Antoine Buetti-Dinh

Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base.

The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising ...

The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.

Supplementary files for the submission: Reverse Engineering Directed Gene Regulatory Networks from Transcriptomics and Proteomics Data of Biomining Bacterial Communities with Approximate Bayesian Computation and Steady-State Signalling Simulations

Supplementary files for the publication: Deep Neural Networks Outperform Human Expert’s Capacity in Characterizing Bioleaching Bacterial Biofilm Composition

Publication data made available for Biotechnology Reports, supplementary data

Proteomics and transcriptomics data tables, sample IDs and description, source code

edit later

Publication data made available for Biotechnology Reports, supplementary data

tbd

Archive contains python scripts for image analysis

Images used for training and validation of deep learning algorithm to determine biofilm composition of mixed species biofilms on mineral grains

just cell counts, the area of the grains is separate.

after shankra, saving the images that could not be analysed earlier. here they are simply treated by imagej change in brightness/contrast. the same can also be done with imagemagic.

TATAA biocenter workshop lecture

Workshop by the fairdomhub team on reproducible and citable data and models