Difference between revisions of "Schedule"

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===[[How to prepare for the Workshop on Molecular Evolution]]===
 
===[[How to prepare for the Workshop on Molecular Evolution]]===
 
===Please download and install the software listed here: [https://molevol.mbl.edu/index.php/Computer_lab_introduction#Downloads Downloads]===
 
===Please download and install the software listed here: [https://molevol.mbl.edu/index.php/Computer_lab_introduction#Downloads Downloads]===
===Make T shirt suggestions [[Shirts2017]] !===
 
  
Shirts from previous years [https://molevol.mbl.edu/index.php/Previous_MBL_Molecular_Evolution_Workshop_T-Shirts here]!
+
===<span style="color:red;">***BELOW IS THE 2017 SCHEDULE; IT WILL BE UPDATED SOON***===
  
===All morning sessions are in [[:file:rowe.jpg|Rowe]], afternoons and evenings will be in room G70 of the [[:file:Loeb.jpeg|Leob building]] ===
+
===Opening Activities: 7 PM Thursday, July 20th, Computer orientation lab & Opening Reception===
 
 
===Opening Activities: 7 PM Sunday, July 20th, <span style="color:#ff0000"> LOCATION CHANGES ===
 
 
 
===Computer orientation lab:===
 
Day: <span style="color:#ff0000">Thursday evening<br/></span>
 
Time: <span style="color:#ff0000">7:00-8:00 PM<br/></span>
 
Location: <span style="color:#ff0000">G70 (downstairs) in the Loeb building</span> (ask about this location when you check in)<br/>
 
Bring your laptop with you to the lab, and try to arrive between 6:45-7:00.  We plan to get started at 7:00pm sharp.<br/>
 
 
 
===Opening Reception:===
 
Day: <span style="color:#ff0000">Thursday evening<br/></span>
 
Time: <span style="color:#ff0000">8:00-10:00 PM<br/></span>
 
Location:  <span style="color:#ff0000">The outdoor terrace of the Swope Building</span> (this is a new location)<br/>
 
Bring an appetite, as this will be your dinner!  There will be plenty of food, drink and fresh air, with great views of Woods Hole and Eel Pond.  <br/>
 
  
 +
===All morning sessions are in [[:file:rowe.jpg|Rowe]], afternoons and evenings will be in room G70 of the [[:file:Loeb.jpeg|Loeb building]] ===
  
 +
===Group photo: Tuesday July 25 at 10:30 outside of Rowe building===
  
 
== First Week ==
 
== First Week ==
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| align="center" width="14.3%" style="background:#DCDCDC" |
 
| align="center" width="14.3%" style="background:#DCDCDC" |
 
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''                <br/>(Phylogenomics & methods)
 
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''                <br/>(Phylogenomics & methods)
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''        <br/>(Model selection)
+
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''        <br/>([http://phylosolutions.com/paup-tutorial/ Model selection])
 
| align="center" width="14.3%" | '''[[John Huelsenbeck|Huelsenbeck]]'''  <br/>(Simulation lab++)
 
| align="center" width="14.3%" | '''[[John Huelsenbeck|Huelsenbeck]]'''  <br/>(Simulation lab++)
 
|-
 
|-
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| align="center" width="14.3%" style="background:#DCDCDC" |
 
| align="center" width="14.3%" style="background:#DCDCDC" |
 
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''                <br/>(Phylogenomics & methods)
 
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''                <br/>(Phylogenomics & methods)
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''        <br/>(PAUP)
+
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''        <br/>([http://paup.phylosolutions.com/ PAUP])
 
| align="center" width="14.3%" | '''[[John Huelsenbeck|Huelsenbeck]]'''  <br/>(Why I like ML & Bayes)  
 
| align="center" width="14.3%" | '''[[John Huelsenbeck|Huelsenbeck]]'''  <br/>(Why I like ML & Bayes)  
 
|-
 
|-
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| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''        <br/>(Sequence homology)
 
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''        <br/>(Sequence homology)
 
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''              <br/>(Branch support & tree tests)
 
