Allen J. Hall

Materials Science & Engineering, Productivity, and Life

Author Archives: Allen

NY-PBS Captures The Struggle Of The Graduate Student

It’s not often that someone goes about deciding to make a film about graduate studies. It just so happens that Thirteen (PBS-NY) has done just that. Their film “Naturally Obsessed: The Making Of A Scientist” is quite an excellent snap-shot of the struggle of graduate students to get their PhD degree and accomplish something very difficult. Of course each of our struggles is unique. We are all dealing with our own situations, with our own fields (some not even in laboratories- the horror- is that real science? hahahah).

Speaking of our own struggles, what most of the public often does not get a feel for is the absolute devotion, almost to insanity, towards finding the solutions we are looking for. Many of the comments by the graduate’s spouses touched home for me. In each of the graduates followed in this film I saw bits of myself. One thing however, that is different, is the struggle for the specific protein structure. Often that struggle is a lot less well-defined. In this situation, you either get the structure of AMPK or you don’t. I guess it’s a lot like their attempts at creating crystals. Sure, you get crystals, but if they don’t have a periodic structure, you’ll never get diffraction. In my situation, the variables in our studies are very difficult to control, and so often one doubts one’s work solely on the question of reproducibility. Many scientists struggle with this same situation. People think that doing things like “measuring temperature” is a very easy thing. In reality, it is a very very difficult thing. Especially in a vacuum. :) That question just arose the other day in discussing our science with a new undergraduate assistant. As we talked more and more on the difficulties of measuring temperature we all saw his eyes grow larger in wonder. The simplest of problems can often be the most difficult. How accurate do you need to measure it? What standard will you use? Do you believe your thermocouple, your thermometer, or your pyrometer? What if the emissivity of the surface changes? :)

This is the life of a scientist. And the film below attempts to capture the lives and struggles of a few graduate students who are hoping for a career in science. It’s a struggle. But, you have heard me say that enough. ;) To learn more about it I strongly suggest you watch this film. For the graduate student, I warn you: you’ll see yourself in this. For those who aren’t scientists: this may end up being a comedy, and I kindly refer you to Marg Simpson’s commentary on graduate students posted earlier in this blog.

My congratulations to Thirteen for doing such an excellent job on this one hour film. They didn’t have a lot of time to share with you everything regarding our struggles and achievements, but they distilled it quite well in the time available.

Equology – A new eco-friendly planner.

ExaclairThe wonderful folks at Exaclair have sent out some items to review. I was a lucky recipient of a few of them, so in the coming posts, I’ll be sharing with you some of their wonderful items for sale. I will be sure to mention both the good and the bad, and in doing so, I hope to entice you to try them out for yourself. [Because I know you'll be coming back to thank me if you do!]

This first review has a time-constraint- in that it is a planner review. Equology is a new eco-friendly planner that Quo Vadis has just started offering. The recycled content list is quite impressive- 88% recycled materials, and 100% post-consumer recycled paper. It’s certified, processed chlorine free, and FSC recycled. Heck, it’s even manufactured using biogas! This isn’t the end of the impressive details- read on to hear my experience using it with Fountain Pens! [recycled paper shrieks in terror here]

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iPod Application: LDAPeople Import/Export

LDAPeopleiPhone/iPod application “LDAPeople” allows your iPod or iPhone to search an LDAP server for contact information, which you can save in your contacts with a single button press. It fills the gap that Apple left in Mail for the iPod with system software os2.x (3.0 includes LDAP support, but not for ssh ldap connections, which LDAPeople supports). LDAPeople has a great, clean, implementation. I highly recommend the application if you’re on the fence about buying it. I use it frequently at my university.

The only barrier to using LDAP people is that, depending on your institution, you have to struggle through proper settings to ensure that you can utilize your organization’s LDAP server to the fullest. The latest update for LDAP people has made a great addition- the import and export of settings files! This is fantastic.

So, without further ado, here’s my settings file for the University of Illinois at Urbana-Champaign’s main LDAP server: UIUC LDAP People Config File. Note that you can search by First name, Last name, and UID/UIN with these settings. The UID is also listed in parentheses after the person’s name to aid in finding the right student or staff-member based upon their e-mail address, etc.

