BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260407T181224Z UID:8414d721-55c0-4361-b8e7-2e7435574987 DTSTART:20260621T090000Z DTEND:20260626T170000Z DESCRIPTION:**This School is co-organized by SIB/ELIXIR Switzerland and [de .NBI/ELIXIR Germany](https://www.denbi.de/)**\n## Overview\nBiodiversity i s fundamental to ecosystem functioning\, yet it is facing unprecedented pr essure. Advances in the generation\, analysis and integration of omics dat a by bioinformatics tools are transforming our ability to study biodiversi ty across scales through comprehensive\, high-throughput molecular profili ng of organisms and ecosystems. This summer school aims to equip life scie ntists with extended knowledge and practical skills to address these chall enges. \n\nIt will follow a hackathon / mini-project format\, with around 20 hours dedicated to hands-on training and collaborative problem-solving. Each participant will work within a single group throughout the week\, fo stering deep engagement\, collaborative problem-solving\, and the exchange of knowledge and expertise. Experienced trainers will guide four groups\, focusing on the following topics:\n\n* **Biodiversity across scales – f rom eDNA to ecosystems**\n* **Pangenomes: Capturing genetic diversity beyo nd a single reference**\n* **Computing genomic essential biodiversity vari ables**\n* **Evolutionary and functional insights from large-scale compara tive genomics** \n\nTo complement the project work\, the programme will in clude lectures and a social activity. Participants will stay together in a comfortable hotel\, creating an environment that encourages informal exch anges and networking beyond the formal sessions. Accommodation and meals a re included in the registration fee\, allowing participants to focus entir ely on training\, collaboration\, and community building. \n\n\n##### Topi c 1: Biodiversity across scales – from eDNA to ecosystems\nThis project introduces the background and conceptual foundations of environmental DNA (eDNA) metabarcoding as a powerful tool for biodiversity assessment. Parti cipants will gain a theoretical overview of key laboratory steps\, from sa mple processing to sequencing\, and explore different bioinformatic pipeli nes that transform raw sequencing reads into taxonomic lists and ecologica l diversity metrics. Emphasis is placed on understanding methodological ch oices\, sources of bias\, and best practices across workflows. The project is designed as a hands-on training\, guiding participants step by step fr om raw sequencing data to interpretable biodiversity results. Each partici pant will build and run their own analysis pipeline\, enabling a practical understanding of metabarcoding data generation and analysis. The course c oncludes by highlighting ecological and applied use cases of metabarcoding in biodiversity research and monitoring.\n**Trainers**\nDr Vera Zizka\, T he State Museum of Natural History\, Karlsruhe\nDr Ameli Kirse\, Leibniz I nstitute for the Analysis of Biodiversity Change\n\n**Skills/experience ne eded for this topic**\n-basic command line experience\n-basic R software e xperience\n-basic knowledge in molecular sequencing data\n\n\n##### Topic 2: Capturing genetic diversity beyond a single reference\nIn this project\ , participants will experience the fundamental workflow of genomic analysi s\, beginning with the quality assessment and de novo assembly of raw sequ encing reads. Participants will proceed to characterize the obtained genom e assemblies through structural and functional gene annotation\, followed by variant calling to identify specific genetic differences. The project c oncludes with the construction of a graph-pangenome to model the full scop e of genetic diversity within a population.\n**Trainers**\nDr Marie Bolger \, Forschungszentrum Jülich\nDr Sebastian Beier\, Forschungszentrum Jüli ch\,\n\n**Skills/experience needed for this topic**\n-basic command line e xperience\n-some experience with sequencing technologies and associated da ta formats (eg.\, fasta\, fastq\, vcf)\n\n##### Topic 3: Computing genomic essential biodiversity variables\nEssential Biodiversity Variables (EBVs) are a set of standardized biological measurements designed to quantify an d report changes in biodiversity across time\, space\, and biological leve ls\, with the goal of informing and influencing policy‑making decisions. In this project\, participants will work in small groups to design and ca rry out a biodiversity genomics analysis aimed at quantifying EBVs. Starti ng from a conservation or management question\, they will use publicly ava ilable genomic datasets and develop an analysis plan\, spanning raw data q uality control\, read mapping\, and variant calling\, through to populatio n structure\, diversity\, inbreeding\, and effective population size metri cs. \nThe project emphasizes reproducible pipeline design using establishe d tools\, standard reference resources\, and careful interpretation of EBV outputs in the context of conservation\, bioeconomy\, and policy-making.\ n**Trainers**\nDr Tristan Cumer\, Department of Ecology and Evolution\, Un iversity of Lausanne\, Switzerland\nDr Chiara Bortoluzzi anb Dr Christian de Guttry\, Environmental Bioinformatics\, SIB Swiss Institute of Bioinfor matics\n\n**Skills/experience needed for this topic**\n-basic command line experience\n-basic R software experience\n**Nice to have:**\n-prior exper ience with sequencing technologies and associated data formats (e.g.\, FAS TA\, FASTQ\, VCF) would be beneficial\n-basic understanding of population genetics may be helpful\n\n##### Topic 4: Evolutionary and functional insi ghts from large-scale comparative genomics \nIn this project\, participant s will work in small groups to design and carry out a comparative genomics study addressing an evolutionary or functional question. Starting from a biological question\, they will identify relevant datasets\, plan appropri ate analyses (e.g. genome quality control\, orthology inference\, gene fam ily evolution\, functional annotation)\, and implement them using existing tools and resources. The project emphasizes methodological choices\, data interpretation\, and critical evaluation of results. Results will be synt hesized and presented at the end of the week.\n**Trainers**\nDr Natasha Gl over\, Comparative Genomics Group\, University of Lausanne and SIB Swiss I nstitute of Bioinformatics\nDr Robert Waterhouse\, Environmental Bioinform atics group\, SIB Swiss Institute of Bioinformatics\n\n**Skills/experience needed for this topic**\n-basic command line experience\n-basic familiari ty with at least one scripting language (Python or R)\n-general understand ing of genomics concepts (genes\, genomes\, annotations)\n *Nice to have:* \n-prior exposure to comparative genomics concepts (orthology\, gene famil ies\, synteny)\n-experience working with omics data (genomics\, transcript omics)\n-familiarity with bioinformatics workflows or pipelines\n-basic da ta visualization skills (R\, Python\, or similar)\n\n\n## Audience\nThis c ourse is designed for PhD students\, postdoctoral and other researchers in the life sciences from both academia and industry who are interested in b iodiversity bioinformatics.\n\n## Learning outcomes\nAt the end of the cou rse\, the participants are expected to:\n* understand the major challenges of biodiversity bioinformatics\n* have gained an in-depth knowledge of th e topic in which they participated\n* have played an active role in a grou p project and delivered a presentation of the results.\n\n## Prerequisites \n##### Knowledge / competencies\nThis course is designed for beginner to intermediate users\, and requires the following general skills/experience: \n\n* Previous experience with sequencing technologies and associated data formats (eg.\, fasta\, fastq\, vcf)\n* Basic command-line usage (Linux/Un ix) \n* Basic familiarity with at least one scripting language (Python or **R**) \n\nMore specific prerequisites are listed in the topics paragraph s above. \n\n\n##### Technical\nParticipants are required to bring their o wn laptop with administrative rights\, allowing them to install software a nd/or packages during the course if needed. However\, we expect all requir ed software—details of which will be communicated later—to be installe d **prior to the course**.\n\n## Schedule - CET time zone\n\nNote that the details of the schedule are informative\, changes are possible.\n\n**Sund ay**\n~18h00 Arrival and registration \n19h00 Dinner\n20h15 Welcome sess ion\n\n**Monday**\n09h00 General introduction + introduction to the 4 top ics\n10h30 Break\n11h00 Introduction to the 4 topics and/or Project work in groups\n12h30 Lunch\n14h00 Project work in groups (including a break )\n17h15 Recap of the day\n17h30 End\n\n**Tuesday**\n09h00 Project work in groups\n10h30 Break\n11h00 Lecture\n11h45 Project work in groups\n1 2h30 Lunch\n14h00 Project work in groups (including a break)\n17h15 Rec ap of the day\n17h30 End\n\n**Wednesday**\n09h00 Project work in groups\ n10h30 Break\n11h00 Lecture\n11h45 Project work in groups\n12h30 Lunch \n14h00 Social Activity\n17h15 Recap of the day\n17h30 End\n\n**Thursda y**\n09h00 Project work in groups\n10h30 Break\n11h00 Lecture\n11h45 P roject work in groups\n12h30 Lunch\n14h00 Project work in groups + proje ct presentation preparation (including a break)\n17h15 Recap of the day\n 17h30 End\n\n**Friday**\n09h00 Project presentations\n10h30 Break\n11h0 0 Project presentations\n11h45 Conclusion\n12h00 Lunch &\; back home \n\n\n## Application\n\nThe registration fees for academics are **900 CHF (~950 EUR)** and **1900 CHF (~2000 EUR)** for for-profit companies. Course fees and hotel accommodation (in single rooms)\, as well as meals are inc luded.\n\nApplicants will be contacted by email after submitting their app lication and invited to provide a **motivation letter** and complete a sho rt **survey** to let us know about your **topic preference(s)**. In the ev ent of oversubscription\, participants will be selected based on several c riteria\, which may extend the time required to confirm registration.\n\nY ou will be informed by email of your registration confirmation. Upon recep tion of the confirmation email\, participants will be asked to confirm att endance by paying the fees within 10 days.\n\nApplications will close on * *31 March 2026**. Deadline for free-of-charge cancellation is set to **2 A pril 2026**. Any cancellation after this date may be subject to penalties\ , depending on the possibility of replacement by someone in the waiting li st.\n\n**Summary of the process:**\n- application using the button at the top of the page\n- you receive an email containing instructions to send ba ck a motivation letter and to complete a survey to let us know your prefer ence(s)\n- validation of your participation or placed on a waiting list\n- payment\n\n\n## Venue and Time\nThe course will take place at the [Dorint Parkhotel Siegen](https://hotel-siegen.dorint.com/en/) in Germany.\n\nTo ensure every participant easy traveling\, the school will start on Sunday around 19h and end on Friday after lunch.\n\nPrecise information will be p rovided to the registered participants in due time.\n\n\n## Additional inf ormation\nCoordination: Helena Schnitzer (de.NBI and ELIXIR Germany) and G régoire Rossier (SIB).\n\n\nAt the end of the course\, we will provide a *Certificate of Achievement* recommending 2 ECTS credits.\n\n\nYou are wel come to register to the SIB courses mailing list to be informed of all fut ure courses and workshops\, as well as all important deadlines using the f orm [here](https://lists.sib.swiss/mailman/listinfo/courses).\n\n\nPlease note that participation in SIB courses is subject to our [general conditio ns](http://www.sib.swiss/training/terms-and-conditions).\n\n\nSIB abides b y the [ELIXIR Code of Conduct](https://elixir-europe.org/events/code-of-co nduct). Participants of SIB courses are also required to abide by the same code.\n\n\nFor more information\, please contact [us](mailto:gregoire.ros sier@sib.swiss\,h.schnitzer@fz-juelich.de). SUMMARY:Biodiversity Bioinformatics Summer School URL;VALUE=URI:https://www.sib.swiss/training/course/20260621_SSBIB END:VEVENT END:VCALENDAR