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41 Publications visible to you, out of a total of 41
The Human Physiome: how standards, software, and innovative service infrastructures are providing the building blocks to make it achievable.

Abstract

Not specified

Authors: David Nickerson, Koray Atalag, Bernard de Bono, Jörg Geiger, Carole Goble, Susanne Hollmann, Joachim Lonien, Wolfgang Müller, Babette Regierer, Natalie J. Stanford, Martin Golebiewski, Peter Hunter

Date Published: 6th Apr 2016

Publication Type: Journal

FAIRDOM approach for semantic interoperability of systems biology data and models.

Abstract

Not specified

Authors: O. Krebs, K. Wolstencroft, NJ. Stanford, N. Morrison, M. Golebiewski, S. Owen, Q. Nguyen, JL. Snoep, W. Müller, C. Goble

Date Published: 2016

Publication Type: Journal

The evolution of standards and data management practices in systems biology

Abstract

Not specified

Authors: Natalie J Stanford, Katherine Wolstencroft, Martin Golebiewski, Renate Kania, Nick Juty, Christopher Tomlinson, Stuart Owen, Sarah Butcher, Henning Hermjakob, Nicolas Le Novère, Wolfgang Mueller, Jacky Snoep, Carole Goble

Date Published: 8th Dec 2015

Publication Type: Journal

SEEK: a systems biology data and model management platform

Abstract (Expand)

Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources … to facilitate the sharing and integration of data, and for linking of data to systems biology models.

Authors: Katherine Wolstencroft, Stuart Owen, Olga Krebs, Quyen Nguyen, Natalie J Stanford, Martin Golebiewski, Andreas Weidemann, Meik Bittkowski, Lihua An, David Shockley, Jacky L. Snoep, Wolfgang Mueller, Carole Goble

Date Published: 1st Dec 2015

Publication Type: Journal

SEEK: a systems biology data and model management platform.

Abstract (Expand)

BACKGROUND: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools … and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. RESULTS: The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. CONCLUSION: The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.

Authors: K. Wolstencroft, S. Owen, O. Krebs, Q. Nguyen, N. J. Stanford, M. Golebiewski, A. Weidemann, M. Bittkowski, L. An, D. Shockley, J. L. Snoep, W. Mueller, C. Goble

Date Published: 15th Jul 2015

Publication Type: Journal

Data extraction for the reaction kinetics database SABIO-RK

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible, manually curated database that has been established as a resource for biochemical reactions and their kinetic properties with a focus on supporting … the computational modeling to create models of biochemical reaction networks. SABIO-RK data are mainly extracted from literature but also directly submitted from lab experiments. In most cases the information in the literature is distributed across the whole publication, insufficiently structured and often described without standard terminology. Therefore the manual extraction of knowledge from the literature requires biological experts to understand the paper and interpret the data. The database offers the literature data in a structured format including annotations to controlled vocabularies, ontologies and external databases which supports modellers, as well as experimentalists, in the very time consuming process of collecting information from different publications. Here we describe the data extraction and curation efforts needed for SABIO-RK and give recommendations for publishing kinetic data in a complete and structured manner.

Authors: Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller

Date Published: 1st May 2014

Publication Type: Journal

Path2Models: large-scale generation of computational models from biochemical pathway maps

Abstract

Not specified

Authors: Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère

Date Published: 1st Dec 2013

Publication Type: Journal

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