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This is an introduction page for the SDCSB Cytoscape Advanced Tutorial.
This tutorial is a shorter version of advanced Cytoscape workshop at VIZBI 2015. The goal of this course is learning how to use Cytoscape from external tool such as IPython Notebook to make your data visualization workflow reproducible. If you have some experience with Cytoscape, and are interested in driving Cytoscape from external tools or scripts, this is the right course for you.
- Learn how to use snapshot of data visualization workspace with Docker
- Understand fundamentals of language-agnostic RESTful API for Cytoscape (cyREST)
- Drive Cytoscape from IPython Notebook
- Some experience with Cytoscape
- Basic Python
- Just basics, such as built-in data types, conditional statements and loops.
- We will use Python as an example programming language to control Cytoscape, but most of the concepts are universal, i.e. language-agnostic.
IMPORTANT: You should install all of the required software BEFORE the meeting. If you have any problem to install those, please send me an email (kono ucsd edu).
- Mac OS X Mavericks or newer
- Windows 7 or 8 (64 bit version ONLY)
- Ubuntu (14.x highly recommended)
Please install ALL of the following before the session
Installing Cytoscape is very straightforward. You just need to install Java and then Cytoscape.
Simply double-click the installers and follow the instructions.
There is only one required App (formerly called Plugins) for this tutorial:
* [cyREST](http://apps.cytoscape.org/apps/cyrest)
- Start Cytoscape 3.2.1
- Open web browser
- Visit this page
- Click Install button
Note: Currently, we have an issue to install latest version of cyREST from App Manager. To install the latest one, please use the Install button on the App Store page.
(You can skip this section if you already have one.)
The entire course materials will be uploaded to this repository. This means you need a GitHub account to fork it.
GitHub has a great collection of documents for users. Please visit their help page if you have problems.
You need git to clone the forked repository.
Important: If you cannot run the following command on your machine after installing Docker, please contact me as soon as possible:
docker run -d -p 80:8888 -v $PWD:/notebooks -e "PASSWORD=you_can_use_your_own_pw" -e "USE_HTTP=1" idekerlab/vizbi-2015
(You can use your own password)
Please read the Homework section in this page to install Docker. For Mac users, here is a step-by-step instruction:
For Windows and Linux, installation should be straightforward (I think...)
We use Docker for this tutorial to use identical data analysis/visualization environment for everyone. This means you can build your own environment if you are an experienced Python user. You can create same IPython Notebook server using virtualenv. If you prefer building data analysis environment directly on your machine, you can install the software one by one manually by reading contents of this file (and its parent):
You need to install about 20 python packages though...
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Make sure you have installed Docker/boot2docker
-
Have you exported required environment variables?
- Type
boot2docker shellinitto display those
- Type
-
Follow this instruction to make sure you have not skipped any important steps:
If you get some random errors related to boot2docker, try the following to create new VM
~/prog/git/sdcsb-advanced-tutorial (master ✔) ᐅ boot2docker stop
~/prog/git/sdcsb-advanced-tutorial (master ✔) ᐅ boot2docker delete
~/prog/git/sdcsb-advanced-tutorial (master ✔) ᐅ boot2docker init
~/prog/git/sdcsb-advanced-tutorial (master ✔) ᐅ boot2docker up
Waiting for VM and Docker daemon to start...
......................ooooooooooooooooooo
Started.
Writing /Users/kono/.boot2docker/certs/boot2docker-vm/ca.pem
Writing /Users/kono/.boot2docker/certs/boot2docker-vm/cert.pem
Writing /Users/kono/.boot2docker/certs/boot2docker-vm/key.pem
To connect the Docker client to the Docker daemon, please set:
export DOCKER_HOST=tcp://192.168.59.103:2376
export DOCKER_CERT_PATH=/Users/kono/.boot2docker/certs/boot2docker-vm
export DOCKER_TLS_VERIFY=1
~/prog/git/sdcsb-advanced-tutorial (master ✔) ᐅ boot2docker status
runningIf you are a Mac or Windows user, you are running Docker on boot2docker virtual machine. To access it, you need to use the VM's IP address. You can get it by typing the following command:
~ ᐅ boot2docker ip
192.168.59.103If you know how to fork and clone repositories, please do so! (but don't worry if you don't know how to do it. I'll show you how in the workshop.)