Sensors, Sensors Everywhere!

This year at the fall meeting of the American Geophysical Union, I presented an education abstract in addition to my normal science content. In this talk, I wanted to raise the awareness of how easy it is to work with electronics and collect geoscience relevant data. This post is here to provide anyone that was at the talk, or anyone interested, with the content, links, and resources!

Sensors and microcontrollers and coming down in price thanks to mass production and advances in process technology. This means that it is now incredibly cheap to collect both education and research grade data. Combine this with the emergence of the "Internet of Things" (IoT), and it makes an ideal setup for educators and scientists. To demonstrate this, we setup a small three-axis magnetometer to measure the Earth's magnetic field and connected it to the internet through data.sparkfun.com. I really think that involving students in the data collection process is important. Not only do they realize that instruments aren't black boxes, that errors are real, and that data is messy, but they become attached to the data. When a student collects the data themselves, they are much more likely to explore and be involved with it than if the instructor hands them a "pre-built" data set.

For more information, watch the 5-minute talk (screencast below) and checkout the links is the resources section. As always, email, comments, etc are welcome and encouraged!

Resources

Talk Relevant Links

- Slides from the talk
- This blog! I post lots of electronics/data/science projects throughout the year.
- Raspberry Pi In The Sky
- Kicksat Project
- Weather Underground PWS Network
- uRADMonitor
- Our IoT magnetometer data stream
- Python Notebooks
- GitHub repository for the 3D Compass demo
- AGU Pop-Up Session Blog

Parts Suppliers

- Adafruit
- Sparkfun
- Digikey
- Element14

Assorted Microcontrollers/Computers

- Beagle Bone
- Raspberry Pi
- Arduino
- Propeller
- MBed
- Edison
- MSP430
- Light Blue Bean

General

- Thingiverse 3D printing repository
- Maker blogs from places like Hackaday, MAKE, Adafruit, Sparkfun, etc

How I Design a Talk

This year I'm co-chairing a session at the American Geophysical Union meeting called "Teaching and Career Challenges in Geoscience." We have been maintaining a blog for the session at keepinggeologyalive.blogspot.com. I wrote a post that I wanted to cross-post here in hopes that you too may find a few tips to help with the next presentation you need to give.

Hello everyone! While I was preparing my talk, I thought I would share my process in the hope that maybe someone will find a useful nugget or two. There are lots of great resources out there. Books like Pitch PerfectTalk Like TED, and the MacSparky Presentations Field Guide are great places to start. With AGU only a couple of weeks away, I wanted to highlight a few ideas on presentation planning.First, close PowerPoint or Keynote. The presentation software is not the place to start preparing a presentation. I like to sit down in a comfortable spot with a stack of index cards and a mug of coffee. While I love technology as a tool, it's just too early. I write out one major thought on the top of each card and put supporting material on as a list. For a short talk, like the pop-ups, this is just a few cards, but I've had stacks over 2 cm high for longer talks. I put everything I might want to bring up on these, pruning the content comes later.  After my cards are made, I lay them out on a big table (or the floor) and play with the ordering. I'll ad-lib sections of a fake talk and see if two thoughts can flow smoothly into each other. Once I'm happy with the general layout, then I'm ready to move on.

After playing with index cards, I'll let technology in. I like using OmniOutliner to help here. I put my index cards into a digital outline. Lots of people start here, which is fine. I like starting on paper because I can sketch things out and feel less constrained. Index cards also don't have email notifications that interrupt your thinking. In OmniOutliner, I break out my thoughts into short bullets. I can drag in content such as a photo of a sketch I think may turn into a graphic, sound bytes of an idea, or quotes I want to include.

Now it is time to decide on supporting graphics. I have an idea of what I'm going to say, so what visual aides will help tell the story? Your slides are not an outline and are not meant to guide you through the content. You and the slides together will guide an audience through your work in a logical way. Graphics can be photos, graphs of data, schematic diagrams, anything! Personally, I like make my graphics using an assortment of applications like PythonAdobe Illustrator, or OmniGraffle. Making graphics is a whole other series of books that you could dive into, including the great books by Nathan Yau: Visualize This and Data Points.

