bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

GATK – why it matters

UPDATE 7th April 2015: the licensing of GATK to commercial partners will now be carried out directly by Broad, Appistry not involved

I realised I was writing a poorly structured rant, and so instead of writing this really long, angry, idiotic blog post, I’m going to put a list of (short) bullet points.

This post is about GATK and the news that commercial entities will require a license to use the software.  This is why I feel that the licensing of GATK to commercial entities is bad:

1. Bioinformatics is special

In fact, it’s amazing.  More often than not, we completely open our code, and let anyone use it for any purpose.  This is awesome.  It means our methods are there for anyone to examine, in all their visceral glory/ugliness.  No other scientific method is as open to scrutiny, which is a fantastic achievement.

2. We give away our competitive advantage

Because we adhere to (1) so much, we are giving away our competitive advantage.  This benefits science immensely.  Instead of those fantastic methods sitting in the hands of the few that developed them, they are now available for everyone to use.  I’ll say it again: this benefits science immensely. It happens far less so in the lab.  Lab techniques are published, yes, but stories of others being unable to reproduce results are common.  Lab techniques can be poorly described, or crucial details left out.  Not so in open-source bioinformatics.  We do something amazing that allows us to crunch data in a way that noone else has ever been able to do – and then we give it away.  So that everyone can benefit from it.  Just stop and think about that for a second.

Seriously, it’s incredible that we do this, and I want to protect it.

3. Commercial science is not bad science

We need commercial entities doing science.  It’s easy to sit in our academic ivory towers and believe we are some kind of benevolent force of nature, carrying out science for the good of humanity, and that commercial science is of a lower order.  It’s not true.  We need commercial companies, we need drugs and treatments, and disease resistant crops, and we need men and women who are driven by money and commercial success to develop them.

Commercial entities create jobs, they employ our friends and family, they drive the economy.

There is absolutely nothing wrong with academic science publishing code that benefits commercial companies.  And there is nothing wrong with us doing that freely, with no expectation of a return on our efforts.

Just as we are doing good by giving our papers and our code freely to the public, we are also doing good by giving our code and papers freely to commercial companies.

4. Not all commercial companies make $billions

This is fairly obvious.  Sure, you might think that GSK or Roche can spare a few $1000s to buy a GATK license, but others will be small start ups, spin outs, people who are just trying to get ahead, trying to make a living.  Small companies with just a few employees, trying to make a difference in a competitive market.

Why should we not let them benefit from our algorithms in the same way academic science does?  If they end up curing a disease, then we have all won.  Humanity has won.  And if they make a little money out of that, is that a bad thing?  No.

5. Broad’s current model won’t work

Currently, academic institutes who collaborate with a commercial entity will not need a license to do so.  This will change, rapidly.  It has to.  Otherwise every single commercial entity will simply partner up with an academic to avoid the license fee.  When Broad realise this, they will change the license.  Again.

6. Support is not the issue

The stated problem is that supporting commercial entities was becoming difficult on limited resources, hence the license.  If support was the issue, then open up the code, give it away free and then charge for support.  Red Hat do this.  MySQL do this.  It works.  I have asked why Broad do not take up this model a few times, and I have not received a valid reply.

7. The role of Broad is not to make money

Their role is to carry out great science (which they do) that benefits the USA, and the rest of the World.  That’s why governments fund academic research, to do stuff that’s important that will benefit us all.

They’re not there to sell stuff.  They’re not there to make money.

You’re going to challenge me on this and say that every university has an office dedicated to the commercialisation of research.  Sure.  So spin out GATK as a software company and sell it.  See how far you get.  See how much money you don’t makeAnd then see how much everyone has failed to benefit from the process.

Ask yourself this: Why don’t the NCBI sell blast?  Why doesn’t EBI license Ensembl?  Why didn’t Sanger sell BWA to companies?

Because it’s not their job to sell stuff.  It’s their job to carry out science that benefits everyone, commercial companies included.

And yes, I’m aware that WUBLAST was commercialised: http://www.advbiocomp.com/blast.html.

Let’s all just sit and think about what an amazing success that has been.

Update – 13:20 GMT, 28/01/2013

It has been pointed out by Daniel MacArtthur, and others agree with him, that part of the problem is start-up companies who add very little value and simply try to make money from OA software with a pretty front-end/GUI:


Whilst at first glance, this argument seems to stand up, actually if you work through the options, it really doesn’t.

Firstly, I am yet to see evidence these companies exist.

