imagine someone invents a new form of surgery this new technique promises to
surgery this new technique promises to
surgery this new technique promises to treat a condition previously considered
treat a condition previously considered
treat a condition previously considered untreatable now along with it they also
untreatable now along with it they also
untreatable now along with it they also create new tools that enable one to
create new tools that enable one to
create new tools that enable one to perform this new procedure then they
perform this new procedure then they
perform this new procedure then they publish a research paper about it get
publish a research paper about it get
publish a research paper about it get mentioned in the news and tens of
mentioned in the news and tens of
mentioned in the news and tens of thousands of people find out about this
thousands of people find out about this
thousands of people find out about this great new innovation that promises to
great new innovation that promises to
great new innovation that promises to improve the lives of so many around the
improve the lives of so many around the
improve the lives of so many around the world
world
world however they keep the new tools that
however they keep the new tools that
however they keep the new tools that they created to themselves in a case
they created to themselves in a case
they created to themselves in a case like this how useful would you say this
like this how useful would you say this
like this how useful would you say this new technique is everybody finds out
new technique is everybody finds out
new technique is everybody finds out about it but very few people are
about it but very few people are
about it but very few people are actually able to use it or benefit from
actually able to use it or benefit from
actually able to use it or benefit from it now I think you can appreciate the
it now I think you can appreciate the
it now I think you can appreciate the fact that being protective of tools that
fact that being protective of tools that
fact that being protective of tools that enable new techniques will not only
enable new techniques will not only
enable new techniques will not only limit the impact these techniques can
limit the impact these techniques can
limit the impact these techniques can have but also it’ll prevent others from
have but also it’ll prevent others from
have but also it’ll prevent others from trying them out and improving upon them
trying them out and improving upon them
trying them out and improving upon them and I’m here to tell you that something
and I’m here to tell you that something
and I’m here to tell you that something exactly like that is happening in
exactly like that is happening in
exactly like that is happening in science and it’s decreasing our chances
science and it’s decreasing our chances
science and it’s decreasing our chances of collaboratively solving some of the
of collaboratively solving some of the
of collaboratively solving some of the most heart important problems we face
most heart important problems we face
most heart important problems we face today I want to talk to you about the
today I want to talk to you about the
today I want to talk to you about the role of openness and collaboration in
role of openness and collaboration in
role of openness and collaboration in science specifically about the movement
science specifically about the movement
science specifically about the movement of open science and within open science
of open science and within open science
of open science and within open science open source just introduce what open
open source just introduce what open
open source just introduce what open science is open science is the movement
science is open science is the movement
science is open science is the movement dedicated at making all scientific
dedicated at making all scientific
dedicated at making all scientific research and data openly and freely
research and data openly and freely
research and data openly and freely accessible to everyone and one of the
accessible to everyone and one of the
accessible to everyone and one of the six core principles of open science is
six core principles of open science is
six core principles of open science is open source referring to open source
open source referring to open source
open source referring to open source software and what is open source
software and what is open source
software and what is open source software it is software for which the
software it is software for which the
software it is software for which the source is made freely available to the
source is made freely available to the
source is made freely available to the general public for use or modification
general public for use or modification
general public for use or modification I’m currently a PhD candidate at MIT
I’m currently a PhD candidate at MIT
I’m currently a PhD candidate at MIT working in computer vision and
working in computer vision and
working in computer vision and the last six years or so I’ve had to use
the last six years or so I’ve had to use
the last six years or so I’ve had to use or write some type of software for my
or write some type of software for my
or write some type of software for my research and I want to share with you a
research and I want to share with you a
research and I want to share with you a few things I’ve learned around open
few things I’ve learned around open
few things I’ve learned around open sharing of software in scientific
sharing of software in scientific
sharing of software in scientific research now you could say that science
research now you could say that science
research now you could say that science has been open for centuries people
has been open for centuries people
has been open for centuries people publish papers in journals and anybody
publish papers in journals and anybody
publish papers in journals and anybody can read these journals and then they
can read these journals and then they
can read these journals and then they can give credit to the original author
