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This comprises the whole LiSyM network
Programme: LiSyM: Liver Systems Medicine
SEEK ID: https://seek.lisym.org/projects/13
Public web page: http://www.lisym.org
Organisms: Rattus norvegicus, Rattus rattus, Mus musculus, Homo sapiens
FAIRDOM PALs: Max Lüdemann, Matthias König, Vincent Moser, Matthias Reichert, Lutz Brusch, Christian Hudert, Janine Koehncke, Madlen Matz-Soja
Project start date: 1st Jan 2016
Related items
- People (112)
- Institutions (35)
- Investigations (0+1)
- Studies (0+1)
- Assays (0+4)
- Data files (8+17)
- Models (1)
- SOPs (1)
- Publications (52)
- Presentations (41+45)
- Events (55+2)
- Documents (1+15)
Projects: LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI), LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), LiSyM network, LiSyM Scientific Leadership Team (LiSyM-LT)
Institutions: University of Freiburg - Institute of Physics, LiSyM programme directorate

Projects: LiSyM network, LiSyM-Krebs
Institutions: HITS gGmbH
This asset is going to be changed later. Its purpose is providing an accessible URL that stays.
Creator: Madlen Matz-Soja
Submitter: Wolfgang Müller
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: None
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Sonja Kleeschulte
Submitter: Sonja Kleeschulte
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Johannes Bausch
Submitter: Johannes Bausch
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Johannes Bausch
Submitter: Johannes Bausch
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
For the spatio-temporal dynamics of bile transport, bile canalicular dilation, mechanical stimulation and transduction of YAP signaling during liver regeneration see the open access publication and its appendix:
Meyer et al. (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985. https://doi.org/10.15252/msb.20198985
The model format is MorpheusML that can readily be loaded and run in the free and open source software
...
Creator: Lutz Brusch
Submitter: Lutz Brusch
Model type: Agent based modelling
Model format: MorpheusML
Environment: Morpheus
Organism: Mus musculus
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
The purpose of this document is to define procedures to follow for exchanging the following items between collaboration partners within the LiSyM network:
a) Exchanging samples of human origin obtained from a natural person (i.e. a patient or other human subject).
b) Exchanging material derived from samples of human origin as defined in a).
c) Exchanging associated data describing samples of human origin and derived material as defined in a) and b).
d) Exchanging data derived from samples of human
...
Creators: Martin Golebiewski, Frank Lammert, Wolfgang Müller
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: Christian H. Holland, Jovan Tanevski, Javier Perales-Patón, Jan Gleixner, Manu P. Kumar, Elisabetta Mereu, Brian A. Joughin, Oliver Stegle, Douglas A. Lauffenburger, Holger Heyn, Bence Szalai, Julio Saez-Rodriguez
Date Published: 1st Dec 2020
Publication Type: Journal
DOI: 10.1186/s13059-020-1949-z
Citation: Genome Biol 21(1),36
Abstract (Expand)
Authors: K. B. Cokan, Z. Urlep, G. Lorbek, M. Matz-Soja, C. Skubic, M. Perse, J. Jeruc, P. Juvan, T. Rezen, D. Rozman
Date Published: 9th Nov 2020
Publication Type: Journal
PubMed ID: 33182326
Citation: Cancers (Basel). 2020 Nov 9;12(11). pii: cancers12113302. doi: 10.3390/cancers12113302.
Abstract (Expand)
Authors: F. E. A. Mohamed, S. Hammad, T. V. Luong, B. Dewidar, R. Al-Jehani, N. Davies, S. Dooley, R. Jalan
Date Published: 25th Jul 2020
Publication Type: Journal
PubMed ID: 32703481
Citation: Pathol Res Pract. 2020 Aug;216(8):152980. doi: 10.1016/j.prp.2020.152980. Epub 2020 May 19.
