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@timosachsenberg timosachsenberg released this 25 Oct 12:10
· 966 commits to develop since this release
Release3.1.0
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Learn about vigilant mode.

Dear OpenMS-Users,

We are excited to share an experimental update with our community, mainly targeted at platforms that depend on Conda packages.
Please note that this is a partial and unannounced release, focused on delivering novel features and major changes that we're actively testing and refining.
While these features are still in an experimental phase, we encourage adventurous users and platform integrators to explore and provide feedback.

The source code and precompiled installers (Windows, Linux, MacOSX) are available at the bottom of this page or here.

Note: the Windows installer has been updated (Nov 16th 2023) to re-establish functionality of the OpenMS GUI tools (like TOPPView, TOPPAS etc) - which were misconfigured in the first release.

Important Notes:

  • Features are experimental and may undergo changes or be removed in future releases based on user feedback and stability.
  • We welcome your feedback and suggestions to help us improve and refine these experimental features.
  • For stability and production use, we recommend sticking with the latest stable release.

Please use this opportunity to test and provide feedback on these new features, as your input will play a vital role in shaping their development.

Thank you for being a part of our community and for helping us make OpenMS even better!

What's new:

  • Major change: removed the distinction between TOPP tool and util and the TOPP and UTIL build targets were merged to a single TOPP target. All utils are considered tools now and categorized as "Utilities".
  • Added SageAdapter. Support for standard identification tasks with sage (https://github.com/lazear/sage) (experimental).
  • Require some advanced instruction sets for x64 CPUs: SSE3 (g++/clang) or AVX (MSVC); and NEON for ARM64 CPUs (#6978)
    and report them via the OpenMSInfo tool (#7022)
  • Base64 encoding/decoding using the SIMDe library (#6978)
  • Filter features in ProteomicsLFQ according to feature p-value (additional parameters feature_with(out)_id_min_score, MBR is automatically active if targeted_only = false)

Fixes:

  • Fix a crash when loading mzML data with multiple threads which contains non-MS spectra, e.g. 'electromagnetic radiation spectrum' (#7011)
  • InternalCalibration: improve visualization of calibration plots (#7064)
  • Restore TOPPAS tutorial (#7076)
  • various low impact UBSan fixes
  • make mzData more robust against wrong 'length' attributes for binary data (#7113)

Misc:

  • Report reading/writing throughput (MiB/sec) when loading/storing mzML (#7035)
  • Add ability to create decoy features in FeatureFinderIdentification
  • Restore developer quick guide in Doxygen docu - see https://openms.de/current_doxygen/html/index.html (#7109)
  • Updated the changelog helper to set LD_LIBRARY_PATH automatically and other fixes
  • Added "area" column to EICextractor output

Cleanup of old/unused tools and code:

  • Removed old tools and associated code in the library for InclusionExclusionListCreator, SvmTheoreticalSpectrumGenerator, PrecursorIonSelector, and MSSimulator
    Note: general SVC and SVR is still supported with the SimpleSVM class.
  • Removed old RT and PT predict code and tools RTModel, RTPredict, PTModel, PTPredict, RTEvaluation and associated library code (SVMWrapper and LibSVMEncoder).
  • Removed PepNovoAdapter
  • Removed CompNovoAdapter and library code
  • Removed simplistic evaluation tools FFEval, LabeledEval, TransformationEvaluation
  • Removed EnzymaticDigestionLogModel
  • Removed FidoAdapter (same functionality now in our own inference engines)

Full Changelog: Release3.0.0...Release3.1.0

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