Tag: computers and chemistry don’t mix

Uncle WikiProf. Delmar Larsen is an recent recent professor in the Chemistry Department at the University of California at Davis. Delmar’s current “labor of love” is developing a new online teaching resource to augment chemistry education while reducing excessive out of pocket costs for students.  We recently consolidated The Chem Wiki as a component of his larger project.  His current project is outlined below and I am working with him in a limited capacity to bring this to the attention to the masses.

Delmar has sent me the following in the hopes that you might be interested  in this project, too.

Currently at American universities, chemistry departments require introductory chemistry textbooks at an average cost of $190 per book. When combined with the accompanied study guide ($70), solutions manual ($50), the online student access kit ($48) and individual instructor Readers ($60), the total cost ranges from $250 to $420 annually per student. With an average of ~1,500 students taking General Chemistry sequences each year for a major department, we ask freshmen Chemistry students to contribute from $375k to $525k total annually per university, which essentially doubles to $1M per year when including O-chem classes. While textbooks are clearly an important and critical component to students’ education, their abusive price tags are not, especially in today’s economy as tuition and other student costs are increasing near exponentially.

Much of the content in chemistry textbooks (especially general and O-chem topics) has essentially not changed for years: thermodynamics has been around for centuries; SN2 reaction basics have been established for decades and even alchemists in the 16th century knew how to titrate properly. Why have we convinced ourselves that shelling out $200 per book for established knowledge is the way to go? Simply because there is no other choice; faculty, not students, determine the required textbooks for classes and for a suitable non-commercial textbook substitute to be viable, it must be off sufficient quality to warrant evaluation AND must be supported especially by faculty.

I am constructing an online freely accessible textbook to address both aspects. As a new Chemistry faculty member at UC Davis, I still remember the pain of textbook costs and I am now positioned to construct/manage and push the ChemWiki project as a viable alternative to conventional textbooks. However, the construction of a textbook is not a trivial task, requiring years of effort to complete. This cannot be done by one person, hence we are constructing the ChemWiki via a massively parallelized plan involving simultaneous development effort on multiple fronts, whereby content is written and re-written by not only by faculty members, but primarily by students and other contributing experts.

I am appealing to the expert (and not-so-expert) readers of the chemistry blogging community to participate in the development of the ChemWiki. We are in our 2nd year of development and many Modules (pages) of content need to be developed, reviewed and edited; the range of topics varies across the entire chemistry field. We are also currently pursuing extending the ChemWiki as a resource to developing countries with difficulties obtaining textbooks, specifically in Africa. This is our attempt to make a contribution (outside of research of course) to the scientific community that is long lasting and significant, but we need help to make the project viable – your help.

Contact Delmar Larsen (dlarsen@ucdavis.edu) or visit the ChemWiki server (http://ChemWiki.ucdavis.edu) for an account.

I purchased a MacBook Pro.  It’s sexy, yes, but that’s not why I bought it.  Let me convince you why you should consider the same purchase.

First of all, you have probably noticed a recent proliferation of polycarbonate and aluminum notebooks floating around the undergraduate masses.  If you’re a parent of a reasonably articulate child, they have undoubtedly asked of some type of brand name Apple accessory, if not the full Monte.  This sudden emergence of omnipresence is more than just a trick on your eyes or a sudden perception – it’s a monumental ground swell occurring under the feet of the Millennial Generation (which would be my generation, I suppose) as the personal computer is increasingly an item of both utility and luxury and those that can afford luxury, buy a more personalized and stylish device.

To the left, you see an increasing percent of Apple computers owned by undergraduates at the University of Virginia as it pushes 40% while a concomitant decrease in the number of PCs owned occurs.  It’s not reading tea leaves – the data is clear – as the hardware market moves, so too does the software market.  Apple already has a hand up academia’s skirt and with the influx of undergraduate consumers, that hand has gone full on into shocker mode.

While the popularity of the computers is promising, the transition to Intel architecture also means that writing code (creating programs) and porting existing software for the mac will be easier and, as the popularity increases, I would anticipate software developers to be less shy about porting their software to OSX since it’s a port between two x86 systems and not from x86 to a RISC system.  It also means that software packages that emulate Windows, like Parallels, can run PC software seamlessly over the OSX environment:

OSX running parallels

From the above image you can see I’m running ACD’s 1D NMR software over OSX with Keynote running in the background.  You can even pop up the Windows Start Menu to launch other Windows applications, all of which run nearly seamlessly (you can’t copy Mac Chemdraw structures into PC Chem3D, for instance, though you can copy text and images to your heart’s delight.)

