1. Publishing and Sharing Sherif Farag University of North Carolina at Chapel Hill, USA

2. Publishing and Sharing Specific aim Documenting your code in a professional way and making it accessible for either the public or to a limited group.

3. Outline What is publishing ? – Dynamic vs Static – Uses of dynamic documentation – Examples of dynamic documentation What is Sharing ? – Importance of sharing source code – How to share your code – Revision control System – Examples of RCS

4. Publishing Creating a document that represent you research code in a professional way that is easy to follow and understand. Embedding code snippets into your document.

5. Publishing Dynamic VS Static StaticDynamic

6. Publishing Dynamic VS Static in Typing int a; a = 5; cout << a + 5 ; cout << b + 7 ; x = 23 print x C++, JavaPython, R ( Good) ( Not Good)

7. Publishing Dynamic VS Static Documentation A living document or dynamic document is a document that is continually edited and updated. A simple example of a living document is an article in Wikipedia, that permits anyone to freely edit its articles. A "dead" or "static" documents, such as an article in a single edition of the Encyclopaedia Britannica.

8. Publishing Uses of Dynamic Documentation A nice and detailed way of reporting/documenting your research code. Makes editing of the document easier and efficient. Can be used on a regular basis by graduate students for delivering class assignments/ lab reports as well as professional writings such as a thesis or a manuscript.

9. Publishing Examples: Knitr Is an engine for dynamic report generation with R. It is a package in the statistical programming language R that enables integration of R code into LaTeX, LyX, HTML, Markdown Knitr (R) LatexHTMLMarkdownLyx

10. Publishing Examples: Latex Before BuildingAfter Building

11. Publishing Examples: Latex Before BuildingAfter Building

12. Publishing Examples: Knitr with Latex Before BuildingAfter Building

13. Publishing Examples: Ipython Notebook IPython Notebook is a web-based interactive computational environment for creating IPython notebooks. An IPython notebook is a JSON document containing an ordered list of input/output cells which can contain code, text, mathematics, plots and rich media. iPynb (Py) LatexHTMLMarkdownPDFPython

14. Publishing Examples: IPython Notebook Before BuildingAfter Building

15. Outline What is publishing ? – Dynamic vs Static – Uses of dynamic documentation – Examples of dynamic documentation What is Sharing ? – Importance of sharing source code – How to share your code – Revision control System – Examples of RCS

16. Sharing

18. Importance of Sharing Code Is a contributing factor to the maturation of people’s programming skills. Help optimizing current version of software by reducing number of bugs within a source code (Two brains better than one !!) Make programing more plannable and more efficient by splitting tasks between programmers. Pair programming: two programmers work as a pair together on one workstation. One, the driver, writes code while the other, the observer, pointer or navigator, reviews each line of code as it is typed in.

19. Sharing How to Share Your Code CD, DVD,SD, Flash drive, …,etc Cloud: Google drive, Dropbox, BOX, StackoverFlow, …,etc Revision Control System (RCS)

20. Sharing Revision Control System (RCS) Is a software implementation of revision control that automates the storing, retrieval, logging, identification, and merging of revisions. RCS is useful for text that is revised frequently, for example programs, documentation, procedural graphics, papers, and form letters.

21. Sharing Examples of RCS SVNGit

22. Links Latex Tutorial: http://www.latex-tutorial.com/http://www.latex-tutorial.com/ Knitr: http://yihui.name/knitr/http://yihui.name/knitr/ Knitr examples: https://github.com/yihui/knitr-examples https://github.com/yihui/knitr-examples Ipython Notebook: http://ipython.org/notebook.html http://ipython.org/notebook.html GIT: https://git-scm.com/https://git-scm.com/ SVN: https://subversion.apache.org/https://subversion.apache.org/