How the Web is
Democratizing Science

(Join in!)


Strange Loop Conference 2015
Abigail Cabunoc Mayes / @abbycabs

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.

Sony PSP video game graphics


De novo sequence assembly

Problem 1

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

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.


Open Science logo by Greg Emmerich / CC-BY-SA

What does 'Open' even mean?

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

“Philosophical Transactions
of the Royal Society”

Established by the Royal Society of London in 1665


“Philosophical” = “natural philosophy” which is equivalent to “science” today

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

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

Fast Forward

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

gforsythe CC BY-NC-SA 2.0
“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…”

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

Science today

(a fictional example)

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

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)

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)




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!

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

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!














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