Category "PhD Process"

August 10, 2006

Birthday Serendipity


I had two serendipitous moments today, both relating to my thesis.

First, I'd been feeling stuck for the past couple of days. I am working on a way to translate this new model approach I've designed into a computational model. This is the last part of the last revision of my thesis, and the phrase "always darkest before the dawn" comes to mind. I've got the logical steps of the model down and now I need to figure out how to represent that in the analytical program I'm using. It's not really a huge deal, since I'm using a very simple add-in to Excel -- not like I'm writing my own code or anything -- but it's proving to have its own challenges.

I'm working on trying to attribute human cases of Salmonella illness among the various food commodities to identify where most of the Salmonella is coming from. Now, there is a lot we don't know about where Salmonella is and how it works its way through the food production systems. It's a bit like a black hole, really. What I'm trying to do is identify ways we can nibble away at the edges of this black hole now, with the data we have, and how we could get even further with more information and better data.

Cutting to the chase, I had come to a point yesterday when I realized I needed to account for all the different combinations of foods the cases had been exposed to just prior to getting ill. I was pretty sure I new how to puzzle this out using simple probability rules, but I went to my book to make sure.

I learned that what I wanted to know was the number of subsets that exist for the nine food categories in my model. It turns out there is a shortcut to calculating this: it is simply 2^n (2 to the nth power). So I learned I would be working with 2^9 = 512 possible combinations. As I continued reading, I also rediscovered how all of these combination ideas fit into Pascal's triangle. I say "rediscovered" because I had learned about Pascal's triangle in math class, but I don't think I really appreciated its beauty until now.

But I haven't even come to the real serendipity yet. There were also a couple of lines in the combinations section that I skimmed over and then re-read, concentrating on their meaning: "A subset may be chosen by deciding for each of the n elements whether that element should belong to the subset, or not. There are n successive choices to be made, with two possible choices at each stage." Those two sentences have given me an idea for a whole new way of setting up this analytical structure -- one that may save me the step of having to create all 512 possible combinations.

The funny thing is that when Ben and I were carpooling into work this morning, and I was complaining about being at a complete mental logjam, Ben said that I would come up with a great idea today to get me unstuck.

Maybe it's all due to birthday karma. Which brings me to serendipitous moment number two.

I don't make a habit of reading my horoscope. But today I decided to see what my birthday horoscope said. Here it is from The Washington Post. (I didn't know the Washington Post had horoscopes, but they do, filed under "Arts & Living".)

Leo July 23 - August 22

For Thursday, August 10 -You have been moving forward on a new goal for quite a while, and should start seeing real progress today. If you don't feel like you are far enough along then backing out of this situation is not an option. You are in the thick of things, and you might as well keep on going -- things will start looking more promising soon. Right now you can try to get more comfortable with your surroundings if you understand the processes going on. Ask a few questions and get informed.

© 1996-2006.

Yes, of course, horoscopes are all about writing something vague that appears to be personal, like the horoscope is directly speaking to you. But even though I'm not a believer, reading it today did give me a nice boost. I especially like that first bit about moving toward a goal for while and starting to see progress. Keep the good mojo working, baby!

Posted by rigd0003 at 5:31 PM | PhD Process

Category "PhD Process"

August 7, 2006

Still here, still writing!

Typing at the laptop

Still here and writing like crazy trying to finish the dissertation. I've discovered that finishing up a thesis is very deceptive. You start with a finishing marker -- you can see that marker and you know where to go. Or at least you think you do. As you make your way to that marker, what looked like a straight path is actually a very winding one. It's like being one peak over from the last peak. You've only a valley and one last climb to do, but you didn't notice all of those darn switchbacks!

I've been working closely with my advisor on tying up some loose ends in this Salmonella attribution model I'm creating. I've finished the final refinements to the logical construct, now I'm working on the final tweaks to the analytical construct.

My goal was to be graduated this summer. But certain problems arose in some of those 'loose ends' that didn't tie up how I thought they would. My new goal is to finish all of my responsibilities -- a complete draft of the thesis -- by the end of summer and send it off to my committee. I'm sure there will be revision work to do before I can defend, but I feel like I really have that final marker is sight!

Posted by rigd0003 at 11:05 AM | PhD Process

Category "Frustrations"

Category "PhD Process"

June 27, 2006

Consolidation Countdown

I posted an article back in April about consolidating your student loans to lock in the interest rate before it goes up on July 1. Haven't done it yet? Neither did I, until two minutes ago! Yes, I'm a horrible procrastinator, but thankfully the process was smooth and easy after I cleared up a problem with my PIN.

The whole consolidation thing had been looming over me for the past couple of weeks, but I kept putting it off. Yesterday, I decided it was finally time to get it done, since I only had until Friday to get it in under the deadline. I have some old loans through Sallie Mae, so I needed to go to the National Student Loan Data System web site to get the necessary information to plug into the consolidation form. To retrieve the information, they ask for your information and your PIN. But when I entered my PIN, I kept getting an error. I even went to the Federal Student Aid PIN site and requested a PIN look-up.

I got a little worried when they confirmed that the PIN I was using was the one they had on file. Why won't it work? Is the site broken or overloaded? What if I couldn't fix it before Friday? And then, of course, I couldn't help but feel immense guilt at not having done this months ago...

But then the extraordinary procrastinator's luck I've had most of my life kicked in. I called the student aid 800 number and got right through to someone after pressing "2" for PIN help. I explained my problem.

She asked "and you got the error message after putting in your 4 digit PIN?"

I replied, "No, I got the error message after I put in my 6 letter PIN."

