diff --git a/content/events/2012/supercomputing_mini_workshop_2012.md b/content/events/2012/supercomputing_mini_workshop_2012.md
index d07402f60437156f3b9708d0500727882f6d0460..29989d6068f96b16331e25d72ed05219a3439540 100644
--- a/content/events/2012/supercomputing_mini_workshop_2012.md
+++ b/content/events/2012/supercomputing_mini_workshop_2012.md
@@ -3,6 +3,11 @@ title = "Supercomputing Mini Workshop 2012"
 description = "Supercomputing Mini Workshop 2012."
 +++
 
+Quick Link: <a href="http://go.unl.edu/supercomputing_mini_2012">http://go.unl.edu/supercomputing_mini_2012</a>
+
+Presentation
+============
+
 [Workshop Presentation](https://unl.box.com/s/qr0p96va5qrkhvvq8lcyvqnzfrz1q2c0)
 
 Submit files, code source files, and example scripts can be found in
diff --git a/content/events/2013/hcc_matlab_workshop_2013.md b/content/events/2013/hcc_matlab_workshop_2013.md
index bf8e21b7c3133ff4ce62f7f4a8fdacb2a5b9cd3d..6ef348f6d65835a80c75586b677a9759e6294241 100644
--- a/content/events/2013/hcc_matlab_workshop_2013.md
+++ b/content/events/2013/hcc_matlab_workshop_2013.md
@@ -3,98 +3,27 @@ title = "HCC Matlab Workshop 2013"
 description = "HCC Matlab Workshop 2013."
 +++
 
-
-Quick link:
-<a href="http://go.unl.edu/hcc_matlab_2013" class="external-link">http://go.unl.edu/hcc_matlab_2013</a>
-
-<span
-class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
-class="expand-control-text">Click here to view presentation...</span>
-
-Timeline
-========
-
 Workshop presentation slides
-&lt;[matlab\_workshop.pdf](attachments/2851357/3178542.pdf)&gt;
-
-Time
-
-Title
-
-Description
-
-UNMC
-
-10am - 11am
-
-Demo/Hand-On Practice
-
-Implementing a MATLAB code on HCC supercomputers
-
-11am - 12pm
+&lt;[matlab\_workshop.pdf](https://unl.box.com/s/lulbnbrnr7xqwufrx5s20gxnyxpykn7j)&gt;
 
-Individual Consultation
+| Time        | Title                   | Description                                      |
+|-------------|-------------------------|--------------------------------------------------|
+| UNMC        |                         |                                                  |
+| 10am - 11am | Demo/Hand-On Practice   | Implementing a MATLAB code on HCC supercomputers |
+| 11am - 12pm | Individual Consultation | Bring your MATLAB code on HCC supercomputers     |
+| UNO         |                         |                                                  |
+| 2pm - 3pm   | Demo/Hand-On Practice   | Implementing a MATLAB code on HCC supercomputers |
+| 3pm - 4pm   | Individual Consultation | Bring your MATLAB code on HCC supercomputers     |
 
-Bring your MATLAB code on HCC supercomputers
-
-UNO
-
-2pm - 3pm
-
-Demo/Hand-On Practice
-
-Implementing a MATLAB code on HCC supercomputers
-
-3pm - 4pm
-
-Individual Consultation
-
-Bring your MATLAB code on HCC supercomputers
-
- 
 
 Password for all demo accounts is **HCC\_matlab2013**.
 Replace `<group name>` with `demo` and `<username>` with `demoXX`
 (e.g. `demo01`).
 
--   Get started with [For Windows Users](For-Windows-Users_2851288.html)
-    or [For Mac/Linux Users](2851290.html).
--   Hands On: [MATLAB on HCC](MATLAB-on-HCC_2851078.html)
+-   Get started with [For Windows Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_windows_users/)
+    or [For Mac/Linux Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/).
+-   Hands On: [MATLAB on HCC](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_matlab_jobs/)
 -   Sample code for MATLAB on HCC:
-    &lt;[matlab\_dir.zip](attachments/2851357/3178543.zip)&gt;
+    &lt;[matlab\_dir.zip](https://unl.box.com/s/u19fy7cjeswfl1wi7h1nkeeie8gl3z90)&gt;
 -   Sample code for Parallel MATLAB Job:
-    &lt;[parallel\_matlab\_dir.zip](attachments/2851357/3178544.zip)&gt;
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[demo\_hcc\_matlab.zip](attachments/2851357/3178541.zip)
-(application/zip)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[matlab\_workshop.pdf](attachments/2851357/3178545.pdf)
-(application/pdf)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[matlab\_dir.zip](attachments/2851357/3178569.zip) (application/zip)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[parallel\_matlab\_dir.zip](attachments/2851357/3178570.zip)
-(application/zip)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[matlab\_workshop.pdf](attachments/2851357/3178546.pdf)
-(application/pdf)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[matlab\_workshop.pdf](attachments/2851357/3178547.pdf)
-(application/pdf)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[matlab\_workshop.pdf](attachments/2851357/3178568.pdf)
-(application/pdf)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[matlab\_workshop.pdf](attachments/2851357/3178542.pdf)
-(application/pdf)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[matlab\_dir.zip](attachments/2851357/3178543.zip) (application/zip)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[parallel\_matlab\_dir.zip](attachments/2851357/3178544.zip)
-(application/zip)  
-
-
+    &lt;[parallel\_matlab\_dir.zip](https://unl.box.com/s/fhl3kf6hg8dmtozkphq3u2r58yexrppe)&gt;
diff --git a/content/events/2013/hcc_mpi_workshop_2013.md b/content/events/2013/hcc_mpi_workshop_2013.md
index 4089b6f61d71870aa49a45639a63eafb97257608..a49977cda3f8fbc51d8e64be78eec4985f4caa4a 100644
--- a/content/events/2013/hcc_mpi_workshop_2013.md
+++ b/content/events/2013/hcc_mpi_workshop_2013.md
@@ -3,18 +3,7 @@ title = "HCC MPI Workshop 2013"
 description = "HCC MPI Workshop 2013."
 +++
 
-Quick
-link: <a href="http://go.unl.edu/hcc_mpi_2013" class="external-link">http://go.unl.edu/hcc_mpi_2013</a>
-
-<span
-class="expand-control-icon"><img src="assets/images/icons/grey_arrow_down.png" class="expand-control-image" /></span><span
-class="expand-control-text">Click here to view presentation...</span>
-
-Presentation
-============
-
-Workshop presentation slides
-&lt;[mpi\_workshop.pdf](attachments/2851569/3178561.pdf)&gt;
+Workshop presentation slides &lt;[mpi\_workshop.pdf](https://unl.app.box.com/file/438884023344)&gt;
 
 | Time    | Title                   | Description                                    |
 |---------|-------------------------|------------------------------------------------|
@@ -25,23 +14,13 @@ Password for all demo accounts is **HCC\_mpi2013**.
 Replace `<group name>` with `demo` and `<username>` with `demoXX` (e.g. `demo01`).
 
 -   Get started with [For Windows
-    Users](For-Windows-Users_2851288.html) or [For Mac/Linux
-    Users](2851290.html).
+    Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_windows_users/) or [For Mac/Linux
+    Users](https://hcc.unl.edu/docs/quickstarts/connecting/for_maclinux_users/).
 -   Sample code for Fortran/C on HCC:
-    &lt;[serial\_dir.zip](attachments/2851569/3178562.zip)&gt;
+    &lt;[serial\_dir.zip](https://unl.app.box.com/file/438858401843)&gt;
 -   Sample code for MPI on HCC:
-    &lt;[mpi\_dir.zip](attachments/2851569/3178563.zip)&gt;
+    &lt;[mpi\_dir.zip](https://unl.app.box.com/file/438885605405)&gt;
 -   For more details of this demonstration, see [MPI Jobs on
-    HCC](MPI-Jobs-on-HCC_2851393.html).
-
-Attachments:
-------------
-
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[mpi\_workshop.pdf](attachments/2851569/3178561.pdf) (application/pdf)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[serial\_dir.zip](attachments/2851569/3178562.zip) (application/zip)  
-<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
-[mpi\_dir.zip](attachments/2851569/3178563.zip) (application/zip)  
+    HCC](https://hcc.unl.edu/docs/guides/submitting_jobs/submitting_an_mpi_job/).  
 
