Squonk Computational Notebook

Computation research made simple and reproducible
We believe that the reason computational tools are not being utilised effectively in R&D is not because of a lack of functionality, but a lack of usability. And we don't just mean standard UI/UX type issues, rather usability of the whole work process. The Computational Notebook is a new breed of software designed around that work process. By integrating best of breed open source and commercial tools and making them interoperable and simple to use, the Squonk Computational Notebook allows scientists to perform complex workflows easily. Not only can you process your data but you can also analyse the results. As you work a record of what you did is automatically built up, providing strong providence and reproducibility. Controlled sharing facilitates secure collaboration with co-workers.

For end-users
For developers
Database / data source, Visualisation tool, Software, Analysis tool, Service, Workflow tool
API Type:
Processing and analysis, Workflow, visualisation and reporting
Applicability domain:
Computational modelling, Bioinformatics, Predictive toxicology
Chemical properties, Risk assessment, Structure-activity relationship (SAR / QSAR), Predictive modelling, Information extraction
Targeted industry:
Chemicals, Nanotechnology, Drugs, Cosmetics, Food
Targeted users:
Software Developers, Risk assessors, Researchers, Students
Relevant OpenRiskNet case studies:
  • DataCure - Data curation and creation of pre-reasoned datasets and searching
  • MetaP - Metabolism Prediction
  • ModelRX - Modelling for Prediction or Read Across
  • RevK - Reverse dosimetry and PBPK prediction
  • SysGroup - A systems biology approach for grouping compounds
  • TGX - Toxicogenomics-based prediction and mechanism identification
References and training materials:
  • https://squonk.it/ 
  • Video from a Squonk user from the XChem project at the Diamond Light Source, showing how the Squonk Computational Notebook is being used to solve problems at Diamond:

Provided by:
Informatics Matters
Apache 2.0
Login required:
Implementation status:
Graphical user interface available, API documentation available (Swagger-OpenAPI v2), Available as web service, Containerised
Technology readiness level:
TRL 9 – actual system proven in operational environment (competitive manufacturing in the case of key enabling technologies; or in space)
Integration status:
Integrated application
Service integration operations completed:
Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer.
Is annotated according to the semantic interoperability layer concept using defined ontologies.
Is containerised for easy deployment in virtual environments of OpenRiskNet instances.
Has documented scientific and technical background.
Is deployed into the OpenRiskNet reference environment.
Is listed in the OpenRiskNet discovery services.
Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR).
Provides legal and ethical statements on how the service can be used.

Resources & Training

WP1 Requirement Analysis, Outreach and Case Studies
13 Dec 2018
Additional materials:
WP1 presentation

Target audience: OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, JGU, CRG, UM, UoB, NTUA, Fraunhofer, UU, VU, IM, INERIS