sed-ml support in jws online
TRANSCRIPT
S E Ssimulation experiment management system
SED-ML support in JWS OnlineUsing SED-ML and COMBINE archives to reproduceSimulation Results
MARTIN PETERS, JACKY SNOEP, DAGMAR WALTEMATHDepartment of Systems Biology & Bioinformatics, University of Rostock
Department of Biochemistry, Stellenbosch University, South Africa
2016
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Table of contents
Reproducing Simulations
About JWS Online
What’s new in JWS Online?
Summary – Achievements and Limitations
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Reproducing FiguresRunning a simulation by reading a paper
values of the total proteins that were determined byquantitative immunoblotting, total concentrations of phos-phorylated STAT5 were calculated with the model. Addition-ally to the observations at the protein level, expression kineticsof CIS and SOCS3 were determined at mRNA levels usingquantitative RT–PCR to validate the data from the microarray
experiments and to improve the temporal resolution at earlytime points for parameter estimation (Figure 3C).To provide the required information content necessary to
disentangle the role of the dual negative feedback regulation,we also performed experiments applying specific perturba-tions. Time-resolved activation of the pathway was monitored
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Quantitative RT–PCR
t = 10 min
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Figure 3 Model calibration with experimental data of JAK2-STAT5 signaling obtained by different experimental techniques. For all experiments, primary CFU-E cellswere starved and stimulated with 5 U/ml Epo. At the indicated time points, samples were subjected to (A) quantitative immunoblotting, (B) mass spectrometry analysis or(C) qRT–PCR. Experimental data (black circles) with estimated standard errors and trajectories of the best fit (solid lines) are represented. Mass spectrometrydata represent replicates of four independent experiments. (For additional experimental data used for the model calibration, see Figure 4 and SupplementaryFigures S11–S23.) In total, 531 data points representing 18 different experimental conditions were used for model calibration. Source data is available for this figure atwww.nature.com/msb.
Dual feedback controls JAK2-STAT5 signalingJ Bachmann et al
& 2011 EMBO and Macmillan Publishers Limited Molecular Systems Biology 2011 5
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Reproducing FiguresDemonstrating the Magic
Demo shows experiment database in JWS Online in action.Try it out here:
https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate
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About JWS Onlineand the circle of reproducibility
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About JWS Onlineand the circle of reproducibility
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About JWS Onlinea platform for curation and sharing
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About JWS Onlinea database for kinetic models
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About JWS Onlinea database for kinetic models
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About JWS Onlineand what we wanted to advance
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About JWS Onlineand SED-ML support
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Introducing SED-MLto JWS Online
• Simulation Experiment Description – Markup Languagehttp://identifiers.org/combine.specifications/
sed-ml.level-1.version-2
• Enabling reproducible in silico experiments since 2007
• Sophisticated multi-model/multi-experiment setups
• Support for experimental data and post-processing
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About JWS Onlineand the single-click reproducibility
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About JWS Onlineand the single-click reproducibility
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About JWS Onlineand COMBINE Archive support
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About COMBINE archivesone file to share them all
• Container format for bundling belonging to modeling or simulation experiment
• Enriched with meta information according to the OMEX standard
• Enable to bundle all necessary resources for reproduction
• http://co.mbine.org/standards/omex
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Achievementsand all the other cool stuff
• Dockerized JWS Onlinehttps://jws-docs.readthedocs.io/10_docker.html
• Introduced a basic set of APIs into JWS Onlinehttps://jws-docs.readthedocs.io/8_rest.html
• Widely extended the handling of Manuscript meta information
• Implemented SED-ML database into JWS Onlinehttps://jjj.bio.vu.nl/models/experiments/
• Enabled import and export of COMBINE Archives
• Introduced Reproduction of Simulation Experiments –by a single click
https://jjj.bio.vu.nl/models/experiments/
bachmann2011/simulate
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Limitationsand all the non-cool stuff
• Only Time-Course Simulations
• No Repeated-Tasks
• Excel Spreadsheets instead of NuML
• Only 2D Plots
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S E Ssimulation experiment management system
That’s it!
SEMS Task Force JWS Team
Fabienne LambuschMartin ScharmDagmar WaltemathMariam Nassar
Tom GebhardtVasundra ToureRon HenkelOlaf Wolkenhauer
Dawie van NiekerkJohann EicherDaniel PalmJacky Snoep
funded by
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S E Ssimulation experiment management system
That’s it!Want to talk? Drop me a message!
@[email protected]@uni-rostock.de
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S E Ssimulation experiment management system
References
• Köhn, Dagmar, and Nicolas Le Novere. 2008. SED-ML–an XML Format for the Implementation ofthe MIASE Guidelines. In Computational Methods in Systems Biology, 176–190. Springer.
• Olivier, Brett G, and Jacky L Snoep. 2004. Web-Based Kinetic Modelling Using JWS Online.Bioinformatics 20 (13): 2143–2144.
• Waltemath, Dagmar, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov,Andrew K Miller, Ion I Moraru, et al. 2011. Reproducible Computational Biology Experiments withSED-ML-the Simulation Experiment Description Markup Language. BMC Systems Biology 5 (1):1.
• Wolstencroft, K, Owen, S, Krebs, O, Nguyen, Q, Stanford, NJ, Golebiewski, M, Weidemann, A,Bittkowski, M, An, L, Shockley, D, Snoep, JL, Mueller, W, Goble, C (2015) SEEK: a systemsbiology data and model management platform. BMC Systems Biology, Issue 9:33, pages 33,2015. DOI:10.1186/s12918-015-0174-y
• Bergmann, Frank T., Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, MartinGolebiewski, Michael Hucka, et al. One File to Share Them All: Using the COMBINE Archive andthe OMEX Format to Share All Information about a Modeling Project. arXiv:1407.4992 [Cs,Q-Bio], July 18, 2014. http://arxiv.org/abs/1407.4992.
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