As a fomer lecturer of CS department at ESPOL, I am really happy that the first Ph.D. program was launched. With this in mind, I want to share with the new students some tips that I found quite useful during my research.
a) Remote copy: There are cases that a file (or directory) needs to be transfer from one computer to another computer via network
scp filename username@computer:location scp -r source_directory username@computer:location
b) Screen command: Launch any script and keep it running in the background. Useful if you need to review the status of your script in a different locations
screen --> new screen-terminal <Ctrl-A> + d --> detach current screen-terminal screen -r name_screen --> reattach to name_screen screen -ls --> list all screen-terminals
c) Subsitute information in text files
sed -i 's/search_pattern/substitution/' input_file
d) Remote mounting
sshfs username@computer:remote_folder mounting_point
e) Join several pdf files
pdfunity filename1 filename2 ... filenameN output_filename
f) ffmpeg: create a video from a set of images (given a pattern)
ffmpeg -r 1/2 -i pattern_image -r 30 output.mp4
g) Academic writing: This was the first advice that I received (thanks Sixto). It sounds obvious but it is a complex task to put your research in words. I can recommend two books: Science Research Writing For Non-Native Speakers Of English: A Guide for Non-Native Speakers of English (Glasman-Deal) and How to Write and Publish a Scientific Paper (Day and Gastel).
I hope this can be useful.