Bioinformatics for the public eye
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Bioinformatics for the public eye

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Bioinformatics training has to scale as NGS becomes commoditsed and interpetation become more challenging.

Bioinformatics training has to scale as NGS becomes commoditsed and interpetation become more challenging.

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    Bioinformatics for the public eye Bioinformatics for the public eye Presentation Transcript

    • Bioinformatics for the Public Eye WEB 2013 ISMBECCB 2013, Berlin 22 July 2013 Wednesday, July 24, 13
    • 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 Translating what we do into readily understandable terms such as “DVD” simplifies the concepts - but not the challenge
    • Data management 5 Wednesday, July 24, 13 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 Wednesday, July 24, 13
    • 7 Experimental data Results Wednesday, July 24, 13 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 Wednesday, July 24, 13 More online resources are appearing, that can assist - if used wisely - our education effort
    • Health 9 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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? 10 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13
    • Personal Incentive to genome variants 14 Wednesday, July 24, 13 My sister has Schizophrenia - I want to know more as to why - her report hints at developmental issues.
    • Informed? 15 Wednesday, July 24, 13 So to be informed, should access to our genomes, and their interpretation be commoditised?
    • One Click Genome 16 Wednesday, July 24, 13
    • Public Information 17 medical practitioners professionals working in the biomedical sciences motivated lay individuals interested in exploring their personal genetic data Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13
    • 20 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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? Wednesday, July 24, 13 Users of bioinformatics are still mostly scientists - only a tiny percentage are lay public citizen scientists
    • Who uses bioinformatics databases? 23 Computational Biolgists Bench Scientists Industry General public? Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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? CSHL two week training course for 500 people? 26 Wednesday, July 24, 13 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? CSHL two week training course for 500 people? Why can’t my postdocs just take a workshop to analyze their data? 26 Wednesday, July 24, 13 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? CSHL two week training course for 500 people? Why can’t my postdocs just take a workshop to analyze their data? Can you help with our analysis today? 26 Wednesday, July 24, 13 We need to develop responsive new models to address the rapid increase in demand for NGS expertise.
    • Addressing the challenge Online resources and practical Simplified online tools Cloudman + Galaxy AWS instance Guided collection of training blogs and resources 27 Wednesday, July 24, 13 Initial approach to online training coupled with dedicated training sessions
    • Online tutorials 28 Wednesday, July 24, 13 online tutorials
    • Training blogs 29 Wednesday, July 24, 13 curated list of blogs
    • Commentary blogs 30 Wednesday, July 24, 13 commentary - including my own - increases awareness of the available approaches to performing bionformatics
    • Guardian Science Blog 31 Wednesday, July 24, 13 controversial statements can be followed up with discussion on key areas
    • Controversy 32 Wednesday, July 24, 13
    • Is most of our DNA devoid of purpose or does it play a major role in our cells? 33 Wednesday, July 24, 13 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 Wednesday, July 24, 13 evolutionary conservation define functional loci vs potential of site to perform function
    • Function Conservation vs Potential 34 Wednesday, July 24, 13 evolutionary conservation define functional loci vs potential of site to perform function
    • 35 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 public spat reveals that access models can have political and financial fallout.
    • Engaging the public 38 Wednesday, July 24, 13
    • Commons and sharing 39 Wednesday, July 24, 13
    • Feedback to the scientists from the sample providers? 40 Wednesday, July 24, 13
    • Some roadblocks Materials for training? Resuable and quality material? 41 Wednesday, July 24, 13 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 Wednesday, July 24, 13 Developing courseware is often performed using existing material in a completely ad hoc manner.
    • Is peer review the answer? 43 Wednesday, July 24, 13
    • Digital Object Identifier 44 Wednesday, July 24, 13 what is micropublication could be enhanced to include course materials?
    • Digital Object Identifier DOI:..... Not just for Publications any more... Provenance Citability 44 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 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 Wednesday, July 24, 13 Looking for a new set of hands...