 
diff --git a/content/events/2013/june_2013_osg_workshop.md b/content/events/2013/june_2013_osg_workshop.md
index f1140b7043c6c278e9346037e958c81641ad67db..215a670f143a0af953aa8b5137f05b8f10ca6b6f 100644
--- a/content/events/2013/june_2013_osg_workshop.md
+++ b/content/events/2013/june_2013_osg_workshop.md
@@ -3,11 +3,7 @@ title = "HCC OSG Workshop, June 2013"
 description = "HCC OSG Workstop, June 2013."
 +++
 
-Quick
-link: <a href="http://go.unl.edu/hccosg2013" class="external-link">http://go.unl.edu/hccosg2013</a>
-
-Location: <span style="line-height: 1.4285715;">Unity Room/212 in the
-Jackie Gaughan Multicultural Center</span>
+Location: Unity Room/212 in the Jackie Gaughan Multicultural Center
 
 | Time    | Title                                                 | Description                                                      |
 |---------|-------------------------------------------------------|------------------------------------------------------------------|
diff --git a/content/events/2013/supercomputing_mini_workshop_february_27_2013.md b/content/events/2013/supercomputing_mini_workshop_february_27_2013.md
index 6f388cc63374dcf4b46adbe6b92c38b036494ccf..fb081292535318d15a2850999bae6d742dcbc5a6 100644
--- a/content/events/2013/supercomputing_mini_workshop_february_27_2013.md
+++ b/content/events/2013/supercomputing_mini_workshop_february_27_2013.md
@@ -15,16 +15,6 @@ framework of the standard supercomputing process and demonstrate that it
 does not require huge efforts for one to take advantage of
 state-of-the-art supercomputing resources. 
 
