Author Archives: Ulrike Wittig

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.

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

COVID-19 Disease Map on FAIRDOMHub

FAIRDOM helps to collect knowledge about the molecular mechanisms of COVID-19 and established a project in FAIRDOMHub for the COVID-19 Disease Map: https://fairdomhub.org/projects/190

 

The COVID-19 Disease Map is an assembly of molecular interaction diagrams established based on literature evidence for virus-host interaction mechanisms specific to the SARS-CoV-2. In the project lists of contributors, data and computational models, and literature is shared.

 

FAIRDOMHub and the data management support for the COVID-19 disease map gets featured in Nature Scientific Data https://www.nature.com/articles/s41597-020-0477-8