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Release Notes for INCA
- Version 2.4
- 09/06/2025
- Implemented minor bug fixes and compatibility upgrades for Matlab 2025a
- Version 2.3
- 06/24/2024
- Added several options to enhance performance of the Monte Carlo parameter uncertainty analysis. First, users may now set an upper limit on the total number of Monte Carlo trials (default=Inf). Second, users may resume a previously unfinished Monte Carlo job by loading intermediate results from a ‘dump’ file that is automatically saved following each iteration. Third, users may select a subset of parameters to test for convergence at each iteration, rather than forcing all parameters to converge to within the specified relative tolerance.
- When using parameter continuation analysis, users may now set a timeout threshold for completing each confidence interval estimate (default=Inf).
- Implemented minor bug fixes and checked compatibility with Matlab 2024a.
- Version 2.2
- 06/18/2023
- Implemented minor bug fixes and compatibility upgrades for Matlab 2023a. No new features added.
- Version 2.1
- 06/19/2022
- Changed nomenclature from metabolite ‘nodes’ to ‘pools’ to be consistent with current terminology.
- Implemented minor bug fixes. No new features added.
- Version 2.0
- 07/01/2021
- 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
- 06/29/2020
- 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
- 07/28/2019
- 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
- 06/20/2018
- 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
- 06/19/2017
- 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
- 06/23/2016
- Minor bug fixes only
- Version 1.4
- 07/08/2015
- 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
- 01/05/2015
- Version 1.0
- 10/17/2013
- Initial Release
Release Notes for ETA
- Version 2.7
- 07/07/2025
- The license expiry date has been extended.
- Version 2.6
- 06/24/2024
- The license expiry date has been extended.
- Version 2.6
- 06/19/2023
- The license expiry date has been extended.
- Version 2.6
- 06/19/2022
- The license expiry date has been extended.
- Version 2.6
- 07/01/2021
- The license expiry date has been extended.
- Version 2.6
- 06/19/2020
- The license expiry date has been extended.
- Version 2.6
- 07/01/2019
- The license expiry date has been extended.
- Version 2.6
- 06/11/2018
- The license expiry date has been extended.
- Version 2.6
- 06/19/2017
- Updated the third-party findjobj.m function. All calls to this function are now made during ETA launch, in order to avoid hang-ups after clicking checkboxes in the user interface. A waitbar is now displayed during ETA launch because of the additional startup time required.
- Fixed position, colors, and legend entries of error bars in grouped bar plots.
- Version 2.5
- 06/23/2016
- New expiry date July 1, 2017
- Made several updates in response to changes in graphics handling introduced in MATLAB 2014b.
- Version 2.4
- 01/05/2015
- Version 2.3
- 10/23/2013
- Bug fixes that have been pointed out by users.
- Version 2.0
- 01/2013
Release Notes for PIRAMID
- Version 1.3.3
- 09/08/2025
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Better Data Support: Now works with Stellar equipment data for smoother processing.
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Improved Data Viewing: Added filters to better display specific data (MS1) from Stellar equipment, fixing issues with complex data sets.
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More Accurate Results: Updated calculations to ensure results add up correctly, even with tricky numbers.
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Enhanced Data Export: Improved how natural abundance data is shown in exports, making it clearer for labeled or unlabeled molecules.
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User Interface Update: Adjusted text in the metabolite panel to match the latest Matlab2025a interface.
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Higher Precision: Improved the resolution algorithm for more accurate data analysis.
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Extended License: Updated the software’s expiration date.
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Quick Fix: Applied a patch to improve the reliability of a key data processing feature.
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Flexible Settings: Made isotopic data more adaptable, allowing updates to settings like carbon or nitrogen tracer purity.
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- Version 1.3
- 02/24/2025
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Added support for parallel reaction monitoring (PRM) datasets
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- Version 1.2
- 06/24/2024
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Fixed a bug with zeros in dual-labeled integration appearing in the theoretical distribution.
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When no metabolites are found due to the resolution, now PIRAMID offers the option to try again when the resolution is changed
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Window resizing was implemented.
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- Version 1.1
- 06/19/2023
- Several algorithms were optimized and implemented minor bug fixes. No new features added.
- Version 1.0
- 01/06/2023
- Initial Release.
