minor fixes to week 11

3mmaRand · Dec 5, 2023 · 8e2bf89 · 8e2bf89
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diff --git a/core/core.qmd b/core/core.qmd
@@ -27,19 +27,5 @@ This week there is a drop-in session where you can ask questions about the mater
 
 ## Week 11 Core 3 Research Compendia and Reproducible Reporting
 
-<!-- Before -->
-<!--  (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown and BIO00058M-Data-science-2020/slides/04_advanced_rmarkdown.html) -->
-<!-- Literate programming -->
-<!-- What is quarto -->
-<!-- markdown basics: text, code chunks, headings -->
-<!-- yaml -->
-<!-- automatic numbering of figures and tables -->
-<!-- cross references -->
-<!-- special characters -->
-<!-- citations -->
-
-<!-- Workshop -->
-
-<!-- practice doing the above with your project and data -->
-
+This week we will cover the “Research compendium” and reproducible reporting which are part of the assessment. Research Compendium that is a documented collection of all the digital parts of the research project including data (or access to data), code and outputs. The Compendium might be a single Quarto/RStudio Project, or it might be a folder including an Quarto/RStudio Project and some additional materials including the description of unscripted processing. The collection is organised and documented in such a way that reproducing all the results is straightforward for another individual. We will also cover reproducible reporting which means using literate programming to weave together code and text together in a single document. Quarto is a multi-language literate programming tool (very like R Markdown).
 
diff --git a/core/week-11/overview.qmd b/core/week-11/overview.qmd
@@ -5,7 +5,7 @@ toc: true
 toc-location: right
 ---
 
-This week we will cover the "Research compendium" which is part of the assessment. A research compendium can be a single RStudio Project but we have broadened the definition. It is a documented collection of all the digital parts of the research project including data (or access to data), code and outputs. The collection is organised and documented in such a way that reproducing all the results is straightforward for another individual.
+This week we will cover the “Research compendium” and reproducible reporting which are part of the assessment. Research Compendium that is a documented collection of all the digital parts of the research project including data (or access to data), code and outputs. The Compendium might be a single Quarto/RStudio Project, or it might be a folder including an Quarto/RStudio Project and some additional materials including the description of unscripted processing. The collection is organised and documented in such a way that reproducing all the results is straightforward for another individual. We will also cover reproducible reporting which means using literate programming to weave together code and text together in a single document. Quarto is a multi-language literate programming tool (very like R Markdown).
 
 ### Learning objectives
 

diff --git a/core/week-11/study_before_workshop.qmd b/core/week-11/study_before_workshop.qmd
@@ -36,12 +36,15 @@ These slides are a guide to Research compendium.
 *Stage 3 Integrated Masters students are expected to submit a Research
 Compendium that is a documented collection of all the digital parts of
 the research project including data (or access to data), code and
-outputs. The collection is organised and documented in such a way that
+outputs. The Compendium might be a single Quarto/RStudio Project, or it
+might be a folder including an Quarto/RStudio Project and some
+additional materials including the description of unscripted processing.
+The collection is organised and documented in such a way that
 reproducing all the results is straightforward for another individual.*
 
 *Students will be assessed on the technical complexity, completeness and
 organisation of their compendium and the completeness, reproducibility
-and clarity of their documentation at the project and code/process
+and clarity of their documentation at the project and the code/process
 level. Marking will focus on the reproducibility of the results and the
 clarity of the decision making processes rather than the interpretation
 of the results which is covered in the report. There is no word or size
@@ -56,18 +59,21 @@ and minimal. Extraneous text, code or files will be penalised.*
 ::: {style="font-size: 65%;"}
 *Stage 3 Integrated Masters students are expected to submit a Research
 Compendium that is a* **documented collection of all the digital parts
-of the research project** *including data (or access to data), code and
-outputs. The collection is* **organised and documented in such a way
-that reproducing all the results is straightforward** *for another
-individual.*
+of the research project including data (or access to data), code and
+outputs.** *The Compendium might be a single Quarto/RStudio Project, or
+it might be a folder including an Quarto/RStudio Project and some
+additional materials including the description of unscripted
+processing.* **The collection is organised and documented in such a way
+that reproducing all the results is straightforward for another
+individual.**
 
 *Students will be assessed on the* **technical complexity, completeness
-and organisation of their compendium** *and the* **completeness,
+and organisation of their compendium and the completeness,
 reproducibility and clarity of their documentation at the project and
-code/process level.** *Marking will focus on the reproducibility of the
-results and the clarity of the decision making processes rather than the
-interpretation of the results which is covered in the report. There is
-no word or size limit for any part of the compendium but its contents
+the code/process level.** *Marking will focus on the reproducibility of
+the results and the clarity of the decision making processes rather than
+the interpretation of the results which is covered in the report. There
+is no word or size limit for any part of the compendium but its contents
 should be concise and minimal. Extraneous text, code or files will be
 penalised.*
 :::

diff --git a/index.qmd b/index.qmd
@@ -6,17 +6,17 @@ toc-location: right
 
 # Overview
 
-You are *either* 
+You are *either*
 
--  an integrated masters student doing BIO00088H Group Research Project *or* 
--  an MSc Bioinformatics student doing BIO00070M Research, Professional and Team Skills
+-   an integrated masters student doing BIO00088H Group Research Project *or*
+-   an MSc Bioinformatics student doing BIO00070M Research, Professional and Team Skills
 
 For students doing BIO00088H, Data Analysis compromises six workshops covering computational skills needed in your project. Three of these are core and taken by everyone and three are specific to your project type. MSc Bioinformatics students do the Core workshops and the 'omics workshops as part of BIO00070M.
 
 The project types are:
 
 | Project                                 | Data Strand                     |
-|-----------------------------------------|---------------------------------|
+|----------------------------------------|--------------------------------|
 | Stem Cells, Jillian Barlow              | 'omics, Emma Rand               |
 | Developmental Biology, Betsy Pownal     | 'omics, Emma Rand               |
 | Microbial Ecology, Kelly Redeker        | 'omics, Emma Rand               |
@@ -26,16 +26,15 @@ The project types are:
 
 The data analysis workshops are:
 
-| Week | Data Strand              |
-|------|--------------------------|
-| 1    | Core 1                   |
-| 2    | Core 2                   |
-| 3    | omics/structure/images 1 |
-| 4    | omics/structure/images 2 |
-| 5    | omics/structure/images 3 |
-| 6    | Core 3                   |
-
-
+| Week | Data Strand                                          |
+|------|------------------------------------------------------|
+| 1    | Core 1 Organising reproducible data analyses         |
+| 2    | Core 2 File types, workflow tips and other tools     |
+| 3    | omics/structure/images 1                             |
+| 4    | omics/structure/images 2                             |
+| 5    | omics/structure/images 3                             |
+| 6    | Drop-in                                              |
+| 6    | Core 3 Research Compendia and Reproducible Reporting |
 
 ## Module Learning Outcome linked to this content
 
@@ -47,11 +46,6 @@ Students who successfully complete this module will be able to
 
 All material is on the VLE so why is this site useful? This site collects everything together in a searchable way. The search icon is on the top right.
 
+## Please cite as
 
-## Please cite as 
-
-```{r}
-#| echo: false
-cffr::cff_to_bibtex("CITATION.cff")
-```
-
+Rand E (2023). Data Analysis for Group Project. https://3mmarand.github.io/BIO00088H-data/.