Streamlining Python Development: A Guide to a Modern Project Setup
140712 antabif egbamm
1. ANTABIF: EGBAMM, 2012
Antarctic Biodiversity Information Facility
Saturday 14 July 12
2. Our vision:
Antarctic biodiversity data are
open, linked, useful, interoperable and safe.
Saturday 14 July 12
3. What’s ANTABIF?
David B, Danis B, Griffiths HJ
Saturday 14 July 12
4. What’s ANTABIF?
• Born as Census of Antarctic Marine Life
as the data, visualization and analysis
component
David B, Danis B, Griffiths HJ
Saturday 14 July 12
5. What’s ANTABIF?
• Born as Census of Antarctic Marine Life
as the data, visualization and analysis
component
• Free and open access to biodiversity data:
taxonomy and biogeography
David B, Danis B, Griffiths HJ
Saturday 14 July 12
6. What’s ANTABIF?
• Born as Census of Antarctic Marine Life
as the data, visualization and analysis
component
• Free and open access to biodiversity data:
taxonomy and biogeography
• SCAR-MarBIN => ANTABIF projects
David B, Danis B, Griffiths HJ
Saturday 14 July 12
7. What’s ANTABIF?
• Born as Census of Antarctic Marine Life
as the data, visualization and analysis
component
• Free and open access to biodiversity data:
taxonomy and biogeography
• SCAR-MarBIN => ANTABIF projects
• Science, conservation and management
David B, Danis B, Griffiths HJ
Saturday 14 July 12
8. What’s ANTABIF?
• Born as Census of Antarctic Marine Life
as the data, visualization and analysis
component
• Free and open access to biodiversity data:
taxonomy and biogeography
• SCAR-MarBIN => ANTABIF projects
• Science, conservation and management
• Networked community developments
David B, Danis B, Griffiths HJ
Saturday 14 July 12
9. What’s ANTABIF?
• Born as Census of Antarctic Marine Life
as the data, visualization and analysis
component
• Free and open access to biodiversity data:
taxonomy and biogeography
• SCAR-MarBIN => ANTABIF projects
• Science, conservation and management
• Networked community developments
• Scientific impact: Citations : 423,
Publications: 58, H-Index: 11
David B, Danis B, Griffiths HJ
Saturday 14 July 12
10. What’s ANTABIF?
• Born as Census of Antarctic Marine Life
as the data, visualization and analysis
component
• Free and open access to biodiversity data:
taxonomy and biogeography
• SCAR-MarBIN => ANTABIF projects
• Science, conservation and management
• Networked community developments
• Scientific impact: Citations : 423,
Publications: 58, H-Index: 11
David B, Danis B, Griffiths HJ
Saturday 14 July 12
11. Progress: Taxonomy
17,098 taxa
The first dynamic Register of Antarctic Marine Species
Taxonomic backbone
Board of 64 editors
Feeds World Register of Marine Species, Catalogue of Life and
Encyclopedia of Life
Saturday 14 July 12
12. Progress: Taxonomy
17,098 taxa
The first dynamic Register of Antarctic Marine Species
Taxonomic backbone
Board of 64 editors
Feeds World Register of Marine Species, Catalogue of Life and
Encyclopedia of Life
Saturday 14 July 12
13. Progress:
Biogeography
• Single access to 900 datasets
• 2.5 million records
• Data back to 1900 (Pygoscelis
adeliae)
• Spatial data on over 5000 taxa
• Downloadable
• Interoperable
• Free and open
Saturday 14 July 12
14. Progress:
Biogeography
• Single access to 900 datasets
• 2.5 million records
• Data back to 1900 (Pygoscelis
adeliae)
• Spatial data on over 5000 taxa
• Downloadable
• Interoperable
• Free and open
Saturday 14 July 12
36. ipt.biodiversity.aq
• Integrated Publishing Toolkit
• standardize and clean your data
• manage primary biodiversity data
• manage associated metadata
• choose collaborators
• generate and submit a Data Paper
• push data and metadata to Information Systems
Saturday 14 July 12
46. Proof of concept
ZooKeys 185: 73–78 (2012)
Antarctic Starfish (Echinodermata: asteroidea) from the ANDEEP3 expedition
doi: 10.3897/zookeys.185.3078 DAtA PAPEr
A peer-reviewed open-access journal
73
www.zookeys.org Launched to accelerate biodiversity research
Antarctic Starfish (Echinodermata, Asteroidea) from
the ANDEEP3 expedition
Bruno Danis1, Michel Jangoux2, Jennifer Wilmes2
1 ANTABIF, 29, rue Vautier, 1000, Brussels, Belgium 2 Université Libre de Bruxelles, 50, av FD Roosevelt,
1050, Brussels, Belgium
Corresponding author: Bruno Danis (bruno.danis@gmail.com)
Academic editor: Vishwas Chavan | Received 13 March 2012 | Accepted 18 April 2012 | Published 23 April 2012
Citation: Danis B, Jangoux M, Wilmes J (2012) Antarctic Starfish (Echinodermata: asteroidea) from the ANDEEP3
expedition. ZooKeys 185: 73–78. doi: 10.3897/zookeys.185.3078
Abstract
This dataset includes information on sea stars collected during the ANDEEP3 expedition, which took
place in 2005. The expedition focused on deep-sea stations in the Powell Basin and Weddell Sea.
