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Last modified by oliviaeriksson on 2022/12/13 14:50
From version 8.1
edited by oliviaeriksson
on 2022/12/08 15:29
Change comment: There is no comment for this version
To version 4.7
edited by oliviaeriksson
on 2022/11/24 11:37
Change comment: There is no comment for this version

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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 +**[[Golden paragraph>>https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/]] **
24 24  
25 -=== Source Code ===
25 +=== **Source Code** ===
26 26  
27 - [[https:~~/~~/github.com/icpm-kth/>>https://github.com/icpm-kth/]] (mirrored on GitLab)
27 +Source code for model processing and Bayesian parameter estimation ([[https:~~/~~/github.com/icpm-kth/uqsa/>>https://github.com/icpm-kth/uqsa/]], mirrored );
28 28  
29 -=== Documentation** ** ===
29 +=== **Documentation ** ===
30 30  
31 -[[https:~~/~~/github.com/icpm-kth/>>url:https://github.com/icpm-kth/]]
31 +Documentation for** **modelling workflow with Bayesian parameter estimation ([[https:~~/~~/github.com/icpm-kth/>>url:https://github.com/icpm-kth/]])
32 32  
33 -=== Examples ===
33 +=== **Examples** ===
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 +Jupyter notebook example of modelling workflow with Bayesian parameter estimation ([[https:~~/~~/github.com/icpm-kth/>>url:https://github.com/icpm-kth/]] )
36 36  
37 -=== Publications ===
37 +=== **Publication** ===
38 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]]
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]] ; 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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