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DTSTART;TZID=Europe/Stockholm:20240220T080000
DTEND;TZID=Europe/Stockholm:20240222T170000
DTSTAMP:20260408T035109
CREATED:20231215T082629Z
LAST-MODIFIED:20231215T082631Z
UID:10001070-1708416000-1708621200@www.scilifelab.se
SUMMARY:Basic Course in Scanning and Transmission Electron Microscopy for Life Sciences
DESCRIPTION:This course covers lectures and practical demonstrations in SEM and TEM techniques\, specifically for life science applications. The contents include principles of electron microscopy\, specimen preparation\, cryo-electron microscopy and correlative light-electron microscopy. For electron microscopy in physical science applications\, there will be a similar-content basic course organised later. \n\n\n\nRead more and register\n\n\n\nApplication deadline: The registration closes on 26 January 2024. \n\n\n\nLocation: Lectures at KBC Building and laboratory demonstrations at UCEM facility\, Umeå University \n\n\n\nParticipants: 18 persons \n\n\n\nInstructors: UCEM staff \n\n\n\nDuration: 3 days \n\n\n\nBreaks/Refreshments: Coffee\, cookies and fruit. \n\n\n\nCosts: No course fee\, but full attendance is required! \n\n\n\nExamination/Credits: Oral and practical examinations are conducted during laboratory demonstrations. A course certificate will be given after participants attend all lectures and laboratory demonstrations for this 3-day course. UCEM recommends PhD program examiners to give 1 ECTS after successful participation.
URL:https://www.scilifelab.se/event/basic-course-in-scanning-and-transmission-electron-microscopy-for-life-sciences-2/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/12/Bild1.jpg
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240311T080000
DTEND;TZID=Europe/Stockholm:20240315T170000
DTSTAMP:20260408T035109
CREATED:20231220T151424Z
LAST-MODIFIED:20240213T125934Z
UID:10001073-1710144000-1710522000@www.scilifelab.se
SUMMARY:RNA-seq data analysis
DESCRIPTION:This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of  lectures and computer practicals. \n\n\n\nTopics covered will include: \n\n\n\n\nRNAseq quality control analysis\n\n\n\nMapping of short reads\n\n\n\nQuantification of gene expression\n\n\n\nExploratory data analysis\n\n\n\nDifferential gene expression\n\n\n\nGene set enrichment analysis\n\n\n\n\nMore details about the course can be found at the previous year webpage: RNAseq course 2023 \n\n\n\nThe course will follow similar structure and topics. \n\n\n\nNOTE: in March 2024\, the course will be a 5-day-course on-site in Uppsala. \n\n\n\nRegister here\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises: \n\n\n\n\nBasic knowledge in Linux and R\n\n\n\nYour own laptop with the following specs:At least 6 GB of RAM.Operating system Win10\, OS X or Linux\n\nAt least 30 GB of free storage\n\n\n\n\n\n\nDesirable: \n\n\n\n\nExperience working with NGS data analysis or completed the NBIS workshop “Introduction to Bioinformatics using NGS data”\n\n\n\nExperience working in R or completed the NBIS course “R Programming Foundations for Life Scientists”\n\n\n\n\nDue to our best practice to have a high teacher to student ratio we have set the number of participants to a maximum of 20 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. \n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK for non-profit organisations 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\nImportant dates:\n\n\n\n\nApplication open: December 19\, 2023\n\n\n\nApplication deadline: February 19\, 2024\n\n\n\n\nResponsible teacher/s:Johan Reimegård\, Julie Lorent\, Nima Rafati \n\n\n\nContact information for questions regarding the courseedu.rnaseq@nbis.se
URL:https://www.scilifelab.se/event/rna-seq-data-analysis-2/
LOCATION:Uppsala University\, Uppsala\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240318T090000
DTEND;TZID=Europe/Stockholm:20240322T170000
DTSTAMP:20260408T035109
CREATED:20231214T083927Z
LAST-MODIFIED:20231214T083931Z
UID:10001069-1710752400-1711126800@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data – ONLINE
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\n\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: 13-December-2023 \n\n\n\nApplication closes: 05-February-2024 \n\n\n\nConfirmation to accepted students: Week 6\, 2024 \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\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 3000 SEK. 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 outcome\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\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-online-4/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240321T080000
DTEND;TZID=Europe/Stockholm:20240322T170000
DTSTAMP:20260408T035109
CREATED:20240125T130718Z
LAST-MODIFIED:20240223T112954Z
UID:10001125-1711008000-1711126800@www.scilifelab.se
SUMMARY:Introductory Course in Organisational learning
DESCRIPTION:How do we build a collaborative and innovative workplace? \n\n\n\nIn the first offering of this two-day course in Organizational Learning\, learn how we can adapt and improve as an organization through gathering\, sharing\, and applying knowledge. This course goes beyond individual skill development to building organizational culture and structure. Through creating and utilizing organizational processes that foster collective learning and development\, we can achieve the workplace we want. \n\n\n\nThe lectures\, discussions\, and exercises of this course will teach foundational principles and theories of Organizational Learning\, including concepts on organizational knowledge\, knowledge management\, and workplace training.We will also give you practical tools and sustainable strategies you can apply beyond the course—such as how to enhance learning at all levels\, from the individual (micro level)\, to group/team (meso level) and organization (macro level). \n\n\n\nWe welcome managers\, coordinators\, and leaders from all career stages to learn how to build a workplace culture of continuous learning in a resource-friendly way using organizational knowledge and collective intelligence! \n\n\n\nRegistration Deadline\n\n\n\nThere is no deadline for application. Applications will be accepted on a rolling basis\, and applicants will be confirmed their enrollment within 5 business days.  \n\n\n\nRegistration\n\n\n\nTargeted level of the training event:\n\n\n\nIntroductory level \n\n\n\nTarget Audience:\n\n\n\nInfrastructure managers\, SciLifeLab affiliated group leaders\, and other staff with managerial roles. \n\n\n\nPrerequisites:\n\n\n\nNo prior knowledge of organisational learning\, management or individual learning is required\, but experience from management is beneficial.  \n\n\n\nLearning Outcomes: \n\n\n\nBy the end of this course\, participants should be able to: \n\n\n\n– explain key concepts in Organisational Learning\, and how these relate to culture\, leadership and organisational processes. \n\n\n\n– identify similarities and differences between individual learning\, group learning and organisational learning \n\n\n\n– identify workplace learning activities\, and recognize how these can be designed to create additional organisational value \n\n\n\n–  identify barriers and promoters for knowledge dissemination and organisational learning \n\n\n\nSyllabus:\n\n\n\nDay 1 (Thursday 21.3.2024):                                          \n\n\n\nModule 1 – Introduction to Organisational Learning \n\n\n\nModule 2 – Basic concepts of Individual learning \n\n\n\nDay 2 (Friday 22.3.2024):                        \n\n\n\nModule 3 – Concepts of Organisational Learning \n\n\n\nModule 4 – How we promote organisational learning \n\n\n\nSpring 2024: \n\n\n\nAfter the course an optional follow-up session will be held online. Exact date will be decided by the participants. \n\n\n\nCourse fee:\n\n\n\nThere is no course attendance fee. Please note that the course does not include any meals or accommodation. \n\n\n\nSelection criteria:\n\n\n\nDue to limited space\, the course accommodates a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria such as correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nImportant dates\n\n\n\nApplication open: Jan 25\, 2024 \n\n\n\nApplication closes: Feb 20\, 2024 \n\n\n\nConfirmation to applicants Feb 23\, 2024 \n\n\n\nFor further questions\, please contact us at traininghub@scilifelab.se.
