The CellML models’ walk through the repository
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This document summarizes a retrospective study of the CellML model repository. It found that the repository grew from around 500 models in 2007 to over 2,500 models in 2013. Version control was implemented to track model development over time, revealing over 18,000 total versions and 15,000 differences between versions. Common operations on models in the repository included updates, deletes, inserts, and moves of components. The study provided insights into the evolution of models in the repository.
![The CellML Model Repository
Growth
2007 2008 2009 2010 2011 2012 2013
05001000150020002500
Number of models in the repository
Avg number of nodes in an XML tree
Dec 3rd, 2010: about 800 models with
mean size of ≈56 nodes per model
in repositories SVP_0000*
“Here we describe the development of an online re-
pository of Standard Virtual Biological Parts (SVPs)
– mathematical model components describing the
function of SBPs [(Standard Biological Parts)] which
can be downloaded, extended and recombined to aid
the design, in silico, of synthetic biological systems.”
Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 9](https://image.slidesharecdn.com/8th-cellml-workshop-nz-scharm-150407081133-conversion-gate01/85/The-CellML-models-walk-through-the-repository-14-320.jpg)
The CellML models’ walk through the repository
- 1. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system The CellML models’ walk through the repository A retrospective study MARTIN SCHARM, DAGMAR WALTEMATH Department of Systems Biology & Bioinformatics, University of Rostock http://sems.uni-rostock.de 8th International CellML Workshop Auckland, New Zealand 2014 Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 1
- 2. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system S E Ssimulation experiment management system Graph Database Version Control ∆ ∆ Retrieval Ranking retrieve rank track development store Version 1 Version 2 latest http://sems.uni-rostock.de/ Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 2
- 3. The CellML Model Repository 2007 2008 2009 2010 2011 2012 2013 05001000150020002500 Number of models in the repository Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 3
- 4. Version Control good news A r C B D cycE/cdk2 RB/E2F RB-Hypo free E2F A r B C D E s RB/E2F RB-Hypo free E2F cycE/cdk2 RB-Phos new insights Waltemath et al.: Improving the reuse of computational models through version control. Bioinformatics (2013) 29(6): 742-728; Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 4
- 5. BiVeS Difference Detection A r C B D cycE/cdk2 RB/E2F RB-Hypo free E2F A r B C D E s RB/E2F RB-Hypo free E2F cycE/cdk2 RB-Phos A r B C D A r B C D E s Biochemical Model Version Control System • compares models encoded in standadized formats (currently: and ) • maps hierarchically structured content • constructs a delta (in XML format) • is able to interprete this diff <XML> Diff moves product of r: C deletes product of r: B inserts species: E product of r: E reaction s </XML> mapping diff construction Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 5
- 6. BudHat Diff Visualization A r C B D cycE/cdk2 RB/E2F RB-Hypo free E2F A r B C D E s RB/E2F RB-Hypo free E2F cycE/cdk2 RB-Phos A r B C D A r B C D E s <XML> Diff moves product of r: C deletes product of r: B inserts species: E product of r: E reaction s </XML> • calls BiVeS to construct the diff • displays the result in various formats • the XML diff • a reaction network highlighting the changes using • a human readable report A r B C D E s Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 6
- 7. The CellML Model Repository for r in $repositories do hg clone $r done ∅CellML Files 2702 Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 7
- 8. The CellML Model Repository M 1 1 M 1 2 M 1 3 M 2 2 M 2 3 M 3 3 ∅CellML Files 2702 ∅Versions 18329 Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 7
- 9. The CellML Model Repository M 1 1 M 1 2 M 1 3 M 2 2 M 2 3 M 3 3 ∆ ∆ ∆ ∅CellML Files 2702 ∅Versions 18329 ∅#Deltas 15626 Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 7
- 10. The CellML Model Repository M 1 1 M 1 2 M 1 3 M 2 2 M 2 3 M 3 3 ∆ ∆ ∆ ∅CellML Files 2702 ∅Versions 18329 ∅#Deltas 15626 ∅#relevant 2833 ∅#operations 355.31 Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 7
- 11. The CellML Model Repository Growth 2007 2008 2009 2010 2011 2012 2013 05001000150020002500 Number of models in the repository Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 8
