Slides for my lightning talk on the SUPERSMART platform to the SSB/SSE/ASN annual meeting, Austin, TX, USA. SSB Spotlight Session: "Next generation phylogenetic inference 2". Monday, June 20th 2016, 3:20PM, Ballroom A.
Hoe leer je een robot soorten te herkennen?Rutger Vos
Guest lecture slides for the bioinformatics student union (Exon) at the university of applied sciences, Leiden, the Netherlands. In this lecture I present the results of a research project at Naturalis Biodiversity Center to identify slipper orchids using image recognition techniques.
Taxonomic classification of digitized specimens using machine learningRutger Vos
Progress in the development of neural networks that classify images of slipper orchids and Javanese butterflies. Talk to LEBEN at Leiden University's biology department, IBL, 20 September 2016.
Hoe leer je een robot soorten te herkennen?Rutger Vos
Guest lecture slides for the bioinformatics student union (Exon) at the university of applied sciences, Leiden, the Netherlands. In this lecture I present the results of a research project at Naturalis Biodiversity Center to identify slipper orchids using image recognition techniques.
Taxonomic classification of digitized specimens using machine learningRutger Vos
Progress in the development of neural networks that classify images of slipper orchids and Javanese butterflies. Talk to LEBEN at Leiden University's biology department, IBL, 20 September 2016.
Natural history research as a replicable data scienceRutger Vos
Keynote presentation to the 2017 GARR conference, 17 November 2017, Venice, Italy. Introduction to natural history data types and analysis examples. Discussion of current practices in promoting reproducibility.
Species delimitation - species limits and character evolutionRutger Vos
Lecture slides for the program orientation Evolutionary Biology at the Institute of Biology Leiden, the Netherlands. Thursday, September 7th, 2017.
Lecture notes are here: https://docs.google.com/document/d/e/2PACX-1vRIv5mKK1fjBby--u97emC7hrqXUbxFQZe63P1FpguuhHLG6xykbwXKeKXCUE5W-LSpakXYCI621xCK/pub
Onderzoek bio-informatica Naturalis. Raad voor Cultuur 2017.Rutger Vos
Presentatie voor leden van de Raad voor Cultuur, 27 juni 2017, Naturalis. Geeft een overzicht van de onderzoeksactiviteiten aan collectiemateriaal met een bio-informatische component.
Presentation about image recognition applied to digitized specimen of the Van Groenendael Krijger collection of Javanese Papilionid butterflies. Occasion: BrainFood, 12 April 2017, Naturalis, Leiden, the Netherlands.
Modeling the biosphere: the natural historian's perspectiveRutger Vos
Natural history collections of specimens are a rich source of data for discovering the patterns of biodiversity in space and time and for furthering our understanding of the underlying processes that generate these patterns. Modeling the biosphere in this manner can help address global challenges in relation to climate change, food security, emerging disease and conservation. (Talk to the 3rd annual eScience symposium, 8 October 2015).
Kunnen we een tomaat van 400 jaar oud proevenRutger Vos
Slides voor mijn college aan de Museum Jeugd Universiteit (http://museumjeugduniversiteit.nl) in Museum Boerhaave (http://www.museumboerhaave.nl), 19 october 2014.
PhyloTastic: names-based phyloinformatic data integrationRutger Vos
Lightning talk to the 2013 TDWG conference symposium on phyloinformatics, brief report on PhyloTastic with special attention to the taxonomic name reconciliation service TaxoSaurus.
NeXML is an exchange standard for representing phyloinformatic data — inspired by the commonly used NEXUS format, but more robust and easier to process.
Full title: "The tree of life as central unifying artefact for the integration of phylogenetic knowledge." This is a brief intro presentation for the 2011 BioHackathon in Kyoto, Japan. I describe a simple workflow built around semantic web services that add metadata to a backbone of the Tree of Life. The take home message is that such a structure can be a useful anchor to which knowledge can be attached, but that there are still issues with standards definition and adoption.
Course slides for computational phyloinformatics, an annual course organized by NESCent in collaboration with hosting organizations across the world. I am the teacher of the Perl section of the course, these are the slides I presented in 2010 at BGI, Shenzhen, PRC.
How to make a monkey: functional adaptation in the primate genomeRutger Vos
Presentation to the "Workshop on Parallel and Distributed Processing of Large Genome Data", 22 February 2011, DBCLS, Tokyo (http://mlab.cb.k.u-tokyo.ac.jp/en/events/lgd/). The presentation describes the methodological issues surrounding the design of a workflow for assigning orthology among primate genomes, testing them for evidence of selection and interpreting the results using the Gene Ontology.
Natural history research as a replicable data scienceRutger Vos
Keynote presentation to the 2017 GARR conference, 17 November 2017, Venice, Italy. Introduction to natural history data types and analysis examples. Discussion of current practices in promoting reproducibility.
Species delimitation - species limits and character evolutionRutger Vos
Lecture slides for the program orientation Evolutionary Biology at the Institute of Biology Leiden, the Netherlands. Thursday, September 7th, 2017.
