So wa e o FAIR da a
S e ano Cozzini , PRP@CERIC coo dina o
A ea Science Pa k
10.11.2025
Agenda
•Da a Wo k low examples:
•The basic: Da a om SEM o epo
•The luxu y: Da a om Ox o d Nanopho e o ORFEO
•FAIR app oach o scien i ic so wa e
•Wha /Why so wa e in esea ch
•So wa e sus ainabili y
•FAIR4RS: Fai p inciples o esea ch so wa e
•Recommenda ion o make so wa e FAIR
•How o make a mode n da a wo k low FAIR ?
•How o make a mode n compu a ional wo k low FAIR ?
So wa e in Resea ch: A pilla o Open Science
•Di e en oles:
•a ool
•a esea ch ou come o esul
• he objec o esea ch
Whe e is so wa e in you daily esea ch ?
Whe e is so wa e in you daily esea ch ?
•so wa e is a componen in ou scien i ic ins umen s
Whe e is so wa e in you daily esea ch ?
•so wa e is he ins umen !
Whe e is so wa e in you daily esea ch ?
•so wa e analyses you esea ch da a
Whe e is so wa e in you daily esea ch ?
•so wa e analyses you esea ch da a
Whe e is so wa e in you daily esea ch ?
•so wa e p esen s you esea ch esul s
Upda ed e sion: aken on 20.10.2024
Upda ed e sion: aken on 11.11.2025
Lo s o wheel ein en ion?
i ’s un and was unded! Sus ainable??
We do need mo e
han one kind o
wheel …
… echnical issues,
ypes o da a,
analysis, use s,
communi ies ….
Analysis Code
one-o me esea ch
P o o ype Tools
Resea ch So wa e
In as uc u e
p o essionalised p oduc
Concep : Thanks o Tom Honeyman, ARDC
Slide aken om Resea ch So wa e Sus ainabili y akes a Village
(zenodo.o g)
o ha e a sus ainable
u u e you mus c ea e
and sus ain a u u e
wo k o ce ha can
de elop, suppo and/o
wan o use you
so wa e.
Image: I Takes a Village: Open Sou ce So wa e Sus ainabili y A Guidebook o P og ams Se ing Cul u al and Scien i ic He i age Feb ua y 2018
Mo e on h ps:// u u e-o - esea ch-so wa e.o g/
So wa e pa chwo k: Ac Local, Think Global
A web o dependencies, a spec um o isibili y.
h ps://xkcd.com/2347/
Use acing shiny hing
Applica ions, ools, sc ip s
Domain speci ic eusabili y
Visible - Rocke
Unde wa e
Pla o ms, in as uc u e, lib a ies
Big codes and li le codes
C oss-domain gene ic eusabili y
O e ly amilia
In isible – Rocke launche
Communi y <-> so wa e closeness
Di ec , indi ec , unconnec ed o he so wa e use o ely on in supply chain
Biologis
Bioin o ma ician
Specialised so wa e de elope
Pla o m de elope
Lib a y main aine
In as uc u e p o ide
In o ms he need o unding
Six di e en so wa e laye o ep oducibili y
1. P ojec speci ic so wa e
W i en by scien is s o a
speci ic esea ch p ojec
2. Domain speci ic esea ch
so wa e.
These a e ools and lib a ies ha i
mplemen models and me hods
which a e de eloped and used by
communi ies anging in size om
a single esea ch lab o
housands o esea che s”
3. Scien i ic in as uc u e
c ea ed speci ically o scien i ic
compu ing, bu no any
pa icula domain.”
