I’m on a lot of dissertation committees. While most of the committees are for students in my department, many are not in my area of operations research. I’m surprised at how hard it can be to follow along to the bigger picture and/or to the technical details. Even when I completely understand the technical details, I usually do not know enough about the specific research niche to characterize the dissertation’s contribution or novelty.

I tell students that the most important part of their thesis or dissertation defenses are the 30 seconds when they summarize the key contributions of their research at the beginning of the dissertation. I’ve been to defenses and proposal defenses where this has been unclear, and confusion follows. A lot of confusion.

The 30 second elevator speech is an important skill, because academics (and non-academics too) spend a lot of time trying to sell their ideas (literally!) to people with technical expertise in another field. The 30 second elevator speech is a necessary but not sufficient first step to communicating with others, and a thesis or dissertation is a great place to get started with this.

Additionally, all committee members want to understand what a student’s research is trying to accomplish and how it will fit into the literature. We need help to get there. Not all committee members seek to understand all the technical ideas, especially if they are outside your area, but we all want the Big Picture. Admittedly, guiding your committee through the Big Picture this will take more than 30 seconds, but doing so will lead to fewer questions later on.

A good thesis offense starts by hitting your committee with a 30 second elevator speech, not a sword. Thesis defense comic courtesy of xkcd.

Related posts:

• do you have a 30 second elevator speech about your research?
• should you do a PhD?
• despite what you have heard, getting a STEM PhD is a good idea

The National Science Foundation (NSF) started to require a data management plan for each new proposal.  The data management plan will require investigators to make their data (including figures, tables, and code) available to encourage collaboration.  An excellent idea! They specifically mention that investigators are required to document their data–not just make it available–so that others could use it, thus creating new opportunities for scientific research.  NSF’s data management plan is similar to NIH’s public access plan, which requires that publications from NIH-funded research are publicly available through Pubmed Central with twelve months of publication.

The research world is moving toward a place where investigators are required to share data and code.  I once wrote about my insecurities surrounding sharing my code.  While I don’t have insecurities about sharing my data (except trying to find extra time to document data better), I do need to think about creating a system for posting my research materials.  I’m not sure what the solution should look like.

What is the best place online for sharing research materials?  How should code be stored and formatted?  Tables, figures, data, and code have different formats.  It’s best if they are all stored (or accessed) in the same location.

My university does not have the best tools for sharing data (at least not that I know of).  Just updating my web site is a pain.  I use my university’s BlackBoard page for my research group that contains my code, papers, references, slides, and whatever else I get tired of emailing students.  However, my BlackBoard site is a closed system that does not allow guests even at my university to have access, so it cannot be used to share data to the public.

Dropbox may be a good place to store many documents, given that a separate page links to all of the stored data, although I am loathe to use my precious Dropbox space for storing data.  Slideshare and Scribd are good places for sharing slides and technical reports, respectively.  Code can be zipped and uploaded elsewhere.  But having to store each type of file in a different account on a different site would not exactly facilitate sharing information with others (and no fun for me to keep track of all the different logins and passwords), but I could create a Google Sites page to manage the information so that it can be accessed from a single page.

How do you share your data?  How do you find time to document your data?

Related posts:

• On sharing code
• Dropbox: a love story

I was recently asked for some of my code that I used in a paper.  First of all, I should firmly state that people should share code. Sharing and openly sharing ideas is, after all, the hallmark of academic research.

I am not often asked for code, and I had a few reactions to a recent request, which was made by a student.  My first reaction was that of a professor: should I give the student a fish or teach the student how to fish?  When I am usually asked for code, the request is extremely short with no context given, meaning that it is hard for me to gauge how hard the student had tried to get the program to work.  Was there a typo in the paper that is causing a problem? Where are they stuck?  What types of programming errors are they getting?  Are they simply being lazy?  I just don’t know.

This particular request relied on code that was about 20 lines of code.   Most of my projects are longer, usually comprising of hundreds or thousands of lines of code (I don’t really count, but they can get hairy).  I found myself wondering if the requester–a graduate student–really had thought about how to run the code or was just emailing me.  I exchanged a few emails with the requester before sending my code to make sure that I wasn’t doing someone’s homework for them.

Another recent request asked for code in a paper that I did the computational work for when I was in graduate school.  I looked at the pseudo-code in the paper draft and wrote the code.  It took me a day or so to get my code working, but it wasn’t particularly painful.  In this case, I was confident that the paper was clear and unambiguous about how to write the code.

