[MORPHMET] Geometric Morphometrics course in Berlin (5-9 March 2018) with Dr. Carmelo Fruciano

[Carlo Pecoraro]

Dear all,

we will run a course on "Geometric Morphometrics" next March (5-9.03.18) with 
our instructor Dr. Carmelo Fruciano (Queensland University of Technology 
(Brisbane, Australia)).


Overview

Geometric morphometrics has become a standard in biological research because it 
combines statistical rigour and ease of interpretation. Through geometric 
morphometrics, biological form is quantified, analysed and the results are 
expressed as easily interpretable and visually impactful shape changes. This 
course covers the main common practices of modern geometric morphometrics, 
including: acquiring data, analysing it, visualizing and interpreting the 
results.


Workshop Format

The course will be delivered over five days and will comprise both lectures and 
hands-on sessions. The lectures will cover both basic theoretical aspects and 
their practical implementation in research practice and software. During the 
hands-on sessions, the attendees will have the chance of both using example 
datasets and applying the knowledge acquired to their own data. The course will 
be focused mainly on 2D data and on easy-to-use software with graphical user 
interface to maximize the ability to understand concepts and apply them. 
However, some information on 3D data and on R implementations will be provided, 
as appropriate.  


Who Should Attend

This course is aimed at beginners and intermediate users. In other words, it is 
aimed at researchers who intend to use geometric morphometrics or who have 
started performing geometric morphometric analyses but feel they need a more 
structured background.


Session content

Monday 5th – Classes from 09:30 to 17:30 

 

Geometric morphometrics: overview and potential applications:

Traditional and geometric morphometrics
An overview of common analyses
Examples of geometric morphometrics applied to biological problems

 

>From biological objects to numerical representation:

Overview of typical devices used to digitalise biological objects 
Landmarks, semilandmarks, outlines and surfaces - different types of geometric 
morphometric data
Most commonly used geometric morphometric software
Data quality, most common pitfalls in study design and data acquisition

 

 Tuesday 6th – Classes from 09:30 to 17:30

Generalized Procrustes analysis (GPA) – the core of most geometric 
morphometrics:


Principal component analysis (PCA)

 
Comparing groups:

Between-group PCA
Canonical variate analysis (CVA)
Tests of difference in means

 

Wednesday 7th – Classes from 09:30 to 17:30

Co-variation between size and shape:

Allometry, regression and general linear models

 
Co-variation between shapes:

Partial least squares analysis (PLS)
Modularity and integration

 

Thursday 8th – Classes from 09:30 to 17:30 

 
Combining analyses in a basic workflow:

Preliminary assessment of data quality
Typical basic workflow

Expanding the basic workflow: variation in geographic space

Expanding the basic workflow: association between shape and environmental 
variables

 

Friday 9th – Classes from 09:30 to 17:30

 
Expanding the basic workflow: elements of phylogenetic comparative analyses

 Review and open discussion

 Presentation of attendees’ analyses on their own data 



Please visit our website to register: 
https://www.physalia-courses.org/courses-workshops/course22/

Best regards,

Carlo Pecoraro, Ph.D

Physalia-courses DIRECTOR

i...@physalia-courses.org

http://www.physalia-courses.org/

Twitter: @physacourses

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[MORPHMET] Course: Geometric Morphometrics. 5-9 March 2018 Berlin (Germany)

[Carlo Pecoraro]

Dear all,

I am delighted to inform you that we will run the first edition of our course 
"Geometric Morphometrics" next March (5-9.03.2018) in Berlin!!

OVERVIEW
Geometric morphometrics has become a standard in biological research because it 
combines statistical rigour and ease of interpretation. Through geometric 
morphometrics, biological form is quantified, analysed and the results are 
expressed as easily interpretable and visually impactful shape changes. This 
course covers the main common practices of modern geometric morphometrics, 
including: acquiring data, analysing it, visualizing and interpreting the 
results.

FORMAT
The course will be delivered over five days and will comprise both lectures and 
hands-on sessions. The lectures will cover both basic theoretical aspects and 
their practical implementation in research practice and software. During the 
hands-on sessions, the attendees will have the chance of both using example 
datasets and applying the knowledge acquired to their own data. The course will 
be focused mainly on 2D data and on easy-to-use software with graphical user 
interface to maximize the ability to understand concepts and apply them. 
However, some information on 3D data and on R implementations will be provided, 
as appropriate.
 
TARGET AUDIENCE
This course is aimed at beginners and intermediate users. In other words, it is 
aimed at researchers who intend to use geometric morphometrics or who have 
started performing geometric morphometric analyses but feel they need a more 
structured background.