Finally, it's time to make your slides. I follow the Michael Alley approach of a slide with a (nearly) complete sentence at the top, followed by graphics. The fewer things that the audience has to read, the closer they will be listening to what you have to say. If you need to document your material to hand-out, produce a small one or two page text document with the necessary graphics (an idea from Edward Tufte). Again, the slides should not be the presentation, but support for it.  If you are stuck for ideas on slide design, head over to Garr Reynold's blog Presentation Zen. Garr has some great examples, as well as his own books.

My last tip regards the ends of your presentation. The beginning and the ending are incredibly important. The beginning is where you gain or loose the audience, and the end is where you make sure that their time was well spent. Nail these. I don't script presentations, it sounds too robotic, but the first and last 30 seconds are written down and well thought out.

I can't wait to hear what everyone has to share and I hope that some of these tips and resources are useful in your preparation!

Breaking the Wishbone - How to Win

The folks over at Michigan Engineering did some modeling, 3D scanning, and experimentation to tell us how to win at the age-old Thanksgiving game of breaking the wishbone. According to the folks over at aaepa.com, the tradition is much older than Thanksgiving, dating back over 2400 years to cultures that believed that birds were capable of telling us the future. There is even suggestion that the phrase "getting a lucky break" can be traced to this tradition.  If you want to win, watch the 76 second video below and remember: choke up, stay stationary, and pick the thick side.

We Are ... Seismic Noise

2014-10-28 13.27.05

Over the last few months construction crews have been hard a work tearing into the building adjacent to mine on the Penn State campus. Lots of demolition has been happening as the old building is completely cleaned out and being rebuilt. Some of the noise has been so strong that we could feel it next-door. As a data-nut, my first thought was "I'm going to look at this on our seismometer!"

At the base of Deike building (the geoscience building), we have a seismometer. The station, WRPS "We aRe Penn State", has been in operation on an isolated pier for some time, so we have lots of data to look at! For our purposes, I downloaded the entire month of October for 2013 and 2014. There are some hours/days that are missing, but we'll ignore those and work with what we have. This is a common problem in geoscience!

First let's just make a plot of this year's data. Each square represents one hour (24 squares in a row), and each row represents one day. Missing data is the lightest shade. The squares are colored by the strength of the seismic energy received during that hour; the darker the square, the more energy received.

WRPS_2014_HourlyYou'll immediately notice that there is always more noise starting about 11 UTC, which is the 7-8 AM hour locally. This is about when people are coming into work, vibrating the ground and buildings on campus as they do. The noise again seems to die off about 21 UTC or the 5-6 PM hour locally. This again makes sense with people leaving work and school. This isn't split finely enough to look for class change times on campus, but that could always be another project.

The other thing to point out is the dates of October 4-5,11-12,18-19,25-26. These are the weekends! You notice there is less of the normal daily noise traffic with fewer people on campus and construction halted. There is a repeating noise event at 11 UTC on the 1st, 12th, 20th, and 27th. I'm not sure what that is yet, but looking at more months of data may indicate if that event is associated with equipment starting up, or is really random.

While these daily life trends are interesting, they have been observed before. This whole discussion started with construction and how it was affecting the noise we saw on our local station. To examine this, I made a stacked power spectral density plot. Basically, this shows us how much energy is recorded at different frequencies. The higher frequencies would be human activity.

WRPS_PSD

We can see that the curves from 2013 and 2014 are very similar, with the exception of the 11-16 Hz range. In that range, the energy is higher in 2014 than in 2013 without construction by about a factor of 10. That range makes sense with construction activity as well! The energy remains elevated even after the main bump out to 20 Hz.

You might be thinking that such a bump could be due to anything. That's not necessarily true considering that we have stacked a month's worth of data for each curve. To show how remarkably reproducible these curves are, I made the same plot for the same times with a station in Albuquerque, New Mexico.

ANMO_PSD

 

In the Albuquerque plot, the two years are very similar, nothing like the full order of magnitude difference we saw in University Park. There are obviously some processing effects near 20Hz, but those are not actual signal differences, just artifacts of being near the corner frequency.

That's it for now! If there is interest, we can keep digging and look at signals resulting from touchdowns in football games, class changes, factories, etc. A big thank you to Professor Chuck Ammon as well for lots of discussion about these data and processing techniques.

