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Extending BACTOME functionality
Dr. Sarah Pohl
Institute for Molecular Bacteriology, TWINCORE, Hanover
Damianos P. Melidis
L3S Research Center, Leibniz University Hanover
June 12, 2020

Motivation
After the first human genome was sequenced, many genome databases and online browsers were created to study each species genomic and transcriptomic landscape. With the same goal, researchers have developed BACTOME [Hornischer et al., 2018], an interactive reference database for the opportunistic pathogen Pseudomonas aeruginosa.

Currently, the BACTOME web portal has three main topics: a general overview of phenotypes of the collected P. aeruginosa strains, interactive tools for identifying genomic variants between the strains, and similar tools to explore the variability of the transcriptomic landscape. In 2019-2020, the whole site has changed. The database was re-designed and repopulated, then the website and the phenotype view were re-designed and implemented using django and javascript.

Aiming to improve the existing new website, we seek to find motivated student assistants that will implement the genome and transcriptome views. Achieving this, the new BACTOME will be ready to be used by researchers through the web. In this effort, we will use and extend already available software packages for web interactive genome viewers. To name a few, general viewers such as the one developed by Cao et al. [2018], or existing browsers tailored for bacterial genomes like the ones by Aurisano et al. [2015], Garanina et al. [2018]. We refer to the work of Pavlopoulos et al. [2015] for a general survey of genome visualization tools. Finally, we will test the system offline and online in order to ensure its applicability.

Goal/Deliverables
Upon successful completion, the student assistant, based on the already implemented django framework, should:

  1. Implement genomic and transcriptomic views
  2. Design, implement and test code
  3. Explain her/his work in a scientific report

A supervisor will always help with major questions, testing of the code and writing of the report.

Prerequisites

  1. Motivation & interest in the topic
  2. Self-contained work in a multi-disciplinary team
  3. Python (Django)
  4. JavaScript
  5. Experience in genomics and transcriptomics is a plus

Contact
Dr. Sarah Pohl: Sarah.Pohl@helmholtz-hzi.de.
Damianos P. Melidis: melidis@l3s.uni-hannover.de.

References

  1. Klaus Hornischer, Ariane Khaledi, Sarah Pohl, Monika Schniederjans, Lorena Pezoldt, Fiordiligie Casilag, Uthayakumar Muthukumarasamy, Sebastian Bruchmann, JanneTh¨oming, Adrian Kordes, et al. Bactome{a reference database to explore the sequence-and gene expression-variation landscape of pseudomonas aeruginosa clinical isolates. Nucleic acids research, 47(D1):D716{D720, 2018.
     
  2. Xiaoyi Cao, Zhangming Yan, Qiuyang Wu, Alvin Zheng, and Sheng Zhong. Give: portable genome browsers for personal websites. Genome biology, 19(1):92, 2018. Jillian Aurisano, Khairi Reda, Andrew Johnson, Elisabeta G Marai, and Jason Leigh. Bactogenie: a large-scale comparative genome visualization for big displays. BMC bioinformatics, 16(11):S6, 2015.
     
  3. Irina A Garanina, Gleb Y Fisunov, and Vadim M Govorun. Bac-browser: the tool for visualization and analysis of prokaryotic genomes. Frontiers in microbiology, 9, 2018. Georgios A Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou, Anton J Enright, and Ioannis Iliopoulos. Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience, 4(1):38, 2015.
     
  4. Irina A Garanina, Gleb Y Fisunov, and Vadim M Govorun. Bac-browser: the tool for visualization and analysis of prokaryotic genomes. Frontiers in microbiology, 9, 2018.
     
  5. Georgios A Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou, Anton J Enright, and Ioannis Iliopoulos. Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience, 4(1):38, 2015.