sQuid: observation and interaction in experimental environments

sQuid is an open-source C++/Qt software application designed to observe environments using FireWire cameras (IEEE 1394), while interacting with these environments through a port interface (e.g. IEEE 1284). We envision that this application will be very useful in scientific research as well as robotics.

As an example, we control a system of LEDs and valves while multiple cameras capture visual information from an experiment. Specifically, fruit flies (Drosophila melanogaster) are placed within a transparent chamber to visualize their behavior (Ramdya et al. 2012). While capturing images from two cameras, we simultaneously control a series of LEDs to excite fluorescence proteins and generate gas flow by controlling a series of valves.

> Author’s project web page

> Fluorescence Behavioral Imaging (FBI)

In silico benchmark generation and performance profiling of network inference methods
An extensible toolkit for modularity detection in networks
Java library for simulating stochastic differential equations

Journal Articles

Fluorescence Behavioral Imaging (FBI) tracks identity in heterogeneous groups of Drosophila

P. P. Ramdya; T. Schaffter; D. Floreano; R. Benton 

PLOS One. 2012. Vol. 7, num. 11, p. e48381. DOI : 10.1371/journal.pone.0048381.

GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods

T. Schaffter; D. Marbach; D. Floreano 

Bioinformatics. 2011. Vol. 27, num. 16, p. 2263-2270. DOI : 10.1093/bioinformatics/btr373.

Revealing strengths and weaknesses of methods for gene network inference

D. Marbach; R. J. Prill; T. Schaffter; C. Mattiussi; D. Floreano et al. 

PNAS. 2010. Vol. 107, num. 14, p. 6286-6291. DOI : 10.1073/pnas.0913357107.

Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

D. Marbach; T. Schaffter; C. Mattiussi; D. Floreano 

Journal of Computational Biology. 2009. Vol. 16, num. 2, p. 229-239. DOI : 10.1089/cmb.2008.09TT.


Numerical Integration of SDEs: A Short Tutorial

T. Schaffter 


Stochastic Simulations for DREAM4

T. Schaffter; D. Marbach