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''              <br/>(Branch support & tree tests)
| align="center" width="14.3%" | '''[[Emily Jane McTavish|McTavish]]'''  <br/>(Large scale phylogenetics)
+
| align="center" width="14.3%" | '''[[Emily Jane McTavish|McTavish]]'''  <br/>([https://molevol.mbl.edu/images/d/d5/ML_search.pdf Maximum likelihood tree searching])
 
|-
 
|-
 
| align="center" width="14.3%" height="30" style="background:#c8ccd1"  | '''20:30-22:00'''
 
| align="center" width="14.3%" height="30" style="background:#c8ccd1"  | '''20:30-22:00'''
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| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''        <br/>(FASTA/BLAST lab)
 
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''        <br/>(FASTA/BLAST lab)
 
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''              <br/>(Branch support & tree tests)
 
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''              <br/>(Branch support & tree tests)
| align="center" width="14.3%" | '''[[Emily Jane McTavish|McTavish]]'''  <br/>(GARLI & RaxML)
+
| align="center" width="14.3%" | '''[[Emily Jane McTavish|McTavish]]'''  <br/>([https://mctavishlab.github.io/MLsearchLab Maximum Likelihood Search])
 
|-
 
|-
 
|}
 
|}
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| align="center" width="5%" style="background:#DCDCDC"|  
 
| align="center" width="5%" style="background:#DCDCDC"|  
 
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]'''    <br/>([https://peterbeerli.com/workshops/mbl/2016/talk1.pdf Introduction to the Coalescence])<br/>   
 
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]'''    <br/>([https://peterbeerli.com/workshops/mbl/2016/talk1.pdf Introduction to the Coalescence])<br/>   
| align="center" width="13.5%" | '''[[David Weisrock|Weisrock]]'''      <br/>(species delimitation and lineage sorting)
+
| align="center" width="13.5%" | '''[[David Weisrock|Weisrock]]'''      <br/>([[:file:Weisrock_WH_species_delimitation.pdf |species delimitation and lineage sorting]])
 
| align="center" width="13.5%" | '''[[Scott Edwards|Edwards]]'''  <br/>(Multilocus phylogeography and phylogenetics)
 
| align="center" width="13.5%" | '''[[Scott Edwards|Edwards]]'''  <br/>(Multilocus phylogeography and phylogenetics)
 
| align="center" width="13.5%" | '''[[Conor Meehan|Meehan]]'''    <br/>(Phylodynamics: the use of phylogeny in epidemiology)
 
| align="center" width="13.5%" | '''[[Conor Meehan|Meehan]]'''    <br/>(Phylodynamics: the use of phylogeny in epidemiology)
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|-
 
|-
 
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''14:00-15:30'''
 
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''14:00-15:30'''
| align="center" width="13.5%" | '''[[Belinda Chang|Chang]]'''<br/>(Adaptive molecular evolution)
+
| align="center" width="13.5%" | '''[[Belinda Chang|Chang]]'''<br/>([https://molevol.mbl.edu/images/3/33/Protein_Evolution_%26_Ancestral_Reconstruction.pdf Protein evolution & ancestral reconstruction])
| align="center" width="13.5%" | '''[[Tracy Heath|Heath]]'''<br/>([http://revbayes.com RevBayes])
+
| align="center" width="13.5%" | '''[[Tracy Heath|Heath]]'''<br/>([https://molevol.mbl.edu/index.php/Total-evidence_analysis_in_RevBayes RevBayes])
 
| align="center" width="5%" style="background:#DCDCDC" |  
 
| align="center" width="5%" style="background:#DCDCDC" |  
 
| align="center" width="13.5%" | '''[[Laura Kubatko|Kubatko]]'''/'''[[David Swofford|Swofford]]''' <br/>(Species Tree Lab I)<br/>
 
| align="center" width="13.5%" | '''[[Laura Kubatko|Kubatko]]'''/'''[[David Swofford|Swofford]]''' <br/>(Species Tree Lab I)<br/>
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|-
 
|-
 
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''15:30-17:00'''
 