can give credit to the original author
can give credit to the original author by citing their paper in any follow up
by citing their paper in any follow up
by citing their paper in any follow up publications
publications
publications however these journals aren’t really
however these journals aren’t really
however these journals aren’t really open and what I mean by that
open and what I mean by that
open and what I mean by that specifically is that if you ever want to
specifically is that if you ever want to
specifically is that if you ever want to read a paper in one of these scientific
read a paper in one of these scientific
read a paper in one of these scientific journals you have to pay often a
journals you have to pay often a
journals you have to pay often a significant amount per paper and the
significant amount per paper and the
significant amount per paper and the worst thing is that you even have to pay
worst thing is that you even have to pay
worst thing is that you even have to pay to read a paper on research that was
to read a paper on research that was
to read a paper on research that was funded by your tax dollars a portion of
funded by your tax dollars a portion of
funded by your tax dollars a portion of the sixty five billion dollars in
the sixty five billion dollars in
the sixty five billion dollars in government funding that goes to
government funding that goes to
government funding that goes to universities and colleges every year in
universities and colleges every year in
universities and colleges every year in the US now fortunately the open science
the US now fortunately the open science
the US now fortunately the open science movement has actually made some progress
movement has actually made some progress
movement has actually made some progress on this issue in the last few years in
on this issue in the last few years in
on this issue in the last few years in fact there’s a bill in the House of
fact there’s a bill in the House of
fact there’s a bill in the House of Representatives right now called the
Representatives right now called the
Representatives right now called the fair access to Science and Technology
fair access to Science and Technology
fair access to Science and Technology Research act or faster which would
Research act or faster which would
Research act or faster which would mandate the public release of publicly
mandate the public release of publicly
mandate the public release of publicly funded research which will hopefully get
funded research which will hopefully get
funded research which will hopefully get passed and become law soon however this
passed and become law soon however this
passed and become law soon however this bill says nothing about the software
bill says nothing about the software
bill says nothing about the software that is created as part of these
that is created as part of these
that is created as part of these publicly funded projects and why is that
publicly funded projects and why is that
publicly funded projects and why is that a problem
a problem
a problem in today’s day and age where computers
in today’s day and age where computers
in today’s day and age where computers and software are becoming more powerful
and software are becoming more powerful
and software are becoming more powerful by the day
by the day
by the day software is beginning to drive a vast
software is beginning to drive a vast
software is beginning to drive a vast majority of research out there we live
majority of research out there we live
majority of research out there we live in a world where it is possible for a
in a world where it is possible for a
in a world where it is possible for a researcher to simulate and analyze let’s
researcher to simulate and analyze let’s
researcher to simulate and analyze let’s say how a nanoparticle releases drug
say how a nanoparticle releases drug
say how a nanoparticle releases drug into the bloodstream
into the bloodstream
into the bloodstream before any actual tests are conducted on
before any actual tests are conducted on
before any actual tests are conducted on animals and oftentimes software exactly
animals and oftentimes software exactly
animals and oftentimes software exactly like this is a key enabler of any
like this is a key enabler of any
like this is a key enabler of any follow-up research in addition this
follow-up research in addition this
follow-up research in addition this software tends to be fairly large
software tends to be fairly large
software tends to be fairly large complex and tedious to replicate so for
complex and tedious to replicate so for
complex and tedious to replicate so for example if a researcher like me had open
example if a researcher like me had open
example if a researcher like me had open access to a paper about
access to a paper about
access to a paper about some software-driven research I would
some software-driven research I would
some software-driven research I would still have to spend several months if
still have to spend several months if
still have to spend several months if not years just recreating that software
not years just recreating that software
not years just recreating that software before I can replicate the published
before I can replicate the published
before I can replicate the published results and as a researcher it is
results and as a researcher it is
results and as a researcher it is critical for me to be able to reproduce
critical for me to be able to reproduce
critical for me to be able to reproduce these results because then only can I
these results because then only can I
these results because then only can I start building upon them now this really
start building upon them now this really
start building upon them now this really undermines some of the key enabling
undermines some of the key enabling
undermines some of the key enabling qualities of software which is one that
qualities of software which is one that
qualities of software which is one that it’s easy to distribute to it produces
it’s easy to distribute to it produces