-**Table of Contents  
-**
-
--   [Preparation](#SupercomputingMiniWorkshop-February27,2013-Preparation)
--   [Serial Job](#SupercomputingMiniWorkshop-February27,2013-SerialJob)
--   [Parallel
-    Job ](#SupercomputingMiniWorkshop-February27,2013-ParallelJob)
--   [Useful
-    Commands](#SupercomputingMiniWorkshop-February27,2013-UsefulCommands)
-
 **Logging In**
 
 ``` syntaxhighlighter-pre
@@ -36,7 +26,7 @@ ssh tusker.unl.edu -l demoXXXX
 Preparation
 -----------
 
-**[Download](attachments/1246451/1179891.zip) the demo code.**
+**[Download](https://unl.box.com/s/kopsfrp6ibnfds65it0g2oe3zmp3jxtx) the demo code.**
 
 Copy the two folders to the clipboard 
 
diff --git a/content/faq/_index.md b/content/faq/_index.md
index ced10c8c43e60640882f27974577e52455e190ca..1090e762238e137bcedf7e5e923bf2848b494010 100644
--- a/content/faq/_index.md
+++ b/content/faq/_index.md
@@ -173,5 +173,5 @@ Of course! We have an open door policy and invite you to stop by
 anytime Monday through Friday between 9 am and 5 pm. One of the HCC
 staff would be happy to help you with whatever problem or question you
 have.  Alternatively, you can drop one of us a line and we'll arrange a
-time to meet (http://hcc.unl.edu/contact-us). 
+time to meet:  [Contact Us](https://hcc.unl.edu/contact-us).
 
diff --git a/content/guides/running_applications/Jupyter.md b/content/guides/running_applications/Jupyter.md
index 6a8d0b3e542bb590295e96c7d8d4c484c2c515d2..442133957028bc65e34a1beefac28eb30ea0cc3b 100644
--- a/content/guides/running_applications/Jupyter.md
+++ b/content/guides/running_applications/Jupyter.md
@@ -24,9 +24,8 @@ weight = 20
 
 	{{< figure src="/images/jupyterPush.png" >}}  
 
-3.	Choose a job profile. Select "Local Jupyter Notebook" for light tasks such as debugging or small-scale testing.
-Select the other options based on your computing needs. Note that a local Jupyter Notebook will save to your "home" 
-directory, while the other options save to your "work" directory.
+3.	Choose a job profile. Select "Noteboook via SLURM Job | Small (1 core, 4GB RAM, 8 hours)" for light tasks such as debugging or small-scale testing.
+Select the other options based on your computing needs. Note that a SLURM Job will save to your "work" directory.
 
 {{< figure src="/images/jupyterjob.png" >}}
 
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
index a709aaefa93ba8595ada3a63a2fdd789a7fb6081..deb9548ce639c06043447c45cc82884cdff53932 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/_index.md
@@ -7,7 +7,7 @@ weight = "52"
 
 [BLAST] (https://blast.ncbi.nlm.nih.gov/Blast.cgi) is a local alignment tool that finds similarity between sequences. This tool compares nucleotide or protein sequences to sequence databases, and calculates significance of matches. Sometimes these input sequences are large and using the command-line BLAST is required.
 
-The following pages, [Create Local BLAST Database](create_local_blast_database) and [Running BLAST Alignment](running_blast_alignment) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.
+The following pages, [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}) and [Running BLAST Alignment]({{<relref "running_blast_alignment" >}}) describe how to run some of the most common BLAST executables as a single job using the SLURM scheduler on HCC.
 
 
 ### Useful Information
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
index 6423e3f0457bd60c536cafabf8d7bf0d4a9868f2..babb649362326e24e93e20d7a42a70545a34b837 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
@@ -28,7 +28,7 @@ $ blastn -help
 These BLAST alignment commands are multi-threaded, and therefore using the BLAST option **-num_threads <number_of_CPUs>** is recommended.
 
 
-HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In order to use these resources, the ["biodata" module] (../../../biodata_module) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
+HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In order to use these resources, the ["biodata" module] ({{<relref "/guides/running_applications/bioinformatics_tools/biodata_module">}}) needs to be loaded first. The **$BLAST** variable contains the following currently available databases:
 
 - **16SMicrobial**
 - **env_nt**
@@ -50,12 +50,13 @@ HCC hosts multiple BLAST databases and indices on both Tusker and Crane. In orde
 - **tsa_nr**
 - **tsa_nt**
 
-If you want to create and use a BLAST database that is not mentioned above, check [Create Local BLAST Database](create_local_blast_database).
+If you want to create and use a BLAST database that is not mentioned above, check [Create Local BLAST Database]({{<relref "create_local_blast_database" >}}).
 
 