REQUIREMENTS
Attendees should have a background in biology and a basic understanding of 
statistical 

PROGRAM
5 March 2018

Geometric morphometrics: overview and potential applications:

-   Traditional and geometric morphometrics
-   An overview of common analyses
-   Examples of geometric morphometrics applied to biological problems


>From biological objects to numerical representation:

-   Overview of typical devices used to digitalise biological objects
-   Landmarks, semilandmarks, outlines and surfaces - different types of 
geometric morphometric data
-   Most commonly used geometric morphometric software
-   Data quality, most common pitfalls in study design and data acquisition


6 March 2018

Generalized Procrustes analysis (GPA) – the core of most geometric 
morphometrics:

Principal component analysis (PCA)

Comparing groups:
-   Between-group PCA
-   Canonical variate analysis (CVA)
-   Tests of difference in means



7 March 2018

Co-variation between size and shape:

-   Allometry, regression and general linear models

Co-variation between shapes:

-   Partial least squares analysis (PLS)
-   Modularity and integration

8 March 2018

Combining analyses in a basic workflow:

-   Preliminary assessment of data quality
-   Typical basic workflow

Expanding the basic workflow: variation in geographic space

Expanding the basic workflow: association between shape and environmental 
variables

9 March 2018

Expanding the basic workflow: elements of phylogenetic comparative analyses

Review and open discussion

Presentation of attendees’ analyses on their own data


Please visit our website to get more information about the course: 
https://www.physalia-courses.org/courses-workshops/course22/


Here is the full list of our courses and Workshops: 
https://www.physalia-courses.org/courses-workshops/

Many thanks for your kind attention.
Best regards,


Carlo Pecoraro, Ph.D

Physalia-courses DIRECTOR

i...@physalia-courses.org

http://www.physalia-courses.org/

Twitter: @physacourses

https://groups.google.com/forum/#!forum/physalia-courses

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[MORPHMET] Course: Exploratory multivariate analysis and visualization of genomic data. Berlin 19-23 March 2018

[Carlo Pecoraro]

Dear all,

we think that our new course on "Exploratory multivariate analysis and 
visualization of genomic data 
" may be of 
your interest.


Place: Berlin


Dates: 19-23 March 2018


*Instructors*: 

Dr. Sebastien Le (Agrocampus Ouest, FR)

Dr. Aubry Marc (University of Rennes1, FR)


*Overview*

This course is divided into two parts.


First, a detailed overview of the classical exploratory methods conceived 
for multivariate data: Principal Components Analysis, Correspondence 
Analysis, and Multiple Correspondence Analysis. From a unified theoretical 
framework, we will see how these methods are linked, as well as their 
specificities in terms of interpretation, due to the nature of the data 
they are dealing with. From a practical point of view, we will see how they 
can be applied to genomic data, and how they can be used to obtain 
meaningful information. We will see notably, how we can add supplementary 
information to get a better understanding of the data.


Second, an overview of methods that handle multivariate data, when 
variables are structured according to groups: generalised canonical 
analysis, and Multiple Factor Analysis. These methods are really useful 
when different points of view on the same set of individuals have to be 
compared. It is the case for instance, when one has at his disposal gene 
expressions on the one hand, and chemical measures on the other hand. 

The methods will be presented from a geometrical point of view. The 
concepts of quality of representation, active versus illustrative 
variables, automatic description of the dimensions provided by the analyses 
will be discussed.



*Format*

Each day will include an introductory lecture with class discussion of key 
concepts. The remainder of each day will consist of practical hands-on 
sessions. These sessions will involve a combination of both mirroring 
exercises with the instructor to demonstrate a skill as well as applying 
these skills on your own to complete individual exercises. After and during 
each exercise, interpretation of results will be discussed as a group. 
Computing will be done using a combination of tools installed on the 
attendees laptop computer and web resources accessed via web browser.
Who should attend

Researchers who would like to investigate multivariate and heterogenous 
data from an exploratory point of view. Researchers who would like to 
invest in methods capable of handling multi-block data, in the sense that 
data are structured into groups of variables.
WHERE

Botanisches Museum, Königin-Luise-Straße 6-8, Berlin


For the detailed program, please visit our website 



Here is the full list 
of our courses and Workshops

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[MORPHMET] Eukaryotic Metabarcoding Workshop in Berlin (February 26th-March 2nd, 2018)

[Carlo Pecoraro]

Dear all,

We are pleased to announce that the 2nd edition of Eukaryotic Metabarcoding 
Workshop will take place from February 26th-March 2nd, 2018 in Berlin 
(Germany): https://www.physalia-courses.org/courses-workshops/course4/


