The Quality of Scientific Plotting Software

I’m going to take a minute here to rant a little bit about the paltry menu of scientific plotting software that is available.

This research project that I’m working on has required me to teach myself the basics of multivariate linear regressions and a few other things. I’ve finally gotten something that I think is legitimate, although I won’t know until tomorrow, when I meet with the physician I’ve been working with. I want to make some simple box-and-whisker plots that show the differences between a few different groups. I’ve been using JMP to do my analysis, but I’d like to produce some publication quality figures so that I can start working on our paper. The problem is that the options for generating publication quality figures absolutely sucks. I’ve spent the past six hours trying to figure out the best way to generate a half dozen plots that don’t look like they were cobbled together in Excel and I’ve gotten nowhere. Screw all of this.

This isn’t the first time I’ve had this type of frustration. Here are the options I’ve tried, that produce crappy results.

• Matlab is nice for working with large datasets, particularly if you’re doing things like Fourier analysis or numerical modeling.  The problem that Matlab has is that it can’t produce reliable figures – what you see on your screen is usually not what you get when you generate an EPS or TIF.  Also, what the hell is with medical journals that don’t want vector images?  I was blown away when I found out that the journal I’m hoping to submit wanted GIF or JPG figures.  At any rate, Matlab is terrible.
• JMP is fine for producing quick plots of various statistical relationships, but its ‘Graph Builder’ is absolutely useless.  Beyond useless.  Honestly, the vast majority of statistical software I’ve used has the most worthless user interface.  It’s enough to make me think that GUI statistical software can shove it.  If I get into a MD / PhD program, I swear I will never use any of this crap – I’ll teach myself to use R and never look back.
• SigmaPlot.  This piece of crap costs a zillion dollars and the interface is nearly impossible to use.  It’s as if these packages are designed by people that don’t actually know anything about how data analysis is done.
• Microsoft Excel.  I hate almost everything Microsoft does, but Excel 2003 was awesome.  Of course, after that, Microsoft changed the interface entirely that is completely useless and makes the simplest tasks a Herculean epic.  Of course, there’s the problem of no capacity to export into a usable format.  Worthless

Seriously.  This is infuriating.  It should not be this difficult to produce properly formatted and sized figures.  Even the most expensive programs do an abysmal job.  All I want to do is make a few box-and-whisker plots with well-defined resolutions, fonts, formats, and sizes.  I have wasted countless hours trying to do this and I’m absolutely fed up with it.  Seriously, fuck this.

Greetings New Readers!

Judging by the enormous swell in the number of hits that my archives page has got, I’d imagine that I have a few new readers.  Hopefully you guys enjoy what I write enough to stick around – my posting frequency is rather short right now, since I’m 25% of the way through studying for the MCAT.  I’ll try to post an update on how that’s going sometime this weekend.  Take care.

One More in the Bag – Part 1

I apologize for not giving a lot of updates the past month or so – things at work have gotten ridiculously busy and I just haven’t had a lot of time to sit down and write out a post of any depth or length.  I’ll give a bit of an update now on how my semester turned out and then sometime in the next week or so, I have some other topics that I want to address.  The first is a discussion about the research I’ve gotten involved with and the other is on ethnicity and how I feel that it relates to the medical profession, particularly the application process.  If either of those topics is of interest to any of you, stay tuned – hopefully, I’ll have something in a couple of weeks.

About six weeks ago, I flew out to Florida to prove out a test method that a coworker and I have been developing over the past year.  Without getting too technical, we were basically trying to measure the attenuation of an enclosed structure to electromagnetic radiation.  There are well-established methods for doing this for small structures, but for larger structures like buildings and planes, those methods tend to break down and you usually get nonsensical results.

