schliessen

Filtern

 

Bibliotheken

Taming the BEAST—A Community Teaching Material Resource for BEAST 2

Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two field... Full description

Journal Title: Systematic biology 2018-01-01, Vol.67 (1), p.170-174
Main Author: Barido-Sottani, Joëlle
Other Authors: Bošková, Veronika , Plessis, Louis Du , Kühnert, Denise , Magnus, Carsten , Mitov, Venelin , Müller, Nicola F , PečErska, Jūlija , Rasmussen, David A , Zhang, Chi , Drummond, Alexei J , Heath, Tracy A , Pybus, Oliver G , Vaughan, Timothy G , Stadler, Tanja
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/28673048
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5925777
title: Taming the BEAST—A Community Teaching Material Resource for BEAST 2
format: Article
creator:
  • Barido-Sottani, Joëlle
  • Bošková, Veronika
  • Plessis, Louis Du
  • Kühnert, Denise
  • Magnus, Carsten
  • Mitov, Venelin
  • Müller, Nicola F
  • PečErska, Jūlija
  • Rasmussen, David A
  • Zhang, Chi
  • Drummond, Alexei J
  • Heath, Tracy A
  • Pybus, Oliver G
  • Vaughan, Timothy G
  • Stadler, Tanja
subjects:
  • Algorithms
  • Bayesian analysis
  • Bayesian inference
  • Biodiversity
  • Computer applications
  • Computer programs
  • Data processing
  • Developmental biology
  • Epidemiology
  • Evolutionary biology
  • Mathematical models
  • MCMC
  • phylodynamics
  • Phylogenetics
  • Phylogeny
  • Software
  • Software for Systematics and Evolution
ispartof: Systematic biology, 2018-01-01, Vol.67 (1), p.170-174
description: Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a black-box method is not sufficient anymore. Instead, biologists are required to be actively involved with modeling decisions during data analysis. The modular design of the Bayesian phylogenetic software package BEAST 2 enables, and in fact enforces, this involvement. At the same time, the modular design enables computational biology groups to develop new methods at a rapid rate. A thorough understanding of the models and algorithms used by inference software is a critical prerequisite for successful hypothesis formulation and assessment. In particular, there is a need for more readily available resources aimed at helping interested scientists equip themselves with the skills to confidently use cutting-edge phylogenetic analysis software. These resources will also benefit researchers who do not have access to similar courses or training at their home institutions. Here, we introduce the “Taming the Beast” (https://taming-the-beast.github.io/) resource, which was developed as part of a workshop series bearing the same name, to facilitate the usage of the Bayesian phylogenetic software package BEAST 2.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