Apparently, the PIN I'd been using for years -- the PIN I was issued by the FSA -- is no longer accepted on the NSLDS web site... they only accept PINs that have four numbers. Fortunately, that was easy enough to fix. You can change your PIN right on the web and can even set it to a number of your choosing. It was odd -- and frustrating -- that there wasn't a note about the incompatibility on the log-in page.

But now I'm all consolidated and happy and ready to procrastinate the next big thing...

Posted by rigd0003 at 1:11 PM | Frustrations | PhD Process

Category "PhD Process"

June 14, 2006

More music to write to...

Still writing!

In addition to Hammond B-3 organ music, I 've found that German operettas like The Merry Widow and Die Fledermaus make for good writing music. Nice tempo, jovial melody, and in a foreign language that is neither too familiar nor unfamiliar to be distracting.

Posted by rigd0003 at 3:53 PM | PhD Process

Category "Computer-related"

Category "PhD Process"

Category "Rant"

May 30, 2006

My Livestrong just died...

My HP Livestrong notebook computer just died. I was waking it up from hibernation last night and suddenly everything went dark, even the power/charging light, and it failed to reboot. It did indeed live strong, but it died quickly, quietly, and without warning. And so young! Not even a year old!

I just took it in for resuscitation. If it needs to go to HP for special surgery, that could take from one to three weeks. Fortunately, I have a mirror backup of the hard drive that I made on Thursday, so only Friday's work is lost. I hope my Livestrong didn't decide to take its own life like the heroic laptop I read about in the Onion recently.

Regardless, I won't let this little set-back slow me down. I certainly have access to several computers, at home and on campus. I probably won't be typing away in the coffee house any time soon, but I'll make do. I'll keep you posted.

Posted by rigd0003 at 11:04 AM | Computer-related | PhD Process | Rant

Category "PhD Process"

May 23, 2006

Thank you for your support

Thanks to everyone for your amazing support and votes of confidence! I've got a lot to do on my thesis this summer, but the end is in sight.

I've gotten into a writing routine (or at least a rough semblance of a routine). I start out at the local coffee house for about an hour in the morning, listening to some B-3 organ jazz through my headphones and trying to get my ideas down. Then I go into my office (I'm so lucky to have work space on campus!) to check my e-mail and unwind for a bit. Then it's back to writing.

Hmm... that all sounds a bit more regimented and productive than it actually is. But I do think I'm making progress. I've got most everything in one big Word document. Seeing it all together emphasizes all the work that I've already done. And I've been using FreeMind for the sections that I get stuck on. Rather than stare at a blinking cursor, I pop over to FreeMind for some free association. I can usually break through a mental log-jam by focusing on the two or three main things I want to say and just write them in my own conversational tone. Something about writing in Word makes me want to rephrase everything before I actually type it. That's very frustrating. I'm hoping I can strike a good balance between un-tethered thoughts and cumbersome or overburdened formal writing in the final draft.

I know I promised pictures of our France trip -- they'll be coming soon. If I get my Model Development chapter delivered to my adviser on Thursday, I'll do some trip blogging on Friday...

Posted by rigd0003 at 11:07 AM | PhD Process

Category "Music"

Category "PhD Process"

April 20, 2006

Music to write to

Billy Holloman CD

I've been trying to dedicate more time to writing recently. This morning, instead of going directly to my office, I spent about an hour at a coffee house near campus. I booted up my laptop and turned off its wireless device so I wouldn't be tempted by e-mail and web browsing.

The coffee house has a nice mix of background busyness. I find I'm distracted both when there's too much going on and also when things are too quiet, so the coffee house in the morning is a happy medium. But I do find myself distracted sometimes by the music they play there. Today, however, I found a good solution: pop in the headphones and have Billy Holloman playing on iTunes.

I didn't always appreciate organ-based jazz, but Ben introduced me to the finer points of the Hammond B3. As a gift last year, I gave Ben This is Organ Night, a CD collection featuring Billy Holloman on organ. The album gets its title from a regular feature at the St. Paul jazz club, the Artists' Quarter. Tuesday night at the AQ is Organ Night, as you can see from their calendar. (We'll have to get down to the AQ one of these Tuesdays...)

As I discovered today, this is great music to listen to while writing. There are no vocals to be distracted by, the fluid tones of the organ serve as good background music, and the tempo of the songs helps keep my thoughts flowing and the fingers typing. I caught myself swaying back and forth, bobbing my head to the music on a few occasions, but that didn't seem to raise any eyebrows -- I'm just glad I wasn't in the library!

I recommend you head on over to the album's CD Baby site where you can listen to decent-sized MP3 samples of the tracks. If you like what you hear, you can order right there (not available from iTunes). CD Baby is great "little online record store" that sells music directly from independent musicians.

Posted by rigd0003 at 12:19 PM | Music | PhD Process

Category "PhD Process"

April 13, 2006

What I learned about student loan consolidation...

stack of money

I attended a quick seminar yesterday morning on student loan consolidation. I'm a bit thick-headed when it comes to finances. There was a lot of talk about consolidation last year, but I was too confused and busy to do anything. And the letters and flyers from banks encouraging me to consolidate now! finally prompted me to go see what this was all about, and I'm glad I did. Here are some key points for others who may feel as confused as I did.

Many student loans have variable interest rates. These rates can be changed (usually they increase) every year on July 1. Students are encouraged to consolidate their loans. The reason I was confused is that I had already consolidated my loans a few years back and took consolidation to mean "combine into one." Well, now I understand that consolidation really means "lock in the interest rate." And you can consolidate just one loan, if you want. What happens is that you take out a new loan that pays off the other(s) and fixes the interest rate. When you consolidate two or more loans with different interest rates, the interest rate for the new loan is a combination of the existing loan rates, calculated as a weighted average. If you have any variable interest rate loans now, you want to consolidate by June because the new interest rate starting July 1 will probably go up from this year's 4.7% to 6.8%!

