From bioinformatics scientist to entrepreneur - Women in Omics - ICG11 - 2016
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Presented by Fiona Nielsen at the International Conference of Genomics at China National Genebank, Shenzhen http://www.icg-11.org I present the "WHY" of what I am doing, and how I got here. A personal story of frustration, science and family. Session chaired by Laurie Goodman, Gigascience
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From bioinformatics scientist to entrepreneur - Women in Omics - ICG11 - 2016
- 1. Fiona NielsenNovember 3 - 2016 Shenzhen, ICG-11 Tweet me @glyn_dk From bioinformatics scientist to entrepreneur
- 2. The frustrated researcher! How did this happen?
- 3. 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
- 4. What do you do? Sequence Read Archive
- 5. What do you do?
- 6. What do you do?
- 7. Yikes What do you do? PubMed?
- 8. What do you do?
- 9. What do you do? Ask your PI Write application Apply for access Wait…Wait…Wait…Wait…
- 10. Access requests can take months
- 11. You are not the only one 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
- 12. 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 Genomes Sequenced ~400k genomes produced And how do you keep up?
- 13. More projects launched every day
- 14. And how do you keep up? Data is uploaded to repository Data is discovered by potential user Data is accessed by potential user
- 15. What IF? You could easily search and discover data? You could rank data by relevance? Registering data was simple to do?
- 16. Search would be easy
- 17. Collaboration would be simple
- 18. You would discover new resources you did not know existed
- 19. https://www.flickr.com/photos/blackzack00/10205948476/ It has taken a while… DNAdigest was founded in March 2013
- 20. Working out what to do Making data discoverable and shareable
- 21. Building through collaboration DNAdigest organises hackathons/workshops 4 times a year
- 22. We founded Repositive To make genomic data accessible for research Adrian Alexa CTO & Data Scientist Fiona Nielsen Founder & CEO
- 23. A portal to search for data Interested? Sign up for our beta at repositive.io
- 24. To make your data visible Interested? Sign up for our beta at repositive.io
- 25. To collaborate Interested? Sign up for our beta at repositive.io Let me show you
- 26. But we are not done yet
- 28. Working towards Open Science • Transparency • Availability • Accessibility • Reusability • Collaboration
- 29. Making your contribution should be easy Supporting best practices: • get credit for making data available • give credit to data producers • Initiate new collaborations
- 30. http://en.wikipedia.org/wiki/Karyotype#mediaviewer/File:Spectralkaryotype98-300.jpg Any questions so far?
- 31. 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
- 33. The future is always uncertain
- 34. I am just doing what it takes
- 35. Team effort
- 36. Presenting to the world
- 37. Reaching out
- 39. 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
- 40. Read more at http://repositive.io and http://DNAdigest.org Thanks for listening!
- 41. 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
Hinweis der Redaktion
- 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
- How did this happen?
- I need data for my analysis
- Go to GEO – but this is only expression data
- Go to GEO – but this is only expression data
- You go to dbGaP -
- You ask a colleague for help
- You go to pubmed to find out what others did
- 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!!!)
- 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
- And how to keep up with the latest data? 400k genomes produced an the large proportion is private
- And how to keep up with the latest data? 400k genomes produced an the large proportion is private
- Searches can be made simple
- And how to keep up with the latest data? 400k genomes produced an the large proportion is private
- 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?
- Searching for relevant data was as easy as finding the right hotel in a city you have not been before?
- Search results can be easy to navigate FIGSHARE
- Collaboration is easy
- You could discover new resources you did not know existed?
- And you are invited Sign up for BETA TESTING
- And you are invited Sign up for BETA TESTING
- And you are invited Sign up for BETA TESTING
- And you are invited Sign up for BETA TESTING
- And you are invited Sign up for BETA TESTING
- And you are invited Sign up for BETA TESTING
- Through your daily work routine you gain visibility for potential collaborators?
- Through your daily work routine you gain visibility for potential collaborators?
- Contribution is easy
- Life as an entrepreneur
- And you are invited Sign up for BETA TESTING