Transcript The 8 Queens Problem (and how to solve it)

Software Project
MassAnalyst
Roeland Luitwieler
Steven Bitter
June 26, 2006
Overview
Reminder
Progress
Demo: Spectre
Conclusion
2
Reminder
Project initiators
Scientific background
The need for software tools
3
Project initiators
Dr. ir. Bas van Breukelen
Dr. ir. Jeroen Krijgsveld
Department of Biomolecular
Mass Spectrometry
4
Scientific background:
Proteomics
Our body consists of cells
Cell functionality and structure is offered by
proteins
Proteomics
Main research areas:
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Identification of proteins
Interaction of proteins
Comparison of protein levels
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Mass Spectrometry (MS)
Technique using a mass
spectrometer
Input: sample of peptides
Output: mass spectrum
Frequencies of particles of certain
masses
 Full peptide sequence can be derived
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Mass Spectrometry (MS)
Improvements for better analysis
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Use chromatography
Spreads input over time
 Output: a sequence of MS’s
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Use “recursive” MS
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Called MS/MS (or MS2 or tandem MS)
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Mass Spectrometry (MS)
Improvements for better analysis (2)
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Use bioinformatics
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Lots of redundant / boring work is taken care of!
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Tools exist, but…
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Lots of different tools to do different things
Functionality not always as desired
They also lack functionality
Not easily extendable
Solution: develop new software
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Progress
Spectre:
Requirements ↔ features
 Our approach
 Planning
 Problems
 Documentation
 Future
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Requirements ↔ features
According to SP site:
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Load raw data files
Visualize data
Filter data
Quantify data
Analyze data (and visualize this)
Export results
Extendable
Well documented
11
Requirements ↔ features
According to SP site:
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Load raw data files
Visualize data
Filter data
Quantify data
Analyze data (and visualize this)
Export results
Extendable
Well documented
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Load raw data files
mzXML → v0.1
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Added optional use of rand. acc. → v0.1.1
pepXML → v?
Wasn’t required, but we tried
 Unexpected problems encountered
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Requirements ↔ features
According to SP site:

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Load raw data files
Visualize data
Filter data
Quantify data
Analyze data (and visualize this)
Export results
Extendable
Well documented
14
Visualize data
Sample list → v0.1
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Added use of workspaces → v0.1
MS (with “stacking” and zooming) → v0.1
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Cross sections → v0.1
MS/MS → v0.1
Peptide information → v?
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Need pepXML for that…
Contrast tool → v0.2
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Requirements ↔ features
According to SP site:
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Load raw data files
Visualize data
Filter data
Quantify data
Analyze data (and visualize this)
Export results
Extendable
Well documented
16
Filter data
Noise filter → v0.1.1
Statistical noise filter → v0.1.1
Added filter manager → v0.1.1
Added finalization → v0.1.1
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Requirements ↔ features
According to SP site:

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
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Load raw data files
Visualize data
Filter data
Quantify data
Analyze data (and visualize this)
Export results
Extendable
Well documented
18
Quantify data
Ratio calculation → v0.2
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Requirements ↔ features
According to SP site:
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Load raw data files
Visualize data
Filter data
Quantify data
Analyze data (and visualize this)
Export results
Extendable
Well documented
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Analyze data (and
visualize this)
Warping → v0.2
Peak detection → v0.2
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Requirements ↔ features
According to SP site:




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
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Load raw data files
Visualize data
Filter data
Quantify data
Analyze data (and visualize this)
Export results
Extendable
Well documented
22
Export results
Images → v0.1
Results quantification → v0.2
Modified mzXML → v?
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We didn’t get to that
Modified pepXML → v?
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You know…
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Requirements ↔ features
According to SP site:








Load raw data files
Visualize data
Filter data
Quantify data
Analyze data (and visualize this)
Export results
Extendable
Well documented
24
Requirements ↔ features
According to SP site:








Load raw data files
Visualize data
Filter data
Quantify data
Analyze data (and visualize this)
Export results
Extendable
Well documented
25
Systematic approach
to the problem
Phased development
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Three versions
Lots of diagrams
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Application of courses MSO, PM
Sub-teams
HCI team and data layer team
 data visualization team
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Extreme Programming
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Planning
Version
0.1
0.1.1
0.2
Planning
week 19
week 23
week 27
Reality
week 18
week 25
week 26
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Problems
PepXML
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Missing Link
Memory usage while loading
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Random access
License
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GPL vs. LGPL
Data formats
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New Version mzXML
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Documentation
Java Doc
Package Doc
Quick Start
Reference document
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Future
Final Release tomorrow
Next year part two ?
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Demonstration
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Conclusion
Spectre: a modular and extendable
program
A combination of many different
requirements
Any questions?
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The structure of
Spectre
GUI
1
1
Processor
*
Workspace
4
Graph
*
Sample
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