BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260407T181316Z UID:9e781765-abfa-4732-809e-f11ce12b29af DTSTART:20250121T090000Z DTEND:20250124T170000Z DESCRIPTION:**This course is now full with a long waiting list.** If you d o not want to miss your chance to be part of the next session and remain i nformed about all training activities at SIB\, we highly recommend you to keep an eye on our list of [upcoming events](https://www.sib.swiss/trainin g/upcoming-training-courses) and subscribe to our courses [mailing list](h ttps://lists.sib.swiss/mailman/listinfo/courses) here (if you haven't done so already).\n\n## Overview\nThis course delves into the cutting-edge fie ld of Spatial Omics\, focusing on Spatially-Resolved Transcriptomics (SRT) technology which provides unprecedented insights into the spatial organiz ation of gene expression within tissues. The rapid and recent advances in SRT technology are transforming our understanding of biological systems\, and this course is designed to equip researchers with the tools to harness the power of SRT\, adding significant value to biological knowledge and o pening new avenues for scientific discovery.\n\nParticipants will explore both imaging-based and sequencing-based SRT technologies\, learning to nav igate the entire workflow of SRT data analysis. The course covers essentia l topics such as pre-processing techniques for data cleaning\, normalizati on\, and quality control\, methods for identifying and characterizing spat ial domains within tissues\, strategies for integrating SRT data with sing le-cell RNA sequencing data\, and statistical approaches to analyze spatia l patterns and relationships. Additionally\, participants will investigate interactions between cells within their spatial context. By the end of th is course\, participants will be equipped with the knowledge and skills to construct a complete workflow for SRT data analysis\, from raw data to me aningful biological insights. The course combines lectures with practical sessions\, ensuring a balanced approach to theory and hands-on experience. \n\nThe course materials will be on the dedicated [GitHub page](https://g ithub.com/elixir-europe-training/ELIXIR-SCO-spatial-omics).\n\n## Audience \nThis 3-day course is addressed to PhD students\, postdocs\, and research ers who are involved (or will be in the near future) in projects including spatially-resolved transcriptomics data\, and want to acquire the skills to get started with spatial data analysis. \n\n## Learning outcomes \nAt t he end of the course\, the participants will be able to:\n* Identify and r ecall key concepts and terminology related to imaging- and sequencing-base d SRT technologies. \n* Assess and evaluate quality of SRT data.\n* Perfor m standard SRT data analysis\, including data cleaning\, normalization\, q uality control.\n* Examine and interpret spatial patterns and relationship s within SRT data using statistical and machine learning approaches.\n* Co nstruct a comprehensive workflow for SRT data analysis\, from raw data to meaningful biological insights.\n\n## Prerequisites\n##### Knowledge / com petencies\nParticipants should be proficient in Python and R\, for basic d ata analysis. \n\nParticipants should be familiar with NGS technologies\, have experience with analyzing (spatial/single-cell) transcriptomics data as well as basic knowledge of machine learning.\n\nParticipants should als o have a basic understanding of working with command line tools on Unix-ba sed systems. You can test your skills with Unix with the quiz here. If you do not feel comfortable with UNIX commands\, please take our Unix fundame ntals e-learning module.\n\n\n##### Technical\nParticipants are required t o bring your own laptop. \n\nWe will be mainly working on an Amazon Web Se rvices (AWS) Elastic Cloud (EC2) server. Our Ubuntu server behaves like a ‘normal’ remote server\, and can be approached through a web browser ( safari\, firefox\, chrome etc.). All participants will be granted access t o a personal workspace to be used during the course. The web interface wil l be approached through http (not https!)\, so make sure you can access ht tp sites. You can validate it [here](http://neverssl.com/).\n\nPlease perf orm these installations PRIOR to the course and contact us if you have any trouble.