PolITiGenomics

I just added the WordPress Mobile Pack plugin to the site. When browsing from a mobile device, you should get a small-screen friendly view (and you won’t see the video below).

If you are at all interested in a government of the people, by the people, and for the people, the presentation below by Lawrence Lessig is well worth the 18 minutes.

Monya Baker recently published a Technology Feature in Nature Methods that discusses the use of cloud computing in genomics. I, along with several other people in the genome informatics community, were interviewed for the article. Until I saw the picture of Vivien Bonazzi in the article, I did not know she played guitar. I guess next time I am in DC I’ll have to challenge her to a guitar duel.

(Note: the video above is just an amusing example of a guitar duel, it is not intended in any way as a comment on Vivien’s or my personality. Vivien is great and me… well, you may have a point there. It is also worth noting that Bobby is not actually playing the “Holy Trinity of Rock ‘n’ Roll”, E-A-B. The chords being played are E-G-A E-G-B♭-A E-G-A-G-E. The older among us will recognize that as the same progression as the main riff from Deep Purple’s classic rock anthem Smoke On The Water.)

Over at Informatics Iron, Matthew Dublin states in his summary of the article that I want to bring everyone “back to square one” because I say that the solution to the computing challenges in genomics will likely involve a mixture of internal and external resources. The current reality is that most people are currently using local resources and, as those resources become more and more underpowered compared to their needs, they will extend their workflows to leverage external resources as well. In other words, researchers are not likely to scrap their current computing infrastructures and migrate entirely to the cloud when their computing needs grow beyond their existing resources. Hopefully by the time most people need to spill over into external resources middleware systems will exist that intelligently schedule jobs to appropriate computational resources, internal or external, with a minimal amount of job metadata from bioinformatician submitting the job.

Here’s a video hint for those who do not understand the reference in the title of this post.

Political commentators play the blame game. Don’t worry, it’s really no one’s fault.

Here a cool video from DNA: The Secret of Life detailing (in real time, just like the PacBio RS!) the central dogma of molecular biology.

Whenever you get asked about a recent genome publication or the latest sequencing technology, the conversation invariably turns to cost. It turns out, cost is a tricky thing. When people talk of the “cost” of the Human Genome Project, they typically quote the cost for the entire project. A cost that includes sequencing instruments (several revisions), personnel, overhead, consumables, informatics, and IT. They contrast this rather large cost to the much lower cost of the $10,000 or $1,000 genome. However, in reality that “$10,000 genome” costs more than $10,000 (same goes for the $1,000 genome). You see, when people talk about the $10,000 genome, they are only accounting for the cost of consumables: flow cells and reagents. Perhaps this focus on consumables has its roots in the days of the Human Genome Project when reagent (BigDye^®) costs dominated sequencing costs. Perhaps the focus is driven by marketers at the sequencing instrument companies who want to draw attention away from the six-figure sequencing instrument costs. Perhaps this focus is driven by the $10,000 recurring cost number specified by the Archon X PRIZE for Genomics, which receives much more attention than the $1 million direct cost cap. Regardless of the reason for the focus on consumables (likely some combination of all of the above), the reality is that consumable costs have fallen much more rapidly than any other cost associated with genome sequencing and can no longer be the only number quoted when stating the cost of a genome; at least if you want that number to actually mean anything.

So, what other costs should be considered? Well, the types of costs and actual values will depend greatly on your situation. Will you be doing the sequencing or will you be contracting at a core facility or sequencing-as-a-service company? Will you be doing the analysis or relying on a third party? How will you be validating your results? How many people will be working on the project at what percent of their efforts? Will you buy everyone a Pet Rock when the project reaches 1 exabases of sequence?

Here I’ll run through a standard cost calculation for a typical academic sequencing and analysis center to sequence and analyze a human genome. The names and costs have been changed to protect the innocent (this means I chose nice, round numbers that are the right order of magnitude). Why not use real numbers? Read the previous paragraph (I’ll wait …): your cost factors and numbers will not be the same as anyone else’s. So you’re going to have to do the calculation for yourself, not just lift the numbers from this post.

