# Open science practices for keeping inventions alive after project ends

Camille Maumet

► To cite this version:

Camille Maumet. Open science practices for keeping inventions alive after project ends. ESMRMB 2023 - 39th Annual Scientific Meeting on European Society for Magnetic Resonance in Medicine and Biology, Oct 2023, Basel (CH), Switzerland. 2023. [hal-04236827](https://hal-04236827)

HAL Id: hal-04236827

https://inria.hal.science/hal-04236827

Submitted on 11 Oct 2023

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
<figure><img src="image_2.png" /></figure>

# Open science practices for keeping inventions alive after project ends

Camille Maumet

Inria, Univ Rennes, Inserm, CNRS, IRISA
Keeping inventions alive...

<figure><img src="image_3.png" /></figure>
# Keeping inventions alive...

Acquisition

<figure><img src="image_4.png" /></figure>

Data preparation

<figure><img src="image_5.png" /></figure>

Derived data

Statistical analysis

<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /></figure>
# Keeping inventions alive...

Acquisition

<figure><img src="image_8.png" /></figure>

Data preparation

<figure><img src="image_9.png" /></figure>

Derived data

Statistical analysis

<figure><img src="image_10.png" /></figure>

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>
# Keeping inventions alive...

Acquisition

<figure><img src="image_13.png" /></figure>

Data preparation

<figure><img src="image_14.png" /></figure>

Derived data

Statistical analysis

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

<figure><img src="image_17.png" /></figure>
# Keeping inventions alive...

Acquisition

<figure><img src="image_18.png" /></figure>

Data preparation

<figure><img src="image_19.png" /></figure>

Derived data

Statistical analysis

<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>
Keeping inventions alive...

ation

aration

data

analysis

<figure><img src="image_22.png" /></figure>

<figure><img src="image_23.png" /></figure>
Keeping inventions alive...

<figure><img src="image_24.png" /></figure>
Keeping inventions alive...

<figure><img src="image_25.png" /></figure>

<figure><img src="image_26.png" /></figure>
# Keeping inventions alive...

<figure><img src="image_27.png" /></figure>

Hum... I can't
reproduce the original
results...

<figure><img src="image_28.png" /></figure>

Which release of
SPM was used?

Which registration
algorithm was
selected?

How was the brain
mask computed?

Did I understand
the method
correctly?

... or is this due to
my use of a
different dataset?

... a different
computing
platform?

... something
else!?
# Keeping inventions alive...

<figure><img src="image_29.png" /></figure>

Hum... I can't
reproduce the or
results...

<figure><img src="image_30.png" /></figure>

Which release of
SPM was used?

Which registration
algorithm was
selected?

How was the brain
mask computed?

or is this due to
ly use of a
different dataset?

different
computing
platform?

... something else!?
<figure><img src="image_31.png" /></figure>
Make your project
**REPRODUCIBLE**

<figure><img src="image_32.png" /></figure>
# Making your project **reproducible**

<figure><img src="image_33.png" /></figure>

**Computational reproducibility**

Ability to reproduce the exact same results using the **same data** and the **same methods**.
Good Practices **for reproducibility**

```ini
# CITATION
# README
# LICENSE
# requirements.txt
# data
  -- birds_count_table.csv
# doc
  -- notebook.md
  -- manuscript.md
  -- changelog.txt
# results
  -- summarized_results.csv
# src
  -- sightings_analysis.py
  -- runall.py
```

[Wilson et. al, PlosCompBio 2017]

* Use **version control**

* Create **1 repository** per manuscript
# Good Practices for reproducibility

```ini
# CITATION
# README
# LICENSE
# requirements.txt
# data
# birds_count_table.csv
# doc
# notebook.md
# manuscript.md
# changelog.txt
# results
# summarized_results.csv
# src
# sightings_analysis.py
# runall.py
```

[Wilson et. al, PlosCompBio 2017]

* Use **version control**

* Create **1 repository** per manuscript

* **Archive** your code for long term preservation

<figure><img src="image_34.png" /></figure>

Software Heritage

zenodo
# Good Practices for reproducibility

```yaml
-- CITATION
-- README
-- LICENSE
-- requirements.txt
-- data
  -- birds_count_table.csv
-- doc
  -- notebook.md
  -- manuscript.md
  -- changelog.txt
-- results
  -- summarized_results.csv
-- src
  -- sightings_analysis.py
  -- runall.py
```

[Wilson et. al, PlosCompBio 2017]

* Use **version control**

* Create **1 repository** per manuscript

* Archive your code for long term preservation

<figure><img src="image_35.png" /></figure>

Software Heritage

<figure><img src="image_36.png" /></figure>

But...

It's not only about the source code but also the **environnement** (versions, OS, etc.) *docker*, *guix*

**10 years computational reproducibility** is an open question!

Perkel, Jeffrey M. "Challenge to scientists: does your ten-year-old code still run?." *Nature* 584.7822 (2020): 656-659.
Make your project
**OPEN**

<figure><img src="image_37.png" /></figure>
Making your project **open**

Acquisition

<figure><img src="image_38.png" /></figure>

Data preparation

<figure><img src="image_39.png" /></figure>

Derived data

Statistical analysis

<figure><img src="image_40.png" /></figure>

<figure><img src="image_41.png" /></figure>

<figure><img src="image_42.png" /></figure>

Credits: Parcels 1, 2 & 4 (CCO), Parcel 3 (CCO), Parcel 5 (CCO).
Making your project **open**

Acquisition

<figure><img src="image_43.png" /></figure>

Data preparation

<figure><img src="image_44.png" /></figure>

Derived data

Statistical analysis

<figure><img src="image_45.png" /></figure>

<figure><img src="image_46.png" /></figure>

<figure><img src="image_47.png" /></figure>

Credits: Parcels 1, 2 & 4 (CCO), Parcel 3 (CCO), Parcel 5 (CCO).
## Good practices: FAIR principles