Secondly, if they can offer interpretation, customer service and data delivery through a nice web front-end – what is wrong with that?  They are still offering something Broad does not.

Thirdly, there are other options to GATK.  There are other free tools that do what GATK does.  If these companies truly add no value and are simply after a fast buck, they will just use something else.

Perhaps that is what Broad want – but why would you want that?  There are three possibilities here:

  1. The other tools are better than GATK.  Then Broad have nothing to sell.
  2. The other tools are as good as GATK.  Then Broad have nothing to sell.
  3. GATK is better than everything else.

If (3) is the case (and it’s a big, unproven “if”), then all Broad are doing is denying paying members of the public access to the best algorithm.  As I said above, if these “vampiric” companies exist solely to offer free tools to a gullible public, then they won’t pay for GATK, they’ll just use Samtools/DINDEL/SoapSNP etc etc etc.  So instead of those gullible members of the public getting access to the best data, they get access to data that is slightly less good.  The companies still exist.  The public still pays.

You haven’t changed anything except less people benefit from GATK.


  1. Agree with Mick, once open source softwares are commercilalised they might not get inputs from research community. It is like a flowing river and a stagnant water, former always has indefinite streams flowing in to recharge it whreas later may dry out.

  2. Bravo.

    To amplify point (4), small companies are able to work quickly and take commercial risks in a way that that Big Pharma can’t or won’t do. Some of the most creative and dynamic parts of the commercial sector will be hit hardest by charging for licences.

  3. Precisely. Commercialising software like this can only stifle creativity and enterprise. Should Broad, a multi-million $, publicly funded research institute, really be trying to make money this way?

  4. While delightfully terse, this post does not describe what parts of GATK are actually going to be relicensed, what the licensing fees are by usage, or exactly how charging companies implies the academic branch is black boxed.

    More importantly, what you haven’t mentioned is that the resellers themselves that have requested this closed branch because they don’t want to abide by a GPL license. You use the Redhat model but Linux is GPL – you can’t resell it without providing the source.

    Perhaps the fee is onerous – you can certainly argue that point and then we can compare it to the fees for Novoalign or Blat…or the Adobe Creative Suite.

  5. I will reiterate Daniel’s point that it annoys people to see other people becoming rich off of building a software that puts a pretty face on someone else’s intellectual work because I think you are underestimating its importance.

    It is one thing to make an intellectually rational argument that this is not a problem. It is another thing all together for the Broad to ask its employees to suck up watching, in many cases, former and more junior colleagues make more money than they are (or at least attempt to) by commercializing the work that they produced. The Broad has to be sustainable as an organization. It cannot put its employees in this position and expect to retain the best talent. It is just too damaging to morale.

  6. So I ask again – why don’t Sanger sell BWA? And EBI Ensembl? Both are sustainable operations, AFAIK.

    If the GATK developers want more money, then take the risk, go commercial and make more money. Your language use doesn’t fill me with joy – those “more junior colleagues” are leaving the very warm, very safe world of academia and entering the cut-throat world of commerce. Do people who take such a risk deserve an award? Damn straight they do. Refer to my “ivory towers” sentence. You are not better than a commercial scientist just by being an academic.

  7. I don’t think GATK was ever GPL was it? Forgive me if I am wrong.

  8. No, GATK v1 was MIT licensed.

  9. Good blog with very good points. Covers the problem well.

    Re ‘vampiric’ companies. There are many examples of proprietary products which are fancy GUIs for OSS programs, but also add a level of additional ‘sophistication’. e.g. Partek, Genomatix and CLC bio IIRC all have some internal functions which are essentially wrappers for something else. Partek and Genomatix wrap several differential gene expression algorithms written in R. They aren’t *just* GUI wrappers, but they don’t do anything you couldn’t do yourself given the right skillset, time and knowledge.

    I presonally don’t see any problem with this. Adding a GUI to a commandline R algorithm is definitely ‘value-added’ and if people are prepared to pay for it then there’s a market for it.

    As bioinformaticians we’re not paid to make nice and shiny tools which can be run by anyone, we write software which solves biological questions that are pertinent to our own needs. If they’re useful to others that’s a bonus. If someone can base a company around it, well, good luck to them.

    Choice of licencing model is a personal choice of the software author and if they choose a closed option which the academic community doesn’t feel is suitable then it will be sidelined by most and alternatives will take their place (see WU-blast vs PSI-BLAST, Quanta vs PyMol, GCG, SRS etc).

