Preparing for my PhD defense

So as many of you know, in January my adviser and I sat down to talk about the timeline for me graduating. Let me first explain the PhD process here so you all know exactly what I am doing. This does vary by school and department, but the process at Illinois in the Chemical and Biomolecular Engineering department is:

1. Enter PhD program during fall semester
This step is probably pretty self explanatory. For me, it meant buying a condo, saying a very teary goodbye to David, riding in a Penske truck / VW R32 caravan halfway across the country with my parents, and starting a new life in a very flat state. I had found a roommate to share my condo with me on criagslist (she was luckily great) and I had no friends. Enter Khush :) Your first semester in graduate school you take a full course load just as you did in undergraduate, and Khush and I had almost the exact same schedule and very compatible personalities. She is now one of my very best friends.

My condo in IL

2. Pass written qual exam the following January
The written qual is a three hour exam with one question each from about 14 topics, some of which are considered "core" topics. You have to answer 8 questions (I think, or maybe 9) and at least 4 of them (I think?) have to be from the list of core topics. You can't go on in your PhD program if you do not pass this exam. Well, out of 14 students, I was the only one who failed. Luckily for me, the department believes in second chances and you are allowed to take it again the following January. I thought I had studied pretty sufficiently for the first one, but it was nothing compared to how I studied for the second one. I holed up for over a month and basically re-taught myself all of the core topics. I was amazed at how much I learned! Where was my brain during my undergraduate classes and how did I ever get a good grade? My understanding of the concepts was so much more organized and clear after studying for round two of the qual. Needless to say, I finished the 3 hour exam in 45 minutes and then sat there checking answers for the remainder of the time. Thankfully, I passed.

3. Pass oral qual exam that spring 
The oral qual is where you present your plan to a group of professors for what more or less will become your masters project. My project was pretty well laid out and I had a good understanding of where I was going, so this was pretty easy for me. Nobody in my year failed this to my knowledge.

4. Deposit master's thesis somewhere between year 2 and 4 (before step 5 though)
Your master's thesis can just be your first published paper, and to save time on writing I opted to go this route. My first paper wasn't published until my 4th year in the PhD program, so I obtained my masters somewhat on the late side.

5. Pass prelim somewhere between year 3 and 5
The prelim is where you present your plan for your official PhD thesis committee. The committee is made up of your research adviser, two other professors from your department, and one out of department professor. My out of department professor is our collaborator who I meet with every single week (by video chat now that I'm in Boston) so it actually takes a lot of pressure off for me that I have such a good relationship with him and he is so up to date on my work. The prelim consists of a 20ish page research proposal (mimics a grant actually) outlining what you intend to do for your thesis. You give the proposal to your committee one week before your actual prelim date, and on your prelim date you give a 45ish min presentation to the committee and allow them to drill you with questions. I get very nervous with presentations, but I actually enjoy the process, so this went well for me. My committee was a little bit worried that my plan was overambitious, but might as well aim high right?

6. Defend your thesis work somewhere between year 4 and 6 
Approximately 1-2 years after you pass your prelim, you reconvene with your committee to show them what you have done for your thesis and they decide whether you are ready to get your PhD. You give them your thesis document one week in advance, and then present your work to them in a 45ish min presentation. The public is allowed to attend and ask questions. There is a period at the end where the public has to leave so your committee can ask you questions. Then everyone but the committee leaves the room while they discuss what they have seen, and then they come out and tell you whether your new title is DR.

7. Actually get your degree from the university
There are a bunch of confusing deadlines about which semester you defend in, whether you defend by the right date, and what that means for when you will actually "graduate" and get your diploma. There are three chances to do this throughout the year - spring, summer, and fall. Even though my defense will be this summer, I missed the summer deadline so I will not actually "graduate" until December. But the main event is my defense.

Q: What is your thesis actually about and what degree will you have when you finish??? Excellent question, I actually don't talk about it much. I will have a PhD in Chemical Engineering, but my research focus is Systems Biology. In the most basic form, Systems Biologists look at challenging questions in biology (e.g., biofuels, medicine) as a big picture, or a system. They use large data sets and computational approaches to try to find patterns in the data that can teach us more about the biological question being studied. My work specifically is modeling the metabolism in a butanol producing bacteria - I built a computer model to predict how carbon flows from glucose (the food source) to butanol (the byproduct made by the bacteria and a potential biofuel). This model is based on the DNA of the bacteria - all of the DNA tell us which reactions can happen in the baceteria's metabolism, and then I model how the carbon goes from one reaction to the other (its basically linear programming). With the model, we can predict what reactions (and therefore genes) we want to cut out (i.e., genetically engineer) to make the flow of carbon from food to butanol more efficient. This would then mean the bacteria makes MORE butanol from the same amount of sugar, making the biofuel more economical. So my thesis is about how I made the model, how I have used the model, and other data I have collected (by running fermentation and analyzing all of the compounds we see in the fermentations, called metabolomics) to help us better understand what's going on metabolically. I currently have 3 publications, 1 pending publication, and I will hopefully have 1 more publication on top of that before everything is said and done - for 5 total publications.

