✎ how_to [oncinfo]

<p>
This is a collection of short answers and links to some miscellaneous questions that we have had while doing research in Oncinfo. This can also be a useful resource for other scholars in the field of computational biology with similar interests and challenges.
</p>
<hr />

</div>

<h3>Measure memory used by GPUs?</h3>
<div class="level3">

<p>
Use <code>torch.cuda.<a href="https://pytorch.org/blog/understanding-gpu-memory-1/?hss_channel=tw-776585502606721024" class="urlextern" title="https://pytorch.org/blog/understanding-gpu-memory-1/?hss_channel=tw-776585502606721024" rel="ugc nofollow">memory</a></code> , e.g., to discover the effect of clearing gradients at the end of each <a href="https://towardsdatascience.com/epoch-vs-iterations-vs-batch-size-4dfb9c7ce9c9" class="urlextern" title="https://towardsdatascience.com/epoch-vs-iterations-vs-batch-size-4dfb9c7ce9c9" rel="ugc nofollow">iteration</a>. With ignite, this can be done using an event handler that calls <code>optimizer.<a href="https://stackoverflow.com/questions/48001598/why-do-we-need-to-call-zero-grad-in-pytorch" class="urlextern" title="https://stackoverflow.com/questions/48001598/why-do-we-need-to-call-zero-grad-in-pytorch" rel="ugc nofollow">zero_grad</a>(set_to_none=True)</code>.<code> </code>
</p>
<hr />

</div>

<h3>Analyze multiomicds data?</h3>
<div class="level3">

<p>
<a href="http://biggsinstitute.org/neurepiomics-2023/#1686596557113-fac33f90-1709" class="urlextern" title="http://biggsinstitute.org/neurepiomics-2023/#1686596557113-fac33f90-1709" rel="ugc nofollow">Neurepiomics</a> workshop in 2023:
</p>
<ol>
<li class="level1"> Shiva's presentation on omics<a href="https://docs.google.com/presentation/d/1W-pJfPy5MkQscPn5iOSJAkOzuyC2-eirBeHHeKHuYyw/edit#slide=id.p" class="urlextern" title="https://docs.google.com/presentation/d/1W-pJfPy5MkQscPn5iOSJAkOzuyC2-eirBeHHeKHuYyw/edit#slide=id.p" rel="ugc nofollow">databases</a></li>
<li class="level1"> Mohsen's <a href="https://docs.google.com/presentation/d/14z2jAkYfmyH6dIH0Rr59ywZk--Kk9ocHzWEDiyd_P4k/edit#slide=id.p" class="urlextern" title="https://docs.google.com/presentation/d/14z2jAkYfmyH6dIH0Rr59ywZk--Kk9ocHzWEDiyd_P4k/edit#slide=id.p" rel="ugc nofollow">presentation</a> for Neurepiomics workshop, 2023-10-09.</li>
<li class="level1"> Habil's <a href="https://docs.google.com/presentation/d/1mGld52Y8TkMXArc5EhcD2XY_0rXvb79BFEgA0YaZwms/edit#slide=id.g63f2c216dd_0_0" class="urlextern" title="https://docs.google.com/presentation/d/1mGld52Y8TkMXArc5EhcD2XY_0rXvb79BFEgA0YaZwms/edit#slide=id.g63f2c216dd_0_0" rel="ugc nofollow">slides</a> on multiomics data integration.</li>
</ol>
<hr />

</div>

<h3>What is the best Linux distribution for biologists?</h3>
<div class="level3">

<p>
<a href="https://archlinux.org/" class="urlextern" title="https://archlinux.org/" rel="ugc nofollow">ArchLinux</a> and <a href="https://wiki.archlinux.org/title/Arch-based_distributions" class="urlextern" title="https://wiki.archlinux.org/title/Arch-based_distributions" rel="ugc nofollow">its derivatives</a>, like <a href="https://manjaro.org/" class="urlextern" title="https://manjaro.org/" rel="ugc nofollow">Manjaro</a>, are the top Linux distributions for biologists. The <a href="https://github.com/BioArchLinux/Packages" class="urlextern" title="https://github.com/BioArchLinux/Packages" rel="ugc nofollow">BioArchLinux community</a> maintains an excellent repository with over 4,000 bioinformatics packages and their dependencies. Regular automated updates ensure the latest versions are available by fetching source code from trusted repositories and compiling releases optimized for the target architecture. Its philosophy is described <a href="https://f1000research.com/posters/11-809" class="urlextern" title="https://f1000research.com/posters/11-809" rel="ugc nofollow">here</a>.
</p>
<hr />

</div>

<h3>Download files to where you cannot login or click using a GUI?</h3>
<div class="level3">

<p>
Login using GUI on another computer. Click to start downloading. While it is downloading, right-click on the page and then click on "Inspect". Then, click on "Network" on the top of the panel and find the file. Get the cURL <a href="https://www.youtube.com/watch?v=udfCVWuobhc" class="urlextern" title="https://www.youtube.com/watch?v=udfCVWuobhc" rel="ugc nofollow">command</a> and run it in terminal to download the file in the other computer.
</p>
<hr />

</div>

<h3>Supercharge your YouTube experience and minimize ads?</h3>
<div class="level3">

<p>
"<a href="https://chrome.google.com/webstore/detail/youtube-enhancer/ejcniippeghnejiodjkkmndlelbagmah" class="urlextern" title="https://chrome.google.com/webstore/detail/youtube-enhancer/ejcniippeghnejiodjkkmndlelbagmah" rel="ugc nofollow">Enhancer</a> 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 <a href="https://chrome.google.com/webstore/detail/autoskip-for-youtube-ads/hmbnhhcgiecenbbkgdoaoafjpeaboine" class="urlextern" title="https://chrome.google.com/webstore/detail/autoskip-for-youtube-ads/hmbnhhcgiecenbbkgdoaoafjpeaboine" rel="ugc nofollow">Autoskip</a> to automatically skip ads that pass the Enhancer filter. <br/>

<br/>

The above solutions reduces the income of the person or the team who created and posted the YouTube video. Better than the above solutions is to use a YouTube <b>premium</b> account. In this way, you a) save your time and focus by avoiding ads and b) support the person who created the video. Youtube <a href="https://support.google.com/youtube/answer/7060016?hl=en#:~:text=How YouTube Premium supports creators,monthly membership fee with creators." class="urlextern" title="https://support.google.com/youtube/answer/7060016?hl=en#:~:text=How YouTube Premium supports creators,monthly membership fee with creators." rel="ugc nofollow">pays</a> creators a little money for every minute we watch their video with a premium account.
</p>
<hr />

</div>

<h3>Prevent Google Colab from being disconnected?</h3>
<div class="level3">

<p>
To prevent disconnection of your Google Colab session, you can use the following script that keeps the session active by clicking on the notebook every 60 seconds:
</p>
<pre class="code">function ClickConnect(){
    console.log("Working");
    document.querySelector("colab-connect-button").click()
}
setInterval(ClickConnect,1000*60)

</pre><p> </p>

<p>
To implement this script, open the developer console in your browser (using Ctrl+Shift+J in Chrome or Ctrl+Shift+I in Firefox or Command+Option+C in Safari), and paste the above script in the console. This will help to ensure that your Colab session remains active and does not disconnect due to inactivity.
</p>
<hr />

</div>

<h3>Plot deep neural network architecture diagrams?</h3>
<div class="level3">

<p>
There are <a href="https://datascience.stackexchange.com/questions/14899/how-to-draw-deep-learning-network-architecture-diagrams" class="urlextern" title="https://datascience.stackexchange.com/questions/14899/how-to-draw-deep-learning-network-architecture-diagrams" rel="ugc nofollow">several</a> <a href="https://datascience.stackexchange.com/questions/12851/how-do-you-visualize-neural-network-architectures" class="urlextern" title="https://datascience.stackexchange.com/questions/12851/how-do-you-visualize-neural-network-architectures" rel="ugc nofollow">apps</a> that would help in this manner which are listed based on their descending qualities:
</p>
<ol>
<li class="level1"> <a href="https://github.com/HarisIqbal88/PlotNeuralNet" class="urlextern" title="https://github.com/HarisIqbal88/PlotNeuralNet" rel="ugc nofollow">PlotNeuralNet</a> (very simple, just generate fixed latex commands, no flexibility in the layers themselves, you need to rewrite models in this <a href="https://github.com/HarisIqbal88/PlotNeuralNet/blob/master/pyexamples/test_simple.py" class="urlextern" title="https://github.com/HarisIqbal88/PlotNeuralNet/blob/master/pyexamples/test_simple.py" rel="ugc nofollow">language</a>) <a href="/lib/exe/fetch.php?tok=f7fe20&media=https%3A%2F%2Fuser-images.githubusercontent.com%2F17570785%2F50308846-c2231880-049c-11e9-8763-3daa1024de78.png" class="media" title="https://user-images.githubusercontent.com/17570785/50308846-c2231880-049c-11e9-8763-3daa1024de78.png"><img src="/lib/exe/fetch.php?w=50&h=18&tok=78bd00&media=https%3A%2F%2Fuser-images.githubusercontent.com%2F17570785%2F50308846-c2231880-049c-11e9-8763-3daa1024de78.png" class="media" loading="lazy" alt="" width="50" height="18" /></a></li>
<li class="level1"> <a href="https://analyticsindiamag.com/how-to-visualize-deep-learning-models-using-visualkeras/" class="urlextern" title="https://analyticsindiamag.com/how-to-visualize-deep-learning-models-using-visualkeras/" rel="ugc nofollow">Visualkeras</a> (plots Keras models) <a href="/lib/exe/fetch.php?tok=d54b37&media=https%3A%2F%2F149695847.v2.pressablecdn.com%2Fwp-content%2Fuploads%2F2021%2F11%2Fimage-37.png" class="media" title="https://149695847.v2.pressablecdn.com/wp-content/uploads/2021/11/image-37.png"><img src="/lib/exe/fetch.php?w=30&h=31&tok=6f98f0&media=https%3A%2F%2F149695847.v2.pressablecdn.com%2Fwp-content%2Fuploads%2F2021%2F11%2Fimage-37.png" class="media" loading="lazy" alt="" width="30" height="31" /></a></li>
<li class="level1"> <a href="http://alexlenail.me/NN-SVG/index.html" class="urlextern" title="http://alexlenail.me/NN-SVG/index.html" rel="ugc nofollow">NN-SVG</a></li>
<li class="level1"> <a href="https://github.com/gwding/draw_convnet" class="urlextern" title="https://github.com/gwding/draw_convnet" rel="ugc nofollow">draw_convnet</a> <a href="/lib/exe/fetch.php?tok=bdaeed&media=https%3A%2F%2Fraw.githubusercontent.com%2Fgwding%2Fdraw_convnet%2Fmaster%2Fconvnet_fig.png" class="media" title="https://raw.githubusercontent.com/gwding/draw_convnet/master/convnet_fig.png"><img src="/lib/exe/fetch.php?w=100&h=32&tok=e818cd&media=https%3A%2F%2Fraw.githubusercontent.com%2Fgwding%2Fdraw_convnet%2Fmaster%2Fconvnet_fig.png" class="media" loading="lazy" alt="" width="100" height="32" /></a></li>
<li class="level1"> <a href="https://github.com/lutzroeder/netron" class="urlextern" title="https://github.com/lutzroeder/netron" rel="ugc nofollow">netron</a> (does not consider ModuleList inside the model in PyTorch) <a href="/lib/exe/fetch.php?tok=a2ef10&media=https%3A%2F%2Fgithub.com%2Flutzroeder%2Fnetron%2Fraw%2Fmain%2F.github%2Fscreenshot.png" class="media" title="https://github.com/lutzroeder/netron/raw/main/.github/screenshot.png"><img src="/lib/exe/fetch.php?w=50&h=34&tok=6f2c65&media=https%3A%2F%2Fgithub.com%2Flutzroeder%2Fnetron%2Fraw%2Fmain%2F.github%2Fscreenshot.png" class="media" loading="lazy" alt="" width="50" height="34" /></a></li>
<li class="level1"> <a href="https://viscom.net2vis.uni-ulm.de/" class="urlextern" title="https://viscom.net2vis.uni-ulm.de/" rel="ugc nofollow">Net2Vis</a> (automatically generates abstract visualizations for convolutional neural networks from Keras code)</li>
<li class="level1"> <a href="https://tikz.net/neural_networks/" class="urlextern" title="https://tikz.net/neural_networks/" rel="ugc nofollow">LaTeX</a> examples of neural networks.</li>
</ol>
<hr />

