Welcome to the developers tutorials!
In here you will find everything that you need to start developing plug-ins for OptFlux.
Contents
- 1 First things first
- 2 Getting the code
- 3 OptFlux Architecture
- 4 Your first basic plug-in
- 5 Deployment and versioning
- 6 How To's
- 6.1 Accessing data from the clipboard
- 6.2 Performing a simulation and retrieving results
- 6.3 Creating a tabular view for your data
- 6.4 Performing an Optimization Procedure
- 6.5 Invoking other operations from your own
- 6.6 Adding results from your operation to the Clipboard
- 6.7 Developing your own GUI for an Operation
First things first
OptFlux is built on top of AIBench meaning that OptFlux itself is no more than set of plug-ins for the AIBench framework.
The AIBench Framework is a joint project by colleagues at University of Vigo and ourselves. You can find specific contacts and documentation for AIBench at its own website.
Version 2.3 (first fully open version of OptFlux) is composed of six main plug-ins all of which are distributed by default in the downloadable archives of OptFlux. Some extra plug-ins are also distributed in the main version although they are not part of what we call "the core".
This six plug-ins are the following:
- optflux.core - the core datatypes, viewers and operations to load/export and interact with models in several formats
- optflux.simulation - simulation related datatypes, operations and views. Wild-type, Gene and Reaction KO. (FBA, MOMA, ROOM, FVA, etc...)
- optflux.optimization - optimization specific datatypes, operations and views (Gene and Reaction KO optimization)
- optflux.biovisualizer - our own visualizer for biochemical networks. Support for CellDesigner layouts
- optflux.saveloadquit - just a save / load / quit project dedicated plug-in. Datatype agnostic as long as data is serializable.
- optflux.extraviewers - some extra viewers that we decided to include in the core release.
OptFlux is being developed using Eclipse IDE. We recommend using Eclipse to create your own plug-ins since we already provide ready-to-go classpath and project configurations for this IDE. You are, however, free to develop in any IDE you see fit. Please contact us if you are willing to provide a tutorial on how to get things going in any other IDE. We would very much appreciate that :)
You can download Eclipse here. We recommend version 3.5.* or above.
Getting the code
The code of OptFlux can be obtained either in specific versions format or, alternatively directly from SVN located at sourceforge.
From version packages
Starting at version 2.3, you can download a "ready-to-go" eclipse configuration of OptFlux.
This will allow you to import this project into Eclipse and start developing new plug-ins with very little effort.
Version specific source code distributions can be found here.