If you make any changes to the settings, I’d love it if you could post below, allowing me to update the file and benefit the rest of the UIUC community. Thank you!

To see other reviews of LDAPeople and/or purchase it, see this app on iTunes: LDAPeople

Related post: iPod Touch Application: LDAPeople

MATLAB and reciprocal space mapping – small update.

Well, I’m one of those guys who believes a picture is usually worth a ton of words. I’ve got a few images to share here on the matlab code I’ve been working on for reciprocal space mapping in MATLAB. I’m still not 100% on my code right now, so I’m not sharing it for the time-being. In particular, I use an import function for .x00 slices for two-axis scans in the Panalytical/Philips XPert system. If you are using XRDML, skip the files for .x00 import that I have in other posts on this blog. In anycase, without much explanation here are the images…

surfacetestusingallomegas2

surfacetestusingallomegas3

qspaceorigtranslateweachomegaload

Latex Hint: Use your computer leverage to output large amounts of data.

After a few weeks of doing cryogenic cathodoluminescence spectroscopy on some of my samples, I have gobs and gobs of spectra to look over, and the task is a bit daunting.  Oh sure, you can do so on the computer in many different ways, but often, I need to see my data on the page (old school) before I can really sort through it.  Sometimes even then there’s just too much of it and playing with the data in MatLab all together is critical.

Here’s what I came up with to help output my data very quickly into a printable document that included numerous graphs.  First, the primary goal of this quick method is to be quick- to get tons of graphics (of same proportions) into a doc for printing or perusing.  Second- it should be relatively minimal typing, if possible.  [We all know we can do it by hand 100x; while grad-student pay rate is low, there's gotta be a better way.]

  1. Get a directory listing for all the items wanted to be included and dump this in a text file.  (ls *.pdf > filelist.tex)
  2. Create a main.tex file which includes the code we’ll need to do this fast.  [You can reuse this file for other directories of graphics needed to be printed.]  My example uses the following:
    \documentclass[%
    ,secnumarabic%
    ,amssymb, amsmath,nobibnotes, aps, prl,superscriptaddress,letterpaper]{revtex4}
    \usepackage[pdftex]{color,graphicx,rotating}
    \setkeys{Gin}{width=0.85\columnwidth}
    
    %Simple way to call images and add filenames to captions - for lots of data.
    \newcommand{\dataimg}[1]{
    \includegraphics[width=3in]{#1}
    Filename: #1
    
    }
    
    \begin{document}
    \title{CL Results\\
    \textit{Internal document not for distribution.}}
    \date{\today}
    \author{Allen Hall}
    \maketitle
    
    \include{filenames}
    
    \printfigures
    \end{document}

    The important code is the “\include{}” line and also the “\newcommand{\dataimg}…” section. This is what is going to do all the work for us.

  3. Now, we need to take your filelist and add at the beginning of each line and end of each line the following:
    \dataimg{

    and at the end:

    }

    One way to do this simply is with a command line gawk command:

    Terminal Prompt> ls |awk '{ print "\\dataimg{"$0"}" }'
  4. So, now each line looks like: \dataimg{filename1.pdf}
  5. Once that is done, you can run the LaTeX compile, and you’ll have your file of graphs!  That’s a heck of a lot easier than writing each line out by hand.  [Use a program like TextMate or Gawk etc. to append and prepend each line with the necessary call.]

The benefit of the \newcommand is that it fills in the needed formatting for each graphics file, and attaches the filename for each graphic beside the graphics file itself.  You can make it prettier, I’m sure, but this is what I was able to do in a very short time frame.

There are many ways to accomplish this little task, you could use Gawk itself to write the latex file for you, I’ve seen some do makefiles to do this type of thing, or perl, or bash shell scripting etc.  But, the critical part is to leverage the computer to output a latex file for typsetting and save yourself some time.

The iHand: Lo-Fi -v- Hi-Fi Methods For Productivity

iHandRecently a friend saw me with my hand covered in notes, and yet, in the same hand was my iPod Touch (a very capable productivity tool by itself).  He laughed hysterically and resisted pointing and laughing with some difficulty.  :)   Instead, he took this photograph to share with others.  [Photo courtesy of Rick Haasch.]

