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removed xsede and swc pages. replaced html code with markdown equivalents

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content/events/2016/hcc_fall_kickstart_2016.md
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...@@ -18,7 +18,7 @@ Materials ...@@ -18,7 +18,7 @@ Materials
Etherpad: no longer supported Etherpad: no longer supported
Software Carpentry Software Carpentry
Lessons: <a href="https://eharstad.github.io/2016-09-08-UNL/" class="external-link">https://eharstad.github.io/2016-09-08-UNL/</a> Lessons: [https://eharstad.github.io/2016-09-08-UNL/](https://eharstad.github.io/2016-09-08-UNL/)
Slides for Thursday intro: Slides for Thursday intro:
......
content/events/2016/hcc_qiime_workshop_2016.md
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...@@ -9,7 +9,7 @@ Where:  NIC Food Innovation Campus room 277 ...@@ -9,7 +9,7 @@ Where:  NIC Food Innovation Campus room 277
             1901 N. 21st St., Lincoln, 68588              1901 N. 21st St., Lincoln, 68588
<a href="https://hcc.unl.edu/hcc-qiime-workshop" class="external-link">Details and Agenda</a> [Details and Agenda](https://hcc.unl.edu/hcc-qiime-workshop)
------------------------------------------------------------------------ ------------------------------------------------------------------------
...@@ -20,7 +20,7 @@ Slides for morning ...@@ -20,7 +20,7 @@ Slides for morning
introduction: [QIIME\_2016\_intro.pdf](https://unl.box.com/s/d2o92uoar7x59a7rxl0f3y7o3ncy0swq) introduction: [QIIME\_2016\_intro.pdf](https://unl.box.com/s/d2o92uoar7x59a7rxl0f3y7o3ncy0swq)
Software Carpentry Unix Shell Software Carpentry Unix Shell
Lessons: <a href="http://eharstad.github.io/shell-novice/" class="external-link">http://eharstad.github.io/shell-novice/</a> Lessons: [http://eharstad.github.io/shell-novice/](http://eharstad.github.io/shell-novice/)
Slides for HCC Slides for HCC
Overview: [2016\_Qiime.pdf](https://unl.box.com/s/4gryu7ny8lo95fs8clyu566k2ubbhtef) Overview: [2016\_Qiime.pdf](https://unl.box.com/s/4gryu7ny8lo95fs8clyu566k2ubbhtef)
...@@ -29,7 +29,7 @@ QIIME ...@@ -29,7 +29,7 @@ QIIME
slides: [QIIME\_Talk\_Oct20.pdf](https://unl.box.com/s/h4zi0h27t1t16u9due3ybfrxmsdebzin) slides: [QIIME\_Talk\_Oct20.pdf](https://unl.box.com/s/h4zi0h27t1t16u9due3ybfrxmsdebzin)
QIIME QIIME
tutorial: <a href="http://bioinformatics.unl.edu/qiime_tutorial.pdf" class="external-link">http://bioinformatics.unl.edu/qiime_tutorial.pdf</a><a href="http://bioinformatics.unl.edu/qiime_tutorial.pdf" class="external-link"></a> tutorial: [http://bioinformatics.unl.edu/qiime_tutorial.pdf](http://bioinformatics.unl.edu/qiime_tutorial.pdf)
------------------------------------------------------------------------ ------------------------------------------------------------------------
...@@ -40,7 +40,7 @@ tutorial: <a href="http://bioinformatics.unl.edu/qiime_tutorial.pdf" class="ext ...@@ -40,7 +40,7 @@ tutorial: <a href="http://bioinformatics.unl.edu/qiime_tutorial.pdf" class="ext
-------------------------------------------------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------
1. To participate in this workshop, you will need to 1. To participate in this workshop, you will need to
<a href="http://hcc.unl.edu/new-user-request" class="external-link">sign up for an HCC account</a> [sign up for an HCC account](http://hcc.unl.edu/new-user-request)
(if you do not already have one). Please complete the account (if you do not already have one). Please complete the account
application and [DUO two-factor authentication application and [DUO two-factor authentication
setup](https://hcc-docs.unl.edu/display/HCCDOC/Setting+up+and+using+Duo) setup](https://hcc-docs.unl.edu/display/HCCDOC/Setting+up+and+using+Duo)
...@@ -55,17 +55,17 @@ tutorial: <a href="http://bioinformatics.unl.edu/qiime_tutorial.pdf" class="ext ...@@ -55,17 +55,17 @@ tutorial: <a href="http://bioinformatics.unl.edu/qiime_tutorial.pdf" class="ext
and [Mac/Linux and [Mac/Linux
Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/). Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/).
