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UltraScan Release Updates

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Borries Demeler edited this page Apr 28, 2024 · 49 revisions

pending updates for next release

Critical updates

Security Updates

  • LIMS web submission forms - numeric fields now validated as numeric

Performance Updates

  • Academic cluster submission - reuse connection when submitting multiple jobs significantly speeds up submission

New features

  • Addition of new buffer components to the UltraScan buffer tables which are commonly used in pharmaceutical formulations. Availability of these components allows more accurate density and viscosity corrections for s20,W and D20,W values:
    1. DTT
    2. HEPES
    3. L-alanine
    4. L-arginine
    5. L-glycine
    6. L-histidine
    7. Sodium nitrate
    8. Sodium perchlorate
    9. Sorbitol
    10. Tween-80
    11. Water
  • The Velocity and Utility menus have been re-organized to arrange module links in a more logical fashion and help the user to find related features more easily
  • UltraScan now includes a new utility that can convert a Beckman-generated tar.gz Optima AUC data archive into openAUC formatted binary files for direct import into the UltraScan LIMS system.
  • A new spreadsheet utility has been added to facilitate the import of ASCII spreadsheets (.dat, .csv, .txt) into any program consuming ASCII formatted numerical data. The new spreadsheet program in UltraScan can be used to read and write ASCII files and sort columns, delete rows and colums, add headers, and reformat ASCII spreadsheets.

2023-Q4 release

Critical updates

Security Updates

  • Operating system update for latest patches

  • Email sending RFC5322 compliance patch

Bug Fixes

  • The problem of resetting the frame color to its original/default state upon reopening the plot configuration has been resolved.
  • Manual buffer correction flag was not being honored. This caused s20,W and D20,W corrections to be performed with regular water corrections, instead of the fixed density and viscosity values in the manual buffer setting.
  • GMP automatic editing of data now has an improved algorithm for initially determining the meniscus position that captures more exception cases when the loading volume doesn't match the protocol-provided value
  • GMP e-Signatures: bug fixed as to proper time to send first informative e-mail to assigned operator
  • R&D data acquisition: bug fixed related to incorrect requirement for GMP submission form at 3. IMPORT stage
  • Several bugs fixed reported by CodeQL
  • GMP | 4. EDIT: long-standing bug fixed related to "Missing Edit Profiles" error in the 5. ANALYSIS stage
  • Import experimental GUI program: The bugs related to editing runID and needing to restart the program to upload a new experiment are fixed.
  • Buffer GUI program: The bug related to updating the viscosity and density of the new buffer is fixed.

New features

  • Update of density and viscosity calculation for standard conditions (20 °C) for Water according to the latest published values (Density - old: 0.998234 g/ml, new: 0.998213 g/mL, see: Patek J, Hruby J, Klomfar J, Souckova M, Harvey AH (2009) Reference correlations for thermophysical properties of liquid water at 0.1 MPa. J Phys Chemical Ref Data 38:21–29. https://doi.org/10.1063/1.3043575, and Viscosity - old: 1.00194 cp, new: 1.0016 cp, see: Rukes B, Dooley RB (2020) Guideline on the use of fundamental physical constants and basic constants of water, IAPWS G5–01 (2020). Int Assoc Properties Water Steam 1–7. http://iapws.org/relguide/fundam.pdf). All density and viscosity calculations are now identical to the values reported in 2023 in the latest version of Sednterp (Philo JS. SEDNTERP: a calculation and database utility to aid interpretation of analytical ultracentrifugation and light scattering data. Eur Biophys J. 2023 Jul;52(4-5):233-266. doi: 10.1007/s00249-023-01629-0. Epub 2023 Feb 15. PMID: 36792822.). Important: Please understand that as a result of this update there may be slight differences in s20,w and D20,w values when plotting previously simulated models, and that methods for the temperature/buffer corrections for systems measured at different temperatures than 20C have also been updated. Manual buffers are not affected, and continue to be honored unadjusted.
  • Save plot configuration: This allows you to save your plot configurations into a JSON files and use the configuration later on to plot another figure in the same style.
  • Query Model RMSDs: A new program used to display the RMSD values for UltraScan models. It includes a flexible tool to sort RMSD values based on various options such as editing profile, analysis number, modeling method, and triple information in order to quickly compare the accuracy of your analyses.
  • LIMS server update - the LIMS now includes an option called Supporting Files: It allows any type of document, zip files, and images to be uploaded into the LIMS database account. Supporting files are categorized by user based on project, buffer, analyte, and solution names. They are easily downloaded, edited, or deleted from the user LIMS account. Selected file types can be viewed directly in the browser (e.g., PDF, image files, text files).
  • The Spectral Analysis utility Spectrum Fitter can now import data from the ThermoFisher Genesys 50 and Genesys S10 spectrophotometers directly.
  • The ABDE experimental data analysis program now has a baseline correction feature to account for CsCl refractive errors.
  • The ABDE normalization program has now capability to be retrieved data from the LIMS database.
  • UltraScan GMP now includes electronic signatures and enhanced reporting features.
  • New program developed to create global lists of reviewers and approvers
  • US Protocol Development: Audit trail generation steps (each stage submission forms, e-Signatures) are implemented for Development GMP runs
  • US Protocol Development: Run name & label are both enforced to be pre-existing, original runName && label in the protocol development runs.
  • GMP Reporting: Run Details now has temperature plot and temperature standard deviation, as requested by users
  • GMP Reporting: UltraScan version info is added to the report header
  • GMP Reporting: Integration limits for selected individual "Type-Method" (combined) distributions are shown as vertical lines for convenience
  • New program "Audit Trail" developed showing logs and user interactions at all GMP processing stages

