This is the summary of what Francesco Serafin did in its first year of doctoral studies, defending for his admission to his second year Ph.D. Undoubtedly he did a lot of work and he program to di even more. Three are the lines of his research: implementing a new flexible structure based on graphs for commanding simulations of interacting systems; implementing a domain specific language for doing environmental models (and particularly to solve ordinary and partial differential equations); deplying a system that makes easier to do replicable science.

1. C R E A T I N G A N E W I N F R A S T R U C T U R E F O R
G E O T O P 3 . 0
D O C T O R A L S C H O O L O F C I V I L ,
E N V I R O N M E N T A L A N D M E C H A N I C A L
E N G I N E E R I N G
X X X I C Y C L E
Admission to the second year
S U P E R V I S O R :
P R . P H D R I C C A R D O R I G O N
C O - A D V I S O R :
P H D O L A F D A V I D
P H D S T U D E N T :
F R A N C E S C O S E R A F I N
24/10/16

2. TOPICS
During this year, I started to dig into mainly three
topics:
• Graphs
• PDEs
• Reproducible research
…all related to Hydrology
24/10/16Serafin F. Admission to the second year

3. GRAPHS
A graph is a set of
vertices and a
collection of edges that
each connect a pair of
vertices.
Algorithms 4th ed. – Sedgewick
& Wayne
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24/10/16Serafin F. Admission to the second year

4. GRAPHS
A graph is a set of
vertices and a
collection of edges that
each connect a pair of
vertices.
Algorithms 4th ed. – Sedgewick
& Wayne
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?
What they got to do with
Hydrology?
24/10/16Serafin F. Admission to the second year

5. GRAPHS
• Hydrological System
http://www.revision.co.zw/the-hydrological-water-cycle/
24/10/16Serafin F. Admission to the second year

6. GRAPHS
• Hydrological System
http://www.revision.co.zw/the-hydrological-water-cycle/
NODES: physical processes
EDGES: processes interactions
24/10/16Serafin F. Admission to the second year

7. GRAPHS
• Hydrological System
Rigon, Serafin, Bancheri – Hydrological cycle as a dynamical system
MASS BUDGET
24/10/16Serafin F. Admission to the second year

8. GRAPHS
• Hydrological System
• Environmental
Model
http://teeic.indianaffairs.gov/er/lhhydro/restech/desc/index.htm
24/10/16Serafin F. Admission to the second year

9. GRAPHS
• Hydrological System
• Environmental
Model
http://teeic.indianaffairs.gov/er/lhhydro/restech/desc/index.htm
NODES: HRUs or subbasins
EDGES: water flow
24/10/16Serafin F. Admission to the second year

10. GRAPHS
• Hydrological System
• Environmental
Model
• Mesh
http://www.innovationresearchfocus.org.uk/Issues/85/IRF85_HR2.html
24/10/16Serafin F. Admission to the second year

11. GRAPHS
• Hydrological System
• Environmental
Model
• Mesh
http://www.innovationresearchfocus.org.uk/Issues/85/IRF85_HR2.html
NODES: cell
EDGES: interaction between cells
24/10/16Serafin F. Admission to the second year

12. 1
2
3
4
GRAPHS
They allow to enable
IMPLICIT
PARALLELIZATION.
This is the reason why
the implementation of a
graph data structure for
environmental
modelling is the right
answer to the request of
computational speed.
24/10/16Serafin F. Admission to the second year

13. Classes Research
— Discrete Maths - DISI
— Complex Networks –
Summer School
— Algorithms & Data
Structures – DISI
— Geostatistics - DICAM
— Ne3: parallel binary
tree – multithreading version
of a binary tree totally designed
around PATTERNS
— OMS v3: Tree Data
Structure – beta version of
the tree data structure which
supports the running of
different component in each
node
GRAPHS
24/10/16Serafin F. Admission to the second year

14. PDEs
Environmental models
should be easier to
implement, to read and
to maintain.
24/10/16Serafin F. Admission to the second year

15. PDEs
Environmental models
should be easier to
implement, to read and
to maintain.
API: expansion of the existing library
DSL: development of a built-in DSL in OMS v3
24/10/16Serafin F. Admission to the second year

16. DSL
A DSL (Domain-
Specific Language) is a
computer language
specialized to a
particular application
domain. This is in
contrast to a GPL
(General-Purpose
Language), which is
broadly applicable
across domains.
https://en.wikipedia.org/
wiki/Domain-
specific_language
DSML model
Idea/Concept
Product
MANUAL
AUTOMATIC
GENERATION
Source code
MANUAL
COMPILE
amountoftimeandeffort
http://www.slideshare.net/chanchaljayaraj/web-based-tool-for-domain-specific-modeling
24/10/16Serafin F. Admission to the second year

17. Classes Research
— Advanced Numerical
Methods – Winter
School
— API based Boussinesq
Groundwater Equation
— Bachelor thesis co-
tutor: A. Iemma – Richards
equation 1D
— Master thesis co-tutor:
N. Tubini – Freezing
Thawing processes study
with numerical model
PDEs
24/10/16Serafin F. Admission to the second year