- 12. The CellML Model Repository Growth 2007 2008 2009 2010 2011 2012 2013 05001000150020002500 Number of models in the repository Avg number of nodes in an XML tree Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 9
- 13. The CellML Model Repository Growth 2007 2008 2009 2010 2011 2012 2013 05001000150020002500 Number of models in the repository Avg number of nodes in an XML tree Dec 3rd, 2010: about 800 models with mean size of ≈56 nodes per model in repositories SVP_0000* Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 9
- 14. The CellML Model Repository Growth 2007 2008 2009 2010 2011 2012 2013 05001000150020002500 Number of models in the repository Avg number of nodes in an XML tree Dec 3rd, 2010: about 800 models with mean size of ≈56 nodes per model in repositories SVP_0000* “Here we describe the development of an online re- pository of Standard Virtual Biological Parts (SVPs) – mathematical model components describing the function of SBPs [(Standard Biological Parts)] which can be downloaded, extended and recombined to aid the design, in silico, of synthetic biological systems.” Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 9
- 15. The CellML Model Repository Growth 2007 2008 2009 2010 2011 2012 2013 05101520 units,imports,components mean num units mean num imports mean num components mean num variables 050100150 variables Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 10
- 16. The CellML Model Repository Types of Operation A B C D E F A B G D E C x=“y” x=“z” q qqqq qqqq qqqq qq qq qqq q qqqqq qq q qqq q qqqqqqq qqqq qqqq qqqq qq qq q qqq qqq qqqq qq q qqq q qq qqq qq qq qqqq qqq q qqqq qq qqq qq qqq q qq qq q qq qq qqqq q q qqq qqqqq qqq qq q q qq qqq qqqq qq q q qqq qqqqqqqqq q qq qq q qqq qqqq qqq q qqq qqqq q q qq qqq qq qq qq qq q qq qqq qq qqqq qqq qq qqq qq qq qq q qq q qqq qqq q q qq qqq q qqq qq q qq qqqq q qqq q qqq qq qqq qq qqqq qqq qqq q q qqqq qqqqqqq qqq qq qqq qq qqq qqqqqqqqq qq qqq q qqqq qq qq qq qq qq q qqqqqqq qq qqqq qq qqq qq qq qq qqq q qqq q qq qq qqq qq q q qqqq q qq qq qq q qq qq qqq qq qqqqq qq qqq qq q qqq qqq qqq qq qqqq q qqqqq qqq qqqq qq qq qq q qqq qq q qq qqq qq qqqq q qqq qqq qqqq qq q qqqq qq qqqqq qqqq q q qqqqqq qq q qqq qqqqq qqq qqqq qq q qqq qq qq qqqqq q qq q qq qqq qq qq q qq qq qq qq qq qqq q qqqqqqq qqqq qqqqqqq q qqq qqqqq qqqq qq qqqqqq qq q qqq qq qqqq q q qqqqq q qqq q qq qqq qqqqqqqqq qqq qq qq qqqq qqqq qq qqqqqqq q q 1 5 10 50 100 500 1000 updates deletes inserts moves median 50% Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 11
- 17. The CellML Model Repository Modification Targets <component name=“Template_Species” > <variable name=“time” units=“second” public_interface=“in”/> <variable name=“concentration” units=“nM” initial_value=“concInit” public_interface=“out”/> <variable name=“JGain” units=“nM_per_s” public_interface=“in”/> <math xmlns=“http://www.w3.org/1998/Math/MathML”> <apply> <eq/> <apply> <diff/> <bvar> <ci>time</ci> </bvar> <ci>concentration</ci> </apply> <ci>JGain</ci> </apply> </math> </component> q qq qq qq qq qqq qq q qqq qqq qqqq q q qqqqq qqq qq qq qq qq qqq qqq q qq qq qq qq qqqqq qq q qq qqq qqqq qq qqqq qqq qq qqqq qqq qqqq q q qqqq qq qqq qqqq qq qq q qq qqqq qq qqq qq qqq qq qq q qq qq qqq qq qq qqqqqqq qqq qqq q qq qqqq qq qq qq qq qqqq qq qqqq q qq q qqqq qqq q qq qqqq q q qqq qqqqq qq qq qqqqqq qq qq qqqqq qq q qq qq qqqqq qqq qqq qq q q qqq qq qq qqq qqq qq q qqq qq qq qq qq qqqq qqqq qqqqqqqq qq qqqqq qqq q qqq qqq qqqqq qq qqqqq q qqq qq qq qqq qqq q qqqqq qq qq qqqq qqqqq q q qq q qqqq qqqqq qq qqq q qqqq q q qqqqq qq qq qqq qqqqqq qq qqq qqqq q qq qq qqqq q qqq qq qq qqqqq qq qqq q qq qqq qqq qq qq qq qqq qq qq q qqqq qq qqqq qqqqqq qq q qqq q qqq qqq qqq qq qq q qq qqq q qqqq q qqqqqq qqq qqq q q qqq q qq qq qq qq qq qqqq qqq qq qq qq qq q qq q qqqq q qqq qq q qqqq qq qq q qq qqq qqqq qqqq qqq qqq q qq q qq qq qqq qq qqqq q qq qq q qqqq q qq qqqqq qq qqqq qqq q qqqq qq qqqq qq qqqqq q qqqq qq q qq q qq 1 5 10 50 100 500 1000 document nodes attributes text nodes Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 12
- 18. The CellML Model Repository Operations Novak 1993 12 updates 20 moves 80 inserts 20 deletes Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 13
- 19. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system Thank you for your attention! SEMS group Dagmar Waltemath Ron Henkel Martin Peters Markus Wolfien Rebekka Alm Olaf Wolkenhauer @SemsProject http://sems.uni-rostock.de Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 14