it’s easy to distribute to it produces almost the exact same result on any
almost the exact same result on any
almost the exact same result on any computer and three that it can be
computer and three that it can be
computer and three that it can be quickly and easily updated and improved
quickly and easily updated and improved
quickly and easily updated and improved not to mention the potentially huge
not to mention the potentially huge
not to mention the potentially huge impact some open source software coming
impact some open source software coming
impact some open source software coming out of science can have consider the
out of science can have consider the
out of science can have consider the example of this machine learning library
example of this machine learning library
example of this machine learning library called scikit-learn and some of you here
called scikit-learn and some of you here
called scikit-learn and some of you here actually might be familiar with this the
actually might be familiar with this the
actually might be familiar with this the original paper about this has been cited
original paper about this has been cited
original paper about this has been cited over 7,000 times which is a lot in just
over 7,000 times which is a lot in just
over 7,000 times which is a lot in just six years and it has enabled research
six years and it has enabled research
six years and it has enabled research across a huge variety of domains all the
across a huge variety of domains all the
across a huge variety of domains all the way from evolutionary biology to
way from evolutionary biology to
way from evolutionary biology to astrophysics to psychology it even helps
astrophysics to psychology it even helps
astrophysics to psychology it even helps power Spotify a service that many of us
power Spotify a service that many of us
power Spotify a service that many of us use pretty much every day now I want to
use pretty much every day now I want to
use pretty much every day now I want to clarify that for software that comes out
clarify that for software that comes out
clarify that for software that comes out of privately funded research or software
of privately funded research or software
of privately funded research or software that forms the basis of a new company
that forms the basis of a new company
that forms the basis of a new company whether that’s made open-source is
whether that’s made open-source is
whether that’s made open-source is purely a business decision I’m only
purely a business decision I’m only
purely a business decision I’m only talking about software as it’s used in
talking about software as it’s used in
talking about software as it’s used in academic research that mostly comes out
academic research that mostly comes out
academic research that mostly comes out of publicly funded projects which if it
of publicly funded projects which if it
of publicly funded projects which if it isn’t shared mostly we’ll just sit on a
isn’t shared mostly we’ll just sit on a
isn’t shared mostly we’ll just sit on a hard drive somewhere before it gets
hard drive somewhere before it gets
hard drive somewhere before it gets thrown out so this culture of being
thrown out so this culture of being
thrown out so this culture of being protective of software that research is
protective of software that research is
protective of software that research is based on is a stumbling block and really
based on is a stumbling block and really
based on is a stumbling block and really slows down the innovation process in a
slows down the innovation process in a
slows down the innovation process in a lot of fields and I can say this from my
lot of fields and I can say this from my
lot of fields and I can say this from my personal experience my research has been
personal experience my research has been
personal experience my research has been based at the intersection of two fields
based at the intersection of two fields
based at the intersection of two fields which are culturally very different
which are culturally very different
which are culturally very different computer science and mechanical
computer science and mechanical
computer science and mechanical engineering now computer science on one
engineering now computer science on one
engineering now computer science on one hand as a field has really adopted this
hand as a field has really adopted this
hand as a field has really adopted this culture of open-source there are a lot
culture of open-source there are a lot
culture of open-source there are a lot of researchers however in mechanical
of researchers however in mechanical
of researchers however in mechanical engineering who are still protective
engineering who are still protective
engineering who are still protective about their software
about their software
about their software so they keep it to themselves access to
so they keep it to themselves access to
so they keep it to themselves access to all of this software coming from the
all of this software coming from the
all of this software coming from the computer science community has enabled
computer science community has enabled
computer science community has enabled me to make very rapid progress however
me to make very rapid progress however
me to make very rapid progress however to implement some of my ideas on the
to implement some of my ideas on the
to implement some of my ideas on the mechanical engineering side I’ve had to
mechanical engineering side I’ve had to
mechanical engineering side I’ve had to recreate over 10,000 lines of software
recreate over 10,000 lines of software
recreate over 10,000 lines of software over almost three years and I’ve heard
over almost three years and I’ve heard
over almost three years and I’ve heard repeatedly over the last five to six
repeatedly over the last five to six
repeatedly over the last five to six years from many of my colleagues at MIT
years from many of my colleagues at MIT
years from many of my colleagues at MIT over and over again that they needed
over and over again that they needed
over and over again that they needed some software to advance their research
