Releases | Open Source Science

BASICO - Release 0.85

This release fixes an issue with the profile likelihood graphs. Additionally, an issue is fixed that made it impossible to overwrite the CopasiSE executable to be used by the processing functions.

Additional new features allow the plotting engine for plots to be specified (QWT / QCustomPlot).

Finally all events of a model can be removed quickly using remove_all_events.

Scientific Software - Peer-reviewed - Python
Published by fbergmann 5 months ago

This release fixes an issue where the LNA task would give a confusing error message, when no steady state was found. It also works around an incompativility when using python-copasi compiled with SWIG 4.3.0.

Scientific Software - Peer-reviewed - Python
Published by fbergmann 8 months ago

BASICO - Release 0.83

This release updates basico to work with the latest version of petab_select. All changes are in the backend, and do not influence how to perform model selection:

Model selection example

Scientific Software - Peer-reviewed - Python
Published by fbergmann 11 months ago

BASICO - Release 0.82

This release upgrades the implementation of the PEtab select package to the latest version. Nothing on the external API has changed, for an example see:

FAMOS Model Selection

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 1 year ago

BASICO - Release 0.81

This is a bug fix release silencing a misleading error message coming from the steady state task

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 1 year ago

BASICO - Release 0.80

This release adds access to the results of the Linear Noise Approximation Task. (it requires an python-copasi > 4.44). For an example of running the task see the:

LNA Task Example

Generally, the LNA is computed runing run_lna the optional argument return_results (default False) indicates whether the full result is returned, or only the status of the computation. To retrieve the results after a computation of the LNA the following methods may be used:

get_lna_status returns the status of the last computation
get_lna_covariance_matrix returns the full covariance matrix
get_lna_reduced_covariance_matrix returns the reduced covariance matrix
get_lna_reduced_b_matrix returns the reduced b Matrix
get_lna_solution returns the tuple: (status, covariance matrix, reduced covariance matrix, reduced b matrix)

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 1 year ago

BASICO - Release 0.79

This issue changes the behavior when running time courses, obtaining values only at specified time points. Previously the first value might have been the first value specified or an earlier time point if the model was not currently at the time. This release changes that behavior to set the output start time to the first specified value.

Additionally, the previously private collect_data method can now be used to obtain values from the current model state using either display names or cns.

This resolves issue #61.

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 1 year ago

BASICO - Release 0.78

This is a bugfix release that fixes an issue that occurs if basico is used with the python-copasi package 4.45 and using optimisation constraints.

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 1 year ago

BASICO - Release 0.77

This release fixes an issue with load_model_from_string, where specific SBML models were mistakenly imported as COPASI models.

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 1 year ago

BASICO - Release 0.76

This release fixes an issue where returning simulation results from run_time_course could not be obtained if multiple model elements were named Time. If this issue is encountered:

basico will no longer try to set the index, and instead issue a warning Duplicate column names in time series consider using use_sbml_id=True, or running ensure_unique_names()
the new function ensure_unique_names() appends a count to the name ensuring uniqueness

This fixes #60 .

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 1 year ago

BASICO - Release 0.75

This release adds a workaround when dealing with the following issues:

when resolving references from display names for reactions containing ')', these are now correctly found.
for testing, added function import_sbml that optionally can modify the XML before loading it. This function is experimental and might be removed in the future.

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 1 year ago

BASICO - Release 0.74

This is a bugfix release, renaming the parameter for run_lyapunov to calculate_divergence.

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.73

This release adds initial support for calculating lyapunov exponents and can be used like:

bash >>> load_example('brusselator') >>> exponents, sums, divergence = run_lyapunov(num_exponents=2) >>> print(exponents) [-0.0007025645113957691, -2.6051942604518477]

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.72

This release adds a set_parameters function the basico PetabSimulator, with that it will be possible to reevaluate many parameters without requiring a reload.

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.71

This release adds support for the new output specifications for scan tasks to get_scan_settings and set_scan_settings. That way more precise control can be gained as to when output is selected.

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.70

This release fixes an issue (#56 ) where mapping a number to a reaction parameter would only work if that parameter was in the first position. Additionally, time course settings are now restored when retrieving simulation results for experiments, issue (#54).

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.69

This release fixes an issue where notes / annotations could not be set on all elements. This fixes #53 .