My second concern about sharing code is–and I’m being honest here–my code is one giant hack.  I am not a software programmer.  I know what good, elegant code looks like, and it’s not mine.  I often have to cobble together multiple programs to solve a problem from beginning to end.  I often write a script to run many copies of the same program with different inputs.  I always write code for analyzing the solutions and creating figures.  Over the years, I have gotten good at making my code readable to me, so that I can come back to it after months or years and figure out what I did.  But that’s not the same thing as being readable to someone else.  This is a long way of saying that I’m a little embarrassed about sharing my code with others.  Maybe I’m just prudent and am being too hard on myself.  But I am married to a software programmer, so I very aware of how high the bar really is for “good” code.

Having someone look at my code is like inviting someone into my house before straightening up first. It’s one thing to show my messy code to a collaborator but it’s another thing to show my messy code to a stranger.  Sharing papers and tech reports is different–they are polished so they are OK to share.  This can be somewhat addressed by commenting code better.  I always start off commenting code well, but during the fog of debugging, my code usually gets a little out of control, and it’s hard to reign in after awhile.  (I’ve seen other people’s code.  I have some good programming habits–my code could be much, much worse).

However, as I am learning in my discrete optimization course this semester, even simple programming assignments such as implementing the Secretary Problem Markov decision process model can be incredibly difficult for PhD students.  They can benefit from looking at my code.  My homework solution code isn’t as wild and unruly as my research code.  I’m getting used to sharing my code for the homework solutions.

On a related note, this post by Panos Ipeirotis reflects on how to make code more robust to changes, since old code often does not run if it relies on old libraries.  Dr. Ipeirotis is a computer scientist, and it sounds like he writes more elegant code than I do.  I’m still in square one, meaning that I try to make my code readable to someone else.

How self-conscious are you about sharing your code?

Last week, I started a new lab notebook.

My first lab notebook was a gift from my MS advisor.  On our first official meeting together, he seemed a little concerned that I wasn’t taking notes during the meeting.  He promptly gave me a lab notebook.  It was a high-quality notebook that was also given to undergraduates taking a senior design course.  I liked it.

After I filled my first notebook, I replaced it with a composition notebook.  I have continued to use composition notebooks ever since.  They are sturdy, frugal, and small–they are exactly what I need.  The pages are small enough that I am not tempted to write two ideas on the same page.  Early on, I discovered the benefit to keeping a Table of Contents (two pages at the end of the notebook).  It doesn’t take much time to maintain, since I can write an entry into the back of the book in just a few seconds after writing a page in the notebook.

I use my notebook less often these days, but I still find it vital for doing research.  In the past few years, I no longer use my lab notebook to crunch numbers, since it became too hard to find mathematical arguments that were correct given all of the dead ends.  I now write endless pages of math on scrap paper, and then copy the legitimate ideas into the notebook.  I also jot ideas into MS OneNote on my tablet PC.  OneNote is a great program that can certainly double as a lab notebook if backed up frequently, but I stick to a real lab notebook.  I print out my OneNote notes and staple them into my lab notebook.  However, I still frequently write down many of my research ideas directly into my notebook before I forget.  That is, after all, why I have a lab notebook in the first place.

The lab notebook seems to have gone the way of the dinosaur.  Are they still needed today?  I think so.

It is still a great idea to organize research thoughts and to write down research ideas before they are forgotten.  The lab notebook is perfect for that.  Dr. Rod Beavon (who offers advice for maintaining a lab notebook) reminds us that “science does not take place on the pages of textbooks or learned journals, but it is recorded [in the lab notebook]. The quality of any work is only as good as the report that remembers it when the test-tubes have long been washed up.”

Another benefit of lab notebook is that they teach students how to be organized researchers.  I have observed first-hand that grad students are not always naturally bent toward organization, partly because we professors often have low expectations for organization (compared to what students can expect in industry).  Organization builds character, and students need it to learn how to approach research in an organized way.

I have found that one drawback to using a lab notebook is that some ideas do not lend themselves to the lab notebook, since they are too sprawling or complicated or better summarized in a snippet of code.  If an idea cannot fit on a page, it is hard to understand later.  Another drawback is that research ideas for pursuing later can get lost in a notebook.  I try to copy those ideas elsewhere so I don’t forget about some of my more interesting and speculative ideas.

These days, my desk, computer, and schedule are cluttered with various tasks and obligations (teaching, service, research, personal).  But my lab notebook remains a special place just for research ideas.  I appreciate the simplicity of that.

My stack of lab notebooks

Links:

• Writing the lab notebook

Tell me about your lab notebook!