Archive of ‘Digital literacy’ category

Reproducibility Librarian

Reproducibility Librarian? Yes, That Should Be Your Next Job
Vicky Steeves (@VickySteeves) is the first Research Data Management and Reproducibility Librarian
Reproducibility is made so much more challenging because of computers, and the dominance of closed-source operating systems and analysis software researchers use. Ben Marwick wrote a great piece called ‘How computers broke science – and what we can do to fix it’ which details a bit of the problem. Basically, computational environments affect the outcome of analyses (Gronenschild et. al (2012) showed the same data and analyses gave different results between two versions of macOS), and are exceptionally hard to reproduce, especially when the license terms don’t allow it. Additionally, programs encode data incorrectly and studies make erroneous conclusions, e.g. Microsoft Excel encodes genes as dates, which affects 1/5 of published data in leading genome journals.
technology to capture computational environments, workflow, provenance, data, and code are hugely impactful for reproducibility.  It’s been the focus of my work, in supporting an open source tool called ReproZip, which packages all computational dependencies, data, and applications in a single distributable package that other can reproduce across different systems. There are other tools that fix parts of this problem: Kepler and VisTrails for workflow/provenance, Packrat for saving specific R packages at the time a script is run so updates to dependencies won’t break, Pex for generating executable Python environments, and o2r for executable papers (including data, text, and code in one).
plugin for Jupyter notebooks), and added a user interface to make it friendlier to folks not comfortable on the command line.

I would also recommend going to conferences:

more on big data in an academic library in this IMS blog
academic library collection data visualization

more on library positions in this IMS blog:

on university library future:

librarian versus information specialist


VR and students with special needs

Bibliography on virtual reality and students with physical and cognitive disabilities

Jeffs, T. L. (2009). Virtual Reality and Special Needs. Themes In Science And Technology Education2(1-2), 253-268.

Lahav, O., Sharkey, P., & Merrick, J. (2014). Virtual and augmented reality environments for people with special needs. International Journal Of Child Health And Human Development7(4), 337-338.

Cai, Y., Chiew, R., Nay, Z. T., Indhumathi, C., & Huang, L. (2017). Design and development of VR learning environments for children with ASD. Interactive Learning Environments25(8), 1098-1109. doi:10.1080/10494820.2017.1282877

Passig, D. (2011). The Impact of Immersive Virtual Reality on Educators’ Awareness of the Cognitive Experiences of Pupils with Dyslexia. Teachers College Record113(1), 181-204.

Ke, F., & Im, T. (2013). Virtual-Reality-Based Social Interaction Training for Children with High-Functioning Autism. Journal Of Educational Research106(6), 441-461. doi:10.1080/00220671.2013.832999

Collins, J., Hoermann, S., & Regenbrecht, H. (2016). Comparing a finger dexterity assessment in virtual, video-mediated, and unmediated reality. International Journal Of Child Health And Human Development9(3), 333-341.

Epure, P., Gheorghe, C., Nissen, T., Toader, L. O., Macovei, A. N., Nielsen, S. M., & … Brooks, E. P. (2016). Effect of the Oculus Rift head mounted display on postural stability. International Journal Of Child Health And Human Development9(3), 343-350.

Sánchez, J., & Espinoza, M. (2016). Usability and redesign of a university entrance test based on audio for learners who are blind. International Journal Of Child Health And Human Development9(3), 379-387.

Rizzo, A. A., Bowerly, T., Shahabi, C., Buckwalter, J. G., Klimchuk, D., & Mitura, R. (2004). Diagnosing Attention Disorders in a Virtual Classroom. Computer (00189162)37(6), 87-89.

Eden, S. (2008). The effect of 3D virtual reality on sequential time perception among deaf and hard-of-hearing children. European Journal Of Special Needs Education23(4), 349-363. doi:10.1080/08856250802387315

Eden, S., & Bezer, M. (2011). Three-dimensions vs. two-dimensions intervention programs: the effect on the mediation level and behavioural aspects of children with intellectual disability. European Journal Of Special Needs Education26(3), 337-353. doi:10.1080/08856257.2011.593827

Lorenzo, G., Lledó, A., Roig, R., Lorenzo, A., & Pomares, J. (2016). New Educational Challenges and Innovations: Students with Disability in Immersive Learning Environments. In Virtual Learning. InTech.

more on virtual reality in this IMS blog

digital assessment session for SCSU faculty

please consider the following opportunities:

  1. Remote attendance through :
  2. Recording of the session: (URL will be shared after the session)
  3. Request a follow up meeting for your individual project:

more on digital assessment in this IMS blog

digital assessment

Unlocking the Promise of Digital Assessment

By Stacey Newbern Dammann, EdD, and Josh DeSantis October 30, 2017

The proliferation of mobile devices and the adoption of learning applications in higher education simplifies formative assessment. Professors can, for example, quickly create a multi-modal performance that requires students to write, draw, read, and watch video within the same assessment. Other tools allow for automatic grade responses, question-embedded documents, and video-based discussion.