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.68

This release fixes an issue that corrupted expressions when replacing CNs with display names. #52

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.67

This release fixes an issue if NaNs are in the list of affected experiments.

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.66

This release fixes an issue, where the compartment dimensions could not be set with a numpy integer. #49 .

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.65

This release fixes issues #45 and #46, where it was not possible to add experiments for model elements that were added (until the experiment was saved). Now the model is compiled before adding experiments solving that issue. Additionally get_simulation_results disables randomize_start_values when calculating the solution statistic.

Finally several changes were made to make basico compatible with upcoming breaking API changes in the COPASI backend.

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 1 year ago

BASICO - Release 0.64

This release fixes an issue when expression contained logical || or && or used e-notation.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.63

Another bug fix release, for retrieving / setting CN's. Now empty references will be given as empty string.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.62

This release fixes the issues #40, where the initial time could not be retrieved or set. #41 and #42 where CNs could not be retrieved for generalized task settings.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.61

This release contains further improvements in translating expressions with names to expressions of CNs as expected by the COPASI C++ API.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.60

Another bug fix release, this time with setting the expressions for a different than the current model. With that species / parameters can now be cloned from dictionary like so:

```python # get from one model species = basico.asdict(basico.getspecies()) params = basico.asdict(basico.getparameters()) # start new model dm = basico.new_model()

    # ensure we have all species
    for s in species:
        basico.add_species(s['name'], s['compartment'])

    for p in params:
        basico.add_parameter(p['name'], p['value'])

    # now set all values as we had them
    for s in species:
        basico.set_species(exact=True, **s)

    for p in params:
        basico.set_parameters(exact=True, **p)

```

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.59

This release fixes an issue, where get_parameters or get_species would return expressions from the current model, rather than from the model that has been passed in. Additionally upon request get functions now return the display_name of elements additionally rather than just the name. Also transition_time is now returned when calling get_species which might be of interest after bringing the model to steady state.

Full Changelog: https://github.com/copasi/basico/compare/v0.58...v0.59

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.58

This release fixes an issue with get_reaction_mappings that on some systems would fail to provide the complete mapping of a reaction element. Additionally an issue is fixed when set_task_settings is used to change Duration / StepNumber of time courses, which unfortunately would sometimes not be correct. Also added two new methods:

get_model_name returns the name of the current model
remove_loaded_models removes all loaded models

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.57

This release fixes an issue in the plotting subroutine for the profile likelihood method.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.56

This release ensures that parameter estimation tasks are executed, even if errors have been previously logged.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.55

This is a bug fix release, that solves an issue (#39) where creating a parameter set could cause other tasks to not run anymore.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 2 years ago

BASICO - Release 0.54

This release fixes compatibility with python 3.12. Additionally it supports parameter scans over parameter sets, as was introduced with COPASI 4.42. It fixes issues when creating events with multiple assignments, and ensures that parametersets are correctly created from the current model state.

Examples:

Working with Parameter Sets

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 2 years ago

BASICO - Release 0.53

This release adds support for the MCA task to basico, for an example on how to use it see:

MCA Example

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 2 years ago

BASICO - Release 0.52

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release adds support for using constraints when running optimization or parameter estimation tasks. They do make things much more difficult to solve, so use with care. I've updated the examples to show how to use them:

Full Changelog: https://github.com/copasi/basico/compare/v0.51...v0.52

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 2 years ago

BASICO - Release 0.51

This release introduces a new method run_scheduled_tasks and the general run_task command, that executes tasks, and aims to produce the output specified. For now basic plotting is implemented, but will be refined in the next versions.

It also includes a number of bugfixes (fixes #34, #35 , #36), thanks to @ayush9pandey for reporting. This should produce more applicable error messages when running simulations, sort an issue where Miriam information could not be retrieved when using python-copasi > 4.35 and clarify issues in the notebooks.

Full Changelog: https://github.com/copasi/basico/compare/v0.50...v0.51

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 2 years ago

BASICO - Release 0.50

This release upgrades the support for petabselect, cleans up logging (not using the root logger anymore), and also supports observable transformations for PEtab problems. Additionally it exposes the Hybrid Runge Kutta method (fixes #33 ) to the `runtimecourse/runtimecoursewith_output` functions.