Those wishing to consolidate are strongly encouraged to do so now and not wait for the June rush. Consolidating your loans isn't too complicated once you understand what you need. First, you need to know what kind of loans you have. To find out, go to the National Student Loan Data System where you will see a history of all of your Federal Title IV Loans by clicking on "Financial Aid Review". To access your loans, you will need to use your FAFSA pin number (the same one you use to access your Federal Student Aid). UPDATE (6/27/06): Make sure your PIN is a four-digit number. The NSLDS web site only accepts 4-digit PINs. If you have a six-letter PIN (or something else), you must got to the PIN web site and change it. I found this out the hard way.

When you log on, you will see a page with a list of your entire loan history. Keep in mind that some of these loans may have been paid off. You only need to worry about those that have "Outstanding Principal" greater than $0 (second-to-last column). It is very important to check this NSLDS site first because it shows all of your loans. The Direct Loan Servicing page of the Federal Student Aid agency only shows your Direct loans. There are two main types of loans when talking about consolidation: Direct and non-Direct. Direct are the "Direct Stafford Subsidized" and "Direct Stafford Unsubsidized" loans. Other, non-Direct, loans don't have the "direct" in the title, like "Stafford Subsidized", etc.

One quick aside: if you have a Perkins Loan, you probably don't want to consolidate it along with the others because there are many forgivenesses -- like if you become a teacher or join the Peace Corp. These forgivenesses are nullified by consolidation because you take out a new loan with new terms.

If you only have Direct loans, you can consolidate any/all of them with a simple phone call. Just call 1-800-557-7392 and they can take care of consolidating your Direct loans. But the operators at the Department of Ed can only see your Direct Loans on their screen -- they can't tell you if you have other loans.

If you have a mixture of Direct and non-Direct, you can consolidate by filling out some forms on-line at the Department of Ed consolidation website. But you need to take some information from the NSLDS web site (the "Financial Aid Review" page I mentioned above). You can find the information you need about each loan by clicking on the round, yellow number button that precedes each loan on the list. It may be helpful to download the paper form to see what information you'll need for the electronic form -- the PDF is here.

The information you need about your loans is:
• Loan Lender Name, Address, and Phone number -- this is at the bottom of the loan page. For all Direct loans, the address is probably not listed (not very helpful), but that information is:
Direct Loan Servicing Center
Borrower Services Department
P.O. Box 5609
Greenville, TX 75403-5609

Loan Type -- Stafford Unsubsidized, Direct Stafford Subsidized, etc.

Account Number -- for all of your loans, this is your Social Security Number

Current Balance -- outstanding principle

Now, with this information, you are ready to complete the on-line consolidation form. Be aware that you don't have to consolidate through the Department of Education. There are many banks and loan servicing companies that are more than happy to have your business, but just keep in mind the DOE is a sound, secure thing. If you do decide to consolidate with a bank, make sure it's a trusted bank with a long, stable history. You don't want to wind up in the situation where your loan is sold and passed around from place to place, because you have to be really on top of things so you don't default. Many servicing companies will offer incentives like reducing your interest after you make a number of on-time payments. But if your loan is sold, you probably won't get that deal anymore or you'll start back at square one. And make sure, whether you consolidate with DOE or someone else,that you fully understand what constitutes an "on time" payment. Finally, if you are looking for a deal (who isn't?) just about anyplace, including the DOE, will give you a quarter point interest rate reduction on your loan repayments when you sign up for automatic electronic payment through your bank account.

Okay, kids, have at it!

Posted by rigd0003 at 11:38 AM | PhD Process

Category "PhD Process"

April 5, 2006

Feelin' a little mentally log-jammed

I've been a bit mentally blocked this week. My modeling project has come down to a few final, but big, revisions and I feel like I'm trying to do all of them at once and not getting anywhere on any of them. You know, like trying to steer your car in three directions at the same time.

I'm also really interested in finding a creative way to display some of my data. Something cool and simple, like the things Edward Tufte talks about. (With all due respect to Dr. Tufte, for someone who champions the simple and elegant, his web site is neither. His ideas -- and his books -- are excellent, though.) But being creative and explorative takes time, and I don't feel like I have time. I've got a poster presentation to create by the end of the month and loads to do before ever hoping to finish in June.

I'm not totally freaking out, mind you. Just a bit of a freak out moment. I'll feel better tomorrow afternoon after I meet with my adviser. My adviser is just the kind of supportive, guiding, "I've got your back" sort of adviser that we all deserve but many of us do not receive. We've got a standing meeting every Thursday, and for the most part we keep it. This is how a lot of my progress has been made, I just do meeting prep work every week. Well, it hasn't been as smooth and easy as that sounds, but I'd really be in a mess without it.

So, I've just got to gather up the week's jumbled thoughts and tasks and prep for tomorrow's meeting...

UPDATE: Things are already looking up! I've been playing around with ways of visualizing my data this morning using a trial copy of OriginLab graphing software, with fairly good success.

Posted by rigd0003 at 12:53 PM | PhD Process

Category "PhD Process"

January 20, 2006

Tools of the trade

While I'm doing a lot of analysis now, I'm also trying to keep up with the writing so I won't be swamped with it all at once as I get closer to the end of the semester. To me, writing is its own special agony. Nothing helps alleviate this--I just have to force myself to plow ahead. But there are tools that help me prepare and get organized. They don't make the writing any easier, per se, but make what is a 'tough row to hoe' at least a straight row and let's me know where I'm going. (Keep in mind that many of these are offered at discounted prices for students and that FreeMind is free!)