URL:https://www.scilifelab.se/event/organisational-learning/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="Training Hub":MAILTO:traininghub@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240410T123000
DTEND;TZID=Europe/Stockholm:20240410T163000
DTSTAMP:20260408T035109
CREATED:20240125T103059Z
LAST-MODIFIED:20240223T112828Z
UID:10001122-1712752200-1712766600@www.scilifelab.se
SUMMARY:SciLifeLab Train the Trainer Course
DESCRIPTION:This course offers guidance\, ideas and tips for designing training/teaching\, development and delivery on training activities\, all based on research-driven educational principles. This course will cover the following topics: \n\n\n\n\nLearning principles and how they apply to training and teaching\n\n\n\nDesign and plan session\, course\, materials\n\n\n\nTeaching techniques to enhance learner engagement and participation\n\n\n\nAssessment and feedback in training and teaching\n\n\n\nCreating and maintaining engagement\n\n\n\n\nCourse dates are: April 10\, April 17\, April 24 and May 2\, held from 12:30-16:30 each day \n\n\n\nRegistration Deadline: \n\n\n\nThe registration deadline is March 22\, 2024.  \n\n\n\nConfirmation to applicants 27-March-2024 \n\n\n\nThis course will be delivered through Zoom. You can find a link to the course pages below. \n\n\n\nRegistration\n\n\n\nNotes: \n\n\n\n\nThe course is highly interactive and hence it is important that you\, as a participant\, actively contribute to all sessions and elements of the course.\n\n\n\nThere are no fees for this course.\n\n\n\n\nAll are welcome to participate. \n\n\n\nLearning Objectives and Learning Outcomes\n\n\n\nLearning Objectives \n\n\n\n\nTo get acquainted with Learning principles and how they apply to training\n\n\n\nTo be able to select and use training techniques that can help enhance learner engagement and participation\n\n\n\nTo learn how to use assessment and feedback in training\n\n\n\nTo learn about session\, course\, and materials design as well as strategies for making learning engaging\n\n\n\n\nLearning Outcomes \n\n\n\nBy the end of this course\, learners will be able to: \n\n\n\n\nName learning principles that a good teacher/instructor should have in mind\n\n\n\nDescribe at least three training techniques\, drawing on learning principles\n\n\n\nDesign a training session and a course\n\n\n\nDevelop assessment questionnaires\n\n\n\nEnumerate types of materials needed for each part of a training session or course\n\n\n\n\nDescribe strategies to promote engagement amongst learners \n\n\n\nTarget Audience \n\n\n\nThis course is directed towards anyone who is interested in becoming a trainer/instructor\, or improving your training skills. \n\n\n\nPrerequisites\n\n\n\nEntry requirements \n\n\n\nThis course is directed towards anyone who is interested in becoming a trainer/instructor\, or improving your training skills. If you have questions like the following ones\, this course may be very helpful to you. \n\n\n\n\nHow learning works?\n\n\n\nHow do I use learning principles and theories to improve my teaching/training?\n\n\n\nHow do I make my teaching/training more engaging and effective?\n\n\n\nHow should I adjust my teaching/training to different types of learners?\n\n\n\nHow do I ensure learning progress?\n\n\n\nHow can I assess whether my students are actually understanding my lessons? Are they actually learning?\n\n\n\nWhat is the best balance between theory and practice?\n\n\n\nHow can I best assess whether learning is occurring and/or has occurred?\n\n\n\nWhat works in a classroom and what doesn’t?\n\n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria: Priority will be given to applicants from SciLifeLab infrastructures\, institutes and organizations across the Nordic research community\, and to participants from Nordic ELIXIR nodes. \n\n\n\nSyllabus\n\n\n\nPlease see the course website\, which will be updated regularly\, for more information: https://scilifelab-training.github.io/train-the-trainer/2403/
URL:https://www.scilifelab.se/event/scilifelab-train-the-trainer-course/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="Training Hub":MAILTO:traininghub@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240415T080000
DTEND;TZID=Europe/Stockholm:20240416T170000
DTSTAMP:20260408T035109
CREATED:20240318T115849Z
LAST-MODIFIED:20240318T120120Z
UID:10001209-1713168000-1713286800@www.scilifelab.se
SUMMARY:A primer on cryo-EM data processing using cryoSPARC on BerzeLiUs
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of cryo-EM data processing using national supercomputing resources. \n\n\n\nApplication\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-03-18Application closes: 2024-04-07Confirmation to accepted students: 2024-04-08 \n\n\n\nCourse Leader and teachers: Tim Schulte \, Piotr Draczkowski \n\n\n\nIn case you miss information on any of the above dates\, please contact: Tim Schulte \, Piotr Draczkowski \n\n\n\nCourse fee\n\n\n\nThe course is free of charge. \n\n\n\nCourse content\n\n\n\nWhat is this about? \n\n\n\nHow to use Berzelius compute cluster for cryo-EM data processing. We will process the beta- galactosidase dataset\, known from the Relion tutorials\, but applying cryoSPARC on BerzeLiUs\, as implemented by the PReSTO team. \n\n\n\nThe main purpose of this training is to learn how to: \n\n\n\n● access and use BerzeLiUs● apply Presto\, especially cryoSPARC on BerzeLiUs to process cryo-EM data \n\n\n\nWho should apply?\n\n\n\nAnyone interested in processing cryo-EM data using national supercomputing resources\, especially BerzeLiUs cluster. This is a primer for data processing on Berzelius\, not an introduction to cryo-EM. We expect applicants to be familiar with the general concepts of cryo-EM and data processing. Participants need to have a computer to access Berzelius remotely. \n\n\n\nLearning outcomes\n\n\n\nUpon completion of this course\, you will be able to:’ \n\n\n\n● apply for the allocation of computational resources on BerzeLiUs cluster● set up and start your cryoSPARC instance on BerzeLiUs● submit jobs to the cluster using the predefined submission lines● manage the jobs● process cryo-EM data on BezleLIUs using a standard data processing pipeline in CryoSPARC \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● Basic knowledge of Linux● Ability to bring your own laptop● Set up an account in NAISS SUPR (supr.naiss.se) \n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n● Experience in processing cryo-EM data using any of the available software packages \n\n\n\nDue to limited space the course can accommodate a maximum of 15 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/a-primer-on-cryo-em-data-processing-using-cryosparc-on-berzelius/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240416T090000
DTEND;TZID=Europe/Stockholm:20240418T170000
DTSTAMP:20260408T035109
CREATED:20240103T100130Z
LAST-MODIFIED:20240103T100350Z
UID:10001098-1713258000-1713459600@www.scilifelab.se
SUMMARY:Workshop on Data Visualization in R
DESCRIPTION:A national course open for PhD students (prioritized)\, postdocs\, researchers and other employees within Swedish universities who are interested in learning to produce publication quality plots using different packages in R. \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Markus Ringner\, Louella Vasquez\, Katja Kozjek \n\n\n\nContact information: edu.plotting.r@nbis.se \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: January 8\, 2024 \n\n\n\nApplication deadline: March 22\, 2024 \n\n\n\nConfirmation to accepted participants: March 25\, 2024 \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website (2023 version)\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThe fee for this on-site workshop is 2000 SEK to be paid by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches\, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. \n\n\n\nNote that travel and accommodation is not included in the fee and must be arranged by the participants. \n\n\n\n\n\n\n\nCourse description\n\n\n\nThis course aims to help researchers to visualize their data in different ways using R. This course will teach how to produce publication grade figures using R. A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of their data. \n\n\n\n\n\n\n\nCourse content\n\n\n\nIn this course you will learn how to visualize your data in R. \n\n\n\nIn particular\, you will learn how to: \n\n\n\n\nformat the data necessary for ggplot\n\n\n\nmake bar-charts\, box-plots and others using ggplot\n\n\n\nmake PCA plots in ggplot\n\n\n\nuse R packages for heatmaps\n\n\n\nplot data on maps using R (optional)\n\n\n\nplot and handle phylogenetic trees in R (optional)\n\n\n\nmake interactive plots in R using Rshiny\n\n\n\nhost a Rshiny app in one of the available servers\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\nBy the end of the course the participant will be able to: \n\n\n\n\nhandle data in R for visualizations\n\n\n\napply the grammar efficiently in ggplot to obtain the desired plot\n\n\n\ncombine different data and/or different plots that are of publication-grade\n\n\n\nwrite your own simple Rshiny app\n\n\n\ndeploy Rshiny apps in public servers. \n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete the plotting exercises: \n\n\n\n\nfamiliarity with using R and Rstudio\n\n\n\na computer with R and Rstudio installed\n\n\n\ninstallation of necessary R packages prior to the start of the course\n\n\n\n\n\n\n\n\nSelection criteria\n\n\n\nThe course can accommodate 25 participants. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry. \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits\, however the estimated credits are just guidelines. 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/workshop-on-data-visualization-in-r/
