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DTSTART;TZID=Europe/Stockholm:20240520T080000
DTEND;TZID=Europe/Stockholm:20240524T170000
DTSTAMP:20260406T173625
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
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240520T090000
DTEND;TZID=Europe/Stockholm:20240524T170000
DTSTAMP:20260406T173625
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
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DTSTART;TZID=Europe/Stockholm:20240527T080000
DTEND;TZID=Europe/Stockholm:20240529T170000
DTSTAMP:20260406T173625
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
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