Bioinformatics for the public eye

Bioinformatics for the Public EyeWEB 2013 ISMBECCB 2013, Berlin22 July 2013

Wednesday, July 24, 13

Bioinformatics for the Public EyeWEB 2013 ISMBECCB 2013, Berlin22 July 2013


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

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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 DataScience, 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

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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.

Volume13 quadrillion DNA bases a year

(stack of DVDs two miles high)

30 000 human genomes in 2012

Several million within 2 years.

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Translating what we do into readily understandable terms such as “DVD” simplifies the concepts - but not the challenge

Data management

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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

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Experimental data Results


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Experimental data Results


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

Public Interaction with BioinformaticsOnline technologies

News/social media

YouTube

Online courses

Online tools

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More online resources are appearing, that can assist - if used wisely - our education effort

Health

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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?

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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?

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Will I get cancer?Informed consentHow to understand my genome data?

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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.

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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.

http://www.guardian.co.uk/film/2013/jun/02/angelina-jolie-mastectomy-grateful-reaction

http://www.guardian.co.uk/film/2013/jun/02/angelina-jolie-mastectomy-grateful-reaction

Genome variants

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

OTC genome variation analysis13


Personal Incentive to genome variants14


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 Genome16


Public Information

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medical practitionersprofessionals 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 Data18


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

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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

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Because Big Data is now mainstream - its interpretation has economic potential. If Goldman Sachs is defining bioinformatics, rest assured it will be monetised.

Hedge FundsWhere can I learn how to estimate the reagents used for Next Gen Sequencers?

Bioinformatics market alone “$38bn” in 2006

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Estimates of NGS technology use keeps hedge fund managers busy - they want education too.

Who uses bioinformatics databases?

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Computational BiolgistsBench Scientists

IndustryGeneral public?


Users of bioinformatics are still mostly scientists - only a tiny percentage are lay public citizen scientists

Who uses bioinformatics databases?

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Computational BiolgistsBench Scientists

IndustryGeneral 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

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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

MOOCsPublic Access vs traditional models

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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

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

Scale and realityWhy can’t you provide us a Khan Academy for NGS?

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CSHL two week training course for 500 people?

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Why can’t my postdocs just take a workshop to analyze their data?

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Why can’t my postdocs just take a workshop to analyze their data?

Can you help with our analysis today?

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Addressing the challengeOnline resources and practical

Simplified online tools

Cloudman + Galaxy AWS instance

Guided collection of training blogs and resources

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Initial approach to online training coupled with dedicated training sessions

Online tutorials28


online tutorials

Training blogs29


curated list of blogs

Commentary blogs30


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

Guardian Science Blog31


controversial statements can be followed up with discussion on key areas

Controversy

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Is most of our DNA devoid of purpose or does it play a major role in our

cells?

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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

FunctionConservation

vsPotential

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evolutionary conservation define functional loci vs potential of site to perform function

FunctionConservation

vsPotential

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evolutionary conservation define functional loci vs potential of site to perform function

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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?

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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

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public spat reveals that access models can have political and financial fallout.

Engaging the public38


Commons and sharing39


Feedback to the scientists from the sample providers?

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Some roadblocks

Materials for training?Resuable and quality material?

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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?

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Developing courseware is often performed using existing material in a completely ad hoc manner.

Is peer review the answer?

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Digital Object Identifier

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what is micropublication could be enhanced to include course materials?

Digital Object Identifier

DOI:.....Not just for Publications any more...ProvenanceCitability

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what is micropublication could be enhanced to include course materials?

Accreditation drives quality - GOBLETAccessible

Peer reviewed

Informed

Preprint > Rating > Leaderboard >Selection for publication > online publication with citation

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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

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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

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There is growing diversity of trainees for bioinformatics

The reality100 > 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?

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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

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The field is evolving in hand with the technologies

Nagging questions

Are we being effective?

How can we translate to the public?

Commodotise training?

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Given all the work and huge number of sequences shouldn’t we be able to do better?

Looking for a visionaryOnline competition for a professional to provide training environment for Harvard researchersWinner will provide the best plan, sample course outline and materials and the most compelling vision!

Apply [email protected]

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Looking for a new set of hands...

mailto:[email protected]

mailto:[email protected]

Education

Bioinformatics for the public eye