MiBiPreT: the Micro-Bioremediation Prediction Tool

Collaborative open-source software development for MIBIREM

At the end of 2024 the MIBIREM consortium joined forces with two Research Software Engineers of the Netherlands eScience Center, when the institution an official partner in the project. But who is this new partner, what do Research Software Engineers do and why does MIBIREM need this?

Who we are

The Netherlands eScience Center is the Dutch centre of expertise in research software engineering [1], with engineers from a wide range of backgrounds and disciplines. Our mission is to work directly with researchers to foster and transfer sustainable software development practices. The engineers collaborate with scientists on the software they develop for their research to bring it to the next level with regards to performance, quality and FAIR-ness [2]. In the process, we try to convey some good practices in research software engineering to the research group.

The story so far

We first got involved when we joined a short hackathon in March 2024 with researchers in the Faculty of Geosciences at Utrecht University. The pleasant and productive atmosphere led to the eScience Center joining the project as a partner around 6 months later, after much administrative wrangling. Since then, we have been actively involved in part of the project called Work package WP4 – Prediction Tool for enhancement and feasibility evaluation of Bioremediation through regular coworking days at the University of Utrecht, where we work on the development of a prediction tool for micro-bioremediation called MiBiPreT [3].

MiBiPreT

The prediction Toolkit for Micro-Bioremediation– MiBiPreT, consists of various software packages and scripts that can be used separately or in unison. At present, we work on three python packages called mibitrans, mibiscreen and mibiremo as well as one workflow collection [4].  mibitrans provides access to a variety of analytical and semi-semianalytical solutions for hydrogeological transport phenomena. mibiscreen is a collection of routines for data analysis on contaminant site data with the goal of predicting if bioremediation is a feasible remediation strategy.  mibiremo, the Microbiome Bioremediation Reaction Module, is a python interface to an existing geochemical model. It is being developed in collaboration with DND Biotech company (Italy) and allows coupling with transport models to simulate reactive transport in porous media. Finally, we are beginning to collect detailed descriptions of the workflows of experimental scientists in this area for the purpose of identifying ways in which our software could help them automate their analyses – a collection we call mibibio.

Challenges

We collaborate with researchers and scientists spread across multiple institutions, working in various domains and located in several countries (most recently connecting to a developer in Australia). Due to the different backgrounds and job roles, our potential user base is diverse and has different use cases. This makes it important to carefully think about the requirements of each of the components. It would be rather a waste of time to build high quality software that nobody uses.

Looking ahead

We will continue our close collaboration with Utrecht University and support of DND Biotech to develop the various components of the micro-bioremediation prediction tool, while collecting input from the rest of the consortium. Since these tools are completely free and open source, they can be used, adapted and further developed by any scientific institute, individual or company to their needs.

 

References:

1. Netherlands eScience Center – https://www.esciencecenter.nl/
2. FAIR principles for Research Software – https://www.nature.com/articles/s41597-022-01710-x
3. Mibipret poster zenodo link – https://zenodo.org/records/15582486
4. Mibipret Github organisation – https://github.com/MiBiPreT

 

Authors:

Robin Richardson and Jaro Camphuijsen