Career talk about how I moved from bioinformatics scientist to become an entrepreneur.
Presented at BioSB2016, pre-conference PhD retreat for young researchers in bioinformatics and systems biology at Congrescentrum De Werelt in Lunteren. #BioSB2016 #BioSB16
Link to event:
http://www.youngcb.nl/events/biosb-phd-retreat-2016/
Read more about my work:
http://DNAdigest.org
http://repositive.io
https://uk.linkedin.com/in/fionanielsen
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
11. 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
19. 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
20. What IF?
You could easily search and
discover data?
You could rank data by
relevance?
Registering data was simple
to do?
39. Read more at http://repositive.io and http://DNAdigest.org
Thanks for listening!
40. 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
Editor's Notes
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
DNA photo from Flickr: https://www.flickr.com/photos/12745914@N00/17200471/
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
Searches can be made simple
And how to keep up with the latest data?
400k genomes produced an the large proportion is private
And you are invited
Sign up for BETA TESTING
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
Through your daily work routine you gain visibility for potential collaborators?
Through your daily work routine you gain visibility for potential collaborators?