Logo
COMS

ARABLAB 2021

Abstract:
 
The shop window for SCIENCE & CHEMICALS, featuring the latest laboratory trends in dedicated show sectors: FOODLAB, BIOLAB, PETROLAB, ENVIROLAB, MEDILAB, CHEMLAB, TESTLAB, DESIGNLAB.
Event listing ID:
 
1397069

Read More
None

Conference: THE 14TH MIDDLE EAST GEOSCIENCES CONFERENCE & EXHIBITION.

For 26 years, the GEO exhibition and conference has been at the forefront of petroleum geoscience. GEO has fast become a next generation energy event, hosting major NOCs, IOCs, manufacturers, technology providers and service companies – all of whom play an active role in the global energy value chain. Conference: 4-7 October 2021 Exhibition: 5-7 October 2021
Read More
international association for the study of Arabia

Friends with Socotra

The 20th Friends of #Socotra Conference & AGM and the 2nd World Dragon Tree Conference will take place in Ghent in September 2021.

Read More
transmitting science

INTRODUCTION TO MACROEVOLUTIONARY ANALYSES USING PHYLOGENIES

COURSE OVERVIEW

Phylogenetic trees have changed the way we study and understand life on Earth. Taking phylogenetic information into account in our analyses is critical to account for the non-independence of biological data. Also, phylogenies allow us to get a deep-time perspective of the processes that have shaped the evolutionary history of groups, including diversification and trait evolution.

This course will introduce participants to the use, modification and representation of phylogenetic trees. Also, we will focus on the use of phylogenetic information to reconstruct ancestral characters and biogeographic histories, using different phylogenetic comparative methods.

This course will also tackle trait evolution modelling and the assessment of phylogenetic signal. Finally, we will learn about the shape of phylogenetic trees and its evolutionary causes, and how to estimate the rates of diversification throughout the history of groups. Participants are encouraged to bring their data sets to use in the practical classes.

The course includes an optional first introductory day to basic R.

Important note: Please bear in mind that this course is not about reconstructing (building) phylogenetic trees.

Software: Mesquite, FigTree, R (ape, TreeSim, TreePar, Geiger, OUwie, BioGeoBEARS).

See the full program here

REQUIREMENTS

Graduate or postgraduate degree in Biology (including palaeontologists no matter the degree).

Participants must have a personal computer (Windows, Mac, Linux) with this software installed:

The use of Webcam and headphones are strongly recommended, and a good internet connection.

CONTACT

courses@transmittingscience.com

Read More
Eurasia Web

International Conference On Environment And Life Science (EUCELS)

About Event

The conference provides a platform for professionals involved in Environment and Life Science to exchange knowledge and gain an insight into the state of the art in the current technology, techniques and solutions in Environment and Life Science as they have been developed and applied in different countries. Participants include a wide variety of stakeholders from research and academia, to industrial sectors as well as government organizations.

Read More
science society

International Conference On Nanomaterials And Biomaterials (EUICNB)

About Event

The conference provides a platform for professionals involved in Nanomaterials and Biomaterials to exchange knowledge and gain an insight into the state of the art in the current technology, techniques and solutions in Nanomaterials and Biomaterials as they have been developed and applied in different countries. Participants include a wide variety of stakeholders from research and academia, to industrial sectors as well as government organizations.

Read More
Physalia courses

INTRODUCTION TO GENOME-WIDE ASSOCIATION STUDIES (GWAS)

OVERVIEW

This course will introduce students, researchers and professionals to the steps needed to build an analysis pipeline for Genome-Wide Association Studies (GWAS). The course will describe all the necessary steps involved in a typical GWAS study, which will then be used to build a reusable and reproducible bioinformatics pipeline.

FORMAT

The course is structured in modules over five days. Each day will include introductory lectures with class discussions 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 instructors to demonstrate a skill as well as applying these skills on your own to complete individual exercises. After and during each exercise, results will be interpreted and discussed in group.