*Instructors*

Dr Owen S. Wangensteen (University of Salford, UK)

Dr Vasco Elbrecht (University of Guelph, Canada)


*Overview:*

Metabarcoding techniques are a set of novel genetic tools for qualitatively 
and quantitatively assessing biodiversity of natural communities. Their 
potential applications include (but are not limited to) accurate water 
quality, soil diversity assessment, trophic analyses of digestive contents, 
diagnosis of health status of fisheries, early detection of non-indigenous 
species, studies of global ecological patterns and biomonitoring of 
anthropogenic impacts. This workshop gives an overview of metabarcoding 
procedures with an emphasis on practical problem-solving and hands-on work 
using analysis pipelines on real datasets. After completing the workshop, 
students should be in a position to (1) understand the potential and 
capabilities of metabarcoding, (2) run complete analyses of metabarcoding 
pipelines and obtain diversity inventories and ecologically interpretable 
data from raw next-generation sequence data and (3) design their own 
metabarcoding projects, including bioinformatic data analysis and planning 
of laboratory work. All course materials (including copies of 
presentations, practical exercises, data files, and example scripts 
prepared by the instructing team) will be provided electronically to 
participants.


*Intended audience:*

This workshop is mainly aimed at researchers and technical workers with a 
background in ecology, biodiversity or community biology who want to use 
molecular tools for biodiversity research and at researchers in other areas 
of bioinformatics who want to learn ecological applications for 
biodiversity-assessment. In general, it is suitable for every researcher 
who wants to join the growing community of metabarcoders worldwide. This 
workshop will review mostly techniques and software useful for eukaryotic 
metabarcoding. Other workshops focused on procedures currently used in 
microbial metabarcoding will be available from Physalia-courses.


*Teaching format:*

The workshop is delivered over ten half-day sessions (see the detailed 
curriculum below). Each session consists of roughly a one hour lecture 
followed by two hours of practical exercises, with breaks at the 
organizer’s discretion.


*Assumed background:*

No programming or scripting experience is necessary, but some previous 
expertise using the Linux console and/or R will be most welcome. All 
examples will be run either in Linux or Mac environments, with some ssh 
connections to remote servers. For Windows users, a virtual box running 
Linux under Windows and/or the installation of an ssh client (e.g. PuTTY) 
will be needed. For MacOSX systems, installation of some additional Python 
packages might be needed for running the OBITools software suite. The 
syllabus has been planned for people which have some previous experience 
running simple commands from a terminal in Linux or Mac and using the R 
environment (preferently RStudio) for performing basic plots and 
statistical procedures. You will need to have a laptop with Python 2.7 
installed for running OBITools, but no experience with Python is necessary. 
If in doubt, take a look at the detailed session content below or send an 
email to us.


*Program:*

Monday 26th – Classes from 09:30 to 17:30

*Session 1*. Introduction to metabarcoding procedures. The metabarcoding 
pipeline.

In this session students will be introduced to the key concepts of 
metabarcoding and the different next-generation sequencing platforms 
currently available for implementing this technology. Some examples of 
results that can be obtained from metabarcoding projects are explained. We 
will outline the different steps of a typical metabarcoding pipeline and 
introduce some key concepts. We will also explain the format of the course. 
In this session, we will check that the computing infrastructure for the 
rest of the course is in place and all the needed software is installed. 
Core concepts introduced: high-throughput sequencing, multiplexing, NGS 
library, metabarcoding pipeline, metabarcoding marker, clustering 
algorithms, molecular operational taxonomic unit (MOTU), taxonomic 
assignment.


*Session 2.* Molecular laboratory protocols. DNA extraction. Metabarcoding 
markers. Primer design. PCR and library preparation. Good laboratory 
practice.

In this session we will learn the basics about molecular laboratory 
procedures needed for metabarcoding. While there will be no hands-on 
laboratory practices, guidelines and best practices for all key laboratory 
steps will be discussed. We will explain sample collection techniques, 
including eDNA and bulk community samples, pretreatment and DNA extraction 

[MORPHMET] Course: "Getting started with R"

[Carlo Pecoraro]

Course: "Getting started with R"

https://www.physalia-courses.org/courses-workshops/course13/



18-22 June 2018, Berlin (Germany)



Application deadline is: May 20th, 2018.





Instructor:



Dr. Alexandre Courtiol (Leibniz Institute for Zoo and Wildlife Research,
Berlin (Germany))

https://www.physalia-courses.org/instructors/t40/







Session content

Monday 18th – Classes from 09:30 to 17:30



Monday is DATA day



This first day will be dedicated to the data. R is software dedicated to
data analysis, so mastering the basics of data manipulation in R is
essential for further steps. It  will be explained how to import data into R
and how to manipulate them (e.g. from adding or removing rows or columns, to
merging tables and using pivot tables). This will be good practice for
students to learn the basics of the R language. We will illustrate how to do
everything using R base (that is R out of the box), but we will also
introduce that allow users to perform some operations on large datasets a
little faster.







