Why i left my job in genomics R&D - Lunteren - april 18 - 2016
-
Upload
fiona-nielsen -
Category
Career
-
view
2.078 -
download
0
Transcript of Why i left my job in genomics R&D - Lunteren - april 18 - 2016
![Page 1: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/1.jpg)
Fiona NielsenApril 18 - 2016
BioSB PhD Retreat in Lunteren
Tweet me @glyn_dk
Why I left my job in genomic
R&D
![Page 2: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/2.jpg)
The frustrated researcher!
How did this happen?
![Page 3: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/3.jpg)
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
![Page 4: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/4.jpg)
What do you do?
Sequence Read Archive
![Page 5: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/5.jpg)
What do you do?
![Page 6: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/6.jpg)
What do you do?
![Page 7: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/7.jpg)
Yikes
What do you do?
PubMed?
![Page 8: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/8.jpg)
What do you do?
![Page 9: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/9.jpg)
What do you do?
Ask your PI
Write application
Apply for access
Wait…Wait…Wait…Wait…
![Page 10: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/10.jpg)
Access requests can take months
![Page 11: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/11.jpg)
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
![Page 12: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/12.jpg)
![Page 13: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/13.jpg)
Access requests can take months
![Page 14: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/14.jpg)
2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
Genomes Sequenced~400k genomes produced
And how do you keep up?
![Page 15: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/15.jpg)
More projects launched every day
![Page 16: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/16.jpg)
And how do you keep up?
Data is uploaded to repository
Data is discovered by potential user
Data is accessed by potential user
![Page 17: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/17.jpg)
https://www.flickr.com/photos/blackzack00/10205948476/
It has taken a while…
DNAdigest was founded in March 2013
![Page 18: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/18.jpg)
Working out what to do
Making data discoverable and shareable
![Page 19: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/19.jpg)
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
![Page 20: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/20.jpg)
What IF?You could easily search and
discover data?
You could rank data by relevance?
Registering data was simple to do?
![Page 21: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/21.jpg)
Search would be easy
![Page 22: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/22.jpg)
Collaboration would be simple
![Page 23: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/23.jpg)
You would discover new resources you did not
know existed
![Page 24: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/24.jpg)
Building through collaboration
DNAdigest organises hackathons/workshops 4 times a year
![Page 25: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/25.jpg)
We founded Repositive
To make genomic data accessible for research
Adrian Alexa CTO & Data Scientist
Fiona NielsenFounder & CEO
![Page 26: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/26.jpg)
A portal to search for data
Interested? Sign up for our beta at repositive.io
![Page 27: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/27.jpg)
To make your data visible
Interested? Sign up for our beta at repositive.io
![Page 28: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/28.jpg)
To collaborate
Interested? Sign up for our beta at repositive.io
![Page 29: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/29.jpg)
But we are not done yet
![Page 30: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/30.jpg)
https://www.flickr.com/photos/blackzack00/10205948476/
Now I am an entrepreneur
![Page 31: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/31.jpg)
![Page 32: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/32.jpg)
The future is always uncertain
![Page 33: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/33.jpg)
https://www.flickr.com/photos/f4/12652885873
I am just doing what it takes
![Page 34: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/34.jpg)
Team effort
![Page 35: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/35.jpg)
Presenting to the world
![Page 36: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/36.jpg)
Reaching out
![Page 37: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/37.jpg)
![Page 38: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/38.jpg)
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
![Page 39: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/39.jpg)
Read more at http://repositive.io and http://DNAdigest.org
Thanks for listening!
![Page 40: Why i left my job in genomics R&D - Lunteren - april 18 - 2016](https://reader036.fdocuments.in/reader036/viewer/2022070521/58f9a837760da3da068b61c5/html5/thumbnails/40.jpg)
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