SOFTWARE COMPETENCE, SELF-SUFFICIENCY, AND
SOVEREIGNTY THROUGH OPEN SCIENCE
D . Adina Wagne
Ins i u e o Neu oscience and Medicine,
B ain & Beha io (INM-7),
Resea ch Cen e Jülich
DOI:
@adswa@mas. o
doi.o g/10.5281/zenodo.17249652
1
WHO AM I?
F ee and open
sou ce so wa e
RSE
Open
(Neu o-)
science
Handbook
AI
RDM me!
2
Science:
I s building blocks:
Image c edi : CC-BY Sc ibe ia and
The Tu ing Way
3
Science:
I s building blocks:
Image c edi : CC-BY Sc ibe ia and
The Tu ing Way
3.1
Science:
I s building blocks:
Image c edi : CC-BY Sc ibe ia and
The Tu ing Way
3.2
Science:
I s building blocks:
Image c edi : CC-BY Sc ibe ia and
The Tu ing Way
3.3
Science:
I s building blocks:
Image c edi : CC-BY Sc ibe ia and
The Tu ing Way
3.4
RESEARCH SOFTWARE IS A SPECTRUM
Resea ch so wa e = So wa e w i en by scien is s, o science
4
RESEARCH SOFTWARE IS A SPECTRUM
Resea ch so wa e = So wa e w i en by scien is s, o science
Indi idual sc ip s
4.1
MY PATH INTO RESEARCH SOFTWARE
5.4
MY PATH INTO RESEARCH SOFTWARE
5.5
MY PATH INTO RESEARCH SOFTWARE
5.6
MY PATH INTO RESEARCH SOFTWARE
5.7
MY PATH INTO RESEARCH SOFTWARE
5.8
RESEARCH SOFTWARE & OPEN, REPRODUCIBLE SCIENCE GO HAND IN HAND
Image c edi : CC-BY Sc ibe ia and
The Tu ing Way
Rep oducibili y Managemen in Neu oscience: Speci ic issues and solu ions
(h ps://doi.o g/10.5281/zenodo.4285927)
6
RESEARCH SOFTWARE & OPEN, REPRODUCIBLE SCIENCE GO HAND IN HAND
Image c edi : CC-BY Sc ibe ia and
The Tu ing Way
Rep oducibili y Managemen in Neu oscience: Speci ic issues and solu ions
(h ps://doi.o g/10.5281/zenodo.4285927)
6.1
RESEARCH SOFTWARE & OPEN, REPRODUCIBLE SCIENCE GO HAND IN HAND
Image c edi : CC-BY Sc ibe ia and
The Tu ing Way
Rep oducibili y Managemen in Neu oscience: Speci ic issues and solu ions
(h ps://doi.o g/10.5281/zenodo.4285927)
6.2
JUST PUT THE CODE ON GITHUB ...
:
Open da a o 38% o N=174 s udies we e no "in p inciple eusable"
24 ou o 35 s udies wi h eusable da a: i ep oducible main esul s wi hou assis ance o he
o iginal au ho s,
13 ou o 24: no exac ly ep oducible e en wi h assis ance
:
N=62 Regis e ed Repo s
36 a icles sha ed bo h da a and code o ep oduce esul s
Ou o hose, main indings o 15 a icles could no be ep oduced
Da a Managemen
mul iple e sions o code
/da a
subop imal da a cu a ion
unclea execu ion o de /en y
poin s
non-po able code
Technical p oblems
w ong so wa e
en i onmen
p op ie a y so wa e
link o /accessibili y
issues
Human e o s
epo ing (copy-pas e) e o s
ambiguous analysis
speci ica ion
Ha dwicke e al., 2018
Obels e al., 2020
How o w i e a ep oducible esea ch a icle
(h ps://zenodo.o g/ eco ds/5508797)
7
"Wo ks on my machine"
Image c edi :
de ickbailey.com
8
"This used o wo k on my machine..."
Image c edi : Based on
de ickbailey.com
10.1
"This used o wo k on my machine..."
Image c edi : Based on
de ickbailey.com
10.2
"This used o wo k on my machine..."
Image c edi : Based on
de ickbailey.com
10.3
"This used o wo k on my machine..."
Image c edi : Based on
de ickbailey.com
10.4
WHEN YOU WRITE RESEARCH SOFTWARE YOU INCREASINGLY
GET...
11
WHEN YOU WRITE RESEARCH SOFTWARE YOU INCREASINGLY
GET...
...
unding
:
Open sou ce as a equi emen o g an s
dedica ed unding o esea ch so wa e e.g., DFG, Klaus-Tschi a-S i ung,
Volkswagens i ung, Helmhol z, ...
11.1
WHEN YOU WRITE RESEARCH SOFTWARE YOU INCREASINGLY
GET...
