Stuart Owen

Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)

Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. Project DigiSal will lay the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining ...

FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.

Collection of training material for SEEK/FAIRDOMHub

Good data and model management improves the longevity and impact of your interdisciplinary research. FAIRDOM offers software and expertise to support you in better managing your interdisciplinary life-science projects, particularly in systems and synthetic biology. If you have never heard of data and model management, or are curious about it, or you are an expert keen to exchange ideas, our user meeting is the place for you!

At our users meeting you can:

• Learn why data and model management is ...

Systems Biology studies the properties and phenotypes that emerge from the interaction of biomolecules where such properties are not obvious from those of the individual molecules. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex ...

Salmon farmed on modern feeds contains less of the healthy, long-chain fatty acids (EPA and DHA) than before. Up until the turn of the millennium, farmed salmon were fed fish oil as a replacement for their omega-3 rich natural prey. However, fish oil is now a scarce resource, and more than half of the fat in modern feeds comes from plant oils that are inexpensive, but devoid of long-chain omega-3 fatty acids. How can we increase the omega-3 content of salmon on sustainable feeds?

One option is ...

The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:

• facilitates and maximises the potential for data exchange between SysMO research groups;
• maximises the ‘shelf life’ and ...

Report of the Data Management Foundry Workshop, 19th-20th of March, 2012, Vienna, Austria

Tutorial given at the Reproducible and Citable Data and Models Workshop, Warnemunde September 14th-16th 2015.

Describes how the DNA was isolated from salmon intestinal samples before preparations of 16S rRNA gene amplicons for the Illumina MiSeq system.

Update about Samples related features in FAIRDOM-SEEK (Flora D’Anna, VIB)

Overview of the latest FAIRDOM-SEEK release (Stuart Owen, University of Manchester)

Presentation of the new roadmap (Stuart Owen, University of Manchester)

Talk given by Olga Krebs at EmPowerPutida project meeting in Bruxeles 23rd November 2016

Slides that were presented alongside a SEEK demonstration at the EraSysApp PALS meeting in Munich - December 2015

Written and presented by Carole Goble (University of Manchester) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Documentation for using FAIRDOMHUB / SEEK for a workshop in Warnemunde, September 2015.

Presentation of data management concepts for ERASysAPP projects at IMOMESIC kick off meeting on 8 th of May 2015 in Heidelberg. Part I presented by Olga Krebs

Carole Goble's talk at ERASysAPP - EXCHANGE Networking and Info Day for research projects of the first ERASysAPP call (a day before PALs meeting)

Poster presented at SWAT4LS - Semantic web applications and tools for life science- in Berlin at 10 of december 2014 by Olga Krebs

The second half of the overview of recent SEEK updates presented and discussed at the PALS meeting in Paris 2013. It is mostly covering infrastructure changes and also the addition of ORCID (http://orcid.org) support.

Carole Goble's KeyNote talk at the 9th Intl Symp on Integrative Bioinformatics 2013 from the 20th Martch 2013

Keynote presentation by Professor Carole Goble at BOSC (Bioinformatics Open Source Conference) Long Beach, California, USA, July 14 2012. Co-located with ISMB, Intelligent Systems in Molecular Biology

Also available on slideshare at http://www.slideshare.net/mygrid/if-we-build-it-will-they-come-13652794

Presentation by Carole Goble at the International Semantic Web Conference 2013 in Sydney Australia about the use of semantic web technology in SEEK and RightField.

Introduction to RightField and Demo were presented at the Virtual Liver Network PALs meeting on 31st of October in Hünfeld, Germany

Katy Wolstencroft's talk at the "3rd Eagle Genomics Symposium:Will Big Data and Bigger Cuts Cripple Bioinformatics?", presented on 21st March 2013.

http://www.eaglegenomics.com/2013/01/eagles-third-symposium-how-the-efficient-bioinformatician-reduces-rd-costs/

The talk presented by Carole Goble and Wolfgang Mueller at the SysMO evaluation conference 2013 in Berlin.

An overview of the RDF work being done with SEEK, given at the PALs meeting, November 2012. It gives a high level explanation of what RDF is, why its useful and can be used for filtering and finding out information about the data in SEEK. This talk proceeded an interactive session where the PALs came up with 20 questions, to help us refine our model and prioritise what we describe.

This document is a summary of the SysMO-DB PALs meeting on the 29-30 November 2012

This talk was presented at the IEEE e-Science conference, Chicago, USA (8-12 October 2012). http://www.ci.uchicago.edu/escience2012/ It describes the latest developments in RightField for both semantic data annotation and extraction to RDF.

The 2011 SysMO Conference.

Agenda: http://www.sysmo.net/lw_resource/datapool/__pages/pdp_157/Agenda_SysMO_Conference_2011.pdf

SAMPLE TYPE to describe samples of CEN.PK-113-7D yeast strain upon metabolic perturbation of the steady state culture by glucose pulse

Sample type representing the old BioSample model available to SysMO and VirtualLiver