Useful tools of thesis-writing trade:

EndNote - reference manager
Adobe Acrobat - not just the Reader but the fully-functional program
Freemind - mind-mapping software
Adobe Photoshop Elements - digital image editor
MS Word - yeah, I know, but I have my reasons (see below)

These software programs can be used in a wonderfully synergistic way. For example, I use EndNote to store all of my references. But it also stores files! I can store one file per reference. Almost all of the references I have are journal articles and reports, and most of these are available in PDF format. So I just insert the Adobe PDF file right into EndNote which adds a unique ID to the file and copies it into the EndNote library folder on your computer.

EndNote screenshot

And I can launch the file right from EndNote. I'm not limited to PDF files. I also store Word files of manuscripts and reports, and JPG files of pictures, tables, and figures I've stored as their own reference entry.

I've already mentioned how useful Adobe Acrobat is for viewing publications, and this can be done with the free Reader version. But there are some nice features of the full Standard version that enticed me to purchase it. For one thing, I can manipulate files a bit more. I can select text for copying, highlight and make comments to the document as I read it, and take screen clippings. Some of these features do not work if the document is locked, but most of the documents I've come across are not locked. Another nice feature is that I can delete pages or add/combine pages in a document. This is handy with really big documents that are offered only in segments--I can combine them into one document on my machine.

An additional feature I've used quite a bit is the web capture. I can open a web page in Acrobat and save it as a PDF. This is a handy way to save web pages as references in my EndNote database. I use this a lot for press releases and federal reports from sites like the USDA or CDC when PDF versions aren't available.

A final feature I've grown to love is the Adobe Acrobat Organizer. This is a place to manage and store PDF files in an organized way. The Organizer keeps a history of recently-viewed files as well as a file manager system. In a way, this overlaps with the EndNote feature as a way of keeping track of PDF files, but sometimes it's easier to find files in the Acrobat Organizer since it keeps a screen shot of the document. It's also a quick way to save something I want to look at later (notice the "To be read" folder).

Acrobat Organizer screenshot

Now that I've got my references all organized, I actually have to start synthesizing that knowledge into my thesis, i.e., I have to start writing. How to begin? I've got all of this stuff swirling around in my head and it never seems to come out in a clear, orderly manner. That's where FreeMind comes in. Wonderful, wonderful FreeMind. I've talked a bit about the program before. It's a way to outline your ideas--to get them down--without having to worry about order right off the bat. That's what I hate about traditional outlines: whether it's bullets or numbers, I'm still fixated with order because I type things one after another. With FreeMind, just jot down your ideas as a bunch of blobs (nodes) around a central blob. I keep the central node something stupidly vague and short, like "methods chapter." Once I've done my first 'mind dump,' I go back and arrange things. I usually keep FreeMind open in the background to add things as they come to me. I've even used FreeMind to take notes as I'm reading a book or journal article.

FreeMind screenshot

One of the great features about FreeMind is that I can insert images and links. When I come across a key table or figure I want to discuss, I just insert it so it's right there for me to take notes on. (I'll create a screen clip and open it into Adobe Photoshop to tweak it, if need be, and save it as a JPG.) The links work well for referencing larger things or to serve as place holders for coming back to. These links can be internal to other nodes in the mind map, external, like links to files on my computer, or hypertext links.

After I've got a good map down, I export it as HTML and bring it in to Word so I can flesh it out into a finished document. It exports as a hierarchical outline. I take each piece of the outline and fill it into a complete paragraph. It helps a lot if I write my FreeMind nodes as paragraph topic sentences to begin with. For more on this, see my previous post or go directly to John Carlis' "Design: The Key to Writing (and Advising) a One-Draft Thesis" (under Selected Papers on his personal web page). I highly recommend it!

The reason I use Word is that it supports EndNote's "Cite While You Write" feature. As I'm writing, I can just plop the necessary citation into my document and EndNote does all the formatting, and even creates a reference list at the end of the document. I've looked into the open source word processors like Open Office Writer. The Writer is very good, but without the easy citation feature, I went back to using Word.

Well, there you have it. It may sound like a cumbersome Rube Goldberg system, but I've found it helpful. Now, back to writing...

Posted by rigd0003 at 12:43 PM | PhD Process

Category "Me"

Category "PhD Process"

Category "Public Health"

Category "Science and Policy"

December 2, 2005

Outbreaks, Dissertation work, and Sprouts

An e-mail newsletter in my Inbox today contained links to two stories. The first story described a recent study by the Center for Science in the Public Interest concluding that produce contributed to more illnesses than poultry, eggs, and other animal products. CSPI studied reports of food-related outbreaks and noted the implicated foods that were the source of the disease-causing organisms.

This report comes at a very influential time in the food safety arena and it raises exactly the questions I am tackling in my dissertation work. There's a great interest in these types of attribution studies that seek to learn where foodborne illness cases are coming from. What types of foods are contributing most to the burden of disease?

But what we really want to know isn't just "what" but also "how" and "where." How are these foods becoming contaminated? Where in the food production, transportation, and preparation steps is this contamination occurring?

In outbreak investigations, the point of contamination can sometimes be difficult to discern. Produce may have been contaminated in preparation, often cross-contaminated from other foods in the kitchen. But there are increasing numbers of multi-state outbreaks where cases crop up in multiple places at about the same time. In these instances, it seems most likely that the implicated food was contaminated on the farm or during processing or shipping. This is where our ability to conduct trace-back investigations is key to solving the mystery of exactly where and how, and, hopefully, preventing similar contamination in the future. CSPI is lobbying for better record-keeping and ID tagging of foods to help in these efforts.

