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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241028T090000
DTEND;TZID=Europe/Stockholm:20241101T170000
DTSTAMP:20260407T225420
CREATED:20240808T121308Z
LAST-MODIFIED:20240809T075123Z
UID:10001316-1730106000-1730480400@www.scilifelab.se
SUMMARY:R Programming Foundations for Data Analysis
DESCRIPTION:The course is addressed to individuals with little or no experience in programming but who are enthusiastic about learning how to use R for data analysis and streamline their work. It is a national course open for PhD students\, postdocs\, researchers and other employees in all Swedish. We also welcome applications from outside of Sweden (EU-zone) and from the non-academic sector\, for more info contact us. NOTE: In October 2024\, the course will be a 5-day-course on-site both in Uppsala and Lund. \n\n\n\n\n\n\n\nVenue – onsite\n\n\n\n\nUppsala University: Experimental room\, Campus Blåsenhus\, von Kraemers allé 1A\, 2nd floor\n\n\n\nLund University: Retina D227\, Biologihuset\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\n\nApplication open: August 08\, 2024\n\n\n\nApplication deadline: September 30\, 2024\n\n\n\nConfirmation to accepted students: October 4\, 2024\n\n\n\n\nResponsible teachers: Nima Rafati\, Guilherme Dias\, Miguel Angel Redondo\, Marcin Kierczak\, Lokeshwaran Manoharan\, Louella Vasquez \n\n\n\nContact for questions: edu.r@nbis.se \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK for non-profit organizations or 15000 SEK for private companies will be invoiced to accepted participants. This includes lunches\, coffee\, snacks\, and one course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\nCourse content\n\n\n\nThe course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting. After introductory lectures on good programming practices\, basic software design theory and a brief overview of R\, we will delve into programming. We start by learning how to use R as a basic calculator\, what are variable types\, how to use data structures\, how to implement repeating actions with and without loops\, and how to take actions based on certain conditions. We gradually proceed to loading data\, importing data from common file formats\, some basic matrix algebra and learning how to perform basic statistical tests and visualize results. You will learn how to document your work and how to generate automatic reports using real-life datasets. During the course you will also be working on a small dataset to apply knowledge you learnt in the course and will present that in a report format towards the end of the workshop. \n\n\n\nTopics covered will include: \n\n\n\n\nVariables and Operators\n\n\n\nMatrices\, lists\, and dataframes\n\n\n\nData manipulation\n\n\n\nVisualization\n\n\n\nR packages\n\n\n\nBioconductor\n\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nDescribe different data structures commonly used in R.\n\n\n\nWork with different data types.\n\n\n\nImport and export data from and to R environment. \n\n\n\nManipulate data.\n\n\n\nWork with dataframes and lists.\n\n\n\nVisualize the data.\n\n\n\nUse R Markdown to create reports containing text\, code\, tables and/or figures.\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nGood general computer literacy is expected\, but no previous experience in programming or R is required. You are expected to know basic concepts in mathematics and statistics\, but the emphasis of the course is to learn how to use R. \n\n\n\nParticipants are expected to use their own computers with pre-installed R and R Studio (detailed instructions will be given upon acceptance). \n\n\n\nDue to our best practice to have a high teacher to student ratio\, there are a maximum number of allowed participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/r-programming-foundations-for-data-analysis/
LOCATION:Uppsala University\, Lund University
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241111T090000
DTEND;TZID=Europe/Stockholm:20241115T170000
DTSTAMP:20260407T225420
CREATED:20240619T091221Z
LAST-MODIFIED:20240920T111426Z
UID:10001282-1731315600-1731690000@www.scilifelab.se
SUMMARY:Introduction to Python - with application to bioinformatics
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of fundamental Python skills. We also welcome applications from outside of Sweden and from the non-academic sector\, for more info contact us! \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-06-11 \n\n\n\nApplication closes: 2024-09-30 \n\n\n\nConfirmation to accepted students: 2024-10-02 \n\n\n\nCourse Leader and teachers: Dimitris Bampalikis (CL)\, Jeanette Tångrot (CL)\, Nanjiang Shu\, Nina Norgren \n\n\n\nContact: edu.intro-python@nbis.se \n\n\n\n\n\n\n\nCourse locations\n\n\n\nSciLifeLab Uppsala\, Entrance C11\, BMC\, Husargatan 3\, Uppsala OR Umeå University\, Naturvetarhuset\, room NAT.D.370 OR Lund University\, Biologihuset\, rooms Cerebrum höger (D215b) and Cerebrum vänster (D215a) \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK  for academic participants and 15000 SEK for non-academic participants will be invoiced to accepted participants. The fee includes lunches\, coffee and snacks\, and course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse content\n\n\n\n This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course\, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs. \n\n\n\nFormat \n\n\n\nThis course runs in parallel on-site in Uppsala\, Umeå and Lund. Lectures will be streamed online from our Uppsala site to the Umeå and Lund