Alessandro Borsoi11.09.2014, EDUCAFE, METID – Politecnico di Milano

SEEK for Science

what it is (1)

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

scientific projects.

what it is (2)

SEEK is an open-source, web-based platform and suite of software tools for the

management, linking, exploration and exchange of Systems Biology data, models

and Standard Operating Procedures (SOPs).

SEEK is designed to facilitate data sharing and collaborations between scientists.

who

Developed by:

- a team at the University of Manchester in the United Kingdom

- the Heidelberg Institute for Theoretical Studies in Germany

Founded by:

- the BBSRC in the UK- the BMBF in Germany

as part of the SysMO-DB project

story

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.

SEEK is now the central hub for the SysMO community to store and share a wide variety of data, from collection to

publication, for both laboratory and computational experiments.

data (1)

SEEK ‘data’ type:

- data generated by high-throughput experiments.- data arising from low throughput, cumulative experiments in the form of:

raw data, i.e. single pieces of data belonging to a larger data series, non-replicated data, non quantified data.experimental results, i.e. reliable, quantified and repeated data series, including high-throughput data.calculated data, i.e. involving further analysis of raw data.image data.

- data arising from biological modelling.- models generated by systems biology approach.- parameterisations of models.- validation data for models.- metadata, i.e. data providing information about one or more pieces of data.- processes used to design the experiments, generate the data, and generate the models,

i.e. standard operating procedures (SOPs), spreadsheets, workflows.

data (2)

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.

As a dynamic service, SEEK aims to expand functionality provided for data types and formats as the needs arise. Where SEEK does not appear to support a data type or format, a request can be placed to extend SEEK for this data.

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

data (3)

Organise and store your data

SEEK has adopted an ISATAB style structure for organising experiments and data.

data (4)

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.

data (5)

Explore and annotate data

Excel spreadsheets can be explored and annotated without the need to download.

data (6)

Using RightField we have produced a wide collection of template files.

Semantic spreadsheet templates

data (7)

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.

data (8)

There is a lot of flexibility and control over who can see, download or edit your items.

Flexible sharing controls

data (9)

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.

SBML models (1)

Simulate SBML models

Most models that conforms to the SBML format can be simulated within SEEK.

SBML models (2)

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.

The JWS Online model simulator presents a schematic diagram of the model, and allows parameters and reactions to be modified for the simulation.Models can also be edited using JWS Online OneStop, and semantically annotated with Miriam annotations, and then saved back to SEEK as a new version.

people (1)

Who's doing what, where?

You can find out what people using, and have expertise in, and how to get in contact with them.

people (2)

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.

people (3)

PALS

SEEK has a varied network of scientists, known as SysMO PALs, who represent a wide but typical user base. Through regular meetings with these PALs we have, and continue, to develop a platform that is tailored in functionality and usability to you, the scientist.

platform

PLATFORM

end

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