Tuesday 19th – Classes from 09:30 to 17:30



Tuesday is PLOTTING day



Plotting is a crucial part of any data analysis no matter how advanced you
are in statistics. It is important to visualise the data before the analysis
(e.g. to visually check the presence of potential errors and for getting a
sense of the distribution of the data), during the analysis (e.g. to check
the distribution of model residuals), and after the analysis (to communicate
findings in the most efficient way). Therefore, knowing how to plot various
kind of data matters a lot. We will thus show how to plot different types of
data in R (points, distributions, rasters...) using different graphic
environments (e.g graphics, lattice, ggplot2).







Wednesday 20th – Classes from 09:30 to 17:30



Wednesday is FUNCTIONS day



As John Chambers -- the grandfather of R -- put it "Everything that happens
in R is a function call". That R allows for so-called functional programming
is one of its great benefits: it allows the implementation of any workflow
of statistical analysis as the succession of simple clearly identified
steps. Each step is described by a function that takes an input and
generates an output. The output of one function is often the input of the
next. On this third day we will show that creating one's own function is
very very easy (yes, even YOU can program!) and can be very very useful. As
a first application we will create our own functions to implement a
randomisation test. As a second application we will show how to create
functions to perform a power analysis (the estimation of the probability of
getting true positives when applying a test) for any statistical test.




Thursday 21st – Classes from 09:30 to 17:30



Thursday is LM day



Many widely used statistical methods (t-tests, anova, ancova, linear
regressions...) are just different type of Linear Models (LM), which is why
LM represent the most useful statistical toolbox to be familiar with if you
are in natural or social sciences. Fitting a LM in R is easy -- but building
models, checking model assumptions, interpreting the outputs, and plotting
predictions correctly requires some know how. After refreshing the most
important concepts surrounding LM, we will go through each of these steps in
detail, working on real datasets. It is important to understand LM quite
well before jumping into the more complex methods which we will see on the
next day.






Friday 22nd – Classes from 09:30 to 17:30



Friday is GLMM day



On this last day we will continue with LM and explore what to do when
everything goes wrong; starting with when the process generating the data is
not gaussian, when the observations are not independent. We will see that
the solution is often to use Generalised Linear Models (GLM) which can
handle binary and count data and to use Linear Mixed-effects Models (LMM)
which can handle non-independence in the data. Both can also be combined
under  Generalised Linear Mixed-effects Models (GLMM). We will show some
specific application of such models (e.g. how LMM can be used to study
heredity). We will then see how to tackle spatial and temporal sources of
independence in the data, non constant residual variance, and other
LM-related pathologies. We will illustrate (G)LM(M) mainly using two R
packages: lme4 and spaMM.







For more information about the course, please visit our website:
https://www.physalia-courses.org/courses-workshops/course20/





Here is the full list of our courses and Workshops:
https://www.physalia-courses.org/courses-workshops/

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[MORPHMET] Re: Course: Geometric Morphometrics. 5-9 March 2018 Berlin (Germany)

[Carlo Pecoraro]

Dear all,
we have the last 5 spots left for the course "*Geometric Morphometrics 
<https://www.physalia-courses.org/courses-workshops/course22/>*" which will 
be held in Berlin next March (5-9.03.2018)!! 

Our instructor is Dr. @CarmeloFruciano 
<https://scholar.google.com/citations?user=0BoHmJYJ=en>



