Open-Source Initiatives in Pharma

What’s Out There & Why You Should Join

Nicholas Masel

I recently turned 40

and this is the age where I hear from people with experience saying things like,

I tweaked my back, getting out of the car or

no, I can’t eat that, it has too much cholesterol.

So now that I’ve joined this group, I set an appointment for a check-up with my doctor.

When I showed up, I found that I have white-coat syndrome.

And that means every time I think about my BP, it goes up!

So the next day, I’m chatting about this with some friends

and one of my buddies insists I go to the gym with him,

he’ll pick me up at 5 am!

He says it very casually, like it’s a normal time to be awake and to be working out.

But I’ve got to do something, so I agree.

5 am comes quickly,

I jump in his truck and we’re off.

Now, I’ve never worked out in a gym in my life, so I don’t know what to expect.

We open the door and this was my experience. SHOW CRAZY VIDEO

And when I think about this now,

it’s a really close parallel to my open-source journey.

• How I found a need to make a change,

• How not making a change would be detrimental to myself and those around me.

• How terrifying it was to start something new.

Now I’d like to share my open-source journey with you!

• In hopes that it will help you along your journey.

And to do that, I’ve lumped that journey into three buckets

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Open-Source Journey

Organizations Thinking About Using Open-Source

Organizations Currently Implementing

Organizations Been There, Done That, Have a T-Shirt

• Organizations thinking about open-source.
• Organizations currently using open-source.
• Organizations that might think of this as old news. I’ve been there, done that, and have the t-shirt to prove it. NEXT SLIDE.

Organization?

VS.

WHY ORGANIZATIONS:

• Some of you may be wondering why are you talking about organizations.
• I’m just a happy bucket, who likes to program.

ORGANIZATIONS ARE PEOPLE:

• Well, organizations are made up of people.
• They’re made up of you.

THINK ORGANIZATIONALLY:

• I want everyone to think about this from the organizational perspective.
• About how your COMPANY can improve, by adopting open-source.

BELIEVE:

• And I want you to believe, you have the ability to drive the use of open-source w/in your org.

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Organizations Thinking of Using Open-Source

So,

For you

as a driver of change, thinking about how you can get your organzation to use OS.

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Questions when Starting Out in OS

• I love R/Python! But how can I gain support to use Open-Source in my everyday work?

• Should I grow an Open-Source team within my organiation? If so, how?

• Where do I start? There are so many options!

You’ll have run into some questions to sort out?

Speak to each incremental bullet.

The best thing to do, is … NEXT SLIDE

Just dive in!

Just Dive In!

• I’ll share some of our story, of just diving in.
• To help you avoid some of those rocks.

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Our Story (of just diving in)

What did we need?

• Show value

• Build credibility

• Expand the team

How did we do it?

• Interactivity is the Key

• Find Quick Wins

• Excel to Shiny

• “Borrow Code”

So, what did we need to do…

And how did we achieve this?

WE NEEDED TO:

• Show value

• Build credibility

• We knew we needed more people, so we use that credibility to EXPAND THE TEAM

HOW DID WE ACHIEVE THIS:

• Interactivity is the Key

• Find some quick wins

• Move Excel to Shiny

• “Borrow code”

• Shiny galleries

Example - Most Frequently Reported AEs

Old Way

TOOK PROCESS USING EXCEL:

• identify AE that exceeded some threshold

PROCESS:

• Open an output
• Copy the contents
• Open excel
• Paste in content
• Slice and dice the data

Example - Most Frequently Reported AEs

New Way

OUR NEW WAY:

• is nothing wild

PROCESS:

• Instead of opening output or excel, you OPEN SHINY APP
• Browse to files
• Load the files
• Slice and dice the data

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Benefits of Shift to Shiny

• Easier to use

• Reduced errors

• Faster and higher quality results

• Saving $250k/year!

So what were the benefits?

• Easier to use.

• Reduced errors (copy/paste and accidental modifications).

