Worldwide, governments are growingly focusing on free and open source software (FOSS) as a move toward transparency and the freedom to run, copy, study, change and improve the software. The European Commission (EC) is also supporting the development of FOSS [...]. In addition to the financial savings, FOSS contributes to scientific knowledge freedom in computational science (CS) and is increasingly rewarded in the science-policy interface within the emerging paradigm of open science. Since complex computational science applications may be affected by software uncertainty, FOSS may help to mitigate part of the impact of software errors by CS community- driven open review, correction and evolution of scientific code. The continental scale of EC science-based policy support implies wide networks of scientific collaboration. Thematic information systems also may benefit from this approach within reproducible integrated modelling. This is supported by the EC strategy on FOSS: "for the development of new information systems, where deployment is foreseen by parties outside of the EC infrastructure, [F]OSS will be the preferred choice and in any case used whenever possible". The aim of this contribution is to highlight how a continental scale information system may exploit and integrate FOSS technologies within the transdisciplinary research underpinning such a complex system. A European example is discussed where FOSS innervates both the structure of the information system itself and the inherent transdisciplinary research for modelling the data and information which constitute the system content. [...