TARGETED AUDIENCE & ASSUMED BACKGROUND

The course is aimed at students, researchers and professionals interested in learning the different steps involved in a GWAS study using them to build a structured pipeline for semi-automated and reproducibile GWAS analyses. It will include information useful for both beginners and more advanced users. We will start by introducing general concepts of GWAS and bioinformatics pipeline building, progressively describing all steps and putting there seamlessy together in a general workflow. Attendees should have a background in biology, specifically genetics; previous exposure to GWAS experiments would also be beneficial. There will be a mix of lectures and hands-on practical exercises using R, Linux command line and custom software. Some basic understanding of R programming and Unix will be advantageous. Attendees should also have some basic familiarity with genomic data such as those arising from NGS experiments.

 

LEARNING OUTCOMES

  • Understanding the different steps involved in a typical GWAS analysis and how to build them together in a general workflow / bioinformatics pipeline

PROGRAM

Monday  2-8  pm Berlin time

 14:00    Lecture 0  General Introduction / Overview of the course

 14:30   Lecture 1   Introduction to GWAS: Linkage disequilibrium and Linear Regression

 15:30   Lecture 2   GWAS: case studies / examples from literature

 16:30  break

 17:00    Lab 2 - part 1  basic Linux and R

 18:00   Lab 2 - part 2  Practicalities and set-up (server, github repo, conda envs, etc) and description of datasets

 18:30   Lab 2 - part 3  basic Linux and R

 19:00   Lab 3     GWAS: basic models

 19:30   Lab 3 (demonstration) GWAS: basic models (linear and logistic regression, population structure, etc.)

 

CURRICULUM

 Monday  2-8 pm Berlin time

 14:00    Lecture 0  General Introduction / Overview of the course

 14:30   Lecture 1   Introduction to GWAS: Linkage disequilibrium and Linear Regression

 15:30   Lecture 2   GWAS: case studies / examples from literature

 16:30  break

 17:00    Lab 2 - part 1  basic Linux and R

 18:00   Lab 2 - part 2  Practicalities and set-up (server, github repo, conda envs, etc) and description of datasets

 18:30   Lab 2 - part 3  basic Linux and R

 19:00   Lab 3     GWAS: basic models

 19:30   Lab 3 (demonstration)GWAS: basic models (linear and logistic regression, population structure, etc.)

             
 Tuesday 2-8 pm Berlin time

 14:00    Lecture 4     EDA: theory

 14:30    Lab 4     EDA practice

 15:00    Lecture 5     data preprocessing: theory

 16:00    Lab 5    data preprocessing: practice

 17:00     break

 17:30    Lecture 6 Imputation of missing genotypes: theory

 18:30    Lab 6 - part 1  practical session on imputation (Beagle)

 19:30    Lab 7 (demonstration) KNNI imputation

             
 Wednesday   2-8 pm Berlin time

 14:00   Lecture 7  GWAS, the full model (all SNPs)

 15:30   Lab 9 (demonstration)   a few steps in the past (GenABEL)

 16:30   Lab 10    GWAS: the stand-alone script(s) for the full model

 17:00 break

 17:30   Lecture 8  GWAS: experimental design and statistical power

 18:30   Lecture 9  The multiple testing issue?

 19:30   Lab 10  revising the steps involved in GWAS
 

 Thursday 2-8 pm Berlin time

 14:00    Lecture 10 Bioinformatics pipelines: a super-elementary introduction

 15:00    Lab 11    Building a pipeline with Snakemake

 15:30    Lab 12    The GWAS pipeline for continuous phenotype

 16:00   Lab 13    The GWAS pipeline for binary phenotype

 16:30     break

 17:00    Lab 14  Introducing the exercise (+ light touch on RMarkdown)

 17:30    Collaborative exercise  Let’s build our own GWAS pipeline on new data

 19:00    Discussion  Q&A on  building pipelines for GWAS


 Friday 2-8 pm Berlin time

 14:00   Lecture 11  GWAS models for categorical traits (a primer)

 15:00   Lecture 12  GWAS models for longitudinal data (a primer)

 16:00: break

 16:30   Lecture 13  A light touch on post-GWAS analysis

 17:30   Lecture 14  A glimpse on ROH-based alternative

 18:00   Kahoot quiz  on what we learned about GWAS!

