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Bio-IT
image-analysis-training-resources
Commits
a4e35a00
Verified
Commit
a4e35a00
authored
Jul 24, 2019
by
Toby Hodges
Browse files
clean up files not needed from Carpentries style
parent
9789038c
Changes
13
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_includes/dc/intro.html
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9789038c
<p>
<a
href=
"{{site.dc_site}}"
>
Data Carpentry
</a>
aims to help researchers get their work done
in less time and with less pain
by teaching them basic research computing skills.
This hands-on workshop will cover basic concepts and tools,
including program design, version control, data management,
and task automation.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.
</p>
<p
align=
"center"
>
<em>
For more information on what we teach and why,
please see our paper
"
<a
href=
"http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745"
>
Best Practices for Scientific Computing
</a>
".
</em>
</p>
_includes/dc/schedule.html
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View file @
9789038c
<div
class=
"row"
>
<div
class=
"col-md-6"
>
<h3>
Day 1
</h3>
<table
class=
"table table-striped"
>
<tr>
<td>
09:00
</td>
<td>
Automating tasks with the Unix shell
</td>
</tr>
<tr>
<td>
10:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
12:00
</td>
<td>
Lunch break
</td>
</tr>
<tr>
<td>
13:00
</td>
<td>
Building programs with Python
</td>
</tr>
<tr>
<td>
14:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
16:00
</td>
<td>
Wrap-up
</td>
</tr>
</table>
</div>
<div
class=
"col-md-6"
>
<h3>
Day 2
</h3>
<table
class=
"table table-striped"
>
<tr>
<td>
09:00
</td>
<td>
Version control with Git
</td>
</tr>
<tr>
<td>
10:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
12:00
</td>
<td>
Lunch break
</td>
</tr>
<tr>
<td>
13:00
</td>
<td>
Managing data with SQL
</td>
</tr>
<tr>
<td>
14:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
16:00
</td>
<td>
Wrap-up
</td>
</tr>
</table>
</div>
</div>
_includes/dc/syllabus.html
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View file @
9789038c
<div
class=
"row"
>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-shell"
>
The Unix Shell
</h3>
<ul>
<li>
Files and directories
</li>
<li>
History and tab completion
</li>
<li>
Pipes and redirection
</li>
<li>
Looping over files
</li>
<li>
Creating and running shell scripts
</li>
<li>
Finding things
</li>
<li><a
href=
"{{site.swc_pages}}/shell-novice/reference/"
>
Reference...
</a></li>
</ul>
</div>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-python"
>
Programming in Python
</h3>
<ul>
<li>
Using libraries
</li>
<li>
Working with arrays
</li>
<li>
Reading and plotting data
</li>
<li>
Creating and using functions
</li>
<li>
Loops and conditionals
</li>
<li>
Defensive programming
</li>
<li>
Using Python from the command line
</li>
<li><a
href=
"{{site.swc_pages}}/python-novice-inflammation/reference/"
>
Reference...
</a></li>
</ul>
</div>
<!--
<div class="col-md-6">
<h3 id="syllabus-r">Programming in R</h3>
<ul>
<li>Working with vectors and data frames</li>
<li>Reading and plotting data</li>
<li>Creating and using functions</li>
<li>Loops and conditionals</li>
<li>Using R from the command line</li>
<li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Reference...</a></li>
</ul>
</div>
-->
<!--
<div class="col-md-6">
<h3 id="syllabus-matlab">Programming in MATLAB</h3>
<ul>
<li>Working with arrays</li>
<li>Reading and plotting data</li>
<li>Creating and using functions</li>
<li>Loops and conditionals</li>
<li>Defensive programming</li>
<li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Reference...</a></li>
</ul>
</div>
-->
</div>
<div
class=
"row"
>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-git"
>
Version Control with Git
</h3>
<ul>
<li>
Creating a repository
</li>
<li>
Recording changes to files:
<code>
add
</code>
,
<code>
commit
</code>
, ...
</li>
<li>
Viewing changes:
<code>
status
</code>
,
<code>
diff
</code>
, ...
