Projektmanagement im Softwarebereich OpenMS 2011

Wiki Seite zum Praktikum Projektmanagement im Softwarebereich - OpenMS 2011.

Zeitplan

01.04.2011 (10.00 Uhr) Vorbesprechung
04.04. - 08.04.2011 C++-Kurs
11.04. - 12.04.2011 OpenMS CodingTutorial
12.04.2011 Projektvergabe
21.04.2011 Projektpräsentation
30.05.2011 Abgabe
31.05.2011 Abschlusspräsentation

Vorbesprechung

  • Projektbeschreibung
  • Templates für Präsentationen + Abschlussbericht(LaTex) siehe unten
  • Homework:
    • installieren von VisualStudio 2008/G++/QtCreator/XCode
    • Paper lesen [SturmEtal08,KohlbacherEtal07] [ALLE] + indiv. Projektliteratur
    • VPN/WLAN

OpenMS Tutorial

Montag

  • Einführung in SVN, CMake, VS/QtCreator/XCode
  • Installieren von OpenMS source
  • Library Structure
    • Coding Convention
    • FAQ
    • Where is what
  • OpenMS External Project HowTo

Dienstag

  • Coding Tutorials
  • TOPPView
  • TOPPAS
  • Project Assignment

Homework

  • talk (21.04)
  • plan the project (milestones)

Projektpräsentation

Vortrag
  • Theorie
  • Ansatz
  • Interface/Interaction
  • Milestone plan

Projekte

Eine genaue Beschreibung der Projekte wird in kürze hinzugefügt

Fractional Averagines

Already implemented in NitPick [RenardEtal08]. Reimplement and benchmark.

Deviations from Averagines

Averagines are the most common mean to assess if a signal orginiates from a peptide. However the model is not perfect. Especially for exotic peptides (sulfur heavy) the deviation is quite large. But how large? Given the averagine model, compute a theoretical digest of a protein database and determine the distribution of deviation from the model given knowledge about the sequence. Determine thresholds which are sensible in real life and find which peptides are affected. Does anything change when using a detectability filter?

Simulation of SILAC Labeling

MSSimulator is a simulator for mass spectrometry measurements integrated into OpenMS. One of its abilities is the simulation of labeled experiments. The SILAC[OngEtal02] technique is currently supported but only in a very elementary way. The aim of the project is the extension of this labeling module to be more realistic (e.g., multi-channel SILAC).

Simulation of ICPL Labeling

MSSimulator is a simulator for mass spectrometry measurements integrated into OpenMS. One of its abilities is the simulation of labeled experiments. The ICPL[SchmidtEtal05] is currently not included and therefor will be implemented in this project.

Robust Estimation of Peak FWHM

PeakPicking is one of the most important signal processing steps in analyzing MS data. One very competitive solution[LangeEtal07] is available in OpenMS. To make this algorithm totally fool-proof the important FWHM (full width at half max) needs to be set properly. Usually this needs to be set by the user, using information from the experimental setup (instrument resolution, instrument type). However, it is also possible to estimate FWHM from the data, thus basically making PeakPicking fully automated in medium to low-res data. We will use simulated data for performance assessment and develop an algorithm that allows to estimate FWHM from data.

Referenzen

[RenardEtal08]
Bernhard Y Renard, Marc Kirchner, Hanno Steen, Judith a J Steen, and Fred a Hamprecht. NITPICK: peak identification for mass spectrometry data. BMC bioinformatics, 9:355, January 2008. [ DOI | http ]
[SturmEtal08]
Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher. OpenMS - an open-source software framework for mass spectrometry. BMC Bioinf., 9:163, 2008. [ DOI | http ]
[LangeEtal07]
Eva Lange, Clemens Gröpl, Ole Schulz-Trieglaff, Andreas Leinenbach, Christian Huber, and Knut Reinert. A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics (Oxford, England), 23(13):i273--81, July 2007. [ DOI | http ]
[KohlbacherEtal07]
Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, and Marc Sturm. TOPP--the OpenMS proteomics pipeline. Bioinformatics (Oxford, England), 23(2):e191--7, 2007. [ DOI | http ]
[SchmidtEtal05]
Alexander Schmidt, Josef Kellermann, and Friedrich Lottspeich. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics, 5(1):4--15, January 2005. [ http ]
[OngEtal02]
Shao-En Ong, Blagoy Blagoev, Irina Kratchmarova, Dan Bach Kristensen, Hanno Steen, Akhilesh Pandey, and Matthias Mann. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Molecular & cellular proteomics : MCP, 1(5):376--86, May 2002. [ http ]

Vorlagen für Abschlussbericht und Präsentationen

Formular für regelmäßiges progress meeting

Comments

 

Topic attachments
I Attachment Action Size Date Who Comment
CodingConvention.pdfpdf CodingConvention.pdf manage 1456.3 K 11 Apr 2011 - 14:11 StephanAiche Coding Convention Slides
GitTutorial.pdfpdf GitTutorial.pdf manage 1058.0 K 11 Apr 2011 - 10:18 StephanAiche Git Slides
Introduction_to_CMake.pdfpdf Introduction_to_CMake.pdf manage 911.1 K 11 Apr 2011 - 09:45 ChrisBielow  
subversion.pdfpdf subversion.pdf manage 751.4 K 11 Apr 2011 - 09:48 ChrisBielow  
Topic revision: r13 - 19 May 2011, ChrisBielow
 
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