First we can consider the consumables (e.g., flow cells and reagents) costs. Let’s say those are $10,000. Then there is the instrument depreciation. Let’s say the instrument costs $600,000, has an expected life of three years, and can do 40 runs per year. Assuming a straight-line depreciation, the instrument depreciation per run is $5,000 (= $600,000 / (3 × 40)). If the instrument supports two flow cells, you would divide the number in half to get $2,500. Now, the DNA doesn’t just hop on the sequencer by itself. DNA has to be acquired, consents signed and approved by institutional review boards (IRBs), and sequencing libraries have to be made. Let’s say sample acquisition costs $100,000 for 50 samples; that’s $2,000 per sample. Shepherding the project and consents through the IRB takes one full-time employee (FTE) at 10% effort one month. We’ll say the cost of one FTE (salary, benefits, etc.) is $60,000 per year. So getting the project through IRB approval costs $500. If the project is able to use all 50 samples, that’s only $10 per sample! If the consumables and personnel time to make a sequencing library is $200, then the total production cost for sequencing our human genome is $14,710. Wait, I forgot the IT and LIMS support! In this scenario we’ll say that each instrument needs one IT FTE and one LIMS FTE, each at 25% effort ($750). And you need disk space for the data ($1,000, you can cut that in half if you throw away everything but the sequence, qualities, and alignments) and compute time ($100) to run alignments and QC. Add to that 50% overhead charges that your institution takes to cover administration, utilities, lab space, etc. (a company would need to determine each of these costs and add them in rather than this overhead multiplier) and your $10,000 genome costs you nearly $25,000. And you haven’t even called a variant yet.

Speaking of variants, let’s assume you want to call SNPs, indels, and structural variations. The first thing you will have to do is align your reads. Let’s say you are efficient and simply use the alignments from the production QC step. Above we assumed $100 for these alignments, but what goes into that number? First you have to determine an average alignment time per genome. Let’s say 90 Gb of sequence (30× coverage of a human genome) in 2×100 base read pairs takes 1,000 core×hr to align to the human reference genome. If you did this on Amazon EC2 ($0.17/core×hr), it would cost you $170 (plus data transfer and storage costs). If you have your own cluster, you need to amortize the cost of your cluster (compute nodes, racks, networking equipment and cabling, PDUs, etc.) per core×hr, add in the cost of your administrators per core×hr, and utilities or overhead per core×hr to get your cost. When you do that calculation, let’s say you get $0.10 per core×hr, so the alignment costs you $100 (but you already paid it above). Merging the BAM files from each lane’s worth of data and marking duplicates takes 50 hours, costing $5. Calling SNPs and indels (including reassembly) takes 100 hours, costing $10. Detecting structural variation using aberrant read pairs takes 200 hours, costing $20. Annotating all the variants across an entire genome takes 100 hours, costing $10. The disk space for all of this costs you $1,000 (again, you’ll need to calculate a cost per GB factoring storage, racks, switches, servers, personnel, etc. to get this number). Finally, somebody needs to run (or automate) this analysis pipeline. Figure that one analyst and one developer each at 10% effort can accomplish this over the course of two weeks; $480. Add all this up and your analysis with overhead runs you about $2300, or about 10% of the cost of generating the data. Of course, human resequencing for variant detection is not the only application of sequencing data. Other types of analysis, e.g., de novo assembly and metagenomic analysis, can have significantly higher costs per base. For example, in metagenomic analysis you may want to classify reads that do not align to known sequences by aligning them in protein space against a database like NCBI nr. If you generate 10 Gb of sequence per sample and 25% of the read pairs do not align to anything else, you will need to align 12.5 million reads. If you use the most common tool for this sort of alignment, NCBI BLAST+ blastx, it would take over 5,500 core×hr, costing about $550 by itself.

Now that you have your sequence data and list of variants, you are going to need to validate them. There are a lot of different ways to validate variants, e.g., PCR, pool, and sequence or Sequenom, so I am not going to go through a detailed cost calculation. It suffices to say that, depending on the number of variants you want to validate, the cost can rise into the thousands of dollars. Whatever platform you choose, you will need to go through a thorough cost calculation (like the one done above for the original sequencing and analysis). For the sake of this post, which is already too long, we’ll say the validation cost is $2,000.