\n\n## Schedule - CET time zone\n**Day 1 (13:00 -17:00)**\n* Welc ome and course introduction\n* Overview of technologies\n* Imaging-based s patial data analysis\n\n **Day 2 (09:00 -17:00)**\n* Segmentation-free ana lysis \n* Sequence-based data analysis \n* Integration with scRNA-seq\, de convolution\, annotation\, imputation\n\n **Day 3 (09:00 -17:00)**\n* Grap h representations and niche reconstruction\n* Spatial domain identificatio n and spatial annotation\n* Spatial statistics \n* Guest lecture by [Maria Brbic](https://people.epfl.ch/maria.brbic) from EPFL\n\n **Day 4 (09:00 -12:30)**\n* Cell-cell communication\n* Course wrap-up\n\n\n## The trainer s\nThe course will feature the following lecturers and trainers:\n\n* Lars Borm (Katholieke Universiteit (KU) Leuven &\; Vlaams Instituut voor Bi otechnologie (VIB)\, BE)\n* Helena Crowell (Centro Nacional de Análisis G enómico (CNAG)\, ES)\n* Francesca Drummer (Helmholtz Zentrum München\, D E)\n* George Gavrillidis (Centre for Research and Technology Hellas (CERTH )\, GR)\n* Geert van Geest (SIB Swiss Institute of Bioinformatics\, CH)\n* Naveed Ishaque (Berlin Institute of Health (BIH)\, DE)\n* Ahmed Mahfouz ( Leiden University Medical Center (LUMC)\, NL)\n* Mark Robinson (University of Zurich (UZH) &\; SIB\, CH)\n* Yvan Saeys (University of Ghent (UGen t) &\; Vlaams Instituut voor Biotechnologie (VIB)\, BE)\n* Rasool Sagha leyni (NBIS/ELIXIR-SE\, SciLifeLab\, SE)\n* Anna Schaar (Helmholtz Zentrum München\, DE)\n* Marco Varrone (University of Lausanne (UNIL) &\; SIB \, CH)\n\n\n ## Application\n**This course is now full with a long waiting list. It is not possible to apply anymore. Thank you for your understandi ng** \n\nRegistration fees are **150 CHF** for academics and **750 CHF** f or for-profit companies.\n\nParticipants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivat ion to attend the course as well as gender and ELIXIR nodes balance.\n\n** To apply to this course and enter the selection process\, please fill in t his [questionnaire](https://forms.office.com/e/4BgWAvVCUg).** \n\nApplicat ions will close **01/11/2024**. The applications selection will start th e week of the **05/11/2024**. Accepted applicants will be notified by ema il by during the week of the **11/11/2024** and they will have until **22 /11/2024** to confirm their attendance by paying the fees. \n\nDeadline fo r free-of-charge cancellation is set to **27/11/2024**. Cancellation after this date will not be reimbursed. \n\n## Venue and Time\nThis course will take place at the University of Lausanne (UNIL).\n\nThe course will start the first day at 13:00. A light lunch will be provided before the start o f the course as well as at the end of the course on the last day. \n\nAll participants are invited to the social dinner\, organized on 21 January 2 025. \n\nPrecise information will be provided to the participants in due t ime.\n\n## Additional information\nThis is an international course hosted by the SIB Swiss Institute of Bioinformatics (ELIXIR-CH) in collaboration with the [ELIXIR Single-Cell Omics community](https://elixir-europe.org/co mmunities/single-cell-omics)\, and trainers’ own institutions and affili ations to ELIXIR nodes (KU Leuven\, VIB\, CNAG\, Helmholtz Zentrum Münche n\, CERTH\, SIB\, BIH\, LUMC\, UZH\, UGent\, NBIS SciLifeLab\, UNIL).\n\nC ourse organizers: \n* Ahmed Mahfouz\, Leiden University Medical Center (L UMC)\, ELIXIR - Netherlands\n* Diana Marek\, SIB Training group\, ELIXIR - Switzerland \n* Patricia Palagi\, SIB Training group\, ELIXIR - Switzerla nd\n* Eija Korpelainen\, CSC\, ELIXIR - Finland\n\n\nThis course is partia lly funded by an [ELIXIR Staff Exchange Programme](https://elixir-europe.o rg/internal-projects/staff-exchange-programme).\n\n\nWe will recommend 0.7 5 ECTS credits for this course (given a passed assessment).\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/postorius/lists/courses.lists.sib.swiss /).\n \nPlease note that participation in SIB courses is subject to our [g eneral conditions](https://www.sib.swiss/training/terms-and-conditions).\n \nCourse organizers and trainers abide by the [ELIXIR Code of Conduct](ht tps://elixir-europe.org/events/code-of-conduct). Participants are also req uired to abide by the same code. SUMMARY:Spatial Omics Data Analysis URL;VALUE=URI:https://www.sib.swiss/training/course/20250121_SPODA END:VEVENT END:VCALENDAR