Now, back to the January conversation I had with my adviser about finishing Step 6. We decided that a summer "defense date" was reasonable, and so I sat down and made an ambitious calendar to do list to help me plan the months to come.

The January plan: 

In March I realized that the only defense date that worked for me, my adviser, and other other members of my committee was JULY 10th. And so the date was set. It soon became apparent that the plan I had made in January was a little over ambitious, and so a few of the smaller items were set aside and it was decided that I would wait and focus on writing the planned publication after my defense was over (not uncommon).

I returned from my March trip to Seattle with the intent to work long hours from then until July 10th so that I could have the best thesis I was capable of compiling. Enter Steven's Johnson Syndrome and long days at Mass General Hospital. In early April my sister developed SJS, a severe allergic reaction to a medication. She was hospitalized for nearly 6 weeks, and could have died, gone blind, had long term joint/skin/organ damage, and who knows what else. It was really very serious, and when she first went into the hospital she was very, very sick. Even if I wasn't needed to help  her and hold her hand, I couldn't have worked on my thesis because my brain and emotions were in too strong a state of worry - I felt nervous and sick for her for weeks. It wasn't until the very beginning of May that it became clear she was going to be OK and so I extracted myself from the healing team and really hunkered down to finish my thesis work.

At that point, I was down to just 2 months of time until July 10th. I had quite a bit of data analysis and interpretation left to do before I could even think about writing, and so I began what is till my present routine of being a hermit and working hard core. My goal had been to finish all of the data analysis by June 3, and then to spend the entire month of June writing my thesis document and preparing my presentation slides. There has been a bit more overlap than that - I have written some of the thesis already,and I am still finishing up a couple of days of data analysis. I think I am on track though, and feel comfortable with the information I have to present. My long hours are paying off. As many of you have probably experienced, having less time than you thought you'd have with a hard deadline can be a serious motivator, and can make your brain much more efficient and effective.

To give you an idea of a typical day, I took some pictures and thought I'd outline a timeline. This more or less happens 7 days a week, though there is a bit less work on the weekend days because David and I have family and house things to take care of. I still have worked several-many hours on every weekend day though.

• 7-9am: Wake up, say good morning to the doggies (always a joy), brush my teeth, take them for a walk, feed them, give Pepper his meds, feed myself.

I usually keep the house very clean, including making the bed. I'm ignoring that these days. 

• 8-10am: Check emails and blogs that I like to follow and make a plan for the day's work. 
• 9/10am -12pm: Work (either data analysis or writing).

Here's what my desk looks like.

• 12pm: Lunch. Take the dogs to the yard and water the plants. 
• 12:30-1:30pm: Work. 
• 1:30pm: Get excited, the mail is here. 
• 1:35-5:30pm: Work. 
• 5:30-6pm: Take the dogs for a walk. Feed them dinner. 

These guys spend there day keeping me company. Ash sits right beside me in the chair, and Pepper sits on another chair by the window and barks whenever something interesting happens outside.

• 6-8pm: Work. 
• 8-9pm: Dinner and a little TV so I don't go crazy. 
• 9-11pm: Work. 
• 11pm-12am: Get ready for bed, let the dogs out to pee, try to take care of dishes, read for a bit, sleep. This bedtime very much depends on what I have been working on as many nights I have stayed up until 2am so that I could finish something that I didn't want to lose a train of thought on. This is why my wake up time is so varied. 

Dishes and laundry are dreaded chores for me to take care of theses days. I try to do the dishes every day (try is the key word), and I manage to get the clothes washed, but the clean, unfolded laundry tends to pile up. If we look a bit rumpled when you see us, you'll know why (the hamper is actually full of clean clothes).



David has been super helpful, though because he has been traveling again its been more limited what he can do around the house. On Sundays though he makes sure we cook enough dinner so that I don't have to cook during the week, he helps with housework, and he does the grocery shopping. Good thing, because when he wasn't around and I was left to do the groceries, our fridge looked like this while I scavenged (actually, looking back at this picture, the fridge was looking pretty populated....there was definitely a more empty point): 

So there you have it! My life in a nutshell as I prepare for my defense, and more info on what it actually means that I am defending. Wish me luck in my final stretch! And stay tuned for the Friday post after July 10th to hear how it all goes down :)