Why Advisors are Awesome

So today started out frustratingly bad. I couldn't code this morning (since I was still stuck), so I started looking up stuff for my introduction that I need to write. I knew I was going to meet with my advisor at 3, so the plan was to be occupied until then. I had requested a late meeting for today (one that takes longer than usual), and I had also asked about starting benchmarking early. Of course, something happened to the firewall (or so I suspect), so I couldn't actually connect to the internet and work on my intro. So I spent a good hour twiddling my thumbs and trying to do other things on my project that did not involve the internet, like look over my algorithm again. This didn't make me feel any better. I even started worry that perhaps my implementation was the only way to do the tree structure and that I'm just going to have to scream it out. What if I'm really, really stuck?

So I walk into the meeting, expecting to be there for three hours at least, and explain how I've been struggling with this underlying tree data structure.

"Why don't you use a 'left-child, right-sibling' tree structure?" she asked. She quickly went over how it worked. I just stared at her. In roughly five minutes, she gave me a flexible tree structure that I'm pretty much will solve all the problems I had with the tree structure I've been wrestling with. Just wow. Can you say awesomeness? :-)

As for benchmarking, I have full permission to go forward, and to start early. She agreed that it would be wise to start benchmarking a week early, since neither of us can tell how long the simulations will run. So I got a bunch of information on how I can continue. I also got a series of deliverables for the end of the week (yay!)

• Read about the Parsimony/Ratchet algorithm: learn it, reimplement tree structure with it. Put aside code.
  
  
• Draft of paper: methodology section must be done, intro should be mostly fleshed out
  
  
• Install IPE/DIA/R on the Windows Machine at work
  
  
• Read the Tree of Life Brochure
  
  
• Read and learn all the necessary PAUP commands for benchmarking.
  

Tomorrow will largely be a play day. In other words, I'll be playing around with PAUP, getting familiar with it, and trying to see how many iterations would be good for the simulations. Right now, I think between 150 - 200 would be a safe number (as by Dr. Williams' suggestion).

This should be a welcomed break. I'm looking forward to having some non-coding fun. For now, I need to do some reading. Oh, and if you're curious, the meeting lasted only an hour and forty-five minutes :-) My advisor is truly awesome. I feel reassured. But I must go read!

Take care!