Software

INTRODUCTION

Software is an important research outcome in the Laboratory of Systems Biology. We develop software for running experimental setups used in our laboratory, for building mathematical models as well as for analyzing experimental data. When possible and reasonable, the software are published in Open Source format.

This page gives a summary of software we have developed as well as software projects where the members of our laboratory are participating or have been participated with considerable source code contribution.

SOFTWARE DEVELOPED IN THE LAB

IOCBIO PROJECT

This is a collection of our latest software that we develop as a set of separate projects related to our research.

IOCBIO Gel – Application for analysis of Western Blots or similar blots

IOCBIO Kinetics – Application for analysis of traces.

IOCBIO Sparks – Semi-automatic calcium sparks detection software.

IOCBIO WebDB – Web framework with the focus on data entry in scientific laboratories.

IOCBIO Deconvolve – C++ and Python library for performing deconvolution on 3D images. Reference: Laasmaa et al, J Microsc 2011.

IOCBIO AnimalDB – Animal facility management system.

OTHER PROJECTS

Former IOCBio – open-source software from the Laboratory of Systems Biology collected targeted software projects developed in our laboratory. This collection is in the form of Python package and it contains the following software:

• IOCBioMicroscope – a Python package for deconvolving 3D microscope images. Deprecated, use IOCBIO Deconvolve instead. Reference: Laasmaa et al, J Microsc 2011.
• IOCBioSarcomereLength – a C library and Python package for estimating fundamental period of a sequence with an application to determining sarcomere length from microscopy images of cardiomyocytes. Reference: Peterson et al, AJP Cell Phys 2013.
• IOCBioOxygenIsotopeEquationGenerator – a Python module for generation of mass isotopologue equations. Reference: Schryer et al, PLoS Comput Biol 2012.
• IOCBioStrathKelvin – a wrapper to Strathkelvin Instruments 929 Oxygen System software.

Here we list software that has more general purpose than software in IOCBio, and therefore, are worth of publishing as separate software projects:

• PyLibNIDAQmx – a Python wrapper to libnidaqmx library.
• PyLibTiff – a Python TIFF library.
• SympyCore – an efficient pure Python Computer Algebra System (originally supported by Simula Research Laboratory).
  • SteadyStateFluxAnalysis – a steady state flux analysis module. Reference: Schryer et al, BMC Syst Biol 2011.
• Simple RPC C++ – a simple RPC wrapper generator to C/C++ functions.
• PyLibDeconv – a Python wrapper of the deconv library.
• LSjuicer – program for squeezing results from linescan images.
• F2PY project – Fortran to Python Interface Generator – 3rd generation

INTERNAL SOFTWARE PROJECTS

Here we list software that have been developed for specific experimental setups, and as such, would be difficult to be used outside of the laboratory.

• Sysbiosoft microscope – a software platform for running experimental protocols on our custom built microscope setups:
  • fluorescence confocal microscope Airy – built around Olympys IX71 microscope with photon counter from PerkinElmer, galvo mirrors from Cambridge Technology. Reference: Illaste et al, Biophys J 2012.
  • fluorescence wide-field microscope Suga – built around Nikon Eclipse Ti-U microscope with Andor Ixon EMCCD camera and high-speed Imperx IPX-VGA210-LMCN CCD camera Reference: Jepihhina et al, Biophys J 2011.
• Cluster Design – a web-based application for finding the optimal configuration for High-Performance Computational clusters.

CONTRIBUTIONS TO EXTERNAL SOFTWARE PROJECTS

• f2py – Fortran to Python interface generator. Author: Pearu Peterson. Reference: Peterson, Int J Comp Sci Eng 2009.
• Scipy – a Python-based ecosystem of open-source software for mathematics, science, and engineering. Co-author: Pearu Peterson.
• Numpy – the fundamental package for scientific computing with Python. Developer: Pearu Peterson .