315 Million Miles From Home, Cold, and Landing on a Ball of Ice

Rosetta's_Philae_touchdown

Image: Wikimedia

Tomorrow (November 12, 2014), the Philae robotic lander will detach from the parent spacecraft, Rosetta, and begin its short trip to the surface of comet 67P/Churyumov–Gerasimenko. This is a big step in technology and spaceflight! I'm sure we'll hear lots of fascinating new discoveries in the coming weeks, but before the lander detaches I wanted to point out how amazing this mission already is and a few things that it has already taught us.

First, let's talk about distance and speed. Space often confounds us with mind-boggling distances, sizes, and speeds. Rosetta was launched in 2004 and made a few loops in the inner solar-system to use gravitational acceleration to help it get out past Mars. As of this writing, Rosetta was about 315 million miles away from Earth, having actually travelled much further (map below). It is orbiting a small body (a comet) that is traveling at about 44,700 miles per hour (20 km/s). It is also orbiting very low to the comet, only about 19 miles (30 km) off the surface.

Image: ESA

Image: ESA

 

In the morning, at about 3:35 AM Eastern Time, the Philae probe will detach from the orbiter and begin the seven hour journey to a landing on the comet's surface. Not only is landing on a moving target far from home difficult, but it is made even more difficult by the small size of the comet. We know that small bodies exert less gravitational attraction on other objects (it's directly proportional to the mass if you remember the Law of Gravitation). Small masses are normally good, because it means that we don't have to be going as fast to escape the gravitational influence of the planet. For example, the escape velocity of Earth is about 25,000 miles per hour (11.2 km/s), while the escape velocity of the moon is only about 5,400 miles per hour (2.4 km/s). The escape velocity of the comet is only about 1.1 miles per hour (0.5 m/s)! Since the spacecraft is descending at about 1 m/s, this presents a problem: it would likely touch the comet, then bounce off, never to be seen again.

To solve the landing problem, Philae has legs with a strong suspension system that utilizes the impact energy to drive ice-screws into the surface. For additional security, two harpoons will be fired into the surface as well.

One of the ice drills securing the lander. Image: Wikimedia

One of the ice drills securing the lander. Image: Wikimedia

 

Once on the comet, the suite of 10 instruments will begin to collect data about the magnetic field, composition, and other parameters. I'm sure the team will have many fascinating discoveries to share, but in the interest of keeping this post short, I'd like to share one result we already have.

Rosetta has been, and will continue, to collect data from orbit with radar units, cameras, magnetometers, and spectrometers. As Rosetta began to get close, scientists noticed a periodic variation in the magnetic field around the comet. These variations are very low in frequency, about 40-50 milli-Hertz. We can't hear anything that low in frequency, but if you artificially bump up the frequency so we can listen to the data, you get the following:

What is most fascinating about this is that it was totally unexpected! Scientists are unsure of the cause. This is one of the many puzzles that Rosetta and Philae will reveal, along with a few of the answers. Best of luck to the team. We'll check in on the spacecraft again in the future and see what we've learned.

One last note: even traveling at the speed of light, the radio signal confirming the spacecraft status will take about 30 minutes to travel from Philae to us! Be sure to watch live tomorrow (here).

 

Doppler On Wheels - A Tour of a Mobile Radar

DOW7_Web

Recently, Penn State was lucky enough to have the "Doppler on Wheels" or DOW visit for two weeks through an NSF education grant! The truck, owned and operated by the Center for Severe Weather Research, is probably familiar to you if you have watched any of the storm chasing television shows or are interested in severe storms.  Dr. Yvette Richardson and Dr. Matt Kumjian were the faculty hosts and incorporated the radar into classes they are teaching.

I've always believed in getting students involved with data collection.  If students collect the data, they are attached to it and begin to see the entire scientific process.  Data doesn't just appear, real data is collected, often with complex instruments, and processed to remove various problems, corrections, etc.  It's not everyday that students get to collect data with a state-of-the-art radar though!

For this entry we're going to try a video format again.  Everyone seemed to like the last video entry (Are Rocks like Springs?).  Keep the feedback coming! It was a bit windy, but I've done what I can with the audio processing.  A big thanks to everyone who let me talk with them!  As always, keep updated on what's happening by following me on twitter (@geo_leeman).  This week I'll be off to New York to hear Edward Tufte talk about data visualization, so expect updates about that!