• Faster and higher quality.

• Saving $250k/year!

SALARY SAVED:

• That’s more than I make a year.
• So, not too bad for a few weeks of work!

SHOW VALUE, QUICKLY:

• We were able to show value, quickly

• and pose the question

QUESTIONS:

• What if we have two people doing this?

• What about three?

• What can we achieve if we invest resources here?

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Implementing within Your Organization

TEAM USING OS:

• So you have a team, using OS to deliver value

SPEAD USE OF OS:

• Eventually, this could expand to how do we spread the use of OS more broadly?
• How could we have a department, adopt the use of OS?

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It’s Not What You Do, but How You Do It!

Regulatory Deliverables

• Are your results reproducible?

• Are people using trusted software?

• Is this getting treatments to patients in need faster?

WHEN YOU GET HERE:

• It’s not what you’re doing,
• but how you’re doing it.

Especially when thinking about Regulatory deliverables.

BUILD HOUSE:

• Sure, we can go build a house
• but when it’s done, and you step back and take a look at it
• if it looks like this
• you’re probably not going to want to live in that house.

QUESTIONS YOU RUN INTO:

• INCREMENT SLIDE UP: Is it reproducible?
• INCREMENT SLIDE UP: Are people using trusted software?
• INCREMENT SLIDE UP: Are you taking full advantage of OS’s capabilities to get treatments to patients faster?

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How We Built Our House

General Contractor

Modernization of Statistical Analytics

Sub-Contractors

R Validation Hub

Home Inspection

Regulatory Submissions WG

So, how did we build our house.

GENERAL CONTRACTOR:

• If you know nothing about building a house.

• Having a general contractor is important.

ROLES:

They understand you need a:

• plumber,
• electrician,
• painter, etc.

ORDER & LANGUAGE OF THE TRADE:

• They understand the order things need to occur.

• They understand the language of each trade.

• Communicating effectively across the roles.

MODERNIZATION OF STATISTICAL ANALYTICS

• The modernization of statistical analysis working group plays this role as a general contractor.

• Now there not going to build your house for you,

• but they can teach you what roles need to be involved,

• the language of each trade,

• so you can effectively drive the building of your home.

SUB-CONTRACTORS:

GENERAL CONTRACTORS ARE NOT PLUMBERS:

• General contractors aren’t plumbers, they aren’t electricians.

• But they know a lot of them,

• And they know who does good work!

SELECTING SOFTWARE:

• And this is how you can think about selecting software,
• And the R Validation Hub, which is a working group w/in the R Consortium, is leading the way here.
• When you pick an electrician,
• You want one who is going to check that
• the light they installed, turns on when you flip the switch.

R VALIDATION HUB:

• The R Validation Hub will guide you in how to pick the right software…
• And how to document that, correctly.

THE HOUSE IS BUILT! LET’S MOVE IN:

• No, we need to make sure it’s safe
• And it’s effective at being a house.
• Little bit of a stretch there, but we’ll make it work :)

REGULATORY AGENCIES:

• This is no different than us submitting to regulatory agencies.
• And the R Consortium has another working group, around submissions,
• To guide you in correctly submitting to agencies,
• While using open-source.

TRANSITION:

• And this is how we built our house.
  
• We leaned on the open-source community,
  
• We joined open-source initiatives,
• We learned from the industry, to overcome challenges.

WHY WE BUILT A NEW HOUSE IN THE FIRST PLACE:

• You already had a house.
• We need to get treatments to patient in need faster.

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Faster to Patients

Standards

Interactivity

No surprise, standards are key to improving efficiency.

PHARMAVERSE:

• group of people, working to curate packages, specific to pharma
• aim to standarize the set of packages regulatory reviewers receive
• reviewers see different, and even proprietary packages each review, opposite of our goal to speed things up
• reviewers continue to see the same set of packages, build trust in packages
• this will help us save time

TRANSITION:

• Moving past packages, to results generated by those and the layout of those results
• If we can worry less about how results are formatted on a page,
• and more about results being correct

It allows things like Caridnal to be built.

