Bioinformatics for the public eye

Bioinformatics for the Public Eye
WEB 2013 ISMBECCB 2013, Berlin
22 July 2013
Wednesday, July 24, 13

Technology overturn
The microscope, invented four centuries ago,
allowed people to see and measure things as never
before — at the cellular level. It was a revolution in
measurement.
Data measurement, is the modern equivalent of the
microscope.
“Google searches, Facebook posts and Twitter
messages, for example, make it possible to measure
behavior and sentiment in ﬁne detail and as it
happens “ Erik Brynjolfsson MIT
2
We are in the early inﬂexion point for the rise of NGS technology as omics functional genomics king. How can we address the rapid rise in demand for
expertise?

Big Data
Science, sports, advertising and public health
— a drift toward data-driven discovery and decision-making.
“It’s a revolution. We’re really just getting under way. But the march of
quantiﬁcation, made possible by enormous new sources of data, will
sweep through academia, business and government. There is no area
that is going to be untouched.”
- Gary King, director of Harvard’s Institute for Quantitative Social Science
8
As educators of the lay public, we need to provide a readily understandable proxy for bioinformatics. People have heard of big data - we should tell them about big biology data needing computational
analysis.

Volume
13 quadrillion DNA bases a year
(stack of DVDs two miles high)
30 000 human genomes in 2012
Several million within 2 years.
4
Translating what we do into readily understandable terms such as “DVD” simpliﬁes the concepts - but not the challenge

Data management
5
Already, online media alerts us to the growing challenge, - twitter FB and G+ are great resources for what’s happening now in our science and what we
can expect soon

6
Experimental data Results

7
Experimental data Results
Bioinformatics makes it possible for bench scientists to understand their own omics data

Public Interaction with Bioinformatics
Online technologies
News/social media
YouTube
Online courses
Online tools
8
More online resources are appearing, that can assist - if used wisely - our education effort

Health
9
The public is primarily interested in its health ﬁrst - this is the major area where bioinformatics intersects with public ‘thirst for knowledge’

Will I get cancer?
10
Either altruists, or the ultimate selﬁes, want to know what’s ‘in there’ for their future. The perception is that sharing genome data might help - perhaps we
should assist the NSA to interpret it?

Will I get cancer?
Informed consent
How to understand my
genome data?
10
Either altruists, or the ultimate selﬁes, want to know what’s ‘in there’ for their future. The perception is that sharing genome data might help - perhaps we
should assist the NSA to interpret it?

Angelina Jolie's BRCA1 gene and
her decision to have a double
mastectomy. It's hard not to be a bit
unnerved. I've always thought it better
to have information than not have
it, and that, anyway, you largely know
from your family history what nasty
diseases are ﬂoating around your gene
pool.
11
Angelina has given us a gift in terms of public perception of the value of genome data. The Guardian UK has featured articles on self genomics - and
describes it in lay terms.

Genome variants
12
The quest is for better understanding of the risk our genomes predict - but this is still a long term goal

OTC genome variation analysis
13

Personal Incentive to genome variants
14
My sister has Schizophrenia - I want to know more as to why - her report hints at developmental issues.

Informed?
15
So to be informed, should access to our genomes, and their interpretation be commoditised?

One Click Genome
16

Public Information
17
medical practitioners
professionals working in the biomedical
sciences
motivated lay individuals interested in exploring
their personal genetic data
This is a great book that you can share with trainees - motivating interest in the exploration of our own code.

Sharing for Personal Genome Data
18
Our code cannot be interpreted if it is siloed - but to share it wisely and effectively needs new platforms - something the Xprize folks are considering for
the next challenge

Economics
19

20
The NYT did us a great favor when it published its commentary on ‘big DNA data’ - allowing us to educate those around us as to our ﬁeld, and to raise
awareness of the work that needs to be done - and how to learn more about our code and its challenges

Bioinformatics
“We believe the ﬁeld of bioinformatics for genetic analysis
will be one of the biggest areas of disruptive innovation in
life science tools over the next few years”
Goldman Sachs
21
Because Big Data is now mainstream - its interpretation has economic potential. If Goldman Sachs is deﬁning bioinformatics, rest assured it will be
monetised.

Hedge Funds
Where can I learn how to estimate the reagents used for Next Gen Sequencers?
Bioinformatics market alone “$38bn” in 2006
22
Estimates of NGS technology use keeps hedge fund managers busy - they want education too.

