News and events


Paper published - Interactive exploration of integrated biological datasets using context-sensitive workflows (20/02/2014)

This work describes novel interactive query functionality for Ondex frontend. The additon of JavaScript-based context sensitve menues allows interactive population of the graph by fetching of additoional information from external webservices. An applictation demonstrated the utility of this new feature using a transcriptome analysis of Aspergillus nidulans dataset.

Ondex 2013 release is now available (31/01/2014)

We are proud to announce that the Ondex-2013 realise is now available for download at www.ondex.org. It incorporates multiple new features, improvements and bug fixes. The 2013 version marks a notable change in philosophy for the development of Ondex Frontend, which now incorporates multiple federated data access features and can support interactive on-the-fly assembly of integrated knowledge graphs. These developments included:

  • Context-sensitive menu powered by Ondex JavaScript engine and support data acquisition and analysis driven by external web services. This was delivered through joint efforts of Rothamsted Research team and our collaborators from the Hans Knoll Institute (HKI), Germany -- Fabian Horn, Martin Rittweger and Reinhard Guthke (Horn et al., 2013).
  • An enhanced interoperability with Semantic Web resources and improved compatibility between Ondex and RDF data models (paper to appear shortly in LNCS)
  • Further improvements to Ondex Web, a Java applet-based viewer for publishing Ondex graphs on the Web (Taubert et al., 2013).

This release also incorporates multiple new features to support chemogenomics analysis delivered as part of the 2-year long TSB project in collaboration with Syngenta. To help you get to grips with these new features, Ondex tutorial has been updated to include new working examples and is available for download here.

  • Support for chemical structure information via EBI CDK library, including support for chemical structure formats and visualisation of structures in the graph view
  • Integration of UniProt and ChEMBL (substances and bioactivity) data via on-the-fly context-sensitive calls to webservices.
  • New parsers (Expasy enzymes, ChEBI, ChemBL as well as SDF, Smiles, InChi formats) and new mapping methods based on chemical similarity (Tanimoto distance)
  • Integration of JalView for the generation and analysis of multiple sequence alignments of proteins

Furthermore, last year saw a successful completion of several biological use-cases where Ondex software has played a significant role, including:

  • A study that looked at network-based candidate gene selection for virulence associated genes in major wheat pathogenic fungi Fusarium graminearum (Lysenko et al., 2013)
  • Genetical genomic Analysis of Brassica rapa under altered calcium (Ca) (Graham et al., 2014, to appear in Plant Physiology later this year)
  • The last year also saw some changes in how Ondex project is developed and supported, most notably the spinning-out of QTLNetMiner and OndexWeb applications. Owning to their great success, these tools have now been established as independent projects supported by their own development teams.

As always we will be very happy to hear your feedback on the latest version of Ondex suite. Although greatest care was taken to test and fix any outstanding issues prior to release, should you encounter any bugs please feel free to report them to us on our issue tracker. We thank you for your continued support and hope that Ondex will continue to serve as a valuable tool for your research.

OndexWeb established as an independent project (25/01/2014)

OndexWeb has now been established as an independent project, supported by a separate development team. Additionally, an application note about OndexWeb functionality has now been published.

Paper published - Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum (04/07/2013)

This work describes how Ondex-driven graph analysis can be used to identify promising candidates for pathogenicity-associated genes. Thesefindings are accompanied by a comprehensive biological review of all candidates of interest and their relevance to current knowledge from domain-specific literature. The analysis was done by cosidering protein-protein interaction, coexpression and sequence similiarity data and exploring gene neighbourhood across these three networks.

Ondex Semantic Web query functionality presented at CIBB 2013 (22/06/2013)

Semantic Web technology offers powerful and flexible solutions for accessing and managing large biological datasets. To take advantage of these developments Ondex frontend was extended to allow on-the-go data import and integration via SPARQL queries. This new functionality was presented at CIBB 2013 event by Dr Artem Lysenko, an advanced draft of the paper is available here.

Ondex release 2012 (25/10/2012)

The latest release of Ondex is now publically available for download here.

Ondex course at the PhytoPath 2012 workshop (20/09/2012)

This course has demonstrated how fungal and chemogenomics datasets can be visualised and analysed using Ondex. The session was part of the PhytoPath training workshop at the EBI and was delivered by Dr Artem Lysenko, Dr Jan Taubert and Prof. Mansoor Saqi.

Ondex course at the EMBO 2012 workshop (19/06/2012)

A course showing how Ondex can be used for plant systems biology applications was delivered at the EMBO Practical Course on Plant Bioinformatics by Dr Artem Lysenko, Dr Jan Taubert and Mr Keywan Hassani-pak. The talks, tutorial scripts and datasets from this event can be downloaded here.