@attributes
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
RANK2.6497521
LOCALfalse
PrimoNMBib
record
control
sourceidjstor_pubme
recordidTN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5925777
sourceformatXML
sourcesystemPC
jstor_id26581925
oup_id10.1093/sysbio/syx060
sourcerecordid26581925
originalsourceidFETCH-LOGICAL-1479t-33d06e5bac40330f040cf60011dcc342705e2485c9f54180e88d59a425a304ad3
addsrcrecordideNqFkUtr3DAUhUVpyatdZpliyCYbN3pL3hQmw_QBKYF2Ct0JjSxnNNjWRJJLZ9cf0V_YX1IZT9M0ULq6F-6nwzk6AJwi-ArBilzGXVw5n8c3yOETcISg4KUk_MvTceekZIiJQ3Ac4wZChDhDB-AQSy4IpPIILJa6c_1tkda2uFrMPi1_fv8xK-a-64bepV2xtNqsR-CDTjY43RYfbfRDMLZofJieFPg5eNboNtoX-3kCPr9ZLOfvyuubt-_ns-sSUVGlkpAacstW2lBICGwghabho63aGEKxgMxiKpmpGkaRhFbKmlWaYqazW12TE_B60t0Oq87WxvYp6FZtg-t02Cmvnfr70ru1uvVfFaswE0JkgYu9QPB3g41JdS4a27a6t36IClWISYmRpBk9f4Rucu4-x8tUhTHHVOBMlRNlgo8x2ObeDIJqLEhNBampoMy_fJjgnv7dSAbII0Hjkk7Oj4Fc-0_ZfS4_bP_r4GxCNzH58McAZxLlXyK_AEjVtvk
sourcetypeOpen Access Repository
isCDItrue
recordtypearticle
pqid1992262472
display
typearticle
titleTaming the BEAST—A Community Teaching Material Resource for BEAST 2
sourceAlma/SFX Local Collection
creatorBarido-Sottani, Joëlle ; Bošková, Veronika ; Plessis, Louis Du ; Kühnert, Denise ; Magnus, Carsten ; Mitov, Venelin ; Müller, Nicola F ; PečErska, Jūlija ; Rasmussen, David A ; Zhang, Chi ; Drummond, Alexei J ; Heath, Tracy A ; Pybus, Oliver G ; Vaughan, Timothy G ; Stadler, Tanja
creatorcontribBarido-Sottani, Joëlle ; Bošková, Veronika ; Plessis, Louis Du ; Kühnert, Denise ; Magnus, Carsten ; Mitov, Venelin ; Müller, Nicola F ; PečErska, Jūlija ; Rasmussen, David A ; Zhang, Chi ; Drummond, Alexei J ; Heath, Tracy A ; Pybus, Oliver G ; Vaughan, Timothy G ; Stadler, Tanja
descriptionPhylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a black-box method is not sufficient anymore. Instead, biologists are required to be actively involved with modeling decisions during data analysis. The modular design of the Bayesian phylogenetic software package BEAST 2 enables, and in fact enforces, this involvement. At the same time, the modular design enables computational biology groups to develop new methods at a rapid rate. A thorough understanding of the models and algorithms used by inference software is a critical prerequisite for successful hypothesis formulation and assessment. In particular, there is a need for more readily available resources aimed at helping interested scientists equip themselves with the skills to confidently use cutting-edge phylogenetic analysis software. These resources will also benefit researchers who do not have access to similar courses or training at their home institutions. Here, we introduce the “Taming the Beast” (https://taming-the-beast.github.io/) resource, which was developed as part of a workshop series bearing the same name, to facilitate the usage of the Bayesian phylogenetic software package BEAST 2.
identifier
0ISSN: 1063-5157
1EISSN: 1076-836X
2DOI: 10.1093/sysbio/syx060
3PMID: 28673048
languageeng
publisherEngland: Oxford University Press
subjectAlgorithms ; Bayesian analysis ; Bayesian inference ; Biodiversity ; Computer applications ; Computer programs ; Data processing ; Developmental biology ; Epidemiology ; Evolutionary biology ; Mathematical models ; MCMC ; phylodynamics ; Phylogenetics ; Phylogeny ; Software ; Software for Systematics and Evolution
ispartofSystematic biology, 2018-01-01, Vol.67 (1), p.170-174
rights
0The Author(s) 2017
1The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. 2017
2The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
3Copyright Oxford University Press, UK Jan 2018
lds50peer_reviewed
oafree_for_read
citedbyFETCH-LOGICAL-1479t-33d06e5bac40330f040cf60011dcc342705e2485c9f54180e88d59a425a304ad3
citesFETCH-LOGICAL-1479t-33d06e5bac40330f040cf60011dcc342705e2485c9f54180e88d59a425a304ad3
links
openurl$$Topenurl_article
openurlfulltext$$Topenurlfull_article
thumbnail$$Usyndetics_thumb_exl
backlink$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28673048$$D View this record in MEDLINE/PubMed
search
creatorcontrib
0Barido-Sottani, Joëlle
1Bošková, Veronika
2Plessis, Louis Du
3Kühnert, Denise
4Magnus, Carsten
5Mitov, Venelin
6Müller, Nicola F
7PečErska, Jūlija
8Rasmussen, David A
9Zhang, Chi
10Drummond, Alexei J
11Heath, Tracy A
12Pybus, Oliver G
13Vaughan, Timothy G
14Stadler, Tanja
title
0Taming the BEAST—A Community Teaching Material Resource for BEAST 2
1Systematic biology
addtitleSyst Biol
descriptionPhylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a black-box method is not sufficient anymore. Instead, biologists are required to be actively involved with modeling decisions during data analysis. The modular design of the Bayesian phylogenetic software package BEAST 2 enables, and in fact enforces, this involvement. At the same time, the modular design enables computational biology groups to develop new methods at a rapid rate. A thorough understanding of the models and algorithms used by inference software is a critical prerequisite for successful hypothesis formulation and assessment. In particular, there is a need for more readily available resources aimed at helping interested scientists equip themselves with the skills to confidently use cutting-edge phylogenetic analysis software. These resources will also benefit researchers who do not have access to similar courses or training at their home institutions. Here, we introduce the “Taming the Beast” (https://taming-the-beast.github.io/) resource, which was developed as part of a workshop series bearing the same name, to facilitate the usage of the Bayesian phylogenetic software package BEAST 2.
