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DTSTART;TZID=Europe/Stockholm:20210503T080000
DTEND;TZID=Europe/Stockholm:20210507T170000
DTSTAMP:20260415T205115
CREATED:20210414T092106Z
LAST-MODIFIED:20210414T093012Z
UID:10000363-1620028800-1620406800@www.scilifelab.se
SUMMARY:Genome Assembly and Annotation 2021 – Online
DESCRIPTION:Elixir course open for PhD students\, postdocs\, researchers and other employees in need of Genome assembly and annotation skills. \n\n\n\nImportant dates\n\n\n\nApplication opens: 30th of March Application closes:19th of AprilConfirmation to accepted students: 26th of April \n\n\n\nResponsible teachers:  Christophe Klopp (FR)\, Lucile Soler (SE)\, Mahesh Binzer-Panchal (SE)\, Nima Rafati (SE)\, Tomas Larsson (SE)\, Henrik Lantz (SE)\, Brane Leskosek (SI)\, Marko Vidak (SI) and Erik Hjerde (NO) \n\n\n\nIf you do not receive information according to the above dates please contact:  Erik Hjerde \n\n\n\nCourse fee\n\n\n\nThe course is free of charge. \n\n\n\nCourse content\n\n\n\nThis course will introduce the best practice bioinformatics methods to assemble and annotate genomes via a series of lectures\, group work and computer practicals. Topics covered will include: \n\n\n\nQuality Assessment of sequencing dataLong read technologies and assemblies and assembly polishingAssembly ValidationHi-C sequencingMethod in Structural AnnotationAbinitio annotationAnnotation with makerAbinitio trainingFunctional annotationSubmission to DBBacterial annotation\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises: \n\n\n\nMandatory to complete a short command line course prior to the event. This will be made available to enrolled participants\n\n\n\nThe course is limited to 25 people\, and maximum 2 participants per national ELIXIR node (except Norway). The course is an advanced course. Based on the information collected upon registration\, the course organizers will enroll participants.
URL:https://www.scilifelab.se/event/genome-assembly-and-annotation-2021-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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DTSTART;TZID=Europe/Stockholm:20210503T080000
DTEND;TZID=Europe/Stockholm:20210507T170000
DTSTAMP:20260415T205115
CREATED:20210414T092540Z
LAST-MODIFIED:20210506T225135Z
UID:10000364-1620028800-1620406800@www.scilifelab.se
SUMMARY:Quick and clean: advanced Python for data science in biology - ONLINE
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of Advanced Python skills within all Swedish universities. \n\n\n\nImportant dates\n\n\n\nApplication is open!Application closes: April 15\, 2021Confirmation to accepted students: April 21\, 2021For questions about the course\, please contact Ashfaq Ali (ashfaq.ali@nbis.se)\, Sergiu Netotea (sergiu.netotea@nbis.se)\n\n\n\nCourse fee\n\n\n\nThe course is free of charge but a no show fee course fee of 2000 SEK will be invoiced to accepted participants who failed to attend the course after accepting to participate. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nThe main aim of this course is to introduce students to the so-called Zen of Python for quick and clean application of python in data science. The workshop is structured around  based on the industry way of classifying big data jobs: data analytics\, data science\, data engineering.  \n\n\n\nParticipants will have an opportunity to learn the following topics \n\n\n\nGeneral overview of computer choke points for various architectures together with a fast paced tutorial on advanced language concepts.Scientific computing\, statistics\, visualization and data mining\, via libraries such as numpy\, pandas\, statmodels and several other “science stack” libraries.Programming with focus on how to perform machine learning\, deep learning\, statistical learning and pattern recognition using python\, via scikit-learn\, tensorflow\, pymc3 and other more exotic libraries.Engineering the computing infrastructure and Python’s role in it. How to run Python on clouds and GPU machinesLearning how Python can be used to organize your workflow with efficiency and reproducibility in mind.Application to research themes where you will either pick one real ‘omics subject from a given task list or you will use Python in your project under our assistance. This is a great time to solidify your knowledge by applying it to your own research scope!\n\n\n\nLearning Outcomes\n\n\n\nAt the end of the course the course participants will have achieved following objectives \n\n\n\nGeneral knowledge about computational workflow using pythonHave knowledge about computer architecture and use of python for efficient computingKnowledge about python libraries for machine learning\, deep learning and statistical learning and their applicationsAbility to apply advanced python libraries in own research field\n\n\n\nWorkshop organization\n\n\n\nWe aim for a balance between lecturing and exercise in Jupyter notebooks (jupyter.org) which is used for taking notes\, self study\, hands on tasks and interaction. Considering that the course is online\, lectures will be delivered via zoom links and exercises will be carried out in zoom breakout rooms with the help of teaching assistants. Course session leaders will be available to answer theoretical and practical questions. Questions are welcome at any time. \n\n\n\nYou will be asked to prepare your laptop a week before the course starts. We will also use a slack channel for communication\, posting links or code tips. \n\n\n\nImportant to Know\n\n\n\nThe workshop covers some of the basic concepts of python programming and each session will have advanced material on the topic that may test the limits of the participant’s knowledge of python and computers. Difficulties during learning are expected and are part of the course design. \n\n\n\nFor the sessions on analyses of your own data\, students are encouraged to send their topic of interest before the start of the course.   \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises \n\n\n\nA computer with any OS.           Python\, R or any other computer language basic knowledge.Basic skills handling your own computer.For those interested in tasks involving cloud computing\, access to Amazon AWS is required. (user configuration)\n\n\n\nDesirable to have \n\n\n\nYou have bioinformatics or systems biology background\, statistical and machine learning skills.Have Linux on your laptop\, or access to a Linux server.You did programming before (not just courses) and can handle the command line.Have a good idea for a task you want to achieve on the fourth day.\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 several criteria including entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nGithub page (older version)
URL:https://www.scilifelab.se/event/quick-and-clean-advanced-python-for-data-science-in-biology-online/
CATEGORIES:Course
LOCATION:https://www.scilifelab.se/event/quick-and-clean-advanced-python-for-data-science-in-biology-online/
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210517T080000
DTEND;TZID=Europe/Stockholm:20210521T170000
DTSTAMP:20260415T205115
CREATED:20210428T093317Z
LAST-MODIFIED:20210428T093423Z
UID:10000368-1621238400-1621616400@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. This workshop is run by the National Bioinformatics Infrastructure Sweden(NBIS) and National Genomics Infrastructure (NGI). \n\n\n\nDue to the Covid-19 situation\, this workshop will be held online. \n\n\n\nIf you have questions regarding the workshop\, please email: edu.intro-ngs@nbis.se \n\n\n\nImportant dates \n\n\n\nApplication opens:  February 01\, 2021 Application closes: April 11\, 2021Confirmation to accepted students:  April 16\, 2021\n\n\n\nResponsible teachers:  Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\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 a 2000 SEK workshop fee**Please note that NBIS cannot invoice individuals \n\n\n\nCourse content \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\nAfter this workshop you should be able to: \n\n\n\nDescribe the basic principles of next generation sequencing.Use the Linux command line interface to manage simple file processing operations\, and organize directory structures.Connect to and work on a remote high performance compute cluster.Apply programs in Linux for analysis of NGS data.Summarise 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.Explain common NGS file formats.Interpret quality control of NGS reads.Explain the steps involved in variant calling using whole genome sequencing data.Independently perform a basic variant calling workflow on example data.Explain the steps involved in differential gene expression using RNA seq data.Independently perform differential gene expression analysis on example data.\n\n\n\nEntry requirements \n\n\n\nA background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to \n\n\n\nHave relevant previous experience in sequencing or analysis.Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others.\n\n\n\nSelection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-online/
CATEGORIES:Course
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210531T080000
DTEND;TZID=Europe/Stockholm:20210611T170000
DTSTAMP:20260415T205115
CREATED:20210413T071434Z
LAST-MODIFIED:20210526T120645Z
UID:10000355-1622448000-1623430800@www.scilifelab.se
SUMMARY:Super-Resolution\, Light-Sheet\, STED-FCS and FRET-FCS
DESCRIPTION:The Advanced Light Microscopy Unit\, ALM\, at Scilifelab gives a two-week course focusing on four new imaging and fluorescence spectroscopy techniques: \n\n\n\nLight-Sheet Imaging\n\n\n\nLong time-lapse imaging of live model organisms with low phototoxicityUltrafast volumetric imaging of cells with lattice light-sheet microscopy\n\n\n\nSuper-Resolution Imaging in Living Cells – MoNaLISA\n\n\n\nSmart probes. 50 nm resolution at 1-2 Hz. 100 x 100 mm field of view. Time lapse imaging\n\n\n\nSTED-FCS\n\n\n\nFluctuation spectroscopy with 30 nm resolutionSub-diffraction dynamics in living cells\n\n\n\nFRET-FCS\n\n\n\nEasy detection of protein-protein interactions in living cellsHighly sensitive detection of rare oligomers in living cells\n\n\n\nLecturers\n\n\n\nSteven EdwardsErdinc SezginIlaria TestaStefan Wennmalm\n\n\n\nCredits: 3 hp for PhD students\, but open for anyone \n\n\n\nLocation: Web-based \n\n\n\nRegistration: stewen@kth.se
URL:https://www.scilifelab.se/event/super-resolution-light-sheet-sted-fcs-and-fret-fcs/
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2019/10/microscope.png
ORGANIZER;CN="Advanced Light Microscopy Unit":MAILTO:stewen@kth.se
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