*Application deadline is: February 10th, 2018.*Best regards,
Carlo


i...@physalia-courses.org

http://www.physalia-courses.org/

Twitter: @physacourses






On Friday, 29 September 2017 18:03:29 UTC+2, Carlo Pecoraro wrote:
>
> Dear all, 
>
> I am delighted to inform you that we will run the first edition of our 
> course "Geometric Morphometrics" next March (5-9.03.2018) in Berlin!! 
>
> OVERVIEW 
> Geometric morphometrics has become a standard in biological research 
> because it combines statistical rigour and ease of interpretation. Through 
> geometric morphometrics, biological form is quantified, analysed and the 
> results are expressed as easily interpretable and visually impactful shape 
> changes. This course covers the main common practices of modern geometric 
> morphometrics, including: acquiring data, analysing it, visualizing and 
> interpreting the results. 
>
> FORMAT 
> The course will be delivered over five days and will comprise both 
> lectures and hands-on sessions. The lectures will cover both basic 
> theoretical aspects and their practical implementation in research practice 
> and software. During the hands-on sessions, the attendees will have the 
> chance of both using example datasets and applying the knowledge acquired 
> to their own data. The course will be focused mainly on 2D data and on 
> easy-to-use software with graphical user interface to maximize the ability 
> to understand concepts and apply them. However, some information on 3D data 
> and on R implementations will be provided, as appropriate. 
>   
> TARGET AUDIENCE 
> This course is aimed at beginners and intermediate users. In other words, 
> it is aimed at researchers who intend to use geometric morphometrics or who 
> have started performing geometric morphometric analyses but feel they need 
> a more structured background. 
>
> REQUIREMENTS 
> Attendees should have a background in biology and a basic understanding of 
> statistical 
>
> PROGRAM 
> 5 March 2018 
>
> Geometric morphometrics: overview and potential applications: 
>
> -Traditional and geometric morphometrics 
> -An overview of common analyses 
> -Examples of geometric morphometrics applied to biological 
> problems 
>
>
> From biological objects to numerical representation: 
>
> -Overview of typical devices used to digitalise biological objects 
> -Landmarks, semilandmarks, outlines and surfaces - different types 
> of geometric morphometric data 
> -Most commonly used geometric morphometric software 
> -Data quality, most common pitfalls in study design and data 
> acquisition 
>
>
> 6 March 2018 
>
> Generalized Procrustes analysis (GPA) – the core of most geometric 
> morphometrics: 
>
> Principal component analysis (PCA) 
>
> Comparing groups: 
> -Between-group PCA 
> -Canonical variate analysis (CVA) 
> -Tests of difference in means 
>
>
>
> 7 March 2018 
>
> Co-variation between size and shape: 
>
> -Allometry, regression and general linear models 
>
> Co-variation between shapes: 
>
> -Partial least squares analysis (PLS) 
> -Modularity and integration 
>
> 8 March 2018 
>
> Combining analyses in a basic workflow: 
>
> -Preliminary assessment of data quality 
> -Typical basic workflow 
>
> Expanding the basic workflow: variation in geographic space 
>
> Expanding the basic workflow: association between shape and environmental 
> variables 
>
> 9 March 2018 
>
> Expanding the basic workflow: elements of phylogenetic comparative 
> analyses 
>
> Review and open discussion 
>
> Presentation of attendees’ analyses on their own data 
>
>
> Please visit our website to get more information about the course: 
> https://www.physalia-courses.org/courses-workshops/course22/ 
>
>
> Here is the full list of our courses and Workshops: 
> https://www.physalia-courses.org/courses-workshops/ 
>
> Many thanks for your kind attention. 
> Best regards, 
>
>
> Carlo Pecoraro, Ph.D 
>
> Physalia-courses DIRECTOR 
>
> i...@physalia-courses.org 
>
> http://www.physalia-courses.org/ 
>
> Twitter: @physacourses 
>
> https://groups.google.com/forum/#!forum/physalia-courses

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[MORPHMET] Geometric Morphometrics course in Berlin

[Carlo Pecoraro]

Dear all,

registration deadline is soon approaching (10.02.18) and we still have
a few spots available for our course "Geometric Morphometrics" 

Where: Berlin (Germany)

When: 5th-9th March 2018

Instructor: Dr. Carmelo Fruciano (ENS, Paris (France)) http://bit.ly/2rxQVFC

 Overview

Geometric morphometrics has become a standard in biological research
because it combines statistical rigour and ease of interpretation. Through
geometric morphometrics, biological form is quantified, analysed and the
results are expressed as easily interpretable and visually impactful
shape changes. This course covers the main common practices of modern
geometric morphometrics, including: acquiring data, analysing it,
visualizing and interpreting the results.

 Format

The course will be delivered over five days and will comprise both
lectures and hands-on sessions. The lectures will cover both basic
theoretical aspects and their practical implementation in research
practice and software. During the hands-on sessions, the attendees will
have the chance of both using example datasets and applying the knowledge
acquired to their own data. The course will be focused mainly on 2D data
and on easy-to-use software with graphical user interface to maximize the
ability to understand concepts and apply them. However, some information
on 3D data and on R implementations will be provided, as appropriate.

Assumed Background

This course is aimed at beginners and intermediate users. In other words,
it is aimed at researchers who intend to use geometric morphometrics
or who have started performing geometric morphometric analyses but feel
they need a more structured background.

Requirements

Attendees should have a background in biology and a basic understanding
of statistical concepts.

