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Fiona NielsenApril 18 - 2016
BioSB PhD Retreat in Lunteren
Tweet me @glyn_dk
Why I left my job
in genomic R&D
The frustrated researcher!
How did this happen?
The long road to results
Raw reads
Read QC
Variant calling
Analysis-ready
reads
Analysis-ready
variants
Variant
Annotation Genotype
Refinement Raw Indels
Raw SVs
Raw SNPs
Mapping
External Data
What do you do?
Sequence Read Archive
What do you do?
What do you do?
Yikes
What do you do?
PubMed?
What do you do?
What do you do?
Ask your PI
Write application
Apply for access
Wait…Wait…Wait…Wait…
Access requests can take months
https://www.flickr.com/photos/blackzack00/10205948476/
How did I end up here?
• Masters in bioinformatics, Odense, Denmark
• Masters project in Nijmegen, CMBI
• Continued as Phd student (junior onderzoeker) with
CMBI and Molecular biology
Then my mother got cancer
Why i left my job in genomics R&D - Lunteren - april 18 - 2016
Access requests can take months
2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
Genomes Sequenced
~400k
genomes
produced
And how do you keep up?
More projects launched every day
And how do you keep up?
Data is uploaded
to repository
Data is discovered
by potential user
Data is accessed
by potential user
https://www.flickr.com/photos/blackzack00/10205948476/
It has taken a while…
DNAdigest was founded in March 2013
Working out what to do
Making data discoverable and shareable
Realising the scope of the problem
T. A. van Schaik et al
The need to redefine genomic
data sharing: a focus on data
accessibility, Applied &
Translational Genomics, 2014
10.1016/j.atg.2014.09.013
Researchers spend months to
find and access genomic data,
and often choose to not access
data at all
What IF?
You could easily search and
discover data?
You could rank data by
relevance?
Registering data was simple
to do?
Search would be easy
Collaboration would be simple
You would discover new
resources you did not
know existed
Building through collaboration
DNAdigest organises
hackathons/workshops 4 times a year
We founded Repositive
To make genomic data accessible for research
Adrian Alexa
CTO & Data Scientist
Fiona Nielsen
Founder & CEO
A portal to search for data
Interested? Sign up for our beta at repositive.io
To make your data visible
Interested? Sign up for our beta at repositive.io
To collaborate
Interested? Sign up for our beta at repositive.io
But we are not done yet
https://www.flickr.com/photos/blackzack00/10205948476/
Now I am an entrepreneur
Why i left my job in genomics R&D - Lunteren - april 18 - 2016
The future is always uncertain
I am just doing what it takes
Team effort
Presenting to the world
Reaching out
Why i left my job in genomics R&D - Lunteren - april 18 - 2016
Consulting
Fundraising
Marketing
Branding
Public Engagement
Financial forecasts
Planning
Software development
Science
Long days
Little financial return
Big satisfaction
Questions?
I would love to hear from you ,
drop me a line at fiona@dnadigest.org
https://www.flickr.com/photos/matthewpaulson/7185380311/
Life as an entrepreneur
Read more at http://repositive.io and http://DNAdigest.org
Thanks for listening!
repositive [ re-poz-i-tiv ], noun;
1. a positive experience of accessing
genomic data repositories
Read more at http://repositive.io and tweet us @repositiveio

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Why i left my job in genomics R&D - Lunteren - april 18 - 2016

Editor's Notes

  1. People are dying from genetic diseases even though the data for their diagnostic and cure is ‘out there’ – but today that data is not accessible I am Fiona Nielsen, we are Repositive and we this is our vision for redefining genomic data sharing
  2. How did this happen?
  3. I need data for my analysis
  4. Go to GEO – but this is only expression data
  5. Go to GEO – but this is only expression data
  6. You go to dbGaP -
  7. You ask a colleague for help
  8. You go to pubmed to find out what others did
  9. You ask your supervisor for permission to apply for access to a dataset in dbGaP You write an application for access You ask your supervisor and possibly your sysadmin to sign the application You submit you access application You wait for a response… (can take up to 6 months!!!)
  10. How did this happen? And what if I want to register my data sets for sharing? Illustration: another complicated process, fit in the boxes, time consuming
  11. DNA photo from Flickr: https://www.flickr.com/photos/12745914@N00/17200471/
  12. How did this happen? And what if I want to register my data sets for sharing? Illustration: another complicated process, fit in the boxes, time consuming
  13. And how to keep up with the latest data? 400k genomes produced an the large proportion is private
  14. Searches can be made simple
  15. And how to keep up with the latest data? 400k genomes produced an the large proportion is private
  16. And you are invited Sign up for BETA TESTING
  17. And how to keep up with the latest data? 400k genomes produced an the large proportion is private
  18. You could search for data in the context of all available data? You could see comments and reactions from your peers on the data they have used? What if you could rank data by quality? What if you could query data directly through API access directly in your scripts and workflows?
  19. Searching for relevant data was as easy as finding the right hotel in a city you have not been before?
  20. Search results can be easy to navigate FIGSHARE
  21. Collaboration is easy
  22. You could discover new resources you did not know existed?
  23. And you are invited Sign up for BETA TESTING
  24. And you are invited Sign up for BETA TESTING
  25. And you are invited Sign up for BETA TESTING
  26. And you are invited Sign up for BETA TESTING
  27. And you are invited Sign up for BETA TESTING
  28. Through your daily work routine you gain visibility for potential collaborators?
  29. Through your daily work routine you gain visibility for potential collaborators?
  30. Contribution is easy
  31. Life as an entrepreneur
  32. And you are invited Sign up for BETA TESTING