L10: FROGS: Facili a ing Rep oducible Open (Geo)Science
Ins uc o
Cou se chai : Debo ah Khide , USC In o ma ion Sciences Ins i u e ([email p o ec ed])
Cou se Ins uc o : Nick McKay, No he n A izona Uni e si y ([email p o ec ed])
Abs ac
Sha ing esea ch da a, so wa e, and wo k low is undamen al o building a Findable,
Accessible, In e ope able, and Reusable (FAIR) open science ecosys em. Indeed, o e
he pas decade, unde s and publishe s ha e in oduced open science policies
emphasizing ep oducibili y, ecognizing inc eased amewo ks ha suppo he sha ing
o ep oducible science p oduc s.
In his cou se, we will co e p inciples o open science in a manne ha p omo es
ep oducibili y:
1. Basic p inciples in documen ing, sha ing, and ci ing all esea ch p oduc s, including
da a, so wa e, and compu a ional p o enance (i.e., desc ibing he wo k low used in a
s udy, which links oge he da a and so wa e wi h hei associa ed pa ame e alues o
ep oducibili y) in acco dance o FAIR p inciples;
2. Gi Hub o code de elopmen (including con inuous in eg a ion) and collabo a ion.
We will also co e linking Gi Hub eposi o y wi h Zenodo o ob ain pe manen iden i ie s
o ci a ion;
3. Con aine iza ion wi h ools including Docke con aine s and myBinde . The cou se
will co e au oma ion o hese p ocesses using Gi Hub ac ions;
4. Publishing so wa e in a so wa e egis y.
The cou se will use an online pla o m (LeapFROGS) wi h a ke nel in Py hon and R.
The pla o m con ains links o ele an esou ces and sel -paced exe cises o es
unde s anding o he concep s. All ma e ials on he LeapFROGS pla o m a e openly
a ailable.
Audience: Resea che s, Lib a ians and adminis a o s, Publishe s
Le el: Beginne
Requi emen s:
● In e ne access o use he LeapFROGS pla o m.
○ Py hon: h ps://linked.ea h/LeapFROGS
○ R: h ps://linked.ea h/RLeapFROGS
○ No e: no knowledge o hese p og amming languages is necessa y. The
pla o m p o ides eaching ma e ials on he subjec .
● A Gi Hub accoun (no knowledge o Gi Hub necessa y beyond c ea ing an
accoun )
● Gi Hub Desk op ins alled and linked o he use ’s Gi Hub accoun [Op ional]
Cou se Lea ning Objec i es
A he end o he cou se, pa icipan s will be able o:
● Unde s and he basics equi emen s o sha e a i ac s o scien i ic esea ch
acco ding o FAIR p inciples
● Use Gi Hub o sha e scien i ic wo k lows
● Use Gi Hub o anspa en p ojec managemen
● Build Docke con aine s o sha e so wa e and wo k lows using Gi Hub ac ions
● Use myBinde o sha e scien i ic wo k lows
● Unde s and p inciples o scien i ic so wa e packaging and dis ibu ion
Cou se Topics
This cou se will be p esen ed o e h ee days o 90min each day and will co e hese
opics:
● Sha ing a i ac s o esea ch: Da a, So wa e, and Wo k low
● Gi Hub o scien i ic esea ch and publishing
● C ea ing con aine s o ep oducible esea ch
● Basics o So wa e Packaging
Cou se Schedule
LIVE ZOOM SESSION SCHEDULE
(All imes Paci ic UTC-7))
4:00pm – 5:30pm
90 minu es
Day 1-3
P esen a ion de ails Day 1:
The i s day will co e undamen al p inciples in scien i ic publishing. Scien i ic
publishing e e s o making all a i ac s o esea ch publicly accessible (no only he
pape bu also he da a, so wa e and wo k low) o ensu e ha all a i ac s o science a e
Findable, Rep oducible, In e ope able, and Reusable (FAIR). The ollowing module will
p o ide an au ho checklis on publishing guidelines and es you unde s anding o he
concep s.
4:00 - 4:10pm : In oduc ion o FROGS and LeapFROGS
4:10 - 4:30pm: Rep oducible Resea ch: Wha is i , why is i impo an , and how do we
do i ?
4:30 - 4:50pm: Concep s in da a and so wa e publishing
4:50 - 5:00pm: B eak
5:00 - 5:15pm: Publishing Rep oducible Wo k lows
5:15 - 6:25pm: Ci ing da a and so wa e in publica ions
6:15 - 6:30pm: W ap-up and links o addi ional esou ces
P esen a ion de ails Day 2
The second day will concen a e on he basics Gi Hub o so wa e and p ojec
managemen and he use o Docke , Binde , and myBinde o he sha ing o
ep oducible wo k lows.
4:00 - 4:20pm : Wha is Gi ? Wha is Gi Hub?
4:20 - 4:50pm: Synch onous Exe cise: c ea ing a eposi o y, b anches, pull eques ,
Gi Hub o p ojec managemen , ob aining a DOI o you p ojec
4:50 - 5:00pm: B eak
5:00 - 5:15pm: Wha a e con aine s? In oduc ion o Docke and myBinde
5:15 - 5:30pm: Synch onous Exe cise: C ea ing a Docke con aine om you Gi Hub
eposi o y using Gi Hub ac ions and eleasing no ebooks on myBinde
No e: No coding expe ience needed. All code will be p o ided o s uden s o be able o
wo k on Gi Hub.
P esen a ion de ails Day 3
The hi d day will ocus on p inciples o so wa e packaging.
4:00 - 4:25 pm : Basics o Packaging
4:25 - 4:50pm: W i ing a good documen a ion and es ing
4:50 - 5:00pm: B eak
5:00 - 5:25pm: Con inuous in eg a ion and publishing
5:25 - 6:30pm: W ap-up
Cou se Ma e ials and Supplies Requi ed
You will need a Gi Hub accoun and Gi Hub Desk op downloaded and ins alled locally.
This las s ep is op ional i s uden s wan o use he web in e ace ins ead.
O he Resou ces
● LeapFROGS:
○ Py hon: h ps://linked.ea h/LeapFROGS
○ R: h ps://linked.ea h/RLeapFROGS