  • Multi-Modal Assessments – create multiple-choice and open-ended items that are distributed digitally and assessed automatically. Student responses can be viewed instantaneously and downloaded to a spreadsheet for later use.
    • ( and
    • Poll Everywhere (
    • Formative ( allows professors to upload charts or graphic organizers that students can draw on with a stylus. Formative also allows professors to upload document “worksheets” which can then be augmented with multiple-choice and open-ended questions.
    • Nearpod ( allows professors to upload their digital presentations and create digital quizzes to accompany them. Nearpod also allows professors to share three-dimensional field trips and models to help communicate ideas.
  • Video-Based Assessments – Question-embedded videos are an outstanding way to improve student engagement in blended or flipped instructional contexts. Using these tools allows professors to identify if the videos they use or create are being viewed by students.
    • EdPuzzle ( and
    • Playposit ( are two leaders in this application category. A second type of video-based assessment allows professors to sustain discussion-board like conversation with brief videos.
    • Flipgrid (, for example, allows professors to posit a video question to which students may respond with their own video responses.
  • Quizzing Assessments – ools that utilize close-ended questions that provide a quick check of student understanding are also available.
    • Quizizz ( and
    • Kahoot ( are relatively quick and convenient to use as a wrap up to instruction or a review of concepts taught.

Integration of technology is aligned to sound formative assessment design. Formative assessment is most valuable when it addresses student understanding, progress toward competencies or standards, and indicates concepts that need further attention for mastery. Additionally, formative assessment provides the instructor with valuable information on gaps in their students’ learning which can imply instructional changes or additional coverage of key concepts. The use of tech tools can make the creation, administration, and grading of formative assessment more efficient and can enhance reliability of assessments when used consistently in the classroom. Selecting one that effectively addresses your assessment needs and enhances your teaching style is critical.

more on digital assessment in this IMS blog

academic library collection data visualization

Finch, J. f., & Flenner, A. (2016). Using Data Visualization to Examine an Academic Library Collection. College & Research Libraries77(6), 765-778.

p. 766
Visualizations of library data have been used to: • reveal relationships among subject areas for users. • illuminate circulation patterns. • suggest titles for weeding. • analyze citations and map scholarly communications

Each unit of data analyzed can be described as topical, asking “what.”6 • What is the number of courses offered in each major and minor? • What is expended in each subject area? • What is the size of the physical collection in each subject area? • What is student enrollment in each area? • What is the circulation in specific areas for one year?

libraries, if they are to survive, must rethink their collecting and service strategies in radical and possibly scary ways and to do so sooner rather than later. Anderson predicts that, in the next ten years, the “idea of collection” will be overhauled in favor of “dynamic access to a virtually unlimited flow of information products.”  My note: in essence, the fight between Mark Vargas and the Acquisition/Cataloguing people

The library collection of today is changing, affected by many factors, such as demanddriven acquisitions, access, streaming media, interdisciplinary coursework, ordering enthusiasm, new areas of study, political pressures, vendor changes, and the individual faculty member following a focused line of research.

subject librarians may see opportunities in looking more closely at the relatively unexplored “intersection of circulation, interlibrary loan, and holdings.”

Using Visualizations to Address Library Problems

the difference between graphical representations of environments and knowledge visualization, which generates graphical representations of meaningful relationships among retrieved files or objects.

Exhaustive lists of data visualization tools include: • the DIRT Directory ( • Kathy Schrock’s educating through infographics ( infographics-as-an-assessment.html) • Dataviz list of online tools (

Visualization tools explored for this study include Plotly, Microsoft Excel, Python programming language, and D3.js, a javascript library for creating documents based on data. Tableau Public©

Eugene O’Loughlin, National College of Ireland, is very helpful in composing the charts and is found here:

p. 771 By looking at the data (my note – by visualizing the data), more questions are revealed,  The visualizations provide greater comprehension than the two-dimensional “flatland” of the spreadsheets, in which valuable questions and insights are lost in the columns and rows of data.

