Monthly Archives: August 2020

SEEK version 1.10.2 released

A new version of the FAIRDOM SEEK software has been made available, version 1.10.2, which includes a few bug fixes since the last release last month.

In particular, it fixes a validation problem with linking to Publications that were added before describing Publication types were available, and do not have a specific type defined.

More details about the changes can be found in the 1.10.2 Release Notes.

Details on installing SEEK can be found in our Documentation, at https://docs.seek4science.org/get-seek.html – including running with Docker.

The upgrade guide can be found in the usual place at https://docs.seek4science.org/tech/upgrading.html

RightField version 0.26 available

A new version of the RightField software has been released, version 0.26.

This version includes the following enhancements

Ability to select invididual terms that will appear within the dropdown list. The previous behaviour forced all subclasses or instances. From the list of terms at the bottom right, multiple terms can be selected by holding down CTRL, or SHIFT to select a range. By default all are selected. Many thanks to Andreas Weidemann for this contribution.

Tooltips are shown to display the term URI when browsing the ontology or selecting terms – this is to help resolves ambiguities.

Increased the default JVM to 1Gb, and increased the timeout limit when loading ontologies. This provides support for larger ontologies.
Please bear in mind, that for some ontologies you may need to be patient for them to load. For example the EFO ontology can take 2-3 minutes on my laptop.

An upgrade of all dependencies, and Apache POI in particular.

The new version can be downloaded from https://rightfield.org.uk/download.html

For some details and background regarding running on Mac OS X please see the Release Forum Post

de.NBI Course: “Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK”

During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The second day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks.

Date: September 21-23, 2020

More details and registration: Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK