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For Academics

Standardised project folder structure

Define and open a standardised project structure in the Finder, to remove mental load in switching between projects.

I keep these commands in a separate file that is kept in Dropbox so that it is synced between computers, and load them from my ~/.profile file with the following

. ~/Dropbox/Automation/bash/projects

Define project structure

The following makes a new project called project1

newproject project1

Customise the folders to what makes sense to you. For example

analysis/input - input files analysis/scripts - scripts that process the input analysis/temp - temporary files that can be deleted because they can be recreated paper/raw - files used to make figures, such as photoshop files paper/old - old versions of manuscripts are archived here reference/reports - reports prior to manuscript format reference/meetings - meeting notes related to project

These are setup with the following function.

function newproject {
mkdir $1
cd $1
mkdir analysis analysis/input analysis/scripts analysis/temp analysis/output
echo $1/analysis >
mkdir paper paper/raw paper/old
mkdir reference reference/reports reference/meetings

Quickly open project folders

The following allows to quickly open multiple folders related to a project in tabs of the same finder window. It allows to quickly get back to working on the project. Each project needs to be setup once.

The naming convention is for all projects to start with pr_ so that tab completion in the terminal can identify them. You must use the full path to all folders. The function calls an appleScript.

function pr_project1()
{ osascript -e 'set paths to {"/Users/username/git/project1", "/Users/username/git/project1/scripts", "/Users/username/git/project1/input", "/Users/username/git/project1/output", "/Users/username/git/project1/reference"}

tell application "Finder" to activate
tell application "System Events"
    keystroke "n" using command down
end tell
repeat with path in paths
    set applePath to POSIX file path    
    tell application "System Events"
        keystroke "t" using command down
    end tell
    delay 1
    tell application "Finder"
        set target of the front Finder window to applePath
    end tell
end repeat'
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Sex chromosome twitter bot

Silene twitter bot

I setup the sexChr_papers twitter bot following Rob Lanfear's instructions.

I am interested in papers on sex chromosome evolution, and thus remove medical search terms. The pubmed search is sex chromosome NOT aneuploidy NOT patient? NOT chronic NOT acute NOT clinical NOT prenatal NOT diagnostic NOT congenital NOT infant? NOT syndrome NOT trisom* NOT sperm.

Casey Bergman is gathering literature Twitter bots here.