Software

Software is a research output of the Laboratory of Systems Biology. We build open-source tools for experimental control, image and time-series analysis, mathematical modelling, research workflows, and the systems that publish and preserve scientific information. This page includes software developed in the lab as well as substantial contributions by its members.

Current Software

Research Workflows

• FITSA analyses fluorescence-intensity transients recorded by confocal microscopy.

• IOCBIO Gel analyses Western blots and similar gel images.

• IOCBIO Kinetics analyses experimental traces.

• IOCBIO Sparks supports semi-automatic detection of calcium sparks.

• IOCBIO Deconvolve is a C++ and Python library for deconvolving three-dimensional images. Reference: Laasmaa et al., J Microsc 2011.

• IOCBIO WebDB is a web framework focused on data entry in scientific laboratories.

• IOCBIO AnimalDB supports animal facility management.

Other Software

• Zotero Cache Server is a self-hosted caching proxy for the Zotero Web API, used by Zotero Plugin for Grav.

• Zotero Plugin for Grav renders Zotero bibliographies in Grav pages through Zotero Cache Server.

• Grav Robots Plugin serves a site's robots.txt rules and adds a sitemap URL resolved from the Grav configuration.

• Grav Read-Only provides paired development and deployment containers for Git-managed Grav websites. It keeps site content, configuration, and the production runtime read-only wherever practical, while isolating transient Grav state.

• Conflict checks publicly recorded evidence of potential conflicts of interest involving reviewers of PhD theses and papers.

Earlier And Specialized Software

The former IOCBio open-source software collection brought together several targeted Python packages developed in the laboratory:

• IOCBioMicroscope is a Python package for deconvolving three-dimensional microscope images. It is deprecated; use IOCBIO Deconvolve instead. Reference: Laasmaa et al., J Microsc 2011.

• IOCBioSarcomereLength is a C library and Python package for estimating a sequence's fundamental period, including sarcomere length from cardiomyocyte microscopy images. Reference: Peterson et al., AJP Cell Phys 2013.

• IOCBioOxygenIsotopeEquationGenerator generates mass-isotopologue equations. Reference: Schryer et al., PLoS Comput Biol 2012.

• IOCBioStrathKelvin wraps the Strathkelvin Instruments 929 Oxygen System software.

Other earlier software includes:

• PyLibNIDAQmx is a Python wrapper for the libnidaqmx library.

• PyLibTiff is a Python TIFF library.

• SympyCore is an efficient pure-Python computer algebra system, originally supported by Simula Research Laboratory. Its SteadyStateFluxAnalysis module supports steady-state flux analysis. Reference: Schryer et al., BMC Syst Biol 2011.

• Simple RPC C++ generates simple RPC wrappers for C and C++ functions.

• PyLibDeconv is a Python wrapper for the deconv library.

• LSjuicer extracts results from line-scan images.

Internal Experimental Systems

Some software was developed for laboratory-specific experimental setups and is not intended for general use:

• Sysbiosoft microscope is a platform for running experimental protocols on custom-built microscopes, including the Airy fluorescence confocal microscope. Reference: Illaste et al., Biophys J 2012.

• Sysbiosoft microscope also supports the Suga fluorescence wide-field microscope. Reference: Jepihhina et al., Biophys J 2011.

• Cluster Design is a web application for identifying suitable high-performance computing cluster configurations.

Contributions To External Projects

• f2py is a Fortran-to-Python interface generator. Pearu Peterson was an author. Reference: Peterson, Int J Comp Sci Eng 2009.

• SciPy is an open-source ecosystem for mathematics, science, and engineering in Python. Pearu Peterson was a co-author.

• NumPy is a fundamental package for scientific computing with Python. Pearu Peterson was a developer.