The Stemformatics Virtual Lab: More than genomic data visualisation in the cloud

Mr Rowland Mosbergen1, Ms Isha Nagpal2, Mr Othmar Korn3, Ms Ariane Mora4, Mr Tyrone Chen5, Ms Chris Pacheco Rivera6, Professor Christine Wells7

1Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia, rowland.mosbergen@unimelb.edu.au

2Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia, isha.nagpal@unimelb.edu.au

3Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia, o.korn@uq.edu.au

4Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia, ariane.mora@uq.net.au

5Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia, tyrone.chen@unimelb.edu.au

6Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia, chris.pacheco@unimelb.edu.au

7The Walter and Eliza Hall Institute, The University of Melbourne, Melbourne, Australia & Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia, wells.c@unimelb.edu.au

ABSTRACT

STEMFORMATICS VIRTUAL LAB

Stemformatics [1] (www.stemformatics.org)  is primarily a web-based pocket dictionary for stem cells biologists running on the NeCTAR cloud [2]. Part of the stem cell community for over 6 years, it allows biologists to quickly and easily visualise their private datasets. They can also benchmark their datasets against 330+ high quality, preprocessed public datasets.

In this presentation we will show that there is more to Stemformatics than just visualisation and how this is changing what end users expect from their online tools.

Stemformatics is also a collaboration tool.  The first major collaboration was when the multi-omics “Project Grandiose” was published with Stemformatics in December 2014, resulting in in 2 Nature papers [3,4] and 3 Nature Communications papers [5,6,7].  Recently, LEUKomics, a blood cancer atlas, was created using the Stemformatics ecosystem [8].  Stemformatics is also part of the Bioplatforms Australia Stem Cell project.

Stemformatics curates public and proprietary data. To ensure community confidence we only allow high quality experiments to be made public. The failure rate of datasets processed by Stemformatics is currently 29.21%. The main reason to fail a dataset in Stemformatics is poor experimental design. The remaining datasets are high quality datasets that are valuable to the community for benchmarking and data mining.

Stemformatics has also started to mine these public datasets. The Rohart Mesenchymal Stromal Cell (MSC) Test [9] was the first publication that used Stemformatics public datasets to use machine learning to create a classification algorithm for MSCs.

Stemformatics is funded by a grant from the Australian Research Council Special Initiative in Stem Cell Science through Stem Cells Australia [10].

REFERENCES

  1. Wells CA et al Stemformatics: Visualisation and sharing of stem cell gene expression. Stem Cell Research, DOI http://dx.doi.org/10.1016/j.scr.2012.12.003
  2. NeCTAR research cloud website http://nectar.org.au/ accessed 6th of June 2017
  3. Hussein, S. M. I., Puri, M. C., Tonge, P. D. et al. Genome-wide characterization of the routes to pluripotency. Nature. DOI: 10.1038/nature14046
  4. Tonge, P. D. et al. Divergent reprogramming routes lead to alternative stem-cell states. Nature. DOI: 10.1038/nature14047
  5. Clancy, J. L. et al. Small RNA changes en route to distinct cellular states of induced pluripotency. Nature Communications. DOI: 10.1038/ncomms6522
  6. Lee, D-S. et al. An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator. Nature Communications. DOI: 10.1038/ncomms6619
  7. Benevento, M. et al. Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks. Nature Communications. DOI: 10.1038/ncomms6613
  8. LEUKomics article in Conversation: http://theconversation.com/how-big-data-is-being-mobilised-in-the-fight-against-leukaemia-74281 accessed 6th of June 2017
  9. Rohart et al. A molecular classification of human mesenchymal stromal cells. PeerJ. 2016 Mar 24;4:e1845. doi: 10.7717/peerj.1845. eCollection 2016.
  10. Stem Cells Australia website: http://www.stemcellsaustralia.edu.au/ accessed 6th of June 2017

Biography

Rowland Mosbergen is a project manager with 18 years experience in it as a developer, analyst/programmer, team leader, software architect and small business owner.

Rowland has worked at the corporate level with large financial institutions like Merrill Lynch and National Australia Bank on their risk management systems and at the small business level to provide computer support. He has been working in the Stemformatics Virtual Lab for the last 6 years.

About the conference

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