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February 3, 2014
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Data Management Services @ Stanford
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Software Carpentry Boot Camp, image by Amy Hodge

Boot Camp coffee break

Software Carpentry Boot Camp

student gets a consult
Bootcamp for Scientists
Finally, a bootcamp that's more about thinking than sweating! 

On January 27 & 28, Data Management Services hosted a Software Carpentry bootcamp for 28 graduate students and post-docs in experimental physics and geophysics.

The goal: teaching basic skills for scientific computing to help researchers get more done in less time, and with less pain.

Attendees learned about:
  • the Unix shell and automating repetitive tasks,
  • programming and scientific computing in Python,
  • growing a program in a modular, testable way,
  • using Git and GitHub to track and share work efficiently,
  • validating and testing software, and
  • creating reproducible research workflows.
Click the "Read More" button below to learn more about the bootcamp and to find out how to work with us to hold one for your group!

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Tool Spotlight: RightField

Most people agree that making metadata isn't much fun. But the RightField spreadsheet tool can help make it a snap!

This tool might be right for you if you:

  • collect data in Excel spreadsheets
  • want to annotate that data directly in the spreadsheet
  • are interested in using existing ontologies and controlled vocabularies
  • use any platform: Mac, Windows, or Linux

RightField allows you to choose categories from your favorite ontologies as the source of approved metadata terms for entering into spreadsheet cells.

  • Studying neurology in zebrafish? Assign the "CNS interneuron" class from the Zebrafish Anatomy and Development Ontology to cells in your spreadsheet to restrict choices to terms in that class, such as "midbrain interneuron" or "spinal cord interneuron."
  • Studying adverse events? Assign the "lung disorder" class from the Ontology of Adverse Events to cells in your spreadsheet to restrict choices to terms in that class, such as "bronchospasm" or "tuberculosis."
There are 100s of ontologies included, or you can import them from you computer or a URL.
Click the "Read More" button below to find out more about RightField and other freely available metadata tools.
 
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Plastic toy with "Hello my name is" written on it, image by Robert Occhialini

 
Tip of the Month: Dates

Dates are often a good piece of information to include in file names, but a useful and consistent format is key!

To easily sort your files by date, try this format:
  • Include the date at the beginning of the file name.
  • Use only numbers for months, not names, e.g. "02," not "February" or "Feb."
  • Format the date as YYYY, then MM, then DD, such as 20140215 for February 15, 2014.
This way, your computer will automatically sort your files in date order, even if they span decades (or the turn of a century)!

For example, these files will automatically be sorted in the correct order:
  • 19970529test.xls
  • 20120315test.xls
However, files with the month listed first will get all jumbled. All files from March -- every March -- will come before all your files from every May:
  • 03152012test.xls
  • 05291997test.xls
Click the "Read More" button below to read more about best practices for file naming.

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New York Times logo

Scientific_American_logo

 
Further Reading:
Reproducible Research & Archiving Articles

The New York Time's Raw Data column by science writer George Johnson explores irreproducibility in science in the January 20th article "New Truths That Only One Can See":
"Replication, the ability of another lab to reproduce a finding, is the gold standard of science, reassurance that you have discovered something true. But that is getting harder all the time."

"If a result appears only under the full moon with Venus in retrograde, is it truly an advance in human knowledge?"

Scientific American's Information Culture blog recently published an article on "Understanding your rights: repositories, websites, and 'self-archiving.'"

This article does a quick, yet thorough, run-through of where you might want to post one of your articles online, and how to figure out which version you are allowed to post.

Click the button below to contact us at sdr-contact@lists.stanford.edu if you are interested in preserving and sharing copies of your articles via the Stanford Digital Repository.

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Amy Hodge
Science Data Librarian
amyhodge@stanford.edu | 650.556.5194
 
 
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