Opendata, web and dolomites


Bioinformatics Services for Data-Driven Design of Cell Factories and Communities

Total Cost €


EC-Contrib. €






Project "DD-DeCaF" data sheet

The following table provides information about the project.


Organization address
postcode: 2800

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Denmark [DK]
 Project website
 Total cost 7˙091˙021 €
 EC max contribution 6˙250˙636 € (88%)
 Programme 1. H2020-EU.2.1.4. (INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies – Biotechnology)
 Code Call H2020-LEIT-BIO-2015-1
 Funding Scheme RIA
 Starting year 2016
 Duration (year-month-day) from 2016-03-01   to  2020-02-29


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
4    GENIALIS D.O.O SI (LJUBLJANA) participant 536˙875.00
5    SILICOLIFE LDA PT (BRAGA) participant 347˙500.00
6    UNIVERSIDADE DO MINHO PT (BRAGA) participant 341˙691.00
7    DSM FOOD SPECIALTIES BV NL (DELFT) participant 323˙750.00
8    BIOBYTE SOLUTIONS GMBH DE (Heidelberg) participant 251˙250.00
9    BIOSYNTIA APS DK (HORSHOLM) participant 250˙000.00


 Project objective

Omics data is not leveraged effectively in the biotechnology industry due to lack of tools to rapidly access public and private data and to design cellular manipulations or interventions based on the data. With this project we aim to make a broad spectrum of omics data useful to the biotechnology industry covering application areas ranging from industrial biotechnology to human health. We will develop novel approaches for integrative model-based omics data analysis to enable 1) Identification of novel enzymes and pathways by mining metagenomic data, 2) Data-driven design of cell factories for the production of chemicals and proteins, and 3) Analysis and design of microbial communities relevant to human health, industrial biotechnology and agriculture. All research efforts will be integrated in an interactive web-based platform that will be available for the industrial and academic research and development communities, in particular enhancing the competitiveness of biotech SMEs by economizing resources and reducing time-to-market within their respective focus areas. The platform will be composed of standardized and interoperable components that service-oriented bioinformatics SMEs involved in the project can reuse in their own products. An important aspect of the platform will be implementation of different access levels to data and software tools allowing controlling access to proprietary data and analysis tools. Two end-user companies will be involved in practical testing of the platform built within the project using proprietary omics data generated at the companies.