Another difficulty is lack of data. This study looked at outbreaks that had both an identified pathogen -- the bacteria, virus, toxin, or parasite was recovered -- and an identified source -- there was conclusive evidence that pointed to a food. But what about the unknown and unidentified? What about the people who become ill and never see a doctor and don't get tested? We don't have great data on the food side, either -- especially produce where no routine testing is done.

My work is to identify the first two of Sec. Donald Rumsfeld's information trilogy -- the known knowns, the known unknowns, and the unknown unknowns -- and give an account of where our knowledge lies in attributing Salmonella cases to foods at the point of production. [Secretary Rumsfeld got a lot of ribbing after that news briefing, but I've found his words very useful in my work and explaining my work to others!]

The other story in that e-mail relates more to a personal joke than the actual news item. The story is about a recent Salmonella outbreak in Ontario from mung bean sprouts. There have been several Salmonella outbreaks from various types of sprouts in the past decade or so. One of the difficulties in preventing these outbreaks is that Salmonella can contaminate the sprout seed itself, as well as during the growing phase.

The joke here is that I'd heard extensive accounts of these sprout-associated outbreaks from one of my major professors, Dr. Craig Hedberg. We'd worked closely on several food safety projects when I first arrived at the U of M. One time when we were on our way to a meeting off campus, we stopped for lunch at a little sandwich shop. I ordered the veggie special but told them to "hold the sprouts." Craig's eyebrow shot up, he gave a wry smile and said, "Don't do that on my account." I gave a snort and replied that if not on his account -- foodborne disease expert, veteran outbreak investigator -- than whose? And I'm not the only one. Our entire department, it seems, is sprout averse from Craig's stories. So, you see why I smiled when I saw that headline today. Craig is now over in Paris for a year, working with French officials on improving their foodborne disease surveillance. I have to wonder if he's sitting in a little French café at this moment, regaling his company with similar stories.

Posted by rigd0003 at 12:19 PM | Me | PhD Process | Public Health | Science and Policy

Category "Cool web stuff"

Category "Me"

Category "PhD Process"

October 28, 2005

Mind maps and Gantt Charts

FreeMind mind map
A simple example of a FreeMind mind map

My thesis project is shifting into high gear now--hurray! But all the ideas that keep popping up, and all the leads I want to chase down, are in serious danger of being lost. I need a place to collect all the various aspects of my work, but in a way that the information is readily accessible, easy to organize, and will give me the ability to see the whole project at once, but also to focus in on a particular point.

The answer to all of this, I believe, is FreeMind. FreeMind is free (open source) concept mapping software that allows you to construct mind maps -- diagrams that depict the aspects of a topic as nodes, and the interrelatedness of the nodes with branches (called "edges") and arrows. Mind maps have a central topic node, with all other nodes radiating out from it. (Note: FreeMind isn't strictly in the Tony Buzan sense of Mind Maps®, but the concept is similar.)

My husband has been using FreeMind for quite a while now and finds it very useful. He uses it to plan projects, to plan meetings, and even to take meeting notes. And we've used it quite a bit at home for planning trips--especially camping trips where there's a lot of gear to keep track of. But I've not really thought about using for my work until now.

FreeMind has recently launched a new version with lots of great features. You have more choices and control over how things look, can add internal and external (web page) links for easy jumping, add notes to any node, and there lots of choices for exporting and publishing your map. There are several HTML and XHTML options, including one with clickable links. I like the "export as Adobe PDF" option for sharing with my committee members. Printing out these maps can be unwieldy, though. I had to print one out recently and wound up printing it on multiple pages in Adobe Acrobat, then cutting and taping the pieces together.

But printing isn't really the point of it all for me anyway. The beauty of FreeMind is that you aren't constrained by a page style, or an outline format, or margins. I can open it up and just start adding things without immediately trying forcing things into a hierarchy. Then when I'm ready to group items, FreeMind makes it easy.

As an aside, when I was talking with my advisor about mind maps, he asked if they were similar to Gantt charts. That was a term I didn't know, so I did a little research. It turns out that I had seen many Gantt charts before without knowing what they were. Gantt charts are used primarily in creating project timelines, something else that might be useful to keep me on track and finishing on time. Perhaps I can use it to create a reverse calendar for my dissertation. If you're interested, there is also a free open source Gantt chart software called GanttProject. Check out their demo--it's pretty good.

Posted by rigd0003 at 2:47 PM | Cool web stuff | Me | PhD Process

Category "Me"

Category "PhD Process"

Category "Scientific interpretation"

August 26, 2005

Daily affirmation: "Matrix algebra is my friend!"

Non-negative definite matrices are also called "positive semi-definite" matrices...

I've been reading a bit about matrix algebra lately. Notice I said reading and not learning. There's a lot in mathematics that I just don't grok. I definitely feel like a non-native speaker. I wonder if people who are really good in mathematics have trouble understanding other things - things that I may be fairly good at - and if they feel as completely disoriented as I do when I'm trying to understand terms like determinant, orthogonal, and classical adjoint.

The reason for this self-flagellation is not so much directly related to my dissertation, but to improve myself as a methodologist. You see, matrix algebra is the foundation for regression analysis. Regression is used a lot in epidemiology to predict associations between exposures and outcomes or diseases. My problem is that I have a growing concern that methods like regression are misused - that they are applied in the wrong instances and leave the epidemiologist with a false confidence in the results.

