MaSyMoS is a tool for finding hidden treasures in model repositories by enabling semantic searches across models, annotations, and associated data. It addresses a common problem researchers face in difficulty managing and accessing their data. MaSyMoS allows users to query model repositories to find models associated with certain publications, genes, or behaviors. It also provides files needed to run simulations from retrieved models. The tool aims to help researchers better discover, organize, and leverage existing computational models.

1. MaSyMoS:
Finding hidden treasures in model repositories
Ron Henkel, December 10, 2014| SWAT4LS Dagmar Waltemath
http://sems.uni-rostock.de

2. “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.

3. Model
Entities, network
of reactions, math
Fig: Goldbeter (1991),
http://www.ncbi.nlm.ni
h.gov/pubmed/1833774
Annotations
Compartment: Cell GO:0005623
Publication: Goldbeter
PMID:1833774
M = inactive CDCD2 Kinase:
UniProt:CDK1a_XENIA
Fig.: BioModels Database
Protocols
Fig.: BioModels Database
Behavior: Oscillation
TEDDY_0000006
Algorithm: Gillespie
KiSAO:000029

4. Which are the most frequently used GO
annotations in my model set?
Which models are annotated with
‘Adenosine tri-phosphate’?
How many models are available for this
PubMed entry?
Give me all the files I need to run
this simulation study.
Modeling the cell division cycle: cdc2 and cyclin interactions, John J. Tyson,
Ø
Ø Ø
Which models contain reactions with
'ATP' as reactant and 'ADP' as product?
Ron Henkel
1991. SBGN Process Description
p-cyclin
cdc2
p-cyclin
cdc2-p
p-cyclin
cdc2k
cdc2k-P
cyclin
totalcdc2
Find good candidates for features describing my
model set. (Alm et al 2014)
Figure courtesy Ron Henkel, https://peerj.com/preprints/376/

5. Modeling the cell division cycle: cdc2 and cyclin interactions, John J. Tyson,
1991. SBGN Process Description
p-cyclin
cdc2
p-cyclin
cdc2-p
p-cyclin
cdc2k
cdc2k-P
cyclin
totalcdc2
Ø
Ø Ø
Tyson 1991 Model (SBML)
Systems Biology Ontology (OWL)
Tyson 1991 Simulation Experiment Description (SED-ML)
Kinetic Simulation Algorithm Ontology (OWL)
Tyson 1991 Model (CellMl)
KISAO:
Ontology
KISAO:097 KISAO:000
KISAO:201
KISAO:019
KISAO:352
KISAO:273 KISAO:433
KISAO:020
KISAO:447
Document
SEDML
Modelref-erence
Output
Data-generator
Task Simulation
Variable Variable
Document
Tyson1991
Cell Cycle 6
var
Kegg
sce04111
Pubmed:
1831270
Reaction3 C2 CP pM Cell
Uniprot:
P04551
GO:
0005623
Interpro:
IPR006670
isDescribedBy
EC-Code:
3.1.3.16
Document
Tyson_1991
CP environment
C2
CP C2 time time C2 CP
time
SBO:
000064
SBO:
Ontology
SBO:0000
SBO:545 SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:064
Figures courtesy Ron Henkel, https://peerj.com/preprints/376/

6. Try it out: https://sems.uni-rostock.de/projects/masymos/
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
Ron Henkel @SemsProject
Rebekka Alm
HERMES-Forschungsförderung
der Universität Rostock