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DTSTART;TZID=Europe/Stockholm:20231204T090000
DTEND;TZID=Europe/Stockholm:20231206T170000
DTSTAMP:20260407T180353
CREATED:20230906T082705Z
LAST-MODIFIED:20231106T132742Z
UID:10000967-1701680400-1701882000@www.scilifelab.se
SUMMARY:Snakemake “bring-your-own-code” (BYOC) workshop - Cancelled
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of skills to write Snakemake workflows for reproducible and scalable bioinformatics data analyses. CANCELLED! \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-09-11 \n\n\n\nApplication closes: 2023-10-29 \n\n\n\nConfirmation to accepted students: 2023-11-06 \n\n\n\nCourse Leader and teachers: Verena Kutschera (CL)\, Marcel Martin\, John Sundh. In case you have any workshop-specific questions\, please contact: edu.byoc-snakemake@nbis.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis online training event has no fee. However\, if you confirm your participation but do not do so (no-show) you will be invoiced 2\,000 SEK*.*Please note that NBIS cannot invoice individuals \n\n\n\n\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\n\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\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 who can demonstrate experience in writing Snakemake workflows and with at least basic Unix/bash knowledge (e.g. being familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.).\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 12 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-online/
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:20231206T080000
DTEND;TZID=Europe/Stockholm:20231208T170000
DTSTAMP:20260407T180353
CREATED:20231002T115541Z
LAST-MODIFIED:20231002T115646Z
UID:10000980-1701849600-1702054800@www.scilifelab.se
SUMMARY:DDLS Biomarker Discovery: from theory to real world examples
DESCRIPTION:National workshop open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of understanding biomarker research and methods. \n\n\n\nWorkshop location:  SciLifeLab\, Tomtebodavägen 23A\, Solna \n\n\n\nVenue:  Air&Fire (G2690) and Milky Way (A2631) \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-10-01 \n\n\n\nApplication closes: 2023-10-30 \n\n\n\nConfirmation to accepted students: 2023-11-15 \n\n\n\n \n\n\n\nCourse Leaders and teachers: Animesh Acharjee\, Clemens Wittenbecher\, Markus Mayrhofer\, Mun-Gwan Hong\, Paul Pyl\, Prasoon Agarwal \n\n\n\nplease contact edu.biomarkers@nbis.se for course-specific questions \n\n\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\nWorkshop fee\n\n\n\nA course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunch and coffee. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nWorkshop content\n\n\n\nThe main purpose of this workshop is to provide a good overview of biomarkers and biomarker studies. This workshop will explore recent research\, showcasing diverse biomarker applications within clinical trials. Methods employed to identify biomarkers through various omics datasets will be reviewed. Participants will engage in discussion on biomarker studies and data analysis exercises that encompass approaches like machine learning methods and other integrative omics strategies used in biomarker discovery. \n\n\n\nTopics covered will include: \n\n\n\n\nBiomarker study design for “context of use”\n\n\n\nTypes of biomarkers\, diagnostic\, prognostic\, and wellness\n\n\n\nBiomarkers are in use for various diseases such as cancer\, cardiovascular diseases\n\n\n\nBiomarker discovery from various omics data including proteome\, microbiome\n\n\n\nBiomarker and multi-omics data integration\n\n\n\nMachine learning methods\, lasso logistic regression and random forest\, to identify biomarkers\n\n\n\nPerformance indicators\, e.g. sensitivity and specificity\n\n\n\nInternal/external validation\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required to be able to follow the workshop and complete the exercises: \n\n\n\n\nAbility to bring your own laptop with R installed for the practical exercises\n\n\n\nBasic Programming/scripting experience in R\n\n\n\nor took an R course NBIS prepared.\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nSome basic knowledge of biostatistics\n\n\n\nPrevious experience in biomarker-related studies\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/ddls-biomarker-discovery-from-theory-to-real-world-examples/
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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