masymos: finding hidden treasures in model repositories
TRANSCRIPT
http://sems.uni-rostock.de
Ron Henkel, Dagmar WaltemathDecember 10, 2014| SWAT4LS
MaSyMoS: Finding hidden treasures in model repositories
“We’ve been hearing a common theme from the academic community– researchers are having difficulty managing and accessing their data. It seems to be an ongoing problem for research scientists” Nature Blogs (2014) Nine Worrying Stats on the Effect of Poor Scientific Data Management.
Model
Entities, network of reactions, math
Fig: Goldbeter (1991), http://www.ncbi.nlm.nih.gov/pubmed/1833774
Annotations
Fig.: BioModels Database
Protocols
Fig.: BioModels Database
Behavior: OscillationTEDDY_0000006Algorithm: Gillespie KiSAO:000029
Compartment: Cell GO:0005623Publication: Goldbeter PMID:1833774 M = inactive CDCD2 Kinase: UniProt:CDK1a_XENIA
Which models contain reactions with 'ATP' as reactant and 'ADP' as product?
Which models are annotated with ‘Adenosine tri-phosphate’?
Give me all the files I need to run this simulation study.
How many models are available for this PubMed entry?
Which are the most frequently used GO annotations in my model set?
Ron Henkel
Find good candidates for features describing my model set. (Alm et al 2014)
Modeling the cell division cycle: cdc2 and cyclin interactions, John J. Tyson, 1991. SBGN Process Description
p-cyclincdc2-p
p-cyclincdc2
cdc2k
p-cyclin
cdc2k-P
cyclin
totalcdc2
Ø
ØØ
Figure courtesy Ron Henkel, https://peerj.com/preprints/376/
Modeling the cell division cycle: cdc2 and cyclin interactions, John J. Tyson, 1991. SBGN Process Description
p-cyclincdc2-p
p-cyclincdc2
cdc2k
p-cyclin
cdc2k-P
cyclin
totalcdc2
Ø
ØØ
Sys
tem
s B
iolo
gy
Ont
olo
gy (
OW
L)
Tys
on 1
991
Sim
ula
tion
Exp
erim
ent
Des
crip
tion
(SE
D-M
L)
Tys
on 1
991
Mo
del (
SB
ML)
Kin
etic
Sim
ulat
ion
Alg
orith
m O
ntol
ogy
(OW
L)
Tys
on
199
1 M
odel
(C
ellM
l)KISAO:
Ontology
KISAO:000
KISAO:019
KISAO:352
KISAO:020
KISAO:097 KISAO:201
KISAO:433KISAO:273
KISAO:447
Document
SEDML
Modelref-erence
OutputData-
generatorSimulationTask
Variable Variable
Document
Tyson1991 Cell Cycle 6
var
C2 pM CellReaction3 CP
Uniprot:P04551
GO:0005623
Interpro: IPR006670
isDescribedBy
EC-Code: 3.1.3.16
Document
Tyson_1991
C2CP
time
environment
timetime CPC2CP C2
SBO:000064
SBO:Ontology
SBO:0000
SBO:544 SBO:236SBO:231 SBO:064SBO:545 SBO:004 SBO:003
Keggsce04111
Pubmed:1831270
Figures courtesy Ron Henkel, https://peerj.com/preprints/376/
Try it out: https://sems.uni-rostock.de/projects/masymos/
HERMES-Forschungsförderung der Universität Rostock
Martin Scharm Martin Peters Markus Wolfien Srijana Kayastha (not in the picture) Vivek Garg (not in the picture)Fabienne Lambusch (not in the picture)Dagmar Waltemath
@SemsProjectRon HenkelRebekka Alm