Category Archives: News

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

During this 3-day online 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: Tuesday 20th – Thursday 22nd April, 2021

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

Keynote talk “Faring with FAIR” by Carole Goble at GMDS Workshop

 

Carole Goble is giving a keynote talk about “Faring with FAIR” at the GMDS Workshop “FAIRe Data Infrastructures” on Thursday, October 15th, 2020.

Abstract of the talk:

Remarkably it was only in 2016 that the ‘FAIR Guiding Principles for scientific data management and stewardship’ appeared in Scientific Data. The paper was intended to launch a dialogue within the research and policy communities: to start a journey to wider accessibility and reusability of data and prepare for automation-readiness by supporting findability, accessibility, interoperability and reusability for machines. Many of the authors (including myself) came from biomedical and associated communities. The paper succeeded in its aim, at least at the policy, enterprise and professional data infrastructure level. Whether FAIR has impacted the researcher at the bench or bedside is open to doubt. It certainly inspired a great deal of activity, many projects, a lot of positioning of interests and infrastructure initiatives such as FAIRDOM. COVID has injected impetus and urgency to the FAIR cause (good), highlighted its politicisation (not so good) and the need to reassure communities that FAIR for health related data is not a contradiction with data privacy. In this talk I’ll reflect on how we are faring with FAIR: as one of the original authors; as a FAIR infrastructure developer for the biomedical sector and as a veteran of FAIR before we had the principles.

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

SEEK version 1.10.1 released

We are pleased to announce a new version of FAIRDOM SEEK is now available, which is version 1.10.1

This minor release contains some bugfixes and small improvements, including:

  • Rails upgrade to the latest Rails 5 release (5.2.4.3), along with some other dependencies
  • Discussion links now have an optional label, to be displayed instead of the raw URL
  • Discussion links are now included in the API
  • Model organism has been included in the API
  • The Model image link has been included in the API
  • An improvement to how Submitter and Other creators are displayed, to be less ambiguous
  • Request resource has now been entirely replaced by the improved ability to request contact
  • A fix to a bug that prevented Assays and Assets being unlinked, if there was only 1 Assay

More details about the changes can be found in the 1.10.1 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