Software




Software Development

Some of our research projects require the development of new tools; since we believe that these tools may be very valuable for the community as a whole, we make them freely accessible for non-commercial use.

SAPling

We have developed a 'Scan-Add-Print' database system, SAPling, to track and monitor asexually reproducing organisms. Using barcodes to uniquely identify each animal, we can record information on the life of the individual in a computerized database containing its entire family tree. SAPling enabled us to carry out large-scale population dynamics experiments with thousands of planarians and keep track of each individual. The database stores information such as family connections, birth date, division date and generation. We show that SAPling can be easily adapted to other asexually reproducing organisms, and has a strong potential for use in large-scale and/or long-term population and senescence studies as well as studies of clonal diversity. The software is platform-independent, designed for reliability and ease of use, and provided open source from our webpage to allow project-specific customization. Original publication:

M.A. Thomas, and E.-M. Schoetz. SAPling: a Scan-Add-Print barcoding database system to label and track asexual organisms (Journal of Experimental Biology 214, 3518-3523 (2011)

New: SAPling 2.0 - a QR-code version of SAPling, see pdf.

 

P-tracker

The P-tracker was developed as an easily implemented alternative to current methods for quantitatively screening planarian locomotion phenotypes using a simple table-top experimental setup and automated center of mass tracking. Please contact us if you are interested in a P-tracker copy. Original publication:

J.A. Talbot, and E.-M. Schoetz.Quantitative characterization of planarian wildtype behavior as a platform for screening locomotion phenotypes (The Journal of Experimental Biology. 2011 Apr 1;214(Pt 7):1063-7.)  

Article summary: Changes in animal behavior resulting from genetic or chemical intervention are frequently used for phenotype characterizations.The majority of these studies are qualitative in nature, especially in systems that go beyond the classical model organisms. Here, we introduce a quantitative method to characterize behavior in the freshwater planarian Schmidtea mediterranea. Wild-type locomotion in confinement was quantified using a wide set of parameters, and the influences of intrinsic intra-worm versus interworm variability on our measurements was studied. We also examined the effect of substrate, confinement geometry and the interactions with the boundary on planarian behavior. The method is based on a simple experimental setup, using automated center-of-mass tracking and image analysis, making it an easily implemented alternative to current methods for screening planarian locomotion phenotypes. As a proof of principle, two drug-induced behavioral phenotypes were generated to show the capacity of this method.