overvew and prior study

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diff --git a/core/core.qmd b/core/core.qmd
@@ -11,7 +11,7 @@ Good organisation is important because you will want to be able to set work asid
 
 ## Week 1 Core 1 Organising reproducible data analyses
 
-This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work. We will also examine some file types and concept of tidy data.
+This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work. We will also examine some file types and the concept of tidy data.
 
 
 ## Week 2 Core 2 Workflow tips

diff --git a/core/week-1/images/reproducibility_court.png b/core/week-1/images/reproducibility_court.png
diff --git a/core/week-1/images/reproducible-matrix.jpg b/core/week-1/images/reproducible-matrix.jpg
diff --git a/core/week-1/overview.qmd b/core/week-1/overview.qmd
@@ -5,14 +5,19 @@ toc: true
 toc-location: right
 ---
 
-xxxxx
+This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work. We will also examine some file types and the concept of tidy data.
+
 
 ### Learning objectives
 
--   dd
--   dd.
--   dd
--   d
+The successful student will be able to:
+
+-   explain the organisation of files and directories in a file systems including root, home and working directories
+-   explain absolute and relative file paths
+-   explain why working reproducibly is important
+-   know how to use a project-oriented workflow to organise work
+-   be able to give files human- and machine-readable names
+-   outline some common biological data file formats
 
 ### Instructions
 
@@ -22,11 +27,6 @@ xxxxx
 
 2.  [Workshop](workshop.qmd)
 
-    i.  💻 dd.
-
-    ii. 💻 ddd
-
-    iii. 💻 ddd
 
 3.  [Consolidate](study_after_workshop.qmd)
 
diff --git a/core/week-1/workshop.qmd b/core/week-1/workshop.qmd
@@ -1,5 +1,5 @@
 ---
-title: "Workshop"
+title: "Workshop - 🚧 still in Construction"
 subtitle: "Organising Reproducible Data Analyses"
 author: "Emma Rand"
 toc: true
@@ -22,54 +22,84 @@ library(tidyverse)
 
 # Introduction
 
-
 ## Session overview
 
-In this workshop you will 
+In this workshop you will
 
 
-::: callout-note
-## Key
 
 
-:::
+# What is reproducibility?
 
-# Getting started
+-   **Reproducible: Same data + same analysis = identical results**. *"... obtaining consistent results using the same input
+data; computational steps, methods, and code; and conditions of
+analysis. This definition is synonymous with "computational
+reproducibility"* [@nationalacademiesofsciences2019]
 
+-   Replicable: Different data + same analysis = qualitatively similar
+    results. The work is not dependent on the specificities of the data.
 
-# Exercises
+-   Robust: Same data + different analysis = qualitatively similar or
+    identical results. The work is not dependent on the specificities of
+    the analysis.
 
+-   Generalisable: Different data + different analysis = qualitatively
+    similar results and same conclusions. The findings can be
+    generalised
 
-🎬 
--   Why reproducibility (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown)
--   Project organisation: folders, files
--   Project oriented workflow
--   Naming things
--   Keeping a lab book
--   Readme
--   File formats
--   Data files. Similarities and differences
-    -   Sequences data
-    -   Image data
-    -   Structure data. 
--   Tidy data reminder
+[![The Turing Way\'s definitions of reproducible research
+[@community2022]
+](images/reproducible-matrix.jpg){fig-alt="Two by Two cell matrix. Columns are Data, either same or different. Rows are Analysis either same or different. Each of cells contain one of the definitions for reproducibility"}](https://the-turing-way.netlify.app/reproducible-research/overview/overview-definitions#rr-overview-definitions)
 
-You're finished!
+# Why reproducibility?
 
-# 🥳 Well Done! 🎉
+(BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown) -
+
+
+# Project organisation
+
+## Project oriented workflow
+
+-  Readme
+-  folders, files 
+
+## Naming things 
 
+
 
+## File formats
+
+Data files.
+-   Sequences data 
+-   Image data 
+-   Structure data
+
+Similarities and differences 
+
+## Tidy data reminder
+
+You're finished!
+
+# 🥳 Well Done! 🎉
 
 # Independent study following the workshop
 
 [Consolidate](study_after_workshop.qmd)
 
 # The Code file
 
-These contain all the code needed in the workshop even where it is not visible on the webpage.
+These contain all the code needed in the workshop even where it is not
+visible on the webpage.
 
-The [workshop.qmd](workshop.qmd) file is the file I use to compile the practical. Qmd stands for Quarto markdown. It allows code and ordinary text to be interleaved to produce well-formatted reports including webpages. Right-click on the link and choose Save-As to download. You will be able to open the Qmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/). Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
+The [workshop.qmd](workshop.qmd) file is the file I use to compile the
+practical. Qmd stands for Quarto markdown. It allows code and ordinary
+text to be interleaved to produce well-formatted reports including
+webpages. Right-click on the link and choose Save-As to download. You
+will be able to open the Qmd file in RStudio. Alternatively, [View in
+Browser](https://github.com/3mmaRand/). Coding and thinking answers are
+marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
 
-Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr], `kableExtra` [@kableExtra]
+Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr],
+`kableExtra` [@kableExtra]
 
 # References
diff --git a/references.bib b/references.bib
@@ -158,3 +158,24 @@ @article{nestorowa2016
   file = {C\:\\Users\\er13\\Zotero\\storage\\UYBU6MJ7\\Nestorowa et al. - 2016 - A single-cell resolution map of mouse hematopoieti.pdf;C\:\\Users\\er13\\Zotero\\storage\\798ZR55F\\A-single-cell-resolution-map-of-mouse.html}
 }
 
+
+@book{nationalacademiesofsciences2019,
+	title = {Understanding Reproducibility and Replicability},
+	author = {National Academies of Sciences, Engineering and Medicine,  and Policy,  and Affairs, Global and Committee on Science, {Engineering, Medicine} and Public Policy,  and Board on Research Data,  and Information,  and Division on Engineering,  and Physical Sciences,  and Committee on Applied,  and Statistics, Theoretical and Board on Mathematical Sciences,  and Analytics,  and Division on Earth,  and Life Studies,  and Nuclear,  and Radiation Studies Board,  and Division of Behavioral,  and Social Sciences,  and Education,  and Committee on National Statistics,  and Board on Behavioral, Cognitive and Sensory Sciences,  and Committee on Reproducibility,  and Replicability, },
+	year = {2019},
+	month = {05},
+	date = {2019-05-07},
+	publisher = {National Academies Press (US)},
+	url = {https://www.ncbi.nlm.nih.gov/books/NBK547546/}
+}
+
+@book{community2022,
+	title = {The Turing Way: A handbook for reproducible, ethical and collaborative research},
+	author = {Community, The Turing Way},
+	year = {2022},
+	month = {07},
+	date = {2022-07-27},
+	publisher = {Zenodo},
+	doi = {10.5281/ZENODO.3233853},
+	url = {https://zenodo.org/record/3233853}
+}