Friday, May 3, 2013

Reordering columns/rows in a shapefile in ArcGIS

I recently created a shapefile in ArcGIS of my oceanic transform fault data. I started off with two separate files: a shapefile of points that simply contained a latitude/longitude and name for each fault; and a polyline shape file that contained the length measurements and the start/end points. I combined these two shapefiles in ArcMap using the "Join Data" command, and selecting to join the data based on spatial location. The result was a single polyline shapefile, that included all the original polyline attributes as well as all the related attributes (name, center lat/long) from the point file.

The problem was that the shapefile was not ordered the way I wanted it. In ArcMap you can reorder rows by ascending/descending values by double-clicking on the column header, or move columns simply by clicking on the header and dragging it over. The problem is that this only applies to your view of the shapefile attribute table, and the reordering is not actually saved to the shapefile itself. If you close out ArcMap, open a new map, reimport the shapefile, everything is back to the original order.

There is a free plugin tool for ArcGIS that is quite powerful and can solve these issues for you: ET GeoWizards. There are both free and paid versions of this toolbox, but I found the free version did exactly what I need. This toolbox is pretty impressive, and includes tools for feature translation, where shapefile objects are moved by a user-specified distance, filling holes in polygons, generalizing features, creating clusters from points, and a whole suite of other functions.

In order to reorder the columns and sort the rows in your shapefile, you can find the necessary commands under "Basic." The "Order Fields" command lets you select which fields you want to use from your original shapefile and specify the order in which they should appear. The "Sort Shapes" command lets you select which columns you want to sort the data by (you can select more than one), and whether you want them in ascending or descending order.

Another great toolbox plugin for ArcMap is Jenness Enterprises' Tools for Graphics and Shapes.  If you are looking for a tool to calculate spheroidal (geodesic) length of features in your shapefile, this is the tool for you. While this toolbox includes many of the same functions as the GeoWizards plugin, it also has many unique tools as well.  I have found that having both toolboxes has made working in ArcMap a much more pleasant experience. I wrote up a blogpost on the Tools for Graphics and Shapes plug-in back in 2010.

Thursday, May 2, 2013

Negotiating a Postdoc Position

UPDATE: The webinar link has now been posted. You can view the webinar yourself here.

On Tuesday evening, April 30th, COSEE (Centers for Ocean Sciences Education Excellence) and IBP (Institute for Broadening Participation) co-hosted a webinar :

“How to Negotiate Your Postdoc Position”

The panel speakers included Dr. Ashanti Johnson (Pyrtle), the executive director of IBP, whom I know from the University of South Florida, where she was faculty member when I was a master's student, and Dr. Edward Krug, Assistant Dean for Postdoctoral Affairs and an associate professor at the Medical University of South Carolina.

The webinar focused on how to negotiate your postdoctoral position in order to make your experience the best one possible. This does not just include salary negotiation, which is frequently a moot point anyway since funding is often provided by grants and is fixed, but also start date/end date, teaching load, student advising, publications, expectations, etc.

I took notes during the webinar and thought I would post them here in case they might be a benefit to others. The webinar also mentioned a few online documents and resources for students to help them in finding and negotiating a postdoctoral position, which I will post below.


2) Pathways to Science, an IBP program that seeks to help connect underrepresented groups to careers in STEM fields, lists a whole bunch of programs from K-8 grade levels all the way through faculty positions. Their listing of postdoc programs is quite extensive. They also provide tips on how to prepare and enhance your application, questions to ask before you start, and links to past webinars (the webinar I just attended should be posted there within the next week). While the primary aim of the program is to help bridge the gender/race/ethnicity gap in science, the website is a great resource for everyone.

3) The National Postdoctoral Association, which seeks to provide a "national voice and seeking positive change for postdoctoral scholars." The website provides a lot of resources to students and current postdocs, including listings of current and upcoming positions, guidelines for responsible conduct in research, and access to a network of current and former postdocs and mentors, research universities, and industry companies. Membership is required to access the majority of their content, and the annual dues amount varies according to your position (student, post doc faulty member, etc.).

Below are the notes I took while each presenter was speaking. I have also included a summary of the  questions and answer portion of the webinar.

