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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**Deadlin
 e for applications is on 16 August 2023**. In the case a minimum of 15 par
 ticipants is not met by this date\, SIB may decide to cancel this course. 
 In this case\, SIB will informe those who have registered and reimburse th
 e fees already paid.\n\nDeadline for of free-of-charge cancellation is **1
 6 August 2023**. Cancellation after this date will not be reimbursed. Plea
 se note that participation in SIB courses is subject to this and other gen
 eral conditions\, available [here](https://www.sib.swiss/training/terms-an
 d-conditions).\n\n\n# Venue and time\nThis course will take place **only i
 n person**\, at the University of Lausanne\, in the Campus Sorge. \n\nThe 
 course will start at 9:00 and end around 17:00. \n\nPrecise information wi
 ll be provided to the participants in due time.\n# Schedule \n\n### Day 1 
 - Natasha Glover and Christophe Dessimoz (UniL and SIB) - Introduction to 
 molecular evolution &amp\; phylogenetics\nInterpret phylogenetic trees and
  alignments\; general understanding of how trees are inferred\; knowing th
 e definition of orthology\, paralogy and their subtypes\; understanding th
 e difference between pairwise and groupwise comparisons\; ability to perfo
 rm orthology inference through tree overlap method\; ability to retrieve o
 rthology information from the OMA database\; ability to infer orthologs us
 ing the OMA standalone pipeline.  **Teaching assistants for practical exer
 cises: Yannis Nevers and Sina Majidian.**\n\n* 9:00-12:00: Lectures - Intr
 oduction to molecular evolution &amp\; phylogenetics\; Inferring Orthology
  and Paralogy \n* 12:00 - 13:00: Lunch break\n*  13:00-17:00: Hands-on - e
 xercises on orthology inference through tree overlap methods\, tree reconc
 iliation\, OMA database\, OMA standalone\n\n\n### Day 2 - Robert Waterhous
 e (UniL and SIB) - Orthology-focused arthropod comparative genomics\nUnder
 stand the principles of graph-based orthology delineation using OrthoDB as
  an example\; learn how to browse and programmatically query OrthoDB\; lea
 rn how to use BUSCO to assess genomics data quality\; learn how to formula
 te comparative genomics questions\, develop and apply approaches to addres
 s them (with a focus on using orthology data)\, and then critically interp
 ret them\, through case studies from arthropods. **Teaching assistant for 
 practical exercises: Giulia Campli and Antonin Thiébaut.**\n\n* 9:00-12:0
 0: Lectures - Introduction to OrthoDB &amp\; BUSCO\; case studies from Art
 hropod Comparative Genomics\n* 12:00 - 13:00: Lunch break\n*  13:00-17:00:
  Hands-on - exercises with BUSCO for phylogenomics and OrthoDB for gene fa
 mily evolution\n\n### Day 3 - Marc Robinson-Rechavi (UniL and SIB) - Dupli
 cation of genes and genomes\, expression\nUnderstand the importance of gen
 e and genome duplication in comparative genomics\; understand the difficul
 ty of comparing “function” between homologous genes\, and know some to
 ols to do so. **Teaching assistant for practical exercises: Marina Braso V
 ives and Alessandro Brandulas Cammarata**\n\n* 9:00-12:00: Lectures - Intr
 oduction to Bgee (curated data\, ontologies\, present calls\, homology\, T
 opAnat)\; patterns of gene and genome duplication\; evolution after duplic
 ation\n* 12:00 - 13:00: Lunch break\n*  13:00-17:00: Hands-on - exercises 
 with gene set enrichment of biased duplicate retention\, expression compar
 ison\, positive selection\, functional shifts\, Bgee SPARQL endpoint \n\n#
  Additional information\nCoordination: Patricia Palagi\n\nWe will recommen
 d 0.75 ECTS credits for this course (given a passed exam at the end of the
  course).\n\nYou are welcome to register to the SIB courses mailing list t
 o be informed of all future courses and workshops\, as well as all importa
 nt deadlines using the form [here](https://lists.sib.swiss/mailman/listinf
 o/courses).\n\nPlease note that participation in SIB courses is subject to
  our [general conditions](https://www.sib.swiss/training/terms-and-conditi
 ons).\n\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-europe.
 org/events/code-of-conduct). Participants of SIB courses are also required
  to abide by the same code.\n\nFor more information\, please contact [trai
 ning@sib.swiss](mailto://training@sib.swiss).
SUMMARY:Biodiversity bioinformatics: from large-scale phylogenomics to gene
  families and functions
URL;VALUE=URI:https://www.sib.swiss/training/course/20230830_COMGE
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