For more information, please visit our website: 
https://www.physalia-courses.org/courses-workshops/course22/ 

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[MORPHMET] Course: GENOME-WIDE SIGNATURES OF SELECTION AND ASSOCIATION STUDIES

[Carlo Pecoraro]

Dear  

all,


we still have a few places left for our course "GENOME-WIDE SIGNATURES OF 
SELECTION AND ASSOCIATION STUDIES", that will take place in the beautiful 
botanical museum in Berlin from the 22nd to the 26th of October 2018. 
  

*Our INSTRUCTORS:*



*Dr. Pablo Orozco-terWengel (Cardiff University, Wales (UK))*

 

*https://scholar.google.co.uk/citations?user=urqxLJgJ=en 
<https://scholar.google.co.uk/citations?user=urqxLJgJ=en>*

 
  

*Dr. Filippo Biscarini (CNR, ITA)*

 

*https://www.researchgate.net/profile/Filippo_Biscarini 
<https://www.researchgate.net/profile/Filippo_Biscarini>*

 

 
  

Overview


This course will introduce students, researchers and professionals into the 
field of using genomics data to identify meaningful genomic regions. The 
course comprises two approaches: one based only on genomic information, 
which will use populations genetics techniques to detect signatures of 
selection (both natural and artificial); the other approach will combine 
genomic and phenotypic data to identify genetic associations for specific 
phenotypes (i.e. GWAS, genome-wide association studies).

 

 

 
  

Format


The course is structured in modules over five days. Each day will include 
an introductory lecture with class discussion of key concepts. The 
remainder of each day will consist of practical hands-on sessions. These 
sessions will involve a combination of both mirroring exercises with the 
instructor to demonstrate a skill as well as applying these skills on your 
own to complete individual exercises. After and during each exercise, 
interpretation of results will be discussed as a group.

 

 

TARGETED AUDIENCE & ASSUMED BACKGROUND


The course is aimed at advanced students, researchers and professionals 
interested in learning how to make use of genomic information to study how 
selection has shaped the genome and how the genome influences measurable 
phenotypes. It will include information useful for both beginners and more 
advanced users. We will start by introducing general concepts of population 
genetics, which will take up most of the first half of the course; the 
second half of the course will be centered mainly on GWAS and related 
aspects.

Attendees should have a background in biology, specifically genetics. There 
will be a mix of lectures and hands-on practical exercises using R and the 
Linux command line, and bespoke software. Some basic understanding of R 
programming and the Linux environment will be advantageous. Attendees 
should have also some familiarity with genomic data such as those arising 
from NGS experiments, including genotyping-by-sequencing (GBS), and 
commercial genotyping platforms.

 
  

 

Please visit our website to have more information about the course content: 
https://www.physalia-courses.org/courses-workshops/course36/curriculum-36/

 

 

Here is the full list of our courses and Workshops*: *
https://www.physalia-courses.org/courses-workshops/

 

 

 

If you have any questions please feel free to contact us.

Best regards,

Carlo



----

*Carlo Pecoraro, Ph.D*


Physalia-courses DIRECTOR

i...@physalia-courses.org

http://www.physalia-courses.org/

Twitter: @physacourses

mobile: +49 15771084054

https://groups.google.com/forum/#!forum/physalia-courses

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[MORPHMET] Course: GENOME-WIDE SIGNATURES OF SELECTION AND ASSOCIATION STUDIES

[Carlo Pecoraro]

Dear all,


we still have a few places left for our course "GENOME-WIDE SIGNATURES OF 
SELECTION AND ASSOCIATION STUDIES", that will take place in the beautiful 
botanical museum in Berlin from the 22nd to the 26th of October 2018.
 

Our INSTRUCTORS:


Dr. Pablo Orozco-terWengel (Cardiff University, Wales (UK)): 
https://scholar.google.co.uk/citations?user=urqxLJgJ=en

 
 

Dr. Filippo Biscarini (CNR, ITA): 
https://www.researchgate.net/profile/Filippo_Biscarini


 

Overview


This course will introduce students, researchers and professionals into the 
field of using genomics data to identify meaningful genomic regions. The 
course comprises two approaches: one based only on genomic information, 
which will use populations genetics techniques to detect signatures of 
selection (both natural and artificial); the other approach will combine 
genomic and phenotypic data to identify genetic associations for specific 
phenotypes (i.e. GWAS, genome-wide association studies).

 


Format


The course is structured in modules over five days. Each day will include 
an introductory lecture with class discussion of key concepts. The 
remainder of each day will consist of practical hands-on sessions. These 
sessions will involve a combination of both mirroring exercises with the 
instructor to demonstrate a skill as well as applying these skills on your 
own to complete individual exercises. After and during each exercise, 
interpretation of results will be discussed as a group.