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 2 years ago

BASICO - Release 0.49

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

New in this release is support for advanced event flags, such as:

fire_at_initial_time: to indicate that an event should trigger at time = t0, (default False)
persistent: to indicate that an event has to remain true between trigger time and delay (default False)
delay_calculation: to indicate that not just the assignment, but also the calculation of the assignment expression should be delayed
priority: a priority expression that decides which event will get priority if multiple ones trigger at the same time (default random)

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 2 years ago

BASICO - Release 0.48

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

New in this release is the plotting for profile likelihood profiles. Have a look at the updated example, by default we draw the 68% and 95% threshold.

Scientific Software - Peer-reviewed - Python
Published by fbergmann over 2 years ago

BASICO - Release 0.47

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

New in this release is the capability to create / edit / update / remove model parameter sets. Have a look at the tutorial:

https://basico.readthedocs.io/en/latest/notebooks/Working_with_ParameterSets.html

This release also fixes some more issue, when using relative filenames for experimental data.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 3 years ago

BASICO - Release 0.46

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release:

fixes an issue with setting up timecourses, where inputs are now automatically converted to the types needed by the C++ api. This allows duration to work also with an np.float value
save_experiments_to_dict, save_model_and_data now use relative filenames for the experiment files. So the files will work readily after copying them to other environments.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 3 years ago

BASICO - Release 0.45

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release has further improvements on the profile likelihood generation. It adds a new convenience function get_profiles_for_model that generates all profiles for the currently loaded model. Additionally processing results now allows for a max_time parameter that stops the calculation of results after the specified timeout in seconds. The example has been updated to reflect that.

When using callbacks it is also possible to specify a max_time argument to automatically cancel longer running operations.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 3 years ago

BASICO - Release 0.44

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release fixes an issue with the validation of reaction mappings. It also adds the option to automatically add separators for non-table reports.

Full Changelog: https://github.com/copasi/basico/compare/v0.43...v0.44

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 3 years ago

BASICO - Release 0.43

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This version adds a function wrap_copasi_string, that makes it easier to add reports with literal strings in report headers. It also fixes an issue with generating separators. Additionally when mapping model elements to reaction kinetics, these values will now be validated.

Full Changelog: https://github.com/copasi/basico/compare/v0.42...v0.43

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 3 years ago

BASICO - Release 0.42

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This version fixes an issue, where changing kinetic functions of reaction would fail, even if a mapping was supplied. Additionally there are minor improvements in plotting profiles.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 3 years ago

BASICO - Release 0.41

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release brings a first version of performing 1d likelihood profiles along and fixes an issue where setting model values would fail, if a model is passed along to the key value args.

Scientific Software - Peer-reviewed - Python
Published by fbergmann almost 3 years ago

BASICO - Release 0.40

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release adds an overload to reset the default handler, that can be used to display status information during long running operations. There is now also an example showing how to use the default handler (that will work of tqdm is installed).

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 3 years ago

BASICO - Release 0.39

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release changes the model editing so that the model is not compiled as often. Especially when creating big models, this reduces the runtime of scripts drastically.

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 3 years ago

BASICO - basico 0.38

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release changes the behavior of add_reaction / set_reaction, when it comes to assigning a function definition to it. Previously, the reaction scheme would already have to have all modifiers of the function listed, before a function could be assigned. Now this is no longer necessary and modifiers will be automatically added to the reaction scheme, as long as the mapping to all modifiers is specified. See also the Editing reaction kinetics example in the documentation. ( fixes #29 )

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 3 years ago

BASICO - basico 0.37

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release fixes an issue, where initial_concentrations would be lost when also setting additional properties using either add_species or get_species. (Issue #28)

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 3 years ago

BASICO - Release 0.36

This release updates the PEtab support to the latest libpetab version, and the latest petab_select library. Now also an example for using PEtab problem / selection problems is online:

https://basico.readthedocs.io/en/latest/notebooks/Working_with_PEtab.html

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 3 years ago

BASICO - Release 0.35

This release ensures, that basico is compatible with the latest COPASI version.

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 3 years ago

BASICO - Release 0.34

This release adds the option to return the fit statistic for each experiment when get_fit_statistic is called with include_experiments=True . The python-copasi package will have to be version 2.37.263 or higher for this to work.

Scientific Software - Peer-reviewed - Python
Published by fbergmann about 3 years ago