from real signal, and at too high of a cutoff, very few side chains are sampled and the results are not very representative of the model as a whole. In order to balance these two considerations, we use a Zscore metric based on the null hypothesis of a random binomial distribution with 39 out of 72 bins being called rotameric.

Zscore Equation

The Z-score is a good metric that is (in our experience) always able to find an ideal threshold to maximize the statistical significance of the result. However, it is biased towards models which are larger to begin with; a 60-mer would have a score more than 7 times larger than the equivalent monomer. To account for this, we rescale the Z-score to the EMRinger Score, which is comparable between sample sizes.

EMRinger Score Equation

The maximum EMRinger score obtained across threshold is the one we use as our final metric, and our evidence (as we discuss in the manuscript) is that it is a robust but sensitive metric for model-to-map fit in very high resolution maps, above around 4 Å. The EMRinger scores of model-map pairs from the EMDB sets up a reasonable expectation for what scores should look like for well-refined structures at high resolution:

There is a strong correlation between resolution and EMRinger score. This is to be expected, given that EMRinger score reports on side chain density, which is only resolvable above about 4.5 Å. In general, for maps above around 3.5 Å resolution, the minimum score that should be expected is around 1, with a benchmark for a very good score lying around 2. Most structures which have been carefully refined, either in real or reciprocal space, score above 1.5, with some structures getting scores above 3. Just like with tools like molprobity, a bad score doesn’t necessarily mean an unusable structure, but it does warrant further consideration and refinement.

At resolutions down near 4 Å and below, things get a little bit trickier, and it is hard to make careful predictions about what the target EMRinger score should be. Sampling of the backbone by EMRinger becomes a problem at these resolutions, which can be partially resolved through B-factor sharpening. We are considering ways to modify the EMRinger procedure to make it more appropriate for use in these intermediate resolutions in the future, and I will hopefully write more about that soon!

Making EMRinger Scores Available

Since the score is straightforward to calculate and better scores are strong indicators of a better-fit model, we hope that this tool will be adopted as a standard “Table 1” metric for structures from cryo-EM, alongside gold-standard FSC resolution and Molprobity scores. To that end, we have made the tool available to colleagues as quickly as possible upon completing the manuscript: we have preprinted our work, and we have published and open sourced our code immediately.

Preprinting with bioRxiv

The first and most important thing we did to increase the availability of EMRinger was to preprint the paper on bioRxiv as soon as we submitted the manuscript for review. BioRxiv is a service maintained by Cold Spring Harbor which allows the public deposition of a manuscript before, or even entirely separately from, the peer review process. This allows us to publically share the work we have been doing without waiting for the peer review process, which has been known to take over a year before publication. Additionally, people unrelated to the official peer review process, but who have suggestions for strengthening the method, can provide commentary on bioRxiv that we can then take into account when revising our paper. The Fraser Lab has recently gotten excited about bioRxiv, and we plan on releasing many of our future papers this way. With many (most?) journals now allowing preprinting of manuscripts before peer review, there is little to lose in doing so. So far, we have primarily heard from colleagues directly about our manuscript, but we are excited to see what comments come out of the public forum available on bioRxiv.

We have been really happy with the reception of the paper on bioRxiv; we’ve had about 80 downloads of the paper in the two weeks since we submitted it. James and I have immediately become obsessed with the article metrics available on the site (particularly the altmetric). We are big twitter users and we take every chance we get to share our progress on EMRinger now that it is available in a public form. More importantly, we’ve been able to share the method directly with our colleagues, and if they want to use the EMRinger Score in their publication they will be able to cite the manuscript on bioRxiv ahead of formal publication.

Publishing code on Github

Along with making the manuscript available, we have released the code to run EMRinger on Github. We have published the main utilities to calculate EMRinger score, perform rolling-window analysis, and confine EMRinger analysis to specific residue groups, which are the main ways we have used EMRinger and expect it to be used in the near future. I am also in the process of cleaning up some of my “jiffy” scripts to generate the figures we used in the manuscript, so that the connection between the output of the EMRinger code and the figures we present is as clear as possible. We hope this will also allow anyone interested in extending the usage of EMRinger into new domains to visualize their results quickly.

I wrote the EMRinger scripts in python using the Phenix software package, which provides a whole host of incredibly nice utilities for working with structural biology data. Phenix has so far been used mostly for data from diffraction experiments, but there are an increasing number of tools available for single particle experiments, and I am hopeful that Phenix will be able to bring together experimentalists from both fields. This has the potential to develop standardization in the tools for modeling and analysis, as well as in the data formats between the two fields.

I wrote a detailed usage guide for generating EMRinger Scores in the Phenix_Scripts folder of the EMRinger github page, where the main utility scripts for EMRinger are housed. However, if you try it out, and encounter any problems that are not covered in the usage guide, or just want to discuss how best to interpret your results, I am happy to communicate by email. Please submit bug reports or feature requests on the github, and general comments on the biorxiv page!

Next steps: Phenix GUI and EMRinger Web Server

We are very happy with the Phenix python scripts on github, but in the long term we want to make our tool as universally accessible as possible, without any need to run scripts from the command line. We have been working hard on making EMRinger more accessible in two main ways. The first is putting the tool into the Phenix GUI: this effort is being driven primarily by our collaborator, Nathaniel Echols. Bringing EMRinger into the GUI will allow the rapid calculation of EMRinger scores, as well as making interactive visualization of the ringer scans possible. Since many other analysis tools, including molprobity, are accessible within Phenix, we hope that this inclusion will allow electron microscopists to do every level of model-based validation within a single software package, without needing to resort to individual scripts.

The second way we are trying to expand the availability of EMRinger is by making a webserver to calculate EMRinger scores on demand. I have been working on this as a side project for a few months, and actually got a proof of principle iteration done as part of a minicourse at UCSF with Kevin Hartman and Andrew Van Benschoten. Users will be able to upload their model and map and the webserver will return a series of visualizations as well as the final EMRinger score. I hope that this serves as the most accessible introduction possible to using EMRinger, as the only software needed will be a modern web browser. I’ll be open sourcing it as soon as I have a working prototype (soon, I hope!), and I’ll probably write another post then about the process of making a scientific webserver. There are unique scalability challenges to operating a webserver that can handle map data (which is frequently hundreds of megabytes in file size), and I hope that the solutions that we come up with will allow for a robust system for electron microscopy analysis on the web.