• Advanced Courses in Life Sciences

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Live Online Course – 1st Edition

Introduction to probabilistic inference of Phylogenetic Comparative Methods (PCM) using Julia

November 9th-17th, 2023

Live sessions will be recorded

REGISTRATION IS CLOSED

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This course offers an advanced understanding of probabilistic inference of Phylogenetic Comparative Methods (PCM), exploiting the capabilities of the Julia language. Participants will gain a deeper knowledge of the stochastic processes, their inference and computation behind PCMs as well as their biological interpretations.
We will start with an introduction to Julia language, a powerful new language for numerical computing that combines high performance with high-level syntax, attaining comparable speeds as C, yet remaining accessible to programming initiates. We will then overview probabilistic inference within a Bayesian framework, reviewing basic probability concepts and posterior parameter estimation. Finally, most of the course will then delve into the main three PCM: trait and biogeographic evolution, and a deeper emphasis on diversification models. Topics covered include basic foundations (i.e., diffusion processes such as Brownian motion, time-continuous Discrete Markov models, birth-death models) to then build-up to the more
advanced models that allow for interdependence between processes (i.e., environmental and geographic diversification, inference of biotic interactions). The course will combine introductory lectures and hands-on exercises.

Day 1. Hands-on introduction to Julia:

  • Types and elementary functions.
  • Control flow.
  • Multiple dispatch.
  • Statistical tools.
  • Integrating with shell, R and Python.
  • Benchmarking.
  • Performance.
  • Parallel computing.

Day 2. Introduction to Probabilistic Inference:

  • Probability and Bayes Theorem.
  • Model and data for probabilistic inference.
  • Maximum Likelihood (ML).
  • Bayesian inference:
    – Posterior probabilities
    – MCMC (Metropolis-Hastings)
  • Estimating parameters using ML and MCMC.

Day 3. Trait and biogeographic evolution:

  • Introduction to PCM.
  • Introduction to trait evolution.
  • Introduction to biogeographic evolution.
  • Joint trait and biogeographic evolution to infer biotic interactions (TRIBE).

Day 4. Diversification I:

  • Introduction to birth-death models.
  • Constant rate birth-death (CBD).
  • Introduction to sampling-through-time birth-death models.
  • Constant rate fossilized birth-death (CFBD).
  • Birth-Death Diffusion (BDD).

Day 5. Diversification II:

  • Introduction to multi-type birth-death models.
  • Geographic diversification (GeoSSE).
  • Environmental and Geographic diversification (ESSE).

Programming skills (e.g., R, Python, Julia) and basic knowledge of probability and phylogenetics. Prior material will be suggested and it is strongly recommended that participants become familiar with it before each lesson.

All participants must use their own computer (Windows, Macintosh, Linux), with access to a good internet connection. The use of webcam and headphones is strongly recommended.

Ignacio Quintero instructor for Transmitting Science

Dr. Ignacio Quintero
Institut de Biologie de l’ENS (IBENS)
France

Dates & Schedule

Online live sessions on 9th, 10th, 13th, 15th, and 17th of November

From 14:00 to 18:00 (Madrid time zone)

Total course hours: 26

20 hours of online live lessons, plus 6 hours of participants working on their own.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

Language

English

This course will be delivered live online

This course will be taught using a combination of live (synchronous) sessions on Zoom, prerecorded lessons, and tasks to be completed in between live sessions on the Slack platform.

Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.

Places

Places are limited to 16 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end.

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science
Greece

Fees & Discounts

  • Course Fee
  • Early bird (until September 30th, 2023):
  • 492 €
    (393.60 € for Ambassador Institutions)
  • Regular (after September 30th, 2023):
  • 576 €
    (460.80 € for Ambassador Institutions)
  • Prices include VAT
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during registration.

We offer discounts on the Course Fee.

Discounts are not cumulative. Participants receive the highest appropriate discount.

We also offer the possibility of paying in two instalments. Please contact us to request this.

Former participants of Transmitting Science courses receive a 5% discount on the Course Fee.

20% discount on the Course Fee is offered to members of certain organisations (Ambassador Institutions). If you wish to apply for this discount, please indicate it in the Registration form (proof will be asked later). If you would like your institution to become a Transmitting Science Ambassador Institution, please contact us at communication@transmittingscience.com

Unemployed scientists, as well as PhD students without any grant or scholarship to develop their PhD, can benefit from a 40% discount on the Course Fee. This applies only to participants based in Spain. If you wish to ask for this discount, please contact us. The discount may apply for a maximum of 2 places, which will be covered by strict registration order.