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2010 in review

The stats helper monkeys at WordPress.com mulled over how this blog did in 2010, and here’s a high level summary of its overall blog health:

Healthy blog!

The Blog-Health-o-Meter™ reads Wow.

Crunchy numbers

Featured image

A helper monkey made this abstract painting, inspired by your stats.

A Boeing 747-400 passenger jet can hold 416 passengers. This blog was viewed about 12,000 times in 2010. That’s about 29 full 747s.


In 2010, there were 22 new posts, not bad for the first year! There were 14 pictures uploaded, taking up a total of 2mb. That’s about a picture per month.

The busiest day of the year was November 14th with 944 views. The most popular post that day was Making your webapp react to emails with Lamson, pt 1.

Where did they come from?

The top referring sites in 2010 were reddit.com, totallysynthetic.com, chemistry-blog.com, coronene.com, and friendfeed.com.

Some visitors came searching, mostly for python imap, python gmail imap, nitrogen triiodide, python imap gmail, and gmail imap python.

Attractions in 2010

These are the posts and pages that got the most views in 2010.


Making your webapp react to emails with Lamson, pt 1 November 2010
1 comment


Python Gmail IMAP : part 4 January 2010


Python Gmail IMAP : part 1 January 2010


Python Gmail IMAP : part 3 January 2010


A Chemistry Fraud Roundup February 2010

This is part 2 in a series, here is part 1.

In the last section, you should have got Zed Shaw’s LamsonProject running successfully through its unit tests.

Now I’ll show you how to make what maybe the *simplest* application with Lamson that you’ll ever see. All our application is going to do is:

  1. Receive emails with Lamson.
  2. Pull the content from the body and subject lines using python.
  3. Send the data to Google Calendar to be turned into a calendar entry using the quickAdd call, again using python.

Because Lamson is built to interact easily with Python code, this is snap. Continue Reading »

(quick install instructions)

If you’re a web programmer … and if you’re not, why are you reading this? … at some point you’ve wished you could integrate email into your webapp.  Now, by integrate, I don’t mean sending emails … that’s trivial.  Any language you can think of, there’s a library that will let you fire off all the html gibberish that fills your little hearts with joy.

The challenge comes when the little light goes off in your head and you think, “How hard could it be to have my app react to incoming email?”  Maybe you’d like people to make forum posts by email, or create mailing lists ( listserv ) dynamically.

The answer used to be hard … very hard.  A nightmarish mishmash of postfix, dovecot, procmail, pipes, and the odd custom script would get you something that might, maybe, let you fire off a script when a new email came in.  Actually passing email data to your app? Forget it.  And after all that, most people would rightly wash their hands of it and say ‘let’s just poll the mail server periodically’ … ick.

Why can’t I just convert emails to HTTP POST’s sent to an endpoint on my webapp?  Oh … wait, I can, thanks to Zed Shaw’s LamsonProject.

But first, before going to the trouble of setting LamsonProject up, please be aware that there exist several semi-respectable SAAS companies trying to do this for you:

  • SendGrid Parse API : Email to POST.  I’ve never heard anything bad about SendGrid ( a fair amount of good stuff ) but the it is a sideline to their main business of outsourcing your SMTP server for you.
  • Email Yak : Email to XML, Email to JSON, Email to POST.  In private beta.  Don’t confuse with yak mail or yak messenger.
  • Cloudmailin : Email to POST … “just like a webhook”.  In beta.

Honestly, if I had two nickels to rub together I’d probably use SendGrid, but I don’t … so here we are.  On with the show!

Continue Reading »

… or an undergrad:

In a previous post, I mentioned Innocentive (wikipedia), a company that posts industrial science challenges with cash rewards for a solution.  As full disclosure, I have previously had a solution bought by Innocentive, so I am a fan boy. To put it another way, it allows anyone with the skills, degree or no, to sell good ideas for thousands of dollars and maybe do some good in the process.  Not a lot of good probably, but in the industrial chemistry world that’s maybe a better outcome than average.

Continue Reading »

Innocentive, for those of you who don’t know, is a company/community where science types can go to get cash awards for solving problems in science.  Innocentive likes to call this the ‘open sourcing of science’ which makes for good PR, but a closer description might be ‘outsourcing the R&D dept.’  As full disclosure, I’ve been a member of the community for several years and have received $10K for my chemistry solutions posted there … I think on balance it’s a great idea executed well.

But the trouble is, they believe their own PR and the write-ups they’ve received in the press (see list below).  Several weeks ago Innocentive created a project to collect ‘emergency response’ ideas to deal with the oil spill.  Not surprisingly, Innocentive received around a thousand and counting proposed solutions.  What they did next is surprising … they dropped all thousand ideas into the lap of BP.  Because more is always better, right?  A quick scenario to consider:

Your car engine is on fire and the only copy of your thesis is stuck inside.