4. In as uc u e so wa e
no speci ic oscien i ic
compu ing....ob ain[ed] om he
wide non-scien i ic so wa e
ma ke ”
5. ope a ing sys em
6. ha dwa e
Resea ch so wa e in a snapsho
So wa e de eloped and used o he pu pose o esea ch: o gene a e,
p ocess, analyze esul s wi hin he schola ly p ocess
Fundamen al in he esea ch p ocess
•Bu
•So wa e will collapse i no main ained
•So wa e bugs a e ound, new ea u es a e needed, new pla o ms a ise
•So wa e de elopmen and main enance is human in ensi e
•Much so wa e de eloped speci ically o esea ch, by esea che s
•Resea che s know hei disciplines, bu o en no so wa e bes p ac ices
•Resea che s a e no ewa ded o so wa e de elopmen and main enance
in academia
• De elope s don’ ma ch he di e si y o use communi y
FAIR4RS:
• eleased in 2022 by he FAIR o Resea ch So wa e (FAIR4RS) Wo king G oup
(WG),
•join ly con ened by
•ReSA · Resea ch So wa e Alliance
•FORCE11 – The Fu u e o Resea ch Communica ions and e-Schola ship
•Resea ch da a alliance: d-alliance.o g
•This miles one e lec s he ma u a ion o he esea ch communi y in
unde s anding he bene i s o ha ing FAIR esea ch so wa e, and coming
oge he as he FAIR4RS WG o achie e his.
• The FAIR4RS WG is a global and in e disciplina y communi y whose
membe s sha e an in e es in he applica ion o FAIR p inciples o esea ch
so wa e, such as esea che s, so wa e use s, de elope s and main aine s,
policy make s, in as uc u e suppo s a , and unde s.
•The FAIR4RS P inciples a e ele an o inc ease anspa ency, ep oducibili y,
and eusabili y o esea ch.
Mo e commen s
•The In e ope able and Reusable FAIR4RS P inciples a e somewha
di e en han he equi alen FAIR da a p inciples
•This because o di e ences be ween so wa e and da a whe e he
FAIR4RS g oup had o choose how o de ine hese e ms in he
con ex o so wa e, eaching he de ini ions shown abo e in he
p inciples.
•They de ine in e ope abili y as how in o ma ion (da a, me ada a,
applica ion p og amming in e aces (APIs)) is exchanged.
•They hen de ine eusabili y as bo h usabili y ( he so wa e can be
execu ed) and eusabili y (i can be unde s ood, modi ied, buil upon,
o inco po a ed in o o he so wa e).
Main e e ence:
•Da a Wo k low examples:
•The basic: Da a om SEM o epo
•The luxu y: Da a om Ox o d Nanopho e o ORFEO
Ten quick ips o building FAIR wo k lows | PLOS Compu a ional Biology
Tip1: egis e he wo k low
•Regis e ing he wo k low o any public eco d, p e e ably one
ha is also indexed by popula sea ch engines, will inc ease
indabili y.
•we ecommend egis ies ha enable sys ema ic scien i ic
anno a ions and a e ca e ing o wo k lows w i en in di e en
languages.
•Examples o hese egis ies a e
•Wo k lowHub
•Docks o e.
Tip 2: Desc ibe he wo k low wi h ich
me ada a
•The me ada a should co e in o ma ion on all da a en i ies ha a e p esen in he
wo k low
•wo k low language iles,
•sc ip s, con igu a ion iles,
•example inpu da a, e c..
• esea ch da a can be packaged along wi h he associa ed me ada a using he RO-
C a e (Resea ch Objec C a e) speci ica ion.
Resea ch Objec C a e (RO-C a e) - Resea ch Objec C a e (RO-C a e) (s ain.gi hub.io)
• A wo k low RO-C a e should ollow he communi y cu a ed Bioschemas [30]
speci ica ion o a compu a ional wo k low, which de ines he wo k low p ope ies
ha a e manda o y o ecommended o be desc ibed [31].
•The me ada a is cap u ed in a JSON-LD ile, using he Linked Da a p inciples [32].
•Following hese p inciples, he me ada a ile desc ibes all da a and con ex ual
en i ies ( esea che s, o ganiza ions, e c.) o he wo k low wi h uni o m esou ce
iden i ie s (URIs). This ensu es ha all en i ies in he RO-C a e a e desc ibed
unambiguously and can be easily sea ched o . Mo eo e , wo k low RO-C a e
objec s can be di ec ly uploaded o Wo k lowHub o egis e he wo k low.
Al oge he , he RO-C a e me hod o e s a good ade-o be ween usabili y (human
eadable o ma s) and ichness (su icien me ada a).
