Jieling Zhao

Projects: Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM network

Institutions: INRIA (French National Institute for Research in Computer Science and Control)

Lutz Brusch pal

Projects: Early Metabolic Injury (LiSyM-EMI - Pillar I), LiSyM PALs, LiSyM network, LiSyM-Krebs Partnering

Institutions: Zentrum für Informationsdienste und Hochleistungsrechnen (ZIH), Technische Universität Dresden

https://orcid.org/0000-0003-0137-5106
Matthias König palproject_administratorasset_housekeeper

Projects: LiSyM PALs, Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), LiSyM network, LiSyM-Krebs Partnering

Institutions: Humboldt-Universität zu Berlin - Institute for Theoretical Biology (ITB)

https://orcid.org/0000-0003-1725-179X
SBML Level 3: an extensible format for the exchange and reuse of biological models
Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), LiSyM network

Abstract (Expand)

Systems biology has experienced dramatic growth in the number, size and complexity of computational models describing biology. To reproduce simulation results and reuse models, researchers need to … exchange precise and unambiguous descriptions of model structure and meaning. SBML (the Systems Biology Markup Language) is a community-developed format for this purpose. The latest edition, called SBML Level 3, has a modular structure, with a core suited to representing reaction-based models, and packages that extend the core with features suited for a variety of model types. Examples include constraint-based models, reaction-diffusion models, logical network models, and rule-based models. SBML and its rich software ecosystem have transformed the way systems biologists build and interact with models, and has played an important role in increasing model interoperability and reuse over the past two decades. More recently, a rise of multiscale models of whole cells and organs, and new data sources such as single cells measurements and live imaging, have precipitated new ways of integrating data and models. SBML Level 3 provides the foundation needed to support this evolution.

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

Specifications of standards in systems and synthetic biology: status and developments in 2020
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology. …Not specified

Authors: Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath

Date Published: 29th Jun 2020

Publication Type: Journal

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Abstract (Expand)

This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together … researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers

Date Published: 29th Jun 2020

Publication Type: Journal

A brief history of COMBINE
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Abstract (Expand)

Standards for data exchange are critical to the development of any field. They enable researchers and practitioners to transport information reliably, to apply a variety of tools to their problems, and … to reproduce scientific results. Over the past two decades, a range of standards have been developed to facilitate the exchange and reuse of information in the domain of representation and modeling of biological systems. These standards are complementary, so the interactions between their developers increased over time. By the end of the last decade, the community of researchers decided that more interoperability is required between the standards, and that common development is needed to make better use of effort, time, and money devoted to this activity. The COmputational MOdeling in Biology NEtwork (COMBINE) was created to enable the sharing of resources, tools, and other infrastructure. This paper provides a brief history of this endeavor and the challenges that remain.

Authors: Chris J. Myers, Gary Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novere, David P. Nickerson, Falk Schreiber, Dagmar Waltemath

Date Published: 1st Dec 2017

Publication Type: Not specified

pSSAlib: The partial-propensity stochastic chemical network simulator
Early Metabolic Injury (LiSyM-EMI - Pillar I)

Abstract (Expand)

Chemical reaction networks are ubiquitous in biology, and their dynamics is fundamentally stochastic. Here, we present the software library pSSAlib, which provides a complete and concise implementation … of the most efficient partial-propensity methods for simulating exact stochastic chemical kinetics. pSSAlib can import models encoded in Systems Biology Markup Language, supports time delays in chemical reactions, and stochastic spatiotemporal reaction-diffusion systems. It also provides tools for statistical analysis of simulation results and supports multiple output formats. It has previously been used for studies of biochemical reaction pathways and to benchmark other stochastic simulation methods. Here, we describe pSSAlib in detail and apply it to a new model of the endocytic pathway in eukaryotic cells, leading to the discovery of a stochastic counterpart of the cut-out switch motif underlying early-to-late endosome conversion. pSSAlib is provided as a stand-alone command-line tool and as a developer API. We also provide a plug-in for the SBMLToolbox. The open-source code and pre-packaged installers are freely available from http://mosaic.mpi-cbg.de.

Authors: Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch, Ivo F. Sbalzarini

Date Published: 4th Dec 2017

Publication Type: Not specified

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
LiSyM Core Infrastructure and Management (LiSyM-PD)

Abstract (Expand)

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special … issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them.

Authors: F. Schreiber, G. D. Bader, P. Gleeson, M. Golebiewski, M. Hucka, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, D. Walthemath

Date Published: 12th Feb 2017

Publication Type: Not specified

Pathway modeling with SBML (LiSyM modeling workshop)
Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), LiSyM network

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

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