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:20240422T080000
DTEND;TZID=Europe/Stockholm:20240426T170000
DTSTAMP:20260408T035109
CREATED:20240124T152112Z
LAST-MODIFIED:20240422T093632Z
UID:10001121-1713772800-1714150800@www.scilifelab.se
SUMMARY:TEM sample preparation practical course
DESCRIPTION:This is a practical course on sample preparation for TEM and includes: \n\n\n\n\nUltra-microtome sectioning\n\n\n\nChemical fixation\n\n\n\nPlastic embedding\n\n\n\nTEM imaging\n\n\n\nHigh-pressure freezing & freeze substitution\n\n\n\nImmunolabeling techniques (Immunogold\, CLEM)\n\n\n\nVolume EM (FIB-SEM & Tomography)\n\n\n\n\nParticipants will practice TEM sample preparation and TEM imaging with a sample from their own project. Lab space limits the number of participants to 8\, chosen by motivation and project aim. Write a short project description\, motivation for participating and what sample you would like to bring for the course. Fixation and plastic embedding take time\, therefore one test-sample should be brought to be prepared before the course\, and a new test-sample is brought for the first day. \n\n\n\nIn addition\, a small presentation about an EM-project idea of your own should be prepared and presented on the last day. \n\n\n\nParticipants should attend all theoretical and practical parts of the course to receive a certificate of 1\,5 hp. \n\n\n\nPre-requisite criterion: Basic EM course at UCEM or previous equal experiences with EM methods. \n\n\n\nTeachers: Sara Henriksson\, Agnieszka Ziolkowska\, Narin Mohamad and Linda Sandblad \n\n\n\nContact: linda.sandblad@umu.se \n\n\n\nApplication deadline: 27 March 2024. \n\n\n\nMore Information and registration
URL:https://www.scilifelab.se/event/tem-sample-preparation-practical-course/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/01/UCEM_logo_pos.png
ORGANIZER;CN="UCEM Ume%C3%A5":MAILTO:hussein.haggag@umu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240422T080000
DTEND;TZID=Europe/Stockholm:20240426T170000
DTSTAMP:20260408T035109
CREATED:20240131T120230Z
LAST-MODIFIED:20240314T093013Z
UID:10001134-1713772800-1714150800@www.scilifelab.se
SUMMARY:Introduction to Biostatistics and Machine Learning
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of biostatistical and machine learning skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical methods. It would also suit those already applying biostatistical methods but have never got a chance to reflect on and truly grasp the basic statistical concepts\, such as the commonly misinterpreted p-value. \n\n\n\nImportant dates\n\n\n\nApplication open: now \n\n\n\nApplication closes: 2024-03-24 \n\n\n\nConfirmation to accepted students:  2024-03-28 \n\n\n\nResponsible teachers:  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\nCourse fee\n\n\n\nA course fee of 3000 SEK 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\nCourse content\n\n\n\n\nProbability theory\n\n\n\nHypothesis testing and confidence intervals\n\n\n\nResampling\n\n\n\nLinear regression methods\n\n\n\nIntroduction to generalized linear models\n\n\n\nModel evaluation\n\n\n\nUnsupervised learning incl. clustering and dimension reduction methods\n\n\n\nSupervised learning incl. classification\n\n\n\n\nEducation\n\n\n\nIn this course we focus on an active learning approach. The course participants are expected to do some pre-course reading and exercises\, corresponding up to 40h studying. The education consists of teaching blocks alternating between lectures\, group discussions\, live coding sessions etc. \n\n\n\nEntry requirements\n\n\n\n\nBasic R programming skills (check your R skills by taking our self-assessment test)\n\n\n\nBYOL (bring your own laptop) with R and RStudio installed\n\n\n\nNo prior biostatistical knowledge is assumed\, only basic math skills (pre-course studying materials will be available upon course acceptance)\n\n\n\n\nThe course can accommodate a maximum of 25 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. \n\n\n\nRegistration
URL:https://www.scilifelab.se/event/introduction-to-biostatistics-and-machine-learning-3/
LOCATION:BMC Trippelrummet\, Husargatan 3\, entrance C11\, Uppsala\, Sweden
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/01/course-image.png
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240422T080000
DTEND;TZID=Europe/Stockholm:20240426T170000
DTSTAMP:20260408T035109
CREATED:20240219T105136Z
LAST-MODIFIED:20240220T100128Z
UID:10001162-1713772800-1714150800@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\nCourse Website\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-02-19 \n\n\n\nApplication closes: 2024-03-18 \n\n\n\nConfirmation to accepted students: 2024-03-22 \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\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. \n\n\n\nContact information: edu.trr@nbis.se
URL:https://www.scilifelab.se/event/nbis-elixir-se-tools-for-reproducible-research-2/
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:20240423T080000
DTEND;TZID=Europe/Stockholm:20240425T170000
DTSTAMP:20260408T035109
CREATED:20231114T122916Z
LAST-MODIFIED:20231115T133031Z
UID:10001032-1713859200-1714064400@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 to provide an introduction to practices for better management of data for PhD students\, postdocs\, researchers\, and other employees within all Swedish universities. The workshop will introduce important aspects of research data management through a series of 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\n\n\n\n\nImportant dates\n\n\n\nApplication closes: 2024-03-22 \n\n\n\nInformation to accepted students will be sent: 2024-04-02 \n\n\n\nContact: edu.intro-dm@nbis.se  \n\n\n\n\n\n\n\nApplication\n\n\n\nWorkshop Website\n\n\n\n\n\n\n\n\n\n\n\nFormat & Content\n\n\n\nThis workshop runs on-site in Solna\, Stockholm. Teachers and teaching assistants will be present all week to help with exercises and questions. \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 (e.g. by using Git & GitHub)\n\n\n\nWriting Data Management Plans\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 2000 SEK invoiced to the participant’s organisation. If you accept a position and do not participate (no-show)\, you will still be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals. \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-6/
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:20240520T080000
DTEND;TZID=Europe/Stockholm:20240524T170000
DTSTAMP:20260408T035109
CREATED:20240219T094821Z
LAST-MODIFIED:20240515T124935Z
UID:10001161-1716192000-1716570000@www.scilifelab.se
SUMMARY:2nd CryoNET course on advanced single particle cryo-EM analysis
DESCRIPTION:CryoNet is a Nordic network in cryogenic electron microscopy that aims to promote collaboration and knowledge sharing across national borders. A main goal is to help establish state-of-the-art cryogenic electron microscopy as a strong pillar of Nordic life science research. \n\n\n\nThe core of the network is constituted by the cryo-EM facilities at University of Copenhagen\, Aarhus University\, Stockholm University and Umeå University. \n\n\n\nWe are happy to announce the 2nd CryoNET course on advanced single particle cryo-EM analysis that will take place in Stockholm on 20-24 May 2024. Aim of the course is to provide training in cryo-EM image processing including latest developments of the field. \n\n\n\nParticipants will receive hands-on training in state-of-the-art techniques for single particle cryo-EM image processing\, model building and validation from a range of international specialist guest lecturers. The course also includes theoretical talks and discussions on the use of cryo-EM to address difficult biological questions\, which can help the participants address their own research problems. New for this year is to include Micro-ED and basic processing of Micro-ED data. \n\n\n\nParticipation in the entire course is mandatory and an attendance certificate will be given at the end of the course. \n\n\n\nCourse Objectives\n\n\n\n\nTo provide training in state-of-the-art techniques for high resolution structure determination by cryo-EM\, including hands-on practical training in latest software suites for image processing\n\n\n\nDiscuss data collection strategies\n\n\n\nTraining in basic principles of structure determination using cryo-EM\n\n\n\nGet an introduction to Micro-ED and softwares used for processing of Micro-ED data\n\n\n\nDevelop problem solving skills through discussions and practical sessions in the presence of international experts in the field\n\n\n\nNetworking with experts\, software developers\, and researchers in cryo-EM and learn of not only the latest but also upcoming developments\n\n\n\n\n\n\n\n\nCourse fee covers \n\n\n\n\nAttendance in the course 20-24 May 2024\n\n\n\nLunches\, coffee and refreshments on the course dates\n\n\n\nCourse materials\n\n\n\nCertificate of attendance\n\n\n\nCourse dinner\n\n\n\n\nPlease note\, the registration fee does not cover hotel\, travel expenses\, breakfasts\, and dinners (expect the course dinner) \n\n\n\nCourse fee payment: The course fee of 2\,500 SEK should be paid either by bank transfer (latest 30th of April)\, or via invoice that has been sent out to those that have selected this option.  \n\n\n\nProgram\n\n\n\nProgram_2nd-CryoNET-course-20-24-may-2024_240515Download\n\n\n\nSupported by\n\n\n\n\nKnut & Alice Wallenberg Foundation\n\n\n\nNovo Nordisk Foundation\n\n\n\nThermo Fisher Scientific\n\n\n\nMiTeGen\n\n\n\n\nOrganising committee\n\n\n\n\nKarin Walldén\, Stockholm University\n\n\n\nMarta Carroni\, Stockholm University\n\n\n\nThomas Boesen\, Aarhus University\n\n\n\nJesper Lykkegaard Karlsen\, Aarhus University\n\n\n\nAndreas Bøggild\, Aarhus University\n\n\n\nTillmann Pape\, University of Copenhagen
URL:https://www.scilifelab.se/event/2nd-cryonet-course-on-advanced-single-particle-cryo-em-analysis/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/02/CryoEM-bild.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240520T090000
DTEND;TZID=Europe/Stockholm:20240524T170000
DTSTAMP:20260408T035109
CREATED:20240119T143959Z
LAST-MODIFIED:20240119T144143Z
UID:10001116-1716195600-1716570000@www.scilifelab.se
SUMMARY:NBIS workshop in Neural Nets and Deep Learning
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of Neural networks and Deep Learning skills within all Swedish universities \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens: 2024-01-25 \n\n\n\nApplication closes: 2024-04-10 \n\n\n\nConfirmation to accepted students:  2024-04-25 \n\n\n\nResponsible teachers:  Claudio Mirabello\, Christophe Avenel \n\n\n\nIf you do not receive information according to the above dates please contact: edu.neural-nets-deep-learning@nbis.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website for updates\n\n\n\n\n\n\n\n\n\nCourse Fee\n\n\n\nA course fee* of 3000 SEK will be invoiced to accepted academic participants. A higher fee applies to applicants from private companies. The fee includes lunches\, coffee and snacks. *Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse content\n\n\n\nThis course will give an introduction to the concept of Neural Networks (NN) and Deep Learning. \n\n\n\nTopics covered will include: \n\n\n\n\nNN building blocks\, including concepts such as neurons\, activation functions\, loss functions\, gradient descent and back-propagation\n\n\n\nConvolutional Neural Networks\n\n\n\nRecursive Neural Networks\n\n\n\nTransformers and attention-based models\n\n\n\nAutoencoders\n\n\n\nBest practices when designing NNs\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\nDistinguish the concepts of “Artificial Intelligence”\, “Machine Learning”\, “Neural Networks”\, “Deep Learning”\n\n\n\nDistinguish between different types of learning (e.g. supervised\, unsupervised\, reinforcement) and recognise which applies to their own problem\n\n\n\nDistinguish between linear and non-linear approaches and recognise which is best suited for application to their own problem\n\n\n\nDescribe what a feed-forward neural network (FFNN) is\, along with its components (neurons\, layers\, weights\, bias\, activation functions\, cost functions)\n\n\n\nExplain how training of a FFNN works from a mathematical point of view (gradient descent\, learning rate\, backpropagation)\n\n\n\nExecute with pen and paper a few steps of training of a very simple FFNN model\n\n\n\nTell the difference between a shallow and a deep network\n\n\n\nExplain broadly how different NN architectures are wired and how they work\n\n\n\nImplement and apply the most appropriate architecture to a given problem/dataset\n\n\n\nAnalyze training curves and prediction outputs to evaluate if the training has been successful\n\n\n\nDebug possible issues with the training and suggest changes to fix them\n\n\n\nExplain the difference between training\, validation and testing\n\n\n\nDefine what overfitting is from a mathematical point of view\, and what issues it causes\n\n\n\nIdentify what constitutes good practices of dataset design and how to avoid introducing information leakage or other biases when building their own datasets\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises: \n\n\n\n\nFamiliarity with Unix/Linux\n\n\n\nAbility to bring your own laptop with Python and Jupyter Notebooks  installed for the practical exercises\n\n\n\nProgramming/scripting experience in Python (e.g. having attended the NBIS workshop in basic Python or equivalent)\n\n\n\nBasic experience of statistics and mathematics (e.g. having attended the NBIS workshop Introduction to Biostatistics and Machine Learning or equivalent)\n\n\n\n\nDesirable: \n\n\n\n\nYou have experience of working with Jupyter Notebooks\n\n\n\nYou have a necessity to work with large datasets (e.g. thousands of samples)\n\n\n\n\nDue to limited space the course can accommodate a maximum of 25 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/nbis-workshop-in-neural-nets-and-deep-learning-3/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240527T080000
DTEND;TZID=Europe/Stockholm:20240529T170000
DTSTAMP:20260408T035109
CREATED:20240221T125831Z
LAST-MODIFIED:20240221T125833Z
UID:10001169-1716796800-1717002000@www.scilifelab.se
SUMMARY:Snakemake “bring-your-own-code” (BYOC) workshop
DESCRIPTION:National workshop open for PhD students (prioritized)\, postdocs\, researchers and other employees at Swedish universities in need of skills to write Snakemake workflows for reproducible and scalable bioinformatics data analyses. This workshop requires previous participation in the NBIS Tools for reproducible research course or experience in writing Snakemake workflows. \n\n\n\nRegistration\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-02-26 \n\n\n\nApplication closes: 2024-04-14 \n\n\n\nConfirmation to accepted students: 2024-04-22 \n\n\n\nCourse Leader and teachers: Verena Kutschera (CL)\, Marcel Martin\, John Sundh\, Per Unneberg \n\n\n\nIn case you have any workshop-specific questions\, please contact: edu.byoc-snakemake@nbis.se \n\n\n\nCourse fee\n\n\n\nThis online training event has no fee. However\, if you confirm your participation but do not show up (no-show) you will be invoiced 2\,000 SEK*. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse content\n\n\n\nAs data analysis projects grow and change over time\, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up\, perform and monitor defined sequences of computational tasks (“workflows”)\, thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows. \n\n\n\nThe NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake. \n\n\n\nThis Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here\, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash\, R or python into a Snakemake workflow\, or B) apply more advanced techniques to their existing Snakemake workflows. \n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nBe able to create Snakemake workflows for bioinformatics data analysis\n\n\n\nDemonstrate knowledge of the structure and syntax of different types of Snakemake workflows\n\n\n\nDemonstrate knowledge of advanced features of the Snakemake workflow language\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required for being able to follow the course: \n\n\n\n\nPrevious participation in the NBIS Tools for reproducible research course. The workshop is also open for participants with experience in writing Snakemake workflows and with at least basic Unix/bash knowledge (e.g. being familiar with the command line and commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, etc.). We will use the information you provide in the application form to assess your Snakemake and Unix/bash knowledge.\n\n\n\nYour own bioinformatics analysis scripts in any programming language that you would like to convert into Snakemake OR your own Snakemake workflow that you would like to improve. \n\n\n\nA computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant\, additional setup will be required).\n\n\n\n\nDue to limited space the course can accommodate a maximum of 16 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/snakemake-bring-your-own-code-byoc-workshop/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240610T080000
