Release Notes for INCA

Version 2.1
19 Jun 2022
  • Changed nomenclature from metabolite ‘nodes’ to ‘pools’ to be consistent with current terminology.
  • Implemented minor bug fixes. No new features added.
Version 2.0
1 Jul 2021
  • Added capabilities to model NMR isotopomer and cumomer measurements.
  • Added Edit samples drop-down menu to allow entire groups of measurements to be activated or inactivated en masse.
  • Changes were made to prevent extreme values of initial parameter guesses (e.g., very high or low) from biasing the flux estimation procedure when using randomized initial guesses.
  • Removed obsolete functions to generate FluxML and OpenFlux input files from INCA models.
  • Changed behavior of tracer simulations to use measurement time points instead of the values provided in the simulation time span option, if there are active experimental measurements with finite time values (i.e., t>0 and t).
Version 1.9
29 Jun 2020
  • Updated the third-party findjobj.m function.
  • When plotting MS data in the Flux estimation screen, each simulated MDV is multiplied by its associated scaling factor prior to plotting. This behavior is different from prior INCA releases, which rescaled the measured MDVs rather than the simulated MDVs prior to plotting. The current behavior is more representative of the MDV values shown in the Goodness of fit table, which are obtained from the flux estimation procedure. In contrast, the MDVs plotted in the Tracer Simulation screen are not multiplied by the measurement scaling factors and therefore represent the simulated values produced from the isotopomer model.
  • Time-course plots were modified to only show simulated MDVs that correspond to experimentally measured time points.
  • Change in terminology: different “compartments” are now used (instead of “phases”) to distinguish spatially segregated metabolites.
Version 1.8
1 Jul 2019
  • Updated the third-party findjobj.m function.
  • Improvements were made to the algorithm for generating random initial parameter guesses.
  • Changes were implemented in the mylsqlin.m function to transition away from the obsolete ‘active-set’ method to the ‘interior-point’ method.
  • The approach for estimating local standard errors of best-fit model parameters was updated to account for active inequality constraints.
Version 1.7
1 Jul 2018
  • Changes were made to address incompatibilities introduced by Matlab 2018a and updates to Optimization Toolbox functions.
  • Replaced the @map user-defined object with @atommap to avoid namespace conflicts
Version 1.6
19 Jun 2017
  • Fixed a bug that was causing data misalignment when parameter continuation jobs were terminated early in a parallel computing environment.
  • Adjusted the confidence interval algorithm to respect user-defined parameter bounds.
  • Adjusted the FCF and FVA algorithms to avoid constraint infeasibility.
  • Updated the third-party findjobj.m function. All calls to this function are now made during INCA launch, in order to avoid hang-ups after clicking checkboxes in the user interface. A waitbar is now displayed during INCA launch because of the additional startup time required.
  • Changes were made to address incompatibilities introduced by Matlab 2017a.
Version 1.5
23 Jun 2016
  • Minor bug fixes only
Version 1.4
8 Jul 2015
  • Made several updates in response to changes in graphics handling introduced in MATLAB 2014b.
  • Added the option to adjust the number of trials per iteration and the relative error tolerance when performing Monte Carlo uncertainty analysis by selecting Options -> Confidence interval parameters.
  • Refactored the queue.m function to include three pre-configured job schedulers and to enable running parallel jobs in the background. This m-file is now provided as source code so that users can modify it to run in their own distributed computing environment
Version 1.3
5 Jan 2015
  • Minor bug fixes only
Version 1.0
17 Oct 2013
  • Initial Build