</li>
<li>
Ignoring files
</li>
<li>
Working on the web:
<code>
clone
</code>
,
<code>
pull
</code>
,
<code>
push
</code>
, ...
</li>
<li>
Resolving conflicts
</li>
<li>
Open licenses
</li>
<li>
Where to host work, and why
</li>
<li><a
href=
"{{site.swc_pages}}/git-novice/reference/"
>
Reference...
</a></li>
</ul>
</div>
<!--
<div class="col-md-6">
<h3 id="syllabus-sql">Managing Data with SQL</h3>
<ul>
<li>Reading and sorting data</li>
<li>Filtering with <code>where</code></li>
<li>Calculating new values on the fly</li>
<li>Handling missing values</li>
<li>Combining values using aggregation</li>
<li>Combining information from multiple tables using <code>join</code></li>
<li>Creating, modifying, and deleting data</li>
<li>Programming with databases</li>
<li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Reference...</a></li>
</ul>
</div>
-->
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-r"
>
Open Refine
</h3>
<ul>
<li>
Introduction to OpenRefine
</li>
<li>
Importing data
</li>
<li>
Basic functions
</li>
<li>
Advanced Functions
</li>
<li><a
href=
"{{site.lc_pages}}library-openrefine/reference"
>
Reference...
</a></li>
</ul>
</div>
</div>
_includes/dc/who.html
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9789038c
<p
id=
"who"
>
<strong>
Who:
</strong>
The course is aimed at graduate students and other researchers.
<strong>
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
</strong>
</p>
_includes/lc/intro.html
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9789038c
<p>
<a
href=
"{{site.lc_site}}"
>
Library Carpentry
</a>
is made by people working in library- and information-related roles to help you:
</p>
<ul>
<li>
automate repetitive, boring, error-prone tasks
</li>
<li>
create, maintain and analyze sustainable and reusable data
</li>
<li>
work effectively with IT and systems colleagues
</li>
<li>
better understand the use of software in research
</li>
<li>
and much more...
</li>
</ul>
<p
align=
"center"
>
<em>
Library Carpentry introduces you to the fundamentals of computing
and provides you with a platform for further self-directed learning.
For more information on what we teach and why, please see our paper
"
<a
href=
"https://doi.org/10.18352/lq.10176"
>
Library Carpentry: software skills training for library professionals
</a>
".
</em>
</p>
_includes/lc/schedule.html
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9789038c
<div
class=
"row"
>
<div
class=
"col-md-6"
>
<h3>
Day 1
</h3>
<table
class=
"table table-striped"
>
<tr>
<td>
09:00
</td>
<td>
Data Intro for Librarians
</td>
</tr>
<tr>
<td>
10:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
12:00
</td>
<td>
Lunch break
</td>
</tr>
<tr>
<td>
13:00
</td>
<td>
Shell Lessons for Libraries
</td>
</tr>
<tr>
<td>
14:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
16:00
</td>
<td>
Wrap-up
</td>
</tr>
</table>
</div>
<div
class=
"col-md-6"
>
<h3>
Day 2
</h3>
<table
class=
"table table-striped"
>
<tr>
<td>
09:00
</td>
<td>
Git Intro for Librarians
</td>
</tr>
<tr>
<td>
10:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
12:00
</td>
<td>
Lunch break
</td>
</tr>
<tr>
<td>
13:00
</td>
<td>
OpenRefine for Librarians
</td>
</tr>
<tr>
<td>
14:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
16:00
</td>
<td>
Wrap-up
</td>
</tr>
</table>
</div>
</div>
_includes/lc/syllabus.html
deleted
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9789038c
<div
class=
"row"
>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-python"
>
Data Intro
</h3>
<ul>
<li>
Intro to data
</li>
<li>
Jargon busting
</li>
<li>
Keyboard shortcuts
</li>
<li>
Plain text formats
</li>
<li>
Naming files
</li>
<li>
Regular expressions
</li>
<li><a
href=
"https://data-lessons.github.io/library-data-intro/reference/"
>
Reference...