If you have any problems logging in, please email us at If you have any problems logging in, please email us at
<a href="mailto:hcc-support@unl.edu" class="external-link">hcc-support@unl.edu</a>. [hcc-support@unl.edu](mailto:hcc-support@unl.edu)
3. On Thursday we will be demonstrating how to transfer files using 3. On Thursday we will be demonstrating how to transfer files using
Globus Connect. Before arriving at the workshop, please log in to Globus Connect. Before arriving at the workshop, please log in to
the the
<a href="https://www.globus.org/app/transfer" class="external-link">Globus Web App</a> [Globus Web App](https://www.globus.org/app/transfer)
using your My.UNL credentials (choose *University of using your My.UNL credentials (choose *University of
Nebraska-Lincoln* from the drop down menu).  Next, install the Nebraska-Lincoln* from the drop down menu).  Next, install the
Globus Connect Personal app on your laptop (directions for Globus Connect Personal app on your laptop (directions for
<a href="https://docs.globus.org/how-to/globus-connect-personal-mac/" class="external-link">Mac OS X</a>, [Mac OS X](https://docs.globus.org/how-to/globus-connect-personal-mac/),
<a href="https://docs.globus.org/how-to/globus-connect-personal-linux/" class="external-link">Linux</a>, [Linux](https://docs.globus.org/how-to/globus-connect-personal-linux/),
and and
<a href="https://docs.globus.org/how-to/globus-connect-personal-windows/" class="external-link">Windows</a>) [Windows](https://docs.globus.org/how-to/globus-connect-personal-windows/)
so that you can begin using Globus to transfer data to and from your so that you can begin using Globus to transfer data to and from your
laptop. laptop.
content/events/2016/hcc_spring_workshop_uno.md
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...@@ -5,10 +5,6 @@ description = "HCC Spring Workshop UNO 2016." ...@@ -5,10 +5,6 @@ description = "HCC Spring Workshop UNO 2016."
**When**: 12:30 pm - 15:00 pm, March 11, 2016 **When**: 12:30 pm - 15:00 pm, March 11, 2016
**Where**:  <span style="color: rgb(91,91,90);">UNO, Criss Library Room **Where**: UNO, Criss Library Room 249
249</span>
**Quick
Link**: <a href="http://jingchaozhang.github.io/2016-03-11-UNO/" class="external-link">http://jingchaozhang.github.io/2016-03-11-UNO/</a>
**Quick Link**: [http://jingchaozhang.github.io/2016-03-11-UNO/](http://jingchaozhang.github.io/2016-03-11-UNO/)
\ No newline at end of file
content/events/2016/instructions_for_52016_allinea_workshop.md
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...@@ -3,7 +3,9 @@ title = "Instructions for 5/20/16 Allinea Workshop" ...@@ -3,7 +3,9 @@ title = "Instructions for 5/20/16 Allinea Workshop"
description = "Instructions for 5/20/16 Allinea Workshop." description = "Instructions for 5/20/16 Allinea Workshop."
+++ +++
<span style="color: rgb(0,0,0);">When: May 20th, 1-2:30PM</span> <span style="color: rgb(0,0,0);">Where: UNL AVH 347 and UNO PKI 250</span> When: May 20th, 1-2:30PM
------------------------------------------------------------
Where: UNL AVH 347 and UNO PKI 250
------------------------------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------------
### Untar the files for the examples ### Untar the files for the examples
...@@ -34,20 +36,16 @@ these instructions to setup the Allinea client on your laptop. ...@@ -34,20 +36,16 @@ these instructions to setup the Allinea client on your laptop.