Ashanti Johnson:

  • you are encouraged to negotiate your first salary 
  • can negotiate full compensation package including research support, benefits, etc., not just salary
  • always start off by responding how pleased you are to receive the offer and ask for a written confirmation of the offer. Confirm with them how long you have to make your decision as to whether or not to accept
  • You should convey enthusiasm the whole time, especially throughout the negotiation process
  • Get final offer in writing after all compensations have been made
  • If you reject the position, remember that these are still potential future colleagues and maintain professionalism and enthusiasm throughout

Edward Krug:

  • Grad school versus Post Doc
    • grad school is really focused on how to address problems while postdoctoral positions show you how to identify and address critical gaps in current knowledge. Survival skills for scientists
  • Fundamental science post docs - NSF is primary funding agency
  • National Postdoctoral Association - professional tools - - helps develop core competencies that postdocs should learn during their tenure:
    • Discipline-specific conceptual knowledge
    • research skill development
    • communication skills
    • professionalism
    • leadership and management
    • responsible conduct of research
  • NIGMS IRACDA Program - for biomedical/behavioral scientists. You apply to the program, not a specific person. You teach 25% of your time. Good for want-to-be academics. Includes a yearly conference. Typically 2 - 3 years
  • MyIDP - My Individual Development Plan - aims to help you find the ideal career position once you have completed your PhD. The website gives you means of self-assesment and then fits you with a possible career match (e.g. being a PI). Once matched, the program:
    • provides you with a list of strategic goals to help you achieve your desired career path
    • help you identify possible your weak points towards achieving your goals
    • gives you access support groups of people with similar goals/challenges
  • Publications are the currency of academia. The majority of postdocs end up in some type of publication disputs with their advisor. So what makes a coauthor versus first author?
    • you should discuss this openly and agree on set guidelines with your advisor from the get-go
    • ask about authorship BEFORE joining a lab. Don't assume your mentor will put you first

Questions from the crowd:

   Q: Can you do something else while doing a post doc - non-profit work that fits in with your career?
        A: maybe 25% of time, but don't let it compromise your Post Doc

   Q: If you want to pursue an Industry position, should you pursue a post doc?
        A: Yes. NSF has an industry/academic program. Post docs can really help you get the ideal position.

   Q: Are salaries generally negotiable?
        A: If funding is through a grant, it may be fixed. You need to research the funding source before trying to negotiate a salary. Some institutions have a post doc office that can help you negotiate your post doc salary.

   Q: Can you take your post doc research with you?
        A: Yes, under some circumstances. You can discuss this with your mentor at the beginning. It may also depend on who the funding was awarded to.

   Q: What are the options for foreign post docs studying at US institutions?
        A: NSF and some institutions have foreign postdoc positions, but not NIH

   Q: When do you inform your advisor of your post doc plans?
        A: It really depends on the relationship you have with your advisor and whether or not you can have an informal conversation about it. Remember, they decide when you're done, not you

   Q: Can you apply for a post doc doing the same thing as your PhD?
        A: Similar is fine, but having a post doc that is different is advantageous to learn new skills. NSF actually encourages you to pursue different, but related topics

   Q: If papers are submitted, but not published, can you still look for a post doc?
         A: Yes! Do not wait. Look often and look early.

   Q: What kind of negotiating power do I have as a first time post doc?
         A: Depends on the position, but you should definitely be your own advocate. There is a new government recommendation of starting salary of 42K for postdoctoral scholars, so use that as a starting off point if you are going to negotiate salary

   Q: How many publications per year is expected?
        A: 1 - 1.5 per year is good, at least in biomedical research fields. Some clinical positions expect 3 - 4 publications per year. Expectations are really dependent on the specific field you are in.

   Q: How does research vary between post doc and PhD
         A: You are now a professional, and this should be reflected in the quality of your work and publications. There is less structure, more self-guided. You have one primary mentor, not a whole committee.
               It is what you make of it, so you need to be able to productive on your own and not be dependent on others. Do not be afraid to go out and seek more mentors that can help coach you professionally and personally as you move through your career. These mentors can help you throughout your post doc and beyond.

    Q: So how do you find those other mentors?
         A: Professional societies can be a great source
              Your PhD advisor can become a lifelong mentor. You are now part of their lineage, and they want you to succeed. If there is someone whose work you are interested in, talk to them. They can become a mentor. Networking is key.

Monday, April 22, 2013

The Iran and China earthquakes as captured by the UNH seismometer

This past week has been has been a tense one for sure. Not only was there the Boston Marathon bombings and the fertilizer plant explosion in Texas, but there were also major earthquakes in both Iran and China.

The 7.8 magnitude event in Iran occurred on April 16th, near the Iran/Pakistan border. Pakistan bore the brunt of the quake, with at least 35 dead and an entire town essentially destroyed. You can view all the scientific/technical details of the event on its USGS page. We can see the earthquake quite clearly on the UNH seismometer. The event hits our station at 10:56 UTC (06:56 am EST). The shaking intensity when the surface wave hits is strong enough that the seismic wave looks clipped in the display (in green).

The magnitude 6.6 earthquake in China struck on April 20th. Although smaller than the Iran earthquake, this earthquake was very shallow and hit a more densely populated area. The latest estimates put the death toll at 188, with over 11,000 people injured and many are still missing. The USGS page for the event can be seen here.

It takes about 13 minutes for the initial P-wave from the earthquake to reach our station, and you can see when it hits if you look at the top black line. Just after the 30-minute mark on the same line, you can see the S-wave hit. The much larger amplitude surface waves can be seen in red, starting about 21:03 EST.

