Welcome to the third edition of the ISMCO tutorial on Current methods and open challenges for structural modeling in cancer immunotherapy!!!
| Activity | Duration (m) | Time (PST) | Time (CST) |
|---|---|---|---|
| Opening | 5 | 3:00 | 5:00 |
| Cellular immunity for cancer immunotherapy | 15 | - | - |
| Exploring IEDB resources | 45 | - | - |
| Break | 15 | 4:05 | 6:05 |
| Downloading structures from PDB | 5 | 4:20 | 6:20 |
| Visualizing pHLA structures w Chimera | 35 | - | - |
| Break | 15 | 5:00 | 7:00 |
| Intro to pHLA modeling | 10 | 5:15 | 7:15 |
| DINC (webserver) | 10 | - | - |
| DockTope (webserver) | 5 | - | - |
| Break | 15 | 5:40 | 7:40 |
| Intro to Google Colab | 5 | 5:55 | 7:55 |
| Running Ape-Gen w Google Colab | 10 | - | - |
| Intro to HLA-Arena | 15 | - | - |
| HLA-Arena workflow 0 demo (ApeGen) | 10 | - | - |
| HLA-Arena workflow 1 demo (DINC) | 5 | - | - |
| HLA-Arena workflow 3 demo (mhcflurry + APE-Gen) | 5 | - | - |
| Conclusion | 5 | 6:45 | 8:45 |
https://riceuniversity.zoom.us/j/96681193182?pwd=MVo3bkt0eW9Vb3NGMm1Ydmt1R1RTUT09
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UCSF Chimera: T04, requires downloading UCSF Chimera
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APE-Gen with Google Colab: T05, requires downloading the notebook and opening it on Google Colab
You will need to install the following programs PRIOR TO THE BEGINNING OF THE TUTORIAL! This is important since the download could take some time depending on your internet connection.
If you have any questions about the installation, please contact mmr9@rice.edu.
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For Microsoft Windows, click here to download and here(https://www.cgl.ucsf.edu/chimera/data/downloads/1.14/win64.html) to follow the instructions on how to install.
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For Mac OS X, click here to download and here to follow the instructions on how to install.
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For Linux, click here to download and here to follow the instructions on how to install.
- Find a intro do Google Colab here.
To run HLA-Arena you will need to first install Docker, unless you already have it. For that, follow the instructions in one of these links:
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Docker for Mac or Windows: https://www.docker.com/products/docker-desktop
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Docker for Linux: https://docs.docker.com/install
Next, in a command prompt, pull the HLA-Arena image from Docker Hub by typing:
docker pull kavrakilab/hla-arena
This step can take hours and it will require about 20 Gb of disk space.
In the command line (or prompt) run the following command:
docker run hello-world
You should see the following output:
Hello from Docker!
This message shows that your installation appears to be working correctly.
To generate this message, Docker took the following steps:
1. The Docker client contacted the Docker daemon.
2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
(amd64)
3. The Docker daemon created a new container from that image which runs the
executable that produces the output you are currently reading.
4. The Docker daemon streamed that output to the Docker client, which sent it
to your terminal.
To try something more ambitious, you can run an Ubuntu container with:
$ docker run -it ubuntu bash
Share images, automate workflows, and more with a free Docker ID:
https://hub.docker.com/
For more examples and ideas, visit:
https://docs.docker.com/get-started/
In the command line (or prompt) run the following command:
docker images
You should see an output like this:
REPOSITORY TAG IMAGE ID CREATED SIZE
kavrakilab/hla-arena latest e6cefe68c72a 2 months ago 20.6GB
Several of HLA-Arena workflows rely on Modeller to perform the homology modeling of a given HLA receptor. This modeling task is integrated into a specific HLA-Arena function (more details here). However, using Modeller requires you to register and obtain your own license key, if you do not already have one. First, follow instructions on the Modeller registration page.
Once you have the key, you can permanently update the HLA-Arena container with your key. For that, you should execute the commands below, replacing MODELLER_KEY with the correct key.
docker run -it kavrakilab/hla-arena
sed -i "s/XXXX/MODELLER_KEY/g" /conda/envs/apegen/lib/modeller-9.20/modlib/modeller/config.py
exit
docker commit $(docker ps -a | sed -n 2p | awk '{ print $1 }') kavrakilab/hla-arena
docker container rm $(docker ps -a | sed -n 2p | awk '{ print $1 }')
For more information on HLA-Arena, you can check the HLA-Arena github repository.
HLA-Arena video tutorial (Part 1)