</div>

<h3>Append multiple videos quickly?</h3>
<div class="level3">

<p>
First, make a text file named <code>mylist.txt</code>  with the following content:
</p>

<p>
Then, run
</p>
<pre class="code">ffmpeg -f concat -safe 0 -i mylist.txt -c copy output.mp4

</pre><p> </p>

<p>
which is fast because it only copies the audio and video codecs. ffmpeg can be <a href="https://phoenixnap.com/kb/ffmpeg-mac" class="urlextern" title="https://phoenixnap.com/kb/ffmpeg-mac" rel="ugc nofollow">installed</a> on MacOS using brew.
</p>
<hr />

</div>

<h3>Extend reads in a bam file to a fixed fragment size to better view peaks with IGV?</h3>
<div class="level3">

<p>
Assume you have <code>input.bam</code>, which contains mapped short single-end sequence reads, but you know the fragment size=<code>100</code>. With the following command, you can make a bam file that has the extended reads, but you will miss the actual reads. This helps to better visualize the actual read signal:
</p>
<pre class="code">bedtools bamtobed -i input.bam | \
awk -F'\t' 'BEGIN {OFS = FS} {if ($6=="+") {$3=$2+99} else {$2=$3-99}; if ($2&lt;0) {$2=0}; print $0;}' | \
bedtools bedtobam -g hg19.chr.sizes -i -&gt; extended_input.bam

</pre><p> </p>

<p>
where <code>hg19.chr.sizes</code>  is a tsv file with two columns containing chr names and sizes. <br/>
 <br/>
NOTE: <code>bedCoverage</code>  command is supposed to do this, but in my case, I got an error about the input bam file, despite the fact that it was a normal mapped bam file.
</p>
<hr />

</div>

<h3>Run simultaneous jobs (on multiple files) in a single mpi on a cluster?</h3>
<div class="level3">

<p>
It can be done using <code>xargs -P &lt;number-of-threads> &lt;command></code>. For example, we assume you are writing a bash script as follows: <br/>
 <br/>
First, write a function (or script) to do the work on a single input file. Second, export the function using
</p>
<pre class="code">export -f my_func_for_single_file

</pre><p> </p>

<p>
 <br/>
Third, use the `find` command (or anything appropriate) and pipe the results to `xargs` like this:
</p>
<pre class="code">find . -type f -name "*.bam" -printf "%f\n" | xargs -P 125 -I {} bash -c 'my_func_for_single_file "$@"' _ {}

</pre><p> </p>

<p>
Where <code>%f</code>  is the basename of the file returned by the <code>find</code>  . This command runs the task with 125 threads in parallel on a node (e.g. with 128 cores). Assuming you have 210 files, It will run all the task in 2 sweeps, which means it costs less almost with a factor of 125.
</p>

<p>
Change 125 as you want, but <b>not</b>  more than the number of available cores in each compute node! :) Also you can adapt this idea to the cases where your function needs other inputs than the simple file name.
</p>
<hr />

</div>

<h3>Plot models of Keras in R on MacOS?</h3>
<div class="level3">

<p>
First, in Terminal , run <a href="https://graphviz.gitlab.io/download/" class="urlextern" title="https://graphviz.gitlab.io/download/" rel="ugc nofollow">this</a> brew command (which is much better than "port"):
</p>
<pre class="code">brew install graphviz

</pre><p> </p>

<p>
Then run this in R:
</p>
<pre class="code">reticulate::py_install("pydot", pip = TRUE)

</pre><p> </p>
<hr />

</div>

<h3>Identify genes of a pathway in R?</h3>
<div class="level3">

<p>
1) <code>ReactomeContentService4R</code>  is Reactome <a href="https://www.biostars.org/p/391386/#9463286" class="urlextern" title="https://www.biostars.org/p/391386/#9463286" rel="ugc nofollow">wrapper</a> in R:
</p>
<pre class="code">library(ReactomeContentService4R)
event2Ids(event.id = "R-HSA-6790901") # can only input id here

</pre><p> </p>

<p>
2) <a href="https://www.biostars.org/p/9978/#13639" class="urlextern" title="https://www.biostars.org/p/9978/#13639" rel="ugc nofollow">Kegg</a>:
</p>
<pre class="code">library(org.Hs.eg.db)
kegg &lt;- org.Hs.egPATH2EG
mapped &lt;- mappedkeys(kegg)
kegg2 &lt;- as.list(kegg[mapped])
keggFind("pathway", "mtor") ## finds the pathway with a key word
ent &lt;- kegg2 [["04150"|]] ##needs id of pathway (mtor), returns entrez id
gene.mapping(id=ent, inputType="ENTREZID", outputType = "SYMBOL")

</pre><p> </p>
<hr />

</div>

<h3>Work with screen sessions?</h3>
<div class="level3">

<p>
There are five main <a href="http://www.pixelbeat.org/lkdb/screen.html" class="urlextern" title="http://www.pixelbeat.org/lkdb/screen.html" rel="ugc nofollow">commands</a> while working with screen session:
</p>
<ol>
<li class="level1"> Start and name a screen: <code>screen -S &lt;NAME of the screen></code></li>
<li class="level1"> Detach from a screen: <code>Ctrl+a d</code></li>
<li class="level1"> See the list of active screens: <code>screen -ls</code></li>
<li class="level1"> Reattach to a screen: <code>screen -r &lt;NAME of the screen></code></li>
<li class="level1"> Quit and kill your screen: <code>Ctrl+a </code>  then <code>Ctrl+\</code></li>
</ol>
<hr />

</div>

<h3>Read and write excel files in R</h3>
<div class="level3">

<p>
Use <a href="https://cran.r-project.org/web/packages/openxlsx/index.html" class="urlextern" title="https://cran.r-project.org/web/packages/openxlsx/index.html" rel="ugc nofollow">openxlsx</a> 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.
</p>
<pre class="code">
E.g. Writing four dataframes in four sheets of excel workbook can be done as follows:
library(openxlsx)
data("mtcars")
listDataFrames &lt;- list("First"=mtcars[1:5,], "Second"=mtcars[10:15, ])
xlsFile &lt;- "~/temp/test.xlsx"
w1 &lt;- write.xlsx(x=listDataFrames, file=xlsFile)

## You can add new sheets:
addWorksheet(w1, sheetName = "New")
writeData(wb=w1, sheet="New", mtcars[,1:3])
saveWorkbook(w1, file=xlsFile, overwrite=TRUE)

## Read a sheet in a data frame:
r1 &lt;- read.xlsx(xlsxFile=xlsFile, sheet="Second")

</pre><p> </p>
<hr />

</div>

<h3>Set local mirror for Rscript</h3>
<div class="level3">

<p>
Put following lines above your script.
</p>
<pre class="code">local({r &lt;- getOption("repos")
r["CRAN"] &lt;- "your mirror, example: http://cran.us.r-project.org "
options(repos=r)
})

</pre><p> </p>
<hr />

</div>

<h2>Add only modified changes and ignore untracked files using git?</h2>
<div class="level2">

<p>
Using newer version of `git` (e.g., >=2.32.1),
</p>
<pre class="code">git commit -am 'minor changes'; git push

</pre><p> </p>

<p>
⚠️ <span style = "color:#e74c3c">Caution</span>: With older versions the -a option will add all files in the directory, which is usually NOT what you want. Instead, use following command, which would have the same effect as above:
</p>
<pre class="code">git ls-files --modified | xargs git add; git commit -m 'minor changes'; git push

</pre><p> </p>

<p>
The <a href="https://stackoverflow.com/questions/7124726/git-add-only-modified-changes-and-ignore-untracked-files" class="urlextern" title="https://stackoverflow.com/questions/7124726/git-add-only-modified-changes-and-ignore-untracked-files" rel="ugc nofollow">above</a> should work if there is no conflict. If there is a conflict at push time, first pull. Now, you need to look for ">>>" in the code, and manually fix the conflict. Then, push again.
</p>
<hr />

</div>

<h3>Create an R package or use a package that is being developed?</h3>
<div class="level3">

<p>
An R package source folder has a predetermined <a href="https://r-pkgs.org/package-structure-state.html" class="urlextern" title="https://r-pkgs.org/package-structure-state.html" rel="ugc nofollow">structure</a>. If you change the content of a packge, you can use the <a href="https://bitbucket.org/habilzare/alzheimer/src/master/code/Habil/utilities/make.package.R" class="urlextern" title="https://bitbucket.org/habilzare/alzheimer/src/master/code/Habil/utilities/make.package.R" rel="ugc nofollow">make.package</a>() function to update (i.e., build, check, and install) the package while preserving its structure like the <a href="https://bitbucket.org/habilzare/alzheimer/src/master/code/senescence/Shiva/packing.R" class="urlextern" title="https://bitbucket.org/habilzare/alzheimer/src/master/code/senescence/Shiva/packing.R" rel="ugc nofollow">senescence</a> and <a href="https://bitbucket.org/habilzare/genetwork/src/master/code/Ghazal/Packing/packing.R" class="urlextern" title="https://bitbucket.org/habilzare/genetwork/src/master/code/Ghazal/Packing/packing.R" rel="ugc nofollow">iNETgrate</a> package examples.
</p>
<hr />