These earthquakes have devastated the villages they have hit, particularly the one in China. Construction in these small towns is often very old and not up to code. Landslides bury entire structures and block roadways, making it hard for aid to get to those who need it the most. 

My thoughts go out to everyone affected by this past's weeks events, both here in the US and abroad.

The UNH seismometer is part of the larger New England Seismic Network. You can visit their page here.

Saturday, April 20, 2013

Proposing a session on oceanic transform fault and intraplate environments at AGU!

Last year, while I was presenting my poster at the AGU Fall meeting, I realized that there is a small, but dedicated community of folks that study fault zone structure and processes related to oceanic transform faults. I had only met a few of them, but I wanted to do something to facilitate bringing everyone together for discussion and possible collaboration. I decided that I was going to propose an AGU session that specifically focused on oceanic transform fault research. I started off by talking to some other folks at the conference about it to gauge interest, and everyone I mentioned it to seemed pretty keen about the idea. Encouraged by the level of interest, I decided to move forward.

A friend of mine, Kasey Aderhold, is a PhD student at Boston University. Her research looks at strike-slip earthquakes in the ocean, both in the intraplate regions and along fracture zones. We decided to team up and propose a joint session, along with our respective advisors. We are pretty stoked about it, and hope that this session is successful in bringing everyone together. It will also be an invaluable experience for us, as students, to be able to convene an AGU session. Our advisors are both influential women in the field, and while I have nothing against all the male geophysicists out there, I am proud that our session is all woman-powered. 

We won't know until June if our session has been approved, but our fingers are crossed. If you know anyone who studies fault structure and/or seismicity in the ocean, feel free to share this with them. The more the merrier. It would be very exciting if we had enough abstract submissions to our session that we can have both a poster and oral session.

Saturday, April 13, 2013

Detecting Earthquakes at UNH

I've decided a great way to get back into blogging would be to show some of the great seismograms the UNH seismometer has been recording since we set it up in 2011.

While most of the signals we record on the station are from passing trains, we have also recorded some pretty impressive earthquakes.

Check out this seismogram from an earthquake swarm near the Solomon Islands on Feb. 8, 2013. In a little over 40 minutes, there were 3 large earthquakes. A magnitude 8.0 struck at 1:12 (UTC), followed by a 7.1 event 11 minutes later, and a 7.0 event 30 minutes after that. In addition, there were smaller magnitude 5's and 6's both preceding and succeeding these larger events. When the surface waves from the 7.0 event hit our station, surface waves from the preceding 7.1 and 8.0 event were already shaking it. In the image below, the signal is so strong that it actually goes off the page!

Remember the Colorado and Virginia earthquakes that occurred back in August of 2011? The UNH
seismometer captured those earthquakes as well:

While we are looking at more local events, let's not forget the small Maine event (magnitude 4.0) that occurred on Oct. 16 of last year. See that impuse response in green at the bottom of the chart in the image below? Well, that's it. The earthquake occurred very close to our station, so the P, S, and surface waves hit at nearly the same time. The response that we see in the long-period signal, therefore, is very sharp. I have to admit, I was quite excited when this earthquake occurred. This was the first earthquake that I really felt and realized what it was while it was occurring -- well, truth be told I first thought my furnace was about to explode, but only for the first second or two. In fact, I not only felt the earthquake, but I heard it. I actually heard the earth rumble.

Finally, let's look at a seismogram from a magnitude 6.9 earthquake that occurred on Feb. 02, 2013 in Japan. This is a great seismogram because we can clearly see when the P, S, and surface waves arrive at the station.

Pretty cool, eh? If you want to check out some seismograms for yourself, you can do so at the New England Seismic Network webpage. To view the UNH stations, click on current seismograms and select DUNH as the station.

Saturday, April 6, 2013

Still Alive!

So I know it has been a while since I have posted anything to my blog, but I was a bit shocked to learn that "a while" is actually almost 2 years.

In the past 2 years a lot has happened:

  • I passed my departmental exams and advanced to candidacy
  • I sailed as member of the scientific party on IODP Expedition 343: Japan Trench Fast Drilling Project (JFAST).
  • I was selected to participate in a NASA Social, during which I was able to go to the Jet Propulsion Laboratory in Pasadena for the landing of Curiosity, the Mars Science Lab rover
  • I got married to Kurt Schwehr, who is much better about updating his blog than I am mine
In the next year, I'll be wrapping up my research and getting ready to defend. As I do so, I am going to make an effort to keep my blog updated. 

I realize that not only has my blog been helpful to me, as I have often referred back to it to remember how I did something, but that it has also been helpful to others as well. Having something that I posted save someone else a lot of grief and head-banging is pretty sweet, and I hope that some of my future posts will continue to be beneficial to people.
So buckle up and hang on to your hats folks, here we go....