Abstract (Expand)
Authors: S. Brunak, C. Bjerre Collin, K. Eva O Cathaoir, M. Golebiewski, M. Kirschner, I. Kockum, H. Moser, D. Waltemath
Date Published: 24th Jul 2020
Publication Type: Journal
PubMed ID: 32827396
Citation: J Integr Bioinform. 2020 Jul 24;17(2-3). pii: /j/jib.2020.17.issue-2-3/jib-2020-0006/jib-2020-0006.xml. doi: 10.1515/jib-2020-0006.
Abstract (Expand)
Authors: SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, FT Bergmann, A Finney, CS Gillespie, T Helikar, S Hoops, RS Malik-Sheriff, SL Moodie, II Moraru, CJ Myers, A Naldi, BG Olivier, S Sahle, JC Schaff, LP Smith, MJ Swat, DT, L Watanabe, DJ Wilkinson, ML Blinov, K Begley, JR Faeder, HF Gómez, TM Hamm, Y Inagaki, W Liebermeister, AL Lister, D Lucio, E Mjolsness, CJ Proctor, K Raman, N Rodriguez, CA Shaffer, BE Shapiro, J Stelling, N Swainston, N Tanimura, J Wagner, M Meier-Schellersheim, HM Sauro, B Palsson, H Bolouri, H Kitano, Akira Funahashi, H Hermjakob, JC Doyle, M Hucka, SBML Community members
Date Published: 1st Jul 2020
Publication Type: Journal
Citation: Mol Syst Biol.
Workshop from LiSyM retreat in January 2020. Additional slides devoted to Social Media for Academics. Developed by Peter Krinenberg from https://naturalscience.careers/
Creator: Olga Vvedenskaya
Submitter: Olga Vvedenskaya
We face a reproducibility crisis and computational science, with most published models neither being accessible nor reproducible.
The Systems Biology Markup Language (SBML) is the de facto standard format for encoding pathway based models, which provides a means for exchanging process based models between researchers and tools.
The talk gives an overview of SBML and SBML-based tools.
Creator: Matthias König
Submitter: Matthias König
ICSB is one of the largest international conferences on systems biology. Since the first conference in Tokyo in 2000, which was organized by Dr. Hiroaki Kitano, it has been held annually in different countries.
Country: United States
City: Hartford, Connecticut
SBMC 2020 was postponed to 10th - 12th of May 2021. Further information will follow soon.
Start Date: 10th May 2021
End Date: 12th May 2021
Event Website: https://sbmc2020.bioquant.uni-heidelberg.de
Country: Germany
City: Heidelberg
The "Computational Modeling in Biology" Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology, systems medicine, synthetic biology and related fields. COMBINE 2020 will be a workshop-style event with invited lectures, oral presentations and posters, but also reserving enough time for afternoon breakout sessions to discuss topics around data and model standardization and integration, as well as harmonization and further
...
Country: United States
City: virtual
The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology, synthetic biology and related fields. HARMONY is a codefest-type meeting, with a focus on development of the standards, interoperability and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people
...
Start Date: 9th Mar 2020
End Date: 13th Mar 2020
Event Website: http://co.mbine.org/events/HARMONY_2020
Country: United Kingdom
City: Hinxton, Cambridge
e:Med brings together leading scientists and exceptional young researchers from all over Germany in the emerging field of Systems Medicine. Systems medicine uses interdisciplinary systems-oriented research on diseases to create a basis for understanding complex physiological and pathological processes for development of innovative personalized diagnosis, therapies, and preventive measures. Key to the appropriate analysis and possibly to the modelling of Big Data derived from information levels
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Start Date: 8th Mar 2020
End Date: 10th Mar 2020
Event Website: http://www.sys-med.de/de/meeting/emed-kick-off-2020/
Country: Germany
City: Bonn
Poster for the PhD retreat in Hofgeismar - Svenja Kemmer
Creator: Svenja Kemmer
Submitter: Svenja Kemmer
Investigations: No Investigations
Studies: No Studies
Assays: No Assays