FuGEFlow
Development of Flow cytometry experimental workflow description based on FuGE
Comments on FuGE: FICCS Comments on FuGE v1(Mar07) Specification
Flow Use Cases: Use cases for flow cytometry data exchange, storage and integration
Mapping rules: from MIFlowCyt to FuGEFlow: Proposal, by Olga (Updated June 9, 2008)
Mapping description syntax and abbreviations of frequently used terms
MIFlowCyt concepts and mapping to FuGE
FuGEFlow model
How to get current version of the FuGEFlow
Diagrams
Diagrams for the Data Analysis section.
Diagrams for Material (draft by Max, Nov 14, 2007; last updated on Jan 31, 2008) ( Change Log)
Equipment Diagrams: FugeFlow_Equipment_20070131.ppt
Diagrams for Instrumentation, Acquisition, and Fluorescent Reagents (draft by Peter)
FuGE Workshop, Manchester University Dec 13,14, 2007
Presentations
FuGEflow: FICCS_PeterWilkinson_20071212.ppt
AnalysisXML: Eisenacher_FuGE_Manchester.ppt
GelML: Frank-GelMl-v1.ppt
spML: spMLpresentation.ppt
symba-full: symba-full.pdf
Other
FuGE that points to 3.2 final: FuGE-v1-profile.mdzip
FuGE paper planning: FuGEPaper.doc
Allyson Lister's notes on her BLOG: http://lurena.vox.com/library/post/fuge-users-workshop-13-14-december-2007.html
* FuGE_bestPractices: Rough list, best practices
Revised
- Updated material and treatment (by Max, November 14, 2007)
- Updated instrument (by Peter, October 31, 2007)
- Updated material and treatment (by Max, October 17, 2007)
- Updated experiment overview (by Olga, October 16, 2007)
- Updated instrument (by Peter, October 2, 2007)
- Updated data analysis (by Josef, September 20, 2007)
FuGE Extensions
Currently, we do have the following FuGE-based (pieces of) models of experimental workflow in flow cytometry:
- Initial FuGE extension done by Josef and Peter (Nov 4, 2006)
- Olga’s gating, transformation, and compensation files extension (Nov 14, 2006)
- Settimo’s approach to gating (Dec 6, 2006)
- Josef’s logicle transformation extension example (Dec 12, 2006)
Olga’s FuGE-motivated approach to encode MIFlowCyt into UML (Dec 22, 2006)
New Development Strategy
All the different approaches of extending FuGE have provided valuable lessons for all of us. The initial models are not quite compatible and not completely valid for use with model-driven architecture tools (AndroMDA). The group has agreed to start refactoring the model using the following strategy:
- We will establish a developer group working directly on the extensions: Josef, Max, Olga, Peter (open to others if someone else is interested)
- Each particular extension shall be
- agreed within the developer group,
- performed by a member (or members) of the developer group,
formally checked/validated against AndoMDA tools (see FuGE-to-XSD guidelines on how to derive XML schemas from FuGE-based UML2 models),
- inspected and agreed by the developer group,
- presented to the broader FICCS community.
High Level Package Hierarchy
Initial step will be high level only: create and agree the UML package structure for further extensions, each package having a "content definition" attached. Proposals to come.
Work in Progress
MDZIP files
Refactored, formally validated UML model, with the Reporter and Detector parts only (as originally suggested during the meeting in Dallas). The extension contains one class diagram only.
The UML2 model:
The XML Schema (xsd) generated from the UML2 model using AndroMDA. The process of generating the XSD served also as automated formal syntax/integrity validation.
Obsoleted materials
Has been moved.