DTEND;TZID=Europe/Stockholm:20240620T170000
DTSTAMP:20260408T035109
CREATED:20240301T094124Z
LAST-MODIFIED:20240425T075210Z
UID:10001181-1718006400-1718902800@www.scilifelab.se
SUMMARY:RaukR\, Advanced R for Bioinformatics workshop
DESCRIPTION:Join us this June in beautiful and historic Visby to improve your R skills and have a nice time! \n\n\n\nIn Life Science and Bioinformatics\, R is increasingly being used to transform and analyse data\, perform statistical analysis and produce publication-ready visualisations. This workshop will focus on advanced R functionality\, to increase the participants skillset and understanding of what is possible to do today. \n\n\n\nYou are very welcome to apply or see the homepage for more information. Please\, help us spread the word to interested participants! \n\n\n\nLink to registration\n\n\n\nLink to course website\n\n\n\n\nReproducible research in R (Quarto\, Rmarkdown\, Renv)\n\n\n\nCollaborative work in R using Git and GitHub\n\n\n\nR code style guide & best practices\n\n\n\nCode debugging\, optimization and profiling\n\n\n\nParallelization and vectorization in R\n\n\n\nCrafting your own functions\n\n\n\nObject oriented programming and R classes: S3\, S4\, R6 and RC\n\n\n\nAnatomy of an R package: Creating your own package from scratch\n\n\n\nTidy data flow using tidyverse\n\n\n\nUsing the language of graphics: ggplot2\n\n\n\nDeveloping web applications using Shiny\n\n\n\nR and Python integration using reticulate\n\n\n\nTeam project work – developing data analyses workflow in R using acquired skills\n\n\n\n\nNote that topics covered may be subject to change. \n\n\n\nThe course is open for researchers at university or in industry such as PhD students\, postdocs\, group leaders\, core facility staff and analysts. \n\n\n\nCourse fee\n\n\n\nA course fee* of 8000 SEK will be invoiced to accepted participants. The fee includes \n\n\n\n\nParticipation in lectures and workshops\n\n\n\nMingle reception with snacks and drinks\n\n\n\nDaily breakfast/coffee\, lunch and afternoon coffee during the workshop\n\n\n\nOne official course dinner\n\n\n\nSurprise social activities\n\n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-02-22 \n\n\n\nApplication closes: 2024-04-14 \n\n\n\nFor late registrations\, contact the course leaders directly! \n\n\n\nConfirmation to accepted students: 2024-04-17 \n\n\n\nCourse Leader and teachers:  \n\n\n\nSebastian DiLorenzo\, CL \n\n\n\nMarcin Kierczak\, CL \n\n\n\nRoy Francis \n\n\n\nJenny Bryan\, guest lecturer\, Posit \n\n\n\nHenrik Bengtsson\, guest lecturer\, University of California \n\n\n\nIn case you miss information on any of the above dates\, please contact: Course leaders at raukr@nbis.se \n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nWork collaboratively and reproducibly in R\n\n\n\nOptimize R code\n\n\n\nUnderstand R code to a greater extent\n\n\n\nCreate better visualizations\n\n\n\nAnd more!\n\n\n\n\nEntry requirements\n\n\n\nThe course is aimed at both Ph.D. students and researchers within Life Sciences who are already using R for basic bioinformatics analyses and who would like to start using R at a more advanced level. In order for you and other participants to benefit the most\, you should consider yourself eligible if you are comfortable with reading and transforming data\, installing and using third-party packages and plotting using standard R graphics. \n\n\n\nWe offer places for participants from all over the world\, but there are a number of places reserved for participants from Sweden.Due to limited space the course can accommodate approximately 45 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/raukr-advanced-r-for-bioinformatics-workshop-3/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240616T080000
DTEND;TZID=Europe/Stockholm:20240620T170000
DTSTAMP:20260408T035109
CREATED:20240219T110329Z
LAST-MODIFIED:20240219T110353Z
UID:10001164-1718524800-1718902800@www.scilifelab.se
SUMMARY:Advanced course in Metabolic Engineering & Systems Biology (MESB)
DESCRIPTION:The advanced course in Metabolic Engineering & Systems Biology (MESB) is organized by the Systems and Synthetic Biology division at Chalmers University of Technology\, and is intended for PhD students\, postdocs\, academic and industrial researchers that are interested in computational aspects of metabolic engineering. \n\n\n\nAim & content\n\n\n\nThe aim of the course is to provide participants with a strong primer of various (computational) aspects of metabolic engineering. In particular\, the course covers the following topics: \n\n\n\n\nConstraint-based genome-scale modelling\n\n\n\nEnzyme-constrained modelling\n\n\n\nFermentation technologies\n\n\n\nProteomics technologies\n\n\n\nRNAseq data generation and analysis\n\n\n\nIntegrative gene-expression data analysis\n\n\n\n\nA central question in all the activities is How can I use this in my metabolic engineering project? \n\n\n\nTeaching format\n\n\n\nThe course is intensive and will require precourse studying of material that will be provided closer to the start date. During the course\, teaching will be via lectures\, while also significant time (most afternoons) is allocated for hands-on computer exercises. \n\n\n\nLecturers\n\n\n\nEduard KerkhovenJosé Luis Martínez RuizPetri-Jaan LahtveeVerena SiewersYun ChenCHALMERS\, SwedenDTU\, DenmarkTalTech\, EstoniaCHALMERS\, SwedenCHALMERS\, Sweden
URL:https://www.scilifelab.se/event/advanced-course-in-metabolic-engineering-systems-biology-mesb/
CATEGORIES:Course
ORGANIZER;CN="SciLifeLab Gothenburg":MAILTO:gothenburg@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240823T080000
DTEND;TZID=Europe/Stockholm:20240823T170000
DTSTAMP:20260408T035109
CREATED:20240823T125432Z
LAST-MODIFIED:20240823T125517Z
UID:10001336-1724400000-1724432400@www.scilifelab.se
SUMMARY:CryoEM sample preparation and data collection course
DESCRIPTION:The purpose of the course is to prepare and train cryoEM facility users in sample preparation methods\, introduce users to the image data acquisition workflow\, expand knowledge about cryoEM methods among researchers and show that everyone can learn how to use cryoEM for structural biology. \n\n\n\nCourse description\n\n\n\nThe course is open for facility users or potential facility users\, such as PhD students\, postdocs\, and researchers within the life sciences who are curious and will profit from cryoEM skills. Swedish and international course participants are welcome. To attend\, the course participants should be familiar with electron microscopy and structural biology. \n\n\n\nThis course is supported by SciLifeLab\, CryoNET and Umeå University and organized by the Umeå Centre for Electron Microscopy (UCEM). \n\n\n\nRead more\n\n\n\n241204-241206_CryoEM_sample_preparation_2024Download\n\n\n\nApplication deadlineApplication should be submitted before November 1st\, 2024 \n\n\n\nCourse organizersSara SandinTanvir Shaikh \n\n\n\nLocationUCEM and Chemical Biological Centre (KBC) BuildingUmeå UniversityLinnaeus väg 6 \n\n\n\nTeachers and course instructors \n\n\n\n\nLinda Sandblad\n\n\n\nSara Sandin\n\n\n\nTanvir Shaikh\n\n\n\nLars-Anders Carlson\n\n\n\nErin Schexnaydre\n\n\n\nJohan Unge\n\n\n\nAdditional teachers t.b.a\n\n\n\n\nCourse content \n\n\n\nThis course will cover practical aspects of cryoEM sample preparation and data acquisition. \n\n\n\nThe following topics will be covered: \n\n\n\n\nOverview of cryoEM methods\n\n\n\nMicroscope design and electron optics\n\n\n\nSample preparation\n\n\n\nData collection for single particle analysis (SPA)\n\n\n\nIntroduction to SPA image processing\n\n\n\n\nThe course consists of lectures\, cryo lab work\, demonstrations and practical exercises for all participants\, hands-on experiences of microscopy operation and discussions. A detailed schedule will be provided to accepted participants. \n\n\n\nCourse literatureHandouts and material online. \n\n\n\nEntry requirements \n\n\n\nPriority will be given to researchers involved in a project where the use of cryo-EM is needed\, which are to be briefly described upon application. \n\n\n\nThe course is suitable for researchers in the life sciences with a master’s or PhD degree\, including graduate students\, postdocs and staff scientists. \n\n\n\nA maximum of 18 participants will be admitted. Please provide a clear description of your research project and motivation for attending the course. \n\n\n\nExamination Participation in all parts of the course\, lectures\, lab\, microscopy demonstrations and evaluation are mandatory. Upon completion\, SciLifeLab and Umeå University will provide a course certificate and a recommendation for 1 ECTS.