Lecture notes are here: https://docs.google.com/document/d/e/2PACX-1vRIv5mKK1fjBby--u97emC7hrqXUbxFQZe63P1FpguuhHLG6xykbwXKeKXCUE5W-LSpakXYCI621xCK/pub
Onderzoek bio-informatica Naturalis. Raad voor Cultuur 2017.Rutger Vos
Presentatie voor leden van de Raad voor Cultuur, 27 juni 2017, Naturalis. Geeft een overzicht van de onderzoeksactiviteiten aan collectiemateriaal met een bio-informatische component.
Presentation about image recognition applied to digitized specimen of the Van Groenendael Krijger collection of Javanese Papilionid butterflies. Occasion: BrainFood, 12 April 2017, Naturalis, Leiden, the Netherlands.
Modeling the biosphere: the natural historian's perspectiveRutger Vos
Natural history collections of specimens are a rich source of data for discovering the patterns of biodiversity in space and time and for furthering our understanding of the underlying processes that generate these patterns. Modeling the biosphere in this manner can help address global challenges in relation to climate change, food security, emerging disease and conservation. (Talk to the 3rd annual eScience symposium, 8 October 2015).
Kunnen we een tomaat van 400 jaar oud proevenRutger Vos
Slides voor mijn college aan de Museum Jeugd Universiteit (http://museumjeugduniversiteit.nl) in Museum Boerhaave (http://www.museumboerhaave.nl), 19 october 2014.
PhyloTastic: names-based phyloinformatic data integrationRutger Vos
Lightning talk to the 2013 TDWG conference symposium on phyloinformatics, brief report on PhyloTastic with special attention to the taxonomic name reconciliation service TaxoSaurus.
NeXML is an exchange standard for representing phyloinformatic data — inspired by the commonly used NEXUS format, but more robust and easier to process.
Full title: "The tree of life as central unifying artefact for the integration of phylogenetic knowledge." This is a brief intro presentation for the 2011 BioHackathon in Kyoto, Japan. I describe a simple workflow built around semantic web services that add metadata to a backbone of the Tree of Life. The take home message is that such a structure can be a useful anchor to which knowledge can be attached, but that there are still issues with standards definition and adoption.
Course slides for computational phyloinformatics, an annual course organized by NESCent in collaboration with hosting organizations across the world. I am the teacher of the Perl section of the course, these are the slides I presented in 2010 at BGI, Shenzhen, PRC.
How to make a monkey: functional adaptation in the primate genomeRutger Vos
Presentation to the "Workshop on Parallel and Distributed Processing of Large Genome Data", 22 February 2011, DBCLS, Tokyo (http://mlab.cb.k.u-tokyo.ac.jp/en/events/lgd/). The presentation describes the methodological issues surrounding the design of a workflow for assigning orthology among primate genomes, testing them for evidence of selection and interpreting the results using the Gene Ontology.
Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa: SUPERSMART
1.
h#p://www.supersmart-‐project.org
Self-‐Updating
Platform
for
the
Estimation
of
Rates
of
Speciation,
Migration,
And
Relationships
of
Taxa
Rutger
Vos,
Naturalis
Biodiversity
Center,
Leiden,
the
Netherlands
@rvosa
5. Effect
of
data
mining
parameterization
h#p://www.supersmart-‐project.org
-‐
@rvosa
0 5 10 15 20
0.050.100.150.20
Averaged posterior probabilities on nodes
Minimum marker coverage per taxon
Maximumaverageduncorrectedpairwisedistance
p
<
0.8
0.8
<
p
<
0.95
p
>
0.95
6. Recovering
a
simulated
tree
Simulated
Tree
Re-estimated
Tree
data sim
0.000.10
data sim
60708090
% of invariant sites
per alignment
%
data sim
0102030
Number of indels
per alignment
count
data sim
04080120
data sim
0200400
data sim
02040
average distance
within alignment
relativeeditdistance
Average size of indels
per alignment
size(nucleotides)
Number of gaps
per sequence
gapcount
% gaps per sequence
%
!" #"
time
(myr)
80 0 0 80
h#p://www.supersmart-‐project.org
-‐
@rvosa
7. Install
a
vagrant
box,
then:
$
smrt [COMMAND] [OPTIONS]
h#p://www.supersmart-‐project.org
-‐
@rvosa
8. Acknowledgements
h#p://www.supersmart-‐project.org
-‐
@rvosa
The
smar,es:
• Alexandre
Antonelli
• Rutger
Vos
• Hannes
He#ling
• Mike
Sanderson
• Bengt
Oxelman
• Karin
Nilsson
• Mats
Töpel
• Hervé
Sauquet
• Henrik
Nilsson
• Daniele
Silvestro
• Fabien
Condamine
• Ruud
Scharn
Thank
you
to:
• Erick
Matsen
• Meg
Pirrung
• You,
the
audience!