Step 5: Start your research and finish up coursework and exams as you can.
Get acquainted with your specific research topic and techniques. Start with the most recent review articles on your topic, and work into more specific literature. Read grant proposals if available from your advisor.
*Discuss and critique the literature.
Ideally, discuss literature with colleagues and your advisor. A journal club where someone presents an article and everyone reads and critiques the article can be great for learning an article in depth and learning to critique the literature.
*Plan your research.
From the literature you've read, you should have been able to form some interesting and unproven hypotheses. Plan experiments to test your hypotheses. Plan experiments that will have interpretable results. Avoid experiments that will only be interpretable if your hypothesis is true. Also, ideally design experiments that utilize techniques that are already working in your lab. Don't underestimate the difficulty of developing a technique from the literature into a working technique in your lab. And remember that redoing something from the literature will get you no credit towards a thesis or a publication. Get as much feedback as possible during these planning stages. A good advisor or colleague can provide excellent perspective and ideas on what hypotheses are interesting to pursue, what experiments are more interpretable, and information about existing techniques and their difficulty.
*Make a super-rough, super-early thesis outline.
This outline is really just to focus your work. The thesis will generally consist of an Introduction, Methods Chapter, 2 or more Results Chapters, and Conclusions and References. Coming up with basic topics for your 2 results chapters will help you be focused and driven towards the ultimate Ph.D. requirement - the dissertation. And getting feedback from your advisor on this outline will help the two of you be on the same page from the beginning. Don't be too attached to this thesis outline, since you are only beginning to test your hypothesis, and want to be led to the most interesting possible research by your experiments.
*Make a super-rough picture outline for a paper.
Simply sit down for an hour and rough out drawings of figures you envision being in a paper. Figures often start with an experimental geometry figure, followed by the key results from your experiments. These results may be in the form of photographs, tables, graphs, or other forms of presenting results. Sometimes papers also include figures explaining key interpretations or models drawn from the results. Roughly draw figures you envision for your paper. Again, don't be too attached to this picture outline! Your experiments will yield the results, and these may lead you to different conclusions and down different paths than you expected. Again, feedback on this picture outline helps to get you and your advisor on the same page for expectations.
*Conduct your experiments, collect and analyze your data, and interpret your results.Plan on the long, intermediate, and short time scales. Make a very rough long-term plan that includes time frames for your planned experiments, analysis, and writing up the results as a paper. This long-term plan must be flexible to incorporate the findings of your day-to-day experiments. Plan on the intermediate-scale, e.g. the weekly time-scale. Choose which days to do which experiments, how much time must be set-aside for analysis, and remember to include time for keeping up with the literature, going to interesting talks, and planning. Plan on the short-time scale, i.e. for the experiment for the day.
In your lab notebook, each day (or the previous evening), write down a goal or goals for the day, and an explanation of the planned methods. Write down and record as much as possible during the day, and close each day with some conclusions drawn from the day. For repetitive tasks with minimal changes, reference a previous page in the notebook, and/or type a template that can be printed and pasted into the notebook. Computer files are excellent resources, but be very careful about noting in your lab notebook where the files can be found. Also be very careful about backing up files, and remember that computer files are very easily changed. This easy changing is good and bad. The easy changes are good for updating files as new information is available, but bad if you need to reference what existed at a certain time. For example, a computer file holding a Methods procedure may be referenced in your lab notebook. Later, you may improve the procedure and update the computer file. But you may still need to know exactly how you performed the procedure for the data in your lab notebook. So, be careful with computer files and develop a system for updating and keeping old copies, and for backing up your files.