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Open Source

Kobe
by

Hanno Rein

on 8 August 2013

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Transcript of Open Source

Open Source in Astrophysics
Advantages
Reproducibility
Open Exoplanet
What I am doing
All my codes are public.

I only use publicly available codes.

As a referee, I do not accept papers where the main result is based on a complex simulation that I cannot verify. The source code is part of the initial conditions.

Use the Open Exoplanet Catalogue!
Large-scale simulation of Formation and
Evolution of Planetary Systems, Kobe 2013

Hanno Rein
Continuity
Code reuse
Recognition
Less bugs
Harold F. "Hal" Levison is a planetary scientist specializing in planetary dynamics. He argued for a distinction between what are now called dwarf planets and the other eight planets based on their inability to "clear the neighborhood around their orbits", although his proposal suggested the terms "unterplanet" and "überplanet" and used the word "dwarf" to mean something else. Among other distinctions, he is the co-author of SWIFT, a commonly used symplectic integrator that solves planetary equations of motion for periods of billions of years. He currently works at the Southwest Research Institute, Boulder, CO, and studies planetary orbits and their evolution through solar system history.
Source: http://en.wikipedia.org/wiki/Harold_F._Levison
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Open Source
Proprietary Code
Less than 100,000

100,000 to 499,999

500,000 to 1 million

More than 1 million
Number of defects per 1000 lines
Source: Coverty 2012 Open Source Report
Common drawbacks of astronomical catalogues
How to do it better
Examples
Impossible to correct typos, add data without sending an e-mail to the person in charge
Closed ecosystem
Centralized
Slow and outdated
It can take days/weeks/months for new planets to be added
Maintainer can be holiday or abandon the project
Web-based
Website are badly written
Requires flash or java plugin
Need a constant internet connection
Restricted to a very limited, predefined set of possible queries
Old-fashioned formats
Static tables are not adequate to represent diverse dataset
Almost impossible to include binary/triple/quadruple systems
Not flexible when adding new data
Unintuitive to parse
Open source philosophy
Unrestrictive MIT license
Community project
Everyone can contribute and modify data
Everyone can expand it
Distributed, no need for a server/website
Private clones with confidential data
694 systems, 61 binary system, 927 exoplanets, solar system objects, thousands of KOI objects
~10 million users!
Ready to go
Distributed version control system
Used by Linux kernel and most other open source projects
Every single value, every change ever made is logged, verifiable
Based on git
Hierarchical data structure
Uses plain XML
Can represent arbitrary configurations in systems with stellar multiplicity >1
Extremely easy and intuitive to parse in almost any language
Compresses extremely well
size ~ 100KB


Python
Dataformat
Over the past decade, before pursuing a particular line of research, scientists (including C.G.B.) in the haematology and oncology department at the biotechnology firm Amgen in Thousand Oaks, California, tried to confirm published findings related to that work. Fifty-three papers were deemed 'landmark' studies. It was acknowledged from the outset that some of the data might not hold up, because
Source: C. Glenn Begley & Lee M.
Ellis, Nature 483, 531–533
papers were deliberately selected that described something completely new, such as fresh approaches to targeting cancers or alternative clinical uses for existing therapeutics. Nevertheless, scientific findings were confirmed in only 6 (11%) cases. Even knowing the limitations of preclinical research, this was a shocking result.
What you should be doing.
Applying the same open-source
principles to an astronomical database
of open source software
Encouraging
collaboration
Helps to find new collaborators.
Does not excluding people.
It's open.
Contribute to it!
Catalogue
http://github.com/hannorein/open_exoplanet_catalogue
http://openexoplanetcatalogue.com
arXiv:1211.7121
import

xml.etree.ElementTree
as
ET, glob
for
filename
in
glob.glob(
"*.xml"
):
planetarysystem = ET.parse(
open
(filename,
"r"
))
planets = planetarysystem.findall(
".//planet"
)

for
planet
in
planets:

print
planet.findtext(
"./name"
)

print
planet.findtext("
./mass"
)
import

xml.etree.ElementTree
as
ET, glob
for
filename
in
glob.glob(
"*.xml"
):
planetarysystem = ET.parse(
open
(filename,
"r"
))
planets = planetarysystem.findall(
".//binary/planet"
)

for
planet
in
planets:

print
planet.findtext(
"./name"
)

print
planet.findtext("
./mass"
)
import

xml.etree.ElementTree
as
ET, glob
for
filename
in
glob.glob(
"*.xml"
):
planetarysystem = ET.parse(
open
(filename,
"r"
))
planets = planetarysystem.findall(
".//binary/star/planet"
)

for
planet
in
planets:

print
planet.findtext(
"./name"
)

print
planet.findtext("
./mass"
)
Full transcript