<figure><img src="image_48.png" /></figure>
Good practices: **FAIR** principles

<figure><img src="image_49.png" /></figure>

<figure><img src="image_50.png" /></figure>

<figure><img src="image_51.png" /></figure>

<figure><img src="image_52.png" /></figure>

<figure><img src="image_53.png" /></figure>

<figure><img src="image_54.png" /></figure>

<figure><img src="image_55.png" /></figure>

<figure><img src="image_56.png" /></figure>

<figure><img src="image_57.png" /></figure>

**Interoperable** Using a common standard/format across tools

<figure><img src="image_58.png" /></figure>

**Findable** we can search for open datasets in each repository

<figure><img src="image_59.png" /></figure>

**Reusable** Including enough metadata to enable reuse. e.g. onsets of the task for task-based fMRI.

<figure><img src="image_60.png" /></figure>

**Accessible** Direct download (e.g. Openneuro) or with Data User Agreement (e.g. Donders)
# Making your project open

<figure><img src="image_61.png" /></figure>
# Making your project open

Acquisition

<figure><img src="image_62.png" /></figure>

Data preparation

<figure><img src="image_63.png" /></figure>

Derived data

Statistical analysis

<figure><img src="image_64.png" /></figure>

<figure><img src="image_65.png" /></figure>

Donders Repository

<figure><img src="image_66.png" /></figure>

<figure><img src="image_67.png" /></figure>

<figure><img src="image_68.png" /></figure>

<figure><img src="image_69.png" /></figure>

Software Heritage

<figure><img src="image_70.png" /></figure>

<figure><img src="image_71.png" /></figure>

zenodo

<figure><img src="image_72.png" /></figure>

<figure><img src="image_73.png" /></figure>

<figure><img src="image_74.png" /></figure>

<figure><img src="image_75.png" /></figure>

<figure><img src="image_76.png" /></figure>

<figure><img src="image_77.png" /></figure>

<figure><img src="image_78.png" /></figure>

NEUROVAULT
<figure><img src="image_79.png" /></figure>

Make your project
**COLLABORATIVE**
Make your project **collaborative**

Beyond technical solutions, open science brings a
culture change

* Making resources available to the scientific community

* Reusing existing resources (datasets, tools) that were created by others

towards more collaborative research

<figure><img src="image_80.png" /></figure>
# But what is **open code**...?

<figure><img src="image_81.png" /></figure>

## Open source

* Choose an open source
  **license**

* Make the code available
  for **download**

* Use an **archive** for
  long-term preservation
# But what is **open code**...?

Who can **see** and **use** the code?

<figure><img src="image_82.png" /></figure>

## Open source

* Choose an open source
  **license**

* Make the code available
  for **download**

* Use an **archive** for
  long-term preservation
# But what is **open code**...?

Who can **see** and **use** the code?

<figure><img src="image_83.png" /></figure>

## Open source

* Choose an open source **license**

* Make the code available for **download**

* Use an **archive** for long-term preservation

Who can
**contribute**?

<figure><img src="image_84.png" /></figure>

## Open development

* Accept external **contributions** (e.g. Github PR)

* Be transparent about **development choices** (e.g. issues, project board)
# But what is **open code**...?

Who can **see** and **use** the code?

<figure><img src="image_85.png" /></figure>

## Open source

* Choose an open source **license**

* Make the code available for **download**

* Use an **archive** for long-term preservation

Who can
**contribute**?

<figure><img src="image_86.png" /></figure>

## Open development

* Accept external **contributions** (e.g. Github PR)

* Be transparent about **development choices** (e.g. issues, project board)

Who can **decide** which contributions are accepted?

<figure><img src="image_87.png" /></figure>

## Open governance

* Be transparency about how **decisions** are made

* Open up pathways to **join the governance**
# But what is **open code**...?

Who can **see** and **use** the code?

<figure><img src="image_88.png" /></figure>

## Open source

* Choose an open source **license**

* Make the code available for **download**

* Use an **archive** for long-term preservation

Who can
**contribute**?

<figure><img src="image_89.png" /></figure>

## Open development

* Accept external **contributions** (e.g. Github PR)

* Be transparent about **development choices** (e.g. issues, project board)

Who can **decide** which contributions are accepted?

<figure><img src="image_90.png" /></figure>

## Open governance

* Be transparency about how **decisions** are made

* Open up pathways to **join the governance**

<figure><img src="image_91.png" /></figure>
<figure><img src="image_92.png" /></figure>

Engage
with existing
COMMUNITIES
MRI Together

<figure><img src="image_93.png" /></figure>

EUROPEAN COOPERATION
IN SCIENCE & TECHNOLOGY

<figure><img src="image_94.png" /></figure>

Networking

<figure><img src="image_95.png" /></figure>

Q&A

<figure><img src="image_96.png" /></figure>

NeuroStars

<figure><img src="image_97.png" /></figure>

Engage
with existing
COMMUNITIES

<figure><img src="image_98.png" /></figure>

Hackathons

<figure><img src="image_99.png" /></figure>
<figure><img src="image_100.png" /></figure>

Make your project
**REPRODUCIBLE**

Make your project
**OPEN**

Engage
with existing
**COMMUNITIES**

Make your project
**COLLABORATIVE**
**Open science** Keeping inventions alive
after project ends

Thank you!

Camille Maumet

<figure><img src="image_101.png" /></figure>

<figure><img src="image_102.png" /></figure>

We are hiring

https://team.inria.fr/empenn/job-offers

**Credit:** Presentation template and icons by SlidesCarnival, adapted