</div>

<h3>Cancel all your jobs on the Stampede?</h3>
<div class="level3">
<pre class="code">squeue -l -u $USER|awk 'FNR&gt;2 {print $1}' |xargs  scancel

</pre><p> </p>
<hr />

</div>

<h3>Install R locally (e.g. on a cluster)?</h3>
<div class="level3">

<p>
Like most of Unix programs, R can be installed from source by a) downloading the <a href="https://cloud.r-project.org/" class="urlextern" title="https://cloud.r-project.org/" rel="ugc nofollow">source</a> code, configuring and compiling the code, and then installing the binaries. If you try this simple approach and your get errors like <a href="https://tdhock.github.io/blog/2017/compiling-R/" class="urlextern" title="https://tdhock.github.io/blog/2017/compiling-R/" rel="ugc nofollow">these</a>, it means the dependencies are not available or updated on your machine. E.g., f you want to install the latest <u>development</u>  version of R on your macOS, first install <a href="https://github.com/fxcoudert/gfortran-for-macOS/releases" class="urlextern" title="https://github.com/fxcoudert/gfortran-for-macOS/releases" rel="ugc nofollow">Fortran</a> if you do not have it. You may also need to update PCRE using brew on <a href="http://superuser.com/a/664326" class="urlextern" title="http://superuser.com/a/664326" rel="ugc nofollow">macOS</a>. Alternatively, you can compile PCRE2 from the <a href="https://www.linuxfromscratch.org/blfs/view/svn/general/pcre2.html" class="urlextern" title="https://www.linuxfromscratch.org/blfs/view/svn/general/pcre2.html" rel="ugc nofollow">source</a>, and then let R where it is <a href="https://unix.stackexchange.com/a/149361" class="urlextern" title="https://unix.stackexchange.com/a/149361" rel="ugc nofollow">using</a> CPPFLAGS and LDFLAGS.
</p>

<p>
If you do not have sudo permissions, like when you are working on a cluster, you should either use the software module, or install R locally in your home directory. E.g., you can install R on Stampede or Maverick TACC clusters as follows:
</p>
<pre class="code">mkdir ~/tempR; cd ~/tempR ## Make a temp directory
wget http://cran.cnr.berkeley.edu/src/base/R-3/R-3.2.2.tar.gz ## Always get the latest version
tar -zxvf ./R-3.2.2.tar.gz; cd ./R-3.2.2 ## Unzip, the rest is by following INSTALL file that is in this folder.
mkdir ~/arch ## You will install here.
./configure --prefix $HOME/arch
make
make check
make install

</pre><p> </p>

<p>
If the above works without any error, you can add $HOME/arch to your path by inserting the following line in your .bachrc file:
</p>
<pre class="code">export PATH=$HOME/arch/bin:$PATH

</pre><p> </p>

<p>
On some clusters, <a href="https://tdhock.github.io/blog/2017/compiling-R/" class="urlextern" title="https://tdhock.github.io/blog/2017/compiling-R/" rel="ugc nofollow">a few </a>libraries might not be installed or they might be too old (e.g., zlib, curl, bzip2, xz, pcre). In particular, the bzip2 issue can be resolved by following <a href="http://pj.freefaculty.org/blog/?p=315" class="urlextern" title="http://pj.freefaculty.org/blog/?p=315" rel="ugc nofollow">these</a> steps on the Lonestar5 cluster. Oncinfo Lab members can use it if they add the following to their .bashrc
</p>
<pre class="code">export PATH=/home1/03270/zare/Install/bin:$PATH

</pre><p> </p>

<p>
Installing R using <a href="https://datascience.stackexchange.com/questions/77335/anconda-r-version-how-to-upgrade-to-4-0-and-later/86905#86905" class="urlextern" title="https://datascience.stackexchange.com/questions/77335/anconda-r-version-how-to-upgrade-to-4-0-and-later/86905#86905" rel="ugc nofollow">conda</a> is only a quick and <a href="https://www.perfectlyrandom.org/2016/04/08/install-xml2-r-package-on-macos/" class="urlextern" title="https://www.perfectlyrandom.org/2016/04/08/install-xml2-r-package-on-macos/" rel="ugc nofollow">dirty</a>, temporary solution. E.g., as of 2021-05-14, the xml2 package that is installed by conda is not compatible with R 4.0 that is installed using conda, therefore, solving the issue in <a href="https://stackoverflow.com/questions/37035088/unable-to-install-r-package-due-to-xml-dependency-mismatch" class="urlextern" title="https://stackoverflow.com/questions/37035088/unable-to-install-r-package-due-to-xml-dependency-mismatch" rel="ugc nofollow">this way</a> moves the R version to from 4.0 back to 3.0! The time you will spend addressing such issues would be possibly more than the time you need to put on to a clean instalation of R from source.
</p>
<hr />

</div>

<h3>Restore a file deleted in a local git directory?</h3>
<div class="level3">

<p>
<a href="http://stackoverflow.com/questions/9305326/why-doesnt-git-pull-bring-back-directories-that-ive-deleted" class="urlextern" title="http://stackoverflow.com/questions/9305326/why-doesnt-git-pull-bring-back-directories-that-ive-deleted" rel="ugc nofollow">Use</a> git reset –hard to completely bring your working directory to HEAD state. However, this is a <a href="http://stackoverflow.com/questions/5473/how-can-i-undo-git-reset-hard-head1" class="urlextern" title="http://stackoverflow.com/questions/5473/how-can-i-undo-git-reset-hard-head1" rel="ugc nofollow">dangerous</a> command because you may loose some local files that are not pushed yet.
</p>
<hr />

</div>

<h3>Get familiar with machine learning and its applications in computational biology?</h3>
<div class="level3">

<p>
- You can enroll in many online machine learning courses. Some of the best courses in ML can be found <a href="https://docs.google.com/spreadsheets/d/1AK8lqS-ztMhh8YoOaQ7ScIZmabrQ5AFxAyXKwYWiT04/edit#gid=0" class="urlextern" title="https://docs.google.com/spreadsheets/d/1AK8lqS-ztMhh8YoOaQ7ScIZmabrQ5AFxAyXKwYWiT04/edit#gid=0" rel="ugc nofollow">here</a>.
</p>

<p>
- Most common ML techniques are very well explained in <a href="https://scikit-learn.org/stable/user_guide.html" class="urlextern" title="https://scikit-learn.org/stable/user_guide.html" rel="ugc nofollow">Scikit learn</a> with <a href="https://scikit-learn.org/stable/modules/decomposition.html" class="urlextern" title="https://scikit-learn.org/stable/modules/decomposition.html" rel="ugc nofollow">illustrations</a> and example Python code. These techniques have been implemented in <a href="https://www.kaggle.com/getting-started/5243" class="urlextern" title="https://www.kaggle.com/getting-started/5243" rel="ugc nofollow">R</a> packages including mlr3 and tidymodels.
</p>

<p>
-<a href="http://www.nature.com/nrg/journal/v16/n6/abs/nrg3920.html" class="urlextern" title="http://www.nature.com/nrg/journal/v16/n6/abs/nrg3920.html" rel="ugc nofollow">This</a> 2015 paper reviews applications of ML in genetics and genomics. Read it and follow its references.
</p>
<hr />

</div>

<h3>Get access to the papers through the library when you are off-campus?</h3>
<div class="level3">

<p>
In any of these two ways: <br/>

a) First add the following to your browser (e.g., Chrome, Safari, or Firefox) bookmarks.
</p>

<p>
<a href="/lib/exe/fetch.php?media=wiki:public:screen_shot_2023-04-24_at_3.36.10_pm.png" class="media" title="wiki:public:screen_shot_2023-04-24_at_3.36.10_pm.png"><img src="/lib/exe/fetch.php?w=800&tok=d66112&media=wiki:public:screen_shot_2023-04-24_at_3.36.10_pm.png" class="media" loading="lazy" alt="" width="800" /></a>
For your convenience, you can write "javascript", and then ":voind()", and copy the following line between the parentheses.  
</p>
<pre class="code">location.href=%22http://libproxy.uthscsa.edu/login?url=%22+location.href

</pre><p> </p>

<p>
Then, on the journal page, click on the bookmark. Login and start reading.
</p>

<p>
b) Use <a href="https://infosec.uthscsa.edu/two-factor-enrollment" class="urlextern" title="https://infosec.uthscsa.edu/two-factor-enrollment" rel="ugc nofollow">GlobalProtect</a>, which is the University VPN.
</p>

<p>
If an articles is not available from the library, it can be ordered via <a href="https://libguides.uthscsa.edu/ill" class="urlextern" title="https://libguides.uthscsa.edu/ill" rel="ugc nofollow">interlibrary loan</a>.
</p>
<hr />

