Merge pull request #1 from TeachBooks/paige_experiments

Merging paige experiments branch

Author: guin0x

book/part1/part1.md

@@ -4,13 +4,13 @@
 
 ### 1a. Learning Objectives & Purpose
 
-This mini module is an opportunity for self-paced, independent learning in several core skills. During class, your instructors will expand upon the module topics and will show you how to apply the skills to much more complex problems in your field of study. The learning in this mini-module will equip you to do the following:
+This mini module is an opportunity for self-paced, independent learning in several core skills. During class, your instructors will expand upon the module topics and will show you how to apply the skills to much more complex problems in your field of study. The learning in this mini-module will equip you to do the following: 
 
-- Recognize the importance of file and folder organisation and relate it to my studies.
+- Recognise the importance of file and folder organisation and relate it to your studies.
 
 - Use appropriate naming conventions to manage project files systemically.
 
-- Structure folders effectively to make elements of a research project findable for collaborators and for my future self.
+- Structure folders effectively to make elements of a research project findable for collaborators and for your future self.
 
 - Explain the concept of a directory tree. 
 
@@ -45,7 +45,7 @@ Before we begin, please take this short pre-quiz (5 questions). The purpose is t
 
 ### 1c. Relevance:
 
-<center><strong>Why should we care about file naming & folder organization?</strong></center><br>
+<center><strong>Why should we care about file naming & folder organisation?</strong></center><br>
 
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       <h3>INSIGHTS INTO YOUR RESEARCH PROCESS</h3>
-      <p>Ideally, files are named and organized in a way that helps document the process or sequence that you followed to gather the data. File names should provide hints about why/how each piece is relevant. Effective file naming and <span style="color: pink;">documentation of file naming schema</span> makes it easier to retrace your steps in a project when it’s time to analyze your results.</p>
+      <p>Ideally, files are named and organised in a way that helps document the process or sequence that you followed to gather the data. File names should provide hints about why/how each piece is relevant. Effective file naming and documentation of file naming schema makes it easier to retrace your steps in a project when it’s time to analyse your results.</p>
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       <h3>INCREASED EFFICIENCY</h3>
-      <p>It’s no fun hunting frantically for that one specific piece of information that you collected last month: spending a little time upfront to organize your files increases their findability. This can save you a lot of time (and lower your stress level) in the long run.</p>
+      <p>It’s no fun hunting frantically for that one specific piece of information that you collected last month: spending a little time upfront to organise your files increases their findability. This can save you a lot of time (and lower your stress level) in the long run.</p>
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       <h3>BETTER ORGANIZATION</h3>
-      <p>File naming and folder organization best practices will help you to be more organised in your BSc thesis research and in general: in your studies you will likely be working with larger quantities of data over longer periods of time. You may have it all in your head now, but forget major details two months from now. It’s helpful to have <b>systemic, <span style="color: pink;">well-documented</span> methods</b> for naming and organising your files now so that your future self can easily understand and locate what you did.</p>
+      <p>File naming and folder organization best practices will help you to be more organised in your BSc thesis research and in general: in your studies you will likely be working with larger quantities of data over longer periods of time. You may have it all in your head now, but forget major details two months from now. It’s helpful to have <b>systemic, well-documented methods</b> for naming and organising your files now so that your future self can easily understand and locate what you did.</p>
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       <h3>EFFECTIVE COLLABORATION</h3>
-      <p>Your file naming choices and folder structure should be so clear that it's possible for a collaborator or supervisor to follow the steps of your research and understand the pieces of your work. There is no single "right" way to name files and organize folders, but your system of organizing data and files needs to work for everyone involved in the work.</p>
+      <p>Your file naming choices and folder structure should help a collaborator or supervisor to follow the steps of your research and understand the pieces of your work. When working on collaborative projects, establishing a common/standard folder structure and naming conventions can facilitate collaborative work because everybody knows where to easily find the data they need for the different pieces of the project, making the collaboration more effective. There is no single "right" way to name files and organise folders, but your system of organising data and files needs to work for everyone involved in the work.</p>
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       <h3>REINFORCING COMPUTER SCIENCE PRINCIPLES</h3>
-      <p>The concepts in this module reinforce skills and habits of thinking that you will need for computer programming. For example, understanding folder structures can help you become a more intuitive user of a <b>command line interface</b>. It can also help you to more intentionally organize and store code and documentation for <b>collaborative projects</b>. Moreover, this mini-module will prepare you to practice better <b>version control</b> by reinforcing habits of systemic naming.</p>
+      <p>The concepts in this module reinforce skills and habits of thinking that you will need for computer programming. For example, understanding folder structures can help you become a more intuitive user of a <b>command line interface</b>. It can also help you to more intentionally organise and store code and documentation for <b>collaborative projects</b>. Moreover, this mini-module will prepare you to practice better <b>version control</b> by reinforcing habits of systemic naming.</p>
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 ### 1d. Your turn to process!
 
