Data Sharing, Distribution and Updating Using Social Coding Community Github and LaTeX Packages in Graduate Research

Data Sharing, Distribution and Updating Using Social
Coding Community Github and LATEX Packages in Graduate Research
Presented at
Integration of the Education and Science: Challenges of the Modern World
Kazakh-Russian International University
Aktobe, Kazakhstan
Polina Lemenkova
pauline dot lemenkova at gmail dot com
May 13, 2015

Table of Contents
Outline
1. Introduction
GitHub. What Does is Mean?
GitHub: Shared Creativity
GitHub: Creative Sharing
2. Advantages of Web-Service GitHub
LATEX: Advantages over Traditional Text Editors
3. How to Create Personal Repository ?
Step 1: Key Generation
Step 2: User Registration
Step 3: Generating Project
Step 4: Maintaining Project Push and Update
4. Typesetting Thesis in LATEX
5. Why Using GitHub ?
Functionality of GitHub
Advantages of GitHub in Academia
System of Control and Revision
Maintained Privacy
Online Feature of GitHub: Data-Sharing
6. A Case Study of Using GitHub
Project Interface in the Github Environment
Example of Research Progress
Adding New Data to the Project
Access to the Project
7. Popularization
8. Conclusion
9. Discussion
10. Résumé
11. Thanks
12. Bibliography
Polina Lemenkova Data Sharing, Distribution and Updating Using ... Github and LATEX May 13, 2015 2 31

Introduction GitHub. What Does is Mean?
Some Facts
• Octocat (Octopus + Cat) is a symbol of
GitHub. It symbolizes sharing a project.
• GitHub is available for free which is useful
for students and researchers
• Slogan of GitHub: ’Social Coding’, i.e. ’let’s
code it together’.
• It refers to the programming, but in this
presentation I show using GitHub for MSc
thesis
• GitHub - a web-service for hosting (i.e.
serving and maintenance) of IT-projects
online, as well as their development by
multiple authors (incl. graduate projects
development).
• GitHub is initially aimed at version control
system Git (used in programming)
• GitHub is written in the programming
language "Erlang" and "Ruby", a framework
Ruby on Rails
• GitHub was created by GitHub, Inc, USA.
The ﬁrst private repository was established
in 2008.

Introduction GitHub: Shared Creativity
GitHub: Shared Creativity
GitHub allows viewing and editing texts: make edits, change current versions in collective access;
work together on the current version of the project; add new colleagues for collective work
(convenient, for example, when a group of students write a common ﬁeldwork report). GitHub
maintains colored syntax highlighting: added parts of code/text are colored green, deleted parts of
code/text – red. Example: below (fragment of my MSc thesis code).

Introduction GitHub: Creative Sharing
GitHub: Creative Sharing
• Github allows adding various data types:
code, graphics, etc.
• Github allows control latest changes,
discuss and discuss work with students,
post any comments directly into the text,
add online comments
• Github allows registered users to add
current version changes to the repository of
the current project.
• Github keeps all update versions in the
current projects online
• Github gives the opportunity for data sharing
• Github enables coworking

Advantages of Web-Service GitHub
Advantages of Web-Service GitHub
• Online repositories
• Possibilities for co-authorship
• Creating PhD/MSc/BSc theses
• Presenting research works
• Writing and updating articles
• Archive of scientiﬁc works
• Sharing with colleagues
• Notiﬁcation of current updates

Advantages of Web-Service GitHub LATEX : Advantages over Traditional Text Editors
LATEX : Advantages over Traditional Text Editors
There are a number of drawbacks when using traditional programs for writing theses (e.g., MS
Word). These difficulties are essential when writing a thesis:
• Continuous numbering of the test and illustrations breaks when changing or adding new ones
in the middle of the text (which must be corrected manually)
• In case of MS Word, student has to double-check all references to literary sources again,
which complicates the work and leads to mechanical difficulties and lengthy monotonous
corrections.
• LATEX has a built-in flexible system of bibliographic cross-referencing in the list of references,
which enables making automatic linking to the bib sources, as well as updating links.
• LATEX has a built-in BibTeX package that enables compiling bibliography in active mode and
leaves hyper refs a d live links toreferences, i.e. Instantly editable if necessary.

How to Create Personal Repository ? Step 1: Key Generation
Step 1: Key Generation

How to Create Personal Repository ? Step 2: User Registration
Step 2: User Registration
git conﬁg - global user.email ’youexample.com’
git conﬁg - global user.name ’Your Name’ set up
user’s account default identity

How to Create Personal Repository ? Step 3: Generating Project
Step 3: Generating Project
Key Commands and Tools: ’git init’ - initiation project from scratch. ’git add
files’ - selecting all files for the project. (texts,
tables, graphs, maps, figures).

How to Create Personal Repository ? Step 4: Maintaining Project Push and Update
Project Push and Update
• git commit -a -m ’name of update’
• e.g.: git commit -a -m ’added tables No 14,
15, 17’
• ’git diff’ - a key command of GitHub,
• ’git diff’ - detects and recognizes all updates
in the text
• ’git diff’ highlights them green/red,
respectively

Typesetting Thesis in LATEX
Typesetting Thesis in LATEX
Example of structuring text in a thesis with the help of mark up language used to highlight text
when writing codes with a high level of nesting, allows you to quickly navigate the work:
paragraphs, highlighting text, indentation, multi-level markings, making tabs, hierarchical
structuring (chapters, sections, sub-sections, paragraphs), multi-level indents from the red line.
This allows to quickly read and navigate within the text.