</div>

<h3>Convert pdf to MS word?</h3>
<div class="level3">

<p>
Try whatever you can to avoid conversion! Instead, educate your team and your collaborators to use <a href="https://www.authorea.com/users/54336" class="urlextern" title="https://www.authorea.com/users/54336" rel="ugc nofollow">Authorea</a>, <a href="https://www.overleaf.com/" class="urlextern" title="https://www.overleaf.com/" rel="ugc nofollow">Overleaf</a> or at least Google Doc. In Google Doc, references can be easily handled using <a href="https://gsuite.google.com/marketplace/app/paperpile/894076725911" class="urlextern" title="https://gsuite.google.com/marketplace/app/paperpile/894076725911" rel="ugc nofollow">Paperpile</a> add-on (NOT the extension), and figures can be automatically numbered using the the <a href="https://gsuite.google.com/marketplace/app/cross_reference/269114033347?pann=cwsdp&hl=en" class="urlextern" title="https://gsuite.google.com/marketplace/app/cross_reference/269114033347?pann=cwsdp&hl=en" rel="ugc nofollow">Cross Reference</a> add-on as suggested in these <a href="https://lcolladotor.github.io/2019/04/02/how-to-write-academic-documents-with-googledocs/#.Xjne6RNKjUI" class="urlextern" title="https://lcolladotor.github.io/2019/04/02/how-to-write-academic-documents-with-googledocs/#.Xjne6RNKjUI" rel="ugc nofollow">guidelines</a> on how to write academic documents with Google Docs. Add-ons are not available when editing .docx files. <u>Only</u> if your biologist collaborators cannot <a href="http://www.dedoimedo.com/computers/latex.html" class="urlextern" title="http://www.dedoimedo.com/computers/latex.html" rel="ugc nofollow">unfortunately</a> edit the LaTeX source, consider using a conversion tool such as Adobe <a href="https://chrome.google.com/webstore/detail/adobe-acrobat/efaidnbmnnnibpcajpcglclefindmkaj" class="urlextern" title="https://chrome.google.com/webstore/detail/adobe-acrobat/efaidnbmnnnibpcajpcglclefindmkaj" rel="ugc nofollow">Acrobat</a> Chrome extension or Acrobat Pro, which can export a .pdf as a .doc file. docs. The docs <a href="https://docs.zone/" class="urlextern" title="https://docs.zone/" rel="ugc nofollow">zone</a> and pdf <a href="https://www.freepdfconvert.com/" class="urlextern" title="https://www.freepdfconvert.com/" rel="ugc nofollow">Converter</a> are online alternatives. If you need to to separate pages, use <a href="https://superuser.com/a/1584919" class="urlextern" title="https://superuser.com/a/1584919" rel="ugc nofollow">pdfjam</a>. If Bibtex is not an option, use <a href="http://www.easybib.com/" class="urlextern" title="http://www.easybib.com/" rel="ugc nofollow">EasyBib</a>.
</p>

<p>
<a href="https://www.docx2latex.com/word-to-latex-converter/" class="urlextern" title="https://www.docx2latex.com/word-to-latex-converter/" rel="ugc nofollow">Docx2LaTeX</a> can convert simple Word or Google Docs to LaTeX.
</p>
<hr />

</div>

<h3>Enable spell check in Emacs on OS X?</h3>
<div class="level3">

<p>
The default Aquamacs spell checker has some issues. To replace it, first <a href="http://stackoverflow.com/questions/19022015/emacs-on-mac-os-x-how-to-get-spell-check-to-work" class="urlextern" title="http://stackoverflow.com/questions/19022015/emacs-on-mac-os-x-how-to-get-spell-check-to-work" rel="ugc nofollow">install</a> Aspell, which is a <a href="https://en.wikipedia.org/wiki/GNU_Aspell" class="urlextern" title="https://en.wikipedia.org/wiki/GNU_Aspell" rel="ugc nofollow">replacement</a> for Ispell:
</p>
<pre class="code">brew install aspell

</pre><p> </p>

<p>
And then add the following line to your emacs <a href="http://www.emacswiki.org/emacs/InitFile" class="urlextern" title="http://www.emacswiki.org/emacs/InitFile" rel="ugc nofollow">initialization</a> file, e.g., ~/Library/Preferences/Aquamacs Emacs/Preferences.el, or ~/.emacs
</p>
<pre class="code">(setq ispell-program-name "/usr/local/bin/aspell")

</pre><p> </p>
<hr />

</div>

<h3>Do microaray analysis or anything else in Bioconductor?</h3>
<div class="level3">

<p>
<a href="http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-Affy" class="urlextern" title="http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-Affy" rel="ugc nofollow">This </a> is an excellent site with many well commented code examples and a lot of handy short-cuts. See also <a href="/doku.php?id=how_to" class="wikilink1" title="how_to" data-wiki-id="how_to">Functional analysis tools</a>.
</p>
<hr />

<p>
<b>Learn to learn?</b> <br/>

Take <a href="https://www.coursera.org/learn/learning-how-to-learn/home/info" class="urlextern" title="https://www.coursera.org/learn/learning-how-to-learn/home/info" rel="ugc nofollow">this</a> online course: Learning How to Learn: Powerful mental tools to help you master tough subjects.
</p>
<hr />

<p>
<b>Improve your writing?</b> <br/>

Read and write a lot. Have someone proofread your write up. Use tips and <a href="http://www.springer.com/gp/book/9783319260921" class="urlextern" title="http://www.springer.com/gp/book/9783319260921" rel="ugc nofollow">resources</a> that can help you improve your writing skills to the next level. E.g., you can find valuable professional resources on <a href="http://www.writingforward.com/" class="urlextern" title="http://www.writingforward.com/" rel="ugc nofollow">Writing</a> Forward website. Coursera has a special course on writing emails in its "Improve Your English Communication Skills <a href="https://www.coursera.org/specializations/improve-english?recoOrder=1&utm_medium=email&utm_source=recommendations&utm_campaign=recommendationsEmail~recs_email_2016_12_04_17%3A58" class="urlextern" title="https://www.coursera.org/specializations/improve-english?recoOrder=1&utm_medium=email&utm_source=recommendations&utm_campaign=recommendationsEmail~recs_email_2016_12_04_17%3A58" rel="ugc nofollow">Specialization</a>".
</p>
<hr />

<p>
<b>Prepare a scientific poster?</b> <br/>

Decide on the main figures that you want to include. Put them in a <a href="/doku.php?id=poster_retreat_2013_habil.ppt&media=poster_retreat_2013_habil.ppt" class="wikilink2" title="poster_retreat_2013_habil.ppt" rel="nofollow" data-wiki-id="poster_retreat_2013_habil.ppt">template</a> and write a caption for each figure. Write your abstract and an appropriate title. Send it to collaborators and ask for their comments at least a week before printing.
</p>
<hr />

<p>
<b>Find a biological database of interest?</b> <br/>

First, look at the <a href="https://en.wikipedia.org/wiki/List_of_biological_databases" class="urlextern" title="https://en.wikipedia.org/wiki/List_of_biological_databases" rel="ugc nofollow">list</a> of biological databases. Also, if you know an important database that is missed in this list, please add it as a service to the community.
</p>
<hr />

</div>

<h3>Begin learning bioinformatics?</h3>
<div class="level3">

<p>
Take a course from the <a href="http://research.omicsgroup.org/index.php/List_of_free_online_bioinformatics_courses" class="urlextern" title="http://research.omicsgroup.org/index.php/List_of_free_online_bioinformatics_courses" rel="ugc nofollow">list</a> of free online bioinformatics courses e.g., the Computational Molecular Biology <a href="http://cmgm.stanford.edu/biochem218/index.html" class="urlextern" title="http://cmgm.stanford.edu/biochem218/index.html" rel="ugc nofollow">Course</a> at Stanford is broad and covers the classic topics but it is not updated, and may become outdated. The same is true for PLOS Translational Bioinformatics <a href="http://collections.plos.org/translational-bioinformatics" class="urlextern" title="http://collections.plos.org/translational-bioinformatics" rel="ugc nofollow">Collection</a> of articles, which are more advanced. Most central topics are covered in some course from the European Bioinformatics Institute (<a href="https://www.ebi.ac.uk/training/online/course-list" class="urlextern" title="https://www.ebi.ac.uk/training/online/course-list" rel="ugc nofollow">EBI</a>). Very useful training materials are available from <a href="https://www.mygoblet.org/" class="urlextern" title="https://www.mygoblet.org/" rel="ugc nofollow">GOBLET</a>. Videos from the Models, Inference & Algorithms Initiative (<a href="https://www.broadinstitute.org/scientific-community/science/mia/models-inference-algorithms" class="urlextern" title="https://www.broadinstitute.org/scientific-community/science/mia/models-inference-algorithms" rel="ugc nofollow">MIA</a>) at Broad are relatively advanced. <br/>
 <br/>
<a href="http://bioconductor.org/help/course-materials/" class="urlextern" title="http://bioconductor.org/help/course-materials/" rel="ugc nofollow">Bioconductor</a> course material provides a walkthrough in specific areas. Also, you can find valuable resources from the <a href="http://stephenturner.us/edu.html" class="urlextern" title="http://stephenturner.us/edu.html" rel="ugc nofollow">list</a> of bioinformatics workshops and <a href="http://www.engr.uconn.edu/~mukul/cbc.htm" class="urlextern" title="http://www.engr.uconn.edu/~mukul/cbc.htm" rel="ugc nofollow">conferences</a>. Following the "Bioinformatics for biologists <a href="/doku.php?id=bioinformatics_for_biologist_workshop" class="wikilink1" title="bioinformatics_for_biologist_workshop" data-wiki-id="bioinformatics_for_biologist_workshop">workshop</a>" does not require expertise in computer programing. Bio-Linux team prepared a good <a href="http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf" class="urlextern" title="http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf" rel="ugc nofollow">introduction</a>, which can be used as a reference too. If machine learning is new to you, <a href="http://www.nature.com/nrg/journal/v16/n6/full/nrg3920.html" class="urlextern" title="http://www.nature.com/nrg/journal/v16/n6/full/nrg3920.html" rel="ugc nofollow">read</a> about its applications in genetics and genomics. You need to have some basic knowledge in <a href="https://www.coursera.org/learn/biostatistics?recoOrder=9&utm_medium=email&utm_source=recommendations&utm_campaign=recommendationsEmail~recs_email_2016_06_26_17%3A57" class="urlextern" title="https://www.coursera.org/learn/biostatistics?recoOrder=9&utm_medium=email&utm_source=recommendations&utm_campaign=recommendationsEmail~recs_email_2016_06_26_17%3A57" rel="ugc nofollow">mathematics</a> and statistics too.
</p>
<hr />

<p>
<b>Decide on appropriate courses for a program in computational biology</b><b>?</b> <br/>

Browse the Online Computational Biology <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003662" class="urlextern" title="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003662" rel="ugc nofollow">Curriculum</a>, which lists hundreds of courses available from Coursera, Edx, etc, and comments on their relevance to computational biology. <a href="http://qb3.berkeley.edu/ccb/research-education/courses/" class="urlextern" title="http://qb3.berkeley.edu/ccb/research-education/courses/" rel="ugc nofollow">Berkeley</a> and <a href="http://compbio.stanford.edu/cs-courses.html" class="urlextern" title="http://compbio.stanford.edu/cs-courses.html" rel="ugc nofollow">Stanford</a> also have lists of relevant courses.
</p>
<hr />

<p>
<b>Establish and maintain a computational biology lab?</b> <br/>

Do not miss About My <a href="http://collections.plos.org/about-my-lab" class="urlextern" title="http://collections.plos.org/about-my-lab" rel="ugc nofollow">Lab</a>, a valuable collection of PLOS articles on how to manage a lab. This is a <a href="http://www.mbg.jhmi.edu/sites/default/files/page_attachments/Tilghman_NathansLect_4.2016.pdf" class="urlextern" title="http://www.mbg.jhmi.edu/sites/default/files/page_attachments/Tilghman_NathansLect_4.2016.pdf" rel="ugc nofollow">fundamentally</a> difficult job.
</p>
<hr />

