BEGIN:VCALENDAR
VERSION:2.0
PRODID:icalendar-ruby
CALSCALE:GREGORIAN
BEGIN:VEVENT
DTSTAMP:20260622T040121Z
UID:d5567326-76c0-40c1-826d-0ad43adebe78
DTSTART:20260325T090000Z
DTEND:20260325T170000Z
DESCRIPTION:Attendance is free of charge\; however\, registration is mandat
 ory.\n\n# Overview\nSingle-cell omics data hold great promise for understa
 nding complex biological processes\, but exploring these data is complicat
 ed by their high-dimensionality and the dominance of measurement noise. St
 andard exploration methods\, like UMAP and t-SNE\, embed the data into two
  dimensions\, which provably distorts structures in the high-dimensional d
 ata and even hallucinates new structures. The consensus in the field seems
  to be that these tools are merely used because there is no better alterna
 tive. \n\nAn alternative\, [Bonsai](https://github.com/dhdegroot/Bonsai-da
 ta-representation) ([preprint](https://www.biorxiv.org/content/10.1101/202
 5.05.08.652944v1))\, reconstructs the most likely tree structure that rela
 tes high-dimensional objects while rigorously accounting for heterogeneous
  measurement noise. Unlike other visualization tools\, Bonsai preserves tr
 ue distances between objects and automatically regularizes noise. We also 
 introduce the accompanying online tool\, [Bonsai-scout](https://bonsai.uni
 bas.ch)\, which enables interactive exploration of the tree structure. \n\
 nIn this 0.5-day course\, we will combine an explanation of the theoretica
 l underpinnings of Bonsai\, with hands-on exercises in which we show how t
 o reconstruct a Bonsai-tree on your own data\, how to interpret the result
 s in Bonsai-scout and\, finally\, how to  turn these into publication-read
 y figures.  \n\n# Audience\nThis course is designed for PhD students\, pos
 tdoctoral and other researchers in the life sciences from both academia an
 d industry who are interested in analysing high-dimensional single-cell da
 ta.\n\n# Learning outcomes\nAt the end of the course\, participants are ex
 pected to: \n* Explain the Bonsai method and its advantages for high-dimen
 sional data exploration.\n* Apply Bonsai to construct trees from high-dime
 nsional data. \n* Explore and interpret Bonsai results using the Bonsai-Sc
 out web server. \n* Use and adapt downstream analyses of examples in Jupyt
 er notebooks\nto generate publication-ready figures from Bonsai output. \n
 \n# Prerequisites\n##### Knowledge / competencies\nThis course is designed
  for beginner level users. Participants should be familiar with single-cel
 l data. \n\nDuring the course\, we offer participants the opportunity to a
 sk questions about the analysis of their own data. In the case of scRNA-se
 q data\, it is recommended to **upload your scRNA-seq data at least a week
  in advance** to the Bonsai-Scout web server at [https://bonsai.unibas.ch]
 (https://bonsai.unibas.ch).\n\nTo facilitate the hands-on experience with 
 tree reconstructions\, participants should already **clone the Bonsai GitH
 ub repository** at [https://github.com/dhdegroot/Bonsai-data-representatio
 n](https://github.com/dhdegroot/Bonsai-data-representation) and follow the
  instructions in the ReadMe to **install the right Conda environments**. W
 e recommend that participants meet the learning outcomes of [Version Contr
 ol with Git](https://www.sib.swiss/training/course/GITVC).\n\n##### Techni
 cal\nParticipants are required to have their own computer with an Internet
  connection.\n\n# Application\nAttendance is free of charge\; however\, re
 gistration is mandatory. Applications will close on **18/03/2026**.\n\nYou
  will be informed by email of your registration confirmation.\n\nPlease no
 te that participation in SIB courses is subject to our [general conditions
 ](https://www.sib.swiss/training/terms-and-conditions).\n\n# Venue and Tim
 e\nThis course will be streamed using Zoom.  \n\nIt will start at 14:00 CE
 T (08:00 EST) and end around 18:00 CET (14:00 EST). \n\nPrecise informatio
 n will be provided to registered participants in due course.  \n\n#  Addit
 ional information\nCoordination: Monique Zahn\, SIB Training group.\n\nYou
  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 usi
 ng the form [here](https://lists.sib.swiss/mailman/listinfo/courses).\n\nP
 lease note that participation in SIB courses is subject to our [general co
 nditions](https://www.sib.swiss/training/terms-and-conditions).\n\nSIB abi
 des 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 [training@sib.swiss](
 mailto://training@sib.swiss).
SUMMARY:Bonsai: Exploratory Analysis of Single-cell Data
URL;VALUE=URI:https://www.sib.swiss/training/course/20260325_BNSAI
END:VEVENT
END:VCALENDAR