18. PDEs
The Boussinesq
Groundwater Equation
24/10/16Serafin F. Admission to the second year

19. Giulio Supino 2016 – Master of Science Award
Acknowledgment to the two best master thesis in Water
Engineering which graduations were held in the biennial July
1st, 2014 - April 30th, 2016.
“Patterns for the application of modern informatics
to the integration of PDEs: the case of Boussinesq
Equation”
The award ceremony was held during the XXXV National
Conference of Hydraulics and Hydraulic Constructions in
Bologna.
PDEs
24/10/16Serafin F. Admission to the second year

20. Software, Hardware … Vaporware
I have been frustrated often with statisticians and computer scientists
who write papers where they develop new methods and seem to
demonstrate that those methods blow away all their competitors. But
then no software is available to actually test and see if that is true. …
In my mind, new methods/analyses without software are just
vaporware … If there is no code, there is no paper.
By Jeff Leek*
http://simplystatistics.org/2013/01/23/statisticians-and-computer-scientists-if-there-is-no-code-there-is-no-
paper/
REPRODUCIBLE RESEARCH
24/10/16Serafin F. Admission to the second year

21. TOOLS
• Git – GitHub
24/10/16Serafin F. Admission to the second year

22. TOOLS
• Git – GitHub
• Gradle
24/10/16Serafin F. Admission to the second year

23. TOOLS
• Git – GitHub
• Gradle
• Travis
24/10/16Serafin F. Admission to the second year

24. TOOLS
• Git – GitHub
• Gradle
• Travis
• GEOframe
24/10/16Serafin F. Admission to the second year

25. TOOLS
• Git – GitHub
• Gradle
• Travis
• GEOframe
http://github.com/geoframecomponents
https://github.com/GEOframeOMSProjects
24/10/16Serafin F. Admission to the second year

26. TOOLS
• Git – GitHub
• Gradle
• Travis
• GEOframe
• Documentation
24/10/16Serafin F. Admission to the second year

27. TOOLS
• Git – GitHub
• Gradle
• Travis
• GEOframe
• Documentation
• Online doc
24/10/16Serafin F. Admission to the second year

28. TOOLS
• Git – GitHub
• Gradle
• Travis
• GEOframe
• Documentation
• Online doc
24/10/16Serafin F. Admission to the second year

29. TOOLS
• Git – GitHub
• Gradle
• Travis
• GEOframe
• Documentation
• Online doc
• BMI - OMS
— BMI (Basic Modelling Interface)
is a simple interface that model
developers are asked to
implement in order to simplify
conversion of an existing model to
a reusable, plug-and-play model
component. In this way a
modeling framework will be able
to:
— Determine if a set of components
provide a complete model
— Connect each component that requires
a certain input variable to another
component in the set that provides that
variable as output
24/10/16Serafin F. Admission to the second year

30. TOOLS
• Git – GitHub
• Gradle
• Travis
• GEOframe
• Documentation
• Online doc
• BMI - OMS
— BMI-OMS provide wrapper for
loading BMI models into OMS
compliant modeling frameworks
and vice-versa.
24/10/16Serafin F. Admission to the second year

31. TOOLS
• Git – GitHub
• Gradle
• Travis
• GEOframe
• Documentation
• Online doc
• BMI - OMS
24/10/16Serafin F. Admission to the second year

32. Target Journals
GMD –
Geoscientific
Model
Development
Computer
Geosciences
EMS –
Environmental
Modeling &
Software
24/10/16Serafin F. Admission to the second year

33. Scientific Output
Papers:
- Bancheri M., Serafin F., Abera W. , Formetta G. & Rigon R. - A well engineered
implementation of Kriging tools in the Object Modelling System v.3 – in preparation
- Rigon R., Serafin F., Bancheri M, A tools deployment for replicable and reproducible
research – Invited - OGRS 2016 Conferences proceedings – in preparation
Conferences:
- M.Bancheri , W. Abera, G. Formetta, R.Rigon & F. Serafin , Implementing a Travel
Time Model for the Entire River Adige: the Case on JGrass-NewAGE, American
Geophysical Union, Fall Meeting 2015, abstract #H11K-03.
- Serafin F., Bancheri M., Rigon R. & David O., A binary tree data structure for
environmental modelling, International Congress on Environmental Modelling and
Software, 2016, presentation
- Bancheri, M, Formetta G., Serafin, F., Rigon R , Green T.R & David O. , Replicability of
a modelling solution using NewAGE-Jgrass., International Congress on Environmental
Modelling and Software, 2016, presentation
- Bancheri M., Formetta G., Serafin, F., and Rigon R., Research reproduciblity and
replicability: the case of JGrass-NewAge, XXXV Convegno nazionale di Idraulica e
Costruzioni Idrauliche, 2016, poster
24/10/16Serafin F. Admission to the second year

34. THANK YOU
FOR YOUR
ATTENTION!

35. 24/10/16Serafin F. Admission to the second year