URL:https://www.scilifelab.se/event/cryoem-sample-preparation-and-data-collection-course/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2024/08/241204-241206_CryoEM_sample_preparation_2024.jpg
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240827T120000
DTEND;TZID=Europe/Stockholm:20241001T120000
DTSTAMP:20260408T035109
CREATED:20240615T115304Z
LAST-MODIFIED:20240615T115305Z
UID:10001278-1724760000-1727784000@www.scilifelab.se
SUMMARY:Data-Driven Life Sciences Course 2024 (Online)
DESCRIPTION:Welcome to the Data-driven Life Sciences 2024 course\, where you will explore the intersection of data science\, artificial intelligence\, and life sciences to drive innovation and discovery. This fully online course culminates in an in-person hackathon\, fostering a vibrant community that gathers the DDLS and SciLifeLab members. \n\n\n\nThe 6 modules aim to introduce learners to computer-driven life sciences\, covering application areas in data-driven life sciences. Guest lecturers (DDLS Fellows\, SciLifeLab fellows\, and SciLifeLab facility training providers) will teach topics including technologies and analysis of data sets from proteomics\, transcriptomics\, biomolecular structure\, molecular dynamics simulations\, and various imaging techniques. These modules present\, analyze\, and discuss models of biological phenomena and related scientific breakthroughs based on such data analysis. \n\n\n\nRegistration\n\n\n\nAs prerequisites for the course\, we recommend that you have a look at the following resources: \n\n\n\n\nPlease have a look at the SciLifeLab Data-Driven Life Science (DDLS) initiative website to understand what data-driven life sciences are\, and how Sweden is investing in this area. Focus in particular on the concept of the data life cycle\, which is central in this class.\n\n\n\nWe will use Python as the main programming language in the computer lab\, so please make sure you know the basics of Python. \n\n\n\n\nFor the computer lab\, you will need a computer with internet access\, and make sure you have the following set up: \n\n\n\n\nInstall the latest browser\, e.g. Chrome\n\n\n\nRegister a Google account for the Google Colab access and use the Google Drive\n\n\n\nRegister a ChatGPT account (Note: No need to subscribe to the paid version of ChatGPT\, using the free version is sufficient for this course)\n\n\n\nRegister a Github account for versioning of the code\n\n\n\n\nLearning objectives:  \n\n\n\n\nDescribe the field of data-driven life sciences\n\n\n\nPresent an overview of various application areas\n\n\n\nProvide examples of applications and their associated analysis methods\n\n\n\nApply statistical and machine learning analysis to biological data sets\n\n\n\nFormulate models of biological phenomena\n\n\n\nPresent and review scientific literature in computer-driven life sciences\n\n\n\nReflect on the ethical consequences of data-driven life sciences\n\n\n\nPractice good data management\, including collection\, handling\, sharing\, and analysis\n\n\n\n\nFor questions\, contact the course leader Wei Ouyang at weio@kth.se
URL:https://www.scilifelab.se/event/data-driven-life-sciences-course-2024-online/
LOCATION:Online event via Zoom
CATEGORIES:Course
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240828T100000
DTEND;TZID=Europe/Stockholm:20240828T150000
DTSTAMP:20260408T035109
CREATED:20240419T094002Z
LAST-MODIFIED:20240422T112735Z
UID:10001236-1724839200-1724857200@www.scilifelab.se
SUMMARY:Data Delivery System (DDS) Workshop for Unit Users
DESCRIPTION:We invite current and future users of the Data Delivery System (DDS) from SciLifeLab units to join us for a workshop.  \n\n\n\nWhen: August 28 in Alfa 2 Milky Way\, SciLifeLab Solna.  \n\n\n\nRegister: Register before Aug 23 24.00  \n\n\n\nMax participants:  20 \n\n\n\nThe workshop will include hands-on introductions to registration\, client installation & project access management\, as well as troubleshooting common issues. There will also be a session looking to the future of DDS: future plans and gathering end-user input (e.g. what are the personas amongst your unit’s data recipients?). \n\n\n\nThis workshop is limited to 20 participants and\, we’d love as many SciLifeLab units as possible to be represented\, so would really appreciate you coordinating within your unit to decide who should attend. If there is sufficient demand\, this workshop will run again in the future. \n\n\n\nRegister\n\n\n\nPractical Information\n\n\n\nThe workshop will take place in-person at the SciLifeLab Solna campus. Participants must bring their own laptops for the hands-on component of the day. Lunch will be provided ( if you have dietary restrictions please note this in the registration) \n\n\n\nPreliminary Agenda\n\n\n\n09:30-10:00Fika10:00-10:10Welcome & practical info10:10-10:25Intro to DDS 10:30-12:00Registration\, client installation & project access12:00-13:00Lunch13:00-13:45Project life cycle & support14:00-15:00Future development & user input\n\n\n\nContact information\n\n\n\n\nFor questions contact the Data Delivery System team at SciLifeLab Data Centre. Contact person: Aishling Cooke\n\n\n\nEmail: delivery@scilifelab.se
URL:https://www.scilifelab.se/event/dds-workshop-for-unit-users/
LOCATION:SciLifeLab Campus Solna\, Tomtebodavägen 23 A\, Solna\, Sweden
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/04/Skarmavbild-2024-04-19-kl.-11.30.56-1.png
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240902T080000
DTEND;TZID=Europe/Stockholm:20240913T170000
DTSTAMP:20260408T035109
CREATED:20240402T105825Z
LAST-MODIFIED:20240604T091422Z
UID:10001222-1725264000-1726246800@www.scilifelab.se
SUMMARY:Integrated Structural Biology course 2024
DESCRIPTION:Welcome to the Integrated Structural Biology course\, 2nd edition \n\n\n\nOrganized by SciLifeLab in collaboration with PPS (Protein Production Sweden)\, ESS (European Spallation Source)\, MAX IV\, ProLinC\, NSC (National Supercomputer Centre)\, SwedNMR and InfraLife. \n\n\n\nSeptember 2-13 in Stockholm\, Linköping\, Lund and Gothenburg \n\n\n\nQuestions regarding the course? Send them to: cecilia.persson@nmr.gu.se. \n\n\n\napply here!\n\n\n\nThis course guides you through the different available techniques within structural biology at infrastructures in Sweden. We will also guide all participants through Sweden\, showcasing several of the infrastructures. In short\, the following techniques will be addressed: \n\n\n\n\nCryo-EM\n\n\n\nNMR\n\n\n\nStructural proteomics\n\n\n\nCrystallography\n\n\n\nSAXS/SANS\n\n\n\nBiophysical characterization\n\n\n\nComputational aspects including AlphaFold\n\n\n\nProtein production\n\n\n\nStudent presentations\n\n\n\nSite visits\n\n\n\n\nThe course will start with 4 days in Stockholm and then finish the first week in Linköping. Second week starts in Lund and finishes with two days in Gothenburg. \n\n\n\nYou can download the course overview here: \n\n\n\n Preliminary schedule pdf. \n\n\n\nThere is a course fee for academic participants of 6000 SEK that includes lodging (4 nights each week)\, meals all days and travel between sites. Industry and healthcare participants are welcome for full or specific day participation. Contact Cecilia for more information about costs depending on degree of participation. Industry also welcome to sponsor part of the event and get exposure and networking possibility. \n\n\n\nTravels between sites will be organized for all as well as lodging and lunch/fika. Participants are asked to arrange their own travels to Stockholm on September 2 (arrival latest at 10)\, from Linköping on September 6\, travel to Lund (arrival September 9 before lunch) and then again final travel home on September 13. \n\n\n\nImportant dates\n\n\n\nThere are still some places left in the course and we have prolonged the last application date so you can apply until June 20\, and we will let you know shortly after if you have secured a place in the course \n\n\n\n \n\n\n\nTeachers\n\n\n\n\nMartin Moche\n\n\n\nTomas Nyman\n\n\n\nEsko Oksanen\n\n\n\nTim Schulte\n\n\n\nMichael Hall\n\n\n\nHanna Barriga\n\n\n\nDean Derbyshire\n\n\n\nMaria Sunnerhagen\n\n\n\nSimon Ekström\n\n\n\nLotta Happonen\n\n\n\nCaludio Mirabello\n\n\n\nWojciech Potrzebowski