Who uses
bioinformatics
databases?
23
Computational Biolgists
Bench Scientists
Industry
General public?
Users of bioinformatics are still mostly scientists - only a tiny percentage are lay public citizen scientists

Popular Press vs. Scientific Press
Students required to choose a gene that had been called the “smart gene,”
“fat gene,” “language gene,” and then compare scientific and popular
press.
Online resources
Twitter search
24
Public Access for Teaching Genomics, Proteomics,
and Bioinformatics - Cambell 2003
By reviewing the original literature and then comparing it to the popular press, students can determine the (a) information that matters to the public (b)
how scientific information is transformed for the public interpretation

MOOCs
Public Access vs traditional models
25
With broad sharing posisbilities of internet access public access comes of age for teaching - should our approaches drive or follow the new models?

Scale and reality
26
We need to develop responsive new models to address the rapid increase in demand for NGS expertise.

Scale and reality
Why can’t you provide us a Khan Academy for NGS?
26

Scale and reality
CSHL two week training course for 500 people?
26

Scale and reality
Why can’t my postdocs just take a workshop to analyze their
data?
26

Scale and reality
Why can’t my postdocs just take a workshop to analyze their
data?
Can you help with our analysis today?
26

Addressing the challenge
Online resources and practical
Simpliﬁed online tools
Cloudman + Galaxy AWS instance
Guided collection of training blogs and resources
27
Initial approach to online training coupled with dedicated training sessions

Online tutorials
28
online tutorials

Training blogs
29
curated list of blogs

Commentary blogs
30
commentary - including my own - increases awareness of the available approaches to performing bionformatics

Guardian Science Blog
31
controversial statements can be followed up with discussion on key areas

Controversy
32

Is most of our DNA
devoid of purpose
or does it play a
major role in our
cells?
33
ENSEMBL debate is still current - stating something major takes major evidence - this time - that evidence was packaged in a way that it could be
questioned

Function
Conservation
vs
Potential
34
evolutionary conservation deﬁne functional loci vs potential of site to perform function

35
training should be performed to generate capacity where it is needed, not where the researchers ﬁnd it most convenient to perform study

Databases data
access?
Does GenBank have a monopoly on the
deﬁnition of open access?
36
access to databases for high proﬁle genetic data is a hot area of discussion

Response
- CDC promotes responsible sharing
of data
- GISAD is not GenBank
- GISAID is open to all
37
public spat reveals that access models can have political and ﬁnancial fallout.

Engaging the public
38

Commons and sharing
39

Feedback to the scientists from the sample providers?
40

Some roadblocks
Materials for training?
Resuable and quality material?
41
All these standard workﬂows are great. Unfortunately, people are creative. Or put in a more positive light, they tend to agree with Ewan’s statement.
That means lots and lots of methods development.

How to ﬁnd training
material that
doesn’t suck?
How do I know that this slideset
was well received?
Who likes it and why?
42
Developing courseware is often performed using existing material in a completely ad hoc manner.

Is peer review the
answer?
43

Digital Object
Identiﬁer
44
what is micropublication could be enhanced to include course materials?

Digital Object
Identiﬁer
DOI:.....
Not just for Publications any more...
Provenance
Citability
44
what is micropublication could be enhanced to include course materials?

Accreditation drives quality - GOBLET
Accessible
Peer reviewed
Informed
Preprint > Rating > Leaderboard >Selection for publication > online
publication with citation
45
GOBLET (global organisation for bioinformatics learning education and training) is considering such a model

How to train at scale but retain
effectiveness?
Flip using online
Generating collateral (the big one)
Developing curriculum
The trainee salon
100 > 10 > 1
46
Our approach to scale: Flip then teach interactively in small groups

Who are we teaching
Budding Bioinformaticians
Researchers who need to interpret their data
Members of the public who want to understand their genomes
Medical and Professional community
47
There is growing diversity of trainees for bioinformatics

The reality
100 > 20 hours to prepare a Cloudman Galaxy instance
4 man team to provide onsite training course
advertising and media
self training is diﬃcult to mentor
expectations and levels of expertise
Can we use social media more eﬀectively?
48
Social media should be used more effectively to encourage/scale/improve/develop teaching delivery and self development.

Next...
Central teaching server for Galaxy
Cloudman AWS?
Dark CPU server?
Monetizing HarvardX
Translating Science - do we teach how to blog?
Recognition of eﬀort and impact
49
The ﬁeld is evolving in hand with the technologies

Nagging questions
Are we being effective?
How can we translate to the public?
Commodotise training?
50
Given all the work and huge number of sequences shouldn’t we be able to do better?

Looking for a visionary
Online competition for a professional to provide training environment for Harvard
researchers
Winner will provide the best plan, sample course outline and materials and the
most compelling vision!
Apply within.
whide@hsph.harvard.edu
51
Looking for a new set of hands...

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