We were reasonably certain that it was going to work out well, but most of the people we needed approval from were very skeptical.  The aerospace industry does not suffer change all that well and since the two of us are relatively low level engineers, there is a bit of a bias against us.  In theory, this is due to a difference in experience but in practice, it’s more of a personal thing.  Older engineers are terrified that innovation and efficiency gains will translate into layoffs, so the pressure to continue doing things the way we’ve always done them is high.  Anyway, when we showed up in Florida, we had a huge gallery of engineers and managers watching what we were doing.  A few were worried that it wouldn’t work, which would set their schedule back a year, while others were hoping it would fail.  Normally, this type of testing takes a long time – almost a month – and we were claiming we could do it in a morning, so you can probably imagine the general attitude.

I won’t go into any of the details about the testing, but suffice to say that the results were fantastic.  Not only did it work exactly as we had been saying that it would, but we had a chance to show some of these managers and chief engineers how all of this electromagnetic attenuation worked.  The test took the morning and afternoon, primarily because of all the questions that we fielded.  Most of these people had no idea how electromagnetics works, so I wound up giving lectures on basic physics to a bunch of chief engineers most of the morning.  Testing went flawlessly and we made believers out of everyone.  At the time, having 30 people watch and question my every word or movement was a little frustrating, but after the fact I realized that it was a blessing in disguise.  None of them believed us and they had showed up to see us fail, but as it turned out, they saw the evidence that we were right and now they can’t question the results or the method.

The results turned out so well that, when we all went out for post-testing libations, neither of us bought drinks at all.  Finally getting some recognition for a years worth of sweat and toil was a really nice feeling, but I knew it wouldn’t last.  As soon as I got home, the old school engineers in my group started sending out emails about how neither of us knew what we were doing and how our results were crap.  Of course, the reason they did this was because it invalidated the test results that they had gotten a few years ago when they did a similar test.  So, I’ve spent the past four weeks explaining antenna theory and electrodynamics to even more people.  It’s a long complicated story about workplace drama, so I’m not going to bore you all with the details.  At the end of the day, what I’ve basically been doing is introducing a level of rigor into the way that this type of testing is done.  One of the engineering managers that was present at the test told me afterwards that our approach felt much more like science than those tests normally felt.  I sort of laughed and told him that it was because I wasn’t an engineer.

I was pretty certain prior to performing our test that it was going to yield good results and I knew that it was the sort of thing that we should submit to IEEE, so I’ve been working on that on the side.  Getting anything published at my company is a Herculean task and requires a lot of bureaucracy – I published a paper at a conference last year and it took me less time to write the paper than it did to collect all the necessary clearances, approvals, and signatures.  I remember sitting at a desk with the VP for Legal Affairs and having to explain to him that Coulomb’s law was not a trade secret – it took at least a day just to get through him.  I’m hoping to get two papers published this year based on some of the work I’ve done for the company, but I have no idea of how the industry will judge our work.  I don’t have a PhD and I imagine that there are just as many politics involved with getting things published by IEEE as there are in medicine.  Anyway, we’ll see what happens.

I just realize that I’ve gotten rather long-winded, so I’ll wrap it up.  I’ll give a summary of how my classes finished up in another post, so check out Part 2.

Quick Updates to the Blogs I Follow

I went through and cleaned out my blog links, which you can read on the right-hand side of your screen.  My actual RSS reader is gigantic and many of the blogs I follow are not all that likely to something any of my readers care about.

For some reason, I’ve been a longtime follower on Action Potential’s blog but I didn’t have her linked in my blogroll.  Easily fixed.  If you don’t follow her, you should.

Mandatory Reading

I don’t often delve into the depths of politics and things like that, but I feel compelled to share this article on the issue of mandatory transvaginal ultrasounds.  I linked it earlier via Twitter, but since a lot of people reading my blog probably don’t do the whole Twitter thing, I wanted to post it here.

Two things I want to point out:

1. The fact that the physician that wrote this piece felt the need to cloak his identity for fear of the repercussions speaks volumes on the state of medicine today.  When every bonehead from Barack Obama, Harry Reid, and Nancy Pelosi to Rush Limbaugh, Mitt Romney and now Santorum and Palin feel it is their right to dictate by fiat how practitioners practice and patients are treated, you know things have really gone off the rails.
2. The silence from the American Medical Association on this is absolutely deafening.  I have yet to read or hear of a position or response from the AMA – where are the appeals for physicians to only order procedures and treatments that are medically indicated?  Why has the AMA been absolutely silent on an issue which rides so roughshod over such trivial notions as patient consent?