First, download and install the remote client software for either First, download and install the remote client software for either
Windows or OS X Windows or OS X
from <a href="https://www.allinea.com/products/forge/download#remote-client" class="external-link">this page</a>. from [this page](https://www.allinea.com/products/forge/download#remote-client).
Start the Allinea software, and choose *Configure...* from the *Remote Start the Allinea software, and choose *Configure...* from the *Remote
Launch* dropdown menu. Launch* dropdown menu.
<span {{< figure src="/images/configure.png" width="300" height="78" class="img-border">}}
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="/images/configure.png" class="confluence-embedded-image confluence-content-image-border" width="300" height="78" /></span>
Click the *Add* button on the new window. Click the *Add* button on the new window.
<span {{< figure src="/images/add.png" width="400" height="322" class="img-border">}}
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="/images/add.png" class="confluence-embedded-image confluence-content-image-border" width="400" height="322" /></span>
To setup a connection to Crane, fill in the fields as follows: To setup a connection to Crane, fill in the fields as follows:
*Connection Name:  *Crane *Connection Name:  *Crane
...@@ -56,8 +54,7 @@ To setup a connection to Crane, fill in the fields as follows: ...@@ -56,8 +54,7 @@ To setup a connection to Crane, fill in the fields as follows:
It should appear similar to this: It should appear similar to this:
<span {{< figure src="/images/filledfields.png" width="500" height="306" class="img-border">}}
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="/images/filledfields.png" class="confluence-embedded-image confluence-content-image-border" width="500" height="306" /></span>
Be sure to replace *demo02* with your HCC username. Be sure to replace *demo02* with your HCC username.
...@@ -81,13 +78,11 @@ ln -s $WORK/.allinea $HOME/.allinea ...@@ -81,13 +78,11 @@ ln -s $WORK/.allinea $HOME/.allinea
To test the connection, choose *Crane* from the *Remote Launch* menu. To test the connection, choose *Crane* from the *Remote Launch* menu.
<span {{< figure src="/images/remoteLaunch.png" width="300" height="114" class="img-border">}}
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="/images/remoteLaunch.png" class="confluence-embedded-image confluence-content-image-border" width="300" height="114" /></span>
A* Connect to Remote Host* dialog will appear and prompt for a password. A* Connect to Remote Host* dialog will appear and prompt for a password.
<span {{< figure src="/images/password.png" width="500" height="310" class="img-border">}}
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="/images/password.png" class="confluence-embedded-image confluence-content-image-border" width="500" height="310" /></span>
The login procedure is the same as for PuTTY or any other SSH program. The login procedure is the same as for PuTTY or any other SSH program.
 Enter your HCC password followed by the Duo login.  Enter your HCC password followed by the Duo login.
...@@ -119,14 +114,12 @@ ddt --connect ...@@ -119,14 +114,12 @@ ddt --connect
On your local machine, a pop-up box should appear prompting you to On your local machine, a pop-up box should appear prompting you to
accept the Reverse Connect request. accept the Reverse Connect request.
<span {{< figure src="/images/reverse.png" width="450" class="img-border">}}
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="/images/reverse.png" class="confluence-embedded-image confluence-content-image-border" width="450" /></span>
Choose *Accept.*  The *Remote Launch *section should change to indicate Choose *Accept.*  The *Remote Launch *section should change to indicate
you are connected via tunnel, similar to: you are connected via tunnel, similar to:
<span {{< figure src="/images/tunnel.png" width="250" class="img-border">}}
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="/images/tunnel.png" class="confluence-embedded-image confluence-thumbnail confluence-content-image-border" width="250" /></span>
Once that happens, Reverse Connect is working successfully and a Once that happens, Reverse Connect is working successfully and a
debugging or profiling session can be started. debugging or profiling session can be started.
......
content/events/2016/software_carpentry_open_science_grid_workshop_unl_january_6_8_2016.md deleted 100644 → 0
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+++
title = "OSG Workshop UNL 2016"
description = "OSG Workshop UNL 2016."