 19:00:  Wrap-up discussion  on GWAS

Read More
king Abdullah of Science and Technology

KAUST Research Conference: Near Zero Carbon Combustion Technology

Organized by William Roberts — Physical Science and Engineering Division (PSE)

Read More
Physalia courses

LANDSCAPE GENOMICS

WORKSHOP OVERVIEW

Landscape genomics is an emerging research field that studies how genetic diversity distributes across space and how environmental features can modify this structure through local adaptation. In this workshop, students will learn the basics of this approach and train using state of the art methods. The course will provide an overview of the type of dataset that can be used for a landscape genomics analysis. Firstly, students will learn how to obtain environmental data from publicly available databases, how to process it with Geographic Information Systems (GIS) and how to use the latter to produce indicators able to describe the characteristics of the landscape. Next, the course will discuss the different approaches to obtain genetic data and subsequently show how to study genetic variation and population structure across space in the R environment. Students will be given an overview of the different statistical approaches to study local adaptation, and will be trained in using two of them, Sambada and LFMM. The course will also cover the critical task of the interpretation and validation of the results. Finally, the workshop will consider the crucial aspects and good habits to account for when planning a landscape genomics experiment (e.g. sampling design). 

TARGETED AUDIENCE & ASSUMED BACKGROUND

This workshop is aimed at all biologists, ecologists, geneticists, veterinarians that want to implement the landscape genomics approach in their own studies of evolutionary biology and conservation. Even though the course is not intended for a specialized audience, basic knowledge in evolutionary biology and population genetics would help. Students will learn how to use GIS, but basic computer skills are desirable (e.g. in the R environment). A basic understanding of statistics is also necessary.

TEACHING FORMAT

The course is organized in ten learning sessions. During the first two sessions, the course will provide a contextualization of the research field. Then, students will be guided through a landscape genomics experiment with sessions that couple brief theoretical introductions with practical work.

PROGRAM

 

Monday – Classes from 2-8 pm Berlin time

 

Session 1-Introduction

 

-          Overview of the course program

 

-          Introduction on Landscape Genomics

 

-          Examples

 

 

Session 2-Dataset

 

-          The environmental data

 

-          The genetic data

SESSION CONTENT

Monday – Classes from 2-8 pm Berlin time

 

 

Session 1-Introduction

 

-          Overview of the course program

 

-          Introduction on Landscape Genomics

 

-          Examples

 

 

Session 2 - Dataset

 

-          The environmental data

 

-          The genetic data

 

 

 

Tuesday – Classes from 2-8 pm Berlin time

 

 

Session 3-Environmental Data 1

 

-          GIS basics

 

-          Main environmental databases

 

-          Derived environmental variables

 

 

Session 4- Environmental Data 2

 

-          Environmental characterization of the samples

 

-          Point versus surface

 

-          Analysis of environmental diversity of samples

 

 

 

Wednesday – Classes from 2-8 pm Berlin time

 

 

Session 5- Genetic Data 1

 

-          Sequencing strategies

 

-          Data filtering

 

 

Session 6- Genetic Data 2

 

-          Spatial genetic variation

 

-          Population structure

 

 

 

Thursday – Classes from 2-8 pm Berlin time

 

 

Session 7-Statistical Analysis

 

-          Overview of statistical methods (univariate, multivariate, w/wo population structure)

 

-          samβada: logistic regression

 

 

Session 8-Interpreting Results

 

-          Spatial autocorrleation

 

-          Process samβada output in R

 

-          Validation of results

 

 

 

Friday – Classes from 2-8 pm Berlin time

 

 

Session 9- Planning a Landscape Genomics Experiment

 

-          Scale and Resolution

 

-          Sampling Design

 

 

Session 10-Conclusion

 

-          Take home messages

 

-          Question time

Read More
king Abdullah of Science and Technology

KAUST Workshop: Machine Learning to illuminate the Earth

Organized by Tariq Alkhalifa — Physical Science and Engineering Division (PSE)

Read More
  • Page 1 of 29