Welcome

New Members

Welcome to the team!

These Wiki pages contain a lot of information, no need to read it all at once, you can always come back to it for reference.

Everyone in our group is happy to assist in whatever is needed. Specifically, in a software development group like ours, we know that big goals could only be achieved when working together.

If you think something in this Wiki should be modified/updated, feel free to make this change yourself or consult someone if you are unsure.

How to start?

• Read our group’s Culture and Values, this information page will give you some understanding of our vision for the group and work ethics that will guide you down the road.

• Get a taste of our world by watching this 30 min talk - Automated Kinetic Model Generation and Refinement: An Ecosystem of Software Tools given by Alon in November 2020.

• Download Slack: Slack is the way we communicate as a team. After downloading, notify us to receive a link to our group workspace.

• Sign up for a Github account: GitHub is where we store and manage software. After creating your account, let us know your GitHub username so we can add you as a developer to our repositories.

• Workspace: Our office is located in the Chemical Engineering Department on the third floor, room 321. This is where graduate students sit. Undergraduate students can use the available computers at the office or work on their own computer. We encourage undergraduate students to work from the office as well to make connections with group members and to ask questions.

• Get Linux: Linux is an excellent platform for programmers, both new and experienced. Our office and lab computers mostly run Linux. If you'd like, you can also convert your own machine to gain even more experience with it. (Practical tips: MS Office is unavailable on Linux, there a free similar software, or you can use Office 365 online.) The Linux flavor we will be using is called “Ubuntu“.

  There are several ways to install Linux:

  • Pure Linux: You can install Linux on your PC/laptop instead of Windows. For that, you’ll need an “Ubuntu live” USB installation drive (so no need to download Ubuntu), ask Alon or Mark for this USB drive. This is the recommended way for experienced users or for those who’d like to become experienced users.
  • Dual Boot: You can configure your computer to be able to boot up both Windows and Ubuntu (one at a time, you’ll need to restart your computer every time you want to switch between them). Setting this up requires some experience, ask us for help.
  • Virtual Machine: This is the recommended way for new users. Your computer will primarily run Windows, and you’ll experience the virtual machine (VM) as an Ubuntu “window” inside Windows. You can easily go back and forth between Ubuntu and Windows. Read here for how to set up a Linux VM on your Windows computer.

• Python: Python is the main programming language we will be using. See "Python" on our Wiki for more information and how to properly install it.

• Bash: “Shell” is an interactive interface that allows users to execute commands on Linux (in a terminal). “Bash” stands for “Born Again Shell”. You should be familiar with some very basic Bash commands. See "bash" on our Wiki for more information.

• Git: Git is a version control tool for software development. You should know git. See "git" on our Wiki

Our office and lab computers come pre-installed with the environments and software tools we develop. Once on Linux, and now that you have Anaconda with Python and you know git, you can also install the software repositories on your own computer, if you'd like:

(Tip: Create a new folder under Home named "Code" and clone all your git repositories there.)

Before installing these software repositories, it’s recommended to type sudo apt install gcc g++ make to make sure you have all the necessary compilers installed.

• RMG: Follow the instructions in this link to install RMG, start from step number 3.

  Note: When you get to step number 6, make sure to add these commands to your .bashrc file. Read here to find out more about what this file is and how to edit it.

  When arriving to step 7 of running RMG for the first time, copy an example RMG input file from the folder /Code/RMG-Py/examples/rmg/super_minimal/. Paste this file in a new folder, e.g., /Code/runs/RMG/example1/. Open the terminal in this new folder, and type the following command to run RMG:

  python ~/Code/RMG-Py/rmg.py input.py

  You’re all set. You can explore the output created in this folder by RMG. Congrats!

• ARC

Once you get to Generating RSA SSH keys and defining servers. Check out Set a password-less access (using an RSA SSH key) for further clarifications.

• T3