Software & Tools

The software tools and codes developed by our team are available on GitHub.

Team GitHubs

• Gabriel Braun
• Mathias Gotsmy
• Julian Libiseller-Egger
• Kevin Mildau
• Michael Predl
• Guido Schlögel
• Diana Széliová

FedBatchDesigner

The aim of FedBatchDesigner is to explore the design space of fed-batch fermentations with a growth-arrested second stage. The feed profile of the first stage is either exponential or constant, while the feed rate is kept constant during the second stage (at a value determined by the maintenance coefficient ρ and growth-independent production rate π0).

PeakBot

PeakBot is a Python package for peak-picking in LC-HRMS profile mode data. It initially finds local-maxima in the LC-HRMS dataset. Each of them is then exported as a standarized two-dimensional area (rt x mz), which is used as the input for a machine-learning CNN model. This model reports whether the respective local-maxima is a chromatographic peak with left/right isomeric compounds or a signal of the background.

ecmtool

With this tool, you can calculate Elementary Conversion Modes (ECMs) from metabolic networks. Combinations of ECMs form all metabolic influences an organism can exert on its environment.

ecmtool can be used in two different modes: either as a standalone command line tool or as a Python library for your own scripts. We will describe how to install and use both modes.

Finger Sweat Analysis

This is the code as discussed in "Finger Sweat Analysis Enables Short Interval Metabolic Biomonitoring in Humans".

Finger Sweat Normalization

Creation and comparison of PQN, PKM, and MIX models for size effect normalization.