 Basic SLURM example of nucleotide BLAST run against the non-redundant **nt** BLAST database with `8 CPUs` is provided below. When running BLAST alignment, it is recommended to first copy the query and database files to the **/scratch/** directory of the worker node. Moreover, the BLAST output is also saved in this directory (**/scratch/blastn_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
 {{% notice info %}}
 **Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+**This example will first copy your database to faster local storage called “scratch”.  This can greatly improve performance!**
 {{% /notice %}}
 
 {{% panel header="`blastn_alignment.submit`"%}}
@@ -95,6 +96,7 @@ The default BLAST output is in pairwise format. However, BLAST’s parameter **-
 Basic SLURM example of protein BLAST run against the non-redundant **nr **BLAST database with tabular output format and `8 CPUs` is shown below. Similarly as before, the query and database files are copied to the **/scratch/** directory. The BLAST output is also saved in this directory (**/scratch/blastx_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
 {{% notice info %}}
 **Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+**This example will first copy your database to faster local storage called “scratch”.  This can greatly improve performance!**
 {{% /notice %}}
 
 {{% panel header="`blastx_alignment.submit`"%}}
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
index 5d1e35101b995a53deeb2535ce4c70be5d6132f3..5b770061ec93f6a78c6ec0a37dfd86ea2306fa08 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/bwa/_index.md
@@ -36,4 +36,4 @@ $  bwa COMMAND
 or check the [BWA manual] (http://bio-bwa.sourceforge.net/bwa.shtml).
 
 
-The page[Running BWA Commands](running_bwa_commands) shows how to run BWA on HCC.
+The page [Running BWA Commands]({{<relref "running_bwa_commands" >}}) shows how to run BWA on HCC.
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
index 92a3208a05dd307f6d6ffeea5a0f43d595db117f..69ac4d03eb4609a8d6f06f160c461c874c874255 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/tophat_tophat2.md
@@ -14,7 +14,7 @@ The basic usage of TopHat2 is:
 {{< highlight bash >}}
 $ [tophat|tophat2] [options] index_prefix [input_reads_pair_1.[fasta|fastq] input_reads_pair_2.[fasta|fastq] | input_reads.[fasta|fastq]]
 {{< /highlight >}}
-where **index_prefix** is the basename of the genome index to be searched. This index is generated prior running TopHat/TopHat2 by using [Bowtie](bowtie)/[Bowtie2](bowtie2). 
+where **index_prefix** is the basename of the genome index to be searched. This index is generated prior running TopHat/TopHat2 by using [Bowtie]({{<relref "bowtie" >}})/[Bowtie2]({{<relref "bowtie2" >}}). 
 
 TopHat2 uses single or comma-separated list of paired-end and single-end reads in fasta or fastq format. The single-end reads need to be provided after the paired-end reads.
 
diff --git a/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md b/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
index 7fd7db27144779be73422683ce4b5600295eaf5d..45f9d16e54f721e0f36814ae66aa650a57fdf13b 100644
--- a/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/biodata_module/_index.md
@@ -80,4 +80,4 @@ cp /scratch/blast_nucleotide.results .
 
 
 The organisms and their appropriate environmental variables for all genomes and chromosome files, as well as for short read aligned indices are shown on the link below:  
-[Organisms](#organisms)
+[Organisms]({{<relref "organisms" >}})
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
index 9399d8e3898979f4917535e1958c921605cc5717..efe441b273cf60f9e5580cbf00438943871e34c3 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/bamtools/_index.md
@@ -36,4 +36,4 @@ $ bamtools help COMMAND
 or check the BamTools web, https://github.com/pezmaster31/bamtools/wiki.
 
 
-The page [Running BamTools Commands](running_bamtools_commands) shows how to run BamTools on HCC.
+The page [Running BamTools Commands]({{<relref "running_bamtools_commands" >}}) shows how to run BamTools on HCC.
diff --git a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
index 0246ba99e4fbd988b0273676ef7983d0e8908aa4..df9a00e249745424df56d468de309da6f4971c81 100644
--- a/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
+++ b/content/guides/running_applications/bioinformatics_tools/data_manipulation_tools/samtools/_index.md
@@ -42,4 +42,4 @@ $ samtools COMMAND
 or check the [SAMtools manual] (http://www.htslib.org/doc/samtools.html).
 
 
-The page [Running SAMtools Commands](running_samtools_commands) shows how to run SAMtools on HCC.
+The page [Running SAMtools Commands]({{<relref "running_samtools_commands" >}}) shows how to run SAMtools on HCC.
diff --git a/static/images/jupyterjob.png b/static/images/jupyterjob.png
index 961c2d9b1189c198eaaec9ec5a6a000add8aa59d..e576aea9fa2de2f20c26a4f66c5ad872bb748497 100644
Binary files a/static/images/jupyterjob.png and b/static/images/jupyterjob.png differ