Glotaran Wiki

acknowledgements

2012-01-13T14:43:44+02:00

General Catharina Hippius, René Williams, and Frank Würthner generously provided a sample dataset which is included in a demo project. The global and target analysis of these data is 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.

application

2010-12-03T15:28:19+02:00

This page is still under construction. Glotaran stands for Global and Target Analysis and, as such, is sometimes also written as GloTarAn. Glotaran was born out of the need for an open-source, platform independent and extensible data-analysis software tool with support for interactive model exploration and visualization of analysis results. Development on Glotaran was started at the physics department of the VU University Amsterdam as a graphical user interface (GUI) for the R-package TIMP [1].…

calender

2012-01-13T18:30:09+02:00

2012 To be announced 2013 To be announced 2014 To be announced

color_and_line_convention

2012-01-31T11:44:33+02:00

All plots that are generated in Glotarn has same rules for using line colors and line styles. The sequence in which colors are used for plots in Glotaran is the following: Name RGB code Example BLACK (0, 0, 0) RED (255, 0, 0) BLUE (0, 0, 255) GREEN (0, 255, 0) MAGENTA (255, 0, 255) CYAN (0, 255, 255) YELLOW (255, 255, …

configuration

2010-12-07T13:46:26+02:00

To make use of all of the functionality in Glotaran requires a working installation of R on the machine, with the R-Packages TIMP and Rserve installed. If you have not yet installed R, please refer to the official R-project website for instruction, before proceeding with these notes.

developers

2010-12-04T10:55:49+02:00

There are many ways to contribute to Glotaran. The best way it to simply use it, and provide feedback by e-mail, phone or in person. Tell the developers what works well and what improvements could be made. Another way is to directly file bug reports if you find bugs or file a feature request if you feel something is really missing. It's possible to file bug reports or feature request in the Issue Tracker called Bugzilla1. Finally it's of course also possible to join the ranks of the developer yo…

faq

2010-12-08T11:36:13+02:00

1. How do I start an analysis? A. Right click the analysis file from the project explorer and select 'Run analysis' from the pop-up menu. 2. Why can't I edit my model? A. It is not (or no longer) possible to edit the model files directly. Rather they are dragged onto the analysis scheme editor from which they can be edited.

file_formats

2012-01-14T23:33:02+02:00

Several file formats for reading in data are supported by Glotaran. Two types of files can be distinguished: * Plain text or ASCII, including the Time explicit format and the Wavelength explicit format which both have extension ”.ascii” and the RAW format which has the extension ”.raw”. * Binary including ”.img” files available from Streak Cameras of Hamamatsu Photonics () and ”.sdt” files with FLIM images from Becker & Hickl Gmbh ()…

installation

2011-11-25T11:47:08+02:00

Before installing Glotaran, please check to see if your system meets the specified system requirements. Glotaran can be downloaded from this location, see also the “Downloads” page on this website. Note that there are different installers for each operating system (Linux, Windows, Mac OS X, ...). Alternatively, a System Independent Zip distribution is also available which runs on any platform that has Java 1.6 or greater installed.

introduction

2010-12-03T15:38:19+02:00

This page is still heavily under construction, please check back in a few days. This document serves as an introduction to the concepts of global and target data-analysis in the context of biophysics. It motivates the development of Glotaran, the primary goal of this project. Section 1.1 functions as a brief introduction to the field of biophysics and science in general. Here the scientific process or loop of hypothesis, experiment and data-analysis is introduced. Also the nature of the data ob…

quick_introduction

2009-11-30T16:22:15+02:00

This is a quick introduction into the working of Glotaran based on a demonstration project included with the program. In the following steps we will 1) start a new project, 2) open a dataset, 3) edit a model, 4) start an analysis and 5) analyse the results.

requirements

2011-07-26T15:21:32+02:00

All platforms * 1+ GHz CPU * 1GB+ of RAM * 250MB of disk space * Java 1.6 Run Time Environment (update 26 or higher recommended). * R-2.6.0 or higher (with the TIMP or higher and Rserve packages installed) Windows specific In principle Glotaran should work on Windows XP, Vista, 7 or higher, provided the latest update of the Java Run Time Environment (JRE) version 1.6 is installed. The latest version can be download from Java.com.

roadmap

2012-01-13T18:26:32+02:00

start

2012-01-30T16:45:07+02:00

Glotaran is a tool for interactive global and target analysis of time-resolved spectroscopy and microscopy data. It is an open source software application on which the development was started at the Biophysics department of the VU University Amsterdam, as part of a NWO funded research project, by Joris Snellenburg and Sergey Laptenok under supervision of Ivo van Stokkum.

theory

2010-12-04T09:24:00+02:00

This page is still very heavily under construction, please check back in a few days. Time-resolved spectroscopy or microscopy is the study of dynamic processes in (bio) molecular systems by means of spectroscopic or microscopic techniques. Generally it involves the use of some source of illumination to change the properties of the system and then observing the effect of these changes by detecting fluorescence or absorption over time as a function of one or more variables. The result is some for…