sites. Several teaching assistants will be present in all three classrooms all week to help with exercises and questions. When registering you will be asked to which site you apply. \n\n\n\nThe course consists of a mix of presentations\, demonstrations\, and practical exercises (either in the lab with assistants or on your own). Prior to the course\, you can read a companion book “Programming Python”\, or “Learning Python”. Such a book will also prove useful for your programming tasks\, after the course is over. It is however not required\, and material will be presented in class. \n\n\n\nTopics covered will include: \n\n\n\n\nCore concepts about Python syntax: Data types\, blocks and indentation\, variable scoping\, iteration\, functions\, methods and arguments\n\n\n\nDifferent ways to control program flow using loops and conditional tests\n\n\n\nRegular expressions and pattern matching\n\n\n\nWriting functions and best-practice ways of making them usable\n\n\n\nReading from and writing to files\n\n\n\nCode packaging and Python libraries\n\n\n\nHow to work with biological data using external libraries.\n\n\n\n\n\n\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nDescribe and apply basic concepts in Python\, such as:LoopsIf/else statementsFunctions\n\nReading/writing to files\n\n\n\n\n\nBeing able to edit and run Python code\n\n\n\nWrite file-processing Python programs that produce output to the terminal and/or external files\n\n\n\nCreate stand-alone python programs to process biological data\n\n\n\nKnow how to develop your skills in Python after the course (including debugging)\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage\, such as navigating through folders and issuing commands at a shell prompt. We will not teach UNIX in detail: Other courses are available at SciLifeLab for it. Make sure your laptop has python installed for the practical exercises. \n\n\n\n\n\n\n\nSelection criteria\n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants in Uppsala and 15 in Umeå and Lund. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance. \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to 1.5 hp credits\, however the estimated credits are just recommendations. If formal credits are crucial\, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/introduction-to-python-with-application-to-bioinformatics/
LOCATION:Uppsala University\, Lund University or Umeå University
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241119T090000
DTEND;TZID=Europe/Stockholm:20241121T170000
DTSTAMP:20260407T225420
CREATED:20240701T075350Z
LAST-MODIFIED:20241007T120309Z
UID:10001291-1732006800-1732208400@www.scilifelab.se
SUMMARY:Introduction to Data Management Practices
DESCRIPTION:National Bioinformatics Infrastructure Sweden (NBIS) gives a course in research data management practices. This workshop in Data Management is a unique event that provides an introduction to practices for better data management for PhD students\, postdocs\, researchers\, and other employees within all Swedish universities. We also welcome applications from outside of Sweden and from the non-academic sector; for more information\, contact us. \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication closes: 2024-10-13 \n\n\n\nInformation to accepted students will be sent: 2024-10-15 \n\n\n\nContact: edu.intro-dm@nbis.se \n\n\n\nVenue: Experimental classroom\, Campus Blåsenhus\, Uppsala University \n\n\n\nFormat: This workshop runs on-site Campus Blåsenhus\, Uppsala. Teachers and teaching assistants will be present all three days to help with exercises and questions. \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 2000 SEK for academic and 9500 SEK for non-academic participants and will be invoiced to the participant’s organisation. This includes lunches\, coffee\, and snacks and one course dinner. If you accept a position and do not participate (no-show)\, you will still be invoiced the full fee. Please note that NBIS cannot invoice individuals. \n\n\n\n\n\n\n\nCourse description\n\n\n\nThe workshop will introduce important research data management aspects through lectures\, demonstrations\, and hands-on computer exercises. The course is intended for researchers who want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. \n\n\n\nTopics covered will include: \n\n\n\n\nOpen Science and FAIR in practice\n\n\n\nOrganising data\, files and folders in research projects\n\n\n\nDescribing data with metadata\n\n\n\nPublishing data to public data repositories\n\n\n\nCleaning tabular data and metadata with OpenRefine\n\n\n\nWriting basic recipes for data analysis and visualisation with R\n\n\n\nVersioning data\, documents and scripts\n\n\n\nWriting Data Management Plans\n\n\n\n\n\n\n\n\nCredits & Certificate\n\n\n\nPlease note that NBIS training events do not provide any formal university credits. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating the topics covered and the duration of the workshop. \n\n\n\nDue to limitations in space and capacity\, the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria\, including correct entry information\, motivation to attend the course\, as well as gender and geographical balance. \n\n\n\nFor more detailed information about the workshop\, please visit the workshop website. \n\n\n\n\n\n\n\nEntry requirements\n\n\n\nNo previous programming experience is required\, but you are required to bring your own laptop with the required software pre-installed. The course organisers arrange a pre-course event approximately one week prior to the first-course day.
