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., Lavracč., Šebih 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]

-mmaximum assays for first phase constraint, default m=5
-cminimum coverage (in %) of the first phase, default c=80
-kcoefficient for the cost function g, default k=21.18
-nconstant for the cost function g, default n=91.82

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:

File head:
- The first line is reserved for column names: meta attribute names and assay names.
  - the first three columns must be named "GMOname", "species" and "probability".
- The second line denotes the data type:
  - d for nominal values
  - c for numbers
- The third line denotes column type:
  - m for meta attributes (GMOname, species and probability)
  - empty for assays
File body:
- Each line is the file's body is one GMO.
  The first column represents GMO names.
  The second column must be species.
  The following columns are the responses of the GMO to the assay:
  - 1 means positive response,
  - 0 means negative response.

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: 20171110