# Glotaran: a graphical user interface for the R-package TIMP

## Introduction

Glotaran stands for Global and Target Analysis. It is designed to be a graphical front end for the R-package TIMP, providing an alternative for the script language used there. However, due to the immense extensibility of the platform on top of which Glotaran was built can potentially provide a lot more functionality than TIMP of the R platform itself would allow for. This functionality includes but it not limited to:

- Interactive data exploration and data selection
- Visual model building
- Interactive data analysis
- Easy extensibility for custom binary/proprietary data support.

Glotaran consists of 2 parts: the core user interface, and the computational engine. The user interface was built using Java based technology and as a result it can potentially run on any operating system for which Java supported exists. The computational engine was built on top of the R-platform. R compiles and runs on a wide variety of UNIX platforms and similar systems (including FreeBSD and Linux), Windows and MacOS. The core user interface and the computational engine communicate via a wrapper library over the standard TCP/IP protocal. This means the engine can run on either the local machine, or on a remote machine connected to the local machine via a network (not yet supported). Detailed system requirements can be found in the next section.

## System requirements

- 1+ GHz CPU
- 1GB+ of RAM
- 250MB of disk space
- Java Run Time Environment
- R Computational Platform

## Installation

### Local machine only

#### Glotaran

Included with this distribution is a so called jar file. In order to execute this file, wether it be on Windows, Linux or Mac you need to have the Java (tm) Runtime Platform installed.
The latest version of the Java Run Time can be downloaded from the official website for Java:
http://www.java.com/getjava/

To install Glotaran either double click the setup.jar file and select "Run using Java" or run for the commandline:
java - jar setup.jar

#### Note for Windows Vista and Windows 7 users

If the installer is not run with elevated administrator rights it is not possible to install Glotaran in the Program Files folder; one should install the program in the personal user folder.

Also, in onder to interface with R, Glotaran needs full network access. Please make sure it is not blocked by the Windows Firewall, or any other personal firewall.

#### R

This program also requires a working installation of R on your machine, with the R-Packages TIMP and Rserve installed.
If you don't have R and the packages TIMP and Rserve installed already, please do so before you proceed with the installation. Instructions follow below:

##### TIMP

To install the R-package TIMP, please take the following steps:

- Start R; either from the command line or start the RGui
- Execute the following command:
- install.packages("TIMP")

##### Rserve

To install the R-package Rserve, please take the following steps:

- Start R; either from the command line or start the RGui
- Execute the following command:
- install.packages("Rserve")

##### Start Rserve

Before you run the Glotaran program it is important that you do the following:

- Start R; either from the command line or start the RGui
- Execute the following commands:
- library(Rserve)
- Rserve() (for Windows and Linux/Unix) or Rserve(args="--no-save") (for Mac OS X)
- Start Glotaran from your application menu. Alternatively you can start Glotaran using the glotaran executable in the bin folder of the installation folder.

Please note that Glotaran communicates with Rserve via TCP/IP, this means that you need to 'unblock' Glotaran and Rserve in your firewall settings. Under Windows your are usually presented with a dialog window the first time your start Glotaran, make sure to select 'unblock' here.

### Using a remote computational server

This functionality is not yet implemented but will be available in the final release.

## Quick start

Additional documentation, examples and screencasts are available from the website timpgui.org.

In addition, included with the program is a sample project for which a quick start tuorial is available on the documentation page of the website.

## Acknowledgments

Catharina Hippius, René Williams, and Frank Würthner generously provided the sample dataset.
The global and target analysis of these demo data are described in Figures 5-9 of:
C. Hippius, I.H.M. van Stokkum, E. Zangrando, R.M. Williams, and F. Würthner.
Excited state interactions in calix[4]arene-perylene bisimide dye conjugates: Global and target analysis of supramolecular building blocks.
Journal of Physical Chemistry C, 111(37):13988-13996, 2007.

Maria Voitovich is thanked for her contribution to writing the functions for reading binary sdt Becker & Hickl files.

Ralf Seger is thanked for his contribution in developing the interface used to communicate with the R computational platform.