Fun Paper Fridays

Image: phdcomics.com

Image: phdcomics.com

In my last post about why I think the expert generalist is crucial in today's highly inter-related world, I mentioned a practice that I've adopted of "Fun Paper Fridays."  Today I want to briefly describe fun paper fridays and invite you to participate.

The Routine
Every friday I go to a coffee shop first thing in the morning and commence my weekly review.  During this time I check the status of projects, emails, etc and make sure that things are not slipping through the cracks.  Those of you familiar with David Allen's Getting Things Done will recognize this.  In addition to reviewing my schedule, I added a self expansion project.

Each week I pick out a paper that isn't directly related to my research and read it.  The paper can be serious, just not about my work (ex: Viking Lander 1 and 2 revisited: The characterization and detection of Martian dust devils), or it can be a completely fun topic (ex: How to construct the perfect sandcastle).  That's it! Just read a paper, no notes unless you want.  You'll be surprised when in some situation you'll recall a fact, method, or comment from one of these papers and be able to apply it to a completely different scenario.

Join Me
I hope that you'll join me in this quest of broadening your knowledge horizons. If you're not involved with science, that's no problem. Just read something that you normally wouldn't. Maybe it's the Art & Culture section of a newspaper or an Article from a popular science magazine. Every Friday I'll be posting the paper I'm reading on Facebook and Twitter. Please join me and use the tag: #FunPaperFriday.

The Rise of the "Expert Generalist"

m4s0n501
Swiss Army Knife

Image: http://www.nature.com/

I've always appreciated the value of having a very broad range of knowledge, but recently I've observed many cases that reminded me how important it is. Growing up I worked on tractors and engines and rebuilt many mechanical devices. Later I learned how to machine metal and weld. As it turned out all of those skills and the knowledge gained have been incredibly helpful in graduate school since I happen to work with large hydraulic and mechanical systems that have all custom parts!

It turns out that as our fields all become more connected through increased interdisciplinary collaboration we all must become an "expert generalist". As geoscientists, we are always faced with writing new code, logging new types of data, or becoming GIS experts. Knowing just a little about many fields opens up entirely new ways that you can start to approach a problem. If that approach looks promising then you can become an "expert" or consult with one, but this novel approach would likely have remained hidden without any knowledge of the field.

The main message of the 99u article (linked at the bottom) is:

One thing that separates the great innovators from everyone else is that they seem to know a lot about a wide variety of topics. They are expert generalists. Their wide knowledge base supports their creativity.

As it turns out, there are two personality traits that are key for expert generalists: Openness to Experience and Need for Cognition.

Let's take a look at the two qualities mentioned and see how we can apply them.

Openness to Experience
Creating new content and ideas is really just a merging of concepts that we already know into a complete framework or mental model of examining the problem at hand. That means that we need a large body of knowledge to draw from. While this sounds like a good idea in practice, it isn't easy to do. We have to be open to meeting with people and learning about concepts that may seem completely irrelevant right now. We have to read papers that are out of our fields and realize that we all work on the same field, just different parts of it.

In an effort to broaden my knowledge I've added a component to my Friday review process: the fun paper reading. Every Friday morning while organizing the end of the week and setting up the next week I find a paper that is out of my research area and read it. These papers range from the geometry of parallel parking, to lightning science, to the fluid dynamics involved with sinking bubbles in a pint of Guinness.

Need for Cognition
The second characteristic described is one that most of us already have. It is the drive to be that person always asking "why?". When driving down the road on a hot summer day and you see the road "shimmer" do you keep going or wonder what is happening? Most of us would go look it up and read all about autoconvection. While some may call this going down the Wikipedia rabbit hole, it is essential to build time into our schedules to allow this kind of free exploration.

What can we as geoscientists take from all of this? We should always be broadening our horizons, making many connections with people in all areas, and not forget that we are all working on the same problem... understanding our world.

99u: Picasso Kepler and the Benefits of Being an Expert Generalist

NSF Graduate Fellowships - Some Thoughts and Tips

While this post may not appeal to the general audience, I thought it would be useful because it is an important topic to any senior undergraduate or first/second year graduate student. Today I want to briefly tell you my experience applying for the NSF Graduate Fellowship in 2012 and 2013.  I learned a lot in the process of applying for this prestigious fellowship and hope that I can pass some of that knowledge down!

