Merge pull request #2 from BinxiePeterson/testing1

Merge changes from Testing1 branch to gh-pages

CONTRIBUTING.md

@@ -69,7 +69,7 @@ and to meet some of our community members.
 There are many ways to contribute,
 from writing new exercises and improving existing ones
 to updating or filling in the documentation
-and and submitting [bug reports][issues]
+and submitting [bug reports][issues]
 about things that don't work, aren't clear, or are missing.
 If you are looking for ideas,
 please see [the list of issues for this repository][issues],
@@ -130,11 +130,11 @@ and have final say over what gets merged into the lesson.
 
 ## Issues Labels
 
-What issue labels in this repository mean? Think if you can asign one of the below labels to your issue.
+What issue labels in this repository mean? Think if you can assign one of the below labels to your issue.
 This will help maintainers to decide how to act and should result in quicker response to the issues.
-If you don't assign the label to an issue it will be assigned by the maintainers.
+If you don't assign the label to an issue, it will be assigned by the maintainers.
 
-- **duplicate**  means there is other issue reporting same problem
+- **duplicate**  means there is another issue reporting the same problem
 - **enhancement** improvement to the existing content
 - **help wanted** maintainers invite contributors to tackle this issue
 - **invalid** is not considered an issue by the maintainers

LICENSE.md

@@ -25,8 +25,8 @@ Under the following terms:
 
 * **Attribution**---You must give appropriate credit (mentioning that
   your work is derived from work that is Copyright © Software
-  Carpentry and, where practical, linking to
-  http://software-carpentry.org/), provide a [link to the
+  Carpentry or Data Carpentry and, where practical, linking to
+  http://software-carpentry.org/ or https://datacarpentry.org), provide a [link to the
   license][cc-by-human], and indicate if changes were made. You may do
   so in any reasonable manner, but not in any way that suggests the
   licensor endorses you or your use.

_extras/guide.md

@@ -28,11 +28,11 @@ some of it can be prevented with good strategies for data collection up front.
 very manual and also not reproducible. That's why we're teaching bash shell scripting!
 * Now let's talk about spreadsheets, and when we say spreadsheets, we mean any program that
 does spreadsheets like Excel, LibreOffice, OpenOffice. Most learners are probably using Excel.
-* Ask the audience any things they've accidentally done in spreadsheets. Talk about an example of your own, like that you accidentally sorted only a single column and not the rest
+* Ask the audience any things they've accidentally done in spreadsheets. Talk about an example of your own, like that you accidentally sorted only a single column and not the rest.
 of the data in the spreadsheet. What are the pain points!?
-* As people answer highlight some of these issues with spreadsheets
-* Go through the point about keeping track of your steps and keeping raw data raw
-* Go through the cardinal rule of spreadsheets about columns, rows and cells
+* As people answer, highlight some of these issues with spreadsheets.
+* Go through the point about keeping track of your steps and keeping raw data raw.
+* Go through the cardinal rule of spreadsheets about columns, rows and cells.
 * Hand them a messy data file and have them pair up and work together to clean up the data.
 
 #### [Planning for NGS projects](../02-project-planning/)
@@ -67,8 +67,8 @@ Excel. So, the presenter's environment will only be the same as some of the lear
 We need better notes and screenshots of how things work on both Mac and PC. But we
 likely won't be able to cover all the different versions of Excel. 
 
-If you have a helper who has experience with the other OS than you, it would be good
-to prep them to help with this lesson and tell people how to do things in the other OS.
+If you have a helper who has more experience with the other OS than you, it would be good
+to prepare them to help with this lesson and tell people how to do things in the other OS.
 
 #### People are not interactive or responsive on the exercises
 

index.md

@@ -7,13 +7,13 @@ Good data organization is the foundation of any research project. It not only se
 
 Organizing a project that includes sequencing involves many components. There's the experimental setup and conditions metadata, measurements of experimental parameters, sequencing preparation and sample information, the sequences themselves and the files and workflow of any bioinformatics analysis. So much of the information of a sequencing project is digital, and we need to keep track of our digital records in the same way we have a lab notebook and sample freezer. In this lesson, we'll go through the project organization and documentation that will make an efficient bioinformatics workflow possible. Not only will this make you a more effective bioinformatics researcher, it also prepares your data and project for publication, as grant agencies and publishers increasingly require this information.
 
-In this lesson we'll be using data from a study of experimental evolution using *E. coli*. [More about this dataset](http://www.datacarpentry.org/organization-genomics/data/). In this study there are several types of files
+In this lesson, we'll be using data from a study of experimental evolution using *E. coli*. More information about this dataset is available [here](http://www.datacarpentry.org/organization-genomics/data/). In this study there are several types of files:
 
 - spreadsheet data from the experiment that tracks the strains and their phenotype over time
 - spreadsheet data with information on the samples that were sequenced - the names of the samples, how they were prepared and the sequencing conditions
 - the sequence data
 
-Throughout the analysis we'll also generate files from the steps in the bioinformatics pipeline and documentation on the tools and parameters that we used.
+Throughout the analysis, we'll also generate files from the steps in the bioinformatics pipeline and documentation on the tools and parameters that we used.
 
 In this lesson you will learn: