From 75ec3181840d86c4c1908b76456311fdb0b24f3f Mon Sep 17 00:00:00 2001 From: Michael Clerx Date: Fri, 30 Aug 2019 12:15:35 +0100 Subject: [PATCH] Updated capitalisation of PINTS and made citation info more prominent in README --- README.md | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 2aea9ac16..a3c0d4c09 100644 --- a/README.md +++ b/README.md @@ -9,11 +9,14 @@ # What is Pints? -Pints (Probabilistic Inference on Noisy Time-Series) is a framework for optimisation and Bayesian inference on ODE models of noisy time-series, such as arise in electrochemistry and cardiac electrophysiology. +PINTS (Probabilistic Inference on Noisy Time-Series) is a framework for optimisation and Bayesian inference on ODE models of noisy time-series, such as arise in electrochemistry and cardiac electrophysiology. -## Using Pints +PINTS is described in [this publication in JORS](http://doi.org/10.5334/jors.252), and can be cited using the information given in our [CITATION file](./CITATION). -Pints can work with any model that implements the [pints.ForwardModel](http://pints.readthedocs.io/en/latest/core_classes_and_methods.html#forward-model) interface. + +## Using PINTS + +PINTS can work with any model that implements the [pints.ForwardModel](http://pints.readthedocs.io/en/latest/core_classes_and_methods.html#forward-model) interface. This has just two methods: ``` @@ -23,11 +26,11 @@ simulate(parameters, times) --> Returns a vector of model evaluations at the given times, using the given parameters ``` -Experimental data sets in Pints are defined simply as lists (or arrays) of `times` and corresponding experimental `values`. -If you have this kind of data, and if [your model (or model wrapper)](examples/writing-a-model.ipynb) implements the two methods above, then you are ready to start using Pints to infer parameter values using [optimisation](examples/optimisation-first-example.ipynb) or [sampling](examples/sampling-first-example.ipynb). +Experimental data sets in PINTS are defined simply as lists (or arrays) of `times` and corresponding experimental `values`. +If you have this kind of data, and if [your model (or model wrapper)](examples/writing-a-model.ipynb) implements the two methods above, then you are ready to start using PINTS to infer parameter values using [optimisation](examples/optimisation-first-example.ipynb) or [sampling](examples/sampling-first-example.ipynb). A brief example is shown below: -![An example of using Pints in an optimisation](example.svg) +![An example of using PINTS in an optimisation](example.svg) _(Left)_ A noisy experimental time series and a computational forward model. _(Right)_ Example code for an optimisation problem. The full code can be [viewed here](examples/readme-example.ipynb) but a friendlier, more elaborate, introduction can be found on the [examples page](examples/README.md). @@ -36,15 +39,11 @@ A graphical overview of the methods included in PINTS can be [viewed here](https ### Examples and documentation -Pints comes with a number of [detailed examples](examples/README.md), hosted here on github. +PINTS comes with a number of [detailed examples](examples/README.md), hosted here on github. In addition, there is a [full API documentation](http://pints.readthedocs.io/en/latest/), hosted on readthedocs.io. -### Citing Pints - -If you use PINTS in any scientific work, please [credit our work with a citation](./CITATION). - -## Installing Pints +## Installing PINTS You'll need the following requirements: @@ -57,13 +56,13 @@ These can easily be installed using `pip`. To do this, first make sure you have $ pip install --upgrade pip ``` -Then navigate to the path where you downloaded Pints to, and install both Pints and its dependencies by typing: +Then navigate to the path where you downloaded PINTS to, and install both PINTS and its dependencies by typing: ``` $ pip install . ``` -To install Pints as a [developer](CONTRIBUTING.md), use +To install PINTS as a [developer](CONTRIBUTING.md), use ``` $ pip install -e .[dev,docs] @@ -75,13 +74,13 @@ To uninstall again, type $ pip uninstall pints ``` -## Contributing to Pints +## Contributing to PINTS -If you'd like to help us develop Pints by adding new methods, writing documentation, or fixing embarassing bugs, please have a look at these [guidelines](CONTRIBUTING.md) first. +If you'd like to help us develop PINTS by adding new methods, writing documentation, or fixing embarassing bugs, please have a look at these [guidelines](CONTRIBUTING.md) first. ## License -Pints is fully open source. For more information about its license, see [LICENSE](LICENSE.txt). +PINTS is fully open source. For more information about its license, see [LICENSE](LICENSE.txt). ## Get in touch