why i left my job in genomics r&d - lunteren - april 18 - 2016
TRANSCRIPT
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 resultsRaw reads
Read QC
Variant calling
Analysis-readyreads
Analysis-readyvariants
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
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 alThe 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 NielsenFounder & 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
The future is always uncertain
https://www.flickr.com/photos/f4/12652885873
I am just doing what it takes
Team effort
Presenting to the world
Reaching out
ConsultingFundraisingMarketingBrandingPublic EngagementFinancial forecastsPlanningSoftware developmentScienceLong daysLittle financial returnBig satisfaction
Questions? I would love to hear from you , drop me a line at [email protected]
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