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DESCRIPTION:# Overview\nThe aims of this biodiversity bioinformatics course
  are to (i) explore key evolutionary concepts\, (ii) examine different met
 hodological approaches\, and (iii) gain hands-on experience in comparative
  genomic analyses\, with an emphasis on characterising protein-coding gene
  evolution and function across multiple animal genomes\, both from model a
 nd non model species.\n\nThis course will focus on concepts and methods fo
 r orthology and paralogy of protein-coding genes\, complemented with pract
 ical examples of applications of comparative genomics approaches to invest
 igate biological and/or evolutionary questions. It will be structured with
  mostly lectures in the mornings followed by mostly hands-on sessions in t
 he afternoons.\n\nThis course may touch on\, but will not cover in any det
 ail\, topics relating to genome sequencing and assembly\, genome annotatio
 n\, population genomics\, or genomics of prokaryotes.\n\n\n\n\n# Audience\
 nThis course is aimed at PhD students\, postdoctoral and other researchers
  in the life sciences who are planning how to proceed with comparative gen
 omics analyses to investigate biological or evolutionary questions of impo
 rtance to their study system\, particularly to leverage comparative genomi
 cs tools and resources to characterise the gene repertoires of their non-m
 odel species.\n\n# Learning objectives\nAt the end of the course participa
 nts should be able to:\n* Interpret phylogenetic trees and sequence alignm
 ents\n* Infer orthologs and paralogs using graph- and tree-based methods\n
 * Design and implement comparative analyses to interrogate genomics data\,
  e.g. phylogenomics or gene family dynamics\n\n# Prerequisites\n##### Know
 ledge / competencies:\nParticipants should have a good understanding of co
 mmand line tools. If you do not feel comfortable with these UNIX commands\
 , please take our [UNIX fundamentals e-learning module](http://edu.sib.swi
 ss/course/view.php?id=82). \n\n\n\n##### Technical:\n\n\nYour computer sho
 uld have an internet connection\, and at least 8 GB RAM\, 50 GB free disk 
 space.\n\n\n # Application\nRegistration fees are **300 CHF** for academic
 s and **1500 CHF** for for-profit companies. \nYou will be informed by ema
 il of your registration confirmation. Upon reception of the confirmation e
 mail\, participants will be asked to confirm attendance by paying the fees
  within 5 days.\n\nYou will be informed by email of your registration conf
 irmation. Upon reception of the confirmation email\, participants will be 
 asked to confirm attendance by paying the fees within 5 days.\n\n\n\nDeadl
 ine for of free-of-charge cancellation is **04 August 2024**. Cancellation
  after this date will not be reimbursed. Please note that participation in
  SIB courses is subject to this and other general conditions\, available [
 here](https://www.sib.swiss/training/terms-and-conditions).\n\n\n# Venue a
 nd time\nThis course will take place **only in person**\, at the Universit
 y of Lausanne\, in the Campus Sorge. \n\nThe course will start at 9:00 and
  end around 17:00. \n\nPrecise information will be provided to the partici
 pants in due time.\n# Schedule \n\n### Day 1 - Natasha Glover and Christop
 he Dessimoz (UniL and SIB) - Introduction to molecular evolution &amp\; ph
 ylogenetics\nInterpret phylogenetic trees and alignments\; general underst
 anding of how trees are inferred\; knowing the definition of orthology\, p
 aralogy and their subtypes\; understanding the difference between pairwise
  and groupwise comparisons\; ability to perform orthology inference throug
 h tree overlap method\; ability to retrieve orthology information from the
  OMA database\; ability to infer orthologs using the OMA standalone pipeli
 ne.  **Teaching assistants for practical exercises: Stefano Pascarelli and
  Athina Gavriilidou.**\n\n* 9:00-12:00: Lectures - Introduction to molecul
 ar evolution &amp\; phylogenetics\; Inferring Orthology and Paralogy \n* 1
 2:00 - 13:00: Lunch break\n*  13:00-17:00: Hands-on - exercises on ortholo
 gy inference through tree overlap methods\, tree reconciliation\, OMA data
 base\, OMA standalone\n\n\n### Day 2 - Robert Waterhouse (UniL and SIB) - 
 Orthology-focused arthropod comparative genomics\nUnderstand the principle
 s of graph-based orthology delineation using OrthoDB as an example\; learn
  how to browse and programmatically query OrthoDB\; learn how to use BUSCO
  to assess genomics data quality\; learn how to formulate comparative geno
 mics questions\, develop and apply approaches to address them (with a focu
 s on using orthology data)\, and then critically interpret them\, through 
 case studies from arthropods. **Teaching assistant for practical exercises
 : Giulia Campli.**\n\n* 9:00-12:00: Lectures - Introduction to OrthoDB &am
 p\; BUSCO\; case studies from Arthropod Comparative Genomics\n* 12:00 - 13
 :00: Lunch break\n*  13:00-17:00: Hands-on - exercises with BUSCO for phyl
 ogenomics and OrthoDB for gene family evolution\n\n### Day 3 - Marc Robins
 on-Rechavi (UniL and SIB) - Duplication of genes and genomes\, expression\
 nUnderstand the importance of gene and genome duplication in comparative g
 enomics\; understand the difficulty of comparing “function” between ho
 mologous genes\, and know some tools to do so. **Teaching assistant for pr
 actical exercises: Marina Braso Vives and Julien Wollbrett**\n\n* 9:00-12:
 00: Lectures - Introduction to Bgee (curated data\, ontologies\, present c
 alls\, homology\, TopAnat)\; patterns of gene and genome duplication\; evo
 lution after duplication\n* 12:00 - 13:00: Lunch break\n*  13:00-17:00: Ha
 nds-on - exercises with gene set enrichment of biased duplicate retention\
 , expression comparison\, positive selection\, functional shifts\, Bgee SP
 ARQL endpoint \n\n# Additional information\nCoordination: Patricia Palagi\
 n\nWe will recommend 0.75 ECTS credits for this course (given a passed exa
 m at the end of the course).\n\nYou are welcome to register to the SIB cou
 rses mailing list to be informed of all future courses and workshops\, as 
 well as all important deadlines using the form [here](https://lists.sib.sw
 iss/postorius/lists/courses.lists.sib.swiss/).\n\nPlease note that partici
 pation in SIB courses is subject to our [general conditions](https://www.s
 ib.swiss/training/terms-and-conditions).\n\nSIB abides by the [ELIXIR Code
  of Conduct](https://elixir-europe.org/events/code-of-conduct). Participan
 ts of SIB courses are also required to abide by the same code.\n\nFor more
  information\, please contact [training@sib.swiss](mailto://training@sib.s
 wiss).
SUMMARY:Biodiversity bioinformatics: from large-scale phylogenomics to gene
  families and functions
URL;VALUE=URI:https://www.sib.swiss/training/course/20240828_COMGE
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