About SEEK

Citing SEEK

If you have been using SEEK in your research then please cite us. The key SEEK publications to cite are:

  • Wolstencroft, K, Owen, S, Krebs, O, Nguyen, Q, Stanford, NJ, Golebiewski, M, Weidemann, A, Bittkowski, M, An, L, Shockley, D, Snoep, JL, Mueller, W, Goble, C (2015) SEEK: a systems biology data and model management platform. BMC Systems Biology, Issue 9:33, pages 33, 2015. DOI:10.1186/s12918-015-0174-y
  • Wolstencroft K, Krebs O, Snoep J.L, Stanford N.J, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reyes S, Straszewski J, Van Niekerk D.D, Williams A.R, Malmström L, Rinn B, Müller W, and Goble C (2016) FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. Nucleic Acids Research, 2016, 10.1093/nar/gkw1032.
    DOI: 10.1093/nar/gkw1032

Please also take a look at our other Publications

What is SEEK?

SEEK is a storage platform designed to facilitate heterogeneous data and model storage and sharing, across multi-group scientific projects.

SEEK was conceived as part of SysMO, a pan-European initiative to record and describe dynamic molecular processes in unicellular organisms: from laboratory to mathematical model. SEEK grew organically with the projects needs, informed by a core user-focus group known as the SysMO PALs. Following on from the SysMO project, the SEEK became a key software resource of the FAIRDOM Research Infrastructure. It is now a resource for supporting interdisciplinary science world wide.

Key Features

Data Catalogue - The data catalogue in SEEK includes raw Datasets, Standard Operating Procedures(SOPs), Models, Publications and Presentations. All data are grouped by projects, and associated with the researchers who produced them. In order to encourage sharing of data we allow researchers flexibility in the formats they upload and share their data in. This means data formats in the SEEK catalogue can vary. We do offer a set of “best practice” guidelines for researchers who want to make their data available and usable to the widest possible audience.
Most common formats allow viewing within the browser, without a download, with additional enhanced features for spreadsheets and SBML models.

All data and information added to SEEK is searchable using key-words.

Versioning - All data is stored using versioning, selectable privacy, and static URLs. Versioning and privacy settings ensure that you can share your most recent data, with who you choose. Static URLs ensure that you can be credited directly for all shared work.

Model simulation and annotation - if models follow the SBML standard, they can be simulated, or annotated and re-added as a new version, all within SEEK.

Access Control - Data will go through a research lifecycle between collection and publication. In a competitive academic environment it is important that the data can be shared with collaborators, and then the wider community at appropriate points within the life-cycle. SEEK allows users to keep their uploaded data entirely private, to share between individuals, then across entire projects, until eventually making it public upon publication.

People index - SEEK contains an index of people where users can browse, or keyword-search, profiles of the projects, groups and people that contribute to the data on the site. People can describe their areas of expertise, which allows other users to quickly identify the right people to approach regarding specialist enquiries and collaboration proposals.

Samples - SEEK has a flexible samples framework that allows users to generate templates for sample metadata. Samples can be data, or laboratory samples. The framework integrates with Rightfield sheets, so that semantically-enhanced title sheets can be included with the data. The default Rightfield sheet uses the JERM and allows automatic generation and linking of the data files to an assay.

ISA and Interlinking – Data in SEEK gain increased value and usability when they are described within the context of an experimental process. Multiple experiments will be carried out as part of a single Study, and that study may be part of a wider overall funded Investigation. In SEEK we adopt the ISATAB structure (Investigation, Studies, Assays) which is a community standard for describing links between Omics experiments. We believe that many aspects of the ISA framework are equally appropriate for describing experiments beyond Omics and Biology, so allow this framework to be applied to all data.

Beyond the ISA framework, SEEK allows data to be interlinked within the site itself in order to describe their relationship.

If research resulted in a publication, this can also be registered with SEEK (including accreditation to relevant people) using a PUBMED identifier or DOI, and linked to the assets involved in that research – allowing other researchers access to use, examine, or validate the data that would otherwise be unavailable through the publication alone.

Bespoke Development

If you are interesting in having features added, or in having SEEK link to specific resources (e.g. an institute or national repository), or other bespoke development, then contact us for a consultation support@fair-dom.org