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edited by oliviaeriksson
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edited by oliviaeriksson
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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/]] **
23 23  
24 24  === Source Code ===
25 25  
26 - [[https:~~/~~/github.com/icpm-kth/>>https://github.com/icpm-kth/]] (mirrored on GitLab)
27 + [[https:~~/~~/github.com/icpm-kth/>>https://github.com/icpm-kth/uqsa/]] (mirrored on GitLab)
27 27  
28 28  === Documentation** ** ===
29 29  
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63 63  
64 64  === Documentation and Examples ===
65 65  
66 -[[https:~~/~~/subcellular-bsp-epfl.apps.hbp.eu/model>>https://subcellular-bsp-epfl.apps.hbp.eu/model]]
67 +https:~/~/subcellular-bsp-epfl.apps.hbp.eu/docs/docs.html
67 67  
68 -=== Publication ===
69 +=== Publication ===
69 69  
70 70  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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