</a></li>
</ul>
</div>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-shell"
>
The Unix Shell
</h3>
<ul>
<li>
Files and directories
</li>
<li>
History and tab completion
</li>
<li>
Counting and sorting contents in files
</li>
<li>
Pipes and redirection
</li>
<li>
Mining or searching in files
</li>
<li><a
href=
"https://data-lessons.github.io/library-shell/reference/"
>
Reference...
</a></li>
</ul>
</div>
</div>
<div
class=
"row"
>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-git"
>
Version Control with Git
</h3>
<ul>
<li>
Creating a repository
</li>
<li>
Configuring git
</li>
<li>
Recording changes to files:
<code>
add
</code>
,
<code>
commit
</code>
, ...
</li>
<li>
Viewing state changes with
<code>
status
</code></li>
<li>
Working on the web:
<code>
clone
</code>
,
<code>
pull
</code>
,
<code>
push
</code>
, ...
</li>
<li>
Where to host work, and why
</li>
<li><a
href=
"https://data-lessons.github.io/library-git/reference"
>
Reference...
</a></li>
</ul>
</div>
<div
class=
"col-md-6"
>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-r"
>
Open Refine
</h3>
<ul>
<li>
Introduction to OpenRefine
</li>
<li>
Importing data
</li>
<li>
Basic functions
</li>
<li>
Advanced Functions
</li>
<li><a
href=
"https://data-lessons.github.io/library-openrefine/reference"
>
Reference...
</a></li>
</ul>
</div>
</div>
</div>
<!--div class="row">
<div class="col-md-6">
<h3 id="syllabus-sql">SQL Intro</h3>
<ul>
<li>What is SQL?</li>
<li>Intro to SQLite Manager</li>
<li>Importing a database</li>
<li>Reading and sorting data</li>
<li>Filtering with <code>where</code></li>
<li>Combining values using aggregation</li>
<li>Combining information from multiple tables using <code>join</code></li>
<li><a href="https://data-lessons.github.io//library-sql/reference/">Reference...</a></li>
</ul>
</div>
</div>
-->
_includes/lc/who.html
deleted
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View file @
9789038c
<p
id=
"who"
>
<strong>
Who:
</strong>
The course is for people working in library- and information-related roles.
<strong>
You don't need to have any previous knowledge of the tools that
will be presented at the workshop.
</strong>
</p>
_includes/sc/intro.html
deleted
100644 → 0
View file @
9789038c
<p>
<a
href=
"{{site.swc_site}}"
>
Software Carpentry
</a>
aims to help researchers get their work done
in less time and with less pain
by teaching them basic research computing skills.
This hands-on workshop will cover basic concepts and tools,
including program design, version control, data management,
and task automation.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.
</p>
<p
align=
"center"
>
<em>
For more information on what we teach and why,
please see our paper
"
<a
href=
"http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745"
>
Best Practices for Scientific Computing
</a>
".
</em>
</p>
_includes/sc/schedule.html
deleted
100644 → 0
View file @
9789038c
<div
class=
"row"
>
<div
class=
"col-md-6"
>
<h3>
Day 1
</h3>
<table
class=
"table table-striped"
>
<tr>
<td>
09:00
</td>
<td>
Automating tasks with the Unix shell
</td>
</tr>
<tr>
<td>
10:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
12:00
</td>
<td>
Lunch break
</td>
</tr>
<tr>
<td>
13:00
</td>
<td>
Building programs with Python
</td>
</tr>
<tr>
<td>
14:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
16:00
</td>
<td>
Wrap-up
</td>
</tr>
</table>
</div>
<div
class=
"col-md-6"
>
<h3>
Day 2
</h3>
<table
class=
"table table-striped"
>
<tr>
<td>
09:00
</td>
<td>
Version control with Git
</td>
</tr>
<tr>
<td>
10:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
12:00
</td>
<td>
Lunch break
</td>
</tr>
<tr>
<td>
13:00
</td>
<td>
Managing data with SQL
</td>
</tr>
<tr>
<td>
14:30
</td>
<td>
Coffee
</td>
</tr>
<tr>
<td>
16:00
</td>
<td>
Wrap-up
</td>
</tr>
</table>
</div>
</div>
_includes/sc/syllabus.html
deleted
100644 → 0
View file @
9789038c
<div
class=
"row"
>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-shell"
>
The Unix Shell
</h3>
<ul>
<li>
Files and directories
</li>
<li>
History and tab completion
</li>
<li>
Pipes and redirection
</li>
<li>
Looping over files
</li>
<li>
Creating and running shell scripts
</li>
<li>
Finding things
</li>
<li><a
href=
"{{site.swc_pages}}/shell-novice/reference/"
>
Reference...
