You already now about ship modules and crew management. Today I'd like to show you how to upgrade them. Only way to get upgrades for your ship is to research specimens you'll find during mining or as a reward for finishing the quests. So how do you upgrade your ship?
First you have to find a specimen. Mining it will create a new research possibility in your science section. Depending on amount of time to complete the research and work speed of a assigned scientist, the research will take some time to finish. Working crew members consumes double the life support so I would recommend to always assign fastest one. After the research is finished, a new upgrade possibility for your ship modules or your crew members will appear in your engineering section. From there, to build the upgrade, you need to mine the resources, assign engineer or medic for a job (depending on type of an upgrade) and wait. After the work is done, your module or crew member is now upgraded.
Most of the upgrades will improve system or resource consumption. Some of them will improve module main operations like engine speed or telescope range, and there are few special upgrades that can even add a new functionality to the modules. Researching unknown extraterrestrial specimens is dangerous and in some cases you will end up with damaged modules or injured crew. So be careful, if you are not prepared, sudden accident like this may spiral into unrecoverable system depletion and dead of your crew.