Building evidence of a warming Arctic prompted Canada to increase and accelerate its national effort in Arctic oceanography. In June 2002, a proposal submitted by a consortium of Canadian universities and federal agencies to transform the 98-m icebreaker CCGS Sir John Franklin into a state-of-the-art research vessel was accepted by the International Joint Ventures Fund of the Canada Foundation for Innovation (CFI). The CFI grant allowed for the retrofit of the decommissioned Sir John Franklin, the completion of major structural transformations to adapt the vessel to its new scientific mission and the acquisition of the diverse pool of scientific equipment attached to the infrastructure. A substantial contribution from Fisheries and Oceans Canada – Coast Guard also assured the completion of the modification of the ship. The new research icebreaker was christened the CCGS Amundsen on August 26, 2003 in honour of the Arctic explorer Roald Amundsen. The CCGS Amundsen's capacity as an Arctic research platform was further consolidated in 2006 by a major grant from the CFI and the provincial governments of Quebec and Manitoba to augment, update and diversify the icebreaker's pool of scientific equipment.

For its first scientific mission, the CCGS Amundsen remained in the Canadian Arctic for an impressive 390 days without calling port. The first part (348 days) of the mission was dedicated to the highly successful CASES circum-annual over-wintering expedition to the Beaufort Sea in 2003-2004. For the second part of the mission (42 days), the CCGS Amundsen was transformed into a floating research clinic to carry out the Qanuippitaa? (How are we?) Inuit Health Survey where doctors, nurses and scientists used the ship to visit the 14 coastal communities of Nunavik (Northern Quebec) and assess the overall health of community members. Since then, the CCGS Amundsen has been the main infrastructure supporting the ArcticNet marine based research program and in July of 2007, the CCGS Amundsen left its home port of Quebec City for an historical 15 month expedition to the Canadian Arctic to support ArcticNet and several projects funded by the Canadian International Polar Year program. Beginning in 2009, the Amundsen has supported partnerships with the oil exploration sector for the collection of new environmental data in the Beaufort Sea.

Since 2003, the vessel has spent over 1700 research days at sea and accommodated over 1500 researchers, technicians, students, professionals and media from over 20 different countries, travelling over 223 000 nautical miles or over 10 times the circumference of the earth.

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