This second point bothers me a lot, the more I think about it.  I cite now directly from the AMA code of ethics, section III:

A physician shall respect the law and also recognize a responsibility to seek changes in those requirements which are contrary to the best interests of the patient.

and section VIII

A physician shall, while caring for a patient, regard responsibility to the patient as paramount.

Whether a physician should deliberately break the law in question is something that is probably a matter of individual choice – personally, I would probably refuse to see such patients rather than commit a crime and potentially lose my medical license.  I should point out that, interestingly, section III requires a respect for the law, not a blind adherence to it.  Regardless, note that the second half of their statement is compulsory – the AMA has a self-imposed mandate to seek changes to legal requirements that are contrary to the interests of a patient.  In what universe does the AMA, as the largest representative of MD and DO physicians not have a duty to act?

What is the American Medical Association doing to, in their words, move medicine forward?  From their own mouths.  Physician reimbursement.  Repeal of the SGR.  Lobbying for physician legislation.  Not a single reference to patients in any way.

Cowards.  If ever there were a time for the AMA to man the ramparts and stand up for their patients, that time is now.

Pictures of the Super Kamiokande Neutrino Detector

Here are a couple of pictures of the Super Kamiokande neutrino detector.  My favorite one is the one on the side which shows the guys in the rowboat out in the middle of what looks like a lake.  That huge chamber is filled with heavy water and then lined on all sides with Cherenkov detectors.  This particular detector is located something like a mile under a mountain in Japan.  Muons created by the interaction of cosmic rays with atoms in the upper atmosphere, probably atomic nitrogen or oxygen, have enough energy to reach the Earth’s surface and that would skew the experiment, so neutrino detectors were first constructed in abandoned salt mines.

The pictures are super high-resolution, so here’s a link;

http://www-sk.icrr.u-tokyo.ac.jp/sk/gallery/index-e.html

An Update on the Electronic Migration

This may actually wind up being two posts in one if I end up getting long-winded.

Before I get into it, I want to say thanks to all my readers – I started this blog a bit over two years ago, a couple of months after I decided I wanted to go to medical school and become a doctor.  I never figured that anyone would actually read it, let alone other intelligent people that are on this road with me.  Comments, emails, dialogue, and discussion are really encouraging and the whole premed / application process can be incredibly demoralizing.  Anyway, thanks a lot for reading everyone.

Alright, onward and upward.  My last post, prior to the start of the term, was on my intent to start taking notes electronically and more or less abandon trying to write everything down during lecture.  I got a lot of comments and suggestions on other people’s perspectives and they were all extremely helpful.  I purposefully avoided giving my thoughts early because I wanted to give it a really solid chunk of time before passing judgment, as one of the commenters had suggested.  Thanks Josh.

A little background on how I’ve been doing all this.  I use a MacBook Pro with a lot of memory, so running multiple apps (as long as it isn’t Microsoft Office) doesn’t really have much of an effect on its performance.  Both of my professors post their lecture notes on the course website prior to class in PowerPoint format.  A PDF would be nicer, but it’s not too much of a problem.  Anyway, here are my thoughts so far.

