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Free workshop on Stan for pharmacometrics (Paris, 22 September 2016); preceded by (non-free) three day course on Stan for pharmacometrics

So much for one post a day…

Workshop: Stan for Pharmacometrics Day

If you are interested in a free day of Stan for pharmacometrics in Paris on 22 September 2016, see the registration page:

Julie Bertrand (statistical pharmacologist from Paris-Diderot and UCL) has finalized the program:

When Who What
09:00–09:30 Registration
9:30-10:00 Bob Carpenter Introduction to the Stan Language and Model Fitting Algorithms
10:00-10:30 Michael Betancourt Using Stan for Bayesian Inference in PK/PD Models
10:30-11:00 Bill Gillepsie Prototype Stan Functions for Bayesian Pharmacometric Modeling
11:00-11:30 coffee break
11:30-12:00 Sebastian Weber Bayesian popPK for Pediatrics – bridging from adults to pediatrics
12:00-12:30 Solene Desmee Using Stan for individual dynamic prediction of the risk of death in nonlinear joint models:
Application to PSA kinetics and survival in metastatic prostate cancer
12:30-13:30 lunch
13:30-14:00 Marc Vandemeulebroecke A longitudinal Item Response Theory model to characterize cognition over time in elderly subjects
14:00-14:30 William Barcella Modeling correlated binary variables: an application to lower urinary tract symptoms
14:30-15:00 Marie-Karelle Riviere Evaluation of the Fisher information matrix without linearization in
nonlinear mixed effects models for discrete and continuous outcomes
15:00-15:30 coffee break
15:30-16:00 Dan Simpson TBD
16:00-16:30 Frederic Bois Bayesian hierarchical modeling in pharmacology and toxicology / about what we need next
16:30-17:00 Everyone Discussion


Course: Bayesian Inference with Stan for Pharmacometrics

The three days preceding the workshop (19–21 September 2016), Michael Betancourt, Daniel Lee, and I will be teaching a course on Stan for Pharmacometrics. This, alas, is not free, but if you’re interested, registration details are here:

It’s going to be very hands-on and by the end you should be fitting hierarchical PK/PD models based on compartment differential equations.

P.S. As Andrew keeps pointing out, all proceeds (after overhead) go directly toward Stan development. It turns out to be very difficult to get funding to maintain software that people use, because most funding is directed at “novel” research (not software development, research, which means prototypes, not solid code). These courses help immensely to supplement our grant funding and let us continue to maintain Stan and its interfaces.


  1. Anonymous says:

    If you guys want to raise some real funds, you should really be doing this in Cambridge Mass.

    • We’re totally open to doing these all over the place. We’re also doing many of these basically for free, like Daniel’s course in Alaska for the ASA chapter and for relatively small donations to NumFOCUS, like Daniel’s and my course at Vanderbilt. And we’re trying to hit up conferences for tutorials, but those don’t pay well. We have some support through Sloan to do this kind of outreach (by which I mean things that aren’t really net positive on cash flow for the project).

      But we’ll definitely be doing something like this in the Boston area, probably early next year after Michael and I are back in the NY area. And probably something in the San Francisco area.


    What about donations?

  3. Rahul says:

    Just a thought: Can you guys put a “price” on Stan or maybe a Stan license but yet offer it for free downloads.

    That way if someone anyways has a $500k project he can easily (voluntarily) show a project expense and pay you $10,000 for a license or whatever. Or maybe there ought to be a varying at choice price.

    Is this possible to structure the right way?

    I know one could always donate but you cannot show a “donation” from a grant. But you can show a license purchase. (Unless the auditor came after u to ask why u paid for something that was free! )

    • If it’s varying at choice, it’s hard to justify to a grant or a project manager why you chose some outlandish number like $10,000. On the other hand, it’s pretty easy to justify “I have to attend this 3 day seminar to find out how Stan works”.

      Feature bounties could be useful. Get people to pledge X dollars when Y feature is implemented. I just hope they are able to continue to find funding, because they’ve been SUPER productive and have produced a FABULOUS piece of software, documentation, and community of people working with the software.

    • We can offer some kind of support, but we’d rather keep to our open-source model where we try to support anyone and everyone for free. The best thing people can contribute is time to help out.

      A better approach is to put us on grants as contractors or co-PIs. That ties into what Daniel Lakeland proposes. We have had various deals with companies like Novartis to add functionality to Stan (that’s where our initial ODE solving capabilities came from). But even better, they now let one of their employees, Sebastian Weber, contribute to Stan, and that’s been even more productive than paying us.

  4. Oh, and I believe there’s a Stan conference in the works for early 2017. I haven’t been involved in planning it, but the first one’s going to be in NYC to make it easy on us (if not the budget of the attendees). Eric or Daniel may chime in with details if a date’s been set.

  5. Shravan says:

    I’m looking forward to attending this three-day course, although I don’t know anything about pharmacometrics (I’ll read up on it in advance).

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