Software

Software developed by the Emonet Lab is available on github: https://github.com/emonetlab

To investigate the connection between molecules and behavior we developed agent-based simulators (AgentCell) and  rule-based computational tools for the stochastic simulation of cellular systems NFSim (with J. Faeder, U. Pittsburgh). To extract quantitative data from experiments we developed MicrobeTracker (with C. Jacobs Wagner). NFsim and MicrobeTracker are freely available and count hundreds of users each. There is now a new version of MicrobeTracker called oufti and NFSim has been integrated into the cell simulator VCell. We have also developed software that is useful in neuroscience, especially in the study of insect olfaction: spikesort  to sort spike efficiently, and kontroller to control experiments using MATLAB. All this software is freely available.

spikesort

spikesort is a framework written in MATLAB to help you sort spikes from single-channel extracellular recordings. It is

  1. highly modular Almost everything is written as a plugin. spikesort is a MATLAB class, and plugins are methods defined within the class.
  2. Accurate Using the t-SNE dimensionality reduction algorithm, spikesort achieves a 99.5% accuracy on test data. For a full report, see this.
  3. Data-agnostic spikesort interfaces to your data through plugins, and spikesort doesn’t care what your data format is.
  4. Bring-your-own-algorithm spikesort splits up the spike sorting problem into two steps: dimensionality reduction and clustering. Every algorithm in either step is written as a plugin, and you can write your and drop it in, with zero modifications to the core code. For example, spikesort can use the amazing mutli-core t-SNE algorithm to embed spike shapes in two dimensions very rapidly.

kontroller

kontroller is a free wrapper for MATLAB’s DAQ toolbox that makes it easy to begin doing experiments. It can act as a software oscilloscope, capture data, control instruments, and is fully programmable – you can write your own code that runs kontroller for complex sequences or optimization routines.   

NFsim (The Network-Free Stochastic Simulator)
A general-purpose, open-source, biochemical reaction simulator with advanced capabilities for coarse-graining reaction mechanisms. NFsim implements a novel agent- and rule-based simulation engine that provides exact stochastic results. For many complex biological systems, NFsim provides orders of magnitude speedup over standard ODE and stochastic methods.

Links and Downloads: 

  • The NFsim web site with examples and software download
  • For beginners we recommend using the integrated framework called RuleBender that integrates a user friendly graphical interface to specify and run models with BioNetGen (rule-based language) and multiple solvers included NFsim (stochastic solver). All this resides on the BioNetGen webpage. Direct downloads to RuleBender is here.
  • NFsim user manual
  • NFsim github repository

MicrobeTracker Suite
A MATLAB-based software package designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them. The Suite consists of the MicrobeTracker program itself, which outlines and tracks the cells, a few tools for spot detection inside cells under the general name SpotFinder. See Mol. Micro., 80(3):612–627, May 2011 (pdf, html, supp. info., supp. movies, source code). MicrobeTracker is no longer supported but you can download the last version 0.937 here: MicrobeTracker_0_937.zip  or MicrobeTracker_0_937_with_examples.zip Explanations on how to use it are available here as as well. A new improved version of this code has been developped under the name oufti

AgentCell
Agent-based simulation framework for modeling cellular behavior. See AgentCell: a digital single-cell assay for bacterial chemotaxis Bioinformatics, 1; 21(11):2714-21 (2005). (pdf, html, supp. info.) and Relationship between cellular response and behavioral variability in bacterial chemotaxis,
Proc. Natl. Acad. Sci., 105(9):3304-9(2008). (pdf, html, supp. info.).