SOP for the exchange of clinical samples and corresponding data between collaboration partners in LiSyM
LiSyM network

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
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Creators: Martin Golebiewski, Frank Lammert, Wolfgang Müller

Submitter: Martin Golebiewski

Towards standardization guidelines for in silico approaches in personalized medicine.
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Abstract (Expand)

Despite the ever-progressing technological advances in producing data in health and clinical research, the generation of new knowledge for medical benefits through advanced analytics still lags behind … its full potential. Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards. Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders. Consequently, there is a need for broadly applicable standards compliant with legal and ethical regulations that allow interpretation of heterogeneous health data through in silico methodologies to advance personalized medicine. To tackle these standardization challenges, the Horizon2020 Coordinating and Support Action EU-STANDS4PM initiated an EU-wide mapping process to evaluate strategies for data integration and data-driven in silico modelling approaches to develop standards, recommendations and guidelines for personalized medicine. A first step towards this goal is a broad stakeholder consultation process initiated by an EU-STANDS4PM workshop at the annual COMBINE meeting (COMBINE 2019 workshop report in same issue). This forum analysed the status quo of data and model standards and reflected on possibilities as well as challenges for cross-domain data integration to facilitate in silico modelling approaches for personalized medicine.

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

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

Open modeling and exchange (OMEX) metadata specification version 1.0
LiSyM network

Abstract (Expand)

A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of … models and data, and enable semantic comparisons between models. Motivated by these potential benefits and guided by consensus across the COmputational Modeling in BIology NEtwork (COMBINE) community, we have developed a specification for encoding annotations in Open Modeling and EXchange (OMEX)-formatted archives. Distributing modeling projects within these archives is a best practice established by COMBINE, and the OMEX metadata specification presented here provides a harmonized, community-driven approach for annotating a variety of standardized model and data representation formats within an archive. The specification primarily includes technical guidelines for encoding archive metadata, so that software tools can more easily utilize and exchange it, thereby spurring broad advancements in model reuse, discovery, and semantic analyses.

Authors: Maxwell L. Neal, John H. Gennari, Dagmar Waltemath, David P. Nickerson, Matthias König

Date Published: 25th Jun 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

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Abstract (Expand)

Computational systems biology involves integrating heterogeneous datasets in order to generate models. These models can assist with understanding and prediction of biological phenomena. Generating … datasets and integrating them into models involves a wide range of scientific expertise. As a result these datasets are often collected by one set of researchers, and exchanged with others researchers for constructing the models. For this process to run smoothly the data and models must be FAIR-findable, accessible, interoperable, and reusable. In order for data and models to be FAIR they must be structured in consistent and predictable ways, and described sufficiently for other researchers to understand them. Furthermore, these data and models must be shared with other researchers, with appropriately controlled sharing permissions, before and after publication. In this chapter we explore the different data and model standards that assist with structuring, describing, and sharing. We also highlight the popular standards and sharing databases within computational systems biology.

Authors: N. J. Stanford, M. Scharm, P. D. Dobson, M. Golebiewski, M. Hucka, V. B. Kothamachu, D. Nickerson, S. Owen, J. Pahle, U. Wittig, D. Waltemath, C. Goble, P. Mendes, J. Snoep

Date Published: 12th Oct 2019

Publication Type: Not specified

Data Formats for Systems Biology and Quantitative Modeling
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Abstract (Expand)

Data standards support the reliable exchange of information, the interoperability of tools, and the reproducibility of scientific results. In systems biology standards are agreed ways of structuring, … describing, and associating models and data, as well as their respective parts, graphical visualization, and information about applied experimental or computational methods. Such standards also assist with describing how constituent parts interact together, or are linked, and how they are embedded in their environmental and experimental context. Here the focus will be on standards for formatting models and their content, and on metadata checklists and ontologies that support modeling.

Author: Martin Golebiewski

Date Published: 2019

Publication Type: InBook

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Abstract (Expand)

Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related … resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year.

Authors: F. Schreiber, G. D. Bader, P. Gleeson, M. Golebiewski, M. Hucka, S. M. Keating, N. L. Novere, C. Myers, D. Nickerson, B. Sommer, D. Waltemath

Date Published: 30th Mar 2018

Publication Type: Not specified

Presentation Data Management at 2nd LiSyM Jamboree
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network
No description specified

Creators: Martin Golebiewski, Wolfgang Müller

Submitter: Martin Golebiewski

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Poster at SBMC 2018: Data Needs Structure: Data and Model Management for Systems Biology and Systems Medicine
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

Poster presentation at SBMC 2018 (Bremen)

Creators: Martin Golebiewski, Olga Krebs, Hadas Leonov, Wolfgang Müller, Stuart Owen, Maja Rey, Natalie Stanford, Andreas Weidemann, Ulrike Wittig, Katy Wolstencroft, Jacky L. Snoep, Carole Goble

Submitter: Martin Golebiewski

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FAIRDOM tutorial workshop SBMC2018 Bremen - Introduction into SABIO-RK
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

LiSyM/de.NBI/ERASysAPP Tutorial: How to Share FAIR — The FAIRDOM Data and Model Management Practice
Introduction into SABIO-RK

Creator: Maja Rey

Submitter: Martin Golebiewski

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FAIRDOM tutorial workshop SBMC2018 Bremen - SEEK_Hands-on-tasks
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

LiSyM/de.NBI/ERASysAPP Tutorial: How to Share FAIR — The FAIRDOM Data and Model Management Practice
Hands-on tasks

Creator: Maja Rey

Submitter: Martin Golebiewski

FAIRDOM tutorial workshop SBMC2018 Bremen - SEEK-slides_Hands-on
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

LiSyM/de.NBI/ERASysAPP Tutorial: How to Share FAIR — The FAIRDOM Data and Model Management Practice
Hands-on slides

Creator: Maja Rey

Submitter: Martin Golebiewski

FAIRDOM tutorial workshop SBMC2018 Bremen - Introduction
LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM network

LiSyM/de.NBI/ERASysAPP Tutorial: How to Share FAIR — The FAIRDOM Data and Model Management Practice
Introduction slides

Creator: Martin Golebiewski

Submitter: Martin Golebiewski

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