List of deliverables.
Results of optimization for selected case-studies Other 2020-03-11 13:04:00
Large-scale kinetic models of relevant production hosts Other 2020-03-11 13:03:58
Bi-directional connectivity of the visualization components with APIs and data sources Other 2020-03-11 13:04:04
First version of the database providing novel functional and enzyme annotations Other 2020-03-11 13:04:22
Large-scale kinetic models of one fungal organism with integrated enzyme biosynthesis module Other 2020-03-11 13:03:57
Novel enzyme and pathway candidates publicly available Other 2020-03-11 13:04:22
3rd annual DeCaF workshop Websites, patent fillings, videos etc. 2020-03-11 13:04:23
Software for designing synthetic microbial communities Other 2020-03-11 13:03:38
Consortium-wide repository of methods, algorithms, software, and web-services that can be deployed as docker containers Other 2020-03-11 13:04:22
Community design software publically available Other 2020-03-11 13:03:58
Integration of the visualization components with public data sources is implemented Other 2020-03-11 13:04:02
Integration of gene and pathway mining components from WP2 Other 2020-03-11 13:04:01
Technology Transfer Activities, including training to SMEs Websites, patent fillings, videos etc. 2020-03-11 13:04:22
Models for quantitative simulation of protein secretion by fungi Other 2020-03-11 13:03:59
Web-based cell factory and community design platform (DeCaF) hosted on CSC infrastructure Other 2020-03-11 13:04:03
1st annual DeCaF workshop Websites, patent fillings, videos etc. 2019-07-22 16:51:21
Models for quantitative simulation of protein secretion by bacterial hosts Other 2019-07-22 16:51:07
Models for quantitative simulation of protein secretion Other 2019-07-22 16:51:05
2nd annual DeCaF workshop Websites, patent fillings, videos etc. 2019-07-22 16:51:25
Upload and access control system for processed omics data Other 2019-07-22 16:51:26
Interactive pathway visualization components are available on the DeCaF platform Other 2019-07-22 16:51:07
Models for yeast, E. coli and two other microorganisms that accounts for protein content Other 2019-07-22 16:51:04
Algorithms for optimization using model with protein synthesis and secretion Other 2019-07-22 16:51:16
Cloud hosting solution for web-services on CSC compute infrastructure Other 2019-07-22 16:51:21
Algorithms for optimization using community models Other 2019-07-22 16:51:07
Functional annotation of gene catalog Other 2019-07-22 08:13:41
Software for simulating metabolic interactions in microbial communities Other 2019-07-22 08:20:50
Large-scale kinetic models of one bacterial organism with integrated enzyme biosynthesis module Other 2019-07-22 08:13:42
Thermodynamically-curated GEMs with integrated metabolomics data Other 2019-07-22 08:20:51
Community model reconstruction pipeline publically available Other 2019-07-22 08:13:30
Functional annotation pipeline established Other 2019-07-22 08:13:39
Metabolic interaction simulation software publically available Other 2019-07-22 08:20:51
A toolbox for integration of metabolomics data into thermodynamically-curated GEMs Other 2019-05-30 13:56:30
General metaheuristics-based optimization framework Other 2019-05-30 13:56:38
Bioinformatics pipeline for building community metabolic models Other 2019-05-30 13:56:35
Press release about the launching of the project Websites, patent fillings, videos etc. 2019-05-30 13:56:30
Algorithms for optimization using large-scale kinetic models Other 2019-05-30 13:56:35
Data Management Plan Open Research Data Pilot 2019-05-30 13:56:39
Identifier translation service for metabolite, enzyme, gene, protein and reaction identifiers Other 2019-05-30 13:56:26
Project website: the report will provide a functional description of the project website, its main sections and how the access to the private area is implemented. Websites, patent fillings, videos etc. 2019-05-30 13:56:38
Periodic newsletters Websites, patent fillings, videos etc. 2019-05-30 13:56:39
Genomic/metagenomic gene catalog database Other 2019-05-30 13:56:25

Take a look to the deliverables list in detail:  detailed list of DD-DeCaF deliverables.


year authors and title journal last update
List of publications.
2019 Carlos G Acevedo-Rocha, Luisa S Gronenberg, Matthias Mack, Fabian M Commichau, Hans J Genee
Microbial cell factories for the sustainable manufacturing of B vitamins
published pages: 18-29, ISSN: 0958-1669, DOI: 10.1016/j.copbio.2018.07.006
Current Opinion in Biotechnology 56 2019-05-22
2018 Mohammad Bahram, Falk Hildebrand, Sofia K. Forslund, Jennifer L. Anderson, Nadejda A. Soudzilovskaia, Peter M. Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H. Medema, Mia R. Maltz, Sunil Mundra, Pål Axel Olsson, Mari Pent, Sergei Põlme, Shinichi Sunagawa, Martin Ryberg, Leho Tedersoo, Peer Bork
Structure and function of the global topsoil microbiome
published pages: 233-237, ISSN: 0028-0836, DOI: 10.1038/s41586-018-0386-6
Nature 560/7717 2019-05-22
2018 Daniel Machado, Sergej Andrejev, Melanie Tramontano, Kiran Raosaheb Patil
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
published pages: 7542-7553, ISSN: 0305-1048, DOI: 10.1093/nar/gky537
Nucleic Acids Research 46/15 2019-05-22
2019 Ilaria Massaiu, Lorenzo Pasotti, Nikolaus Sonnenschein, Erlinda Rama, Matteo Cavaletti, Paolo Magni, Cinzia Calvio, Markus J. Herrgård
Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains
published pages: , ISSN: 1475-2859, DOI: 10.1186/s12934-018-1052-2
Microbial Cell Factories 18/1 2019-05-22
2018 Douglas McCloskey, Julia Xu, Lars Schrübbers, Hanne B. Christensen, Markus J. Herrgård
RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli
published pages: 383-392, ISSN: 1096-7176, DOI: 10.1016/j.ymben.2018.04.009
Metabolic Engineering 47 2019-05-22
2019 Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven, Jens Nielsen
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
published pages: , ISSN: 1752-0509, DOI: 10.1186/s12918-018-0673-8
BMC Systems Biology 13/1 2019-05-22
2018 Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
published pages: , ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty499
Bioinformatics 2019-05-22

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