Funding or Firing!

Scientific research has entered the age of "get funded or get fired." Since my position depends on "soft-money" (which means I'm supposed to fund 90% of my salary in grants) my job is in jeopardy. While this isn't a fun place to be, I have always known the risks and possibility of this happening. That's life—if you want to have fun and do science, you accept the risk that your nation will choose to expend its resources on senseless conflict and drain the pool of cash for research and development. :-) I guess you can see where my biases might lie.

So, much like my last post, I'm working very hard as often as possible. The summer is always very busy with students populating the lab and, my chief tech moved on to another lab this past summer. Very hairy time. Nonetheless, I have been in the lab far more lately than in the past five years or so and that's been fun for me (maybe less so for the students!) as I have been revamping my laboratory's focus and working to make the lab a leaner/meaner, agile tool.

I have continued to refine my workflow issues and have become far better at managing my time than in years past. I am still relying on a mix of emacs org-mode for a master priority list and paper calendar sheets for daily tasking (stuck into the back of my lab notebook). This seems to work well and keeps me very organized. I have done very little manuscript writing this summer but I have been reviewing papers from a bunch of different journals on an almost weekly basis. Unfortunately, due to the volume, I am often late getting my comments back to the editor and that's an ongoing source of frustration (for me as much as for them!). I've cut back on the number of papers that I am willing to review but that has been balanced by the increase in requests. Frankly, if a paper is within my areas of expertise, I usually say `yes' and I find that I learn a lot about current state-of-the-art in my field. It seems to me that I exist in an interesting niche with expertise in Physiology/Neurophysiology, developmental Neuroscience, and computational modeling.

In other news I've been learning R as I can't afford to pay staff statisticians a whole bunch of money to build statistical models for me. Nargh. Luckily, we have a class through Epidemiology and Biostatistics on R programming so I'm muddling through. The class is taking a HUGE chunk of my time but this is good for me and I find it interesting and very useful—potentially. Also, there's a great add-on for emacs called ess which stands for "emacs speaks statistics" and this has been a life-saver. I can run R within an emacs window and have all the editingfeatures and syntax highlighting that I know and love available.

I suppose that's all for now. I realize this has been a long gap but I have been extremely busy and, even now, I'm avoiding programming homework to post. LOL!

Workflow and "refactoring"....

I am coming off a 9 week jag of, essentially, continuous work. And here I mean that at least 6 to 8 hours (more like 10 to 16!) per day, every day, has been dedicated to work. My wife and I have BOTH been on this crazy work schedule and it put a damper on our holidays and most of the beginning of this year. Most unfortunate. The result has been two manuscripts submitted, a small-ish grant, and some preliminary work on two other grants.

However, trying to manage this much work has initiated a strong desire to revise my work-flow. I usually use Emacs' org-mode to build my "to do" lists and take notes in lectures or meetings. I have been reading a lot of time-management books a la Dave Allen's Getting Things Done because, mostly since the divorce from my first wife, I've had a real issue with procrastination at times. This is much less a problem now than when I was in grad school but, occasionally, I can feel overwhelmed and it's hard to get started on a project until deadline pressure starts to weigh heavily upon me. So org-mode helps me stay organized and it works well for outputting thoughts to html or LaTeX for incorporation into larger documents. I've also started using it to outline papers/grants.

The big problem with the last few weeks has centered on the use of tools that I'm not all that familiar with. One of the manuscripts we were working on was being written by the first author in Mickeysoft Word. I really, really dislike Word. I have good reasons for disliking Word that go all the way back to when I was working on my thesis in DeScribe (a fantastic word processor and page-layout program!) and had a horrible time trying to export it in a format that Word 2.x for Windoze wouldn't munge up and destroy the table of contents and figures I had painstakingly laid out. I currently have Word 2011 for Mac (ver. 14.02) and it still fails and crashes with documents that are larger than about 10 megabytes. I also find the interface in Office/Word for Windows confusing and difficult to navigate. I download new versions of Office as they become available to the university and check to see if my pet-peeves have been sorted out but the majority of my problems with Word remain.

I've started using OpenOffice to have some compatibility with my colleagues who use Word (while still maintaining some of my OpenSource cred!) but, unfortunately, symbols (like Greek mu and beta) are different between Mac and Win fontsets (at least the subset used by OO and MS Office) so I usually end up with emails back saying, "Hey, your symbols are all monkeyed up! Why can't you just use Word like a normal person!?" etc. OpenOffice is ok—it even has many shortcut key combinations in common with Emacs so I can use it just fine. I also don't have much trouble finding some of the more sophisticated things I need (which I can't say for Word!). I use OpenOffice when I need to work with someone who comes from the WYSIWYG word processing world and I've mandated that everyone in my lab use OpenOffice and store lab-wide documents in either ascii text or OO formats.

