The FAIRDOM Platform uses a stack of software platforms to provide a “Project Commons” – that is, a shared place where projects can organised their own data, models, protocols, workflows in their own managed space.
Organising and Sharing Project Assets
The SEEK platform is FAIRDOM’s web-based resource for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes. It preserves associations between them, along with information about the people and organisations involved. The research can be organised into investigations, studies and assays (experiments) based on the ISA-Tools format. When paired with our openBIS platform it provides data management support from instrument collection through to publication. Norwegian users benefit from a functional integration with the NeLS Bioinformatics compute platform. An API simplifies upload and download of files.
The SEEK can be downloaded, installed, and managed locally as a solution to data sharing within groups and consortia. In addition, publicly released assets can be made available in the FAIRDOMHub.
Integrating Data Infrastructures
The SEEK is designed to organise data held on different data infrastructures.
OpenBIS is an open, distributed system for managing biological information. The main goal is to support biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. When paired with the FAIRDOM-SEEK it provides data management support from instrument collection through to publication.
NeLS is the Norwegian e-Infrastructure for Life Sciences. When paired with the FAIRDOM-SEEK it provides a way for organising and publishing data collected by the ELIXIR-Norway data and analysis services.
Supporting Analysis and Modelling
JWS Online is a systems biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models. It can be used online, and is also integrated into the SEEK platform, to support model management.
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Work is on-going with a number of EU projects to integrate the SEEK with Galaxy: to manage workflows, launch them and manage their data outputs.
Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. Using the SEEK API it is easy to integrate the SEEK with your notebook.
Helping with Metadata Management
Rightfield is an open-source tool for adding ontology term selection to Excel spreadsheets. Rightfield is used by a ‘Template Creator’ to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, Rightfield or the ontologies used. Rightfield embedded templates are used within the Samples framework of the SEEK.