</div>

<h3>Install Salmon on OSX?</h3>
<div class="level3">

If you do not have autoconf, <a href="http://mac-dev-env.patrickbougie.com/autoconf/" class="urlextern" title="http://mac-dev-env.patrickbougie.com/autoconf/" rel="ugc nofollow">install</a> it. Following the installation guidelines, for OSX you need to first <a href="http://stackoverflow.com/questions/3181468/how-do-you-install-intel-tbb-on-os-x" class="urlextern" title="http://stackoverflow.com/questions/3181468/how-do-you-install-intel-tbb-on-os-x" rel="ugc nofollow">install</a> Thread Building Blocks (TBB) (brew install tbb) and then check that the installation was successful (brew list). Download the latest <a href="https://github.com/COMBINE-lab/salmon/releases" class="urlextern" title="https://github.com/COMBINE-lab/salmon/releases" rel="ugc nofollow">version</a> of Salmon source code and uncompress it. Follow Salmon's installation <a href="http://salmon.readthedocs.org/en/latest/building.html#installation" class="urlextern" title="http://salmon.readthedocs.org/en/latest/building.html#installation" rel="ugc nofollow">guidelines</a>. The cmake command in the guidelines will be something like the following for OSX:
</p>
<pre class="code">cmake -DFETCH_BOOST=TRUE -DTBB_INSTALL_DIR=/usr/local/lib -DCMAKE_INSTALL_PREFIX=/usr/local/

</pre><p> </p>

<p>
Follow the rest of the guidelines. You may need to use (sudo make install) if you get a permission error.
</p>
<hr />

</div>

<h2>Write a scientific paper?</h2>
<div class="level2">

<p>
Put the figures together and then <a href="http://www.scidev.net/global/publishing/practical-guide/how-do-i-write-a-scientific-paper-.html" class="urlextern" title="http://www.scidev.net/global/publishing/practical-guide/how-do-i-write-a-scientific-paper-.html" rel="ugc nofollow">draft</a> different <a href="https://www.nature.com/articles/nmeth.4532?WT.ec_id=NMETH-201712&spMailingID=55474826&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1285409878&spReportId=MTI4NTQwOTg3OAS2" class="urlextern" title="https://www.nature.com/articles/nmeth.4532?WT.ec_id=NMETH-201712&spMailingID=55474826&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1285409878&spReportId=MTI4NTQwOTg3OAS2" rel="ugc nofollow">sections</a>. Focus the <a href="http://www.grantcentral.com/strategies-for-avoiding-common-problems-with-research-manuscripts/" class="urlextern" title="http://www.grantcentral.com/strategies-for-avoiding-common-problems-with-research-manuscripts/" rel="ugc nofollow">Discussion</a>. Be careful about <a href="http://colah.github.io/posts/2019-05-Collaboration/index.html" class="urlextern" title="http://colah.github.io/posts/2019-05-Collaboration/index.html" rel="ugc nofollow">authorship</a>. It might be easier to write the <a href="https://plos.org/resource/how-to-write-a-great-abstract/?utm_medium=email&utm_source=internal&utm_campaign=modnewsletters&utm_content=modnewsletter" class="urlextern" title="https://plos.org/resource/how-to-write-a-great-abstract/?utm_medium=email&utm_source=internal&utm_campaign=modnewsletters&utm_content=modnewsletter" rel="ugc nofollow">abstract</a><em>after</em>  other sections are drafted. You can use your <a href="https://www.nature.com/articles/d41586-018-02404-4" class="urlextern" title="https://www.nature.com/articles/d41586-018-02404-4" rel="ugc nofollow">own</a> voice.
</p>

<p>
Many journals require vectorized figures and different tweaks to the fonts and colors. So, make sure your figures are easily reproducible. At the submission stage, you can change to a <a href="https://docs.google.com/document/d/1L49DoVzBfhJaavIvW5CvrxmwV-RHNDJcuFIZy39dS2g/edit" class="urlextern" title="https://docs.google.com/document/d/1L49DoVzBfhJaavIvW5CvrxmwV-RHNDJcuFIZy39dS2g/edit" rel="ugc nofollow">vectorized</a> format like eps or pdf using different tools including <a href="http://blog.linuxgrrl.com/2013/08/12/how-to-produce-vector-eps-with-cmyk-color-using-free-software/" class="urlextern" title="http://blog.linuxgrrl.com/2013/08/12/how-to-produce-vector-eps-with-cmyk-color-using-free-software/" rel="ugc nofollow">Inkscape</a>.
</p>
<hr />

</div>

<h2>Prepare or review computational biology papers for Nature methods?</h2>
<div class="level2">

<p>
Read their "Reviewing computational methods" (<a href="http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3686.html" class="urlextern" title="http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3686.html" rel="ugc nofollow">2015</a>) and "Guidelines for algorithms and software in Nature Methods" (<a href="http://blogs.nature.com/methagora/2014/02/guidelines-for-algorithms-and-software-in-nature-methods.html" class="urlextern" title="http://blogs.nature.com/methagora/2014/02/guidelines-for-algorithms-and-software-in-nature-methods.html" rel="ugc nofollow">2014</a>) articles. Provide source code, pseudocode, compiled executables, and the mathematical description. Softwares must be accompanied with documentation, sample data and the expected output, and a license (e.g., GPL≥2). Have a look at <a href="/doku.php?id=the_list_of_computational_biology_papers_in_nature_methods" class="wikilink1" title="the_list_of_computational_biology_papers_in_nature_methods" data-wiki-id="the_list_of_computational_biology_papers_in_nature_methods">The list of computational biology papers in Nature Methods</a> published in 2015, and the <a href="https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=0ahUKEwic2Oum3dvJAhUGeSYKHWurD-EQFghQMAg&url=http%3A%2F%2Ford.ntu.edu.tw%2Ftc%2Fincludes%2FGetFile.ashx%3FmID%3D253%26id%3D1744%26chk%3De15262f3-87bf-4a7e-be6a-4103cbc61968&usg=AFQjCNHfNXyryLDQMWBRrInOpJVKIL0LCA&sig2=8C9UE1arY4vi2q_CUdsdiQ" class="urlextern" title="https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=0ahUKEwic2Oum3dvJAhUGeSYKHWurD-EQFghQMAg&url=http%3A%2F%2Ford.ntu.edu.tw%2Ftc%2Fincludes%2FGetFile.ashx%3FmID%3D253%26id%3D1744%26chk%3De15262f3-87bf-4a7e-be6a-4103cbc61968&usg=AFQjCNHfNXyryLDQMWBRrInOpJVKIL0LCA&sig2=8C9UE1arY4vi2q_CUdsdiQ" rel="ugc nofollow">hints</a> by an editor of Nature Communications. Several <a href="https://en.wikipedia.org/wiki/Computational_biology#Research" class="urlextern" title="https://en.wikipedia.org/wiki/Computational_biology#Research" rel="ugc nofollow">journals</a> publish papers in this field.
</p>
<hr />

</div>

<h2>Set the default width of fill mode (line length) in emacs?</h2>
<div class="level2">

<p>
<a href="http://stackoverflow.com/questions/3566727/how-to-set-the-default-width-of-fill-mode-to-80-with-emacs" class="urlextern" title="http://stackoverflow.com/questions/3566727/how-to-set-the-default-width-of-fill-mode-to-80-with-emacs" rel="ugc nofollow">Use</a> 'M-x customize-variable' to set 'fill-column' (100 in Oncinfo). Use DejaVu Sans Mono (~<a href="http://www.leancrew.com/all-this/2009/10/the-compleat-menlovera-sans-comparison/" class="urlextern" title="http://www.leancrew.com/all-this/2009/10/the-compleat-menlovera-sans-comparison/" rel="ugc nofollow">Menlo</a> on MacOS) size 18-20 is an <a href="http://ergoemacs.org/emacs/emacs_unicode_fonts.html" class="urlextern" title="http://ergoemacs.org/emacs/emacs_unicode_fonts.html" rel="ugc nofollow">appropriate</a> font for programming in Emacs. To do so, you may need to manually edit your .emacs in <a href="https://stackoverflow.com/questions/4821984/emacs-osx-default-font-setting-does-not-persist" class="urlextern" title="https://stackoverflow.com/questions/4821984/emacs-osx-default-font-setting-does-not-persist" rel="ugc nofollow">macOS</a>, and add the following <a href="https://stackoverflow.com/questions/4879785/can-i-break-the-long-line-in-emacs-non-windows-to-the-next-line" class="urlextern" title="https://stackoverflow.com/questions/4879785/can-i-break-the-long-line-in-emacs-non-windows-to-the-next-line" rel="ugc nofollow">line</a>:
</p>
<pre class="code">(setq truncate-lines nil)

</pre><p> </p>
<hr />

</div>

<h3>Get older versions using git?</h3>
<div class="level3">

<p>
<a href="https://githowto.com/getting_old_versions" class="urlextern" title="https://githowto.com/getting_old_versions" rel="ugc nofollow">Use</a> "git log" to see the previous commits and the corresponding hashes, "git checkout &lt;hash>" to get an older version, and "git checkout master" to get back.
</p>
<hr />

</div>

<h3>Learn about linear models and ANOVA in R?</h3>
<div class="level3">

<p>
Review Advanced Statistical Methods II lecture <a href="https://www.utdallas.edu/~ammann/stat6338/stat6338.html" class="urlextern" title="https://www.utdallas.edu/~ammann/stat6338/stat6338.html" rel="ugc nofollow">notes</a> by Dr. Larry Ammann at UT Dallas.
</p>
<hr />

</div>

<h2>Convert gene or protein IDs?</h2>
<div class="level2">

<p>
<a href="https://biodbnet-abcc.ncifcrf.gov/db/db2db.php" class="urlextern" title="https://biodbnet-abcc.ncifcrf.gov/db/db2db.php" rel="ugc nofollow">bioDBnet</a>, BioMart - Ensembl, or <a href="https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html" class="urlextern" title="https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html" rel="ugc nofollow">AnnotationDbi</a> package in R to convert between Entrez Gene, RefSeq, Ensemble, and many more.
</p>
<hr />

</div>

<h2>Prepare attractive, scientific presentations ?</h2>
<div class="level2">

<p>
Use a "home slide". Also, learn about other tips from Susan <a href="https://www.youtube.com/watch?v=Hp7Id3Yb9XQ" class="urlextern" title="https://www.youtube.com/watch?v=Hp7Id3Yb9XQ" rel="ugc nofollow">McConnell</a>.
</p>
<hr />