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''15:30-17:00'''
| align="center" width="13.5%" | '''[[Belinda Chang|Chang]]'''<br/>(Adaptive molecular evolution)
+
| align="center" width="13.5%" | '''[[Belinda Chang|Chang]]'''<br/>([https://molevol.mbl.edu/images/a/a3/Adaptive_Protein_Evolution.pdf Adaptive protein evolution])
| align="center" width="13.5%" | '''[[Tracy Heath|Heath]]'''<br/>([http://revbayes.com RevBayes])
+
| align="center" width="13.5%" | '''[[Tracy Heath|Heath]]'''<br/>([https://molevol.mbl.edu/index.php/Total-evidence_analysis_in_RevBayes RevBayes])
 
| align="center" width="5%" style="background:#DCDCDC" |  
 
| align="center" width="5%" style="background:#DCDCDC" |  
 
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]'''<br/>([https://peterbeerli.com/workshops/mbl/2016/talk2.pdf Extensions to coalescence])
 
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]'''<br/>([https://peterbeerli.com/workshops/mbl/2016/talk2.pdf Extensions to coalescence])
| align="center" width="13.5%" | '''[[David Weisrock|Weisrock]]''' <br/>(Intro to RADseq)
+
| align="center" width="13.5%" | '''[[David Weisrock|Weisrock]]''' <br/>([[:file:Weisrock_WH_RADseq.pdf |Intro to RADseq]])
| align="center" width="13.5%" |  '''Workshop team'''<br/>(Species Tree Lab III: *BEAST)<br/>
+
| align="center" width="13.5%" |  '''[[Conor Meehan|Meehan]]'''<br/>(Species Tree Lab III: *BEAST2)<br/>
 
| align="center" width="13.5%" |  '''Open lab'''
 
| align="center" width="13.5%" |  '''Open lab'''
 
|-
 
|-
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| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''19:00-20:30'''
 
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''19:00-20:30'''
 
| align="center" width="13.5%" | '''Open lab'''
 
| align="center" width="13.5%" | '''Open lab'''
| align="center" width="13.5%" style="background:#F2E0CE" | '''Course dinner party'''<br/>Lobster Boil, MBL Club<br/>Starts at 5pm
+
| align="center" width="13.5%" style="background:#F2E0CE" | '''Course dinner party'''<br/>Lobster Boil, Terrace<br/>Starts at 6pm
 
| align="center" width="5%" style="background:#DCDCDC" |  
 
| align="center" width="5%" style="background:#DCDCDC" |  
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]''' <br/>( [http://peterbeerli.com/workshops/mbl/2016/tutorial migrate tutorial])<br/>
+
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]''' <br/>( [http://peterbeerli.com/workshops/mbl/2017/tutorial/ migrate tutorial])<br/>
 
| align="center" width="13.5%" | '''[[Deren Eaton|Eaton]]''' <br/>(pyrad and RADseq analysis)
 
| align="center" width="13.5%" | '''[[Deren Eaton|Eaton]]''' <br/>(pyrad and RADseq analysis)
 
| align="center" width="13.5%" | '''[[Lacey Knowles|Knowles]]''' <br/>(Evolutionary applications of genomic data)
 
| align="center" width="13.5%" | '''[[Lacey Knowles|Knowles]]''' <br/>(Evolutionary applications of genomic data)
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| align="center" width="13.5%" style="background:#F2E0CE" |  '''Course dinner party'''
 
| align="center" width="13.5%" style="background:#F2E0CE" |  '''Course dinner party'''
 
| align="center" width="5%" style="background:#DCDCDC"|   
 
| align="center" width="5%" style="background:#DCDCDC"|   
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]''' <br/>( [http://peterbeerli.com/workshops/mbl/2016/tutorial migrate tutorial])<br/>
+
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]''' <br/>( [http://peterbeerli.com/workshops/mbl/2017/tutorial/ migrate tutorial])<br/>
 
| align="center" width="13.5%" | '''[[Deren Eaton|Eaton]]''' <br/>(pyrad and RADseq analysis)   
 
| align="center" width="13.5%" | '''[[Deren Eaton|Eaton]]''' <br/>(pyrad and RADseq analysis)   
 
| align="center" width="13.5%" | '''[[Lacey Knowles|Knowles]]''' <br/>(Evolutionary applications of genomic data)
 
| align="center" width="13.5%" | '''[[Lacey Knowles|Knowles]]''' <br/>(Evolutionary applications of genomic data)

