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The paper focuses on the end-to-end science operations for the first and only European Mars mission to-date, describing the approaches to science and mission planning and the challenges imposed by the operations constraints. It includes the activities of the instrument and science planning teams to plan and process the collected data. The Mars Express spacecraft has been in orbit around Mars since late 2003. An elliptical, near polar orbit has been chosen as the best trade-off between low-cost launch with little remaining fuel, science operations close to the targets on the Red Planet, and long periods required for transmitting the science data with an affordable communications system. The chosen orbit precesses around Mars, allowing the mapping of the complete surface of Mars at low altitude and good resolution. A high-resolution stereo camera, a mineralogical mapping spectrometer, two atmospheric/surface thermal mapping spectrometers, an energetic neutral atoms analyser, a sub-surface sounding radar and communications equipment in support of lander operations are mounted on the payload face of the spacecraft and compete for observation time, pointing preference and downlink time. The science planning facility performs the trade-off between the competing instrument science requests, planning within an envelope imposed by the power, thermal and illumination resource constraints, as well as the on-board data storage capacity and ground station availability. Different seasonal constraints apply due to the geometry between Mars and Earth, Mars and Sun, but also because of anomalies on the spacecraft that impact the power resource. Once a consolidated science plan has been generated and distributed in the form of a pointing timeline and payload operations requests, the Mars Express mission planning and flight dynamics teams validate the feasibility of the plan. The analysis includes the detailed power usage, spacecraft slew rates, reaction wheel off-loading parameters,- illumination and thermal constraint checks. Based on the pointing timeline, orbital events, like eclipses and occultations, and the allocated ground station antennas from the tracking network of the European Space Agency and the Deep Space Network of NASA, the mission planning team generates a communications plan which consists of the switching of the transmitter, downlink and commanding opportunity windows. Tools have been developed within the team to ease and automate the mission planning processes. The tools include the first-ever application based on artificial intelligence technology in mission operations at the European Space Operations Centre (for computing the irregular downlink and uplink plans). Several days prior to execution, the instrument operations requests are updated with detailed and fine-tuned operations parameters. Due to the planning of the instrument operations relative to an orbit event, the execution time uplinked to the instrument is aligned to the latest orbit prediction providing very good accuracy of the orbital events. Once the instrument observations have taken place, the data stored in the on-board mass memory is transferred to the control centre according to the `dump plan', from where the instrument teams pick up the science and housekeeping data for further processing, analysis and publication of the scientific results.