The FAIRDOM-SEEK platform uses a stack of software platforms to provide a shared place where projects can organise their own data, models, protocols, workflows in their own managed space.
Integrating Data Infrastructures
The FAIRDOM-SEEK is designed to organise data held on different data infrastructures.
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.
Helping with Metadata Management
Rightfield is an open-source tool for adding ontology term selection to Excel spreadsheets. It 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 FAIRDOM-SEEK.
Supporting Analysis and Modelling
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 FAIRDOM-SEEK platform, to support model management.
Workflows
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 FARIDOM-SEEK with Galaxy: to manage workflows, launch them and manage their data outputs.
Executable Notebooks
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 FAIRDOM-SEEK API it is easy to integrate the FAIRDOM-SEEK with your notebook.