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ToDo

Dave Brondsema

OpenMS TODO List

Release 2.0 TODOs and Feature Requests

  • Consistent support for mzIdentML and mzTab (FileConverter?), rethink default formats
  • Rethink use of template classes (un-templatize FeatureFinder?, for example)
  • Complete missing tests for TOPP tools
  • Refactor the messy structure of the map alignment tools
  • Refactor FeatureLinker? to be more memory efficient
  • Remove GSL dependencies in all classes

Release 1.9 TODO list

File I/O restrictions:

  • use only types that are known to FileHandler::NamesOfTypes?[]! Otherwise the INI-file cannot be written! We need to think of a fix for OpenMS 1.10...
  • No restrictions attribute for ITEM 'out' in AdditiveSeries?
  • No restrictions attribute for ITEM 'html' No restrictions attribute for ITEM 'mapping_file' No restrictions attribute for ITEM 'cv_files' in CVInspector
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'in' No restrictions attribute for ITEM 'contaminants' in DecoyDatabase?
  • No restrictions attribute for ITEM 'out' in Digestor
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'in' in DigestorMotif?
  • No restrictions attribute for ITEM 'pair_in' in ERPairFinder
  • No restrictions attribute for ITEM 'out_roc' in FFEval
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'out_tsv' in FileInfo?
  • No restrictions attribute for ITEM 'in1' No restrictions attribute for ITEM 'in2' in FuzzyDiff?
  • No restrictions attribute for ITEM 'out_csv' in HighResPrecursorMassCorrector?
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'in' in IDExtractor
  • No restrictions attribute for ITEM 'in' in IDFileConverter
  • No restrictions attribute for ITEM 'precursor_out' No restrictions attribute for ITEM 'fragment_out' No restrictions attribute for ITEM 'in' No restrictions attribute for ITEM 'id_in' in IDMassAccuracy
  • No restrictions attribute for ITEM 'output_name' in IDPosteriorErrorProbability
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'in' No restrictions attribute for ITEM 'sequences_file' in IdXMLEvaluation
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'rt_model' in InclusionExclusionListCreator?
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'inspect_output' No restrictions attribute for ITEM 'in' No restrictions attribute for ITEM 'inspect_input' in InspectAdapter?
  • No restrictions attribute for ITEM 'ref_peaks' in InternalCalibration?
  • No restrictions attribute for ITEM 'out' in MapStatistics?
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'in' in MascotAdapter?
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'in' in MassCalculator?
  • No restrictions attribute for ITEM 'pair_in' in MRMPairFinder
  • No restrictions attribute for ITEM 'pepnovo_executable' in PepNovoAdapter?
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'in' No restrictions attribute for ITEM 'model_file' No restrictions attribute for ITEM 'peptide_db_file' in PILISIdentification
  • No restrictions attribute for ITEM 'db_path' in PrecursorIonSelector?
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'feature_in' in PrecursorMassCorrector?
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'peptide_out' in ProteinQuantifier?
  • No restrictions attribute for ITEM 'out' in PTModel
  • No restrictions attribute for ITEM 'svm_model' in PTPredict
  • No restrictions attribute for ITEM 'out' in RTModel
  • No restrictions attribute for ITEM 'file' No restrictions attribute for ITEM 'in_text' No restrictions attribute for ITEM 'svm_model' in RTPredict
  • No restrictions attribute for ITEM 'in' No restrictions attribute for ITEM 'mapping_file' in SemanticValidator?
  • No restrictions attribute for ITEM 'in_database' No restrictions attribute for ITEM 'in_peptides' in SequenceCoverageCalculator?
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'info' in SpecLibCreator?
  • No restrictions attribute for ITEM 'lib' in SpecLibSearcher?
  • No restrictions attribute for ITEM 'model_output_file' No restrictions attribute for ITEM 'in_spectra' No restrictions attribute for ITEM 'in_identifications' in SvmTheoreticalSpectrumGeneratorTrainer?
  • No restrictions attribute for ITEM 'out' No restrictions attribute for ITEM 'consensus_centroids' No restrictions attribute for ITEM 'consensus_elements' No restrictions attribute for ITEM 'consensus_features' in TextExporter?
  • No restrictions attribute for ITEM 'ref_masses' No restrictions attribute for ITEM 'tof_const' in TOFCalibration
  • No restrictions attribute for ITEM 'out' in TransformationEvaluation?
  • No restrictions attribute for ITEM 'in' No restrictions attribute for ITEM 'schema' in XMLValidator
  • No restrictions attribute for ITEM 'database' No restrictions attribute for ITEM 'xtandem_executable' No restrictions attribute for ITEM 'default_input_file' in XTandemAdapter

TODOS after Retreat Kühlungsborn 09/2010

Update CDash investigate {seg.fault|(Xvfb vs. TOPPViewTest)} in automatic builds ...

TODOS after Retreat Cornwall 03/2010

The PLANNING can be found under wiki.reinert.ws.

We use this to compile the todos during the retreat.

