Last modified by oliviaeriksson on 2022/12/13 14:50
From version 11.1
edited by oliviaeriksson
on 2022/12/08 15:46
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To version 4.5
edited by oliviaeriksson
on 2022/11/24 11:22
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12 12  (((
13 13  == Introduction ==
14 14  
15 -The subcellular modeling and simulation services consist of tools for building and simulating subcellular level models. Such models often describe molecular signaling pathways within the cell. The service contains two different projects. //The subcellular model building and calibration tool set// (1) is focused on model calibration (parameter estimation) using simpler, one compartmental, models. //The subcellular simulation webapp (2),// allows the user to construct more detailed compartmental models using the [[STEPS>>https://steps.sourceforge.net/STEPS/default.php]] or [[BioNetGen>>https://bionetgen.org]] simulators. The tools are interoperable so that e.g. models can be constructed and calibrated using (1) and then simulated with more details in (2). The calibration toolset also allows uncertainty quantification and sensitivity analysis.
15 +The subcellular modeling and simulation services consist of tools for building and simulating subcellular level models. Such models often describe molecular signaling pathways within the cell. The service contains two different projects. //The subcellular model building and calibration tool set// (1) is focused on model calibration (parameter estimation) using simpler, one compartmental, models. //The subcellular simulation webapp (2),// allows the user to construct more detailed compartmental models using the STEPs or BioNetGen simulators. The tools are interoperable so that e.g. models can be constructed and calibrated using (1) and then simulated with more details in (2). The calibration toolset also allows uncertainty quantification and sensitivity analysis.
16 16  
17 17  == (% class="row" %)1. Subcellular model building and calibration tool set(%%) ==
18 18  
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20 20  
21 21  [1] Lubitz, T., Hahn, J., Bergmann, F.T., Noor, E.,. Klipp, E, Liebermeister, W. (2016). SBtab: A flexible table format for data exchange in systems biology. Bioinformatics, 15;32(16), 2559-61.
22 22  
23 -[[**Golden paragraph **>>https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/Molecular%20and%20subcellular%20level%20description/]]
23 +=== **Source Code** ===
24 24  
25 -=== Source Code ===
25 +Source code for model processing and Bayesian parameter estimation ([[https:~~/~~/github.com/icpm-kth/uqsa/>>https://github.com/icpm-kth/uqsa/]]);
26 26  
27 - [[https:~~/~~/github.com/icpm-kth/>>https://github.com/icpm-kth/]] (mirrored on GitLab)
27 +=== **Documentation ** ===
28 28  
29 -=== Documentation** ** ===
29 +Documentation for** **modelling workflow with Bayesian parameter estimation ([[https:~~/~~/github.com/icpm-kth/>>url:https://github.com/icpm-kth/]])
30 30  
31 -[[https:~~/~~/github.com/icpm-kth/>>url:https://github.com/icpm-kth/]]
31 +=== **Examples** ===
32 32  
33 -=== Examples ===
33 +Jupyter notebook example of modelling workflow with Bayesian parameter estimation ([[https:~~/~~/github.com/icpm-kth/>>url:https://github.com/icpm-kth/]] )
34 34  
35 -Jupyter notebook example of modelling workflow with Bayesian parameter estimation can be found[[ here>>https://github.com/icpm-kth/uqsa/blob/master/UQ.ipynb]].
35 +=== **Publication** ===
36 36  
37 -=== Publications ===
38 -
39 -Santos, Pajo, et al (2021), Neuroinformatics; **20**, 241–259, [[https:~~/~~/doi.org/10.1007/s12021-021-09546-3>>url:https://doi.org/10.1007/s12021-021-09546-3]] ;
40 -
41 -Eriksson, et al (2019), Bioinformatics, 35(2), 284-292, [[https:~~/~~/doi.org/10.1093/bioinformatics/bty607>>url:https://doi.org/10.1093/bioinformatics/bty607]]__; __
42 -
43 -Church, et al (2021),__ __//eLife// **10**:e68164, [[https:~~/~~/doi.org/10.7554/eLife.68164>>url:https://doi.org/10.7554/eLife.68164]]
37 +Santos, Pajo, et al (2021), Neuroinformatics; **20**, 241–259, [[https:~~/~~/doi.org/10.1007/s12021-021-09546-3>>url:https://doi.org/10.1007/s12021-021-09546-3]] ; Eriksson, et al (2019), Bioinformatics, 35(2), 284-292,[[ >>url:https://doi.org/10.1093/bioinformatics/bty607]][[https:~~/~~/doi.org/10.1093/bioinformatics/bty607>>url:https://doi.org/10.1093/bioinformatics/bty607]]__; __Church, et al (2021),__ __//eLife// **10**:e68164, [[https:~~/~~/doi.org/10.7554/eLife.68164>>url:https://doi.org/10.7554/eLife.68164]]
44 44  )))
45 45  
46 46  
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53 53  
54 54  )))
55 55  )))
56 -
57 -== 2. Subcellular Simulation Webapp ==
58 -
59 -An online tool for configuring and running compartmental subcellular simulations. This tool allows import of SBML model files from the subcellular model building and calibration toolset workflow or other external sources. The tool ([[https:~~/~~/subcellular.humanbrainproject.eu>>url:https://subcellular.humanbrainproject.eu/]]) allows users to setup and configure BioNetGen and STEPS simulations. Users can populate mesh models of spines and other neural structures, and run stochastic simulations of signalling pathways.
60 -
61 -=== Source Code ===
62 -
63 -[[https:~~/~~/github.com/bluebrain/bluenaas-subcellular>>url:https://github.com/bluebrain/bluenaas-subcellular]]
64 -
65 -=== Documentation and Examples ===
66 -
67 -[[https:~~/~~/subcellular-bsp-epfl.apps.hbp.eu/model>>https://subcellular-bsp-epfl.apps.hbp.eu/model]]
68 -
69 -=== Publication ===
70 -
71 -Santos, Pajo, et al (2021), Neuroinformatics; [[https:~~/~~/doi.org/10.1007/s12021-021-09546-3>>url:https://doi.org/10.1007/s12021-021-09546-3]] ;
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