</div>

<h3>Access a Bioconductor package source code?</h3>
<div class="level3">

<p>
It is always better to a install the latest version of a package as directed in the corresponding Bioconductor page (e.g., <a href="https://bioconductor.org/packages/Pigengene" class="urlextern" title="https://bioconductor.org/packages/Pigengene" rel="ugc nofollow">Pigengene</a>). If you need to see more details in the source code, or you need the development version. If the package maintainer adds your public ssh <a href="https://git.bioconductor.org/BiocCredentials/" class="urlextern" title="https://git.bioconductor.org/BiocCredentials/" rel="ugc nofollow">key</a>, then you can clone the source from the Bioconductor using the "Source Repository (Developer Access) " command, which is posted on the corresponding package <a href="https://bioconductor.org/packages/release/bioc/html/Pigengene.html" class="urlextern" title="https://bioconductor.org/packages/release/bioc/html/Pigengene.html" rel="ugc nofollow">page</a>, e.g.,
</p>
<pre class="code">mkdir ~/proj; cd ~/proj
git clone git@git.bioconductor.org:packages/Pigengene

</pre><p> </p>

<p>
Now, you can build the package fom the source using:
</p>
<pre class="code">R CMD REMOVE Pigengene; R CMD build Pigengene

</pre><p> </p>

<p>
If the build is successful, a tarbal will be created. You can install the new package using:
</p>
<pre class="code"> R CMD INSTALL Pigengene_&lt;Version&gt;.tar.gz

</pre><p> </p>
<hr />

</div>

<h3>Use git via proxy or vpn?</h3>
<div class="level3">

<p>
Use <a href="https://github.com/apenwarr/sshuttle" class="urlextern" title="https://github.com/apenwarr/sshuttle" rel="ugc nofollow">sshuttle</a>, e.g., sshuttle -r h_<a href="mailto:mailto:z14@nyx.cs.txstate.edu" class="mail" title="mailto:z14@nyx.cs.txstate.edu">mailto:z14@nyx.cs.txstate.edu</a> 0.0.0.0/0 -vv<br/>

The list of servers at Texas Sate University are listed <a href="https://cs.txstate.edu/resources/labs/accounts/linux/" class="urlextern" title="https://cs.txstate.edu/resources/labs/accounts/linux/" rel="ugc nofollow">here</a>.
</p>
<hr />

</div>

<h3>Enable autocomplete and the tab bar in Emacs?</h3>
<div class="level3">

<a href="https://www.emacswiki.org/emacs/InstallingPackages#toc2" class="urlextern" title="https://www.emacswiki.org/emacs/InstallingPackages#toc2" rel="ugc nofollow">Install</a> the auto-complete and tabbar packages from <a href="https://www.emacswiki.org/emacs/MELPA" class="urlextern" title="https://www.emacswiki.org/emacs/MELPA" rel="ugc nofollow">MELPA</a>. In OS X, you may need to edit your init file (usually it is .emacs but you can use C-H v user-init-file RET to <a href="https://stackoverflow.com/questions/189490/where-can-i-find-my-emacs-file-for-emacs-running-on-windows" class="urlextern" title="https://stackoverflow.com/questions/189490/where-can-i-find-my-emacs-file-for-emacs-running-on-windows" rel="ugc nofollow">check</a>) file to remove auto-complete from the package-selected-packages list and instead add the following lines:
</p>
<pre class="code">
(require 'auto-complete)
(global-auto-complete-mode t)

</pre><p> </p>

<p>
Also, read the packages instructions to learn how to <a href="https://www.emacswiki.org/emacs/InstallingPackages#toc4" class="urlextern" title="https://www.emacswiki.org/emacs/InstallingPackages#toc4" rel="ugc nofollow">configure</a> and use them.<br/>

Update 2024-08-14: tabbar can take 50%-90% CPU usage! Use <code>tab-bar-mode</code> in Emacs >=27.
</p>
<hr />

<p>
<b>Cite references?</b> <br/>

Find the <a href="http://www.nature.com/nmeth/journal/v14/n3/full/nmeth.4219.html?WT.ec_id=NMETH-201703&spMailingID=53531675&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1120169529&spReportId=MTEyMDE2OTUyOQS2" class="urlextern" title="http://www.nature.com/nmeth/journal/v14/n3/full/nmeth.4219.html?WT.ec_id=NMETH-201703&spMailingID=53531675&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1120169529&spReportId=MTEyMDE2OTUyOQS2" rel="ugc nofollow">original</a> paper that is most relevant. Setup recommendation engines not to miss recently published work.
</p>
<hr />

<p>
<b>Resubmit an NIH grant?</b> <br/>

<a href="http://ctsi.ucla.edu/education/files/view/training/docs/study-sections-adams.pdf" class="urlextern" title="http://ctsi.ucla.edu/education/files/view/training/docs/study-sections-adams.pdf" rel="ugc nofollow">Address</a> ALL reviewers' comments. Write a strong <a href="http://www.regis.edu/~/media/Files/University/OAG/Learning-Resources/Create_Winning_Resubmission_Application_NIH_Report.ashx" class="urlextern" title="http://www.regis.edu/~/media/Files/University/OAG/Learning-Resources/Create_Winning_Resubmission_Application_NIH_Report.ashx" rel="ugc nofollow">introduction</a> [<a href="/lib/exe/fetch.php?media=resubmittinggrantfelson10january2012.ppt" class="media mediafile mf_ppt" title="resubmittinggrantfelson10january2012.ppt (1.8 MB)">ppt</a>  ]. Watch NIH <a href="https://public.csr.nih.gov/ForApplicants/InitialReviewResultsAndAppeals/csrwebinar" class="urlextern" title="https://public.csr.nih.gov/ForApplicants/InitialReviewResultsAndAppeals/csrwebinar" rel="ugc nofollow">Webinars</a> for Applicants.
</p>
<hr />

<p>
<b>Silence a gene?</b> <br/>

Small interfering (si) RNAs and miRNAs <a href="https://www.youtube.com/watch?v=cK-OGB1_ELE" class="urlextern" title="https://www.youtube.com/watch?v=cK-OGB1_ELE" rel="ugc nofollow">bind </a>to mRAN and prevent it from being translated.
</p>
<hr />

<p>
<b>Compare the data resources on a gene across databases?</b> <br/>

<a href="https://xenabrowser.net/" class="urlextern" title="https://xenabrowser.net/" rel="ugc nofollow">Xena</a> provides heatmaps for one gene using databases selected from a list of tens of databases from TCGA,1000 genomes, etc. Cancer Genome <a href="http://docs.cancergenomicscloud.org/" class="urlextern" title="http://docs.cancergenomicscloud.org/" rel="ugc nofollow">Cloud</a> allows the user to integrate their own tools with theplatform and run it on, say, TCGA in the cloud. <a href="http://seek.princeton.edu/" class="urlextern" title="http://seek.princeton.edu/" rel="ugc nofollow">Seeks</a> orders thousands of datasets based on how concordant the expression of the input genes are.
</p>
<hr />

<p>
<b>Save Powerpoint in high resolution on OS X?</b> <br/>

<a href="https://answers.microsoft.com/en-us/msoffice/forum/msoffice_powerpoint-mso_mac/how-do-i-save-powerpoint-slide-as-a-high/1baa460e-8ecb-4f44-a48f-425504d8d25a" class="urlextern" title="https://answers.microsoft.com/en-us/msoffice/forum/msoffice_powerpoint-mso_mac/how-do-i-save-powerpoint-slide-as-a-high/1baa460e-8ecb-4f44-a48f-425504d8d25a" rel="ugc nofollow">Select</a> all, open Preview > File > New from Clipboard. DPI is <a href="https://99designs.com/blog/tips/ppi-vs-dpi-whats-the-difference/" class="urlextern" title="https://99designs.com/blog/tips/ppi-vs-dpi-whats-the-difference/" rel="ugc nofollow">different</a> from PPI.
</p>
<hr />

<p>
<b>Download TCGA normal data?</b> <br/>

Use "Add cases <a href="https://www.biostars.org/p/204897/" class="urlextern" title="https://www.biostars.org/p/204897/" rel="ugc nofollow">filter</a>" link to add sample_type as a filter.
</p>
<hr />

<p>
<b>Know about the immune system?</b> <br/>

It is a <a href="https://www.youtube.com/watch?v=CTQwB63-cgI" class="urlextern" title="https://www.youtube.com/watch?v=CTQwB63-cgI" rel="ugc nofollow">prerequisite</a> (2012) to understand <a href="https://www.youtube.com/watch?v=3hlGq-3F1uQ" class="urlextern" title="https://www.youtube.com/watch?v=3hlGq-3F1uQ" rel="ugc nofollow">immunotherapy</a> (2015). <a href="https://www.youtube.com/watch?v=r9fVKcNOkUE" class="urlextern" title="https://www.youtube.com/watch?v=r9fVKcNOkUE" rel="ugc nofollow">CAR-T Cells</a> (2014) are engineered outside the body to express receptors specific to a patient's particular cancer. Immune <a href="https://www.youtube.com/watch?v=tv_ztPgAUp0" class="urlextern" title="https://www.youtube.com/watch?v=tv_ztPgAUp0" rel="ugc nofollow">checkpoint</a> (2017) inhibitors can release the break of the immune system.
</p>
<hr />

<p>
<b>Use computational biology in immunotherapy?</b> <br/>

A) Mine the gene expression or mutation databases to discover tumor <a href="http://www.tandfonline.com/doi/full/10.1586/17512433.2013.811814" class="urlextern" title="http://www.tandfonline.com/doi/full/10.1586/17512433.2013.811814" rel="ugc nofollow">antigens</a> (targets of immune system). B) Combine these data with mass spectrometric data from tumor <a href="https://www.nature.com/nm/journal/v18/n8/full/nm.2883.html#affil-auth" class="urlextern" title="https://www.nature.com/nm/journal/v18/n8/full/nm.2883.html#affil-auth" rel="ugc nofollow">specimens</a>, or sera, to identify <a href="https://en.wikipedia.org/wiki/Immunogenicity" class="urlextern" title="https://en.wikipedia.org/wiki/Immunogenicity" rel="ugc nofollow">immunogenic</a> (actionable) antigens. C) Analyze gene expression profiles to predict which patients will benefit (also, have benefitted) from a specific treatment (e.g., infer <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1028-7" class="urlextern" title="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1028-7" rel="ugc nofollow">infiltration</a> of immune cells in tumors). D) "Evaluation of humoral response against a diverse set of self-antigens can be explored rapidly using the high-content protein or peptide microarrays" (Thakurta et al.). E) Assess the diversity of the vast 10^14 possibilities for T-cell receptors using proteomics or sequencing. Many tools have been developed to address these needs (<a href="https://www.biorxiv.org/content/biorxiv/early/2017/06/22/152264.full.pdf" class="urlextern" title="https://www.biorxiv.org/content/biorxiv/early/2017/06/22/152264.full.pdf" rel="ugc nofollow">2017</a> review).
</p>
<hr />