some software to advance their research
some software to advance their research and they were not able to gain access to
and they were not able to gain access to
and they were not able to gain access to it all this for software that has been
it all this for software that has been
it all this for software that has been written multiple times in multiple labs
written multiple times in multiple labs
written multiple times in multiple labs as part of multiple projects a lot of
as part of multiple projects a lot of
as part of multiple projects a lot of which were taxpayer funded so perhaps we
which were taxpayer funded so perhaps we
which were taxpayer funded so perhaps we need to start thinking about another
need to start thinking about another
need to start thinking about another bill that would mandate the release of
bill that would mandate the release of
bill that would mandate the release of software also that comes out of these
software also that comes out of these
software also that comes out of these publicly funded projects now I want to
publicly funded projects now I want to
publicly funded projects now I want to make a point that appeals to the
make a point that appeals to the
make a point that appeals to the researchers here you guys might be
researchers here you guys might be
researchers here you guys might be wondering well why is it that some
wondering well why is it that some
wondering well why is it that some researchers in some of these fields feel
researchers in some of these fields feel
researchers in some of these fields feel the need to be protective like this they
the need to be protective like this they
the need to be protective like this they published papers openly but why not also
published papers openly but why not also
published papers openly but why not also release software and the answer to this
release software and the answer to this
release software and the answer to this question lies in the way the academic
question lies in the way the academic
question lies in the way the academic community evaluates researchers
community evaluates researchers
community evaluates researchers researchers get evaluated based on the
researchers get evaluated based on the
researchers get evaluated based on the number of papers they publish and how
number of papers they publish and how
number of papers they publish and how influential those papers are and one of
influential those papers are and one of
influential those papers are and one of the strongest indicators of how
the strongest indicators of how
the strongest indicators of how influential a paper is is how many
influential a paper is is how many
influential a paper is is how many citations it has that is how many other
citations it has that is how many other
citations it has that is how many other research papers make a reference to it
research papers make a reference to it
research papers make a reference to it so researchers sometimes feel if they
so researchers sometimes feel if they
so researchers sometimes feel if they keep the software they create to
keep the software they create to
keep the software they create to themselves then they will be the only
themselves then they will be the only
themselves then they will be the only ones who can publish more papers based
ones who can publish more papers based
ones who can publish more papers based on that software and then more papers
on that software and then more papers
on that software and then more papers will translate to a better academic
will translate to a better academic
will translate to a better academic profile now what if I were to tell you
profile now what if I were to tell you
profile now what if I were to tell you that it might actually be in a
that it might actually be in a
that it might actually be in a researchers best interest to open-source
researchers best interest to open-source
researchers best interest to open-source the software that they write there are
the software that they write there are
the software that they write there are literally hundreds of examples of papers
literally hundreds of examples of papers
literally hundreds of examples of papers out there with which software was
out there with which software was
out there with which software was released which are also the all-time
released which are also the all-time
released which are also the all-time single most cited paper of their authors
single most cited paper of their authors
single most cited paper of their authors often by a significant margin now
often by a significant margin now
often by a significant margin now citation data is not easily accessible
citation data is not easily accessible
citation data is not easily accessible even a preliminary survey tends to show
even a preliminary survey tends to show
even a preliminary survey tends to show that open sourcing your software can
that open sourcing your software can
that open sourcing your software can actually get you a lot of citations and
actually get you a lot of citations and
actually get you a lot of citations and if other people find your software
if other people find your software
if other people find your software useful then you become more visible in
useful then you become more visible in
useful then you become more visible in your community and that further pushes
your community and that further pushes
your community and that further pushes your reputation plus it’s easier than
your reputation plus it’s easier than
your reputation plus it’s easier than ever these days to publish a paper
ever these days to publish a paper
ever these days to publish a paper solely about a software package through
solely about a software package through
solely about a software package through new journals like the Journal of open
new journals like the Journal of open
new journals like the Journal of open source software now some of you might be
source software now some of you might be
source software now some of you might be thinking well making software shareable
thinking well making software shareable