A.  Your best friend comes up, details how to put the fire out and offers to help.

B.  An acquaintance comes up, lists 80 possible ways to put the fire out ( some involving things you don’t have on hand, some of which might not work ) and then asks why you aren’t using one of their ideas.

Innocentive is a great font of ideas, but it takes time to sort the wheat from the chaff, to convince companies that the new solutions might work, and to test.  Innocentive’s challenges usually last several weeks, starting from well defined and tractable problems.  After that is a testing phase that last months.  If they were working on a solution for the next oil spill, I’d applaud it as forward thinking.

If they have a working idea, put it out there … say to the media, “We’ve an idea we’ve tested and think is a great solution … but we don’t want to overburden the people out in the field who are trying their best.”  Complaining to the government that the engineers at BP aren’t taking you seriously, and then to the media (see email to Innocentive members) in the middle of a crisis when you know you can’t push a solution out the door fast enough just feels like chasing ambulances for the sake of PR.

I know everyone’s feelings are running hot about the spill, so please feel free to tell me where I’m wrong in the comments.  If people are interested, I’m also thinking about writing a more positive entry on Innocentive showing how it works well for undergrads.

Continue Reading »

In the second of what appears to be a series of commentary on the Science, Technology, Engineering and Math hearings being held by the US House subcommittee for Science, I’d like to draw your attention to a few points in “Reform in K-12 STEM Education”.

First the funny bits, brought to you today by Dr. Gordon Gee, president of Ohio State University:

  • “Mathematics is very intimidating.  Every time I go and visit with our Math department … I take Valium before I go over … they scare the hell out of me.” (1:18:43)  … So remember kids, if your PI asks why you’re dropping X before group meeting, tell ’em Dr. Gee said it was cool.  Honestly, I think most group meetings would be improved by a little X.
  • “If you can’t be a lawyer, if you can’t be a doctor … you can always be a teacher.” (1:10:06I kid, I kid.

Continue Reading »

Inspired by a conflux of events: a post about demos in Mitch’s chemistry community, followed by a dangerous chemistry demo listed in About.com (below the jump), and ‘Things I won’t work with: FOOF’. I thought I’d mention a series of books near to my heart, full of exciting demos for any precocious high school student with an indulgent teacher or any teachers in the audience.

Bassam Shakhashiri’s Chemical Demonstrations : A Handbook for Teachers of Chemistry, along with vols. 2,3,4 are the absolute best demo books out there. Check them out on Google book’s preview, then buy, borrow, or steal them if you do demos.

However, there are provisos I would offer to a high school student.  For example, when using cent pieces for their copper content … don’t.  The newer (1981+) American cent coins have a zinc core.  Just grab some copper wire from a hardware store … it’s quite cheap.

All of this brings us to my point … Bassam includes in the book (never intending it for unsupervised student use) the recipe for nitrogen triiodide.

… stop …

Look down at your hands.  Pick your two least favorite fingers … now imagine them reduced to a chunky mist about 6 inches to the right of your body.  If you make nitrogen triiodide without knowing what the hell you are doing that image will become reality.  Ask one of its discoverers: Pierre Dulong ( who discovered NCl3, thanks for the kind note Ender!).

Continue Reading »

A Chemistry Fraud Roundup

For reasons I don’t entirely understand, this post is trending high on Google searches for ‘chemistry fraud’.  I’d actually like to do a follow up on some of these cases, so if you’re interested in seeing that, have other cases you’d like listed, or know any of the participants, please contact me in the comments or at: chemistrystatistics AT gmail DOT com
– verpa , 10/20/2010

After reading about the IUCr scandal with some 70 structures invalidated followed by another one this month for another set, it got me thinking about the chemistry scandals that have come to light in the past few years.  It seems as though the number of massive frauds is increasing … or are they just getting becoming more public?  A quick review of some of the biggies ( only chemistry, mind you ): Continue Reading »

VMD and NAMD are two closely linked molecular dynamics tools from the UIUC Computational Biophysics Group.  As you can probably guess from the ‘Biophysics’ header, the emphasis for this suite is on large-scale macromolecular clusters such as proteins or even lipid bilayers, meaning CHARMM and force field models are the order of the day.

Despite the emphasis on biochemistry, there is an interesting tutorial on simulating water permeation through carbon nanotubes.  When I stumbled across that tutorial on the same day I saw a post about desalinization using carbon nanotubes, I thought ‘kismet!’.

Continue Reading »