    One thing I haven’t been able to address myself is, ‘Why can’t Broad (or whoever) monetise a project to generate an income for further R&D so that they are less dependent on (hard to acquire) public funds?’ Surely, it’s a good use of public money? Is’nt it? /How/ the Broad have chosen to do this with GATK is probably the bigger issue here, than the principle. I think.

    This reply has turned into a blog post. I should have a blog… 🙂

  10. No it was MIT aka “do-whatever-just-give-us-credit license”. GPL would be an decent arrangement where everyone could benefit from the work done by resellers a la Redhat. The resellers don’t want a two-way street, but they will agree to a one-way street with tolls. Sounds fair to me.

  11. The path from a good piece of software like GATK to a software that can be used by a wet lab scientist that has designed and executed an experiment (usually over months to years) is long. The companies that “just become rich of putting a pretty face on someones else’s intellectual work” do not really exist. In fact the companies that do become rich on others intellectual work have put in a substantial amount of work too, possibly even intellectual… It might not be lines of code, but it certainly has been things without which nobody would become rich. This concept of most companies just becoming rich is a myth like the one of the eternal happiness of Hollywood actors, as pointed out by some comments here.

  12. I think if a company wants to resell a parallelized/GPU/mobile/kid-friendly/etc version of BWA then Sanger should see some of that revenue. How that is implemented is up for grabs.

  13. Well, they don’t. I can think of an example: Eagle Genomics. One of the services these guys used to offer was essentially enterprise level support for Ensembl (installation, upgrade, maintenance etc) – plus extra development if needed. I can think of one very large pharmaceutical company they provided this service to. As far as I know, EBI/Sanger didn’t demand or receive any revenue for this. Noone sees Eagle in a bad light, many of the developers are ex EBI/Sanger and they all still get along. It’s a system that has worked out for everyone.

    I just don’t *get* this frothy mouthed approach of “someone’s gettin’ rich off the back o’ my hard work”. Do you realise how clogged up bioinformatics would be if everyone took this approach?! If every company had to pay $ for BLAST, BWA, Samtools, TopHat, Ensembl etc etc etc. Sheesh. Science would be worse off. Humanity would be worse off.

  14. Sean Eddy has the right idea with hmmer – he gives it away to everyone for free under the mindset that “people who work at companies are people too.” More people should follow his example.

  15. Mick did an excellent job summarising many of the objections to the Broad’s GATK licensing changes – I touched on a few more points in my blog post about this:

  16. Hi Mick, thanks for an interesting post. These reasoned arguments are helpful to us and to the discussion in general. I’ll try to respond briefly to your points; we probably won’t reach an agreement but I think it’ll be good to see where we stand — and I expect there is actually not that much distance between us on many of those points.

    1. We agree that opening up the code to show the innards of the machine is crucial for the advancement of methods research. That’s why we reversed our earlier decision to keep some tools closed-source, which was clearly a mistake. The code will now be fully accessible to the community that drives bioinformatics methods development (ie the academic research community).

    2. I’m not sure this is entirely true in reality, because even if you share all the code, developers always retain the home field advantage to some extent, particularly for large codebases. In our case, we’re not really that worried about competition by people who would take the GATK code and outcompete us with it — as proof, the GATK framework (which represents a huge amount of code and a very powerful, valuable resource) remains completely open under the MIT license. The GATK codebase is very complex and despite our best efforts to document it, really coming to grips with it takes time, effort and a lot of one-on-one knowledge transfer. Actually, we should probably have a rule about Mark and the senior devs never getting onto an airplane together!

    3. We completely agree that there’s nothing wrong with commercial research. There’s also nothing wrong with giving your results and code freely for companies to use in their research. But I’m not sure I understand how this means that we should be compelled to give them everything for free, every time.

    4. It is true, not all companies are big powerhouses. My best friend works for a small biotech startup (here in Boston you can’t throw a rock without hitting one), and I can tell that it’s a tough world out there. They work really hard to develop the right idea, value proposition and business plan to survive, and they constantly have to prioritize resources. But they know the value of good tools & materials, and absolutely expect to have to pay for them. Now, there have been comments that the price of the single user license is too high for small outfits, and if that is the case it’s something people should discuss with Appistry (http://www.appistry.com/gatk/contact) — but saying the price is too high is not the same as saying there should not be any price at all.