Sea stars were collected using an Agassiz trawl (3m, mesh-size 500µm), deployed in 16 stations
during the ANTXXII/3 (ANDEEP3, PS72) expedition of the RV Polarstern. Sampling depth ranged
from 1047 to 4931m. Trawling distance ranged from 731 to 3841m. The sampling area ranges from
-41°S to -71°S (latitude) and from 0 to -65°W (longitude). A complete list of stations is available from
the PANGAEA data system (http://www.pangaea.de/PHP/CruiseReports.php?b=Polarstern), including a
cruise report (http://epic-reports.awi.de/3694/1/PE_72.pdf ).
The dataset includes 50 records, with individual counts ranging from 1-10, reaching a total of 132
specimens.
The andeep3-Asteroidea is a unique dataset as it covers an under-explored region of the Southern
Ocean, and that very little information was available regarding Antarctic deep-sea starfish. Before this
study, most of the information available focused on starfish from shallower depths than 1000m. This
dataset allowed to make unique observations, such as the fact that some species were only present at
very high depths (Hymenaster crucifer, Hymenaster pellucidus, Hymenaster praecoquis, Psilaster charcoti,
Freyella attenuata, Freyastera tuberculata, Styrachaster chuni and Vemaster sudatlanticus were all found below
-3770m), while others displayed remarkable eurybathy, with very high depths amplitudes (Bathybiaster
loripes (4842m), Lysasterias adeliae (4832m), Lophaster stellans (4752m), Cheiraster planeta (4708m), Er-
emicaster crassus (4626m), Lophaster gaini (4560m) and Ctenodiscus australis (4489m)).
Even if the number of records is relatively small, the data bring many new insights on the taxonomic,
bathymetric and geographic distributions of Southern starfish, covering a very large sampling zone. The
dataset also brings to light six species, newly reported in the Southern Ocean.
The quality of the data was controlled very thoroughly, by means of on-board Polarstern GPS sys-
tems, checking of identification by a renowned specialist (Prof. Michel Jangoux, Université Libre de Brux-
Copyright Bruno Danis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC-
BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Saturday 14 July 12
47. Proof of concept ZooKeys 185: 73–78 (2012)
Antarctic Starfish (Echinodermata: asteroidea) from the ANDEEP3 expedition
doi: 10.3897/zookeys.185.3078 DAtA PAPEr
A peer-reviewed open-access journal
73
www.zookeys.org Launched to accelerate biodiversity research
Antarctic Starfish (Echinodermata, Asteroidea) from
the ANDEEP3 expedition
Impact Factor: 0.514 Bruno Danis1, Michel Jangoux2, Jennifer Wilmes2
1 ANTABIF, 29, rue Vautier, 1000, Brussels, Belgium 2 Université Libre de Bruxelles, 50, av FD Roosevelt,
1050, Brussels, Belgium
Corresponding author: Bruno Danis (bruno.danis@gmail.com)
Academic editor: Vishwas Chavan | Received 13 March 2012 | Accepted 18 April 2012 | Published 23 April 2012
Citation: Danis B, Jangoux M, Wilmes J (2012) Antarctic Starfish (Echinodermata: asteroidea) from the ANDEEP3
expedition. ZooKeys 185: 73–78. doi: 10.3897/zookeys.185.3078
Abstract
This dataset includes information on sea stars collected during the ANDEEP3 expedition, which took
place in 2005. The expedition focused on deep-sea stations in the Powell Basin and Weddell Sea.
Sea stars were collected using an Agassiz trawl (3m, mesh-size 500µm), deployed in 16 stations
during the ANTXXII/3 (ANDEEP3, PS72) expedition of the RV Polarstern. Sampling depth ranged
from 1047 to 4931m. Trawling distance ranged from 731 to 3841m. The sampling area ranges from
-41°S to -71°S (latitude) and from 0 to -65°W (longitude). A complete list of stations is available from
the PANGAEA data system (http://www.pangaea.de/PHP/CruiseReports.php?b=Polarstern), including a
cruise report (http://epic-reports.awi.de/3694/1/PE_72.pdf ).