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CARDINAL:

• Is a package of
• table-generating functions to report results in a standard way
• If we as an industry can agree to a standard layout.
• We can reuse code to generate results at an industry level

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INTERACTIVITY:

• Interactive frameworks, like teal and rhino provide a standard way to give interactivity to your stakeholders.
• This, allows them to answer questions in real time.
• Helping to more quickly understand and summarize their findings.

Been There, Done That, Got the T-Shirt

A jocular, sarcastic, or condescending expression of familiarity or boredom with a certain situation or thing.

YOU’VE BUILT AN OS TEAM

YOU’VE EXPANDED THE SCOPE OF USE FOR OS TO DEPARTMENTS:

• and successfully used for submission

YOU MIGHT THINK:

• I’ve been there done that and I have the t-shirt
• When I talk to organizations that I think think fall in this bucket,
• I’ve found that they don’t think they do have the t-shirt yet.

There is a lot LEFT to do!

People and New Technology

CHANGE MANAGEMENT:

• JUST BECAUSE YOU HAVE THE HOUSE
• DOESN’T MEAN ANYONE IS GOING TO MOVE IN

MARKS PRESENTATION:

• I encourage you to check out Mark’s presentation earlier today around CM, to help get people to move in.

NEW TECHNOLOGY / ERIKS TALK:

• New technologies, like what Erik covered with WebAssembly
• Show we need to stay up to date, to learn new things
• As a way to simplify, remove the roadblocks
• we face as an industry.

There is a lot LEFT to do!

Keep R Sustainable

Contribute to Your Package Pipeline

Contribute to Core R

Join the R Consortium

Now that R has become a key part of your pipeline.

We want to make sure R stays sustainable.

Contribute to Your Package Pipeline:

• The first package I ever contributed toward was while building our house
• I asked how we would cover logging in R.
• We were not sure, so I found a group working on a logging package in the Pharmaverse.
• I reached out to the authors, engaged witht the group, and still to this day
• It’s my favorite package to work on. It’s just a great group, and a lot of fun.

Contribute to Core R:

• Check out STRENGTHNING THE R ECOSYSTEM this afternoon
• Including Heather Turners Talk about Contributing to the R Project

Join the R Consortium:

• Basically the R Consortium supports social and infrastructure projects.
• To spread the use of R and to fund projects to keep infrastructure stable.
• This helps to set up our industry for long-term success!
• Examples of their efforts are the RUGS programs and infrastructure grants they provide.

There is a lot LEFT to do!

Grow R

Share Your Story

Share Your Story

Share Your Story

Organize & Lead

Organize & Lead

We don’t just want to sustain R, we also want to grow it!

SHARE YOUR STORY:

• Like at Posit Conf
• Or if you like something a little more informal:
  • Rachel Dempsy runs the Data Science Hangout each week
  • Pharmaverse Blog

ORGANIZE & LEAD:

• If you see a gap or roadblock not addressed at industry level, create a group to sort this out!

R Consortium - WG Guidance

PHUSE:

• PHUSE is another, they have been around, supporting the pharma industry
• OS Working group, overseeing OS projects
• New Project Form

“Failure isn’t fatal, but failure to change might be”
- John Wooden

Now, to end my story around my blood-pressure and this crazy gym.

I’m still waking up at 5 am and working out, for clsoe to a year now.

My blood-pressure is way down and I’m in great health.

And the analogy seems stronger than ever, you have to change in order to survive and thrive.

So I hope you find a reason to make a change,

Just dive in,

become a leader in moving your organization to Open-Source,

remembering there are many people to help you along your journey,

and remembering to be good stewards of Open-Source

to maintain stability and ensure success, as our industry

adopts Open-Source to get treatments

to patients in need, in time.

Thank you.

Thank You

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