Standards

standard_SEVA

SEVA

WEBSITE
standard_SBOL

SBOL

WEBSITE

Software & repositories

SynBioHub

SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources.

WEBSITE

SEVAhub

The SEVA database (SEVA-DB) is a resource for implementation of a standard for physical assembly of vector plasmids and for their non-ambiguous nomenclature as well as the index for a repository of functional sequences and actual constructs available to the community. This resource, SEVAhub, is an instance of the SynBioHub design repository providing access to SEVA-DB converted to the Synthetic Biology Open Language (SBOL).

WEBSITE

DiSCUS

The software DiSCUS (Discrete Simulation of Conjugation Using Springs) is designed to simulate bacterial growth and communication through horizontal gene transfer (conjugation). The software (v1 – released 2012) can be downloaded from here. DiSCUS paper, which explains parameters and dynamics can be found here.

FlowScatt

A tool to transform an ensamble of flow cytometry data experiment in a scattering dependent and non-dependent part.

WEBSITE

CellShape

Image analysis software with sub-pixel accuracy.

WEBSITE

GitHub

WEBSITE

Selected presentations & posters

  • Biocomputing with synthetic biological systems. MEETING LIFE.HUB.CSIC – ORIGINS & SYNTHESIS of LIFE (7-11/03/2022)
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  • Design of electroactive bacteria by coupling genetic networks to redox environments. 5th European Meeting of the International Society for Microbial Electrochemistry and Technology (ISMET) 13th – 15th September 2021
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  • Control of environmental context to fine-tune genetic performance. Designer Biology, September 8-10, 2021
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  • Characterising contextual information for circuit design. The “Computational Modeling in Biology” Network (COMBINE) 11-15 October 2021
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  • Network visualization of synthetic biology designs. International Workshop on BioDesign Automation (IWBDA). Sep 20th-24th
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  • Genetic circuits beyond genes. CELLS: Workshop on Computing among Cells. October 8th, 2021 Video
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  • The Synthetic Biology Open Language. Standards & Synbio in the Biotech sector. 1st October 2020.
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  • Characterising relationships between model parameters for biocircuit design. Electrical Cell Biology 28/29 March 2019. Radcliffe Conference Centre, University of Warwick, Coventry, UK
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  • Spatiotemporal Principles of Genetic Circuit Design. Synthetic Biology Congress November 8 – 9, 2018 – London UK
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  • Engineering genetic circuits in both space and time. Synthetic Biology 7.0. 13-16 June 2017 Singapore
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Dissemination video

What are the limits of biocomputing?