By looking at data visualized in different combinations, library collection development teams can clearly compare important considerations in collection management: expenditures and purchases, circulation, student enrollment, and course hours. Library staff and administrators can make funding decisions or begin dialog based on data free from political pressure or from the influence of the squeakiest wheel in a department.

more on data visualization for the academic library in this IMS blog

Software Carpentry Workshop

Minnesota State University Moorhead – Software Carpentry Workshop

Reservation code: 680510823  Reservation for: Plamen Miltenoff

Hagen Hall – 600 11th St S – Room 207 – Moorhead



Jeff – certified Bash Python, John

what is shall and what does it do. language close to computers, fast.

what is “bash” . cd, ls

shell job is a translator between the binory code, the middle name. several types of shells, with slight differences. one natively installed on MAC and Unix. born-again shell

bash commands: cd change director, ls – list; ls -F if it does not work: man ls (manual for LS); colon lower left corner tells you can scrool; q for escape; ls -ltr

arguments is colloquially used with different names. options, flags, parameters

cd ..  – move up one directory .      pwd : see the content      cd data_shell/   – go down one directory

cd ~  – brings me al the way up .        $HOME (universally defined variable

the default behavior of cd is to bring to home directory.

the core shall commands accept the same shell commands (letters)

$ du -h .     gives me the size of the files. ctrl C to stop

$ clear . – clear the entire screen, scroll up to go back to previous command

man history $ history $! pwd (to go to pwd . $ history | grep history (piping)

$ cat (and the file name) – standard output

$ cat ../

how to edit and delete files

to create new folder: $ mkdir . – make directory

text editors – nano, vim (UNIX text editors) .      $ nano draft.txt .  ctrl O (save) ctr X (exit) .
$ vim . shift  esc (key)  and in command line – wq (write quit) or just “q”

$ mv draft.txt ../data . (move files)

to remove $ rm thesis/:     $ man rm

copy files       $cp    $ touch . (touches the file, creates if new)

remove $ rm .    anything PSEUDO is dangerous   Bash profile: cp -i

*- wild card, truncate       $ ls analyzed      (list of the analyized directory)

stackoverflow web site .


head command .  $head (check only the first several lines of a large file

$ for filename in basilisk.dat unicorn.dat . (making a loop = multiline)

> do (expecting an action) do

> head -n 3 $filename . (3 is for the first three line of the file to be displayed and -n is for the number)

> done

for doing repetitive functions


$ for filename in *.dat ; do head -n 3$x; done

$ for filename in *.dat ; do echo $filename do head -n 3$x; done

$ echo $filename (print statement)

how to loop

$ for filename in *.dat ; do echo $filename ; echo head -n 3 $filename ; done

ctrl c or apple comd dot to get out of the loop


$ for filename in *.dat

> do

> $filename

> head -n  10 (first ten files ) $filename | tail  -n 20 (last twenty lines)

$ for filename  in *.dat

>> echo  $filename
>> done

$ for filename in *.dat
>> do
>> cp $filename orig_$filename

history > something else

$ head something.else


another function: word count

$ wc *.pdb  (protein databank)

$ head cubane.pdb

if i don;t know how to read the outpun $ man wc

the difference between “*” and “?”

$ wc -l *.pdb


wc -l *.pdb > lenghts.txs

cat lenghts.txt

$ for fil in *.txt
>>> do
>>> wc -l $fil

by putting a $ sign use that not the actual text.


nano . The entire point of shell is to automate

$ bash (exectubale) to run the program

rwx – rwx – rwx . (owner – group -anybody)


$ file

$path .

$ echo $PATH | tr “:” “\n”








$ export PATH=$PWD:$PATH

(this is to make sure that the last version of Python is running)

$ ls ~ . (hidden files)        

$ ls -a ~

$ touch .bach_profile .bashrc

$history | grep PATH

   19   echo $PATH

   44  echo #PATH | tr “:” “\n”

   45   echo $PATH | tr “:” “\n”

   46   export PATH=$PWD:$PATH

   47  echo #PATH | tr “:” “\n”

   48   echo #PATH | tr “:” “\n”

   55  history | grep PATH


wc -l “$@” | sort -n ($@  – encompasses eerything. will process every single file in the list of files


$ chmod (make it executable)


$ find . -type d . (find only directories, recursively, ) 