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-8/
LOCATION:Campus Blåsenhus\, von Kraemers allé 1A\, 750 02 Uppsala
CATEGORIES:Course
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241124T090000
DTEND;TZID=Europe/Stockholm:20241129T170000
DTSTAMP:20260407T225420
CREATED:20240703T145519Z
LAST-MODIFIED:20240703T145521Z
UID:10001292-1732438800-1732899600@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within Swedish academia\, introducing the analysis of next generation sequencing data. \n\n\n\nThe course is organized by: National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI) \n\n\n\nResponsible teachers: Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\nContact information: edu.intro-ngs@nbis.se  \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens: July 4\, 2024 \n\n\n\nApplication closes: Oct 13\, 2024 \n\n\n\nConfirmation to accepted participants: 1 week after application deadline \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 3000 SEK for academic participants and 15 000 SEK for non-academic participants\, invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced at the standard fee. Please note that NBIS cannot invoice individuals.  \n\n\n\n\n\n\n\nCourse description\n\n\n\nThis intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform\, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures.  \n\n\n\n\n\n\n\nCourse content\n\n\n\nBriefly\, the workshop covers the followings major topics: \n\n\n\n\nWorking on the UNIX/LINUX command line\n\n\n\nBioinformatic/NGS data formats and QC\n\n\n\nDNA variant calling workflow essentials\n\n\n\nRNA sequence analysis workflow essentials\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\nAfter this workshop you should be able to: \n\n\n\n\nDescribe the basic principles of next generation sequencing.\n\n\n\nUse the Linux command line interface to manage simple file processing operations\, and organise directory structures.\n\n\n\nConnect to and work on a remote high performance compute cluster.\n\n\n\nApply programs in Linux for analysis of NGS data.\n\n\n\nSummarise the applications of current NGS technologies\, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.\n\n\n\nExplain common NGS file formats.\n\n\n\nInterpret quality control of NGS reads.\n\n\n\nExplain the steps involved in variant calling using whole genome sequencing data.\n\n\n\nIndependently perform a basic variant calling workflow on example data.\n\n\n\nDemonstrate hands-on experience with handling raw RNA sequencing data\, QC and quantification of gene expression.\n\n\n\nExplain the steps involved in differential gene expression using RNA seq data.\n\n\n\n\n\n\nEntry requirements\n\n\n\nTo be able to follow the workshop you need to: \n\n\n\nBYOL\, bring your own laptop configured according to precourse instructions. \n\n\n\nHave a background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable. \n\n\n\nTo get the maximum benefit from the workshop you should: \n\n\n\nHave a research project where you are currently using or are planning to use next generation sequencing.  \n\n\n\n\n\n\n\nSelection criteria\n\n\n\nDue to limited space the course can accommodate a maximum of 30 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers\, and we will prioritise applications  from Swedish academia.
