Filter and export

Publications

What is a Publication?
5 Publications matching the given criteria: (Clear all filters)
Author: Olga Krebs5
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

Abstract (Expand)

This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together … researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers

Date Published: 29th Jun 2020

Publication Type: Journal

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: 4th Jan 2017

Publication Type: Journal

Parallel DNA Polymerase Chain Reaction (PD-PCR)

Abstract (Expand)

This protocol describe an approach in which the first primer binds in a parallel complementary orientation to the single-stranded DNA, leading to synthesis in a parallel direction. Further reactions … happened in a conventional way leading to the synthesis of PCR product having polarity opposite to the template used. Here in FAIRDOM we use this SOP as an example/template

Authors: vikash bhardwaj, Vikash bhardwaj, Kulbhushan Sharma

Date Published: 5th May 2016

Publication Type: Journal

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report … summarizes the topics and activities of the fourth edition of the annual COMBINE meeting, held in Paris during September 16-20 2013, and attended by a total of 96 people. This edition pioneered a first day devoted to modeling approaches in biology, which attracted a broad audience of scientists thanks to a panel of renowned speakers. During subsequent days, discussions were held on many subjects including the introduction of new features in the various COMBINE standards, new software tools that use the standards, and outreach efforts. Significant emphasis went into work on extensions of the SBML format, and also into community-building. This year’s edition once again demonstrated that the COMBINE community is thriving, and still manages to help coordinate activities between different standards in computational systems biology.

Authors: Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, , Martin Golebiewski, Michael Hucka, Nick Juty, , Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet

Date Published: 15th Mar 2014

Publication Type: Journal

RightField: Scientific Knowledge Acquisition by Stealth through Ontology-Enabled Spreadsheets

Abstract (Expand)

RightField is a Java application that provides a mechanism for embedding ontology annotation support for scientific data in Microsoft Excel or Open Office spreadsheets. The result is semantic annotation … by stealth, with an annotation process that is less error-prone, more efficient, and more consistent with community standards. By automatically generating RDF statements for each cell a rich, Linked Data querying environment allows scientists to search their data and other Linked Data resources interchangeably, and caters for queries across heterogeneous spreadsheets. RightField has been developed for Systems Biologists but has since adopted more widely. It is open source (BSD license) and freely available from http://www.rightfield.org.uk

Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Wolfgang Mueller, Finn Bacall, Jacky Snoep, Franco du Preez, Quyen Nguyen, Olga Krebs, Carole Goble

Date Published: 2012

Publication Type: Journal

Powered by
 (v.1.16.2)
About FAIRDOMHub | Funding and Programmes | Credits | Terms & Conditions | Imprint | Cookie preferences
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH