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

Contributor: Martin Golebiewski

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, Martin 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

Journal: Methods Mol Biol

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

Journal: Encyclopedia of Bioinformatics and Computational Biology

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, Martin Golebiewski, M. Hucka, S. M. Keating, N. L. Novere, C. Myers, D. Nickerson, B. Sommer, D. Waltemath

Date Published: 30th Mar 2018

Journal: J Integr Bioinform

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

Contributor: 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

Contributor: 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

Contributor: 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

Contributor: 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

Contributor: Martin Golebiewski

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