Department of Knowledge Technologies National Institute of Biology
GMOtrack

Generator of cost-effective GMO testing strategies

Description

GMOtrack is a command line utility that implements the GMOtrack algorithm. It generates cost-effective testing strategies for traceability of genetically modified organisms (GMO). Given a table of GMOs (along with the probabilities of their presence, the genetic elements present in their genome and a linear cost function) GMOtrack computes the optimal set of screening assays for a two-phase testing strategy.

GMOtrack is distributed free under GPL and can be downloaded from this web page.

Publications

Kralj Novak P., Gruden K., Morisset D., Lavrač N., Š©tebih D., Rotter A., ®Žel J.
GMOtrack: generator of cost-effective GMO testing strategies
Journal of AOAC International 2009, Nov-Dec;92(6):1739-1746
[pdf], supplementary material [pdf], [bib]

Download

Windows executable: GMOtrack.zip
Download data here: [data]
Real-time PCR analysis costs: PCRcosts.pdf is a document with the cost schema
For developers: Python source code GMOtrack-sources.zip which is developed with Orange version 0.9.64.

Installation

Unzip the file GMOtrack.zip. GMOtrack is a command-line utility so run it from the command line as described below. To start the command line, you can use the run.bat script, which is enclosed in the GMOtrack.zip archive.

Usage

GMOtrack is a command-line utility. GMOtrack usage:
GMOtrack filename [-m int][-c float][-k float][-n float]

The program returns for each number i up to m the combination of i screening assays with the lowest expected total cost.

Sample output

sample output

Data

We have prepared the sample datasets.
They were used for the experiments in the paper.

dataset year  frequency   # GMOs   # screening assays 
GMO_EU_1997.tab 1997 all 7 18
GMO_EU_1999.tab 1999 all 15 22
GMO_EU_2002.tab 2002 all 17 24
GMO_EU_2005.tab 2005 all 20 24
GMO_EU_2008.tab 2008 all 22 25
GMO_EU_2008-food.tab 2008 food 22 25
GMO_EU_2008-feed.tab 2008 feed 22 25
GMO_EU_beyond2008.tab 
beyond 2008 all 37 32

Here we describe how you can prepare your own data to be used with GMOtrack. We recommend to take one of the available datasets (above) and modify it in a spreadsheet program (e.g. MS Excel). Be careful when saving, since the file must be a "Tab delimited" text file and the filename must end with ".tab".
how to save the data

GMOtrack uses the ".tab" data format with some additional specifics.
The data must be in a tab separated text file with following format:

Example input data

data preparation

Funding

Funding was provided by the Slovenian Research Agency (P4-0165, P2-0103); the Slovenian Ministry of Agriculture, Forestry and Food; and the Slovenian Ministry of the Environment and Spatial Planning (V4-0314).

Last update: 20130725