Adding new page -- use examples -- and a slight update to 'getting started'

.gitignore

@@ -1,2 +1,3 @@
 env/
 site/
+.venv/

docs/using/community_examples.md

@@ -0,0 +1,23 @@
+# Community Usage Examples
+
+This collects [github gists][github_gists] which HTCF users have written to 
+serve as examples of HTCF usage patterns. We encourage you to write your own 
+gists which describe common tasks you do on the cluster, and share them. This 
+is a good way of keeping a record of how you use HTCF for yourself and future 
+lab mates, and can help the whole HTCF community improve and optimize usage. 
+Feel free to ask questions of the gist writer through the github interface.
+
+- [Turning Exploratory Data Analysis into containerized cmd line scripts in R][eda_to_containerized_cmd]
+
+	> This gist describes a method of interactively exploring data in R in a way that 
+allows the user to simultaneously develop a command line script. Critically, this 
+describes how to use [renv][renv_link] to manage a virtual environment. 
+This makes it simple to create a [docker][docker_link] container. Since 
+[singularity][singularity_link] can run docker containers, this means that you 
+can easily turn EDA into reproducible results which may be easily run on HTCF.
+
+[github_gists]: https://docs.github.com/en/get-started/writing-on-github/editing-and-sharing-content-with-gists/creating-gists
+[renv_link]: https://rstudio.github.io/renv/articles/renv.html
+[docker_link]: https://www.docker.com/
+[singularity_link]: https://sylabs.io/singularity/
+[eda_to_containerized_cmd]: https://gist.github.com/cmatKhan/e08a262b45bed5465301530b7319e6b3

docs/using/getstarted.md

@@ -20,6 +20,8 @@ The login server, `login.htcf.wustl.edu` is accessible via ssh.
 
 Before using the HTCF, it's important to read through and understand:
 
+1. The difference between [login, interactive and compute](#jobs) nodes
+
 1. The [HTCF Storage](../storage/index.md)
 
 2. Using [software](../software.md) on the HTCF
@@ -48,11 +50,20 @@ High Throughput Storage is a distrubuted file system able to handle tens of GBs/
 
 ## Jobs
 
-### Resources
+When you first log in to HTCF, you are interacting with a part of the cluster 
+which is specifically designated for users to log in, log off, submit jobs and 
+move data between storage spaces (eg `scratch` and `lts`).  
 
-The number of CPUs and MBs of RAM per node can be found using the Slurm sinfo command:
+!!! Note
+    Do not do any analysis or computation on the login node
 
-    $ sinfo -N -p general -o '%n %c %m'
+If you need to prototype or do some interactive work (eg, exploratory data analysis) 
+on HTCF, then you should use an [interative session](#Interactive)  
+
+The ultimate goal this type of interactive work is to automate tasks such that 
+they may be submitted to the SLURM scheduler and run on the `compute` nodes. 
+The majority of the compute resources on HTCF are these general compute nodes. 
+Scheduling on these nodes is achieved using the command `sbatch`.
 
 ### Interactive 
 
@@ -155,3 +166,10 @@ $ srun --ntasks-per-node=1 --jobid=12345 nvidia-smi
 |    0                12043      C   guppy_basecaller                 4753MiB |
 +-----------------------------------------------------------------------------+
 ~~~~
+
+### Resources
+
+The number of CPUs and MBs of RAM per node can be found using the Slurm sinfo command:
+
+    $ sinfo -N -p general -o '%n %c %m'
+

mkdocs.yml

@@ -70,3 +70,4 @@ nav:
   - Examples:
     - 'software/examples/r_mpi/index.md'
 # - R+MPI: 'software/examples/r_with_mpi.md'
+- "Use Examples": 'using/community_examples.md'