As we said on the first class, this course will have a lot of homework. They are mandatory, even if you are doing the course for a second time. One of the key ideas of this course is structure. We begin with structured documents, which we write in the RStudio system using the RMarkdown format.
Each one has to download a paper from the list at the end of this page, and create a RMarkdown document with the same content and the same structure. It does not need to look similar, but must have the same structure. You must be able to Knit the document and get a correct HTML output. I recommend that you copy-and-paste the paper into RStudio text editor.
Please follow the instructions we gave on class 2 and class 3. It is also a good idea to use the RMakrdown Cheatsheet and the RMarkdown Reference Guide. Both can also be found under the Help menu in RStudio. You may also watch the following videos:
Send your answers to andres.aravena+cmb@istanbul.edu.tr. If you have any question, ask it on the forum at https://groups.google.com/d/forum/iu-cmb. Each student will do a different document, depending on the last digit of his/her student number. For example, if your student number is 0405123456, then you should work on the document number 6. Our University has access to many journals. All these documents can be downloaded at the University. If you cannot download them at home, try at the university.
The set of documents is this:
- Alon, Uri. “How To Give a Good Talk.” Molecular Cell 36, no. 2 (October 23, 2009): 165–67. https://doi.org/10.1016/j.molcel.2009.10.007.
- Alon, Uri. “How To Choose a Good Scientific Problem.” Molecular Cell 35, no. 6 (2009): 726–28. https://doi.org/10.1016/j.molcel.2009.09.013.
- Haak, Wolfgang, Iosif Lazaridis, Nick Patterson, Nadin Rohland, Swapan Mallick, Bastien Llamas, Guido Brandt, et al. “Massive Migration from the Steppe Was a Source for Indo-European Languages in Europe.” Nature 522, no. 7555 (2015): 207–11. https://doi.org/10.1038/nature14317.
- Hunnicutt, Barbara Jeanine, and Martin Krzywinski. “Points of View: Neural Circuit Diagrams.” Nature Methods 13, no. 3 (2016): 189. https://doi.org/10.1038/nmeth.3777.
- Sarner, Moya. “Unanswered Emails Were the Bane of My Life - until I Spent a Month in Search of Inbox Nirvana.” The Guardian, 2018. https://www.theguardian.com/technology/2018/feb/08/unanswered-emails-inbox-nirvana-bane-of-life.
- Munafò, Marcus R., and George Davey Smith. “Repeating Experiments Is Not Enough.” Nature 553 (2018): 399–401. https://doi.org/10.1038/d41586-018-01023-3.
- “Is Coffee Consumption Associated With Lower Risk for Death?” Annals of Internal Medicine, 2017, 936426. https://doi.org/10.7326/P17-9041.
- Walkowiak, Malte, and Andreas Nehring. “Using ChemDuino, Excel, and PowerPoint as Tools for Real-Time Measurement Representation in Class.” Journal of Chemical Education, 2016, acs.jchemed.5b00923. https://doi.org/10.1021/acs.jchemed.5b00923.
- Wong, Victor S. C. “Lessons from a Postdoc Gone Wrong.” Science 363, no. 6424 (2019): 314–314. https://doi.org/10.1126/science.363.6424.314.
- Ioannidis, John P A. “Why Most Published Research Findings Are False.” PLoS Med 2, no. 8 (2005). https://doi.org/10.1371/journal.pmed.0020124.