• For note-taking purposes, I’ve been using the free version of EverNote, which is limited to 60 MB of online space per month.  I honestly don’t use the web clipper or insert a lot of images in my notes, so I haven’t found this to be a problem.  If I eventually wind up using a lot of images and things off the web, this might change.
• Multiple desktops are a necessity when note-taking, at least for me they are.  I was raised on Unix, so I suppose it might only be a personal thing.  Mac OS and all the flavors of Unix can do it – Apple calls them spaces – but I’ve no idea if the current iteration of Windows is capable or not.  I find that keeping EverNote maximized in one space and PowerPoint in the other works pretty well.  I follow along in the notes and when I want to document something from the lecture, I can quickly switch to the other and do so without having to deal with minimizing or shuffling windows around.
• As I had suspected, having all my notes from the entire semester in one place without having to worry much about organization is absolutely incredible.  Without a doubt, one of the biggest bonuses to taking notes digitally.  I use EverNote when I’m doing the reading and it’s great to be able to quickly look things up there.  I keep two different notebooks for each class – one for reading assignments and one for lectures.
• Having Google at the ready during lecture is a convenience that I never realized until I actually had it.  Looking up a key term or asking Google for an image of something referred to during lecture is really cool.  Resisting the temptation to use the internet recreationally hasn’t been too difficult, although lectures tend to get stuffy sometimes – genetics is particularly prone to this, since my professor tends to just read the slides at us.  Also, since both professors are notorious for posting lecture slides 10 minutes before class, it helps to be able to get to class and just download the lecture notes.
• By default, EverNote stores my notes on the cloud and can be synced with my iPhone.  This is really nice, since I spend about 45 minutes on the train each way.  I tend to review things (e.g., biochemical pathways) while I’m commuting, so being able to quickly look something up on my phone is nice.  So far, I haven’t had any issues syncing or connecting – sometimes, I can’t connect to the wireless router in the classroom, but EverNote caches the latest copy on my machine and I’ve never had any problems accessing my notes.

Nothings perfect though – now for the bad.

• The text formatting in EverNote is terrible.  Even though font sizing has a key-binding, it doesn’t usually work too well – trying to separate things out by text, typeface, or things like is a real pain.  This is doubly true if you’re trying to keep a color scheme going on.  For instance, the color “blue” in my notes means that it’s something I want to look up or review from the text or elsewhere.  “Red” is used for a topic that I should bring up in recitation or in an email to the professor.  I’ve yet to find an efficient way to do this without removing my fingers from the keyboard and hunting around for the formatting ribbon, which sucks.  Then, once I’ve finished typing and select the normal font again, it usually doesn’t actually change the typeface.  Electronic note-taking seems to be all about efficiency and for lots of text, EverNote isn’t all that efficient.  I’m not too bent about this right now, since I’m sure there are ways to make it faster and I just haven’t found them.  Once I do, this whole problem will go away.
• The copy-and-paste feature doesn’t work all that well.  It has no problem copying images in from the web, but if you try it from other applications like Preview, Adobe Reader, and others, it usually shrinks the images down which is annoying because of the lack of a zoom feature.  For small images, charts or diagrams that have text, this can be really annoying.
• The lack of a zoom feature like every other application in the universe has is more than a little bit annoying.  I honestly have no idea how none of their beta testers didn’t whine about this incessantly.  Once you can click-zoom in one application, you just sort of start to expect it.  Even Office has a zoom feature.
• No ability to do subscripts or superscripts is just plain stupid.  There are something like a billion fonts available, but when it comes to typefaces, you get standard, bold, and italics.  No support for superscripts or subscripts.  Granted, EverNote has the ability to recognized and render LaTeX markup, but most of the time, that’s overkill.
• EverNote has the ability to make tables, which is nice.  The only problem is that, once you’ve defined the number of rows and columns in your table, you can’t alter or extend it.  Seriously?  Have any of the designers actually made a table before?
• The screen capture / web clipper only copies images to a new note.  There is no option to insert it to an active or most recent note.  Instead, you have to clip it to a new note, then switch and find the note, copy it from there and then paste it into the note you want.  Afterwards, you have to go back and delete the new note that was created, otherwise you’ll get a lot of duplicates.  I don’t use the clipper much, so this is only mildly irritating, but if I used it a lot, I’d be ready to throw my laptop through a window.

Those are most of my thoughts at this point.  Admittedly, I get spun up and irritated by little things so I should be clear that I’ve really appreciated the transition to a digital format.  The organizational benefit alone has been huge, particularly with my notes from the reading always a click or two away.  Also, the convenience of having the internet available during class is often really useful.

A couple of parting thoughts and then I promise I’ll stop – I guess I got long-winded after all.