Why Using GitHub ? Functionality of GitHub
Syntax Coloring
• Important feature of Github: built-in color
management for updated code
• All recent updates are syntactically
highlighted green in the command line
• Added text, lines and whole fragments and
paragraphs of paragraphs are colored green
• On the contrary, selected sections of text
deleted from the last session are colored
red.

Why Using GitHub ? Advantages of GitHub in Academia
Advantages of GitHub in Academia
Time Monitoring
Using GitHub facilitates monitoring research progress and to assess the work done recently, to
timely response to the comments and corrections of colleagues.
Retrospective Editing
Retrospective and comparative editing of texts in the Github environment allows to return to the
old, previous version of the work, saved a while ago, to cancel updates.

Why Using GitHub ? System of Control and Revision
System of Control and Revision
All versions and changes of the thesis are recorded and available in the system. Thus, using
GitHub revision control system and text code management, the project was regularly updated.
Hence, supervisors can regularly monitor the project.

Why Using GitHub ? Maintained Privacy
Unpublished Works
Both public and private repositories are maintained: the colleague/co-author/supervisors may
receive private links to the current version of research and have access to the work.

Why Using GitHub ? Online Feature of GitHub: Data-Sharing
Online Feature of GitHub: Data-Sharing
Github’s use of the standard command line
interface in programming
• Adding current version changes to the
repository of the current project.
• Supports both a public repository and a
closed one in limited access (private).
• Keeping closed unpublished works, with
restricted access to coworkers.
• Successfully defended dissertations,
master’s projects and theses can be posted
in open access.
• Access is conﬁgured for both the general
public and the university archive.
• Data can be stored there for an unlimited
time.

A Case Study of Using GitHub
A Case Study of Using GitHub
A case study of using GitHub: my MSc thesis.
• MSc Thesis “Seagrass Mapping and Monitoring
Along the Coasts of Crete, Greece”, defended in
Netherlands, University of Twente, Faculty of GIS
and Earth Observation, 2011.
• Written using text editor LATEX using GitHub
• Original source: on my GitHub webpage.

A Case Study of Using GitHub Project Interface in the Github Environment
Project Interface in the Github Environment
Opportunities
GitHub: excellent opportunities in academia for supervisors, students, lecturers, researchers.
Monitoring
The use of LATEX and Github provided timely access for the project’s supervisors to monitor
research progress
Examples
Updating Unlike traditional MS Word, combination of LATEX and Github allowed supervisors to
check current progress on-line as updates, comments and corrections made.

A Case Study of Using GitHub Example of Research Progress
Example of Research Progress
New text is highlighted in green, deleted
paragraphs are highlighted in red.
Current research progress can be easily
monitored and speciﬁc project updates
highlighted and commented

A Case Study of Using GitHub Adding New Data to the Project
Adding New Data to the Project

A Case Study of Using GitHub Access to the Project
Access to the Project

Popularization
Actuality of Using GitHub
Audience
Despite obvious advantages and prospects of the GitHub service, the majority of its users are
programmers and IT specialists. Using GitHub in academia is still limited.
Popularization in Academia
There is an need to popularize and demonstrate the GitHub service and environment in the
student and academic environment: in research centers, universities, institutes.
Examples
Geologists: Getting acquainted with GitHub would be of especial advantage for faculties of natural
and Earth sciences, since they often have common ﬁeldwork data and projects.

Conclusion
Conclusion
Current problem with GitHub and LATEX is their non-popularity in academia caused by following
reasons.
Student Works
Some students are not informed about the LATEX or GitHub and do not know how to use them. The
functionality of these tools, multifunctional environments should be popularized.
Difﬁculty of Learning Curve
GitHub and LATEX are sometimes regard ed as difﬁcult programs. The basics of using LATEX and
GitHub should be initially studied for some time, but it is rewarding. Further advantages of using
TEX and GitHub are obvious and worth the efforts and time to master them.
Examples
Advantages: Joint combination of using LATEX and GitHub facilitates writing, typesetting and
managing versions upgrades while working on a project.

Discussion
Discussion
Opportunities
Traditional for IT industry and programmers, GitHub offers great opportunities for effective
collaboration such as ’student-supervisor’ or ’group of students’ or ’group of colleagues’. Unlike
traditional programs, the use of innovative technologies of text editors, such as LATEX and data
archiving such as GitHub allows supervisor to monitor student’s research progress.
Advantages
A great advantage of GitHub consists in its color syntax and maintaining history of updates
versions. The presentation demonstrated conceptual principles of the Github and LATEX.
Possibilities
The possibilities for collaborative data sharing, research progress updating and creative works are
illustrated. Current work is a technical illustration of using IT in education.

Résumé
Résumé
Résumé
This work aimed to give an example of the effective use of the GitHub web service specifically in
an academic environment. The case study was given to a MSc thesis that was written completely
using LATEX and GitHub. The presentation illustrated how specifically one can apply new
technologies and innovative approaches in the educational environment.
Highlights
Technical issues of running project, creating repositories, making updates, adding new files to the
system are demonstrated with a series of screenshot illustrations of the process. Important
conceptual features and advantages of using Github and LATEX in the academic environment are
listed and discussed.

Thanks
Thanks
Thank you for attention !

Bibliography
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