 
 

TARGETED AUDIENCE & ASSUMED BACKGROUND


The course is aimed at advanced students, researchers and professionals 
interested in learning how to make use of genomic information to study how 
selection has shaped the genome and how the genome influences measurable 
phenotypes. It will include information useful for both beginners and more 
advanced users. We will start by introducing general concepts of population 
genetics, which will take up most of the first half of the course; the 
second half of the course will be centered mainly on GWAS and related 
aspects.

Attendees should have a background in biology, specifically genetics. There 
will be a mix of lectures and hands-on practical exercises using R and the 
Linux command line, and bespoke software. Some basic understanding of R 
programming and the Linux environment will be advantageous. Attendees 
should have also some familiarity with genomic data such as those arising 
from NGS experiments, including genotyping-by-sequencing (GBS), and 
commercial genotyping platforms.

 


Please visit our website to have more information about the course content: 
https://www.physalia-courses.org/courses-workshops/course36/curriculum-36/

 
 

Here is the full list of our courses and Workshops: 
https://www.physalia-courses.org/courses-workshops/

 

 

If you have any questions please feel free to contact us.

Best regards,

Carlo



----

Carlo Pecoraro, Ph.D


Physalia-courses DIRECTOR

i...@physalia-courses.org

http://www.physalia-courses.org/

Twitter: @physacourses

mobile: +49 15771084054

https://groups.google.com/forum/#!forum/physalia-courses

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[MORPHMET] Course: Getting started with R (Berlin, 18-22/06/18)

[Carlo Pecoraro]

 

Dear all,

we are offering the 2th edition of the course "Getting started with R".

Instructor: * Dr. Alexandre Courtiol * (Leibniz Institute for Zoo and 
Wildlife Research, Berlin (Germany))

Dates: June 18th-22nd 

Place: BGBM, Freie University, Berlin (Germany)



Course overview

R is the statistical software the most used in the world. It is extremely 
powerful, free of charge and open source. Despite these benefits, many 
avoid R, or struggle with it, as writing computer code to do any operation 
-- a requirement in R -- is at first both difficult and intimidating. 
This course aims at overcoming those challenges by providing solid basics 
in R. At the end of the course, participants should feel much more at ease 
writing a computer script in the R language which covers the entire 
spectrum of a statistical analysis: reading data, editing them, plotting 
them, and analysing them. Because linear models are the dominant 
statistical tool in many fields, the part of the course focusing on 
analyses per se (see schedule) will focus on those, but principles seen 
during the class should greatly help those interested in other kind of 
analyses as well. The course will be presented over five days and will mix 
explanations and guided exercises. Students are free to practice with their 
own datasets during the course.

For more information, please visit our website: 
https://www.physalia-courses.org/courses-workshops/course13/


Best regards,

Carlo


----

*Carlo Pecoraro, Ph.D*


Physalia-courses DIRECTOR

i...@physalia-courses.org

http://www.physalia-courses.org/

Twitter: @physacourses

mobile: +49 15771084054

https://groups.google.com/forum/#!forum/physalia-courses

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[MORPHMET] Physalia-courses Geometric Morphometrics course in Berlin

[Carlo Pecoraro]

Dear all,

we will run the second edition of our course on "Geometric morphometrics" 
with Dr Carmelo Fruciano next March (18-22) in Berlin. 


The course will be delivered over five days and will comprise both lectures 
and hands-on sessions. The lectures will cover both basic theoretical 
aspects and their practical implementation in research practice and 
software. During the hands-on sessions, the attendees will have the chance 
of both using example datasets and applying the knowledge acquired to their 
own data. The course will be focused mainly on 2D data and on easy-to-use 
software with graphical user interface to maximize the ability to 
understand concepts and apply them. However, some information on 3D data 
and on R implementations will be provided, as appropriate.


This course is aimed at beginners and intermediate users. In other words, 
it is aimed at researchers who intend to use geometric morphometrics or who 
have started performing geometric morphometric analyses but feel they need 
a more structured background. 

  


For more information, please visit the course website: 
https://www.physalia-courses.org/courses-workshops/course22/


Here is the full list of our courses and Workshops: 
https://www.physalia-courses.org/courses-workshops/



For any questions, please feel free to contact us at : 
i...@physalia-courses.org


Best,

Carlo

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[MORPHMET] Discussing about GM with Carmelo Fruciano

[Carlo Pecoraro]

Really want to say thanks to Carmelo Fruciano for his time and availability 
in replying to our questions about #GeometricMorphometrics 
!


