Docker container for E-Cell3
Docker allows software to be packaged into containers: self-contained environments that contain everything needed to run the software. Containers can be run anywhere (containers run in modern Linux kernels, but can be run on Windows and Mac as well using a virtual machine called boot2docker). E-Cell3's Docker image is stored in Docker Hub; the source Dockerfile is in Github. Our E-Cell3 image is based on ecell/spatiocyte.
E-Cell3 with CUI To run E-Cell3 docker container, run
docker run -i -t ecell/spatiocyte /bin/bash Now you are in E-Cell3 container, next run
ecell3-session
E-Cell3 with GUI To start ecell3-session-monitor (GUI simulation monitor), you need to use VNC. In this case, run docker with
docker run -p 5901:5901 -i -t ecell/spatiocyte /bin/bash After going to E-Cell3 container, run
vncserver :1 -geometry 1360x768 -depth 24 If you use boot2docker, connect VNC server for
192.168.99.100:5901 otherwise
localhost:5901 To connect VNC server, you need to install VNC client software like UltraVNC. Mac OS X has a built-in VNC client.
Vagrant box
We moved to docker from vagrant! We have created an E-Cell3 vagrant box to run out of the box in a virtual machine. To run a virtual version of E-Cell3 on your machine, follow these steps
download and install Oracle's Virtual Box from http://www.oracle.com/technetwork/server-storage/virtualbox/downloads/index.html download and install Vagrant from http://www.vagrantup.com/ To start ecell3-session, start Terminal and run following commands vagrant box add ecell3 http://dev.e-cell.org/downloads/ecell3.box vagrant init ecell3 vagrant up vagrant ssh ecell3-session If you would like to start ecell3-session-monitor, you need to install and run Xserver(Xquartz in Mac, Xming in Windows). And use ssh X-forwarding with following commands vagrant ssh -- -X ecell3-session-monitor
Source code
All the source code from the E-Cell project is now available on https://github.com/ecell. You will also find the source code of the E-Cell 3 project under the same organization. E-Cell has been developed using SourceForge's subversion repository since its inception, but we think that now is a good time to switch to a distributed version control system, and we chose GitHub. The development of E-Cell now continues on GitHub. The previous Subversion repository will be abandoned. We think that migration to GitHub will make it much easier for users to contribute to our project and also help us reach our next milestone more gracefully.
E-Cell IDE
E-Cell IDE (Integrated Development Environment) is a GUI application that aims to support development of diverse biological models. IDE, the term originally coined by the software development industry, refers to a tool that provides comprehensive functions required in wide ranges of product development. E-Cell IDE provides a foundation for typical biological modeling processes on top of the state-of-the-art biological simulator, E-Cell System. E-Cell IDE 1.1 release (Windows 32bit installer) E-Cell IDE 1.1 release (Windows 64bit installer) E-Cell IDE consists of three major components, pathway designer, simulator and analytical toolkit that are tightly integrated with each other.
SYSTEM REQUIREMENTS
E-Cell IDE currently runs on .NET Framework 2.0 or later versions. Supported operating systems include: Windows XP, Windows Vista and Windows 7.