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
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

Journal: 2017 Winter Simulation Conference (WSC)

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

Journal: PLoS Comput Biol

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, Martin Golebiewski, M. Hucka, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, D. Walthemath

Date Published: 12th Feb 2017

Journal: J Integr Bioinform

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

Contributor: Matthias König

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