</a></li>
</ul>
</div>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-python"
>
Programming in Python
</h3>
<ul>
<li>
Using libraries
</li>
<li>
Working with arrays
</li>
<li>
Reading and plotting data
</li>
<li>
Creating and using functions
</li>
<li>
Loops and conditionals
</li>
<li>
Defensive programming
</li>
<li>
Using Python from the command line
</li>
<li><a
href=
"{{site.swc_pages}}/python-novice-inflammation/reference/"
>
Reference...
</a></li>
</ul>
</div>
<!--
<div class="col-md-6">
<h3 id="syllabus-r">Programming in R</h3>
<ul>
<li>Working with vectors and data frames</li>
<li>Reading and plotting data</li>
<li>Creating and using functions</li>
<li>Loops and conditionals</li>
<li>Using R from the command line</li>
<li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Reference...</a></li>
</ul>
</div>
-->
<!--
<div class="col-md-6">
<h3 id="syllabus-matlab">Programming in MATLAB</h3>
<ul>
<li>Working with arrays</li>
<li>Reading and plotting data</li>
<li>Creating and using functions</li>
<li>Loops and conditionals</li>
<li>Defensive programming</li>
<li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Reference...</a></li>
</ul>
</div>
-->
</div>
<div
class=
"row"
>
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-git"
>
Version Control with Git
</h3>
<ul>
<li>
Creating a repository
</li>
<li>
Recording changes to files:
<code>
add
</code>
,
<code>
commit
</code>
, ...
</li>
<li>
Viewing changes:
<code>
status
</code>
,
<code>
diff
</code>
, ...
</li>
<li>
Ignoring files
</li>
<li>
Working on the web:
<code>
clone
</code>
,
<code>
pull
</code>
,
<code>
push
</code>
, ...
</li>
<li>
Resolving conflicts
</li>
<li>
Open licenses
</li>
<li>
Where to host work, and why
</li>
<li><a
href=
"{{site.swc_pages}}/git-novice/reference/"
>
Reference...
</a></li>
</ul>
</div>
<!--
<div class="col-md-6">
<h3 id="syllabus-sql">Managing Data with SQL</h3>
<ul>
<li>Reading and sorting data</li>
<li>Filtering with <code>where</code></li>
<li>Calculating new values on the fly</li>
<li>Handling missing values</li>
<li>Combining values using aggregation</li>
<li>Combining information from multiple tables using <code>join</code></li>
<li>Creating, modifying, and deleting data</li>
<li>Programming with databases</li>
<li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Reference...</a></li>
</ul>
</div>
-->
<div
class=
"col-md-6"
>
<h3
id=
"syllabus-r"
>
Open Refine
</h3>
<ul>
<li>
Introduction to OpenRefine
</li>
<li>
Importing data
</li>
<li>
Basic functions
</li>
<li>
Advanced Functions
</li>
<li><a
href=
"{{site.lc_pages}}library-openrefine/reference"
>
Reference...
</a></li>
</ul>
</div>
</div>
_includes/sc/who.html
deleted
100644 → 0
View file @
9789038c
<p
id=
"who"
>
<strong>
Who:
</strong>
The course is aimed at graduate students and other researchers.
<strong>
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
</strong>
</p>
fig/.gitkeep
deleted
100644 → 0
View file @
9789038c
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