$ find . -type f (files, instead of directories)

$ find . -name ‘*.txt’ . (find files by name, don’t forget single quotes)

$ wc -l $(find . -name ‘*.txt’)  – when searching among direcories on different level

$ find . -name ‘*.txt’ | xargs wc -l    –  same as above ; two ways to do one and the same




Link to the Python Plotting :

C and C++. scripting purposes in microbiology (instructor). libraries, packages alongside Python, which can extend its functionality. numpy and scipy (numeric and science python). Python for academic libraries?

going out of python $ quit () .      python expect beginning and end parenthesis

new terminal needed after installation. anaconda 5.0.1

python 3 is complete redesign, not only an update.

jupyter crashes in safari. open in chrome. spg engine maybe

to start python in the terminal $ python

>> variable = 3

>> variable +10

several data types.

stored in JSON format.

command vs edit code.  code cell is the gray box. a text cell is plain text

markdown syntax. format working with git and github .  search explanation in

hackMD (use your GIthub account)

PANDOC – translates different data formats.

print is a function

in what cases i will run my data trough Python instead of SPSS?

python is a 0 based language. starts counting with 0 – Java, C, P

atom_name = ‘helium ‘
print(atom_name[0])                  string slicing and indexing is tricky

atom_name = ‘helium ‘
atom_name = ‘helium ‘
print(atom_name[7])                python does not know how to slice it
synthax of python is        start : end : countby/step
string versus list .   string is in a single quote, list will have brakets
strings allow me to work not only w values, revers the string
atom_name = ‘helium lithium beryllium’
muillyreb muihtil muileh
Atom_name = ‘helium’
len (atom_name)                                     6 .             case sensitive
to clean the memory, restart the kernel
objects in Python have different types. adopt a class, value may have class inherent in its defintion
print (type(’42’)) .   Python tells me that it is a string
print (type(42)) .    tells e it is a string
to combine integer and letter: print (str(1) + ‘A’)
converting a string to integer . : print (1 + int(’55’)) .    all the same type
translation table. numerical representation of a string
print (‘half is’, 1 / 2.0)
built in functions and help
print is a function, lenght is a function (len); type, string, int, max, round,
Python does not explain well why the code breaks
ASCI character set – build in Python conversation
libraries – package:
function “import”
 Saturdady afternoon
reading .CSV in Python
**For windows users only: set up git 
python is object oriented and i can define the objects
python creates its own types of objects (which we model) and those are called “DataFrame”
method applied it is an attribute to data that already exists. – difference from function . is function – it does not take any arguments
data.columns . is a method
print (data.T) .  transpose.  not easy in Excel, but very easy in Python
print (data.describe()) .
%matplotlib inline teling Jupyter notebook

import pandas

data = pandas.read_csv(‘/Users/plamen_local/Desktop/data/gapminder_gdp_oceania.csv’ , index_col=’country’)

GD plot 2 is the most well known library.

xelatex is a PDF engine.  reST restructured text like Markdown.  google what is the best PDF engine with Jupyter

four loops .  any computer language will have the concept of “for” loop. In Python: 1. whenever we create a “for” loop, that line must end with a single colon

2. indentation.  any “if” statement in the “for” loop, gets indented

pedagogically sound Minecraft examples

FridayLive!! Oct 27 THIS WEEK 2:00 PM EDT 

Minecraft for Higher Ed? Try it. Pros, Cons, Recommendations? 

Description: Why Minecraft, the online video game? How can Minecraft improve learning for higher education?
We’ll begin with a live demo in which all can participate (see “Minecraft for Free”).
We’ll review “Examples, Not Rumors” of successful adaptations and USES of Minecraft for teaching/learning in higher education. Especially those submitted in advance
And we’ll try to extract from these activities a few recommendations/questions/requests re Minecraft in higher education.


Minecraft Education Edition:
(more info:


Minecraft empathy skills 

coding w MineCraft

Minecraft for Math

Higher Ed: 

Minecraft Higher Education?

Using MCEE in Higher Education

Why NOT to use minecraft in education:

College Students Get Virtual Look at the Real World with ‘Minecraft’

Carnegie Mellon University uses the game-based learning tool to help students demonstrate engineering skills. SEP182017

Using Minecraft in Higher Education!topic/minecraft-teachers/cED6MM0E0bQ

Using MinecraftEdu – Part 1 – Introduction

Physics with Minecraft example

Chemistry with Minecraft example


other disciplines


Does learning really happen w Minecraft?