• Both of my classes use PowerPoint lectures prepared beforehand.  I’m not sure how easy this would be if no lecture slides were available at all.  My guess is that it would depend a lot on the nature of the material
• By my estimation, a few classes wouldn’t work too well with this approach – physiology, organic chemistry, anything from the physics or math departments, and certain sections of biochemistry.  Anything with lots of diagrams, structures, or mechanisms seems unlikely to be amenable to this type of thing, but I suppose craftier people than I may be able to find a way to make it work.

Anyway, so far the experiment has been a relative success – I haven’t felt like I was missing anything in lecture and the organizational advantage has been a really nice study aid.

Happy New Year!

I just wanted to take a few seconds to wish all of my followers a Happy New Year!  My girlfriend is here for another day and we’re off to a friends house for a few hours and then back here for dinner and a few episodes of BSG.  Hope everyone that follows me out there is enjoying the evening.  If you’re driving, be safe!

Inbox Assault

So, I don’t normally check my email all that often – at least, not the email address tied to my blog or my Twitter feed.  For some reason I logged in this afternoon and checked it out…seriously.  Why have I been assaulted by Republican primary candidates?!?!  My inbox was stuffed full of requests for campaign contributions from pretty much everyone on the Republican ticket.

Now, I tend to swing more or less towards the libertarian side of politics – I favor a small government, personal responsibility, and a rather conservative view of social contract theory.  That being said, I have to wonder how on Earth I ever showed up on the radar of people like Michelle Bachman and Mitt Romney.  Do these characters really believe that by carpet bombing America’s inbox they will ultimately win the Republican nomination and later the presidency?!?  What goes on in their brains?  I mean, sure, I ignore all the V14gR4 and penis enlargement advertisements, but I’m totally going to show up to support your crackpot “vaccines cause retardation” platform.

At this point in the game, it’s obvious to everyone that only two real primary candidates exist for Republicans.  Why are people like Bachmann, Perry, and the rest of the Republican 3-ring circus still around?  Seriously – even if I wanted to give to a person’s presidential campaign (which I don’t), why would I throw my money towards a candidate with a shelf life of less than a month?

There’s a Do-Not-Call list for my telephone – is there one for my email account as well?  Please.  Leave me alone!

A Quick Thought on Analytical Uncertainty

When I first started working for Big Aerospace, I was shocked at the standard approach to presenting experimental or test results.  A single data point at a particular frequency or temperature was taken as gospel.  Every distribution was normal.  Steps were to taken to avoid multiple measurements.  And I have yet to see, in my four and a half years of being surrounded by rocket scientist types, a plot, graph, or Powerpoint presentation with error bars.  I find that hilarious, since it seems like every single engineer I meet has one color of belt or another in Six Sigma-jitsu.

A mathematician friend of mine from undergrad wound up applying to medical school a couple of years ago and is about halfway through his first year at a school just down the street from me (probably my first choice, too).  We hooked up a couple of weeks ago for lunch and he talked about how a lot of medical research takes, at best, a shoddy approach to statistics, although his description was a bit more florid.  I had to suppress a small laugh when I told him the same sort of thing happens all over the place in engineering companies too.  I have to admit that a lot of scientific research gets a pass on statistical and logical rigor.  It shouldn’t happen.  The scientific community really should police itself, but it doesn’t.  Too often, the purported research from people like Hwang Woo-Suk or Andrew Wakefield, gets through the filter for various reasons.  I’m getting a little bit off-track here and I don’t want this to turn into a rant  about the failures by the gatekeepers of scientific fact – and I have to get back to work.

Inspired by this post by Petulant Skeptic on the perils of p-value, I decided to take it upon myself to start teaching myself statistics at work.  This is partially because I don’t want to be a moron when it comes to statistics as a physician someday and also because I’m working on a couple of projects at work which really do require a statistical approach.  Sadly, everyone I’ve turned to at my company for a basic discussion on statistics, particularly measurement and experimental uncertainty, hasn’t really had a clue what I was asking about or why it was important.  That, I suppose, brings me to the real point of my post, which was to share a useful link on uncertainty which I ran across provided by NIST.  I found it a useful read and figured others might be interested.