Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas

pedrorvc

Pedro Vila-Cerqueira • M. Ramirez Lab

iMM Computational Biology and Bioinformatics Day

2020/10/21

Is there an outbreak?

What data to share?

  • Allelic profiles?
  • Raw data?

Strict privacy laws may prevent the users from sharing raw data. Unpublished data is also a matter of concern.

  • Schemas?

Schemas can be created with different parameters, requiring the users to share their configurations.

Profiles are generated based on the schema, which may contain private data, making it hard to share and obtain the same results.

What data to share?

  • Integration with chewBBACA allows users to perform analyses in their local machines.

Chewie-NS: a nomenclature server

  • Share and compare allelic profiles within the community at a global level.
  • Allow the simple communication of results while providing an interface for users to easily explore the allelic diversity within species.

Chewie-NS: a nomenclature server

Git, Docker and Docker-compose to run multi-container Docker applications.

apt-get install git
apt-install docker-ce
curl -L "https://github.com/docker/compose/releases/download/1.25.3/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
git clone https://github.com/B-UMMI/Chewie-NS.git

Clone the repo

Deploy Chewie-NS

docker-compose -f docker-compose-production.yaml up --build

Docker Compose

Chewie-NS: a nomenclature server

https://github.com/B-UMMI/Chewie-NS

Special thanks to Rafael Mamede, Inês Mendes, Mickael Silva, João André Carriço and Mário Ramirez.

https://github.com/B-UMMI/chewBBACA

This work was partially supported by the following projects: the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI – ‘Fundos Europeus Estruturais e de Investimento’ from ‘Programa Operacional Regional Lisboa 2020’ and by national funds from FCT – ‘Fundação para a Ciência e a Tecnologia’, BacGenTrack (TUBITAK/0004/2014) [FCT/Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBİTAK)] and LISBOA-01-0145-FEDER-007391, project cofunded by FEDER, through POR Lisboa 2020 - Programa Operacional Regional de Lisboa, PORTUGAL 2020, and Fundação para a Ciência e a Tecnologia.

Thank you for your attention!

https://github.com/B-UMMI/Chewie-NS_tutorial

Chewie-NS: Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas

By Pedro Cerqueira

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Chewie-NS: Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas

iMM Computational Biology and Bioinformatics Day 2020: 3min Pitch-talk Presentation

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