Updated the setup intructions

_episodes/01-introduction.md

@@ -10,7 +10,6 @@ title: "1. Day 1: Opening and setups, Libra overview, Presentations"
 
 # 2. Logistic and setups
 
-
 # 3. Libra overview
 [Slides](../files/Alexey_Akimov/Libra-July8.pdf)
 

setup.md

@@ -1,10 +1,166 @@
 ---
 title: Setup
 ---
+
 <a name="toc"></a>
-# Coming up soon
+Table of Contnet 
+
+1. [Getting the CCR accounts and VPN](#1)
+2. [Libra](#2)
+3. [Terminal](#3)
+4. [Text editors](#4)
+5. [Molecular visualization and editing tools](#5)
+
+
+
+<a name="1"></a>[Back to TOC](#toc)
+# 1. Getting the CCR accounts and VPN
+
+Below are the steps you’ll need to take to get the accounts setup. This is a little confusing because you actually have two accounts.
+One is an account that gets you access to the University at Buffalo’s VPN network and the other is the account you’ll use to access CCR’s cluster.
+Please **read these steps and the instructions on the links shared here carefully.**  If you run into trouble, I recommend reviewing the steps again 
+to ensure you completed them all. If you have questions or problems, please contact [email protected]. 
+
+
+## Step 1:  Setup two factor authentication for your UB VPN account. 
+
+The username for this account is: **given to you by the CCR staff**
+
+Password: **sent in a separate email**
+
+Instructions can be found [here](https://ubccr.freshdesk.com/support/solutions/articles/13000094126-external-collaborator-industry-business-customer-access)
+
+
+## Step 2:  In order to connect to our machines, you have to be on the UB network.  You'll need to download and install **UB's Cisco VPN client.** 
+You will be receiving a separate email from Globus with the link to download this software.  If you do not already have a Globus account, 
+you will be instructed to create one at this point.  The UB account will not work for the Globus service. 
+
+NOTE: this link is only accessible using the email address this is getting sent to. 
+
+
+## Step 3:  Connect to the CCR VPN – instructions are in the first link above.
+
+When you start the Cisco software the first time you will need to enter the following in the "Connect to:" box: vpn.buffalo.edu and then 
+select CCR from the group drop down menu.  Enter the UB VPN username and password from above and use Duo as your two step verification.
+
+Now that you have setup the UB account and connected to the VPN, you’ll be able to move forward with your CCR account. 
+
+
+## Step 4 (optional): If you’re unsure of your CCR account password you can reset it. Make sure you’re connected to the UB VPN and go to 
+[CCR’s identity management portal](https://idm.ccr.buffalo.edu), enter your CCR username and click the Next button.
+Then click the “forgot your password?” link to generate a one-time password reset link.  The link contained in this email only lasts for 15 minutes. 
+
+Your account has two factor authentication enabled.  If you have trouble remembering how to use it, please refer 
+to [the documentation](https://docs.ccr.buffalo.edu/en/latest/2fa/)
+
+
+## Step 5: FINALLY…Connect to CCR!
+
+There are two ways to connect to our systems:
+
+    * [OnDemand web portal](https://ondemand.ccr.buffalo.edu)
+
+    * If you choose to use a SSH client, you may login to our pool of front end servers with the address: vortex.ccr.buffalo.edu.  
+      You must use SSH keys as we do not accept passwords over SSH.  We have information about this [here](https://docs.ccr.buffalo.edu/en/latest/hpc/login/)
+
+All documentation for using our systems can be found [here](https://docs.ccr.buffalo.edu)
+
+
+<a name="2"></a>[Back to TOC](#toc)
+# 2. Libra and other Python libraries
+
+This workshop will be focused on the [Libra](https://github.com/Quantum-Dynamics-Hub/libra-code/tree/devel) package developed by the 
+[Akimov group](https://akimovlab.github.io/). 
+
+Although Libra and some of its strong and weak dependencies are already installed on UB CCR and will be directly accessible via
+the Jupyter notebooks on OnDemand, you may want/need to install them locally. Since most of the calculations we'll be doing 
+are not too intensive computationally, runnig most of them on your laptop shall not be a problem. 
+
+You may want to use this option, if you want to follow the hands-on exercises with Libra, but you have not been accepted as a fully-fledged 
+participant (the participant without full access to UB CCR resources, which may be because of your geographic location at the moment).
+
+Please follow the [installation instructions](https://github.com/Quantum-Dynamics-Hub/libra-code/tree/devel) to build the corresponding 
+environment, install all needed dependencies and packages, and build and install the Libra code itself. **Make sure to use the "devel" branch**. 
+
+
+<a name="3"></a>[Back to TOC](#toc)
