The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable

Abstract (Expand)

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level … through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.

Authors: D. Nickerson, K. Atalag, B. de Bono, J. Geiger, C. Goble, S. Hollmann, J. Lonien, W. Muller, B. Regierer, N. J. Stanford, M. Golebiewski, P. Hunter

Date Published: 7th Apr 2016

Publication Type: Not specified

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

Abstract (Expand)

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. … It is a web-accessible repository for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship.

Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble

Date Published: 3rd Dec 2016

Publication Type: Not specified

Poster at SBMC 2018: Data Needs Structure: Data and Model Management for Systems Biology and Systems Medicine

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/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/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/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/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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