firstMEM software

The present software is a simplified, but general purpose, module that uses the Maximum Entropy Method to analyse the fluorescence kinetic data. It is written in Java in order to run on different platforms.

The software was developed by Eugene Novikov in 2002, when he was working together with Daniel Lavalette in the Molecular Biophysics Department of the Institute Curie in Orsay, France. At the moment, with permission of the developer, the software is supported and updated by SSTC team. For any questions regarding the software please contact us.

General description

The software package has been developed as a cross-platform envelope for the MemSys5 routine (Maximum Entropy Data Consultants Ltd) facilitating its use in biophysical applications. The MemSys5 routine had been originally delivered in FORTRAN. Therefore, to avoid any platform-specific features, MemSys5 had also been rewritten in Java. Besides import/export, data visualization and basic MEM-processing functionality, the software includes a simulation module to mimic real kinetics data. The MEM User Manual and MEM Video Manual (AVI, 25.6 MB) explains in detail the structure and the use of the software.

Installation

The software is delivered as a stand-alone compressed Java jar file, which nowadays can be run on virtually all machines and operating systems. First, one has to install Java Runtime Environment (JRE) or Java Development Kit (JDK), freely available on https://java.com/en/download/, before running the software.

Current limitations

The analysed data is not allowed to contain a negative amplitude. Therefore, a rising part such as the buildup of acceptor fluorescence upon donor excitation in FRET systems cannot be treated with this version. In addition, the software does not provide for deconvolution from the impulse response function. Here, the impulse response function is assumed to be a delta function.

Input requirements

The input file with the kinetic data should have three tab-separated columns with a one-line header as shown below for three data points:

Time:	Experiment:	Sigma:
2.5	8269	90.93404203
2.50	8193	90.5151921
2.51	8411	91.71150419
...

The first column contains time (in any units, e.g. seconds or nanoseconds), the second - experimental data (e.g. decay intensity) and the third - weighing factors, i.e. standard deviation of experimental data. You can further refer to the MEM User Manual for all details about input and output data. Since the software supports neither deconvolution nor negative pre-exponential factors the rising part of the data has to be cut.

The software is offered freely to the research community in order to promote and popularize the powerful and rigorous MEM approach. In spite of porting MemSys5 routine to Java this is a co-called derivative work and the license to MemSys5 is still required.

For MEMSys5 contact:
Maximum Entropy Data Consultants Ltd
South Hill, 42 Southgate St
Bury St Edmunds, Suffolk, IP33 2AZ, ENGLAND.
Email: sales@maxent.co.uk

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, ARISING FROM THE USE OF THE SOFTWARE.

To download the software use the provided link.

For any work reporting results obtained by firstMEM software you should use one of the following citations:

Maximum entropy analysis of polarized fluorescence decay of (E)GFP in aqueous solution. Eugene G. Novikov, Victor V. Skakun, Jan Willem Borst and Antonie JWG Visser. Methods Appl. Fluoresc. 6 (2018) 014001
Catherine Tetreau, Eugene Novikov, Martine Tourbez, and Daniel Lavalette. Kinetic Evidence for Three Photolyzable Taxonomic Conformational Substates in Oxymyoglobin, Biophys J. 82 (2002) 2148-2155.

History of updates:

01.2019 - version 1.3. Import of first kinetic point in a case of time zero is fixed (was skipped before). Clearing of analysis results after import of new data.
04.2018 - version 1.3. Update of the graphical representation. Preview kinetics in three modes: log(Rate), log(Lifetime) and Lifetime with correct rescaling of kinetics. Option to calculate an area and average lifetime (sum(p*tau)/sum(p)) in a specified interval (in order to compare with results of the ordinary discrete analysis of fluorescence kinetics).
04.2017 - version 1.2. Update of the original code to new Java version. Release on the sstcenter.com web site.