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FAQ

FAQ


Why this name?

Quetzalcoatl, the Feathered Serpent, was a powerful divinity from Mesoamerica who created the world (it still took him 600 years to reach a satisfying version, and we strongly identify to this part of the tale).

The god’s name is a combination of two Nahuatl words:

  • quetzal refers to the Resplendant Quetzal (an emerald bird symbol of freedom)
  • coatl basically means snake (remember, all that glitters is not gold…) and conveniently fits to Coalescence Template Library.

But the full name is quite difficult to pronounce, so feel free to focus on the glitter when you use Quetzal.


Who maintains the library?

Maintainer: Arnaud Becheler


How to cite?

Founder article: Access on Wiley

Citation:

Becheler, A, Coron, C, Dupas, S. The Quetzal Coalescence template library: A C++ programmers resource for integrating distributional, demographic and coalescent models. Mol Ecol Resour. 2019; 19: 788– 793. https://doi.org/10.1111/1755-0998.12992

Becheler, A., & Knowles, L. L. (2020). Occupancy spectrum distribution: application for coalescence simulation with generic mergers. Bioinformatics, 36(10), 3279-3280.


How to contribute?

Clone: git clone https://github.com/Becheler/quetzal.git

Community: IRC channel #quetzal on Freenode

Contribute: Check our Github repository and use the Pull Request system


Why a library and not a program ?

Simply because programs are not always the right level of configurability.

Programs are super handy, because they act as nice black-boxes eating data and digesting them in a process that can be adjusted through a neat user interface (configuration files, Graphical User Interface…). Thanks to black-box programs, biologists do not need to worry about programming languages, design or architecture.

But what if the options of a program do not meet our need ?

In that case, one would have to open the box and modify the code of the program, to extend it towards one’s need, and in that case programming language, design and architecture of course matter to ease this (quite painful) experience.

Quetzal existence stems from the fact it was impossible to customize the behavior of a pre-existing program in the desired way using the available options: we had to re-implement everything.

In short, programs are not the right level of granularity when it comes to reusing the work of other coders.

The key to fast development, correctness, efficiency, and maintainability is to use a suitable level of abstraction supported by good libraries. -Stroustrup


Wait, are you saying that programs are useless?

Nooooo… Programs are still very usefull and user-friendly, so we are currently using Quetzal to develop various programs!

The principal activity of a researcher is to explore new questions. Using simulations to explore new complex models is a powerful technique, but it requires a solid code base that can adapt to theoretical changes.

If the software breaks at each minor change, the exploration would be painful, almost impossible!

Quetzal allows the researcher to widen the limits of the traditional spatially explicit and coalescence-based simulators by allowing the customization of key aspects of the problem: populations reaction to landscape heterogeneity and genes genealogies simulations details.

As nothing is never free is this wild world, this flexibility comes at a cost: using Quetzal requires technical knowledge in C++, so perhaps you would need a Research Software Engineer to code your model.

Or you can use available Quetzal-EGGS!


What is a Research Software Engineer?

You do not know if you are or not a RSE?


I’m not sure if I should use Quetzal?

Do you have to implement or extend a coalescence-based simulator specified by a researcher?

Well, here are some bad news:

  • Reusing or adapting existing code bases for structured coalescence is hardly feasible.
  • We never have time to re-code everything from scratch.
  • Supposing you succeed to write the correct program in a reasonable amount of time (which is not yet certain) sooner or later the model will change, and you will have to start all over again.

Walking on water and developing software from a specification are easy if both are frozen. -Edward Berard

We all know that there is no such thing as frozen specification. Building a system in a changing environment is challenging, and you need the right tools.

But here are the good news:

As an open-source set of C++ abstractions (template classes, functions, algorithms, concepts) Quetzal provides a nice starter-pack to write your own simulation program.

You will probably not find everything that you need.

But you will surely spare time by not re-inventing the wheel.


I don’t understand why the library components are so abstract?

Small components libraries allow to tailor the code to your needs.

When a scientific question leads to change a minor detail in the simulation model, we never want to have to recode everything. So it means that this very level of detail should be the right unit of code. In this way it is possible to only replace a piece of code by another in a very easy way.

This is the meaning of components libraries.

And as we never want to pay computation time for flexibility, the C++ template mechanism is used in Quetzal to build these components. In this way they can be reused, adapted and extended to other contexts with maximal efficiency.

This is the meaning of a C++ template library: flexible, efficient, extensible.

It’s easier than you think: we designed Quetzal so the code can be very expressive and compact.


I have another question?

Sure! Feel free to add a comment, I’ll add your question to the list!