This picture speaks volumes with respect to how easy it is to input data into the iPod and iPhone.  I hate to say it, but the simple stylus was quicker on the Palm platforms.  People are just used to using pens and pencils.  My inked up hand is a very clear indication of this.  To some extent, you can get around this problem with the phone service Jott; however, it also is not as quick as a pen.  Why do the options and computer voice always take soo long in voicemails and these new speech to text services?  [Incidentally, I love Jott for the following: On the go (driving) e-mails and SMS, Expense account additions during the actual payments of said items, and quick notes to myself when anything other than a voice-call is possible.]

The notes in question were taken in typical mid-hallway quick conversation mode, when there just wasn’t enough time to try and open the iPod, turn on an application, and start using the little funky button keyboard.

Incidentally, I also carry a Shirtpocket Briefcase ala Levenger, which always holds a series of 3×5 cards for lo-fi inbox notes.  The 3×5 card is the killer productivity app.  I’ll have to comment on these types of methods in future posts.  Let’s just say there’s a reason most old guys carry around a stack of 3×5′s in rubber bands, or monkey-clips, always in their breast pocket with a pen.

I would love to hear from you about your own methods of Hi-Fi and Lo-Fi productivity and difficulties in their intersections.

Today’s Earworm: “Saint – Saens Concerto Pour Piano N°5 <<Egyptien>> En Fa Majeur, Opus 103 Allegro Animato” performed by Aldo Ciccolini/Orchestre De Montpellier Languedoc – Roussillon from the album Saint – Saens Concerto Pour Piano N°4 Et N°5

How to backup/save/resurrect your Stanza iPod/iPhone eBook Library

calibre_stanzaA recent Stanza update for the iPod Touch and iPhone left me with a completely blank ebook library!  horror!! So, not being content with doing things the most straight forward way, and redownloading every book, I decided to see if you could get all your books back from Stanza somehow.  To learn how, join me after the jump…

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Software For Scientists: Engauge Digitizer

In the time I’ve been doing my research work at the Univ. of IL, I’ve come across a number of graphs from various past researchers, older papers, stuck on the side of machines (calibration curves), and even hand-drawn or chart-recorder graphs in my numerous projects.  The only major problem with those graphs I’ve found is that they aren’t in a digital form for further use with other data (instrument response functions) or to include in your own work as a reference.  So, what to do?

Well, there’s an easy solution.  It’s not the perfect solution, as it’s a bit slow, I’ll get to that in a second, but it’s a great solution to the problem, and has worked for me a number of times now.  To top it off, it’s open-source, donation-ware, and cross-platform: Engauge Digitizer (see post at LifeHacker.com).  Don’t let the website and lack of recent updates deter you.  Tools that can do what Engauge does are few and far between.  So, it is definitely worth a try.  Here’s an example of how I’ve used it just the other day (prompting this post- I’ve used it for years now, but the recent use reminded me I should share it with others).  [click "More" to see an example use and learn more]

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LaTeX Tip: NewCommand

For those friends of mine currently attempting to work in LaTeX to code Materials Science and Engineering related tidbits…

Here’s a quick tip. Tired of typing all those crazy math commands for your material’s name? Simply use a new command. Here’s are a couple examples…

%Simpler way of writing CUINSE2:
\newcommand{\cis}{CuInSe$_{2}$}

%Simpler way of writing CUINGASE2:
 \newcommand{\cigs}{CuIn$_{(1-x)}$Ga$_{x}$Se$_{2}$}

%Simpler way of writing CUGASE2:
\newcommand{\cgs}{CuGaSe$_{2}$}

To see how this looks in compiled LaTeX output and another example, click “More”…
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Apple’s “InEar Headphones” – broken and support difficult. (updated 01/26/09)

Well, interestingly, the strain-relief on the right-ear of my new In Ear Headphones (the dual-driver $80.00 ones for the new iPods) has broken. (to hear more and read the conclusion, click more…)

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A Quick Introduction...

I'm a graduate student (PhD Candidate) at the University of Illinois at Urbana-Champaign.

I've studied and researched in two fields of Materials Science and Engineering (Polymers and Semiconductors). My interests are as diverse as my musical tastes and I usually have my hand in some crazy project during my free time.

I'm available for consulting and have access to a world-renown materials research user-facility supported by the D.O.E. If you would like to know more, please contact me.

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