Revision

It feels like I totally have abandoned this site, I’ve posted so infrequently.  That is not the case but I need to revise the site a little to better serve its purpose.

These days I have too many sites to work on or maintain, including all the social media sites.  I’m not a daily visitor, or even weekly, so I feel like they are abandoned pets when I see them, and maybe they are :(.

I’ve been more frequent to do blogging or writing at least on my github pages (ngreen-gt.github.io) site rather than here.  I feel like practicing markup is good for my writing when I need to intermix data and writing.  Wordpress is good for just writing with pictures.

I’ll wrap up here, but look for more activity in the near future.

 

Short post

I am trying not to write short posts, as I  prefer to write in longer form post that take on a topic or otherwise solve a daily issue, but it has become apparent that it will take a lot more motivation for me to keep up, and I haven’t written a new published post (notwithstanding incomplete drafts) for the last six weeks.  My intention is to make two long form post per month on topics that fit well in a longer format.  I want to continue to document what I am doing or learning to do, and to cover even some far diversions with care and detail that you’d expect from a scientist and engineer.

I have plans to change how I post pictures on this site.  I have several older albums from my research, studies, travel, and personal life that I’d like to share.  I have decided to update the Google+ Photos site that I have put many at, and to link to the albums through photos on this site (which is written in free WordPress).  I had considered using Imgur or another site, but this will work best for me because of my familiarity with Picasa for uploaded photo.  Here is a photo link

https://goo.gl/photos/fMeq8N568Dt1tUup6

My other plans involve this site,  moleculrkitchn.wordpress.com, which I am using to share my experiences as a home cook.  I’ve been experimenting in the kitchen since I was little, and I am intrigued with how to continue that, to have a record and memory of what things I try to make, which ones are great and which fail.  I take inspiration from the chefs at the America’s Test Kitchen and the Pioneer Woman.  And some other people like Julia Childs, Gordon Ramsey, and all the time I watched Top Chef.  I love the experience and togetherness that a great meal creates, and so I practice to be an adequate cook.  The online food world has exploded with so many food bloggers.  Laura Vitale was a new one I learned of this week. So I am surprised I am one.  But getting recipes, substitutions, and results done on digital paper is the best way that I can keep up with my endeavors in the kitchen.

I’ve been busy at nights providing some guidance to a FRC team, the Panther Robotics team, as they prepare for their competition.  It has been nice working with smart, dedicated students as they work through the challenges of completing this engineering project.  I’ve helped with building a catapult and other parts, and have helped with a website to cover their work, pantherrobotics.wordpress.com.

 

So long for now!  I’ll have more content in the next couple weeks if all goes to plan.

New Year’s Resolutions

I’ll keep this short but wanted to get something down before too much time passes.  There is a lot to work toward for 2016.

Foremost, is finishing writing articles of all sorts.  In no particular order, although I know there is a definite order:

1. Minneapolis paper – DOM from the Mississippi (with S. Driver)
2. Compilation of papers for final thesis.
3. Odds and ends (Involvement in Satilla and earlier projects)
4. New directions (R software and LMMs master list)

This last part is in my further interest in the data analysis pipeline for mass spectra within the R programming language.  Data analysis of these sets, particular with interest to the globally collected and discussed datasets, can tell us more about the changes in composition that are to be expected with various perturbations to the natural movement and degradation of DOM.  And also the real challenge of compiling disparate data sets, derived from different extraction and analytical methods, with different sample compositions and with instruments of different capabilities.  This is a continual challenge to the humic sciences because the heterogeneity prevents instrument calibration and method validations for the wide difference in composition.

For the New Year, I want most of my software contributions to be open source and have used GitHub to begin doing that.  I hope to contribute to other projects as I work with R. My projects in software are, again in no order:

1. LMM algorithm (in C++) in R language package.
2. Contributing to package for DOM MS analysis.
3. Further analysis of multiple datasets.