URL:https://www.scilifelab.se/event/integrated-structural-biology-course-2024/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="Integrated Structural Biology Platform at SciLifeLab":MAILTO:cecilia.persson@nmr.gu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240916T080000
DTEND;TZID=Europe/Stockholm:20240920T170000
DTSTAMP:20260408T035109
CREATED:20240426T103029Z
LAST-MODIFIED:20240426T103031Z
UID:10001243-1726473600-1726851600@www.scilifelab.se
SUMMARY:Epigenomics Data Analysis: from Bulk to Single Cell – ONLINE
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of  Epigenomics data analysis skills. We also welcome applications from outside of Sweden and from the non-academic sector\, for more info contact us! \n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-04-26 \n\n\n\nApplication closes: 2024-08-28 \n\n\n\nConfirmation to accepted students: 2024-08-30 \n\n\n\nCourse Leaders : Agata Smialowska and Louella Vasquez \n\n\n\nContact information:  edu.epigenomics@nbis.se \n\n\n\nCourse fee\n\n\n\nThis online training event has no fee for academic participants. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2 000 SEK. For non-academic participants a course fee* of 12 000 SEK  will be invoiced. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse content\n\n\n\nThis workshop aims to introduce the best practice bioinformatics methods for processing\, analyses\, visualisation and integration of epigenomics and functional genomics data. \n\n\n\nTopics covered include: \n\n\n\n\nData processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;\n\n\n\nChIP-seq: peak calling\, peak independent / dependent quality metrics\, differential binding analysis; DNA motif enrichment;\n\n\n\nATAC-seq: peak calling\, peak independent / dependent quality metrics\, differential accessibility analysis;\n\n\n\nQuantitative ChIP-seq using spike-ins;\n\n\n\nCUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;\n\n\n\nFunctional analysis\, including finding nearest genes and custom features\, GO terms and Reactome pathways enrichment;\n\n\n\nBasic multi-omics exploration and integration;\n\n\n\nVisualisations of epigenomics datasets;\n\n\n\nIntroduction to analysis of single cell functional genomics data (scATAC-seq);\n\n\n\nIntroduction to nf-core pipelines for processing and analysis of epi- and functional genomics data : Methylseq\, ChIP-seq\, ATAC-seq.\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the workshop and complete the computer exercises: \n\n\n\n\nBYOL\, bring your own laptop with R and RStudio installed;\n\n\n\nBasic knowledge in Linux;\n\n\n\nBasic programming experience\, preferably in R.\n\n\n\n\nDesirable: \n\n\n\n\nExperience working on the SNIC center Uppmax or another HPC. We encourage participants to run the linked Uppmax tutorial before the workshop;\n\n\n\nPrevious experience with NGS data analyses;\n\n\n\nCompleting NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Foundations for Life Scientists” or equivalent.\n\n\n\n\nDue to limited space the course can accommodate a maximum of 25 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. \n\n\n\nLink to application\n\n\n\nhttps://forms.gle/BbmWmLwZFS1ed8EeA
URL:https://www.scilifelab.se/event/epigenomics-data-analysis-from-bulk-to-single-cell-online-4/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240918T080000
DTEND;TZID=Europe/Stockholm:20240919T170000
DTSTAMP:20260408T035109
CREATED:20240411T132838Z
LAST-MODIFIED:20240603T163446Z
UID:10001229-1726646400-1726765200@www.scilifelab.se
SUMMARY:Training Material made FAIR by Design
DESCRIPTION:This 2 day course is based on the FAIR training handbook and 10 simple rules to make material FAIR publication. All sessions are structured in a way that complement each other aiming to introduce participants with a theoretical & hands-on approach of how to design FAIR training material. \n\n\n\nPlease see the course website\, which will be updated regularly\, for more information \n\n\n\n \n\n\n\nTopics covered will include:\n\n\n\n\nFAIR vs OPEN training material\n\n\n\nTraining material documentation and reproducibility \n\n\n\n(ontology\, Learning Outcomes\,etc)\n\n\n\nIllustrations\, keeping it FAIR\n\n\n\nE-learning and videos\, challenges and solutions to keep it FAIR\n\n\n\nUnique identifiers and version control\n\n\n\n\nActivities are intended to increase the technical skills and critical thinking during the development of a new training course. From A to Z participants are going to be challenged to work in a group to build a FAIR lesson on a topic to be presented at the end of the course. Come inspired! \n\n\n\nImportant Dates\n\n\n\nApplication open: 11-April-2024Application closes: 23-August-2024 \n\n\n\nConfirmation to applicants 30-August-2024 \n\n\n\nRegistration\n\n\n\nCourse website\n\n\n\nNote: The course is highly interactive and hence it is important that you\, as a participant\, actively contribute to all sessions and elements of the course.  \n\n\n\nParticipants need to bring a laptop.There are no fees for this course. \n\n\n\nAll are welcome! Particularly interesting for trainers and instructors that design-develop-deliver short-format training. \n\n\n\nLearning Objectives\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\ncreate FAIR and open training material from the start\n\n\n\napply FAIR principles to all elements of training material\n\n\n\nuse AI tools in content creation of FAIR training material\n\n\n\n\nPrerequisites\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\nBe familiar with GitHub If not\, we advise you to have a look at the GitHub Skills pages and/or Github courses in Glittr.org in order to acquire the following:\n\nBasic knowledge: To be able to make commits\, create branches and issues\, make pull requests.\n\n\n\n\n\nDesirable\, but not essential skills increasing the output of the course include:\n\nPre-reading the FAIR Training Handbook\n\n\n\nPre-reading 10 simple rules to make material FAIR publication
URL:https://www.scilifelab.se/event/fair-training-material-by-design/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="SciLifeLab Training Hub%2C NBIS%2C and VIB":MAILTO:traininghub@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241001T080000
DTEND;TZID=Europe/Stockholm:20241003T170000
DTSTAMP:20260408T035109
CREATED:20240529T151443Z
LAST-MODIFIED:20240529T151527Z
UID:10001270-1727769600-1727974800@www.scilifelab.se
SUMMARY:Basic Course in Scanning and Transmission Electron Microscopy (SEM/TEM) for Life Sciences
DESCRIPTION:This course covers lectures and practical demonstrations in SEM and TEM techniques. The contents include principles of electron microscopy\, specimen preparation\, cryo-electron microscopy and correlative light-electron microscopy. The main focus will be on imaging biological samples\, but the course may also be suitable for material scientists interested in high-resolution electron microscopy. \n\n\n\nRead more\n\n\n\nApplication deadline:10 September 2024 \n\n\n\nLocation:Lectures at the KBC Building and laboratory demonstrations at UCEM. \n\n\n\nParticipants:18 persons \n\n\n\nInstructors:UCEM staff \n\n\n\nDuration:3 days \n\n\n\nBreaks/Refreshments:Coffee\, cookies and fruit. \n\n\n\nCosts:No course fee\, but full attendance is required! \n\n\n\nExamination/Credits:Oral and practical examinations are conducted during laboratory demonstrations. A course certificate will be given after participants attend all lectures and laboratory demonstrations for this 3-day course. UCEM recommends PhD program examiners to give 1 ECTS after successful participation.