subject
0Algorithms
1Bayesian analysis
2Bayesian inference
3Biodiversity
4Computer applications
5Computer programs
6Data processing
7Developmental biology
8Epidemiology
9Evolutionary biology
10Mathematical models
11MCMC
12phylodynamics
13Phylogenetics
14Phylogeny
15Software
16Software for Systematics and Evolution
issn
01063-5157
11076-836X
fulltexttrue
rsrctypearticle
creationdate2018
recordtypearticle
recordideNqFkUtr3DAUhUVpyatdZpliyCYbN3pL3hQmw_QBKYF2Ct0JjSxnNNjWRJJLZ9cf0V_YX1IZT9M0ULq6F-6nwzk6AJwi-ArBilzGXVw5n8c3yOETcISg4KUk_MvTceekZIiJQ3Ac4wZChDhDB-AQSy4IpPIILJa6c_1tkda2uFrMPi1_fv8xK-a-64bepV2xtNqsR-CDTjY43RYfbfRDMLZofJieFPg5eNboNtoX-3kCPr9ZLOfvyuubt-_ns-sSUVGlkpAacstW2lBICGwghabho63aGEKxgMxiKpmpGkaRhFbKmlWaYqazW12TE_B60t0Oq87WxvYp6FZtg-t02Cmvnfr70ru1uvVfFaswE0JkgYu9QPB3g41JdS4a27a6t36IClWISYmRpBk9f4Rucu4-x8tUhTHHVOBMlRNlgo8x2ObeDIJqLEhNBampoMy_fJjgnv7dSAbII0Hjkk7Oj4Fc-0_ZfS4_bP_r4GxCNzH58McAZxLlXyK_AEjVtvk
startdate20180101
enddate20180101
creator
0Barido-Sottani, Joëlle
1Bošková, Veronika
2Plessis, Louis Du
3Kühnert, Denise
4Magnus, Carsten
5Mitov, Venelin
6Müller, Nicola F
7PečErska, Jūlija
8Rasmussen, David A
9Zhang, Chi
10Drummond, Alexei J
11Heath, Tracy A
12Pybus, Oliver G
13Vaughan, Timothy G
14Stadler, Tanja
generalOxford University Press
scope
0TOX
1NPM
2AAYXX
3CITATION
4K9.
57X8
65PM
sort
creationdate20180101
titleTaming the BEAST—A Community Teaching Material Resource for BEAST 2
authorBarido-Sottani, Joëlle ; Bošková, Veronika ; Plessis, Louis Du ; Kühnert, Denise ; Magnus, Carsten ; Mitov, Venelin ; Müller, Nicola F ; PečErska, Jūlija ; Rasmussen, David A ; Zhang, Chi ; Drummond, Alexei J ; Heath, Tracy A ; Pybus, Oliver G ; Vaughan, Timothy G ; Stadler, Tanja
facets
frbrtype5
frbrgroupidcdi_FETCH-LOGICAL-1479t-33d06e5bac40330f040cf60011dcc342705e2485c9f54180e88d59a425a304ad3
rsrctypearticles
prefilterarticles
languageeng
creationdate2018
topic
0Algorithms
1Bayesian analysis
2Bayesian inference
3Biodiversity
4Computer applications
5Computer programs
6Data processing
7Developmental biology
8Epidemiology
9Evolutionary biology
10Mathematical models
11MCMC
12phylodynamics
13Phylogenetics
14Phylogeny
15Software
16Software for Systematics and Evolution
toplevel
0peer_reviewed
1online_resources
creatorcontrib
0Barido-Sottani, Joëlle
1Bošková, Veronika
2Plessis, Louis Du
3Kühnert, Denise
4Magnus, Carsten
5Mitov, Venelin
6Müller, Nicola F
7PečErska, Jūlija
8Rasmussen, David A
9Zhang, Chi
10Drummond, Alexei J
11Heath, Tracy A
12Pybus, Oliver G
13Vaughan, Timothy G
14Stadler, Tanja
collection
0Oxford Journals Open Access Collection
1PubMed
2CrossRef
3ProQuest Health & Medical Complete (Alumni)
4MEDLINE - Academic
5PubMed Central (Full Participant titles)
jtitleSystematic biology
delivery
delcategoryRemote Search Resource
fulltextfulltext
addata
au
0Barido-Sottani, Joëlle
1Bošková, Veronika
2Plessis, Louis Du
3Kühnert, Denise
4Magnus, Carsten
5Mitov, Venelin
6Müller, Nicola F
7PečErska, Jūlija
8Rasmussen, David A
9Zhang, Chi
10Drummond, Alexei J
11Heath, Tracy A
12Pybus, Oliver G
13Vaughan, Timothy G
14Stadler, Tanja
formatjournal
genrearticle
ristypeJOUR
atitleTaming the BEAST—A Community Teaching Material Resource for BEAST 2
jtitleSystematic biology
addtitleSyst Biol
date2018-01-01
risdate2018
volume67
issue1
spage170
epage174
pages170-174
issn1063-5157
eissn1076-836X
notes
0These authors contributed equally.
1Associate Editor: David Bryant
2Senior author.
abstractPhylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a black-box method is not sufficient anymore. Instead, biologists are required to be actively involved with modeling decisions during data analysis. The modular design of the Bayesian phylogenetic software package BEAST 2 enables, and in fact enforces, this involvement. At the same time, the modular design enables computational biology groups to develop new methods at a rapid rate. A thorough understanding of the models and algorithms used by inference software is a critical prerequisite for successful hypothesis formulation and assessment. In particular, there is a need for more readily available resources aimed at helping interested scientists equip themselves with the skills to confidently use cutting-edge phylogenetic analysis software. These resources will also benefit researchers who do not have access to similar courses or training at their home institutions. Here, we introduce the “Taming the Beast” (https://taming-the-beast.github.io/) resource, which was developed as part of a workshop series bearing the same name, to facilitate the usage of the Bayesian phylogenetic software package BEAST 2.
copEngland
pubOxford University Press
pmid28673048
doi10.1093/sysbio/syx060
oafree_for_read