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Most scientists keep a research notebook. You should too. You've probably been told this in every science class since fifth grade, but it's true. Different systems work for different people; experiment. You might keep it online or in a spiral notebook or on legal pads. You might want one for the lab and one for home.
Record in your notebook ideas as they come up. Nobody except you is going to read it, so you can be random. Put in speculations, current problems in your work, possible solutions. Work through possible solutions there. Summarize for future reference interesting things you read.
Read back over your notebook periodically. Some people make a monthly summary for easy reference.
What you put in your notebook can often serve as the backbone of a paper. This makes life a lot easier. Conversely, you may find that writing skeletal papers-title, abstract, section headings, fragments of text-is a useful way of documenting what you are up to, even when you have no intention of ever making it into a real paper. (And you may change your mind later.)
You may find useful Vera Johnson-Steiner's book Notebooks of the Mind, which, though mostly not literally about notebooks, describes the ways in which creative thought emerges from the accumulation of fragments of ideas.
A whole lot of people at MIT