<p>
<b>Discover immunogenic antigens (<a href="http://www.nature.com.libproxy.uthscsa.edu/nrg/journal/v17/n8/full/nrg.2016.67.html?foxtrotcallback=true" class="urlextern" title="http://www.nature.com.libproxy.uthscsa.edu/nrg/journal/v17/n8/full/nrg.2016.67.html?foxtrotcallback=true" rel="ugc nofollow">neoantigens</a>) suitable for immunotherapy?</b> <br/>

Identify the somatic mutations in expressed genes, <a href="https://link.springer.com/article/10.1007%2Fs00262-012-1354-x" class="urlextern" title="https://link.springer.com/article/10.1007%2Fs00262-012-1354-x" rel="ugc nofollow">predict</a> epitope <em>in silico</em> using publicly available databases, and <a href="http://cancerres.aacrjournals.org/content/72/5/1081" class="urlextern" title="http://cancerres.aacrjournals.org/content/72/5/1081" rel="ugc nofollow">immunize</a> mice with long peptides encoding the mutated epitopes to determine immunogenicity.
</p>
<hr />

<p>
<b>Avoid misinterpretation of biological experiments?</b> <br/>

<a href="https://www.nature.com/nrc/journal/v17/n7/full/nrc.2017.32.html" class="urlextern" title="https://www.nature.com/nrc/journal/v17/n7/full/nrc.2017.32.html" rel="ugc nofollow">Reasoning</a> must be logical. Report enough details of the methods to reproduce the results. Assess the robustness of the findings with respect to minor perturbations to the experimental settings. To prove that drug A targets protein X, it is not sufficient to confirm that treatment with A leads to killing cells that have X. Maybe the cells are killed because of some other mechanism. Use "rescue experiments" as in the A=imatinib X=BCR–ABL case. Always, avoid <a href="https://elifesciences.org/articles/48175" class="urlextern" title="https://elifesciences.org/articles/48175" rel="ugc nofollow">these</a> ten common statistical mistakes.
</p>
<hr />

<p>
<b>Analyze single cell RNA-seq data</b><b>?</b> <br/>

<a href="https://hemberg-lab.github.io/scRNA.seq.course/introduction-to-single-cell-rna-seq.html" class="urlextern" title="https://hemberg-lab.github.io/scRNA.seq.course/introduction-to-single-cell-rna-seq.html" rel="ugc nofollow">Map</a> the reads <a href="https://www.nature.com/news/single-cell-sequencing-made-simple-1.22233" class="urlextern" title="https://www.nature.com/news/single-cell-sequencing-made-simple-1.22233" rel="ugc nofollow">similar</a> to bulk RNA-seq data, exclude <a href="https://hemberg-lab.github.io/scRNA.seq.course/construction-of-expression-matrix.html#identifying-confounding-factors" class="urlextern" title="https://hemberg-lab.github.io/scRNA.seq.course/construction-of-expression-matrix.html#identifying-confounding-factors" rel="ugc nofollow">outlier</a> cells and genes, <a href="https://hemberg-lab.github.io/scRNA.seq.course/biological-analysis.html#clustering-introduction" class="urlextern" title="https://hemberg-lab.github.io/scRNA.seq.course/biological-analysis.html#clustering-introduction" rel="ugc nofollow">cluster</a> the cells, and <a href="https://hemberg-lab.github.io/scRNA.seq.course/biological-analysis.html#projecting-scrna-seq-data" class="urlextern" title="https://hemberg-lab.github.io/scRNA.seq.course/biological-analysis.html#projecting-scrna-seq-data" rel="ugc nofollow">project</a> the cells onto an annotated reference such as Human Cell Atlas. The broken links can be found in the <a href="https://www.singlecellcourse.org/index.html" class="urlextern" title="https://www.singlecellcourse.org/index.html" rel="ugc nofollow">Sanger's</a> course.
</p>
<hr />

<p>
<b>Make interactive 3D plots in R?</b> <br/>

Use plot3D::<a href="http://www.sthda.com/english/wiki/impressive-package-for-3d-and-4d-graph-r-software-and-data-visualization#basic-scatter-plot" class="urlextern" title="http://www.sthda.com/english/wiki/impressive-package-for-3d-and-4d-graph-r-software-and-data-visualization#basic-scatter-plot" rel="ugc nofollow">scatter3D</a> to create the graph:
</p>
<pre class="code">
scatter3D(x=iris$Sepal.Length, y=iris$Petal.Length, z=iris$Sepal.Width, clab = c("Sepal", "Width (cm)"))
plotrgl()

</pre><p> </p>

<p>
and then use plot3Drgl::<a href="http://www.sthda.com/english/wiki/impressive-package-for-3d-and-4d-graph-r-software-and-data-visualization#interactive-plot" class="urlextern" title="http://www.sthda.com/english/wiki/impressive-package-for-3d-and-4d-graph-r-software-and-data-visualization#interactive-plot" rel="ugc nofollow">plotrgl</a> to interactively zoom and rotate it.
</p>
<hr />

<p>
<b>Improve the ranking of your institution better than MIT?!</b> <br/>

<a href="https://liorpachter.wordpress.com/2014/10/31/to-some-a-citation-is-worth-3-per-year/" class="urlextern" title="https://liorpachter.wordpress.com/2014/10/31/to-some-a-citation-is-worth-3-per-year/" rel="ugc nofollow">Hire</a> scholars who are frequently cited as adjunct professors.
</p>
<hr />

<p>
<b>Rescue US biomedical research from its systemic flaws?</b> <br/>

<a href="http://www.pnas.org/content/111/16/5773" class="urlextern" title="http://www.pnas.org/content/111/16/5773" rel="ugc nofollow">Hypercompetition</a> has damaging effects. Reduce the number of PhD students and postdocs. Revise funding mechanisms to encourage "path-breaking ideas that, by definition," are <a href="https://www.nature.com/articles/426389a" class="urlextern" title="https://www.nature.com/articles/426389a" rel="ugc nofollow">risky</a>. Support <a href="https://nexus.od.nih.gov/all/2018/05/04/the-issue-that-keeps-us-awake-at-night/" class="urlextern" title="https://nexus.od.nih.gov/all/2018/05/04/the-issue-that-keeps-us-awake-at-night/" rel="ugc nofollow">early</a>-stage investigators.
</p>
<hr />

</div>

<h3>Test an R function that you have extracted from a script?</h3>
<div class="level3">

<p>
Sometimes you have a working script but some part of it is useful also elsewhere. You extract that portion and make a function f(x,y) out of it. Now, in the script you call that function. You run your modified script and the output is exactly the same as before. Is this a sufficient test for the function you just wrote? No! What if you forget to include one of the variables as an input argument of the function? Then, that variable, which is still defined somewhere in the script before you call the function, is used in the function as a "global variable" without any explicit error. However, when the function is used in a different context, that global variable may not be defined, or worse, it may have an irrelevant value. To avoid this issue, use codetools::<a href="https://rdrr.io/cran/codetools/man/findGlobals.html" class="urlextern" title="https://rdrr.io/cran/codetools/man/findGlobals.html" rel="ugc nofollow">findGlobals</a>(…, merge=FALSE) to identify and remove all global variables from your function. A cumbersome and less accurate way to identify global variables follows:
</p>
<ol>
<li class="level1"> Put a browser in the script right before calling the function.</li>
<li class="level1"> Save the function and its inputs in a temporary file, e.g., save(x,y, f, file="~/temp/f1.RData")</li>
<li class="level1"> Remove all objects in this R session using rm(list=ls()).</li>
<li class="level1"> load("~/temp/f1.RData").</li>
<li class="level1"> Type "c" and "Enter" to run the rest of the script. The output must be exactly the same.</li>
<li class="level1"> If the function uses a global variable, while running it this way, you will probably get an error like "object 'z' not found". Then, either compute z in f, add it as an input argument of f, or modify the line that uses z.</li>
<li class="level1"> Repeat until you get no errors, and then, check that the output is exactly the same as before.</li>
</ol>
<hr />

</div>

<h3>Separate the reads corresponding to each individual cell from a single-cell RNA-Seq fastq file?</h3>
<div class="level3">

<p>
 <br/>
<a href="http://www.arrayserver.com/wiki/index.php?title=Preprocess_of_SingleCell_RNA-Seq_Data" class="urlextern" title="http://www.arrayserver.com/wiki/index.php?title=Preprocess_of_SingleCell_RNA-Seq_Data" rel="ugc nofollow">Use</a> the barcodes and Unique Molecular Identifiers (UMIs).
</p>
<hr />

</div>

<h3>Copy from your prior clipboard history?</h3>
<div class="level3">

<p>
Use a clipboard manager like <a href="https://clipy-app.com/" class="urlextern" title="https://clipy-app.com/" rel="ugc nofollow">Clipy</a> (developed based on ClipMenu) or JumpCut. Clipy allows you to save lists of favorite or frequent text snippets for later use.
</p>
<hr />

