diff --git a/docs/cite.rst b/docs/cite.rst index f474b52..a5f3a98 100644 --- a/docs/cite.rst +++ b/docs/cite.rst @@ -3,8 +3,8 @@ How to cite Thank you for using PhysioFit and citing us in your work! It means a lot to us and encourage us to continue its development. - PhysioFit: quantifying cell growth parameters and uptake and production fluxes. + PhysioFit: a software to quantify cell growth parameters and extracellular fluxes. Le Grégam L., Guitton Y., Bellvert F., Jourdan F., Portais J.C., Millard P. - **doi**: https://doi.org/10.1101/2023.10.12.561695 + bioRxiv preprint, doi: https://doi.org/10.1101/2023.10.12.561695 diff --git a/docs/faq.rst b/docs/faq.rst index 0e21b95..dde06fc 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -76,7 +76,7 @@ The quality of the fit can be evaluated based on: What is a χ² test? ------------------------------------------------------------------ -A χ² test describes how well a model fits a set of observations. Measures of goodness of fit typically summarize the discrepancy between observed values and the values expected under the model used in PhysioFit (see the :doc:`models` section). It is calculated as the sum of differences between measured and simulated values, each squared and divided by the simulated value. +A χ² test describes how well a model fits a set of observations. Measures of goodness of fit typically summarize the discrepancy between observed values and the values expected under the model used in PhysioFit (see the :doc:`method` section). It is calculated as the sum of differences between measured and simulated values, each squared and divided by the simulated value. A good fit corresponds to small differences between measured and simulated values, thereby the χ² value is low. In contrast, a bad fit corresponds to large differences between simulations and measurements, and the χ² value is high. The resulting χ² value can then be compared with a χ² distribution to determine the goodness of fit. The p-value of one-tail χ² test is calculated by PhysioFit from the best fit and is given in the log file (have a look to the :doc:`usage` section). A p-value close to 0 means poor fitting, and a p-value close to 1 means good fitting (keeping in mind that a p-value very close to 1 can be an evidence that standard deviations might be overestimated). A diff --git a/docs/method.rst b/docs/method.rst index 8dd360e..2d0b555 100644 --- a/docs/method.rst +++ b/docs/method.rst @@ -52,8 +52,8 @@ more details on the interpretation of the khi2 test results. Sensitivity analysis ********************* -To determine the precision on the fit and on the estimated parameters (including fluxes), PhysioFit performs a Monte Carlo analysis. Briefly, several -noisy datasets are generated from the simulated dynamics of the best fit (i.e defined in parameter :samp:`number of iterations` of the GUI) and calculate fluxes and other growth +To determine the precision on the fit and on the estimated parameters (including fluxes), PhysioFit performs a Monte Carlo analysis. Briefly, PhysioFit generates several +datasets by adding noise to the dynamics simulated from the best fit, and calculated fluxes and other growth parameters for each of these synthetic datasets. This enables PhysioFit to compute statistics (mean, median, standard deviation and 95% confidence interval) for -each parameter. We recommend always running a sensitivity analysis when using PhysioFit. +each parameter (including fluxes). We recommend always running a sensitivity analysis when using PhysioFit. diff --git a/docs/models.rst b/docs/models.rst index fe4ae0d..8c2b47b 100644 --- a/docs/models.rst +++ b/docs/models.rst @@ -1,6 +1,12 @@ Models ========= +Some common flux calculation models are provided with PhysioFit, and users can also build their own models. + +.. note:: We would be happy to broaden the types of models shipped with PhysioFit. If you have developed a new model, it might be + usefull and valuable to the fluxomics community! Please, keep in touch with us to discuss and see if we can include your + model in the built-in models shipped with PhysioFit! :) + Models shipped with PhysioFit ****************************** diff --git a/physiofit/ui/gui.py b/physiofit/ui/gui.py index a0c3a20..fa600b6 100644 --- a/physiofit/ui/gui.py +++ b/physiofit/ui/gui.py @@ -34,6 +34,7 @@ def start_app(self): st.set_page_config(page_title=f"PhysioFit (v{physiofit.__version__})") st.title(f"Welcome to PhysioFit (v{physiofit.__version__})") + st.write("Documentation available at [https://physiofit.readthedocs.io](https://physiofit.readthedocs.io).") self.update_info = st.empty() self.check_uptodate() self.select_menu = st.selectbox( @@ -220,8 +221,13 @@ def _initialize_opt_menu_widgets(self, file_extension): model_options = [ model.model_name for model in self.io.models ] - if self.config_parser.model: - idx = model_options.index(self.config_parser.model["model_name"]) + if self.config_parser: + if self.config_parser.model: + try: + idx = model_options.index(self.config_parser.model["model_name"]) + except Exception: + st.error("Error while reading model name from configuration file") + raise else: idx = None model_name = st.selectbox( diff --git a/pyproject.toml b/pyproject.toml index 0f460ef..d11c968 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "physiofit" -version = "3.3.0" +version = "3.3.1" description = "Calculate extracellular fluxes from metabolite concentrations and biomass data" authors = ["llegregam "] license = "GNU General Public License (GPL)"