BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260407T181506Z UID:8a3b228a-9f71-424b-b303-df0244e3ac05 DTSTART:20240830T090000Z DTEND:20240830T170000Z DESCRIPTION:The recordings of this course are available on YouTube:\n1. [IS MARA: Theory and overview of the results](https://www.youtube.com/watch?v= oma9RDHk9ww)\n2. [CREMA: Theory and overview of the results](https://www.y outube.com/watch?v=jth2iKiX5d8)\n3. [Using the ISMARA and CREMA web interf aces](https://www.youtube.com/watch?v=oGxQoeo80Pg)\n \n\n## Overview\nMoti f Activity Response Analysis (MARA) is a powerful method that automaticall y infers the most important regulatory interactions acting in a given biol ogical system of interest from either gene expression or chromatin state d ata. It takes as input either gene expression (i.e. RNA-seq or micro-array )\, chromatin accessibility (i.e. ATAC-seq or DNase-seq) or epigenome (i.e . ChIP-seq of histone modifications)\, typically in the form of raw sequen cing data files\, and then models these data in terms of computationally p redicted transcription factor binding sites. In this way\, the method infe rs the key regulators acting in the system of interest\, how they change t heir activity across the input samples\, the genomic target regions and ge nes of each regulator\, and so on. MARA analysis has been completely autom ated and is provided through two online tools: [ISMARA](https://ismara.uni bas.ch/mara/) and [CREMA](https://crema.unibas.ch/crumara/). Researcher ca n simply upload their raw data and obtain a comprehensive report on the re gulatory network structure within an interactive graphical web interface.\ nIn this 1-day course\, participants will learn how to use the online tool s with their own data\, including all the functionalities that the interfa ce provides\, how to explore the results that the system produces\, how to perform tailored downstream analyses\, and how to interpret the various r esults and predictions.\n\n\n## Audience\nThis course is aimed at PhD stud ents\, post-docs and researchers in life sciences wanting to make computat ional inferences about gene regulation from gene expression data\, chromat in accessibility and epigenetic mark data. The course is targeted to a wid e audience ranging from computational biologists and bioinformatics resear chers who regularly analyse transcriptome and epigenome data\, to experime ntal researchers interested in inferring key regulatory interactions in th eir own data.\n\n## Learning outcomes\nAt the end of the course\, the part icipants are expected to:\n* Describe the analysis approach used by ISMARA and CREMA.\n* Use the ISMARA and CREMA web server.\n* Use the interactive web interface to generate tailored analyses.\n* Gain a detailed understan ding of the meaning and interpretation of the results and predictions prov ided by these methods.\n\n\n## Prerequisites\n##### Knowledge / competenci es\nParticipants are expected to be familiar with the molecular biology of gene regulation in higher eukaryotes.\n\nNo specific bioinformatics skill s are necessary. \n\n##### Technical\nThis webinar will be streamed\; you are thus required to have your own computer with an Internet connection.\n \n**To optimally benefit from the course\, participants are highly encoura ged to upload their own datasets at least a week in advance. This will all ow them to explore the results of these analyses on their own data.**\n\n\ n## Schedule - CET time zone\n9:00 – 10:30 Introduction to Motif Activit y Response Analysis. Transcription factor binding site predictions\, proce ssing of raw high-throughput data\, and the MARA model. \n10:30 – 11:0 0 Coffee break \n11:00 – 12:30 Using ISMARA and CREMA: supported species and data types\, different ways of data uploading. Overview of the basic results provided by the tools: list of key regulators\, their activities\, lists of target genes\, and core networks. \n12:30 – 13:30 Lunch break \n13:30 – 15:00 Advanced interactive features. Exploring the regulation of specific target genes. Pathways targeting by specific regulators. Aver aging across replicate samples. Calculating contrasts between subsets of s amples. \n15:00 – 15:30 Coffee break \n15:30 – 17:00 Hands-on exercise s in which users explore results using their own datasets.\n\n\n## Applica tion\nAttendance is free-of-charge\; however\, registration is mandatory.\ n\nYou will be informed by email of your registration confirmation.\n\n## Venue and Time\nThis course will be streamed.\n\nThe course will start at 9:00 CET and end around 17:00 CET.\n\nPrecise information will be provided to the participants in due time.\n\n\n## Additional information\nCoordina tion: 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 wor kshops\, as well as all important deadlines using 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](h ttps://www.sib.swiss/training/terms-and-conditions).\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 [training@sib.swiss](mailto://tr aining@sib.swiss). SUMMARY:ISMARA and CREMA: automatically inferring gene regulatory networks from gene expression\, chromatin accessibility or epigenome data URL;VALUE=URI:https://www.sib.swiss/training/course/20240830_ISMCM END:VEVENT END:VCALENDAR