Application 2012 - No award

My first year at Penn State, I applied with the traditional three documents of research statement, personal statement, and research proposal.  I sought the edits of those who had been awarded the fellowship in the past and thought I had a convincing packet assembled.  After reading, re-reading, and re-reading, it was time to submit.  I submitted the application, then made the mistake of reading over it again a week later and finding things I wished I had changed.  Months went by and seemed to drag on until the award announcements came.  I was not selected for an award.  While I was of course disappointed, it was time to kick it into high gear and make an even better application for my next (and final) try.

Application 2013 - Award Offered

For my second application I had lots of debates with myself.  Should I change my research proposal topic? Were my personal and research statements too similar? How can I improve the writing? Should I include figures?

To settle these debates, I turned to the wealth of online information that I hadn't sought out the previous year.  I talked with those who had received the award, I read funded research proposals from various professors and researchers, and I went down to the bare bones of the document.  While I'll discuss specific tips below, I'll just say that I started earlier, took more pauses between writing sprints, and sought more people for reading.

My tips

In writing two proposals, I learned a lot about how to effectively structure my research and emphasize the specific angle of attack I'll take on a research question and why it's different.  Here are some things I found to be helpful:

MY PROCESS

  • Start Early - Think it's too soon? Wrong! You need lots of time to organize your thoughts, revise, rewrite, and think about your application.
  • Read the Announcement - Print out the announcement document and read it critically.  You can look at the 2014 announcement here.  Don't just read it, mark on it. Highlight what they specifically are looking for, underline the buzzwords and key phrases of the call.  Also, draw a big box around the application deadline and then plan to beat it by one week.  Why? Computer problems, server crashes, unexpected medical emergency, etc.  You don't know what could happen, so make sure that your application gets in early!
  • Make a FastLane Account - Go to the online application and make an account.  Get familiar with FastLane, you'll use it for most all of your NSF proposals unless they change sometime in the future! Look at the application.  Go ahead and fill in the boxes with your name, address, etc.  Now you can mark down progress on your application and have momentum to move forward with the hard work.
  • Write the Requirements for your statements out on Paper - This one is huge.   In the application, pull up the research proposal and background/personal statement "prompts."  Print them, read them many times, and finally write them down on a notepad.  Break the prompt up into small chunks and then think about how to answer each piece.  Don't worry about flow, just think.
  • Brain Dump - Now write each one of the pieces of the question on the top of a page and begin to outline the points that you will make to address it.  Again, don't worry about order or how many points you have! Just write and write and write.
  • Organize into an Outline - Take a break, a day or so, then come back to your brain dump afresh and think about how you can piece it together into one coherent story - your story.  The story of a proposed research project and the story of you and your life in science.
  • Make a Draft - It does not need to be pretty, organized, the right length, etc.  Just get complete sentences onto the page.  Do this on paper or in a plain text editor.  Don't worry about formatting, length, spacing, margins... Those are things for later in a word processor.  I like using Textastic, Sublime, TextWrangler, or Editorial.
  • Read it and Have Lots of People Read it - Don't be afraid to ask everyone to read and edit your document.  Do not ask them to re-write the document for you! Remember this needs to come from your brain, but it is fine to gather suggestions and comments.  I also went to the graduate writing center and had some great suggestions from the coach there.  As scientists, we are not used to marketing ourselves and we often think the need for our research is obvious.... That won't work.
  • Talk to Your Reference Writers - You'll need letters of reference.  These take lots of time to write, so make things easy on your mentors and writers.  They have done a lot for you and are about to help out again.  I went through the application, figured out what I thought would be important to my application reviewers and then composed an email to my writers (see below).
  • Do NOT Cram - Whitespace is a dear friend to someone who is reading many pages of documents... like your judges.  Don't pack every single word you possibly can into the pages.  Economy of words shows great thought and restraint when writing.  Edit down over and over.  Leave white space between paragraphs.  If you use figures, text wrapping is a fine way to reclaim space, but leave a sufficient margin.  Look at books and other professionally formatted documents for inspiration.

MY APPLICATIONS FROM BOTH YEARS

Here are links to documents I produced for both applications, of course don't plagiarize, but hopefully they are helpful!