-This section discussed many reasons to expand your knowledge of file naming and folder organization. The next parts of this module aim to provide tools and guidelines which will be immediately applicable to your bachelor’s coursework.
+This section discussed many reasons to expand your knowledge of file naming and folder organisation. The next parts of this module aim to provide tools and guidelines which will be immediately applicable to your bachelor’s coursework.
 
 Before proceeding, please reflect on which of the reasons discussed is most important for you and why:
 
-
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-<br>
+<br>

book/part2/part2.md

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 ### 2a. Relevance
 
-<b>Why assign naming rules to research data and files?</b>
+<b>Why assign naming rules to files and folders?</b>
 
-Consistent file naming can help you to clearly organize all the information for your projects.
+Consistent file naming can help you to clearly organise all the information for your projects.
 
 At the beginning of a project, it’s helpful to determine an FNC (File Naming Convention), or “file naming schema,” for each type of information that you will gather, create, or store to work with. An FNC is the pattern that you establish and follow for naming the files associated with a project. Without an FNC, you might end up with a mysterious list of file names that looks something like this:
 <center>
 <img src="../figures/2Aa_documents_cartoon.png" alt="Documents Cartoon" style="width: 200px; height: auto;"/>
 <p style="font-size: small;"><em>"Documents" by xkcd is licensed under CC-BY-NC.</em></p>
 </center>
 
-
 File naming conventions help you stay organized so you can quickly identify your files. In a shared or collaborative group file-sharing setting, it will help others more easily navigate your work.
 
 <div style="border: 2px solid orange; padding: 10px; background-color: #fff3cd; border-radius: 5px; display: flex; align-items: center; margin: 10px 0;">
   <span style="font-size: 24px; color: orange; margin-right: 10px;">⚠️</span>
-  <span style="margin-left: 5px;">It is <b>essential</b> to establish a convention <b>before</b> you begin creating files or collecting data. Having a clear FNC at the start of a project prevents a backlog of unorganized content.</span>
+  <span style="margin-left: 5px;">It is <b>essential</b> to establish a convention <b>before</b> you begin creating files or collecting data, and to adjust it as needed during the research while documenting any changes accordingly. Having a clear FNC at the start of a project prevents a backlog of unorganised content.</span>
 </div>
 
-In this module we’ll share general recommendations for file naming that apply across academic disciplines. Please note, <b>there’s no single “right” way to name your files</b>. However, also be aware that different fields of study may have their own specific conventions for naming different types of files. For example, biologists may adhere to standardized 4-letter abbreviations for species names.
+In this module we’ll share general recommendations for file naming that apply across academic disciplines. Please note, <b>there’s no single “right” way to name your files</b>. However, also be aware that different fields of study may have their own specific conventions for naming different types of files. For example, biologists may adhere to standardised 4-letter abbreviations for species names.
 
 ### 2b. Rules of Thumb for File Naming
 
 <b>How do I develop an FNC (file naming convention) for my files?</b>
 
-Read the basic rules of thumb to learn more about recommended file naming practices. Afterwards, you’ll be asked to analyze several examples
+Read the basic rules of thumb to learn more about recommended file naming practices. Afterwards, you’ll be asked to analyse several examples
 
 #### #1 Be consistent
 - At the start of a project, choose a naming pattern for all files of the same type. Then stick with it!
@@ -40,7 +39,7 @@ Read the basic rules of thumb to learn more about recommended file naming practi
     - Type or purpose of document (e.g. data, progress report, questionnaire, interview)
     - If working collaboratively, the initials of the person who ran the test
 - "Final" is <b>NOT</b> a descriptive name
-- Use abbreviations that are commonly unterestood by collaborators.
+- Use abbreviations that are commonly unterestood by collaborators, and document these abbreviations.
 
 <b>Describing data in a series:</b>
 
@@ -103,6 +102,7 @@ Practice applying the first two file naming rules of thumb to a research scenari
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 #### #3 Keep file names short
+
 - Try to limit names to 32 characters or less. Shorter names are easier to quickly scan to know what the file is. For a visual:
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 - Try to shorten file names as much as possible by using abbreviations or acronyms (but make sure others in your field understand them)
 
 #### #4 Avoid spaces
-- Some operating systems and command line programs don’t recognize spaces in file names. Spaces can cause problems when you’re transferring files between systems.
 
+- Some operating systems and command line programs don’t recognise spaces in file names. Spaces can cause problems when you’re transferring files between systems.
 - Recommended: use underscores _ or hyphens - instead of spaces.
 
 #### #5 Avoid "weird" characters
+
 - <b>Use periods only at the end of the file name</b>, right before the *extension (*extension: the last 2-3 characters that tell you the file format)
 
 - Some characters carry meanings within a computer programming environment, so it’s better to avoid them. These characters can be confusing for machines:
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 #### #6 Versioning matters: Track versions of your work
-
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