Carmelo talks about his path in this research field, the experience in Jim 
Rohlf's lab in Stony Brook, the current work in Paris and his Workshop here 
in Berlin (https://www.physalia-courses.org/courses-workshops/course22/)


Here is the link: https://www.physalia-courses.org/news/n14/


Happy reading!

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[MORPHMET] Geometric Morphometrics course in Berlin, Germany

[Carlo Pecoraro]

2nd edition of the Course "Geometric morphometrics"

Where: FU University Berlin


When: 18-22 March 2019 

  

Instructor: Dr. Carmelo Fruciano (Ecole Normale Superieure, Paris - IBENS - 
CNRS)

  

topic: Introductory and intermediate geometric morphometrics.

This course covers the main common practices of modern geometric 
morphometrics, including: acquiring data, analysing it, visualizing and 
interpreting the results. 

  

The course will be delivered over five days and will comprise both lectures 
and hands-on sessions. The lectures will cover both basic theoretical 
aspects and their practical implementation in research practice and 
software. During the hands-on sessions, the attendees will have the chance 
of both using example datasets and applying the knowledge acquired to their 
own data.  

  

This course is aimed at beginners and intermediate users. In other words, 
it is aimed at researchers who intend to use geometric morphometrics or who 
have started performing geometric morphometric analyses but feel they need 
a more structured background.




For more information about the course, please visit our website: 
https://www.physalia-courses.org/courses-workshops/course22/



Here is the full list of our courses and Workshops: 
https://www.physalia-courses.org/courses-workshops/

Best regards,

Carlo
------

Carlo Pecoraro, Ph.D

Physalia-courses DIRECTOR

i...@physalia-courses.org

http://www.physalia-courses.org/

Twitter: @physacourses

mobile: +49 17645230846

https://groups.google.com/forum/#!forum/physalia-courses

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[MORPHMET] New course -DNA-sequence data and phylogenies in biodiversity- in Poland

[Carlo Pecoraro]

Dear all,


This course might be of interest for people in this list: "DNA-sequence 
data and phylogenies in biodiversity", 15-18 July 2019.


For the 1st time we will run this course in Poland (University of Lodz).


Instructor: Dr. Diego Fontaneto (CNR, ITALY)




This course will introduce scientists interested in biodiversity to the use 
of DNA-sequence data to address questions that cannot be addressed by using 
only morphological and ecological data in their studies. After a short 
introduction on how to obtain DNA sequences and reliable molecular 
phylogenies, the focus of the questions that could be addressed will be on 
taxonomy, community ecology, and comparative methods.





LEARNING OUTCOMES


   - Understand how to read, interpret and obtain molecular phylogenies, 
   with a focus on the concepts and rationale behind phylogenetic methods 
   - Learn tools from DNA taxonomy 
   - Learn how to include phylogenies in the analyses of community ecology 
   and in comparative analyses 
   - Hand-on experience on all the steps 
   - Being comfortable with using R when including molecular phylogenies in 
   ecological analyses 


For more information about the programme, please visit our website: 
https://www.physalia-courses.org/courses-workshops/course28/

Should you have any questions, please feel free to contact us: 
i...@physalia-courses.org

All the best,
Carlo


----

Carlo Pecoraro, Ph.D


Physalia-courses DIRECTOR

i...@physalia-courses.org

http://www.physalia-courses.org/

Twitter: @physacourses

mobile: +49 17645230846

https://groups.google.com/forum/#!forum/physalia-courses



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[MORPHMET] Geometric morphometrics course in Berlin with Carmelo Fruciano

[Carlo Pecoraro]

Dear all,

just wanted to inform you that we still have a few places available for our 
Geometric morphometrics course.

Where: Free University of Berlin (Germany)

When: 18-22 March 2019

Instructor: Dr. Carmelo Fruciano (Ecole Normale Superieure, Paris (France))

Course Website: https://www.physalia-courses.org/courses-workshops/course22/



This course covers the main common practices of modern geometric 
morphometrics, including: acquiring data, analysing it, visualizing and 
interpreting the results. 

The course will be delivered over five days and will comprise both lectures 
and hands-on sessions. The lectures will cover both basic theoretical 
aspects and their practical implementation in research practice and 
software. During the hands-on sessions, the attendees will have the chance 
of both using example datasets and applying the knowledge acquired to their 
own data. The course will be focused mainly on 2D data and on easy-to-use 
software with graphical user interface to maximize the ability to 
understand concepts and apply them. However, some information on 3D data 
and on R implementations will be provided, as appropriate.


If interested, please have a look at the program: 
https://www.physalia-courses.org/courses-workshops/course22/curriculum-22/


Should you have any questions, please feel free to contact us: 
i...@physalia-courses.org


Many thanks and Best Regards,

Carlo





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