+++
**When**: January 6-8, 2016
**Where**:  UNL Campus, Avery Hall 119
**Quick
Link**: <a href="https://swc-osg-workshop.github.io/2016-01-06-UNL/" class="external-link">https://swc-osg-workshop.github.io/2016-01-06-UNL/</a>
**Materials**
=============
**Etherpad**: no longer supported
**Shell
Lesson**: <a href="http://swc-osg-workshop.github.io/2016-01-06-UNL/novice/shell/" class="external-link">http://swc-osg-workshop.github.io/2016-01-06-UNL/novice/shell/</a>
**Git
Lesson**: <a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
**Python
Lesson**: <a href="https://djw8605.github.io/python-novice-inflammation/" class="external-link">https://djw8605.github.io/python-novice-inflammation/</a>
**Open Science Grid
Lesson**: <a href="http://swc-osg-workshop.github.io/2016-01-06-UNL/novice/DHTC/" class="external-link">http://swc-osg-workshop.github.io/2016-01-06-UNL/novice/DHTC/</a>
content/events/2016/software_carpentry_workshop_uno_july_14_15_2016.md deleted 100644 → 0
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+++
title = "SWC Workshop, July 14-15, 2016"
description = "SWC Workshop, July 14-15, 2016."
+++
**When**: July 14-15, 2016
**Where**: UNO Campus, PKI 160
**Quick
Link**: <a href="https://npavlovikj.github.io/2016-07-14-UNO/" class="external-link">https://npavlovikj.github.io/2016-07-14-UNO/</a>
**Materials**
=============
**Etherpad**: no longer supported
**Shell Lesson**: <span
style="color: rgb(24,54,145);"><a href="http://swcarpentry.github.io/shell-novice/" class="external-link">http://swcarpentry.github.io/shell-novice/</a></span>
**Git Lesson**: <span
style="color: rgb(24,54,145);"><a href="http://swcarpentry.github.io/shell-novice/" class="external-link">http://swcarpentry.github.io/git-novice/</a></span>
**HCC Lesson**: [pdf](https://unl.box.com/s/p5mpahszbu4mwnxas3xzgc6e4ypnthja)
**MatLab Demo**: [matlab](https://unl.box.com/s/z9ihn225txqt7s6xx3d0mfj9o5q6jc7h)
**Python Lesson**: <span
style="color: rgb(24,54,145);"><a href="https://djw8605.github.io/python-novice-inflammation/" class="external-link">https://djw8605.github.io/python-novice-inflammation/</a></span>
content/events/2016/xsede_workshop_big_data_november_2016.md deleted 100644 → 0
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+++
title = "XSEDE Big Data, Nov. 2016"
description = "XSEDE Big Data, Nov. 2016."
+++
When:   November 1st, 2016
Where:  Hardin Hall 901, UNL East Campus
             3310 Holdrege St., Lincoln, 68583
<a href="http://hcc.unl.edu/xsede-hpc-workshop-big-data" class="external-link">Details</a><a href="https://portal.xsede.org/course-calendar/-/training-user/class/518/session/1096" class="external-link"></a>
Etherpad (no longer supported)
------------------------------------------------------------------------
Materials
---------
| Agenda |   |
|--------|------------------------------------------------------------------------------------------------------------------------------------------------|
| 10:00 | Welcome |
| 10:25 | Intro to Big Data |
| 10:45 | Hadoop |
| 12:00 | Lunch break |
| 1:00 | Spark intro |
| 3:15 | A Big Big Data Platform |
| 4:00 | Adjourn |
content/events/2016/xsede_workshop_openacc_december_2016.md deleted 100644 → 0
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+++
title = "XSEDE OpenACC, Dec. 2016"
description = "XSEDE OpenACC, Dec. 2016."
+++
When:   December 6th, 2016
Where:  Animal Science C210, UNL East Campus
            3940 Fair St., Lincoln, 68583
<a href="https://hcc.unl.edu/xsede-hpc-workshop-openacc" class="external-link">Details</a>
<a href="https://unl.box.com/s/cmz1xchbm3irqnbr0gro9ndnpyjvngwa" class="external-link">Exercises</a>
Etherpad (no longer supported)
 
------------------------------------------------------------------------
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