open-science-strangeloop-2015

How the Web is Democratizing Science

(Join in!)

Strange Loop Conference 2015 Abigail Cabunoc Mayes / @abbycabs

Thank organizers, it's an immense honour to be here - diversity scholarships

Hi! I'm abbycabs

I work for the Mozilla Foundation where I'm lead developer for the Mozilla Science Lab.

I use the web to move science forward.

Building a better Internet: promoting openness, innovation & opportunity on the Web.

Helping researchers leverage the open web.

Science Lab - applying Mozilla's mission to a very interesting community of practice. Where they have some very interesting and specific problems:

Sony PSP video game graphics

De novo sequence assembly

These both run algorithms that push the limit of the memory that's available to them. 64B. Jared's story

Problem 1

Visualizing protein interactions in open worm data to help us understand human diseases.

I wanted to introduce you to some problems I care about, and our community cares about.

Problem 2

Analyzing open genetic data to better understand how virus and bacteria interact.

Problem 3

Collecting and curating open astronomy datasets to facilitate data analysis and discovery.

These problems (& more), are usually tackled daily by academics with very little formal computing training. But I think that the people in this room are better equiped to solve these problems -- even without the domain knowledge.

Open Science logo by Greg Emmerich / CC-BY-SA This talk is really about 'open science'. I know I title it 'democratization of science', which is one of the outcomes... But I'm really excited to show you how can be a part of this movement, which is really changing how research is done today.

What does 'Open' even mean?

open source
open access
open data
open standards
open government
open science

We've seen this used for... and I think the word 'open' is starting to loose it's meaning When I first heard 'open science' it was vague and I thought it meants something like 'free science'. I want to look back and see how this term came to inspire so many movements and try to bring back some of the meaning & power behind 'open'. And I would argue that a lot of the fundamental ideas behind 'openness' today originates in science!

Welcome to the scientific revolution! Colbert Presenting the Members of the Royal Academy of Sciences to Louis XIV in 1667. At this time, there were a lot of scientific discoveries being made. But people realized they needed a platform to share and collaborate on research.

“Philosophical Transactions of the Royal Society”

Established by the Royal Society of London in 1665

“Philosophical” = “natural philosophy” which is equivalent to “science” today Coming out of the scientific revolution, the first academic journal devoted to science...

Henry OldenburgThe Royal Society’s first secretary, Henry Oldenburg, wrote a series of letters giving us insight into the values driving the creation of the journal.

Credit & Documentation

“We must be very careful as well of regist’ring the person and time of any new matter, as the matter itselfe, whereby the honor of the invention will be reliably preserved to all posterity”24 November 1664

Sharing

“…all ingenious men will thereby be incouraged to impact their knowledge and discoverys ”3 December 1664

Participation

“ … being first revised by some of the members.”Royal Society of London, Council Minutes, 1 March 1665 Need to share discoveries in order to build on them. Science is better with more eyes

Science embraced a culture of working together and sharing discoveries to further human knowledge.

This has enabled many scientific breakthroughs. Today, almost all advances in science appear in a journal article.

WormBase - C. elegans

Fast Forward

The Web + Free Software = New Meaning of 'Open'

some ideas around working open start to appear in the 90s

gforsythe CC BY-NC-SA 2.0 Essay on the state of free software at the time. Linux

“Linus Torvalds’s style of development—release early and often, delegate everything you can, be open to the point of promiscuity—came as a surprise. No quiet, reverent cathedral-building here—rather, the Linux community seemed to resemble a great babbling bazaar of differing agendas and approaches... out of which a coherent and stable system could seemingly emerge…” Inspired Netscape...

Mozilla

In 1998, the Netscape Corporation released the Netscape browser suite as free software.

This became the basis of the Mozilla Project and sparked the label open source.

Working Open

Public and participatory. This requires structuring efforts so that "outsiders" can meaningfully participate and become "insiders" as appropriate.

Working Open, Mozilla Wiki Let's compare this definition of working open with some of the practices we see in science today.

Science today

(a fictional example)

Gretta Grad Student

Strange Loop University

Gretta Grad Student

Strangus Loopi

Gretta wants to study a population in western Africa

Strangus Loopi

Sequencing

(read the DNA code in the bacteria)

($100 / strain) x 250 strains = $25K

$5K x 1 strain (S. loopi STL) = $5K(on a special long-read PacBio sequencer)

Gretta Grad Student

Gretta has spent $30K and now has lots of data!

Gretta goes to her first scientific meeting

S. Loopi International Meeting

Gretta discovers that two other research groups have also sequenced the S. loopi STL strain using PacBio

Resource loss: $10K savings had they shared their data!(+ PacBio cost of $700K)

It's kinda weird they all look alike... but way to go women in science!

Gretta meets Tucker who is also studying S. loopi in West Africa. They don't share a lot of their discoveries since they're both scared of being scooped.

Knowledge loss & Resource loss($25K if they shared data)

Gretta: time to analyze data!

But she has never written code!

She spends 6 months teaching herself python and bioinformatics to make sense of her data.

Gretta and Tucker independently teach themselves python and run the same analysis on their data. They never share their code.

Neither one realizes that a python library exists for this.

Software loss & Time loss

Results

There is a potentially dangerous strain of S. loopi in West African populations.

Time to publish!

Gretta is published in a high impact journal!

She gets a prestigious fellowship.

Her research is paywalled and inaccessible by the West African community she studied.

They don't take preventative measures to handle the dangerous strain of S. loopi. An outbreak happens.

John R. McKiernan, CC BY-NC-ND

loss of resources, software, time and lives

In research today, we see a loss of... So, I called this the democratization of science. And this is why I will..

I will fight for democracy in science! (if it means open)

Where we see open science today

Problem 1

Visualizing protein interactions in open worm data to help us understand human diseases.

WormBase & Cytoscape.js

WormBase is the glue that holds the C. elegans research community together. Many in the field start their day with a cup of coffee and WormBase; for many WormBase stays open all day on their computer as a constant companion. There’s simply no more efficient way to integrate all of the new data generated in the field.

Problem 2

Analyzing open genetic data to better understand how virus and bacteria interact.

Problem 3

Collecting and curating open astronomy datasets to facilitate data analysis and discovery.

http://trillianverse.org/

Astronomy produces extremely large data sets from ground-based telescopes, space missions, and simulation. The problem is that no one institution can host all of this data, let alone have the resources to properly manage it. The result is that applying analyses against full data sets across the wide range of wavelengths available is either beyond the resources of most astronomers or currently impossible. Trillian will make this simple and straightforward.

+ many more problems like these! These problems (& more), are usually tackled daily by academics with very little formal computing training. But I think that the people in this room are better equiped to solve these problems -- even without the domain knowledge.

Source www.reactiongifs.com

Acknowledgements

Madeleine Bonsma, Angelina Fabbro, Max Franz, Todd Harris, Elizabeth Huynh, Amy Lee, Josh Matthews, Erin McKiernan, John R. McKiernan, Bill Mills, Demitri Muna, Jared Simpson, Lincoln Stein

(+ the Mozilla Science Lab! Kaitlin Thaney, Arliss Collins, Zannah Marsh, Steph Wright)

Science is for everyone!

mozillascience.org/volunteer

How the Web is Democratizing Science (Join in!) Strange Loop Conference 2015 Abigail Cabunoc Mayes / @abbycabs Thank organizers, it's an immense honour to be here - diversity scholarships

How the Web is Democratizing Science – (Join in!)

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