Finally, somebody has to be running this show. Let’s say project management personnel costs $20,000, or $400 per sample. Put this all together and your $10,000 genome costs about $30,000. In other words, the often quoted consumables number only accounts for about 50% of the total cost (Note: overhead applies to consumables also, so while $10,000 looks like 1/3 of $30,000, it is actually half). Again, none of the numbers I use above are real (but they are in the ball park) and all sequencing and analysis facilities are going to have different contributors to their costs resulting in varying contributions from consumables. However, regardless of the cost contribution of consumables at present, the cost of consumables are projected to fall below $5,000 by the end of this year, and they won’t stop there. As such, it is already meaningless to only quote consumable costs when stating the price of sequencing a genome. By the end of the year, it will be ridiculous.

Update: Clarified Archon X Prize cost accounting.

The same news commentators who defended the previous administration’s shortcomings now use those same incidents to label the current administration’s difficulties (starting at about 5:00). So are they now saying that the previous administration had failures, or that the current administration is handling them well? I suppose what they are really saying is that there are limits to their powers of persuasion (“Rosebud!”).

Lawrence Lessig uses Sen. Scott Brown’s (R-MA) inability to explain why he opposes the financial reform bill as further reason that the way we fund elections (or, rather, politicians) needs to be reformed.

Scott Brown, Massachusetts’ new senator, opposes legislation in Congress that would strengthen regulations for Wall Street.

But when a reporter recently asked him why he’s against this bill, Brown couldn’t give an answer. He’s against financial reform, but he has no idea why.

Let me help Senator Brown: During his campaign last year, Brown received half of his campaign contributions from Wall Street and business executives. He benefited from another million dollars in issue ads by the U.S. Chamber of Commerce. They oppose the bill, so Senator Brown opposes the bill. It’s no wonder Pew recently found that trust in Congress is at its lowest point ever.

I focused on Scott Brown, but the influence of special interest money pervades both parties in both chambers. Americans are right to suspect that their representatives are merely doing the bidding of those funding their campaigns.

Last week, I recorded a new episode of the Change Congress Chronicles, talking about Scott Brown, the economy of influence in Washington, and the path to reform. Take a few minutes to watch, and then please share it with anyone you know who is fed up with our electoral system:

Congress can fix our campaign finance system right now by passing the Fair Elections Now Act, which would create an opt-in system of citizen-funded elections. But to get this bill written into law, we must build enough grassroots support so that Congress has no choice but to listen.

Whatever your party affiliation, whatever change you seek — it won’t happen until we Change Congress.

So head over to Fix Congress First and take action.

A previous cloud post, Puff piece, has gotten a bit of attention from Jason Stowe and Informatics Iron. While the Informatics Iron piece was positive, Mr. Stowe took issue with some of the points I made. First, he says that my claim that IT and software engineering is needed to get things running on the cloud is inaccurate.

You are implying that to get running in the cloud, an end user must worry about the “IT expertise” and “software engineering” needed to get applications up and running. I believe this is a straw-man, an incorrect assertion to begin with.

One of the major benefits of virtualized infrastructure and service oriented architectures is that they are repeatable and decouple the knowledge of building the service from the users consuming it. This means that one person, who creates the virtual machine images or the server code running the service, does need the expertise to get an application running properly in the cloud. But after that engineering is done once, a whole community of end-users of that service can benefit without knowledge of the specifics of getting the application to scale.

For example, does everyone that uses GMail/Yahoo/Hotmail know every line of software code to make it run? Do they know every operational aspect of how to make mail scale to tens of thousands of processors across many data centers?

Definitely not, and the point is they don’t have to. The same is true for high performance and high throughput computing. To give examples of free services that don’t require end user software engineering or IT expertise to do bioinformatics/proteomics/etc.:

• The NIH Website for BLAST has, for years, been running BLAST as a service so that researchers can use GUIs to run queries on parallel back-end infrastructure (see http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9606) This requires no complicated knowledge or software engineering for scientists to run BLAST as a Service.
• Tools like ViPDAC have 2-minute tutorial videos to run proteomics on Amazon Web Service.