Callaghan, N. (2016). Investigating the role of Minecraft in educational learning environments. Educational Media International53(4), 244-260. doi:10.1080/09523987.2016.1254877

Noelene Callaghan dissects the evolution in Australian education from a global perspective. She rightfully draws attention (p. 245) to inevitable changes in the educational world, which still remain ignored: e.g., the demise of “traditional” LMS (Educase is calling for their replacement with digital learning environments and so does the corporate world of learning: ), the inevitability of BYOD (mainly by the “budget restrictions and sustainability challenges” (p. 245); by the assertion of cloud computing, and, last but not least, by the gamification of education.

p. 245 literature review. In my paper, I am offering more comprehensive literature review. While Callaghan focuses on the positive, my attempt is to list both pros and cons:


  1. 246 General use of massive multiplayer online role playing games (MMORPGs)

levels of interaction have grown dramatically and have led to the creation of general use of massive multiplayer online role playing games (MMORPGs)

  1. 247 In teaching and learning environments, affordances associated with edugames within a project-based learning (PBL) environment permit:
  • (1)  Learner-centered environments
  • (2)  Collaboration
  • (3)  Curricular content
  • (4)  Authentic tasks
  • (5)  Multiple expression modes
  • (6)  Emphasis on time management
  • (7)  Innovative assessment (Han & Bhattacharya, 2001).

These affordances develop both social and cognitive abilities of students


Nebel, S., Schneider, S., Beege, M., Kolda, F., Mackiewicz, V., & Rey, G. (2017). You cannot do this alone! Increasing task interdependence in cooperative educational videogames to encourage collaboration. Educational Technology Research & Development65(4), 993-1014. doi:10.1007/s11423-017-9511-8

Abrams, S. S., & Rowsell, J. (2017). Emotionally Crafted Experiences: Layering Literacies in Minecraft. Reading Teacher70(4), 501-506.

Nebel, S., Schneider, S., & Daniel Rey, G. (2016). Mining Learning and Crafting Scientific Experiments: A Literature Review on the Use of Minecraft in Education and Research. Source: Journal of Educational Technology & Society, 19(192), 355–366. Retrieved from

Cipollone, M., Schifter, C. C., & Moffat, R. A. (2014). Minecraft as a Creative Tool: A Case Study. International Journal Of Game-Based Learning4(2), 1-14.

Niemeyer, D. J., & Gerber, H. R. (2015). Maker culture and Minecraft : implications for the future of learning. Educational Media International52(3), 216-226. doi:10.1080/09523987.2015.1075103

Nebel, S., Schneider, S., & Daniel Rey, G. (2016). Mining Learning and Crafting Scientific Experiments: A Literature Review on the Use of Minecraft in Education and Research. Journal of Educational Technology & Society, 19(192), 355–366. Retrieved from


Wilkinson, B., Williams, N., & Armstrong, P. (2013). Improving Student Understanding, Application and Synthesis of Computer Programming Concepts with Minecraft. In The European Conference on Technology in the Classroom 2013. Retrieved from

Berg Marklund, B., & Alklind Taylor, A.-S. (2015). Teachers’ Many Roles in Game-Based Learning Projects. In Academic Conferences International Limited (pp. 359–367). Retrieved from

Uusi-Mäkelä, M., & Uusi-Mäkelä, M. (2014). Immersive Language Learning with Games: Finding Flow in MinecraftEdu. EdMedia: World Conference on Educational Media and Technology (Vol. 2014). Association for the Advancement of Computing in Education (AACE). Retrieved from

Birt, J., & Hovorka, D. (2014). Effect of mixed media visualization on learner perceptions and outcomes. In 25th Australasian Conference on Information Systems (pp. 1–10). Retrieved from

Al Washmi, R., Bana, J., Knight, I., Benson, E., Afolabi, O., Kerr, A., Hopkins, G. (2014). Design of a Math Learning Game Using a Minecraft Mod.

more on Minecraft in this IMS blog

effective presentations and AR

augmented reality takeover. It’s played out at Snapchat and Facebook, at Google and Apple. Companies are using AR to design carssell furniture, make little digital sharks swim around your breakfast table. What if Prezi could apply that same technology to make better presentations?
the product isn’t ready for a public launch yet. Prezi has enlisted a select group of influencers to try out the AR tools and offer feedback before the company releases a beta version.

more on effective presentations in this IMS blog

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