2023-Q1 updates

Critical updates

  • Autoflow analysis will get stuck on submission when only one channel parameter is defined. Fixed

Security Updates

  • Operating system update for latest patches

  • Operating system upgrade to Oracle Linux 8.7 release notes or RedHat 8.7 release notes

    • for RedHat system updates performed after 19 May 2023:
    • for Oracle Linux system updates performed after 3 June 2023:

  • User passwords longer than 15 characters would fail to connect to the database from the GUI. Fixed

New features

  • US-SOMO update to revision 6730
  • GMP protocol editing feature introduced
  • ABDE fitter for automatically fitting ABDE experiments for AAV CsCl gradient sedimentation
  • Support for Discrete Model GA Monte Carlo Parallel Threads
  • GMP Reporter - report readability improvements
  • Pseudo-absorbance noise processing module added for removal of time invariant noise from time invariant data
  • MWL-fitter now has a residuals viewer for spectral deconvolutions

Bug fixes

  • Mixed optical system runs would under certain circumstances fail to assign correct triple descriptions
  • UltraScan Gradient Descent fitting algorithm - new initialization defaults for spectrum fitter for better convergence
  • improved GUI interactions for UltraScan graph editing controls

2022-Q3 updates

Critical updates

  • If an administrator submitted analysis jobs as another user using a certain unusual sequence of steps, the models generated would have the wrong ownership (they would belong to the administrator instead of user) making them unusable.

Security Updates

  • Operating system update for latest patches
  • Oracle Linux systems - Conversion to RedHat kernel vs Oracle's UEK Kernel
    • due to ongoing boot issue with grub2 and with Oracle's UEK kernel

Bug Fixes

  • Repeated emails on timeouts
  • Queue viewer delete job logic redone
  • Bug fixes and feature enhancements in the GMP analysis software: ** 4. EDIT stage -- proper plot generations reflecting excluded scans set in the protocol ** 6. REPORT | GMP Report program -- added more flexibility in user controls on variety of generalized report items selections; also, a more logical separation of the report's sections..

New features

  • Configurable run and submit timeouts for analysis jobs

Major Enhancements

  • An option added in the GMP Autoflow framework to mark run as 'failed' and restart from acquisition phase and proceed through all stages; helpful when run stuck/failed for any (stage-specific) reason; does not require creation of a new protocol and restarting from scratch.

2022-Q2 Updates

Critical updates

  • Fixed an issue with record counters in GMP Autoflow that could cause a loss of historical data.

Security Updates

Bug Fixes

  • Bug fixes and feature enhancements in the GMP analysis software

Enhancements

  • New noise processing software.
  • New analysis job manager. The previous version could get congested under heavy load. This has been rewritten and provides more job specific management tools.
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