...
unding
:
Open sou ce as a equi emen o g an s
dedica ed unding o esea ch so wa e e.g., DFG, Klaus-Tschi a-S i ung,
Volkswagens i ung, Helmhol z, ...
...
ecogni ion
:
so wa e is academic ou pu : The San F ancisco Decla a ion on Resea ch
Assessmen ( ), he Ag eemen on Re o ming Resea ch Assessmen
( ), he DFG, and Helmhol z (soon).
DORA
CoARA
11.2
WHEN YOU WRITE RESEARCH SOFTWARE YOU INCREASINGLY
GET...
...
unding
:
Open sou ce as a equi emen o g an s
dedica ed unding o esea ch so wa e e.g., DFG, Klaus-Tschi a-S i ung,
Volkswagens i ung, Helmhol z, ...
...
ecogni ion
:
so wa e is academic ou pu : The San F ancisco Decla a ion on Resea ch
Assessmen ( ), he Ag eemen on Re o ming Resea ch Assessmen
( ), he DFG, and Helmhol z (soon).
DORA
CoARA
...
ci a ions
:
Dedica ed So wa e Jou nals
o make e en indi idual sc ip s ci able
CITATION.c
s anda d
11.3
WHEN YOU WRITE RESEARCH SOFTWARE YOU INCREASINGLY
GET...
...
unding
:
Open sou ce as a equi emen o g an s
dedica ed unding o esea ch so wa e e.g., DFG, Klaus-Tschi a-S i ung,
Volkswagens i ung, Helmhol z, ...
...
ecogni ion
:
so wa e is academic ou pu : The San F ancisco Decla a ion on Resea ch
Assessmen ( ), he Ag eemen on Re o ming Resea ch Assessmen
( ), he DFG, and Helmhol z (soon).
DORA
CoARA
...
ci a ions
:
Dedica ed So wa e Jou nals
o make e en indi idual sc ip s ci able
CITATION.c
s anda d
...
ca ee s
:
Technical skills a e alued
Resea ch So wa e Enginee (RSE) posi ions
11.4
12
CAPTURE COMPUTATIONAL PROVENANCE
Which da a was needed a which e sion, as inpu in o which code, unning wi h
wha pa ame e iza ion in which compu ional en i onmen , o gene a e an
ou come?
# execu e any command and cap u e i s ou pu
# while eco ding all inpu e sions oo
% da alad un --inpu ... --ou pu ... <command>
17
EXHAUSTIVE CAPTURE ENABLES PORTABILITY
P ecise iden i ica ion o da a and compu a ional en i onmen s combined wi h
p o enance eco ds o m a comp ehensi e and po able da a s uc u e, cap u ing
all aspec s o an in es iga ion.
# ans e da a and me ada a o o he si es and se ices
# wi h ine-g ained access con ol o da ase componen s
% da alad push -- o <si e-o -se ice>
18
REPRODUCIBILITY STRENGTHENS TRUST
Ou comes o compu a ional ans o ma ions can be alida ed by au ho ized 3 d-
pa ies. This enables audi s, p omo es accoun abili y, and s eamlines au oma ed
"upg ades" o ou pu s
# ob ain da ase (ini ially only iden i y,
# a ailabili y, and p o enance me ada a)
% da alad clone <u l>
# immedia ely ac ionable p o enance eco ds
# ull abs ac ion o inpu da a e ie al
% da alad e un <commi | ag| ange>
19
ULTIMATE GOAL: (RE-)USABILITY
Ve i iable, po able, sel -con ained da a s uc u es ha ack all aspec s o an
in es iga ion exhaus i ely can be ( e-)used as modula componen s in la ge
con ex s — p opaga ing hei ai s
# decla e a dependency on ano he da ase and
# e-use i a pa icula s a e in a new con ex
% da alad clone -d <supe da ase > <u l> <pa h-in-da ase >
20
WHERE DO I PUT MY STUFF?
Se ices
make * he* di e ence o ad e isemen , disco e y, con enience, openess
o en chosen based on ( ee) a ailabili y, cus oms in he lab o ield, ins i u ional
equi emen o o e
21
WHERE DO I PUT MY STUFF?
Se ices
make * he* di e ence o ad e isemen , disco e y, con enience, openess
o en chosen based on ( ee) a ailabili y, cus oms in he lab o ield, ins i u ional
equi emen o o e
Bu : Imply dependencies
21.1
WHERE DO I PUT MY STUFF?
Se ices
make * he* di e ence o ad e isemen , disco e y, con enience, openess
o en chosen based on ( ee) a ailabili y, cus oms in he lab o ield, ins i u ional
equi emen o o e
Bu : Imply dependencies
Make su e da a/me ada a a e sel -con ained and po able
o acili a e/enable ansi ion o ano he se ice!