So, I'm going back and reviewing regression from scratch. I'm reading a new book by David Freedman, a well-known statistics professor at UC Berkeley, and someone whom I've heard to be critical of how certain statistical tools are used in practice. I was heartened to read in the book's preface:

Much of the discussion [in this book] is organized around published studies... Some may find the tone of the discussion too skeptical. If you are among them, I would make an unusual request: suspend belief until you finish reading the book. (Suspension of disbelief is all too easily obtained, but that is a topic for another day.) [Emphasis added]

I'm looking forward to reading what he has to say. For now, it's back to

If G is non-negative definite rather than positive definite, that is, x'Gx = 0 for some x ≠ 0, then G is not invertible...

Posted by rigd0003 at 3:30 PM | Me | PhD Process | Scientific interpretation

Category "PhD Process"

July 19, 2005

Blogging and the workplace, revisited

Thanks to a comment on my earlier post, Naomi has pointed me to some good resources on blogging in the workplace and how to blog anonymously. First, the EFF story, How to Blog Safely has some good tips and talks about anonymizing technologies (never knew there were such things). There are links to more good stuff at the bottom of the story, including CNET's Guide to workplace blogging that is in Q&A format and includes reasons why you might want to use those anonymizing technologies.

Posted by rigd0003 at 10:57 AM | PhD Process

Category "PhD Process"

July 10, 2005

Blogging and the job search -- incompatable?

UPDATE: See Naomi's comment for link to good information on anonymous blogging...

An interesting piece in the Chronicle of Higher Learning, thanks to Perry of Six Impossible Things Before Breakfast.

The article, "Bloggers Need Not Apply," by Ivan Tribble (pseudonym of a humanities professor at a small liberal arts college in the Midwest, U.S.A) describes the author's experience on his college's faculty hiring committee. The committee found out about the applicant's blogs through interviews, applications, and the help of Google. But after surveying the blogs of their applicants, they came away with a decidedly negative opinion. They found a range of things that concerned them, including one applicant who misrepresented his research and another whose real professional interests were far from that of the open position. Their conclusion:

Job seekers who are also bloggers may have a tough road ahead, if our committee's experience is any indication.

Perry brings up some interesting points on this in her post, so I won't re-hash that here, except for a few quick points:

I'd bet that none of the hiring committee had a blog and that none had read a blog before this experience

Anyone who rants on his or her blog -- especially about coworkers -- better have an anonymous blog (and the UThink blogs here at the U of M are not anonymous)

The most worrisome part of this article was the statement that:

The content of the blog may be less worrisome than the fact of the blog itself [emphasis added]. Several committee members expressed concern that a blogger who joined our staff might air departmental dirty laundry (real or imagined) on the cyber clothesline for the world to see. Past good behavior is no guarantee against future lapses of professional decorum.

In essence, guilt by association. As if I don't have enough job search anxiety as it is...

Posted by rigd0003 at 6:29 PM | PhD Process

Category "Cool web stuff"

Category "PhD Process"

July 6, 2005

Reference eBooks through University library

Ebook gif

Here's a nice reference option I stumbled upon at the U of Minnesota's libraries that I thought I'd share.

I'm doing a little preliminary data analysis now. Well, mostly cleaning up the database and seeing what's there. I decided to use MS Access for these simple database management tasks. It's been a long while since I've used Access and I forgot some of the basic language the program uses for running queries. I wasn't up for trying to navigate the program's "help" so I did a little search on the University library's web page. I thought I might dash over to the library and look a few things up. It turns out I didn't have to leave my chair...

The library has a subscription to, an eBook web site with a built-in reader and note-taker. I could just "check out" an Access reference book and do a search for the query language I was looking for right on my laptop. So cool! But there are some drawbacks. Here are some pointers:

You need to have a University account (except for the public titles--see below).

In addition, you need to create a separate netLibrary account to read the eBooks -- see this FAQ for instructions.

Mostly, the library's eBooks are reference and how-to books, although netLibrary has 3400 books that are publicly accessible to everyone.

The search function at netLibrary is good, but the browsing function is a bit limited. You can browse titles under broad categories like Agriculture, Arts, Chemistry, etc., but it doesn't seem like all 7411 available books (including the public ones) fit under these categories.

Once you find a title you're interested in, you can add it to your list for easy reference or check it out immediately (under the "eContent Details" tab). Only one person can read a certain title at a time, so netLibrary manages this by allowing you access to it for 4-hour intervals.

The reading interface is less than ideal. Your browser screen is split into two panes -- a tool pane on the left and the book content pane on the right. While you can slide the divider to make the book content pane larger, it still doesn't seem like enough room for large books like computer program manuals.

Some of the features: the ability to add notes (limited to a title and 500 word content); a content search function; and an integrated dictionary, encyclopedia, web, and eContnet search functions by highlighting a word and right-clicking.

Happy reading!

Posted by rigd0003 at 10:49 AM | Cool web stuff | PhD Process

Category "PhD Process"

Category "Scientific interpretation"

June 15, 2005

I'm just guessing here...

I just realized something about my dissertation project: I'm just guessing. I'm working on something that I know will not give me one true, definitive answer. When you get down to it, isn't that what all probability models are? Sure you have weights and likelihoods for the different outcomes in different situations, but you're just guessing. It may be an educated guess; it may be a guess that's come out of a very sophisticated algorithm or model. But it's still just a guess.

It's not that this 'revelation' has freaked me out or anything. It's just made me realize the simplicity of the truth. Guessing is okay (said in my best Stuart Smalley "Daily Affirmation" voice*). And acknowledging that I'm guessing leads to some good questions: What is the benefit of guessing? What is the harm? What would I need to know to improve my guess? What is the ideal that I'm working towards? It's actually kind of nice. It gets away from that 'know-it-all' posturing and gets down to the heart of it -- seeking answers that will help us improve.