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-4/
LOCATION:Linköping\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241125T080000
DTEND;TZID=Europe/Stockholm:20241129T170000
DTSTAMP:20260407T225420
CREATED:20240823T090255Z
LAST-MODIFIED:20240823T090341Z
UID:10001335-1732521600-1732899600@www.scilifelab.se
SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research
DESCRIPTION:NBIS / ELIXIR-SE course open for PhD students\, postdocs\, group leaders and core facility staff at all Swedish universities interested in making their computational analysis more reproducible. \n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-08-26 \n\n\n\nApplication closes: 2024-10-18 \n\n\n\nConfirmation to accepted students: 2024-10-25 \n\n\n\nCourse Leader and teachers: \n\n\n\n\nJohn Sundh (CL)\n\n\n\nErik Fasterius (CL)\n\n\n\nEstelle Proux-Wéra\n\n\n\nLokeshwaran Manoharan\n\n\n\nTomas Larsson\n\n\n\nCormac Kinsella\n\n\n\nMahesh Binzer-Panchal\n\n\n\n\nIn case you miss information on any of the above dates\, please contact:  edu.trr@nbis.se \n\n\n\nApply here\n\n\n\nContact information: edu.trr@nbis.se \n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK will be invoiced to accepted participants. The fee includes lunches\, coffee/tea and snacks as well as a course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse content\n\n\n\nThis course will introduce best practices in making research reproducible – from code tracking to software packaging and documentation – via short lectures and hands-on tutorials. \n\n\n\nTopics covered will include: \n\n\n\n\nGood practices for data analysis\n\n\n\nVersion control and collaborative code development\n\n\n\nPackage and environment management\n\n\n\nWorkflow management\n\n\n\nDocumentation and reporting\n\n\n\nContainerized computational environments\n\n\n\n\nLearning Outcomes \n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nOrganize and structure computational projects\n\n\n\nTrack changes and collaborate on code using Git\n\n\n\nInstall packages and manage software environments using Conda\n\n\n\nStructure computational steps into workflows with Snakemake and Nextflow\n\n\n\nCreate automated reports and document their analyses with Quarto and Jupyter\n\n\n\nPackage and distribute computational environments using Docker and Singularity\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required for being able to follow the course and complete the exercises: \n\n\n\n\nFamiliarity with using the terminal (e.g. be familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.)\n\n\n\nSome knowledge in R and/or python is beneficial but not strictly required\n\n\n\n\nDue to limited space the course can accommodate a maximum of 20 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/nbis-elixir-se-tools-for-reproducible-research-3/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241125T090000
DTEND;TZID=Europe/Stockholm:20241129T170000
DTSTAMP:20260407T225420
CREATED:20240918T091340Z
LAST-MODIFIED:20240918T091341Z
UID:10001358-1732525200-1732899600@www.scilifelab.se
SUMMARY:Biostatistics and Machine Learning II
DESCRIPTION:National course for PhD students\, researchers\, and other employees across Swedish universities who seek to deepen their biostatistical and machine learning skills.  Building on the Introduction to Biostatistics and Machine Learning course\, this course expands on common life science data analysis methods\, including dimensionality reduction techniques beyond PCA\, mixed-effects models for analysis of repeated measures\, and survival analysis. We will also dive deeper into machine learning\, covering more classification algorithms\, ensemble techniques\, optimization strategies and PLS methods for single and multi-omics data analysis. \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: now \n\n\n\nApplication closes: 2024-10-18 \n\n\n\nConfirmation to accepted students:  2024-10-25 \n\n\n\nResponsible teachers:  Payam Emami\, Olga Dethlefsen\, Eva Freyhult \n\n\n\nIf you do not receive information according to the above dates please contact edu.ml-biostats@nbis.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee of 3000 SEK for academic participants and 15 000 SEK for non-academic participants will be invoiced to accepted participants. The fee includes lunches\, coffee and snacks. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse content\n\n\n\n\nDimensionality reduction techniques beyond PCA\n\n\n\nClassification algorithm and ensemble techniques\n\n\n\nMachine learning optimization strategies\n\n\n\nPLS-based methods for single and multi-omics data analysis\n\n\n\nMixed-effects models for repeated measures\, longitudinal studies and nested designs\n\n\n\nSurvival analysis\n\n\n\nIntroduction to neural networks\n\n\n\n\n\n\n\n\nEducation\n\n\n\nIn this course\, we focus on an active learning approach. The education consists of teaching blocks alternating between lectures\, group discussions\, live coding sessions etc. \n\n\n\n\n\n\n\nEntry requirements\n\n\n\n\nBasic R and Python data science skills (for more details see course website)\n\n\n\nHaving attended the Introduction to Biostatistics and Machine Learning course or having equivalent knowledge\n\n\n\nBYOL (bring your own laptop)\n\n\n\n\nThe course can accommodate a maximum of 24 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/biostatistics-and-machine-learning-ii/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS & Training Hub":MAILTO:traininghub@scilifelab.se
END:VEVENT
END:VCALENDAR