This brings me back to Emacs. I used vi for about 10 years before switching to Emacs and it's been about 15 years since I made the switch to Emacs. I like Emacs—the command keys for most of the editing I do are embedded in my motor memory and the control over fonts/colors/syntax highlighting makes my life much easier. Since I prefer to use LaTeX and BibTeX for my writing, Emacs is a good editor for those environments and that makes my life easier. Also, I can do just about everything from within Emacs (even though I don't unless I'm on an old or low-spec machine like some of the ancient Linux boxes that are scattered about the lab) and that just appeals to me philosophically. Emacs used to be considered a big program but in today's world of 64 bit architectures, gigabytes of RAM and terabytes of storage, Emacs is very lightweight when compared to Office or other gui text editors.

If I run top (a *nix command) and look at how much real and virtual memory that Emacs is occupying it comes out to about 30 megabytes of each. Word is taking up about 82 megabytes total and OpenOffice is occupying about 110 megabytes. So Emacs "wins" in regard to smaller memory footprint. I still rely on a lot of paper notes (laboratory notebook, my journal, day-planner sheet for each day, etc.) but most of my self-authored documents are written in Emacs and then exported and prettified for others if needed. I use TeXShop and BibDesk too so those count as gui tools that make my life easier. I find it helps to have a giant monitor that I can plug my laptop into when I sit down to work also. My lovely wife bought me a gorgeous 22" Samsung for my study at home and I have a 23" Viewsonic that I bought for myself at work. These huge monitors allow me to take my laptop with me to meetings and take notes or go seek some peace and quiet in my favorite library on campus and then come back to my desk for larger scale editing and graphics work. This is very nice!

So my tools are in place and I just need to figure out a more disciplined way to distribute my workload and get more done. I have been very encouraged by the amount of work that I've managed to complete in the last few weeks but I had to abandon submission of one of the big grants I was working on and embarrass myself in the eyes of my co-authors because I wasn't organized enough to get that grant in shape for them to work on—not pretty and I need to do a better job on this kind of collaborative project. :-(

Computers: Love 'em, or NOT...

Whether you love or hate computers, they're a necessary tool in today's world. I gave up on Windoze back in the days of Windows 3.1 and have never really looked back. My day-to-day computer use is with a Mac (MacBook Pro 13.3", 15", or a MacPro quadcore at my desk). I am always amused when people sneer at my use of Macs and say that they're "too expensive."

I have done many cost comparisons of Macs vs. generic laptops and the costs are about the same for equivalent horsepower. Yes, you can get a cheaper tower or desktop from the PC world and run Linux and you'll have a machine that's roughly equivalent in reliability and speed to my Mac. I can work fluidly in both the Mac and Linux worlds because they're both *nix-based environments and I'm very comfortable using *nix tools.

One reason I have no trouble moving back and forth between Linux and Mac is that I use, essentially, the same tool-set on both platforms. I use Emacs, LaTeX, Python, Firefox, Gimp, Inkscape (though on the Mac I prefer Illustrator as Inkscape just isn't quite there yet), and OpenOffice. Yes, these programs also run in Windoze but I haven't had any need to use Windoze for my daily work in over a decade.

There are a few programs that I find quite handy in the Mac world that don't have direct equivalents in the Linux world: Kaleidagraph, IgorPro, and Skim (a pdf viewer/editor). I also use a program called Papers for managing my voluminous collection of pdfs. There may be roughly equivalent packages in the Linux world or the Windoze world but I haven't found them yet and I haven't needed to go looking.

My lab personnel are perfectly happy using Windoze and I haven't made any strong efforts to pull them away from the platform. We have one section of our lab that is very computer ignorant and they have weekly problems with viruses and hardware failures, largely due to their unwillingness to do the things that I (and my support engineer!) have suggested to prevent their computer headaches. They suffer because they refuse to be more sensible and learn how to use the tool more effectively and safely.

Contrary to popular belief, I don't hate Windoze—I just find the user environment (yes, even Windoze 7!) unnecessarily obtuse and illogically organized. Yes, I'm sure I would "get used to it" over time if I were forced to use Windoze but, luckily, I'm not in that position. I can use whatever operating system and applications I like as long as I'm productive. I choose to use a computing environment that makes it easier for me to be productive and Mac/Linux/Unix tools are the foundation for my productivity.

Winter falls....

I just got back from one of the BIG annual meetings (in San Diego this year) and it was a blast. I met a lot of great new people, saw some good work, and learned some new things about Python and some other good scientific software.

The weather here in Cleveland has been very warm since I got back from the Left Coast and that's always surprising during this time of year. Even though Winter is the most challenging season for us since we aren't particularly keen on a five month period of grey and cold, we DO have our indoor hobbies to keep us occupied. I have two guitars to build this winter, well one to finish and one to start and complete. So, with the Winter hobbies, the long cold-grey is at least bearable.