    5. I have a hard time believing that “partnering up with an academic” is so straightforward; I can think of several companies’ business models that could not feasibly accommodate that. But I know very little of these things, so I’ll refrain from making any big predictions. All I will say is that this model was conceived by business development professionals, and I am fairly confident that they considered this possibility at the time…

    6. Support is a major part of the issue. You seem fairly dismissive of this point, but I can tell you as the person in charge of support for thousands of academic users, it’s not a trivial matter. The problem is that we freely offer support to anyone who asks for it. That includes anyone from commercial companies who needs help — and that adds up to non-negligible amounts of support requests. Now, we could say hey, if you are a commercial user and you want support, you’ll have to start paying for it. But what’s to stop commercial users from asking questions in our general user support forum? Should I start verifying people’s email addresses for commercial domains before I answer their questions? Then what’s to stop people from signing up with Gmail accounts and posing as academics to ask their questions? Should I draw lines and stop answering some types of question that are of more interest to the commercial folks? Won’t that impose unfair limits on non-commercial users? The pure “paid support” model only works if you’re not offering any (decent) free/open-to-all support. But we care strongly about providing the best support we possibly can to the academic research community. So to prevent our free support bandwidth from getting overloaded (and having everyone in the research community suffer the consequences), we’re drawing a line and saying that a subset of people need to subscribe to a separate service. And we’re enforcing it with the license requirement. It is true that this is probably going to lead to some commercial users being forced to pay for a higher level of service they don’t necessarily want. That is regrettable, but it is the only sustainable way for us to move forward and keep providing good service to the academic research community.

    7. True, our mission is to do good science, not make money. And we’re not expecting to make a lot of money off of the GATK. Hopefully we’ll get a little bit of revenue that we can reinvest into, you know, doing good science. But the key gain for us (and here I’m talking about the dev team) is that we’ll have offloaded all the burden of dealing with commercial users and, knowing that they are well taken care of and their needs are being met (personally, I am SO glad I won’t have to worry about providing support for CLIA pipelines and the like), we can focus on the rest of the research community that we are trying to serve.

    Re: update: I was amused by Daniel’s tweet on those annoying startups, and I might have retweeted it. But they’re really not our problem. As you say, if they’re not providing any value, hopefully the market will take them down soon enough. We might resent them a little bit on a personal level, to be honest. And we also worry how many customers will have been misled or even cheated in the meantime by bass-ackwards implementations that spit out worthless results — because whether the tools are GATK or others, implementation matters, and the no-value-added outfits are likely to be less than stellar on that front. But ultimately they are irrelevant, and not the reason we are doing what we’re doing.

    Finally, yes, we’d like to think that GATK is better than all the other tools — but we may be biased! 😉

    We work hard to develop it and ultimately we’d like everyone to use it, so we also work hard to make it accessible. We’re hoping that what we’ve changed will lead to better service for the overwhelming majority of our users. We’re sorry if some of the smaller commercial players feel like they’re being asked to pay more than is fair, and I strongly encourage them to contact Appistry (http://www.appistry.com/gatk/contact) to express that concern.

  17. What risk are they taking? They are repackaging useful software that someone else has already developed, tested, and proven useful. That isn’t innovation. It’s like Napster for genomics software, and yes, they do exist.

    I cannot imagine ANY responsible CFO, auditor, or member of a board of directors letting a US non-profit give up a potential revenue stream. It would be financial mismanagement.

    And that revenue will go back into the Broad, maybe even into the annual bonuses for the people who actually wrote the software! And if they make a little money out of that, is that a bad thing? No.

    And frankly I can’t believe that a company that can’t afford a few thousand for a license has a viable business model in the first place.

  18. “In fact the companies that do become rich on others intellectual work have put in a substantial amount of work too, possibly even intellectual…” in developing a beautiful web user interface!

  19. So I guess I don’t understand what was wrong with MIT? So the reseller wants to branch GATK, improve it and not release their updates; fine, that rules out GPL. But it sounds like MIT, BSD etc and any number of other permissive licenses would allow the reseller to take GATK and do whatever they like.

  20. It is OK to agree to disagree, and this is what we will do 🙂

    My final point is just to ask you to think about what bioinformatics would look like if all the big centres did this – if Sanger, BGI, WashU, Baylor, EBI, JGI etc etc – if all of them licensed their software to commercial entities. It would be horrible. It would restrict science.