I should have started this on a forward-looking trajectory, rather than back to re-analysis of old data.  So in that thought, my resolution is creating better partnerships with researchers looking into properties of complex substances to better understand their relation in chemical and biological system.  Reading much more (daily) is a start, and reaching out, staying open to opportunities and looking for gaps in current data is where the difference can be made.

I wanted to conclude by a simple list of some things (mostly non-science) I recall from 2015 that I enjoyed, and want to remind myself of for this year.

• Working with teens, particular robotics students preparing their paper submissions.
• Cooking a good meal.  Soups and chilis.  Farm fresh ingredients.
• Gardening (really my father) and taking items to the county fair.
• Watching my nephew and new niece. Helping kid’s art at Salina festival.
• Open development of software in GitHub, and learning some R.
• Spending time with family.  Brother’s law school graduation.  Pool time with nephew.  Sunday dinner with Grandma.  And others.

Addressing Xmas cards

Season’s greetings

Around this season, there are many things to be done, and reaching out to old friends and colleagues is an important time-honored tradition.  As I recently found out that preparing the list and addressing the cards can be a major challenge, especially for someone like my 83-year-old Grandma.

Holiday card…and it should read Dunder and Blixem.

To help her for the coming years, I made a new address list using pictures taken with her Ipad mini.  I faced a couple challenges to getting to a nice enough looking printable list that I decided I should share the process here.

Preparing photos from addressed cards

Having consistent, well-lit photos is the key to later having nice address list.  To do this, I put together a photo box using a fruit crate (basically a 3-sided box) in which a hole was cut to allow the iPad mini camera to shoot below.  The surface below was well-lit using a desk lamp.  Tape markings were used to consistently place the cards.

Basic lightbox

From photo to address list

After moving photos onto my computer, I need to crop them to size, fix discoloration, and size the pictures to fit into my list.

I cropped the photos to just the address manually in the Office Picture Manager.  Also rotating the photos as necessary.

Most of the pictures has a grayish background which needed removing before they would be printable.  I found that `convert` from ImageMagick did a reasonably good job of removing this discoloration. Using the command line, you can automate this task for all the photos.

convert *.jpg -auto-level -white-threshold 78% x-%04d.jpg

I found that 58% worked well for my photos, but you can adjust as needed.

Before

After

 The last part was getting all the addresses into a list in Word.  On first try the pictures were too large, so again using the picture manager, the photos were reduced to 30% of the original size.  The first thing I figured out was that the image size was way too big.  Back in the picture manager, I resized them all to 30% their original size.  The next issue was how to get all these pictures to the same width in Word. 

Adjusting the picture width in Word was tedious, but a bulk solution was not apparent.  It became much easier once I learned about the <F4> key function.  I’d recently learned that it can be used to repeat the last action for Excel, and also Word. To use it here first I selected the size of the first picture (3.5 in width; lock relative dimensions), and after I select the next picture hitting <F4> repeats the resizing.  

Future holidays

In the end, I have a list of all the cards that went out this year.  No digging in address books or in my Grandma’s case through several years of earlier lists. For those that are more technically-inclined, this is a nice starting point to digitize your card list and this same process can be followed with return addresses of cards you received this year.

Accepted!

Our paper describing the negative quadrants of the van Krevelen diagram  has been accepted into Analytical Chemistry.

With the low-mass moieties ( CH4O-1 and C4O-3, for example), all the chemical formulae in the compostional space can be related.  This leads to efficient programs to find the chemical formula of a molecule from its mass (mass spectrometry).

For studying natural organic matter, mass spectrometry (with really high resolution) has produced a great amount of molecular information which is being analyzed to better understand the samples and the processes in nature that affect the samples.  The step to assign formulae is only one of several steps from sample collection to data analysis, but improving the efficiency should lead to higher throughput in the future.

This is the first of two papers, the second of which has be revised and submitted.  The second deals with the practical aspects of assigning chemical formulae.  There is still much too be done on the uniqueness problem encountered during formulae assignment, whether by future instrument improvements, more rigorous standards in analysis, or better heuristics.  The resulting samples and growing sample number leave much to be done on data analysis, from the myriad of statistical test and mining that can be done to pull out biogeochemical trends.