OpenCon2014 - Sumatra as an Open Science tool

-as an Open Science tool

Presented by

Felix Hoffmann@Felix11Hfelix11h.github.io/

Slides

Slideshare:tiny.cc/opencon-smtSource:tiny.cc/github-slides

Resources on Sumatra

Website:neuralensemble.org/sumatra/Getting started:packages.python.org/Sumatra/Repository:bitbucket.org/apdavison/sumatra/Mailinglist:tiny.cc/smt-userMaintainer: Andrew Davison

This work is licensed under a Creative Commons Attribution 4.0 International License.

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,—–

—–

if only!

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,—–

—–

if only!

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,—–

—–

if only!

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,—–

—–

if only!

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,same machine, —–

—–

if only!

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,same machine, —–same researcher

—–

if only!

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,same machine, —–same researcher

—– Easy!

if only!

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,same machine, —–same researcher

—– Easy! if only!

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,same machine, —–same researcher

—– Easy! if only!

Spectrum of Reproducibility

... in Computational Research

reproduction fromdescriptions inresearch article

—–Tough!

same code,same machine, —–same researcher

—– Easy! if only!

The problems...

... the solution –

Which version of mycode did I use?

What parameters?

“Why did I do that?”

“It worked yesterday.”

“Piled Higher and Deeper” by Jorge Chamwww.phdcomics.com

... in traditional, experiment-basedresearch.

The problems...

... the solution –

Which version of mycode did I use?

What parameters?

“Why did I do that?”

“It worked yesterday.”

“Piled Higher and Deeper” by Jorge Chamwww.phdcomics.com

... in traditional, experiment-basedresearch.

The problems...

... the solution –

Which version of mycode did I use?

What parameters?

“Why did I do that?”

“It worked yesterday.”

“Piled Higher and Deeper” by Jorge Chamwww.phdcomics.com

... in traditional, experiment-basedresearch.

The problems...

... the solution –

Which version of mycode did I use?

What parameters?

“Why did I do that?”

“It worked yesterday.”

“Piled Higher and Deeper” by Jorge Chamwww.phdcomics.com

... in traditional, experiment-basedresearch.

The problems... ... the solution –

Which version of mycode did I use?

What parameters?

“Why did I do that?”

“It worked yesterday.”

... in traditional, experiment-basedresearch.

The problems... ... the solution –

Which version of mycode did I use?

What parameters?

“Why did I do that?”

“It worked yesterday.”

laboratory notebook

©Wellcome Library, London CC BY 4.0

... in traditional, experiment-basedresearch.

The problems... ... the solution –

Which version of mycode did I use?

What parameters?

“Why did I do that?”

“It worked yesterday.”

laboratory notebook

©Wellcome Library, London CC BY 4.0

... in traditional, experiment-basedresearch.

-- -Simulation Management Tool

“An automated lab notebook forcomputational projects”

⇒ assumes that code is underversion control

⇒ capture information aboutcomputation

⇒ make the informationaccessible through acommand line and webinterface

-- -Simulation Management Tool

“An automated lab notebook forcomputational projects”

⇒ assumes that code is underversion control

⇒ capture information aboutcomputation

⇒ make the informationaccessible through acommand line and webinterface

-- -Simulation Management Tool

“An automated lab notebook forcomputational projects”

⇒ assumes that code is underversion control

⇒ capture information aboutcomputation

⇒ make the informationaccessible through acommand line and webinterface

-- -Simulation Management Tool

“An automated lab notebook forcomputational projects”

⇒ assumes that code is underversion control

⇒ capture information aboutcomputation

⇒ make the informationaccessible through acommand line and webinterface

©Jason Long CC BY 3.0

-- -Simulation Management Tool

“An automated lab notebook forcomputational projects”

⇒ assumes that code is underversion control

⇒ capture information aboutcomputation

⇒ make the informationaccessible through acommand line and webinterface

smt run

-- -Simulation Management Tool

“An automated lab notebook forcomputational projects”

⇒ assumes that code is underversion control

⇒ capture information aboutcomputation

⇒ make the informationaccessible through acommand line and webinterface

- -- a tool for Reproducible Research

By capturing

- version of the code

- input data

- output data

- parameters ————

Full replicability ofresults

- -- a tool for Reproducible Research

By capturing

- version of the code

- input data

- output data

- parameters ————

Full replicability ofresults

- -- a tool for Reproducible Research

By capturing

- version of the code

- input data

- output data

- parameters ————

Full replicability ofresults

- -- a tool for Reproducible Research

By capturing

- version of the code

- input data

- output data

- parameters ————

Full replicability ofresults

- -- a tool for Reproducible Research

By capturing

- version of the code

- input data

- output data

- parameters ————

Full replicability ofresults

- -- a tool for Reproducible Research

By capturing

- version of the code

- input data

- output data

- parameters ————

Full replicability ofresults

- -- as an Open Science tool

..computational research project

.

scientific code

.

input data

.

output data

....

Dataprovenance!

- -- as an Open Science tool

..computational research project.

scientific code

.

input data

.

output data

....

Dataprovenance!

- -- as an Open Science tool

..computational research project.

scientific code

.

input data

.

output data

....

Dataprovenance!

- -- as an Open Science tool

..computational research project.

scientific code

.

input data

.

output data

....

Dataprovenance!

- -- as an Open Science tool

..computational research project.

scientific code

.

input data

.

output data

.

...

Dataprovenance!

- -- as an Open Science tool

..computational research project.

scientific code

.

input data

.

output data

..

..

Dataprovenance!

- -- as an Open Science tool

..computational research project.

scientific code

.

input data

.

output data

...

.

Dataprovenance!

- -- as an Open Science tool

..computational research project.

scientific code

.

input data

.

output data

...

.

Dataprovenance!

- -- as an Open Science tool

..computational research project.

scientific code

.

input data

.

output data

....

Dataprovenance!

Thank you!

Presented by

Felix Hoffmann@Felix11Hfelix11h.github.io/

Slides

Slideshare:tiny.cc/opencon-smtSource:tiny.cc/github-slides

Resources on Sumatra

Website:neuralensemble.org/sumatra/Getting started:packages.python.org/Sumatra/Repository:bitbucket.org/apdavison/sumatra/Mailinglist:tiny.cc/smt-userMaintainer: Andrew Davison

This work is licensed under a Creative Commons Attribution 4.0 International License.