    And the problem is there are 1000s of tech transfer offices around the World watching this with beady eyes – I hope you are not successful, not for any personal reason, but because if you are, then we’re all in for a hard time from, all of us bioinformaticians will have our legal departments insisting we don’t use permissive licenses, and then the entire fabric of bioinformatics will be threatened.

    It may sounds over the top, but from small acorns….

  21. Hah, indeed. I’m a Belgian, I’m all about compromise and agreeing to disagree.

    I guess I just don’t buy this vision of a dystopian future in which licensing to companies leads to paralysis. I see the potential pitfalls, but I also see good things come out of this. Much of the effort put into the commercial version involves quality assurance processes, and goodness knows a lot of bioinformatics software could use some of that. To paraphrase a hobbit, I don’t believe half of bioinformaticians test half their code half as well as it deserves.

  22. How about those of us who write GUIs around GATK and similar tools, but then release them under open-source licenses: http://stormseq.org/ 😀

  23. I agree the licensed model of GATK stinks but Geraldine had the one sentence line as to why it is needed. Clinical genomics is coming, CLIA, shops will be bigger than all academia soon and they need fixed versions, that are documented and well tested. So one could argue for the good of humanity Sanger might need to license BWA else Novoalign or similar will be the mainstay in the clinic

  24. ** while recovering from the pricing offer of Appistry ** Might I add that not all bioinformaticians working for pharma 1) have huge budgets to their disposal 2) need Appistry-level support (seqanswers will do just fine) 3) have direct commercial benefit from using GATK 4) are sometimes fighting hard to get their companies to use open academic tools versus black-box commercial software? Love the tool, will have to learn to live without.
    Opinion is my own, not my company’s.

  25. Most startups out there have less funding than academic labs and usually are more resource constrained. Some day academia will understand that

  26. I really, really, really still struggle to see how Broad see this as a good, positive move. It basically lessens the impact of GATK.

    Less people benefit and Broad get richer.

  27. There is no rule that states that support and quality and open source don’t work together. If the CLIA labs need reliable software, they will pay for commercial support, which can be done (and has been done many many times) open source solutions. The university can also benefit from that by developing the appropriate business relationships.

  28. It sounds like they are asking too much. Is the price confidential or something?

  29. “I will reiterate Daniel’s point that it annoys people to see other people becoming rich off of building a software that puts a pretty face on someone else’s intellectual work because I think you are underestimating its importance.”

    Which companies do that, though? I honestly can’t think of a single example.

  30. And as Chris mentions below, putting a GUI on top of complex software, in such a way that patients can understand the outputs, is innovation of a kind.

  31. Re: putting a GUI on top of software like GATK, I would think the point is to help clinicians run it. Helping patients understand the outputs and implications is a whole other ballgame — requiring a level of educational outreach that’s not going to be solved by pretty buttons. In the commercial space it’s what companies like 23andMe are trying to do; and if it’s done well I personally think that’s of great value to society.

    Returning to the clinicians, one worry is that GUIs make it easier to run complex software as a black box, without proper understanding of the importance of well-chosen inputs and parameter settings, which can lead to meaningless results. I see great potential value in a GUI that would be designed to make the experimental consequences of option choices more explicit rather than glossing over them for simplicity. The other worry, which is a consequence of the nature of research software, is that it’s very hard for GUI developers to keep up with frequent changes such as we make to the GATK, regularly adding and modifying arguments and functionalities. Having a stabilized/ delayed-release commercial version with less frequent changes should help a lot with that, so I would expect any GUI-adding companies to welcome the Appistry product with open arms.

  32. http://www.nytimes.com/2013/02/03/business/knomes-new-machine-to-aid-labs-in-genomic-analysis.html

    If Knome is actually marketing this Big-Ass Server™ as a revolutionary new appliance you can be rest assured they will rebrand GATK with a slew of marketing buzzwords to clinicians who are not bioinformatics savvy.

    Worse, anyone who has worked in this field can easily see that we will be stuck dealing with these proprietary kGAP-generated files for years to come. This is GenomeStudio all over again. At least one academic group that has contributed tools of significance can extract some cash up front from Knome now.

