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DTSTART;TZID=Europe/Stockholm:20221114T080000
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DTSTAMP:20260408T232327
CREATED:20221031T165001Z
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UID:10000725-1668412800-1668790800@www.scilifelab.se
SUMMARY:TEM sample preparation practical course part II
DESCRIPTION:TEM sample preparation course – Chemical fixation\, high pressure freezing\, plastic embedding and staining methods including practice on ultra-microtome sectioning\, TEM imaging and an introduction to CLEM (Correlative Light and Electron Microscopy)\, FIB-SEM (Focused Ion Beam) and electron tomography. \n\n\n\nRead more\n\n\n\nPre-requisite criterion: Basic EM course at UCEM or equal previous experiences of EM methods. \n\n\n\nParticipants will practice EM sample preparation and EM imaging with one sample from their own project. Our lab space limits the number of participants to 8 so we will select participants based on your motivation and how your project aims fits to the course content. Please write a short project description\, a motivation for participating and what sample you would like to process during the course. \n\n\n\nPlease\, look at the program and the methods that are covered in this course. Make sure you have time to participate full days and the entire week. Since the fixation and plastic embedding takes time\, you should bring one test-sample to Agnieszka on Monday 7 of November\, and a new test-sample on the first course day\, 14 November. \n\n\n\nPreliminary Program:The course preliminary program will be announced here once it is organised. \n\n\n\nLocation:Lectures at KBC and laboratory demonstrations at UCEM – Level 5\, 6 + new EM building (Level 1)\, Umeå University. \n\n\n\nParticipants:8 persons. Open to all research students\, postdocs and staff. \n\n\n\nInstructors: \n\n\n\nSara Henriksson – EM research engineerGayathri Vegesna – EM research engineerAgnieszka Ziolkowska – EM research engineerCamilla Holmlund – EM research engineerLinda Sandblad – EM facility director\n\n\n\nDuration:5 days \n\n\n\nBreaks/Refreshments:Coffee\, cookies and fruit will be served. \n\n\n\nCosts:No course fee\, but full attendance is required! \n\n\n\nCredits:Students that attend all theoretical and practical parts of the course\, will receive a certificate for 1\,5 hp.
URL:https://www.scilifelab.se/event/tem-sample-preparation-practical-course-part-ii/
LOCATION:Kemiskt Biologiskt Centrum\, Umeå University\, Linnaeus väg 6\, Umeå\, 90736
CATEGORIES:Course
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
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DTSTART;TZID=Europe/Stockholm:20221121T090000
DTEND;TZID=Europe/Stockholm:20221125T153000
DTSTAMP:20260408T232327
CREATED:20220906T074137Z
LAST-MODIFIED:20220907T061609Z
UID:10000670-1669021200-1669390200@www.scilifelab.se
SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research - ONLINE
DESCRIPTION:NBIS / ELIXIR-SE course is open for PhD students\, postdocs\, group leaders and core facility staff interested in making their computational analysis more reproducible. International applications are welcome\, but we will give approximately half of the participant slots to applicants from Swedish universities at minimum\, due to the national role NBIS plays in Sweden. \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: John Sundh\, Erik Fasterius \n\n\n\nContact information: edu.trr@nbis.se \n\n\n\n\n\n\n\n\n\nApply here\n\n\n\n\n\nCourse webpage\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Sep 5\, 2022 \n\n\n\nApplication deadline: Oct 21\, 2022 \n\n\n\nConfirmation to accepted participants: Oct 28\, 2022 \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 2\,000 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse description\n\n\n\nOne of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis\, e.g. bioinformatics or computational biology\, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete\, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study\, all the code and/or computational notebooks needed to produce results from the raw data\, and the computational environment or a complete description thereof. \n\n\n\nReproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly\, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self! \n\n\n\n\n\n\n\nCourse content\n\n\n\nTopics covered \n\n\n\nGood practices for data analysisVersion control and collaborative code developmentPackage and environment managementWorkflow managementDocumentation and reportingContainerized computational environments\n\n\n\n\n\n\n\nLearning outcomes \n\n\n\nBy the end of the course the student will be able to: \n\n\n\nOrganize and structure computational projectsTrack changes and collaborate on code using GitInstall packages and manage software environments using CondaStructure computational steps into workflows with Snakemake and NextflowCreate automated reports and document their analyses with RMarkdown and JupyterPackage and distribute computational environments using Docker and Singularity\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete computer exercises: \n\n\n\nFamiliarity with using the terminal (e.g. be familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.)A computer with a webcamYou will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the courseSome knowledge in R and/or python is beneficial but not strictly required\n\n\n\n\n\n\n\nSelection criteria\n\n\n\nThe course can accommodate 20 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/nbis-elixir-se-tools-for-reproducible-research-online-2/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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