Daily Life in an Ivory Basement

On Thursday, May 15th, I finished my post-doc position at Caltech.

On Friday, May 16th, I officially started as an Assistant Professor split between Computer Science & Engineering and Microbiology & Molecular Genetics at Michigan State University.

On Friday evening and Saturday, we hung out down at the Caltech Marine Lab and partied.

As I type, I'm on a plane flying from California to Michigan, where my cat and I will spend our first night in our new house.

My wife and daughter will join me on Wednesday.

All of our stuff is en route and will arrive later in the week.

On Monday, I will start "directing" my new lab: I already have several local summer students, as well as a part-time research assistant. Two graduate students and a postdoctoral fellow will be starting with me later in the summer.

Hooray!

--titus

I've been hit by a few different e-mail-related problems over the last few months, and it's becoming intensely frustrating.

Some servers seem to randomly drop messages from me, for no obvious reason; at least, people don't get one message and then do get another, a day later. gmail may be at the center of this but it's not clear. (Changing my public From: address to ctb@msu.edu may have contributed to the lossage rate, but cannot be the only cause.)

Yahoo at first decided to mark messages as spam, then drop messages, and now likes me again.

As I write, caltech.edu seems to be bitch-slapping a select subset of my messages. Either they're grey-listing and waiting to forward some messages on, or they've dropped some messages entirely.

My daily e-mail load has grown to the point where I appear to be hand-deleting real messages from my inbox when my eye gets them confused with spam or automated notices. I know of at least two messages that I've deleted in the last month -- I found them in my received-not-spam folder (where I save all incoming messages) but have no recollection of having read them. Before this month, I can't recall having accidentally deleted two e-mails in the last 5 years. And it's not like my spam filter has a high false negative rate: I barely get any spam at all in my inbox.

Now I'm trying to start sending messages to people in my lab, and some of them are not responding or acknowledging the messages. Maybe they're not getting them. Maybe they're out to lunch. Maybe they don't like me, or authority, or something. I don't want to hassle people who don't want to respond, but I also want to make sure they got the $!%#$#$ message! Ah well, I will be physically there soon...

All of this goes to say that for a variety of reasons -- increasing amounts of e-mail, increasing amount of SPAM e-mail, increasingly random and annoying anti-spam measures implemented by the big inbox providers -- e-mail has become unreliable enough that I have to think about it. Even worse, the number and variety of anti-spam measures in play mean that neither I nor the receiver may have any ability to affect the spam filter that is dropping e-mail (translation: I don't know what to do to make things more reliable).

Grr.

I think the time is coming where a reputable SMTP forwarder could make some $$; I'd be willing to pay a $ or $$ for a bonded SMTP provider! Anything like that out there that actually works?

--titus

p.s. In a largely unrelated side note, the number of blog comment spammers attempting to post to my blog continues to hit record highs on a daily basis. I've never approved a spam comment -- yet they continue to try. It's mind-bogglingly stupid and it just goes to show that stupid behavior will continue indefinitely if it's approximately zero-cost to the commit-ee. Grr x 2.

So, err, drop me a line if you wrote a witty comment that didn't get posted, and if I don't accidentally delete your e-mail I will approve your comment.

I've been on the run for well over a year -- I started writing my PhD thesis in July '06, just after I got back from teaching at Woods Hole. At the time I was also interviewing for a faculty position at MSU (since offered & accepted). Since then I've defended my thesis, finished writing it, switched to my post-doc lab and started a whole new batch of projects, taught a few more courses (at LLNL and Woods Hole), and spoken at a few conferences. This month, I've written a 25 page NIH grant, too.

What I have not been able to do is finish off much of anything, other than the grant! In addition to letting some of my computational science lapse, I've completely dropped the ball on twill and figleaf as well as the subprocess patch, and my systems administration is not going well either... I even have two consulting gigs that aren't really proceeding at the moment, although conveniently I've managed to partly shuffle those off onto someone else's shoulders.

The real kicker is that I have a nice deadline coming up: Tracy and I are having a baby, probably sometime in the next two weeks, and I'm going to take the next month or two off. I certainly won't be doing experimental work, and I probably won't get much done on the computational side, either.

The result of all of this is that my TODO list hit a bit of a zenith this last week: I'd been pushing all the non-grant stuff into it while I finished the grant proposal, and it reached 500 messages. As tempting as e-mail emancipation sounds, I think it's really bad manners; and heck, these were all messages I was interested in! My life, except for some of the personal/family bits, is organized through e-mail -- and it's a large part of being an effective scientist these days, I think. So I spent about 8 hours going through and sorting the messages.

The twill/figleaf/testing-TODO stuff got put in my twill-todo folder. (Sorry folks, at the moment the baby and the science get priority.)

I went through all of the journal ToCs and downloaded the papers I was interested in. They're all in my DEVONthink folder now, waiting to be skimmed and renamed appropriately.

A bunch of stuff got moved back into my inbox, which is where I keep my short-term TODO list. This includes messages about the tutorials I'm hoping to write for the biology-in-python list, as well the consulting work -- I'm gonna try to finish that stuff off before the baby arrives.

The interesting & informative e-mails that I'd been saving for a good read all went into DEVONthink, appropriately tagged, so that I will find them if I search for anything related.

The long-term collaboration/data work that I've been saving in my TODO list also went into DEVONthink, under my lab management folder hierarchy. This is fodder for undergrads, masters students, and PhD students -- I'm not going to get to this data anytime soon, and it's always good to have a dozen or so projects lined up for students that get lured into my net.

Everything else -- about 70-80 messages -- I kept in my TODO folder, awaiting random chance and/or some attention from me.

The two points of this blog entry, such as they are, are:

• don't expect much of out of me for the next few months. If someone wants to step up and integrate patches into figleaf and twill, I'd be very happy; other than that, rest assured that I will get to your e-mails some day... but maybe not soon ;(.
• DEVONthink is becoming more and more important a part of my life. It's a very handy way to organize both random and structured textual data, and it supports the kind of serendipitous discovery of linked research interests that I've started to rely on in my scientific work. I highly recommend it for people who are drowning in information.

--titus

Just a short note to say that I've taken a faculty position at Michigan State University, in Lansing, Michigan. The position is split 65%/35% between the Computer Science and Microbiology & Molecular Genetics departments, and I expect to be working on a fairly wide range of problems. My computational "focus" (such as it is) will be on applying effective computational techniques to biological data; I also will be doing experimental (wet-bench) research in vertebrate developmental gene regulatory networks.

One of the big changes that the MSU Computer Science department is contemplating is changing their intro CSE classes over to some mix of Python and C++. I'll probably be helping with that. Also, I think one of the reasons they hired me to is to introduce more open source and "agile" testing technology into the CSE curriculum there, so expect to see some posts about that soon.

I'll be starting at MSU in August 2008, a year and a half from now.

If you're interested in getting a Masters or PhD in computer science, and like the look of MSU's CSE department please contact me. I'd very much like to attract open source/Python/Web people to the department, and you wouldn't necessarily have to work with me -- there's plenty of other people there. I'm not so familiar with other people yet, but my friend Charles Ofria runs the Digital Evolution Lab, which does fantastic research.

(And, obviously, if you're interested in gene regulatory networks, developmental biology, regulatory genomics, and bioinformatics in general then we should talk...)

--professor titus