21.2
PORTABILITY
"FAIRly big": A la ge-scale da a p ocessing amewo k, buil on he ounda ion
o ully po able da a analyses.
P ocess 50k subjec s on a supe -compu e in a day, o on a egula clus e in 6
weeks - o ake any subjec and ecompu e on you lap op
FAIRly big: A amewo k o compu a ionally ep oducible p ocessing o la ge-scale da a.
Wagne e al., 2022
22
PORTABILITY
"FAIRly big": A la ge-scale da a p ocessing amewo k, buil on he ounda ion
o ully po able da a analyses.
P ocess 50k subjec s on a supe -compu e in a day, o on a egula clus e in 6
weeks - o ake any subjec and ecompu e on you lap op
FAIRly big: A amewo k o compu a ionally ep oducible p ocessing o la ge-scale da a.
Wagne e al., 2022
22.1
THE INFRASTRUCTURE WE RELY ON...
Ma 2025
www.404media.co/nih-a chi es- eposi o ies-ma ked- o - e iew- o -po en ial-modi ica ion
23
OPEN SCIENCE PRACTICES FIT DIGITAL SOVEREIGNTY
Open science p inciples o esea ch ools
Accessible
Open o ma s and s anda ds
Cus omizable
In e ope able
Open sou ce
,
www.so e eign. ech/ eu-s .open o umeu ope.o g
27
OPEN SCIENCE PRACTICES FIT DIGITAL SOVEREIGNTY
Open science p inciples o esea ch ools
Accessible
Open o ma s and s anda ds
Cus omizable
In e ope able
Open sou ce
,
www.so e eign. ech/ eu-s .open o umeu ope.o g
... bu isn' his o en also mo e complex?
27.1
COMPLEX OR UNFAMILIAR, CONVENIENCE OR LOCK-IN?
28
COMPLEX OR UNFAMILIAR, CONVENIENCE OR LOCK-IN?
28.1
CHOOSE YOUR TOOLS WISELY
Open sou ce: You can ha e he code, cus omize, o k, sel -hos
In e ope abili y ins ead o lock-in: Fa ou open o ma s, ex ensibili y
Un amilia does no necessa ily mean unin ui i e/complica ed
Cen alized hings ha e a single poin o ailu e
Communi y s anda ds (e.g. BIDS) > idiosynch a ic solu ions
Whe e you can' choose, ha e a Plan B in place (Lab equi es Ma Lab? Make
su e coded also uns in oc a e!)
29
EXAMPLE: OPEN TOOLS IN MEDICINE
: Collabo a ion be ween uni e si y clinics in NRW and esea che s in
INM-7. P o ides open sou ce esea ch so wa e s ack o da a acquisi ion/pa ien
moni o ing, RDM, and analysis
D
eci
s
i
on
C
o
llec
i
on
P
o
ce
ss
i
n
g
A
n
a
l
ys
i
s
AB
CD
abcd-j.de
30
NEUROSCIENCE IS AT THE FOREFRONT OF OPEN SOURCE
DEVELOPMENT
... and many mo e
31
INCLUSIVE, COLLABORATIVE, EDUCATIONAL SPACES
B ainhack: In e disciplina y con e ence o ma wi h educa ional sessions &
componen s om hacka hons & uncon e ences
Fi s B ainhack e e : He e in Leipzig!
, , , ,
Top le : , Top igh : ,
Bo om le : , Bo om igh :
(C addock e al., 2016)
OHBM B ainhack B ainhack Global Neu ohackademy SIPS hacka hons Tu ing Way bookdashes
OHBM B ainhack Neu ohackademy
Da aLad Handbook con ibu o coun Tu ing Way bookdash
32
TAKE HOME MESSAGES
So wa e is a key ing edien o a scien i ic esul .
Sha able and sha ed code imp o es e iciency, accessibili y, ep oducibili y o
science - bu mo e han any hing else, he science in you nex p ojec .
Wo king on and wi h so wa e is echnical and complex. The skills you'll ge
om ha help o make you independen in science and beyond.
Open science and open sou ce go hand-in-hand: Fo anspa ency and
ep oducibili y, o science-speci ic equi emen s, o open o ma s, o e-use,
and o enable in e ope abili y ac oss ools. And o digi al so e eign y.
33
-25. Oc 2025
-25. Oc 2025
Düsseld
Düsseld
4
4
Dis ibi s 2025
23.-25. Oc obe
In e na ional con e ence on dis ibu ed da a managemen echnologies
2 day con e ence, one day hacka hon
@ Haus de Uni e si ä Düsseldo
In-pe son and emo e ia li es eam
ee!
DISTRIBITS.LIVE
34