NSF 2012 (No Award)
Personal Statement | Previous Research | Proposed Research

NSF 2013 (Award Offered)
Research Statement | Personal & Background Statement |
Letter to Reference Writers

LINKS

There are several other helpful webpages out about the application process.  Remember, what you read on the program site is the final word, but these pages have more useful tips.

GRFP Essay Insights (Missouri)
Alex Lang's Website
Jennifer Wang's Website
Reid Berdanier's Website
The Official NSF GRFP Page
NSF PAPP Guide Book

Remember, if you don't get the award, take the feedback you get and start improving! Try, try again and don't be afraid to seek help from mentors, writers, friends, and family.  Please leave any useful comments below. Best of luck!

Getting Up and Running with a 3D Printer

I recently received some money to purchase a 3D printer to aid my laboratory experiments. I thought that it would be good to share how I decided on the printer that I did and how hard/easy it was to setup. Currently I've only run a few simple test prints, but will be printing some mounting equipment for laboratory experiments within a few weeks.

2014-08-16 05.08.30

Choosing a Printer

When choosing a printer, there are many factors to consider. The consumer 3D printer movement is still very young, so there are many different designs available that require different amounts of tinkering to work and have vastly different capabilities. To help decide, I made a few requirements and decision points :

1. I must be able to print something that is at least 8"x8"x8". Print area is an important consideration and is one of the biggest influences on cost. With this print size I can make most prototypes, brackets, etc that we need. Larger parts can always be printed in sections and joined, but it's not the strongest or easiest thing to do.
2. Print material and method. There are printers that can print in many types of plastic and even in wood. Some printers fuse plastic in layers in an "addictive manufacturing" process. Others can fuse a liquid into a plastic with a process referred to as stereo lithography. Most consumer level machines with a large print area are the type that extrude plastic. There is a large matrix of advantages and disadvantages, but we will just leave it at this for now.
3. The final factor I considered is the development of the machine. Informally this is the "tinker factor." How much are you willing to modify and experiment with the machine to get increased versatility vs. how much do you want a machine that is a push button that just works? I've always been the tinkering type but there is a balance. Some more experimental and low cost machines are not as reliable as I would prefer, but something that is fully developed like the MakerBot line doesn't leave as much versatility. The other portion is the licensing of the software and hardware. I've always been a proponent of the free and open source movement. It's how we are going to advance science and technology. Companies like MakerBot are not fully open source and that just doesn't sit well as it prevents the community from fixing problems in a piece of equipment that was rather expensive.

With all of those considerations and lots of research, I decided on the Taz 4 printer by Lulzbot. You can purchase the printer from Amazon, but I decided to purchase through Sparkfun Electronics since they are a small(ish) business that really supports education and the maker movement. I ordered the printer within a few hours of passing my comprehensive exams and it was on the way!

Setting up the printer

I received the printer and followed all of the setup instructions. This involved assembling the axes and removing the packing protection. I've never done this before, but overall it was very straightforward and took about 45 minutes. The next steps were what made me nervous.

To get quality prints the printer surface must be level with relation to the print head track. There are various end stops and leveling screws to adjust. Using a piece of printer paper as a gap gauge, I just followed the instructions and had the print bed leveled in about 20 minutes. There is also a test print pattern that prints two layers of plastic around the base plate to let you make sure the level is right on. Everything must be kept clean and adjusted as with any precision bit of gear, but overall I was impressed with the design.

The printer ships with an octopus test print that was my first object. I loaded up the file and hit print. The printer ran for about an hour and at the end I had the print shown below!

2014-08-14 22.01.49

What's Next

I've got some plans for what to print next. Currently I'm designing some new brackets to hold sensors in place during experiments and a few new parts like shields and pulleys to improve the quality of some of our demonstration apparatuses in the lab. I'm sure some of the results will end up as their own blog posts, but you can always see what's new by following me on Twitter (@geo_leeman). I also would like to thank Hess energy and Shell energy for their support of various aspects of these projects and of course the National Science Foundation for supporting me and many aspects of my lab research. Everything I've said is of course my own opinion and does not reflect the views of any of those funding organizations. Next post we will likely return to more general topics like seeing trends in data or go back and look at more Doppler radar experiments.

Update!

I was able to print my first laboratory parts, a set of brackets to make a magnetic holder for a displacement transducer.  I will be posting the cad files to my github account under an open license.

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