Revision as of 10:06, 21 November 2017

How to prepare for the Workshop on Molecular Evolution

Please download and install the software listed here: Downloads

***BELOW IS THE 2017 SCHEDULE; IT WILL BE UPDATED SOON***

Opening Activities: 7 PM Thursday, July 20th, Computer orientation lab & Opening Reception

All morning sessions are in Rowe, afternoons and evenings will be in room G70 of the Loeb building

Group photo: Tuesday July 25 at 10:30 outside of Rowe building

First Week

Thursday
(20 July)
Friday
(21 July)
Saturday
(22 July)
Sunday
(23 July)
09:00-10:30 Yoder
(Welcome, Introduction &
1 min Student Presentations)
Lewis
(ML phylogenetics)
Lewis
(Bayesian phylogenetics)
10:30-12:00 Hillis
(Power, efficiency, consistency)
Lewis
(ML phylogenetics)
Lewis
(Bayesian phylogenetics)
12:00-14:00 Lunch break
14:00-15:30 Dunn
(Phylogenomics & methods)
Swofford
(Model selection)
Huelsenbeck
(Simulation lab++)
15:30-17:00 Dunn
(Phylogenomics & methods)
Swofford
(PAUP)
Huelsenbeck
(Why I like ML & Bayes)
17:00-19:00 Dinner break
19:00-20:30 Computer lab, room G70 Loeb (basement) Pearson
(Sequence homology)
Holder
(Branch support & tree tests)
McTavish
(Maximum likelihood tree searching)
20:30-22:00 Opening reception
Swope Terrace
Pearson
(FASTA/BLAST lab)
Holder
(Branch support & tree tests)
McTavish
(Maximum Likelihood Search)


Second Week

Monday
(24 July)
Tuesday
(25 July)
Wednesday
(26 July)
Thursday
(27 July)
Friday
(28 July)
Saturday
(29 July)
Sunday
(30 July)
09:00-10:30 Bielawski
(Codon models, Parts1and2)
Heath
(Integrative Bayesian Analyses)
Beerli
(Introduction to the Coalescence)
Weisrock
(species delimitation and lineage sorting)
Edwards
(Multilocus phylogeography and phylogenetics)
Meehan
(Phylodynamics: the use of phylogeny in epidemiology)
10:30-12:00 Bielawski
(Codon models, Part3)

(Part4)

Heath
(Divergence-time estimation and Biogeography])
Kubatko
(Species Tree Estimation)
dos Reis
(Bayesian species delimitation)
Edwards
(Multilocus phylogeography and phylogenetics)
Meehan
(Participant discussions)
12:00-14:00 Lunch break
14:00-15:30 Chang
(Protein evolution & ancestral reconstruction)
Heath
(RevBayes)
Kubatko/Swofford
(Species Tree Lab I)
dos Reis
(BPP Tutorial)
Edwards
(Species Tree Lab II)
Open lab
15:30-17:00 Chang
(Adaptive protein evolution)
Heath
(RevBayes)
Beerli
(Extensions to coalescence)
Weisrock
(Intro to RADseq)
Meehan
(Species Tree Lab III: *BEAST2)
Open lab
17:00-19:00 Dinner break
19:00-20:30 Open lab Course dinner party
Lobster Boil, Terrace
Starts at 6pm
Beerli
( migrate tutorial)
Eaton
(pyrad and RADseq analysis)
Knowles
(Evolutionary applications of genomic data)
20:30-22:00 Open lab Course dinner party Beerli
( migrate tutorial)
Eaton
(pyrad and RADseq analysis)
Knowles
(Evolutionary applications of genomic data)