Hi all Speaking of project templates, I just ran into this little gem: https://raoofphysics.github.io/phd-starter-kit/
I found it to be a concise, yet quite complete list of the required tools to keep a project such as a PhD on track. I for one would have welcomed such advice back when I started my own research. Which I just realized this very moment was more than *twelve *years ago. Oh my. t. On Tue, Feb 3, 2015 at 7:24 PM, Scott Ritchie < [email protected]> wrote: > Hi all, > > I was recently introduced to the ProjectTemplate > <http://projecttemplate.net/> package in R by a colleague which also > creates a nice project directory structure (and automates some of the > repetitive tedious parts like library loading and reading in data). > > Regards, > > On 4 February 2015 at 09:19, Loyall, David <[email protected]> > wrote: > >> Aron, >> >> >> >> If you have an existing github account, you can just click “edit” on his >> script and it will automatically fork the repo, let you make changes, and >> then present you with the option of sending them back to Dan in the form of >> a Pull Request. >> >> >> >> This has already happened once! The script now will refuse to operate if >> no argument was provided. :) >> >> >> >> Cheers, >> >> >> >> Dave Loyall >> >> State of Nebraska >> >> Office of the CIO >> >> Web Development Team >> >> [email protected] >> >> (402) 471-0677 >> >> >> >> *From:* Discuss [mailto:[email protected]] *On >> Behalf Of *Aron Ahmadia >> *Sent:* Tuesday, February 03, 2015 4:03 PM >> *To:* Daniel Chen >> *Cc:* [email protected] >> *Subject:* Re: [Discuss] Script to organize computational biology >> projects >> >> >> >> Very cool Dan! My only suggestion would be to create a top-level README >> file describing the directory structure (and possibly referring back to >> your script's URL), or print that out to the screen for the user to create >> their own file or append to their own. >> >> The shell experts will probably want to add a little error-handling. At >> minimum, the script should probably turn clobbering off before writing to >> files. >> >> >> >> On Tue, Feb 3, 2015 at 4:59 PM, Daniel Chen <[email protected]> wrote: >> >> Ever since Ivan showed Noble's PlosONE article [1] at the Harvard >> workshop, I began to follow the template and teach it in workshops. >> >> >> >> I created a quick bash script [2] since I just started another project, >> and thought it'd share with everyone. The code isn't pretty, but it does >> the job. Improvements welcome! >> >> >> >> And hopefully it'll be a less barrier to entry for people to setup >> project folders after they attend a workshop. >> >> >> >> >> >> [1] >> http://journals.plos.org/ploscollections/article?id=10.1371/journal.pcbi.1000424 >> >> [2] https://github.com/chendaniely/computational-project-cookie-cutter >> >> >> >> >> >> - Dan >> >> >> _______________________________________________ >> Discuss mailing list >> [email protected] >> >> http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org >> >> >> >> _______________________________________________ >> Discuss mailing list >> [email protected] >> >> http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org >> > > > > -- > ---- > Scott Ritchie, BCompSci, MSc, > Ph.D. Student, > Medical Systems Biology Group, > Department of Pathology, > Faculty of Medicine, Dentistry, and Health Sciences, > The University of Melbourne > Parkville, Victoria, Australia > W: http://www.inouyelab.org > P: +61 3 9035 8916 > E: [email protected] > > Research Community Co-ordinator for the Life Sciences & > Software Carpentry Instructor for R and Data Science. > Department of Research Platforms, > The University of Melbourne. > W: http://resbaz.tumblr.com/ > W: http://software-carpentry.org/ > > President, > Bioinformatics Graduate Student Association (BGSA), > The University of Melbourne. > W: http://bioinformatics.asn.au/bgsa/ > F: https://www.facebook.com/groups/BGSA.melbourne/ > E: [email protected] > > General Committee, > COMBINE: The Regional Student Group (RSG) Australia; > for the International Society for Computational Biology (ISCB) > W: http://combine.org.au/ > http://www.iscb.org/ > ---- > > _______________________________________________ > Discuss mailing list > [email protected] > > http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org >
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