The dataset includes 50 records, with individual counts ranging from 1-10, reaching a total of 132
specimens.
The andeep3-Asteroidea is a unique dataset as it covers an under-explored region of the Southern
Ocean, and that very little information was available regarding Antarctic deep-sea starfish. Before this
study, most of the information available focused on starfish from shallower depths than 1000m. This
dataset allowed to make unique observations, such as the fact that some species were only present at
very high depths (Hymenaster crucifer, Hymenaster pellucidus, Hymenaster praecoquis, Psilaster charcoti,
Freyella attenuata, Freyastera tuberculata, Styrachaster chuni and Vemaster sudatlanticus were all found below
-3770m), while others displayed remarkable eurybathy, with very high depths amplitudes (Bathybiaster
loripes (4842m), Lysasterias adeliae (4832m), Lophaster stellans (4752m), Cheiraster planeta (4708m), Er-
emicaster crassus (4626m), Lophaster gaini (4560m) and Ctenodiscus australis (4489m)).
Even if the number of records is relatively small, the data bring many new insights on the taxonomic,
bathymetric and geographic distributions of Southern starfish, covering a very large sampling zone. The
dataset also brings to light six species, newly reported in the Southern Ocean.
The quality of the data was controlled very thoroughly, by means of on-board Polarstern GPS sys-
tems, checking of identification by a renowned specialist (Prof. Michel Jangoux, Université Libre de Brux-
Copyright Bruno Danis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC-
BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Saturday 14 July 12
48. afg. biodiversity.aq
• Identification aid
• High quality (useful) pictures
• Expert Descriptions
• Built on-the-fly from various sources
• Generates a pdf for taxa/area of interest
Saturday 14 July 12
53. atlas.biodiversity.aq
• Biogeographic Atlas of the Southern Ocean
Saturday 14 July 12
54. atlas.biodiversity.aq
• Biogeographic Atlas of the Southern Ocean
• Redo of Hedgepeth 1969 Folio
Saturday 14 July 12
55. atlas.biodiversity.aq
• Biogeographic Atlas of the Southern Ocean
• Redo of Hedgepeth 1969 Folio
• Predictive approach
Saturday 14 July 12
56. atlas.biodiversity.aq
• Biogeographic Atlas of the Southern Ocean
• Redo of Hedgepeth 1969 Folio
• Predictive approach
• Static and dynamic versions
Saturday 14 July 12
57. atlas.biodiversity.aq
• Biogeographic Atlas of the Southern Ocean
• Redo of Hedgepeth 1969 Folio
• Predictive approach
• Static and dynamic versions
• Modelization loops are ready
Saturday 14 July 12
58. Slope
94 Interpolated data layers Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
+
ANTABIF Occurrence
records
Saturday 14 July 12
59. Slope
94 Interpolated data layers Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
+
ANTABIF Occurrence
records
Saturday 14 July 12
60. Slope
94 Interpolated data layers Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
+
ANTABIF Occurrence
records
Saturday 14 July 12
65. atlas.biodiversity.aq
• Outcomes of the Villefranche workshop
• BRT models on 13 spp of penguins and 15 spp of seals
(sub-ant and ant)
Saturday 14 July 12
66. atlas.biodiversity.aq
• Outcomes of the Villefranche workshop
• BRT models on 13 spp of penguins and 15 spp of seals
(sub-ant and ant)
• Some models are doing ok, but needs refinement
Saturday 14 July 12
67. Arctocephalus gazella
Arctocephalus.gazella − BRT
−40
−50
Arctocephalus.gazella
FALSE
TRUE
pred
−60
lat
0.8
0.6
0.4
0.2
−70
−80
−90
−100 0 100
Saturday 14 July 12 lon
68. Hydrurga leptonyx
Hydrurga.leptonyx − BRT
−40
−50
pred
0.8
0.6
0.4
−60
lat
0.2
Hydrurga.leptonyx
FALSE
TRUE
−70
−80
−90
−100 0 100
Saturday 14 July 12 lon
69. Aptenodytes forsteri
Aptenodytes.forsteri − BRT
−40
−50
pred
0.8
−60
0.6
0.4
lat
0.2
Aptenodytes.forsteri
−70 FALSE
TRUE
−80
−90
Saturday 14 July 12 −100 0 100
70. Pygoscelis adeliae
Pygoscelis.adeliae − BRT
−40
−50
pred
0.8
−60
0.6
0.4
lat
0.2
Pygoscelis.adeliae
−70 FALSE
TRUE
−80
−90
Saturday 14 July 12 −100 0 100