Linking files to database
August 9, 2016 12:45 PM   Subscribe

Help me organize my lab's data: make a database that is somewhat robust and very easy in its links to files.

My lab has an organization problem. In particular, we have a several types of data files, each with some associated data we can't directly attached. The example here is for sequencing data, but we have a couple other examples.

My lab has a few hundred plasmids (circular pieces of DNA), each well described by a sequence file (snapgene .dna file, though I don't think it matters). Each plasmid also has two physical locations - one that we use regularly and another in a backup box stored in another location.

We currently have an excel file listing the plasmids, organized by location. We have a bunch of useful information here (antibiotic resistance, etc).

We need some reasonable system to link the .dna files to the location list. We have tried using excel, keeping everything on one shared computer. However, the links keep getting broken when people move things (because much of the work is done on their own computers). Moreover, excel is really annoying (for this).

The opposite is relatively straightforward (we can put the locations in a note file in the .dna file). However, this restricts us to using this software, which I am not that thrilled with (the sequence information in the .dna file is very portable between software, but I don't trust the metadata to be). More importantly perhaps, we currently have files of both plasmids we've designed but not yet made, and those we've actually made.

I'm looking for recommendations of either software or workflows. I really think we primarily have a workflow problem.

For example, the best I've come up with is putting the list and all the sequence files of completed plasmids into a google drive folder, and then right clicking on each sequence file and copying the sharable link. Then we could insert that link into the spreadsheet of the list of physical locations. This seems like it would solve the problem, but is cumbersome. For example, we'd have to download the .dna file each time to open it (or keep the folder of files in a google drive folder on our computers). (One problem here is that no one wants to leave their personal google drive folder open on the shared lab computer, though a dummy account could solve that).

We also have access to microsoft onedrive. Though not having used it, I don't know how it compares to google drive.
posted by lab.beetle to Work & Money (5 answers total) 3 users marked this as a favorite
 
However, the links keep getting broken when people move things (because much of the work is done on their own computers).
Can the files be accessed in the existing folder and not moved around? You may need to explicitly share the folder and then have each person map a network drive to that folder. Instead of moving the files, they should be copying them to their machines and then copying them back to the original location if the file has been modified.
posted by soelo at 1:20 PM on August 9, 2016 [1 favorite]


Have you considered Open Science Framework?
posted by unknowncommand at 1:55 PM on August 9, 2016


However, the links keep getting broken when people move things (because much of the work is done on their own computers).

Can you use a lab dropbox for this purpose?
posted by Maecenas at 3:27 PM on August 9, 2016


Response by poster: I'll look into Opens Science Framework, but haven't yet really considered it. Thanks.
posted by lab.beetle at 11:12 PM on August 9, 2016


simple cms with tagging instead of relational location. get the files off of the file system and into a controlled data store.
posted by j_curiouser at 11:38 PM on August 9, 2016


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