Compatibility and fear of being on a lonely island being excluded, the final two points are cost and power and, not surprisingly, they are related.  The laptop I own is top-of-the line (no shit) running a 15″ LED display at 3.06 GHz with 6MB of L2 Cache.  That setup isn’t even possible through Toshiba direct, let alone there are no other vendors of laptops that contain dual graphics cards, one with 512 MB of RAM.  The only company that could produce such a beast would be Lenovo – a company that also produced great laptops.  If you build a comparable system (you can’t get an LED display and a 500 GB  hard drive) you end up spending $100 more than I did with my Developer discount (if you use an educational discount, you’ll spend $100 more for the Apple product.)

In short, you pay a very high price for a very high end system and, because the lowest end laptop Apple sells is still spec’d out well above the average Toshiba you find sitting in Best Buy, you get the feeling Apple is ripping you off…  but that’s not really the case.  And speaking of case, the whole laptop weighs about 3-8 pounds less than what you would get from Lenovo (depending on the specific brand.)

I’ll admit it:  I got an Apple because I wanted something different, too.  Something to change the scenery and something new to play around with.  I’ve been faithfully using a PC since I was given one in the 4th grade by my super-smart-kids elementary school and I’ve never had any beef with them.  Windows XP is a great OS (Vista can suck my nuts) and seems to be as stable as Mac OSX, if not more so, assuming you’re not retarded and download random shit with Internet Explorer (which, like Safari, is inferior when compared to Firefox.)

For the last few days I have been trying to figure out how I can do a simple Monte Carlo simulation on my computer without much success.

In the last few months I have become convinced that by doing my own computer modeling I could probably avoid making a lot of unnecessary molecules.  Indeed, I see no reason why the notion hasn’t struck me in the same way the concept of checking a sample after a reaction for purity why should I check the reaction before I do it to see how well it might work?

Firstly, it’s become pretty obvious that computational chemistry is a giant fucking black box.  There are lots of force fields and data sets and letters followed by ** and shit and not a goddamn easy way to deal with ANY of it.  Let’s say I want to model a transition state, what do I do?  Call a computational chemist?  I’m sure they’ve got shit they want to do, too.  Not only that, but after a couple decades of ripening, I’d like to think the ability to do simple computational analysis should be in the hands of the average schmuck like me.

So, I want to do a Monte Carlo simulation.  This, as I have come to appreciate it, simply means I want to find a global minimum for a structure – i.e. the lowest energy configuration something sits in, but there’s no easy way to figure out how to do this.  In so far as I can tell, you can do the following things:
Draw something in chemdraw and either import it into Chem3D if you own a PC or into Avogadro if you own a Mac (which will convert chemdraw .cdx files into 3D coordinate files).  Do a minimization using whatever they have.  Avogadro is clearly better at this (and it works for PC) and has a number of different choices.  The problem with both of those program is that they really don’t find a global minimum.  Insofar as I can tell, if you start with a shitty structure, both of them will find a minimum of that shitty structure.  True Monte Carlo, as I understand it, means it will rebuild the structure and keep searching.

Then I discovered a program called Tinker… it has a bunch of force fields and shit in it, all prime and ready to use (and it even works on Windows and Mac) but no clear path from Avogadro or Chem3D to a minimization is presented.

I don’t understand why computational chemists don’t want other chemists to do computational chemistry with a graphical user interface and dialog boxes and all those smart things that can be made using Visual Basic or Apple script… It just seems to me that, a lab like Jay Ponder‘s or Dan Gezelter’s could really make a difference by making a user application that would allow the simple importation of a Cartesian coordinate file and allow the user to select a Force Field, Algorithm and a good stopping point to do their own “back of the napkin” calculations before they run off into the lab…  If I had the wherewithal to do it, I’d have done it by now.

UPDATE:  Re: Collaborate with a computational chemist:

I have done that before, put his name on the paper and everything.  The problem is that I’m *JUST* starting out in my little Post-Doc adventure and so I don’t really have systems in mind that I would want to bother someone with.  I.E. some of them are likely patently absurd – simply won’t work for reasons I don’t need a computer to tell me… but I have a chemdraw folder full of them and a billion other (more pressing) things to be doing.  I also have a pretty ass kickity computer that has no problem crunching numbers all day, both at home and at school.

I also want to obtain some degree of self sufficiency.  I feel as though, in this modern era, I don’t need to run to an NMR chemist to take a sample of, what will normaly turn out to be ethyl acetate, so why should I need to run to a computational chemist to do something so very trivial.  It’s a waste of her time to do my calculations for me on a compound that has a 1% shot of even being made!