thinking well making software shareable and usable it takes a lot of extra time
and usable it takes a lot of extra time
and usable it takes a lot of extra time and effort and I totally agree it does
and effort and I totally agree it does
and effort and I totally agree it does but it seems like the more effort you
but it seems like the more effort you
but it seems like the more effort you put into making your software usable the
put into making your software usable the
put into making your software usable the higher the chances that it will come
higher the chances that it will come
higher the chances that it will come back and get you a bunch of citations
back and get you a bunch of citations
back and get you a bunch of citations and consider the fact for a moment that
and consider the fact for a moment that
and consider the fact for a moment that maybe your papers aren’t really complete
maybe your papers aren’t really complete
maybe your papers aren’t really complete without the software anyway because that
without the software anyway because that
without the software anyway because that is preventing other researchers from
is preventing other researchers from
is preventing other researchers from rapidly reproducing your results as I
rapidly reproducing your results as I
rapidly reproducing your results as I close I’d like to ask you all to take
close I’d like to ask you all to take
close I’d like to ask you all to take some action to help this cause of open
some action to help this cause of open
some action to help this cause of open source in science as researchers and the
source in science as researchers and the
source in science as researchers and the entire academic community you should
entire academic community you should
entire academic community you should adopt the culture of open source and
adopt the culture of open source and
adopt the culture of open source and released the software that you write if
released the software that you write if
released the software that you write if nothing then for your own academic
nothing then for your own academic
nothing then for your own academic profile this doesn’t always happen but I
profile this doesn’t always happen but I
profile this doesn’t always happen but I believe that open source is one of those
believe that open source is one of those
believe that open source is one of those few things that ensures everybody wins
few things that ensures everybody wins
few things that ensures everybody wins and let’s try and change this culture
and let’s try and change this culture
and let’s try and change this culture slowly because that type of change can
slowly because that type of change can
slowly because that type of change can only come from within the community and
only come from within the community and
only come from within the community and as citizens you should expect and demand
as citizens you should expect and demand
as citizens you should expect and demand openness from taxpayer-funded research
openness from taxpayer-funded research
openness from taxpayer-funded research this will ensure that appropriate
this will ensure that appropriate
this will ensure that appropriate legislation such as faster gets drafted
legislation such as faster gets drafted
legislation such as faster gets drafted and passed even if a single researcher
and passed even if a single researcher
and passed even if a single researcher does not have to spend months
does not have to spend months
does not have to spend months replicating software all of your tax
replicating software all of your tax
replicating software all of your tax dollars going into research will go much
dollars going into research will go much
dollars going into research will go much further and most importantly this will
further and most importantly this will
further and most importantly this will ensure that you have the choice to
ensure that you have the choice to
ensure that you have the choice to access any of these publications if you
access any of these publications if you
access any of these publications if you ever feel the need to so just like that
ever feel the need to so just like that
ever feel the need to so just like that surgeon who knows about a new technique
surgeon who knows about a new technique
surgeon who knows about a new technique but does not have access to the required
but does not have access to the required
but does not have access to the required tools researchers in a lot of fields
tools researchers in a lot of fields
tools researchers in a lot of fields these days don’t have access to the
these days don’t have access to the
these days don’t have access to the tools they need to advance their
tools they need to advance their
tools they need to advance their research
research
research and these days oftentimes that tool is
and these days oftentimes that tool is
and these days oftentimes that tool is some type of software so whenever
some type of software so whenever
some type of software so whenever possible let’s put the tools that
possible let’s put the tools that
possible let’s put the tools that surgeons and researchers need back in
surgeons and researchers need back in
surgeons and researchers need back in their hands and let’s all help advance
their hands and let’s all help advance
their hands and let’s all help advance our society to become a place where not
our society to become a place where not
our society to become a place where not just new techniques and discoveries but
just new techniques and discoveries but
just new techniques and discoveries but also the tools that enable them are
also the tools that enable them are
also the tools that enable them are openly shared so that we can not just
openly shared so that we can not just
openly shared so that we can not just solve problems we face but also make
solve problems we face but also make
solve problems we face but also make amazing new discoveries together thank
amazing new discoveries together thank
amazing new discoveries together thank you very much
you very much
you very much [Applause]
”
Be First to Comment