Difference between revisions of "Conor Meehan"

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(Lecture and Lab files)
(Other lectures/labs)
 
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====Contacting me====
 
====Contacting me====
 
Email: cmeehan@itg.be<br>
 
Email: cmeehan@itg.be<br>
 +
Twitter: @con_meehan
  
 
I will be at the course for the entire time
 
I will be at the course for the entire time
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==Lecture and Lab files==
 
==Lecture and Lab files==
My lectures given at MolEvol 2017:<br />
+
===Phylodynamics lecture===
Phylodynamics
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[[:Media:MolEvol_Phylodynamics_2017.pdf |Phylodynamics]]
  
 +
===*BEAST tutorial===
 
The *BEAST tutorial is part of the Taming the BEAST workshop tutorials set.<br>
 
The *BEAST tutorial is part of the Taming the BEAST workshop tutorials set.<br>
 
The whole set of tutorials can be found (and followed for free) at [https://taming-the-beast.github.io/tutorials/ https://taming-the-beast.github.io/tutorials/]<br>
 
The whole set of tutorials can be found (and followed for free) at [https://taming-the-beast.github.io/tutorials/ https://taming-the-beast.github.io/tutorials/]<br>
 
We will specifically use the [https://taming-the-beast.github.io/tutorials/StarBeast-Tutorial/ *BEAST2 tutorial].
 
We will specifically use the [https://taming-the-beast.github.io/tutorials/StarBeast-Tutorial/ *BEAST2 tutorial].
  
Some past work:
+
Can download BEAST2 from [http://www.BEAST2.org BEAST2.org]
 +
 
 +
If you want to run the lab on the cluster, you can create input in BEAUti on your computer and then upload to class server or copy premade xml file by
 +
<pre>
 +
cp /class/molevol-shared/StarBeast-Tutorial/xml/gopher.xml .
 +
</pre>
 +
(Do not mv, only cp)
 +
 
 +
You can then run BEAST2 with
 +
<pre>
 +
beast gopher.xml
 +
</pre>
 +
 
 +
 
 +
If everything goes wrong, you can get all the input and output files by using
 +
<pre>
 +
cp -r /class/molevol-shared/StarBeast-Tutorial/ .
 +
</pre>
 +
(Do not mv, only cp)
 +
 
 +
Another note: BEAST2 comes with a faster, more robust version of *BEAST called *BEAST2. You can get this in BEAUti through the 'manage packages' menu under 'file'
 +
 
 +
===Other lectures/labs/links===
 +
Some past or good lectures/labs:
 
A tutorial I wrote for the Molecular Evolution course in Cesky Krumlov on BLAST+ can be found  
 
A tutorial I wrote for the Molecular Evolution course in Cesky Krumlov on BLAST+ can be found  
 
[http://evomics.org/learning/bioinformatics/blast-laboratory/ here]
 
[http://evomics.org/learning/bioinformatics/blast-laboratory/ here]
  
A brief overview presentation on short read alignment can be viewed [[Media:SRA.pdf|here]]
+
A brief overview presentation on short read alignment can be viewed [[Media:SRA.pdf|here]]<br>
 +
An alignment lecture can be found [[File:MSA.pdf|here]] and a lab from Mark can be found [[Alignment_tutorial|here]]
 +
 
 +
For extra checking of Bayesian logs you can use [http://king2.scs.fsu.edu/CEBProjects/awty/awty_start.php AWTY] or [https://github.com/danlwarren/RWTY RWTY]
  
 
===Other interests===
 
===Other interests===
 
Besting [[Emily_Jane_McTavish]] at leg wrestling at MolEvol11
 
Besting [[Emily_Jane_McTavish]] at leg wrestling at MolEvol11
 
[[File:ConorBestsEmily.jpg|500px|left]]
 
[[File:ConorBestsEmily.jpg|500px|left]]

Latest revision as of 20:25, 29 July 2017

Conor Meehan.jpg

Conor Meehan

Research fellow at the Institute of Tropical Medicine working on Mycobacteria, primarily epidemiology and drug resistance.

Time at course

I will be here from July 20th until July 30th (the entire course).

Contacting me

Email: cmeehan@itg.be
Twitter: @con_meehan

I will be at the course for the entire time

Current projects

  • Transmission of M. tuberculosis and M. ulcerans in highly endemic areas
  • Epidemiological cut-offs for exploring transmission clusters
  • Phylodynamic modelling of bacteria
  • Evolution and transmission of drug resistance

Other work-related interests

  • Species concepts in prokaryotes and units of diversity
  • Protein structure variation and effect on function
  • HIV coreceptor usage and envelope structure
  • Microbial community interactions and lateral gene transfer

My Lab's Web Page

Lecture and Lab files

Phylodynamics lecture

Phylodynamics

*BEAST tutorial

The *BEAST tutorial is part of the Taming the BEAST workshop tutorials set.
The whole set of tutorials can be found (and followed for free) at https://taming-the-beast.github.io/tutorials/
We will specifically use the *BEAST2 tutorial.

Can download BEAST2 from BEAST2.org

If you want to run the lab on the cluster, you can create input in BEAUti on your computer and then upload to class server or copy premade xml file by

cp /class/molevol-shared/StarBeast-Tutorial/xml/gopher.xml .

(Do not mv, only cp)

You can then run BEAST2 with

beast gopher.xml


If everything goes wrong, you can get all the input and output files by using

cp -r /class/molevol-shared/StarBeast-Tutorial/ .

(Do not mv, only cp)

Another note: BEAST2 comes with a faster, more robust version of *BEAST called *BEAST2. You can get this in BEAUti through the 'manage packages' menu under 'file'

Other lectures/labs/links

Some past or good lectures/labs: A tutorial I wrote for the Molecular Evolution course in Cesky Krumlov on BLAST+ can be found here

A brief overview presentation on short read alignment can be viewed here
An alignment lecture can be found File:MSA.pdf and a lab from Mark can be found here

For extra checking of Bayesian logs you can use AWTY or RWTY

Other interests

Besting Emily_Jane_McTavish at leg wrestling at MolEvol11

ConorBestsEmily.jpg