In other news, I now have a car. For the first time since 2004. I'm not a big fan of cars in general because they end up as money pits and I find driving with four wheels on the ground quite boring. My motorcycle will always be my favorite form of transportation. In this case, because my wife and I are zooming around with crazy schedules, a second car is going to be very handy. We had already been talking about buying a second car when a deal came along that I couldn't pass up. Ruth's friend Walt was visiting from Florida and mentioned that he needed to unload his Audi A4 due to neighborhood association rules (typical BS!) and did we happen to know anyone that would be interested in buying the car? I quickly made him aware that we were keen on buying it and would be happy to help him out.

Walt drove the car up last Friday and I took it to the shop today to get it checked out and have some small things fixed but it looks like a nice little car. I'll let you know how it does. I find it strange to drive a car after being without for so long and having Ruth do most of the driving. Yet, like riding a bicycle, it comes back quickly.

Summertime, and the living ain't easy...

Forgive my bastardization of that classic standard's first line but, as I've mentioned before, Summer is the busiest time of the year for me. My laboratory takes in students from various programs and I have promised my chief tech that I would back off from taking in more students. So, I did—by one when compared to last year. ;-) However, in my defense, we have some EXCELLENT students in the lab this Summer.

Aside from trying to get them up and running, all is proceeding apace and I hope to even get some time in the lab for my own experiments. We have the newest version of RTXI up and running so we'll FINALLY be able to do some of the dynamic clamp experiments I've been dying to do for a few years.

In other news, I'm trying to figure out what my "minimal software set" is for my Macintosh. I have a laundry list of proprietary and open source software that I use and I want to pare that down to the minimum. I'll keep you posted!

Work, work, work...

I am still catching up from the trip in February! That's life. My rule of thumb has been that, for every day I'm gone, it takes me three days to catch up. I think that ratio may no longer be true and it may be more like 1:4 or 1:5. I am not sure why this has shifted, frankly. Much of the blame probably relies with me and how I process my tasks.

I have been working on improving my efficiency so I have been reading a lot of management-type books that are focused on streamlining task management and improving one's ability to deal with a "To Do" list. Dave Allen's "Getting Things Done" method is useful and, while I've read the book before, I have a renewed commitment to using his methods to handle my work load more effectively.

A big help in this area has been org-mode for emacs. I've been using emacs for about a decade now and I find it the most sensible way for me to work. I like using plain text for all of my files but I have a difficult time getting collaborators to work with LaTeX/TeX files that I produce and, after using org-mode for a few months, I've moved away from writing straight LaTeX and instead, I'm using org-mode for my note taking and outlines for manuscripts. I haven't yet played with the spreadsheet features in org-mode but I am getting more interested in using webdav to publish my To Do list to my iPod Touch so I have the updated version on hand all of the time.

I use iCal at work on my main desktop computer so I am tied to an Apple product for my calendar needs (at the moment). Org-mode has a nice agenda minor mode that would probably be more sensible for me to switch to since I use various computers throughout the week and they aren't all Mac OS based. So when I'm using Linux or (on very rare occasions) Windoze, I need to have some way to deal with my calendar that is multi-platform. I do have my iCal calendar publish to my Google cloud apps so I have access to it as long as I have web access but it would be more sensible to have it pushed out to a device (either my CrackBerry or the iPod Touch that I carry). I'll keep you posted on how this all goes.

In the mean time, please feel free to send any ideas or comments about work efficiency. I really need to become more productive just to keep up with my work responsibilities. Of course this would help me keep on top of things that I need to get done at home too! :-)

Two weeks

The last two weeks have been tough. My grandmother and my great uncle both passed away. They were in their late 80s and had been devoted and hard-working. They had good lives and I was very gratified to see so many people come for the funerals and share their stories and appreciation for my grandmother and uncle.

We drove down to Florida for my grandmother's funeral and then we came up through Georgia, S. Carolina, N. Carolina, and Maryland (I was to give a couple of talks at Johns Hopkins) before heading for Cleveland last Thursday morning. Friday was spent catching up on emails, to the best of my abilities, and then Saturday I received the call from my Mom about my uncle passing. I made reservations to fly down to Dallas, meet my Mom, pick up a rental car, and then drive to Corsicana for the funeral on Monday morning.

The funeral was sad but it was very good to see my cousins and more extended family, many of whom I haven't seen in over 20 years. So we helped each other get through the sad parts and enjoyed catching up with each other.

One ripple triggered by these events has been a renewed commitment on both Ruth's and my part to put our families and friends higher on our list of priorities. We feel like we've neglected many people whom we have been close to and have been very supportive of us over the years. Frankly, we need to change and do a better job of showing our appreciation for people we care deeply about. I'm afraid that we're both bad about writing and sending "thank yous" and holiday cards. We will have to do better.