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DD-DeCaF SIGNED

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

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

DD-DeCaF project word cloud

Explore the words cloud of the DD-DeCaF project. It provides you a very rough idea of what is the project "DD-DeCaF" about.

integrative economizing chemicals interoperable companies identification components model industrial service practical competitiveness enzymes broad software mining factories health reuse academic industry communities leveraged market bioinformatics tools agriculture manipulations interactive proteins metagenomic public standardized respective private cell platform microbial ranging time levels oriented smes spectrum biotech omics lack proprietary data web interventions cellular reducing human biotechnology efforts

Project "DD-DeCaF" data sheet

The following table provides information about the project.

Coordinator	DANMARKS TEKNISKE UNIVERSITET Organization address address: ANKER ENGELUNDSVEJ 1 BYGNING 101 A city: KGS LYNGBY postcode: 2800 website: www.dtu.dk 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	http://dd-decaf.eu/
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

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	DANMARKS TEKNISKE UNIVERSITET DANMARKS TEKNISKE UNIVERSITET Organization address address: ANKER ENGELUNDSVEJ 1 BYGNING 101 A city: KGS LYNGBY postcode: 2800 website: www.dtu.dk contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DK (KGS LYNGBY)	coordinator	1˙776˙110.00
2	EUROPEAN MOLECULAR BIOLOGY LABORATORY EUROPEAN MOLECULAR BIOLOGY LABORATORY Organization address address: Meyerhofstrasse 1 city: HEIDELBERG postcode: 69117 website: http://www.embl.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (HEIDELBERG)	participant	1˙457˙952.00
3	CHALMERS TEKNISKA HOEGSKOLA AB CHALMERS TEKNISKA HOEGSKOLA AB Organization address address: - city: GOETEBORG postcode: 41296 website: www.chalmers.se contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	SE (GOETEBORG)	participant	861˙412.00
4	GENIALIS D.O.O GENIALIS D.O.O Organization address address: KOPRSKA ULICA 72 city: LJUBLJANA postcode: 1000 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	SI (LJUBLJANA)	participant	536˙875.00
5	SILICOLIFE LDA SILICOLIFE LDA Organization address address: RUA DO CANASTREIRO 15 city: BRAGA postcode: 4715 387 website: www.silicolife.com contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	PT (BRAGA)	participant	347˙500.00
6	UNIVERSIDADE DO MINHO UNIVERSIDADE DO MINHO Organization address address: LARGO DO PACO city: BRAGA postcode: 4704 553 website: www.uminho.pt contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	PT (BRAGA)	participant	341˙691.00
7	DSM FOOD SPECIALTIES BV DSM FOOD SPECIALTIES BV Organization address address: ALEXANDER FLEMINGLAAN 1 city: DELFT postcode: 2613 AX website: www.dsmfoodspecialties.com contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	NL (DELFT)	participant	323˙750.00
8	BIOBYTE SOLUTIONS GMBH BIOBYTE SOLUTIONS GMBH Organization address address: Bothestrasse 142 city: Heidelberg postcode: 69126 website: www.biobyte.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (Heidelberg)	participant	251˙250.00
9	BIOSYNTIA APS BIOSYNTIA APS Organization address address: KOGLE ALLE 6 city: HORSHOLM postcode: 2970 website: www.biosyntia.com contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DK (HORSHOLM)	participant	250˙000.00
10	UNIVERSIDAD POLITECNICA DE MADRID UNIVERSIDAD POLITECNICA DE MADRID Organization address address: CALLE RAMIRO DE MAEZTU 7 EDIFICIO RECTORADO city: MADRID postcode: 28040 website: www.upm.es contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	ES (MADRID)	participant	104˙095.00
11	ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE Organization address address: BATIMENT CE 3316 STATION 1 city: LAUSANNE postcode: 1015 website: www.epfl.ch contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	CH (LAUSANNE)	participant	0.00

Map

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.

Deliverables

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.

Publications

List of publications.
year	authors and title	journal	last update
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, PÃ¥l Axel Olsson, Mari Pent, Sergei PÃµlme, 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. HerrgÃ¥rd Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-Î³-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 SchrÃ¼bbers, Hanne B. Christensen, Markus J. HerrgÃ¥rd 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	BenjamÃn J. SÃ¡nchez, 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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