Tip 3: Make sou ce code a ailable in a public
code eposi o y
•Mul iple con en ional eposi o y se ices o so wa e
de elopmen a e a ailable such as Gi Hub, Gi Lab, and Bi bucke
•Sou ce code should be w i en ollowing widely used s yle
con en ions, e.g., PEP 8 o Py hon and he Google S yle Guide o
a a ie y o p og amming languages
•Code analysis ools ha can assis wo k low de elope s in
adhe ing o hese s yle con en ions a e a ailable
•These ools should be in eg a ed in he wo k low de elopmen
ou ine, o example, h ough au oma ic es ing p o ocols.
F om:
h ps://google.gi hub.io/s yleguide/shellguide.h ml
Tip 4: P o ide example inpu da a and esul s
along wi h he wo k low
•Accessibili y o he wo k low’s inpu da a and associa ed esul s will help
he end-use o unde s and how he wo k low should unc ion and
imp o es ep oducibili y. Example da a can be p o ided along wi h he
wo k low, o example, when using RO-C a e o package he wo k low
•Al e na i ely, he wo k low documen a ion should gi e guidance on how
o e ie e he da a, p e e ably om a FAIR da a eposi o y.
•example da a can be used o e i y he use s’ con igu a ion. Running a
pipeline in ano he compu a ional en i onmen can equi e adjus men s
o he con igu a ion ile (see Tip 8). The example da a wi h esul s can be
used o e i y ha he wo k low uns co ec ly wi h his new con igu a ion
p o ile.
• es unc ions can be inco po a ed in he wo k low o gua an ee a p ope
wo k low execu ion and, i no execu ed co ec ly, e eal quickly whe e
he execu ion hal s
•Uni es s a e small es s ha can be implemen ed in a wo k low o es
he execu ion o single sc ip s o e en unc ions wi hin a sc ip . Fo
popula p og amming languages, he e a e lib a ies a ailable ha a e
designed o implemen uni es s,
Tip 5: The ools in eg a ed in a wo k low
should adhe e o ile o ma s anda ds
•Adop ing s anda dized ile o ma s inc eases in e ope abili y. No
only wo k low in- and ou pu iles, bu also in e media e iles ha
a e exchanged by p ocesses wi hin he wo k low should be
w i en in s anda dized o ma s whe e possible.
•I is impo an o ealize ha cu en da a s anda ds migh no be
pe sis en o e ime. Using da a s anda ds does no mean being
blind o eme ging da a s anda ds ha possibly o e mo e
ad an ages.
• In he long un, i is a communi y e o o de e mine which
domain-speci ic s anda ds should be e ained o eplaced by
be e al e na i es. The e o e, we ecommend closely keeping
ack o he la es de elopmen s in he espec i e ield ha a
esea che is wo king in.
A e e ence o ep oducible compu a ional
esea ch
Ten Simple Rules o Rep oducible Compu a ional Resea ch | PLOS
Compu a ional Biology
A e e ence o so wa e ool wo k low-
eady ?
Ye ano he example
A inal no e…
This Pilo aining ac i i y has been unded by he Eu opean Union –Nex Gene a ionEU wi hin he PNRR p ojec s unded pu suan o A icle 11, pa ag aph1, o No ice 594/2024:
•“NFFA-DI cod. IR0000015, Missione 4, “Is uzione e Rice ca” – Componen e 2, “Dalla ice ca all'imp esa” – Linea di in es imen o 3.1, “Fondo pe la ealizzazione di un sis ema
in eg a o di in as u u e di ice ca e inno azione” – Azione 3.1.1, “C eazione di nuo e IR o po enziamen o di quelle esis en i che conco ono agli obie i i di Eccellenza Scien i ica di
Ho izon Eu ope e cos i uzione di e i” (CUP B53C22004310006).
•“EFC cod. SSU2024-00002, Missione 4 "Is uzione e ice ca" - Componen e 1, “Po enziamen o dell'o e a dei se izi all'is uzione: dagli asili nido all'uni e si a'” -
In es imen o 3.4 “Dida ica e compe enze uni e si a ie a anza e” - Sub-In es imen o “Ra o zamen o delle scuole uni e si a ie supe io i” (CUP: G97G24000100007).
E-ARGO
Thanks o he a en ion
