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A beginner’s guide to conducting reproducible research

This is a rather good read for anyone interested in reproducible research (i.e., everyone who tries to become a researcher as a career)

TLDR:

Why reproducible research

  1.  reproducible research helps researchers remember how and why they performed specific analyses during the course of a project.
  2.  reproducible research enables researchers to quickly and simply modify analyses and figures.
  3.  reproducible research enables quick reconfiguration of previously conducted research.
  4.  conducting reproducible research is a strong indicator to fellow researchers of rigor, trustworthiness, and transparency in scientific research.
  5.  reproducible research increases paper citation rates (Piwowar et al. 2007, McKiernan et al. 2016) and allows other researchers to cite code and data in addition to publications.

A three-step framework for conducting reproducible research

Before data analysis: data storage and organization

  1. data should be backed up at every stage of the research process and stored in multiple locations.
  2. Digital data files should be stored in useful, flexible, portable, nonproprietary formats.
  3. It is often useful to transform data into a “tidy” format (Wickham 2014) when cleaning up and standardizing raw data.
  4. Metadata explaining what was done to clean up the data and what each of the variables means should be stored along with the data.
  5. Finally, researchers should organize files in a sensible, user-friendly structure and make sure that all files have informative names.
  6. Throughout the research process, from data acquisition to publication, version control can be used to record a project’s history and provide a log of changes that have occurred over the life of a project or research group.

During analysis: best coding practices

  1. When possible, all data wrangling and analysis should be performed using coding scripts—as opposed to using interactive or point-and-click tools—so that every step is documented and repeatable by yourself and others.
  2. Analytical code should be thoroughly annotated with comments.
  3. Following a clean, consistent coding style makes code easier to read.
  4. There are several ways to prevent coding mistakes and make code easier to use.
    1. First, researchers should automate repetitive tasks.
    2. Similarly, researchers can use loops to make code more efficient by performing the same task on multiple values or objects in series
    3. A third way to reduce mistakes is to reduce the number of hard-coded values that must be changed to replicate analyses on an updated or new data set.
  5.  create a software container, such as a Docker (Merkel 2014) or Singularity (Kurtzer et al. 2017) image (Table 1) for ensuring that analyses can be used in the future

After data analysis: finalizing results and sharing

  1. produce tables and figures directly from code than to manipulate these using Adobe Illustrator, Microsoft PowerPoint, or other image editing programs. (comment: for example, can use csvsimple package in latex)
  2. make data wrangling, analysis, and creation of figures, tables, and manuscripts a “one-button” process using GNU Make (https://www.gnu.org/software/make/).
  3. To increase access to publications, authors can post preprints of final (but preacceptance) versions of manuscripts on a preprint server, or postprints of manuscripts on postprint servers.
  4. Data archiving in online general purpose repositories such as Dryad, Zenodo, and Figshare

Useful Links

Ford Foundation Fellowship Programs

The National Academies of Sciences, Engineering, and Medicine is accepting applications for the 2023 Ford Foundation Fellowship Programs. Eligibility and online application information are available on the Ford Foundation Fellowship Programs website.

 

Through its program of fellowships, the Ford Foundation seeks to increase the diversity of the nation’s college and university faculties by increasing their ethnic and racial diversity, maximize the educational benefits of diversity, and increase the number of professors who can and will use diversity as a resource for enriching the education of all students.

 

Please encourage eligible candidates at your institution to apply to be a part of the Ford Fellows and celebrate the legacy of this impactful program!

 

Eligibility Requirements: 
  • U.S. citizens, U.S. nationals, and U.S. permanent residents (holders of a Permanent Resident Card); individuals granted deferred action status under the Deferred Action for Childhood Arrivals Program (DACA) program;¹ Indigenous individuals exercising rights associated with the Jay Treaty of 1794; individuals granted Temporary Protected Status; asylees; and refugees, regardless of race, national origin, religion, gender, age, disability, or sexual orientation;
  • Individuals with evidence of superior academic achievement (such as grade point average, class rank, honors or other designations); and
  • Individuals committed to a career in teaching and research at the college or university level in the U.S.
1Eligibility includes individuals with current status under the DACA Program, as well as individuals whose status may have lapsed but who continue to meet all the USCIS guidelines for DACA.

 

Stipends: 
  • Predoctoral: $27,000 per year for three years
  • Dissertation: $28,000 for one year
  • Postdoctoral: $50,000 for one year

 

Application Deadline Dates: 
  • Predoctoral: December 15, 2022 (5:00 PM EST)
  • Dissertation: December 8, 2022 (5:00 PM EST)
  • Postdoctoral: December 8, 2022 (5:00 PM EST)

 

Supplementary Materials Deadline Date (Submitted Applications): 
  • January 5, 2023 (5:00 PM EST)

 

Thank you for your assistance in forwarding this message to prospective applicants!

 

Sincerely yours,

 

Elizabeth Prescott, D.Phil.
Director, Fellowships Office
500 5th Street, NW
Washington, DC 20001

 

Graduate Study Center Opening November 1st and 2nd

The time has finally arrived to open the Graduate Student Study Center on the 3rd and 4th floors of Devon Energy Hall. This area is open only to graduate students and is a quiet study area where you can meet your fellow ECE colleagues, make new friends and help one another as you become engineers.
This event is sponsored by the ECE Graduate Student Society. There will be drinks, snacks and of course a giveaway!
If you would like to choose a desk, please meet the new ECE GSS and faculty advisor Dr. Sangpil Yoon along with the ECE staff on November 1, 2022, from 3pm-5pm at the DEH large team room 345 or November 2, 2022, from 2pm-5pm at the DEH large team room 326. Selections for both the 3rd and 4th floors will be done here.
The configuration has changed. If you had a spot previously, you will be choosing a new spot. If you have a refrigerator or microwave, on either floor please contact Dr. Keele, rckeele@ou.edu. If you are unable to make either date, please contact Stephanie Gill, srg@ou.edu on November 3rd. Desks will be chosen on a first come first served basis.

Seeking outstanding female PhD candidates within two years of completion

The Norman chapter of P.E.O. (a women’s philanthropic organization) is looking for an outstanding female PhD candidate.  Their mission is to support women in the attainment of their educational goals.  The P.E.O. Scholars Award (PSA) a $20k grant for PhD students within two years of completion of their degree, with a well-defined research project and within at least a year to completion: https://www.peointernational.org/peo-scholar-awards . The deadline for us to submit a candidate in 11/13.

OU Engineering Information Session

 
When the first president of the University of Oklahoma stepped off the train to look at his new environment, he exclaimed, “What possibilities!” 
 
At the Gallogly College of Engineering, we’re still exploring what’s possible.
 
Join us!
OU Engineering Information Session
 
Be part of the next generation of researchers
 
Join us to learn about:
Graduate Programs
Research and Opportunities
Financial Support and Scholarships
Alumni Engagement
And more!
 
Monday, October 24, 2022
9:00am CDT
 
Zoom link will be provided upon registration.
 
 
For more information visit ou.edu/coe
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