+# 3. Terminal 
+
+The terminal is an interface in which you can type and execute text based commands. It is important to use the terminal to 
+run many computational chemistry software packages. There are several different types of terminal interfaces, called shells.
+In this tutorial, we will focus on using one of the most common shells, the bash shell. 
+How you acquire a bash shell terminal depends on the type of computer you have.
+
+## 3.1. Linux
+If you are using a Linux computer, you probably already know how to open the terminal window. 
+If the Terminal is not shown in menu of programs, you can use the key combination CTRL + ATL + T to open the terminal window.
+
+## 3.2. Mac OS X
+On Mac OS X, a Terimanl application is built into your system. Open the Terminal from Applications -> Utilities -> Terminal.
+
+## 3.3. Windows 11
+Windows has a built in command line interface. To access it, click the Windows Key + R, type cmd, press Enter.
+**However,** this interface is not a bash application. Therefore, the commands for navigating and creating files discussed below
+ will not be the same. We recommend you installing the [Windows Subsystem for Linux](https://devblogs.microsoft.com/commandline/learn-about-windows-console-and-windows-subsystem-for-linux-wsl/) instead. Please follow [these instructions](https://docs.microsoft.com/en-us/windows/wsl/install-win10) to install 
+ it for your system. This will allow you having a fully-fledged Linux/Unix terminal experience while still working on Windows 10.
+
+## 3.4. Resources
+- [Using the command line](https://ryanstutorials.net/linuxtutorial/commandline.php)
+- [Navigation in bash](https://ryanstutorials.net/linuxtutorial/navigation.php)
+- [Making and removing directories, copying and deleting files](https://ryanstutorials.net/linuxtutorial/filemanipulation.php)
+
+
+<a name="4"></a>[Back to TOC](#toc)
+# 4. Text Editors
+
+You will often need to create or read text files.  Opening a text file in a word processing program,
+like Microsoft Word or Google Docs, introduces a lot of formatting that is not needed. 
+You need to use a text editor to read and write these files. There are many choices. You don't need to learn to 
+use all of these at the beginning, just find one that works for you. 
+
+## 4.1. Vi/vim
+Vi/vim is one of the most ubiquitous text editors. It is installed on virtually every Linux computer in the world, 
+so if you ever log on to a unfamiliar machine, it will be available to you. 
+Vi is accessed from the command line; it doesn't have or need a graphical interface so it can operate on the most bare bones computers.
+However, it is not intuitive to use and can be difficult for beginners.
+- [Interactive vim tutorial](https://www.openvim.com/)
+- [Getting started with vi](https://ryanstutorials.net/linuxtutorial/vi.php)
+
+## 4.2. Far 3
+[Far3](https://www.farmanager.com/) is a very handy file and archive manager. Features rather convenient graphical interface and some
+convenient manipulation options such as cutting any blocks of text, syntax highlightling, remote drive access, etc. Don't get
+scared by its old-style "Norton/Midnight Commander" look. You'll love it. If you run Windows, this is definitely our recommendation. 
+
+![](/fig/setup/far.png){:width="80%"}
+
+
+## 4.3. Atom
+[Atom](https://atom.io/) is a modern text editor that is very intuitive to use. You probably don't even need 
+to read the tutorial below to figure out how to create and save files. Standard downloads are available for Linux, Mac, and Windows.
+- [Getting started with atom](https://flight-manual.atom.io/getting-started/sections/atom-basics/)
+
+## 4.4. Emacs
+Similar to vi/vim, emacs is a command line text editor that is already part of almost all Linux distributions.
+Emacs can also be used as an RSS reader or file manager.
+- [Emacs tutorial](https://www.gnu.org/software/emacs/tour/) The section called Beginner tips near the bottom of the page is particularly helpful.
+
+## 4.5. Sublime
+[Sublime](https://www.sublimetext.com/) is an intuitive text editor that makes looking at files with multiple sections easy. 
+t allows split screen editing and is very customizable.
+
+
+<a name="5"></a>[Back to TOC](#toc)
+# 5. Molecular visualization and editing tools
+
+|   |   |
+|---|---|
+| [VESTA](https://jp-minerals.org/vesta/en/) | ![](/fig/setup/vesta.png){:width="80%"} | [Tutorials by Brendan Smith](https://github.com/compchem-cybertraining/Tutorials_Editing_Visualization) |
+| [VMD](https://www.ks.uiuc.edu/) | ![](/fig/setup/vmd.png){:width="80%"} |
+| [IQmol](http://iqmol.org/)  | ![](/fig/setup/IQmol.png){:width="80%"} | [Tutorial by Alexey Akimov](https://youtu.be/BXtPtkUJVqc) |
+| [Avogadro](https://avogadro.cc/) | ![](/fig/setup/avogadro.png){:width="80%"} |
+
+
 
----
 
 
 {% include links.md %}