Look for my best guess at Salmonella attribution to be published this winter! (Do you think the journal editors will be as opened minded to the whole 'guessing' thing?)

*Wikipedia rocks! I can't believe they have a minor pop culture reference like Stuart Smalley!

Posted by rigd0003 at 10:23 AM | PhD Process | Scientific interpretation

Category "Frustrations"

Category "PhD Process"

Category "Rant"

June 13, 2005

Just no pleasing everybody

I competed for one of the University's Doctoral Dissertation Fellowships for next year. It's a really great funding opportunity for doctoral students to focus on completing their dissertation in their last year as a student.

I thought I'd be a bit of a long-shot and heard a few weeks ago that my proposal wasn't accepted. (You can flat out say it was "rejected" but in these times of good feelings towards all, the language has been altered ever-so-slightly. Kind of like how the Academy Awards are now announced, exchanging "And the winner is..." for "And the Oscar goes to...")

I'd just gotten around to reading the reviewer comments. I don't know why I get nervous about such things, maybe it's because I have a bit of trouble with criticism. Actually, it's not the criticism that's the problem, it's the anticipation of criticism. And as criticism goes, this wasn't so bad.

For example, all four reviewers thought that my writing was very good. (I am a good writer when I put my mind to it, and it's carried me through a lot of otherwise tough spots in my professional career.) My application was "well written" with a "strong personal statement"; best of all, it was "lucid."

Most of the criticism was regarding two acknowledged weak points: my lack of publications and the vagueness of my proposed methodology. As to the first, that's a common problem which I am trying to remedy. This reinforces my need to get some publications before I enter the job market, but overall it wasn't a shocker. As to the second weakness, that's kind of inherent in what I'm doing for my dissertation. I'm devising a model -- a method -- for linking human illnesses with pathogen rates on certain food and animal sources. I've never done anything like this before and there's no step-by-step formula. So, yeah, the methodology was a bit vague because that's the meat of my dissertation -- coming up with the method! I knew this was going to be a problem and didn't know how else to describe what I was doing, so this wasn't a big shocker, either.

While that was the heart of the criticism, there were some other little tidbits that seemed to reflect the idiosyncrasies of the individual reviewers. One that has caught in my craw a bit is the following:

"Weak undergrad GPA (3.16); never commented upon."

Well, thanks to the personal soap box that is my blog, allow me to comment on what Reviewer #4 considers to be a glaring omission. First of all, I was floored by the idea that anyone cared what I did in undergrad as long as I had graduated. I thought that my exceptional academics through my Masters and PhD careers might over-shadow my solid B average in undergraduate studies. But now that the subject has come up, let me tell you, dear Reviewer #4, why my GPA was probably so "weak":

• My microbiology major was very hard, requiring many high-level mathematics and chemistry classes in addition to the micro classes and labs,

• I wanted to challenge myself, so I took classes like Multivariate Calculus,

• I believed in a strong liberal arts education, so I took challenging non-science classes like History of 19th century China and Contemporary British Literature,

• I wanted to challenge myself physically, so I became a member of the Tae Kwon Do club and worked my way up to a green belt, something I never thought I'd do since was not an athletic kid,

• Grade inflation may be rampant now, but it wasn't in the sciences and mathematics departments at Iowa State University in the early 1990s,

• Many of these classes kicked my butt, but I got through them, earning my B or C and am proud of what I accomplished and that I never had to retake a class (except for Library, which is a hilarious tale in and of itself).

Jeez! It's this type of nit-picking mentality in academia that sours me on the whole profession. But despite my rant, it hasn't gotten me down. Criticism isn't so bad as long as you put it into perspective.

Posted by rigd0003 at 7:30 PM | Frustrations | PhD Process | Rant

Category "PhD Process"

June 6, 2005

Calling all procrastinators...

The Now Habit

Procrastination is a common occurrence, but over the years I had become a pathological procrastinator. Now that I'm ABD (all but dissertation) and I've set my sights on finishing my Ph.D. over the summer, I've realized I need some serious help. And I may have just found it in the form of a self-help book.

The Now Habit by Neil Fiore bills itself as "a strategic program for overcoming procrastination and enjoying guilt-free play."

Sounds good, but how? Fiore starts out by trying to explain what's behind the procrastination and the feelings of laziness and guilt that go along with it. He describes it as a defense mechanism for fear of failure, fear of being overwhelmed, fear of finishing, or resentment towards a boss or your job. These manifest as thoughts of "I should be working on that report" or "I have to get that literature review finished" that plague us procrastinators non-stop.

The next step is to own up to where we are now, stop being a "should be" victim, and start making choices. After all, I want to -- I actively choose -- to earn this Ph.D. every day that I'm still here at the University. That's all well and good, but up to this point there's a lot of thought but no substance. All pop and no corn, so to speak.

The heart of the book is what Fiore calls the Unschedule. This is a motivating tool that insists upon:

• scheduling time for play: exercising, socializing, reading, gardening
• shifting your focus to starting (not finishing)
• replacing your "To Do" list with a "To Start" list
• aiming for only 30 minutes of uninterrupted, quality work at a time

Starting with a blank 24-hour week, first fill in time committed to meals, sleeping, meetings, and appointments. Also fill in time committed to exercising, free time, and recreation. This shows you how much time you really have to work on those big projects. Then fill in your Unschedule with periods of work on your project that you've spent at least an uninterrupted half-hour on. When you've completed 30 minutes, you may choose to continue, or reward yourself by switching to another, more enjoyable task.