His argument is absolutely correct when dealing with established systems, applications, and work flows. For use cases like email and running BLAST, there is no need for additional software engineering or IT expertise (other than getting on the internet). In fact, The Genome Center has long offered a BLAST service for anyone to use. Further, over the past few weeks, several prepackaged bioinformatics work flows that run on the cloud (or some approximation thereof) have been announced: Mr. Stowe’s company Cycle Computing announced CycleCloud for Life Sciences, GenomeQuest SDM, Cloud Bio-Linux from Bio-Team, ChIP-seq and RNA-seq analysis pipelines from DNAnexus, the work flows available in Galaxy, and of course the previously published Crossbow. Unfortunately, canned analyses are not the norm in bioinformatics. Bioinformaticians love to tinker, trying to get just a little more biological information out of their data sets. The result is that bioinformatics applications and work flows are constantly being tweaked, updated, and improved. Because of this, maintenance of these pipelines is a huge burden. The supporters of these generic pipelines must work constantly to update and verify software or the users will constantly be waiting for the latest fix to be applied or latest feature to be available (anyone who installs each new version of velvet can attest to this). The saving grace in all of this is that as the use of sequencing becomes more widespread, the percentage of the people doing the analysis that classify as bioinformaticians will decrease (greatly). This means that a larger and larger percentage of people with sequence data to analyze will likely not be interested in tweaking analysis pipelines but will just want to run something and get an answer. It is this ever growing group of people that will greatly benefit from easy to use analysis tools, whether they be deployed on the cloud or not. Both Mr. Stowe and I agree that creating easy to use tools for non-bioinformaticians to use is a very worthwhile goal. Unfortunately the proliferation of existing tool options (e.g., maq, bwa, bowtie, bfast, soap, novoalign, etc.) now layered with a proliferation of cloud offerings will make it even more difficult for non-experts to chose which pipeline is the best to use. Therefore approaches like those taken by Cycle Computing and GenomeQuest that provide default analysis pipelines and the ability for bioinformaticians to create and share their own work flows are the most likely to be successful. The development of these generic, distributed analysis frameworks that also provide useful defaults is an even more worthwhile goal because it achieves two important ends: ease of use for non-experts and the ability for bioinformaticians to tinker. Bioinformaticians are more likely to find tools like these useful and therefore will be early adopters, choose the best platforms, establish best-practices on these platforms, publish results using these platforms, and then the non-experts will follow.

Mr. Stowe’s other objection related to my point that no process scales linearly with the number of cores. He concedes that point but points out

In fact, regardless of whether the job is linearly scalable, most companies and research institutions don’t have 1 cluster to 1 user scenarios. There are multiple users with multiple jobs each. What if you have 10 crossbow users with 10 runs to do on various genomes? Then you can get 100x performance on the *workflow as a whole*.

Again, this is true, but, to be fair, that is not the same point he made in his original article. His original point was that if you needed your analysis to run faster you could just provision more nodes. I just pointed out that this is true, but you would likely pay a premium for that because nothing scales linearly. It may seem like a fine distinction, but with all the misinformation around clouds nowadays, it’s an important one to make. It should also be noted that without good software engineering and system administration, even algorithms that should scale nearly linearly might not. The take-home message is that if someone has done that software engineering and systems administration work to make a program scale well and run well in a cloud envrionment and made it available to you, great. If not, someone is going to have to do it.

I had the opportunity to meet Mr. Stowe at the XGen Congress and have talked more with him this week at Bio-IT World Conference and Expo (my talk is tomorrow at 11 a.m. EDT in Track 3: Bioinformatics and Next-Gen Data). We had a good discussion about cloud computing and its role in bioinformatics (they’ve got a cool solution to the Amazon storage problem). As you can hopefully tell from this post, we are largely in agreement: engineering is needed, but once it is done, everyone benefits. Cycle Computing certainly has a lot of good expertise in the cloud, so if you need some engineering done, shoot him an email. Unfortunately, they probably will not be able to help you access the largest cloud computing service.

NPR has a series this week about the current level of distrust Americans have with government. The latest installment, Americans Distrust Congress? That’s No Surprise, ties some of the low opinion of Congress to the highly partisan rhetoric. What the story hints at, but does not state explicitly, is that partisan rhetoric is a positive feedback loop. Those who pay attention to politics, and therefore fund campaigns and watch political shows, tend to be more partisan. This encourages politicians and political pundits to be more partisan (to increase their base/donations and viewership, respectively). This in turn gives credence to and reinforces those more partisan views of their constituents and viewers. Unfortunately, the articles fails to mention the fact that all of this partisan rhetoric is mere theater; a means to get elected and re-elected in perpetuity. It is a means to distract the general public from the fact that partisanship only exists on the fringes of the political debate. Both parties are happy to do the bidding of the same lobbyists on issues that actually matter.