Retreat 2009 Oberjoch

TOPPView

  • spectrum browser (Mathias)
    • add functionality to display peptide identifications for MS2 specta
    • make configurable (context menu)
  • add option to color feature and consensus feature lines and labels according to feature icon color
  • allow direct import of CSV files containing RT, m/z and label (e.g. as feature layer)
  • layer bar should allow drag-and-drop for resorting layers (Johannes)

File formats

  • traML: add support for inclusion/exclusion lists (Alexandra, Andreas posts feature request)
  • discuss mzQuantML - what requirements do WE have (DISCUSS in mzQuantML)

OpenMS and TOPP

  • unique feature IDs for ConsensusMaps? and everything else (Chris, Clemens) [please see Ticket ]#21 for more details
  • some TOPP tools crash on wrong input data e.g. MS1 vs. MS2 data (ALLE) => revise every tool/algorithm (1. check data, 2.warn, 3.try to correct error 4. abort with an exception if data cannot be corrected)
  • adapt calibration procedures to allow for a list of given masses ... talk about different calibration methods (Alexandra, Erhan)
  • replace OpenMS DB by mzML XML database support (DISCUSS)
  • PeakPicker?: peak width dependent on m/z (DISCUSS)
  • FeatureLinker?
    • new labeled algorithm for tuples with more than 2 elements
    • add algorithm for MRM (Andreas)
    • add algorithm applicable to ConsensusXML e.g. simple merging or improve file converter (Clemens)
  • FeatureLinker?: generate seed list for FeatureFinder? based on known missing features (Clemens)
  • quality assessment of algorithm/tool performance (ALLE)
    • report written to DataProcessing? meta data and Logger
    • FeatureFinder?: % explained signal, number of assigned identifications
    • PeakPicker?: % explained signal
    • IDMapper: % assigned peptides, distribution of assigned and unassigned peptide score
  • new UTILS tool mzMLDiff (Andreas)
    • Numerische Unterschiede in Peaks werden korrekt behandelt => Calibration TOPP tests wieder möglich
    • danach Umstellung float/int arrays als 32-bit?
  • problems with SequestAdapter? and MascotAdapter? (Andreas, Sandro)

Website

  • public Wiki for stuff that does not fit into the tutorials or FAQs on SF if possible
    • Place to store TOPPAS workflows and external tool description
    • Place to store parameter set for different tools and instrument types
    • Contribute section => allow users to contribute missing documentation and insufficient descriptions
  • Produce many screen casts (Knut, Oliver, Stephan)

Misc

  • Commits to the HEAD (ALLE) => Every new class/functionality is tested and documented when committing
  • Bugfix commits (ALLE) => Add 'BUGFIX' keyword to SVN commit message and bug tracker number => Bugfixes are merged into the release branch when a bugfix release is created => update internal FAQ
  • Review TODOs in doxygen - are they still valid? (ALLE)

Neue Maintainer

  • VISUAL
  • FEATUREFINDER (Chris?)
  • MAPMATCHING (Clemens)

Dortmund Visit

On 21-23/10/09 we demonstrated three example OpenMS pipelines (iTRAQ, SILAC, RT Prediction) at the ISAS in Dortmund.
René Zahedi, Urs Lewandrowski and Stefanie Wortelkamp compiled the following list of feature requests:

To Do List
feature requests and bugs for OpenMS
Dortmund meeting 21-23/10/09
Rene Zahedi, Lars Nilse

+++ TOPPView +++
(1) 2D Bereich in TOPPview ausgeschnitten, dann mit Rechts Klick "save visible layer data" -> File Endung *.mzML wurde nicht angehaengen.
(2) Datenpunkte in 2D View sind zu klein bzw. schlecht erkennbar.

+++ INIFileEditor +++
(10) Cut & Paste fuer Transfer von Abschnitten zwischen verschiedenen .ini Files. (TOPPBase kann etwas ähnliches bereits (-write_ini -ini gleichzeitig)... müsste man nur in eine funktion auslagern)
(11) Oder Parameter ueber Rechts-Klick aus einem anderen .ini File importieren.
(12) Open -> Recent File request

+++ MapAligner? +++
(15) Beim Schreiben des .ini files muss der Typ angegeben werden z.B. MapAligner? -type apply_given_trafo -write_ini par.ini Dieser Type selbst erscheint im .ini File und ist editierbar, sollte es aber nicht.
(16) Die Anwendungsbereiche der verschiedenen Typen ist unklar. Docu vervollstaendigen.

+++ MascotAdapterOnline? +++
(18) Mascot server im INIFileEditor definieren. Dann werden
- database
- enzyme
- instrument
- taxonomy
- modifications (!)
vom Server geholt und erscheinen als Drop-Down Menues.
(19) PTMs sollten vom Server geholt werden und im INIFileEditor als DropDown? angezeigt werden. Alternative: vom User selbst definierbar.
(20) Weniger oft verwendete PTMs als hidden im ini File verstecken, siehe 'advanced parameters'.
(21) Nicht jedesmal auf NEW klicken, um weitere Mod hinzuzufuegen, sondern ueber STRG mehrere in einem "Abwasch" auswaehlen.
(22) Evtl das Fenster zur Auswahl vergroessern, da sehr viele Modifikationen vorhanden sind.
(23) Mascot Ergebnisse in csv Format (nach TextExporter? Konvertierung). Wichtige Infos fehlen und gehen entweder in MascotAdapterOnline? oder TextExporter? verloren:
- Massenabweichung aus Mascot (ppm oder Da)
- expectancy score
- Aminosaeuren n- und c-terminal von Schnittstellen sollten in Peptidsequenz angezeigt werden: R.ELVISLIVESK.A (entspricht before und after) => wichtig fuer quasi alle Journals
- Accession sollte bei JEDEM Peptid stehen

Related

Wiki: GSLRemoval
Wiki: Home

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