If this sounds like kindergarten psychology -- giving yourself a gold star for every 30 minutes of work -- I totally agree. And yet, I find myself looking forward to the end of the half-hour when I can take my yellow highlighter and fill in another 30 minute block of project time. Plus, Fiore is right -- I'm able to enjoy some down time without feeling guilty, and I'm ready to start my next half-hour block. I think in a different job setting, I wouldn't need to reward myself for every 30 minutes I managed to do my job. But this Ph.D. thing was starting to kick me around, and now I really feel some momentum.

If you're struggling with a project, I'd recommend giving The Now Habit a try. It's a quick read and since it's been around for a while (published 1989) it's probably at your local library.

Posted by rigd0003 at 4:30 PM | PhD Process

Category "PhD Process"

April 20, 2005

PhD web forum and support group

Are you experiencing blocks in your dissertation work? Want to vent your anxiety or frustration about your thesis progress? Have a question other students might be able to help you with? This web site might be for you...

A friend just told me about an on-line forum and support group for PhD students. It's called PhinisheD and it's filled with neat stuff. There are three main tools: basic forums and chat rooms for introducing yourself or posting a question or problem, goal-setting tools for making contracts with yourself and sharing goals and milestones, and resources and links provided by other students.

And it seems to be well attended. I put up a post and got a response fairly quickly. It feels good to know there are so many of us linked together in this experience.

Posted by rigd0003 at 11:31 AM | PhD Process

Category "PhD Process"

March 22, 2005

Helping you along your thesis path...

Everyone's path to a Masters or PhD is different. Maybe that's why so many of us feel a bit adrift when it comes to charting our course of progress. There have been lots of books on the subject of thesis writing, but I've always felt too busy to read them. Here, then, are some tools I've found useful to have along for the journey.

A Progress Journal

In the same vein as a lab notebook, keeping a progress journal lets you look back to see what you've done and the reasoning behind the decisions you've made. Here are some of the things I use my journal for:

There a lots of journal software out there, many of them with free trial periods (journals at, EJournal, the Journal). I use i*write. I like it because every entry is stored by the entry date and the entry category. Plus, I can insert document short-cuts (or entire documents) so I can keep track of all the files that pertain to that particular entry. It also has a good search function.

One-Draft Thesis

John Carlis, a Computer Science & Engineering professor here at the U of M, has written a guide for PhD students and faculty called, "Design: The Key to Writing (and Advising) a One-Draft Thesis." His goal in the guide is to help students develop an effective and efficient way to work. It's an easy read with a lot of good ideas. Check it out at his personal web site (a link to download a PDF of the document is listed under "Selected Papers"). Here are some gems from the guide:

Dissertation Calculator

The University of Minnesota has designed a Dissertation Calculator. Here's how it's described:

The Dissertation Calculator is a tool that helps demystify the process of completing your dissertation or thesis. The Calculator breaks down the dissertation process into manageable deadlines and provides you with important resources and advice. Using this tool can help you develop your specific process in collaboration with your department, advisor, writing group, and others.

To start, you type in a target date of completion. Then you get a list of stages along with a desired deadline for completing the stage. Each stage has a link that describes why the stage is important, the tasks for that stage, and links to more resources. If you are a U of M student, you can sign up to have reminders sent to you by e-mail.

A Support Network

I get by with a little help from my friends...
               - Lennon/McCartney

This is a very important part of dissertation work. In fact, it is a dedicated stage in the aforementioned Dissertation Calculator. There are many ways to seek support and group contributions: a writing group, a regular get-together with your PhD-seeking friends, or attending group support sessions.

It's incongruous, I know, but a nice ending to this post.

Another milestone
Resting only a moment
Enjoying the view

         Copyright 2004, by Joseph Rohrbach

You cannot get where
You are destined to go without
Leaving where you are

         Copyright 2004, by Joseph Rohrbach

Posted by rigd0003 at 4:01 PM | PhD Process

Category "PhD Process"

March 4, 2005

A model is a set of assumptions

As you might know, my thesis work consists of evaluating current models, then using what I like about them and fixing what I don't like about them to create one of my own. It doesn't matter what sort of models I'm looking at or even what questions I want to answer about them, I'm learning from my adviser and my own experience that they all boil down to the same thing - assumptions.

For the most part, models are just short-hand for how you get from one place to another, from A to B. You start out with certain climate data and you end up with a weather prediction; you start with your personal and financial situation and wind up with an investment strategy; you start with exposure and illness information and wind up with a measure of causal association. The model you use tells the story of how all of these data relate to one another and how they come together to give you the outcome - the answer to your question . This "telling of the story" is just a description of your assumptions: this is a linear relationship, these follow a Normal distribution, this decays at this given rate.

I find I'm having a really hard time excavating assumptions from some of the models I am reviewing. Part of the problem is that modeling is a whole new field for me and I don't have much experience. Another part of it is that I hadn't been trained to identify the assumptions in the models I used through most of my schooling (mostly statistical models). But a large part of my trouble is also that many people are not accustomed to laying out their assumptions in a straight-forward manner.

So the next time someone wants you to use a model - a tool - to do some work for you or solve a problem for you, simply ask, "what are the assumptions this model is making to take me from A to B?" They you can decide for yourself if the path the model is taking is one you can accept. But if they can't answer your question, then you've got a REAL problem.

Posted by rigd0003 at 11:48 AM | PhD Process

Category "PhD Process"

February 24, 2005

Getting it RIGHT or getting it DONE?

Which is more important to a PhD student working on her thesis? Are they mutually exclusive? Is this the work on which I'll be judged for the rest of my life, or is having that piece of paper and those three letters after my name the bigger key to opening doors?

Such are the anxieties of life.

Posted by rigd0003 at 2:20 PM | PhD Process