Open source and open hardware projects at UNLOCK 

UNLOCK attaches great importance to Open Science. Open Science is important because it promotes transparency, collaboration, and accessibility in research. By making scientific data, methods, and results openly available, it allows researchers worldwide to build upon each other’s work, increasing efficiency and innovation. Open Science also enhances reproducibility, reducing the risk of errors or biases in research. Additionally, it fosters public trust in science by making knowledge accessible to everyone, including policymakers and citizens. Ultimately, Open Science accelerates scientific progress and ensures that research benefits society as a whole. 

UNLOCK provides hardware, software, and expertise for conducting the wet- and dry-lab experimental procedures complementing the expertise and equipment of the user in microbial research.

By default, we aim to use open-source software technologies and products. We also archive the exact versions of all external (open source) programs used. Version control will be used for all custom scripts and computational workflows. Furthermore, we provide public access to the inhouse developed hardware designs and software source-code through gitlab at http://gitlab.com/m-unlock 

Examples: 

FAIR Data station  

The FAIR Data Station is a simple, yet powerful metadata registration tool designed to support experimentalists and data producers in managing their data according to the FAIR Guiding Principles. These principles emphasize machine-actionable metadata to ensure data can be found, accessed, interoperated, combined, and reused with minimal human intervention. 

To improve data quality and maximize reuse potential, metadata must be sufficient and unambiguous. The FAIR Data Station facilitates this by enabling users to record metadata following Minimum Information Standards, ensuring compliance with community-accepted checklists and structured data formats for machine-actionability. 

 

Key Features of the FAIR Data Station: 

  1. Selection of metadata standards – Users choose appropriate metadata standards, generating a tailored spreadsheet template. 
  2. Metadata recording – Data producers record metadata using the structured template. 
  3. Validation – The system checks metadata for completeness and correctness based on the defined template. 
  4. FAIRification – Metadata is transformed into a machine-actionable FAIR resource for seamless integration and reuse. 

The metadata schema follows the ISA Standard, which integrates the Just Enough Results Model (JERM) and Minimum Information About a Plant Phenotyping Experiment (MIAPPE). Additionally, metadata selection leverages a package subsystem based on the Minimum Information about any (x) Sequence (MIxS) standard from the Genomic Standards Consortium. Beyond its core functions, the FAIR Data Station also supports researchers working with microbial community samples, including those obtained from in vivo sources such as faecal samples. All documentation can be found at https://docs.fairbydesign.nl  

FAIR Computational Workflows 

UNLOCK supports the user community by providing controlled access to the experimental (meta)data, and state-of-the-art dockerized modular workflows for data analysis and discovery. Workflows are specified in the Common Workflow Language and contribute to the FAIR data principles by tracking and integrating parameter configurations and output data provenance with the experiment (meta)data of the complex experimental data generated.​ The workflows that are in development can be found at http://gitlab.com/m-unlock/cwl/. Published workflows are shared via the workflow hub https://workflowhub.eu/projects/16  

Microbiome cultivation tools 

The in-house developed Bio-C biocontroller is designed to provide researchers with the tools and flexibility they need to experiment with their cultivation setups and interact with a diverse range of peripherals. The controller has connections for multiple digital pH, pO2, ORP and conductivity sensors, multiple mass flow and back pressure controllers, stirrers, analog inputs and digital outputs, as well as support for balances and water baths. This, combined with smart software, allows for an enormously flexible control system suitable for a large range of bioreactor research. 

The biocontroller will be paired with the BCS SCADA system. BCS, or Bioreactor Control System, is a SCADA system supporting a range of bio controllers and related equipment, allowing advanced recipes to control the bioreactors.  

Hardware designs and software source-code for these and other projects can be found here. 

 

Raman Assisted Microfluidic Cell Sorting Unit 

Enables the sorting and characterization of cells from a target population of interest for downstream cultivation. 

The system is composed of four main units: Raman microscope, optical tweezers, microfluidics cell sorter & single cell cultivation. Single cells are trapped while flowing through a microfluidic device using integrated optical tweezers. Raman interrogation determines whether the cell has a characteristic of interest (e.g., isotopic labelling) to sort or discard. Individual cells can be characterized and sorted on the basis of their metabolic functions and genetic identity within a complex microbial community. UNLOCK has developed a software solution, tying the knot between different hardware’s and software. It can be found here.