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how_to [2023/10/09 18:54] – [Neurepiomics workshop 2023] mohsenhow_to [2024/04/05 20:25] (current) – [Supercharge your YouTube experience and minimize ads?] admin
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-==== Neurepiomics workshop 2023 ====+==== Measure memory used by GPUs? ====
  
-Link to slides:+Use ''torch.cuda.[[https://pytorch.org/blog/understanding-gpu-memory-1/?hss_channel=tw-776585502606721024|memory]]'' , e.g., to discover the effect of clearing gradients at the end of each [[https://towardsdatascience.com/epoch-vs-iterations-vs-batch-size-4dfb9c7ce9c9|iteration]]. With ignite, this can be done using an event handler that calls ''optimizer.[[https://stackoverflow.com/questions/48001598/why-do-we-need-to-call-zero-grad-in-pytorch|zero_grad]](set_to_none=True)''.'' ''
  
-  - [[https://docs.google.com/presentation/d/1W-pJfPy5MkQscPn5iOSJAkOzuyC2-eirBeHHeKHuYyw/edit#slide=id.p|Databases]]+---- 
 + 
 + 
 +==== Analyze multiomicds data? ==== 
 + 
 +[[http://biggsinstitute.org/neurepiomics-2023/#1686596557113-fac33f90-1709|Neurepiomics]] workshop in 2023: 
 + 
 +  - Shiva's presentation on omics[[https://docs.google.com/presentation/d/1W-pJfPy5MkQscPn5iOSJAkOzuyC2-eirBeHHeKHuYyw/edit#slide=id.p|databases]]
   - Mohsen's [[https://docs.google.com/presentation/d/14z2jAkYfmyH6dIH0Rr59ywZk--Kk9ocHzWEDiyd_P4k/edit#slide=id.p|presentation]] for Neurepiomics workshop, 2023-10-09.   - Mohsen's [[https://docs.google.com/presentation/d/14z2jAkYfmyH6dIH0Rr59ywZk--Kk9ocHzWEDiyd_P4k/edit#slide=id.p|presentation]] for Neurepiomics workshop, 2023-10-09.
 +  - Habil's [[https://docs.google.com/presentation/d/1mGld52Y8TkMXArc5EhcD2XY_0rXvb79BFEgA0YaZwms/edit#slide=id.g63f2c216dd_0_0|slides]] on multiomics data integration.
  
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 ==== What is the best Linux distribution for biologists? ==== ==== What is the best Linux distribution for biologists? ====
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 ==== Supercharge your YouTube experience and minimize ads? ==== ==== Supercharge your YouTube experience and minimize ads? ====
  
-"[[https://chrome.google.com/webstore/detail/youtube-enhancer/ejcniippeghnejiodjkkmndlelbagmah|Enhancer]] for YouTube" is a popular browser extension that enhances the YouTube viewing experience by providing additional features and customization options. While it doesn't explicitly focus on blocking ads, it offers some options to minimize or hide them.+"[[https://chrome.google.com/webstore/detail/youtube-enhancer/ejcniippeghnejiodjkkmndlelbagmah|Enhancer]] for YouTube" is a popular browser extension that enhances the YouTube viewing experience by providing additional features and customization options, but it may contains malware! While it doesn't explicitly focus on blocking ads, it offers some options to minimize or hide them. Use [[https://chrome.google.com/webstore/detail/autoskip-for-youtube-ads/hmbnhhcgiecenbbkgdoaoafjpeaboine|Autoskip]] to automatically skip ads that pass the Enhancer filter.
  
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 Use [[https://cran.r-project.org/web/packages/openxlsx/index.html|openxlsx]] package to read, write and edit xlsx files in R. Package's integration with C++ makes it faster and easier to use. Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java. Use [[https://cran.r-project.org/web/packages/openxlsx/index.html|openxlsx]] package to read, write and edit xlsx files in R. Package's integration with C++ makes it faster and easier to use. Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.
- 
 <code> <code>
 +
 E.g. Writing four dataframes in four sheets of excel workbook can be done as follows: E.g. Writing four dataframes in four sheets of excel workbook can be done as follows:
 library(openxlsx) library(openxlsx)
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 writeData(wb=w1, sheet="New", mtcars[,1:3]) writeData(wb=w1, sheet="New", mtcars[,1:3])
 saveWorkbook(w1, file=xlsFile, overwrite=TRUE) saveWorkbook(w1, file=xlsFile, overwrite=TRUE)
 +
 +## Read a sheet in a data frame:
 +r1 <- read.xlsx(xlsxFile=xlsFile, sheet="Second")
 +
 </code> </code>
  
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 ==== Set local mirror for Rscript ==== ==== Set local mirror for Rscript ====