Topic,Homework,Deadline,URL
[Syllabus](https://svenbuerki.github.io/EEB603_Reproducible_Science/index.html),,,[Syllabus](https://svenbuerki.github.io/EEB603_Reproducible_Science/index.html)
[Chapt. 1 - part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#23_What_is_Reproducible_Science),Read the syllabus carefully and ask questions if you need any clarification,,[Chapter 1](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#2_Chapter_1) & [Chapter 2](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#3_Chapter_2)
[Chapt. 1 - part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#23_What_is_Reproducible_Science),Read your assigned publication for Chapter 1 - part A and identify its reproducibility challenges,,[Part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#partA)
[Chapt. 1 - part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#24_What_Factors_Break_Reproducibility),Read Baker (2016) and Summary (pages 5-19) of the Reproducibility and replicability in science report (from The National Academies Press),,[Part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#partA) & [Part B: Set your R Markdown environment](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#233_Set_your_R_Markdown_environment)
[Chap. 2 - part A: Learning the basics](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#32_PART_A:_Learning_the_Basics),[Install software](https://svenbuerki.github.io/EEB603_Reproducible_Science/index.html#82_Installing_Software) and Sign up for bioinformatics tutorial (see [Syllabus](https://svenbuerki.github.io/EEB603_Reproducible_Science/index.html#1013_Google_Sheet) ),,"[Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#13_PART_B:_Tables,_Figures_and_References)"
Review Chap. 2 - part A and [Chap. 2 - part B: Setting Your R Markdown Document](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#33_PART_B:_Setting_Your_R_Markdown_Document),Complete Chapter 2 - part A,,"[Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#13_PART_B:_Tables,_Figures_and_References)"
"Complete [Chap. 2 - Part B: Setting Your R Markdown Document](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#33_PART_B:_Setting_Your_R_Markdown_Document) (we will start at the ""Install R Dependencies and Load Packages"" section)",Complete the sections of Chapter 2 – Part B up to the end of the “YAML Metadata Section.” Read the “Install R Dependencies and Load Packages” section to familiarize yourself with its content and purpose,,"[Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#13_PART_B:_Tables,_Figures_and_References) & [Part C](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#14_PART_C:_Advanced_R_and_R_Markdown_settings)"
"Start [Chap. 2 - Part C: Tables, Figures, and References](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#34_PART_C:_Tables,_Figures_and_References) and complete it until the end of the ""Cross-reference Tables and Figures in the Text"" section","Make sure that your ""Chapter2_partB.Rmd"" file knits successfully and includes all the material from Chapter 2 - Part B",,[Part D](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#15_PART_D:_User_Defined_Functions_in_R)
"Complete [Chap. 2 - part C: Tables, Figures and References](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#34_PART_C:_Tables,_Figures_and_References) (we will start at section 3.4.7 ""Cite References in the Text"")","Make sure that your `Chapter2_partC.Rmd` file knits successfully and includes all the material up to the end of section [3.4.6 ""Cross-reference Tables and Figures in the Text""](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#346_Cross-reference_Tables_and_Figures_in_the_Text). Refer to section 3.4.4.2 ""Double Table in Caption"" for guidance on how to debug this issue if needed",,[Part D](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#15_PART_D:_User_Defined_Functions_in_R)
[Chap. 2 - part D: Advanced R and R Markdown settings](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#35_PART_D:_Advanced_R_and_R_Markdown_settings),"Complete Chap. 2 - part C: Tables, Figures and References",,[Publications and Resources for bioinformatic tutorials](https://svenbuerki.github.io/EEB603_Reproducible_Science/index.html#7_Publications__Textbooks)
[Chap. 2 - part E: User-Defined Functions in R](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#36_PART_E:_User-Defined_Functions_in_R),Read material presented in Chap. 2 - part E: User-Defined Functions in R,,[Chapter 3](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#4_Chapter_3)
"Complete [Chap. 2 - part E: User-Defined Functions in R](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#36_PART_E:_User-Defined_Functions_in_R) (we will start at section 3.6.8 Create, Name, and Access Elements of a List in R)","Complete Chap. 2 - part E up to section 3.6.8 Create, Name, and Access Elements of a List in R",,[Chapter 4](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#5_Chapter_4)
[Chap. 3: A roadmap to implement reproducible science](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#4_Chapter_3),Read material presented in Chapter 3,,[Chapter 5 - Part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#partDM)
[Chap. 4: Open science and CARE principles](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#5_Chapter_4),Read material presented in Chapter 4,,[Chapter 5 - Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#repcode)
Complete Chap. 4 (group activities on [CARE Principles and comparing FAIR & CARE Principles](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#551_%F0%9F%A4%9D_Group_Sharing_and_Discussions)),Read material presented in Chapter 5 - Data Management,Turn in tutorial for Chap. 7,[Chapter 6 - Part A](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#getpub)
[Chap. 5: Data Management](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#partDM),Read material presented in Chapter 5 - Reproducible Code,Upload tutorial of Chap. 7 on Google Drive,[Chapter 6 - Part B](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#writpub)
Complete [Chap. 5: Data Management](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#partDM) and [Chap. 5: Reproducible Code](https://svenbuerki.github.io/EEB603_Reproducible_Science/Chapters.html#repcode),Read material presented in Chapter 5 - Reproducible Code,Turn in tutorial for Chap. 8,
Bioinfo. tutorial - Chap. 7,Students work on bioinformatics tutorials and their individual projects,Upload tutorial of Chap. 8 on Google Drive,
Bioinfo. tutorial - Chap. 8,Students work on bioinformatics tutorials and their individual projects,Turn in tutorial for Chap. 9,
Bioinfo. tutorial - Chap. 8,Students work on bioinformatics tutorials and their individual projects,Upload tutorial of Chap. 9 on Google Drive,
Bioinfo. tutorial - Chap. 9,Students work on bioinformatics tutorials and their individual projects,Turn in tutorial for Chap. 10,
Bioinfo. tutorial - Chap. 9,Students work on bioinformatics tutorials and their individual projects,Upload tutorial of Chap. 10 on Google Drive,
Bioinfo. tutorial - Chap. 10,Students work on bioinformatics tutorials and their individual projects,Turn in tutorial for Chap. 11,
Bioinfo. tutorial - Chap. 10,Students work on bioinformatics tutorials and their individual projects,Upload tutorial of Chap. 11 on Google Drive,
Bioinfo. tutorial - Chap. 11,Students work on bioinformatics tutorials and their individual projects,Turn in tutorial for Chap. 12,
Bioinfo. tutorial - Chap. 11,Students work on bioinformatics tutorials and their individual projects,Upload tutorial of Chap. 12 on Google Drive,
Bioinfo. tutorial - Chap. 12,Students work on bioinformatics tutorials and their individual projects,,
Bioinfo. tutorial - Chap. 12,Students work on bioinformatics tutorials and their individual projects,,
Individual projects - Q&A,Students work on bioinformatics tutorials and their individual projects,,
Individual projects - Q&A,Upload slides of individual projects (on [Google Drive](https://drive.google.com/drive/folders/1MZt5kNKusCv6OeZpjuuPxUiqBaoQVQAc?usp=sharing)),Turn in ind. projects (on [Google Drive](https://drive.google.com/drive/folders/1MZt5kNKusCv6OeZpjuuPxUiqBaoQVQAc?usp=sharing)),
Oral presentations of individual projects,,,
Oral presentations of individual projects,,,