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DTSTAMP:20260407T181529Z
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DTSTART:20250825T090000Z
DTEND:20250827T170000Z
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 non-model s
 pecies.\n\n# Learning objectives\nAt the end of the course participants sh
 ould be able to:\n* Interpret phylogenetic trees and sequence alignments\n
 * Infer orthologs and paralogs using graph- and tree-based methods\n* Desi
 gn and implement comparative analyses to interrogate genomics data\, e.g. 
 phylogenomics or gene family dynamics\n\n# Prerequisites\n##### Knowledge 
 / competencies:\nParticipants should have a good understanding of command 
 line tools. If you do not feel comfortable with these UNIX commands\, plea
 se take our [UNIX fundamentals e-learning module](http://edu.sib.swiss/cou
 rse/view.php?id=82). \n\n\n\n##### Technical:\n\n\nYour computer should ha
 ve an internet connection\, and at least 8 GB RAM\, 50 GB free disk space.
 \n\n\n # Application\nRegistration fees are **300 CHF** for academics and 
 **1500 CHF** for for-profit companies. \nYou will be informed by email of 
 your registration confirmation. Upon reception of the confirmation email\,
  participants will be asked to confirm attendance by paying the fees withi
 n 5 days.\n\nYou will be informed by email of your registration confirmati
 on. Upon reception of the confirmation email\, participants will be asked 
 to confirm attendance by paying the fees within 5 days.\n\nIn the case a m
 inimum of 15 participants is not met by this date\, SIB may decide to canc
 el this course. In this case\, SIB will informe those who have registered 
 and reimburse the fees already paid. \n\nDeadline for of free-of-charge ca
 ncellation is **31 July 2025**. Cancellation after this date will not be r
 eimbursed. Please note that participation in SIB courses is subject to thi
 s and other general conditions\, available [here](https://www.sib.swiss/tr
 aining/terms-and-conditions).\n\n\n# Venue and time\nThis course will take
  place **only in 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 will be provided to the participants in due time.\n# Schedule
  \n\n### Day 1 - Natasha Glover and Christophe Dessimoz (UniL and SIB) - I
 ntroduction to molecular evolution &amp\; phylogenetics\nInterpret phyloge
 netic trees and alignments\; general understanding of how trees are inferr
 ed\; knowing the definition of orthology\, paralogy and their subtypes\; u
 nderstanding the difference between pairwise and groupwise comparisons\; a
 bility to perform orthology inference through tree overlap method\; abilit
 y to retrieve orthology information from the OMA database\; ability to inf
 er orthologs using the OMA standalone pipeline.  **Teaching assistants for
  practical exercises: Stefano Pascarelli and Athina Gavriilidou.**\n\n* 9:
 00-12:00: Lectures - Introduction to molecular evolution &amp\; phylogenet
 ics\; Inferring Orthology and Paralogy \n* 12:00 - 13:00: Lunch break\n*  
 13:00-17:00: Hands-on - exercises on orthology inference through tree over
 lap methods\, tree reconciliation\, OMA database\, OMA standalone\n\n\n###
  Day 2 - Robert Waterhouse (UniL and SIB) - Orthology-focused arthropod co
 mparative genomics\nUnderstand the principles of graph-based orthology del
 ineation using OrthoDB as an example\; learn how to browse and programmati
 cally query OrthoDB\; learn how to use BUSCO to assess genomics data quali
 ty\; learn how to formulate comparative genomics questions\, develop and a
 pply approaches to address them (with a focus on using orthology data)\, a
 nd then critically interpret them\, through case studies from arthropods. 
 **Teaching assistant for practical exercises: Giulia Campli.**\n\n* 9:00-1
 2:00: Lectures - Introduction to OrthoDB &amp\; 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 phylogenomics and OrthoDB for gene
  family evolution\n\n### Day 3 - Marc Robinson-Rechavi (UniL and SIB) - Ev
 olutionary study of gene function\nUnderstand the importance of gene and g
 enome duplication in comparative genomics\; understand the difficulty of c
 omparing “function” between homologous genes\, and know some tools to 
 do so. **Teaching assistant for practical exercises: Alessandro Brandulas 
 Cammarata and Marion Nyamari**\n\n* 9:00-10:00 Lecture - Function in model
  vs non-model organisms\n* 10:15-11:00 Hands-on Exercise - Finding informa
 tion about gene function at small scale\n* 11:15-12:15 Lecture - Function 
 at large scale\n* 12:15 - 13:15: Lunch break\n* 13:15-14:15 Hands-on Exerc
 ise - Finding information about gene function of a group of genes\n* 14:30
 -15:30 Lecture - Gene and genome duplication\n* 15:45-17:00 Hands-on Exerc
 ise - Function of duplicate genes\n\n# Additional information\nCoordinatio
 n: Valeria Di Cola\, SIB Training Group.\n\nWe will recommend 0.75 ECTS cr
 edits for this course (given a passed exam at the end of the course).\n\nY
 ou are welcome to register to the SIB courses mailing list to be informed 
 of all future courses and workshops\, as well as all important deadlines u
 sing the form [here](https://lists.sib.swiss/postorius/lists/courses.lists
 .sib.swiss/).\n\nPlease note that participation in SIB courses is subject 
 to our [general conditions](https://www.sib.swiss/training/terms-and-condi
 tions).\n\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-europ
 e.org/events/code-of-conduct). Participants of SIB courses are also requir
 ed to abide by the same code.\n\nFor more information\, please contact [tr
 aining@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/20250825_COMGE
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