</div>

<h3>Review a paper?</h3>
<div class="level3">

<p>
Read the journal guidelines, and the Nature's quick and concise <a href="https://www.springer.com/gp/authors-editors/authorandreviewertutorials/howtopeerreview?utm_source=hybris&utm_medium=email&utm_content=internal&utm_campaign=AEXS_1_PF_ReviewerThankYou_tutorial&sap-outbound-id=37A4EBB275E142189BFB59083911E79615029EBE" class="urlextern" title="https://www.springer.com/gp/authors-editors/authorandreviewertutorials/howtopeerreview?utm_source=hybris&utm_medium=email&utm_content=internal&utm_campaign=AEXS_1_PF_ReviewerThankYou_tutorial&sap-outbound-id=37A4EBB275E142189BFB59083911E79615029EBE" rel="ugc nofollow">tutorial</a>. The PLOS Open Reviewer <a href="https://genweb.plos.org/RR/PLOSOpenReviewerGatewayInfosheet.pdf" class="urlextern" title="https://genweb.plos.org/RR/PLOSOpenReviewerGatewayInfosheet.pdf" rel="ugc nofollow">Gateway</a> can be helpful if you are interested in becoming a reviewer for PLOS journals. Read <a href="https://www.biomedcentral.com/getpublished/peer-review-process?sap-outbound-id=96A0B5635C39747973E5643D05210092E64D31E6&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030108_CONR_JRNLS_REP1_GL_PHSS_034NC_NATMAINRC2&utm_content=EN_56237_20240820&mkt-key=42010A0550671EEA9BA13B2C4609D4AD" class="urlextern" title="https://www.biomedcentral.com/getpublished/peer-review-process?sap-outbound-id=96A0B5635C39747973E5643D05210092E64D31E6&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030108_CONR_JRNLS_REP1_GL_PHSS_034NC_NATMAINRC2&utm_content=EN_56237_20240820&mkt-key=42010A0550671EEA9BA13B2C4609D4AD" rel="ugc nofollow">BMC</a> or <a href="https://www.springernature.com/gp/authors/campaigns/how-to-peer-review?sap-outbound-id=96A0B5635C39747973E5643D05210092E64D31E6&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030108_CONR_JRNLS_REP1_GL_PHSS_034NC_NATMAINRC2&utm_content=EN_56237_20240820&mkt-key=42010A0550671EEA9BA13B2C4609D4AD" class="urlextern" title="https://www.springernature.com/gp/authors/campaigns/how-to-peer-review?sap-outbound-id=96A0B5635C39747973E5643D05210092E64D31E6&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030108_CONR_JRNLS_REP1_GL_PHSS_034NC_NATMAINRC2&utm_content=EN_56237_20240820&mkt-key=42010A0550671EEA9BA13B2C4609D4AD" rel="ugc nofollow">Nature</a> introduction, and take the Nature's Focus on Peer Review <a href="https://masterclasses.nature.com/focus-on-peer-review-online-course/16605550?sap-outbound-id=96A0B5635C39747973E5643D05210092E64D31E6&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030108_CONR_JRNLS_REP1_GL_PHSS_034NC_NATMAINRC2&utm_content=EN_56237_20240820&mkt-key=42010A0550671EEA9BA13B2C4609D4AD" class="urlextern" title="https://masterclasses.nature.com/focus-on-peer-review-online-course/16605550?sap-outbound-id=96A0B5635C39747973E5643D05210092E64D31E6&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030108_CONR_JRNLS_REP1_GL_PHSS_034NC_NATMAINRC2&utm_content=EN_56237_20240820&mkt-key=42010A0550671EEA9BA13B2C4609D4AD" rel="ugc nofollow">course</a>.<br/>

Get credit for your reviews via Web of Science Reviewer <a href="https://authorservices.wiley.com/Reviewers/journal-reviewers/recognition-for-reviewers/publons.html" class="urlextern" title="https://authorservices.wiley.com/Reviewers/journal-reviewers/recognition-for-reviewers/publons.html" rel="ugc nofollow">Recognition</a> Service (publons).
</p>
<hr />

</div>

<h3>Adjust the acceleration and speed of a Logitec mouse?</h3>
<div class="level3">

<p>
 <br/>
Install and <a href="https://apple.stackexchange.com/questions/253111/how-to-disable-scroll-acceleration-in-macos-sierra" class="urlextern" title="https://apple.stackexchange.com/questions/253111/how-to-disable-scroll-acceleration-in-macos-sierra" rel="ugc nofollow">use</a> the Logitech Control Center.
</p>
<hr />

</div>

<h3>Encrypt a folder?</h3>
<div class="level3">

<p>
Encrypt a <code>largeFolder</code> folder using <a href="https://www.cyberciti.biz/tips/linux-how-to-encrypt-and-decrypt-files-with-a-password.html" class="urlextern" title="https://www.cyberciti.biz/tips/linux-how-to-encrypt-and-decrypt-files-with-a-password.html" rel="ugc nofollow">tar</a> and compress it using <code>gpg</code> based on the AES-256 encrypting algorithm. You will obtain the <a href="https://crypto.stackexchange.com/a/71078" class="urlextern" title="https://crypto.stackexchange.com/a/71078" rel="ugc nofollow">strongest</a> security with these options:
</p>
<pre class="code">
tar -cvz largeFolder | gpg --s2k-mode 3 --s2k-count 65011712 --s2k-digest-algo SHA512 --s2k-cipher-algo AES256 --symmetric --no-symkey-cache -o largeFolder.tgz.gpg

</pre><p> </p>

<p>
The <code>–no-symkey-cache</code> option is available in <a href="https://unix.stackexchange.com/a/557051" class="urlextern" title="https://unix.stackexchange.com/a/557051" rel="ugc nofollow">version</a> >=2.2.7. On macOS, you need to first install <a href="https://sourceforge.net/p/gpgosx/docu/Download/" class="urlextern" title="https://sourceforge.net/p/gpgosx/docu/Download/" rel="ugc nofollow">GnuPG</a>. An alternative approach is to use <a href="http://www.dzhang.com/blog/2018/03/11/using-7-zip-create-aes-256-encrypted-zip-files-command-line" class="urlextern" title="http://www.dzhang.com/blog/2018/03/11/using-7-zip-create-aes-256-encrypted-zip-files-command-line" rel="ugc nofollow">7z</a>, which can be installed using <a href="http://molecularsciences.org/content/installing-and-running-7-zip-from-mac-terminal/" class="urlextern" title="http://molecularsciences.org/content/installing-and-running-7-zip-from-mac-terminal/" rel="ugc nofollow">homebrew</a>, however, 7z is windows based and thus not recommended.<br/>

<br/>

To decrypt and uncomperess,
</p>
<pre class="code">
gpg --decrypt --no-symkey-cache largeFolder.tgz.gpg | tar -xv

</pre><p> </p>

<p>
<code>tar</code> may need <code>-z –no-same-owner</code>.
</p>

<p>
A good password should have at least 12 characters, include both small and capital letters, and at least one digit and one special character such as !@#$%^&*(). Do not use dictionary words in your password, instead, use a <a href="https://cybernews.com/best-password-managers/how-to-create-a-strong-password/" class="urlextern" title="https://cybernews.com/best-password-managers/how-to-create-a-strong-password/" rel="ugc nofollow">passphrase</a> "to create strong passwords".
</p>
<hr />

</div>

<h3>Upload a file to Oncinfo and link to it?</h3>
<div class="level3">

<p>
<a href="/lib/exe/fetch.php?media=screen_shot_2019-02-12_at_12.38.39_pm.png" class="media mediafile mf_png" title="screen_shot_2019-02-12_at_12.38.39_pm.png (1.2 MB)">Set</a>  the link type to "internal media", click on "Browse Server", and then on "Choose File" and "Update".
</p>
<hr />

</div>

<h3>Aks people's opinion?</h3>
<div class="level3">

<p>
Create a <a href="https://doodle.com/" class="urlextern" title="https://doodle.com/" rel="ugc nofollow">Doodle</a> to find a common time for scheduling events. For longer surveys, use <a href="https://www.surveymonkey.com/" class="urlextern" title="https://www.surveymonkey.com/" rel="ugc nofollow">SurveyMonkey</a> for offline, and <a href="https://www.pollev.com/" class="urlextern" title="https://www.pollev.com/" rel="ugc nofollow">Poll</a> Everywhere for online interaction with audience.
</p>
<hr />

</div>

<h3>Disable scroll acceleration in macOS?</h3>
<div class="level3">

<p>
Install and <a href="https://www.reddit.com/r/osx/comments/6kx6zb/how_to_disable_mouse_scrolling_acceleration/" class="urlextern" title="https://www.reddit.com/r/osx/comments/6kx6zb/how_to_disable_mouse_scrolling_acceleration/" rel="ugc nofollow">use</a> USB <a href="http://www.usboverdrive.com/USBOverdrive/Information.html" class="urlextern" title="http://www.usboverdrive.com/USBOverdrive/Information.html" rel="ugc nofollow">Overdrive</a> to set Wheel up and down "Speed" of your mouse to say, 6 lines. The following <a href="https://apple.stackexchange.com/questions/253111/how-to-disable-scroll-acceleration-in-macos-sierra" class="urlextern" title="https://apple.stackexchange.com/questions/253111/how-to-disable-scroll-acceleration-in-macos-sierra" rel="ugc nofollow">command</a> does NOT work:
</p>
<pre class="code">defaults write .GlobalPreferences com.apple.scrollwheel.scaling -1

</pre><p> </p>

<p>
Logitech Control Center may help on the <a href="https://support.logi.com/hc/en-gb/articles/360025297833-Logitech-Control-Center-for-Macintosh-OS-X" class="urlextern" title="https://support.logi.com/hc/en-gb/articles/360025297833-Logitech-Control-Center-for-Macintosh-OS-X" rel="ugc nofollow">Logitech</a> MX mice older than 2019.
</p>
<hr />

</div>

<h2>Choose a solid state (SSD) external drive?</h2>
<div class="level2">

<p>
The non-volatile memory express (NVMe) devices are <a href="https://ssd.borecraft.com/SSD_Buying_Guide_List.pdf" class="urlextern" title="https://ssd.borecraft.com/SSD_Buying_Guide_List.pdf" rel="ugc nofollow">better</a> than SATA solid state drives. Good brands include <a href="https://smile.amazon.com/gp/product/B07X6CKHH1/ref=ox_sc_act_title_1?smid=A29Y8OP2GPR7PE&psc=1" class="urlextern" title="https://smile.amazon.com/gp/product/B07X6CKHH1/ref=ox_sc_act_title_1?smid=A29Y8OP2GPR7PE&psc=1" rel="ugc nofollow">Sabrent</a> (Nano is smaller than Pro but gets hot when extensivly used), Seagete, Addlink, and Team. As of 2020, a speed of 1000 Mb/s is possible using USB 3.2.
</p>
<hr />

</div>

<h2>Search for public domain images?</h2>
<div class="level2">

<p>
<a href="https://unsplash.com/" class="urlextern" title="https://unsplash.com/" rel="ugc nofollow">Unsplash</a> is among the best <a href="https://wcmshelp.ucsc.edu/about-images/finding-public-domain-images.html" class="urlextern" title="https://wcmshelp.ucsc.edu/about-images/finding-public-domain-images.html" rel="ugc nofollow">resources</a> with many hi-resolution images, which are frequently used by media.
</p>
<hr />

</div>

<h2>Identify Senescence in Cells and Tissues?</h2>
<div class="level2">

<p>
Watch <a href="https://cellsignal.wistia.com/medias/p9khwp3hzx" class="urlextern" title="https://cellsignal.wistia.com/medias/p9khwp3hzx" rel="ugc nofollow">this</a> quick 6-minute introduction to the senescence concept, and learn about the common markers and kits.
</p>
<hr />

</div>

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