  33. The price is quite high for most small companies and even for some of the larger ones.
    I work for a small company and we sell commercial bioinformatics software. It’s not making us super rich but it does pay the rent. Any sound business tries to make 10 dollars for every 1 dollar spent. So if we can’t do this using GATK then we can find alternatives. There goes another would-be commercial licensee.
    It’s also important to note that the seemingly large companies are composed of smaller groups with tight budgets. Therefore these are compelled to use whatever is freely available or not prohibitively expensive to get their project milestones met. Another lost opportunity.
    If Broad does not seek to make a huge amount of money off GATK then they should at least be mindful of the price point that makes GATK affordable enough so that it proliferates commercially. Let’s face it its not a huge market and if you look at aligners as an example perhaps 90% of that small market use Bowtie or BWA because they are free. Those who pay for the remaining 10% know that they need that little extra in terms if features and support for a reasonable fee.

  34. I’m sorry but what price are you being quoted? I would agree $40k/yr is way too high for a small business (<10 employees). Tibco Spotfire Pro is $1000/yr per user/per client, whatever that means. Adobe Creative Cloud is $840/yr per seat, and is clearly a lot more fun to use than GATK.

  35. AFAIK (caveat: it’s not my turf) this 40k figure is several multiples of the actual price of the single-user license from Appistry.

  36. Wherd did the $40k figure come from?

  37. Twitter msg from a clinical exome service provider. Perhaps some details from Joke Reumers and Bertyz would be helpful.

  38. $40k per annum is ridiculous….

  39. Sorry guys, don’t know if I’m allowed to quote our price here. Let’s just say (and this holds in general) that working for big pharma after working in academia, if noticed prices sometimes going up an order of magnitude. And even in big pharma companies, it’s only a few people who will effectively use GATK. And I would certainly defend paying for it if the price would have been fair. We happily pay for CLCBio, which provides much more functionality than GATK and also provides company grade support. As stated before, personal opinion, not company statement.

  40. Sorry guys but I know the price but it’s not my place to reveal it on a public forum. In agreement with Joke Reumers I can say that it is above what SME or medium-sized companies can afford. We would certainly make our customers absorb that cost if we licensed it. Perhaps sequencing vendors could be offered something more favorable to ensure delivery of results processed with GATK is affordable to the end-user who can’t process the data themselves.

  41. The GATK team here at Appistry has been following this post with interest. While we don’t agree with all of the comments made, we appreciate the animated discussion and the opportunity to gain insights that we can use to improve our services. We want to set the record straight, however, about the vastly exaggerated numbers being quoted for licensing in these comments. Geraldine is correct that the number mentioned here and on Twitter is about 5x the cost of a single-user license, and our site licenses (which are scaled by organizational size and provide unlimited usage of the GATK) are on par with prices charged by other providers for similar analysis tools with “company-grade” support. I would suggest that anyone interested in licensing GATK contact Appistry directly to discuss your organization’s situation and needs, rather than acting based on the incorrect information circulating here.

  42. Trevor: Yeah, I would encourage Appistry to be as transparent as possible with regard to pricing – especially since the discussion can then be shifted away from arguing over the closed-licensing principle. IMHO, I don’t think $8k/yr/seat is unreasonable if the person in that seat processes thousands of exomes.

  43. What company out there is making a profit on a GATK with a “pretty front end”? Excuse me, but GATK does nothing of any use to someone without extensive genetics and bioinformatics training.

    Why are my tax dollars going to the Broad so they can produce a product to sell to companies? If Broad wants to sell their products they should be treated as the exact same kind of commercial entity that all of the ivory tower academics love to look down upon, because that’s exactly what it will be!

    A publicly funded organization should be allowed to only create products that the tax paying, and that includes ESPECIALLY corporate tax money, public can use free of charge.

    Broad and all other academic/publicly funded software …developers(companies) are having their cake and eating it too.

  44. Great post. Open source software for bioinformatics should be free. Other sources of revenue should be found. Sell hardware or seq data, not open software. Apple and Google give their software away for free – makes it hard for consumers to pay for already “free”/open software.

  45. Now that GATK commercial licensing is back at the Broad, it doesn’t really change much except that we won’t have to deal with the, um, hard-charging sales people from Appistry. Ironically (given the comments above about companies selling “GATK with a GUI,” making money on OA software w/o adding value), the most recent call I got from an Appistry salesperson was about exactly that – they’ve done the same thing and now are marketing the GUI they put on top of GATK… which looks a lot like the GUI from Bina, Curoverse, GenomeNext or any number of other companies who’ve done similar things, each with their own spin on why it’s not “just a GUI,” which in most cases is actually true.

  46. I always thought Broad should recover some funds for GATK but it’s obvious in retrospect that Appistry was not a good choice to with which to partner. The lack of pricing transparency was especially distasteful.

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