Question: recommendation on lab notebook for bioinformatics/data analysis work
5
gravatar for unkwown_0912
3.3 years ago by
unkwown_091250
unkwown_091250 wrote:

Does anyone have any good suggestion on how they document their bioinformatics/data analysis work? Any suggestion for lab notebook and their corresponding default privacy setting? If the default privacy setting is public, is it possible to change it to private?

Thanks!!

assembly blast next-gen R • 2.7k views
ADD COMMENTlink modified 3.3 years ago by 5heikki8.5k • written 3.3 years ago by unkwown_091250
3
gravatar for Shicheng Guo
3.3 years ago by
Shicheng Guo7.7k
Shicheng Guo7.7k wrote:

After I used evernote and Google+. I can tell you, the No 1 choice is openwetware :website. Of course, you can also build you own Wikimedia. Then local Wikimedia is also very good choice. You can also try to use github or gitlab. I also recommend biostar to open a section for "Protocol and Pipeline". Third, you can also try to use R markdown or Knitr to record everything and steps of your analysis and then share it in github. Finally, I also recommend rpubs to share all the examples for others. I also want to share Microsoft TFS (Team Foundation Server), my IT department recommend it to me and now I am trying to test it to replace Gitlab since TFS is integrated with Azure. sharepoint is also very interesting to be tested. for the data management IRods is a nice recommendation.

ADD COMMENTlink modified 13 months ago • written 3.3 years ago by Shicheng Guo7.7k
2

Our group runs its own Wiki server via MediaWiki, it's useful since then you can have fine grained user control with different groups, i.e., interns can do less damage, you can set everything to private so that only group members can see wiki pages etc. It's probably overkill for one person, in that case I'd use something like tiddlywiki, which is just one HTML file + browser extension.

ADD REPLYlink written 3.3 years ago by Philipp Bayer6.4k
2
gravatar for Alessandro Guida
3.3 years ago by
Italy
Alessandro Guida40 wrote:

I think it comes down pretty much to a personal preference. I tried in the past options like evernote, dokuwiki but what I found works best for me is git. My institute is hosting a gitlab server and it has soon become my number one choice. It forces you to slip projects into repositories which are backup online on the remote server; you can easily share your progress with colleagues in a structured way and work together on the same project. Also, it keeps your code versioned.

When I use gitlab as a lab notebook, I create a new project as well as a README.md file where I explain the structure of the repository, objective and other general info. A doc folder for extra documentation I am collecting during my research (like .pdf files, related papers, etc.. ), a script folder to store all the code. If you are working with R, I strongly recommend implementing your analysis using Rmarkdown. It takes a little bit of extra effort to write your documentation together with your code, but having both of them on the same page pays off on the long run (or one month later when you want to check exactly what you did on that project).

ADD COMMENTlink written 3.3 years ago by Alessandro Guida40

+1 for the git and the gitlab. I would definitely advice this but then again it depends if the institute is having the gitlab server or not. Else one can always put the code in github and make pdf or docs and store them in stipulated folders project-wise. For R , the Rmarkdown is strongly recommended. I usually use gitlab for project specific information and share it with colleagues and for personal codes I put stuffs in github and share it with community.

ADD REPLYlink written 3.3 years ago by ivivek_ngs4.8k

Would you please provide any link for Rmarkdown tutorial where the usage is neatly explained. I have seen some but unable to grasp it properly.

ADD REPLYlink written 3.3 years ago by venu6.2k

Take a look at these links below and see if it is of help to you:

1 . Rmarkdown

2 . Knitr

3 . SciRNotebook. Already an electronic Scientfic notebook format based on RMarkdown

ADD REPLYlink written 3.3 years ago by ivivek_ngs4.8k

There is a good class on coursera that covers pretty much what mentioned in the post. https://www.coursera.org/learn/reproducible-research

ADD REPLYlink written 3.3 years ago by Alessandro Guida40
0
gravatar for 5heikki
3.3 years ago by
5heikki8.5k
Finland
5heikki8.5k wrote:

Be free, Org-mode in Emacs

ADD COMMENTlink written 3.3 years ago by 5heikki8.5k
1

I think google should build such kind of software and build google into it.

ADD REPLYlink written 13 months ago by Shicheng Guo7.7k
1

You can launch google searches from Emacs

ADD REPLYlink written 13 months ago by 5heikki8.5k
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