URL:https://www.scilifelab.se/event/basic-course-in-scanning-and-transmission-electron-microscopy-sem-tem-for-life-sciences/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2024/05/241001_241003_Basic-TEM-SEM-Life-Sciences-2024.jpg
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241014T080000
DTEND;TZID=Europe/Stockholm:20241025T170000
DTSTAMP:20260408T035109
CREATED:20240617T081347Z
LAST-MODIFIED:20240617T081528Z
UID:10001279-1728892800-1729875600@www.scilifelab.se
SUMMARY:New Super-Resolution\, Light-Sheet\, and FCS-Methods at Scilifelab
DESCRIPTION:The Advanced Light Microscopy Facility\, ALM\, at Scilifelab gives a two-week PhD-level course on four new imaging and fluorescence spectroscopy techniques: \n\n\n\nDepletion-based Super-Resolution Imaging \n\n\n\n\nSTED-imaging\, 2D and 3D\, 30-50 nm resolution\n\n\n\nIn Living Cells – MoNaLISA\, 1-2 Hz\, 100 x 100 mm field of view\n\n\n\n\nMINFLUX \n\n\n\n\nImaging with 3 nm resolution\n\n\n\nTracking single molecules at 10 kHz\n\n\n\n\nLight-Sheet Imaging \n\n\n\n\nLong time-lapse imaging of live model organisms with low phototoxicity\n\n\n\nUltrafast volumetric imaging of cells with lattice light-sheet microscopy\n\n\n\n\nFCS-Methods \n\n\n\n\nMeasurements of concentrations\, diffusion coefficients\, molecular dynamics and interactions\, in solution or living cells\n\n\n\nCross-correlation\, FRET-\, STED-\, and line-scan-FCS are covered\n\n\n\n\nLecturers: \n\n\n\nSteven Edwards \n\n\n\nErdinc Sezgin \n\n\n\nAna Agostinho \n\n\n\nFrancesca Pennacchietti \n\n\n\nHans Blom \n\n\n\nStefan Wennmalm \n\n\n\nDates: Monday October 14th – Friday October 25th 2024 \n\n\n\nCredits: 3 hp for PhD students \n\n\n\nLocation: Gamma 3\, Scilifelab\, Solna \n\n\n\nRegistration: stewen@kth.se latest September 30th
URL:https://www.scilifelab.se/event/new-super-resolution-light-sheet-and-fcs-methods-at-scilifelab/
LOCATION:Gamma 3\, Tomtebodavägen 23 A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="Advanced Light Microscopy Unit":MAILTO:stewen@kth.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241014T090000
DTEND;TZID=Europe/Stockholm:20241018T170000
DTSTAMP:20260408T035109
CREATED:20240326T120939Z
LAST-MODIFIED:20240403T083011Z
UID:10001215-1728896400-1729270800@www.scilifelab.se
SUMMARY:Omics Integration and Systems Biology
DESCRIPTION:National course open for PhD students\, postdocs\, researchers\, and other employees in all Swedish universities\, in need of a general description of different approaches for working with multiple types of biological data. 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: 2024-08-05 \n\n\n\nApplication closes: 2024-09-16 \n\n\n\nConfirmation to accepted students: 2024-09-23 \n\n\n\nCourse Leader and teachers: \n\n\n\nNikolay Oskolkov (Lund University\, course leader) \n\n\n\nRasool Saghaleyni (Chalmers University of Technology\, course leader) \n\n\n\nSergiu Netotea (Chalmers University of Technology\, course lecturer) \n\n\n\nJennifer Fransson (Uppsala University\, course lecturer) \n\n\n\nYuan Li (Lund University\, TA) \n\n\n\nNima Rafati (Uppsala University\, TA) \n\n\n\nIn case you miss information on any of the above dates\, please contact: \n\n\n\nNikolay Oskolkov\, nikolay.oskolkov@scilifelab.se \n\n\n\nRasool Saghaleyni\, rasools@chalmers.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\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 all coffee breaks\, all lunches and 1 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\nThe aim of this workshop is to provide an integrated view of data-driven analysis of biological data through machine learning\, graph and network analysis as well as constraint-based modeling integration methods. A general description of different approaches for working with multiple layers of biological information\, i.e. Omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing their advantages and pitfalls. The techniques will be discussed in terms of their rationale and applicability. \n\n\n\nTopics covered will include: \n\n\n\n\nData pre-processing\, cleaning and feature selection prior to integration;\n\n\n\nApplication of key machine learning methods for multi-omics analysis including deep learning;\n\n\n\nMulti-omics factor analysis\, dimension reduction and clustering;\n\n\n\nSingle Cell and Spatial transcriptomics integration;\n\n\n\nBiological network inference\, community and topology analysis and visualization;\n\n\n\nCondition-specific and personalized modeling through Genome-scale Metabolic models for integration of transcriptomic\, proteomic\, metabolomic and fluxomic data;\n\n\n\nIdentification of key biological functions and pathways;\n\n\n\nIdentification of potential biomarkers and targetable genes through modeling and biological network analysis;\n\n\n\nApplication of network approaches in meta-analyses;\n\n\n\nSimilarity network fusion and matrix factorization techniques;\n\n\n\nIntegrated data visualization techniques\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\nIdentify key methods for analysis and integration of omics data based on a given dataset;\n\n\n\nPerform  feature selection and dimension reduction techniques; \n\n\n\nUnderstand strengths and pitfalls of key machine learning techniques in multi-omic analysis;\n\n\n\nApply unsupervised and supervised machine learning data integration techniques;\n\n\n\nBuild biological networks based on different omics data including integrated multi-omics networks;\n\n\n\nPerform centrality and community analyses in graphs;\n\n\n\nApply network approaches in meta-analyses;\n\n\n\nApply similarity network fusion of patient data;\n\n\n\nCompare different cell-types or conditions through the application of different biological network analysis techniques;\n\n\n\nSimulate biological functions using constraint-based models and flux balance analysis;\n\n\n\nIdentify potential confounding factors and sources of bias.\n\n\n\n\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\nBasic knowledge in R or Python;\n\n\n\nBasic understanding of frequentist statistics;\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nExperience with NGS and omics analysis\n\n\n\nCompleting “Introduction to bioinformatics using NGS data” and “Introduction to biostatistics and machine learning” NBIS courses\n\n\n\n\n\n\n\n\nDue to limited space the course can accommodate a maximum of 35 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/omics-integration-and-systems-biology/
LOCATION:Lund University\, Lund\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241028T090000
DTEND;TZID=Europe/Stockholm:20241101T170000
DTSTAMP:20260408T035109
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:20260408T035109
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:20260408T035109
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:20260408T035109
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:20260408T035109
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
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