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Hi everyone!

I started working in my current lab 5 years ago. I started with one box in the refrigerator and one in the freezer... Easy to keep track of things.

But today, I have several dozen in each!!! I've been trying to keep track of everything with an excel file, but it's not very efficient.

Also, a recent event in my lab also makes me want to get a good system working: my boss has been going crazy over some serum samples from Africa that nobody could find! It took over a year to find them in all the boxes people have accumulated over the years...

How do you keep track of your collection of cells, primers, plamsids, sera etc.? Do you use spreadsheets (Excel/OpenOffice), databases (Access, MySQL, FileMaker Pro), pen and paper or something else?

I know of different LIMS (Laboratory Information Management System) options, but they all seem to be overkill and mostly too expensive...

Please share your successes as well as your failures ;)

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@WS: I rolled back because my question is meant to be focused on freezer organization and not on ELNs... I see these as very different things. Whether one uses an ELN system or regular lab notebooks is not directly related to freezer and sample management in my mind. I'd like to keep the question that way ;) – Nicojo Jul 6 at 7:10
sorry. ally I wanted to say is that some ELNs, as they are technically databases, offer tools for managing storage – WS Jul 6 at 7:38

2 Answers

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Dear Nicojo,

probably, the best and easiest thing is to keep everything in your mind and have someone else's as backup :-).

That means, in practice (at least in my experience) record keeping does not work as well as it should unless there is a very insisting lab manager who is keeping an eye on everything and everyone and is able to keep track of it for a longer time.

In a lab where I once worked as postdoc, this was very well organized: The chief technician kept records where the master stocks of cells, plasmids and primers were. If you were to use something new, you would obtain an aliquot and propagate it by yourself for your needs, if necessary. Orders of new primers were only accepted when you presented a database sheet where you had entered all details (concept, sequence, application, PCR parameters etc.). When a student / scientist / technician changed the lab or left the institute, (s)he had to provide documentation on all new plasmids and cell lines (s)he made. Of course, all this paperwork was a bit tedious, but it was easy to retrieve all the necessary information when you started to work with something new and -surprise- the information was quite reliable.

Basically, as PI you need to set up appropriate rules, everybody simply has to follow. Don't give anyone a degree or a testimonial unless (s)he has completed all the paperwork. I know this sounds mean, but in my experience nothing else works in the beginning, until some lab culture is established, where the newbies obtain guidance by the experienced.

Of course this requires some set-up work in the beginning like creating some databases, setting up backup folders in print, organizing freezers, fridges and storage by assigning them coordinates etc. Some electronic lab notebooks (ELN) provide basic database capabilities for this and make lab life easier, but usually, they are quite expensive. Setting up an SOP might be a good start.

How you organize your storage (if you e.g. put all your primers in one set of boxes or store them together with the DNA samples of the respective projects or if you organize your fridge by the sample date) depends on your preferences. Probably some mixed mode is the most practical solution: Samples organized by projects, primers and master stocks organized in an individual storage and important things having at least one backup in a place that probably won't be destroyed in the same power or equipment failure/fire/earthquake/flooding/burglary.

HTH & good luck!

Wo

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Thanks for the detailed reply and for sharing your experience! I'll edit my question to give some reasons why I'm asking... I know labs that do the very tedious work of recording all this on paper. But surely with databases or even spreadsheets we should be able to get things working in a better way, don't you think? – Nicojo Jul 6 at 7:12
I strongly prefer electronic record keeping, as it is easy to edit and search the entries. In the lab I was referring to, we had files with printed versions of all primer, plasmid and cell datasheets. For easy reference when some else occupied the computer that held the database (it was not networked for security reasons) and to have a backup in case of database failure or unwanted deletion of records. – WS Jul 6 at 7:41
Definitely it has to be electronic these days... And backup systems are easier to set up now too. What I need to figure out is what is the best way of setting this up ;) I hope more people will share their experience! – Nicojo Jul 6 at 8:02
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I agree that you need an electronic database and you need to force everyone to enter complete data about their reagents. Having one long-term lab member, like a lab manager, in charge of stocks is a good idea. If you don't have someone like that, then you might have to do that yourself. Institutional memory is crucial for this kind of thing.

For the physical organization, I agree with Wolfgang that master stocks should be centralized and each person should take an aliquot to propagate or use as needed, replacing it if possible (e.g., freezing new cells). That way you only need to worry about the organization of the master stocks rather than everyone's personal boxes. Personally, I like to store things by type so that all primers are together, all DNA stocks are together, etc, but I can see the value of storing things by project as well. As long as it's consistent, it doesn't really matter.

I think it comes down to a question of motivation. People tend to want to expend the minimum possible effort, especially at the end of an experiment when they're putting things away. Keeping everything organized requires more up-front effort but can save a lot of time and effort down the road. So you just have to convince people that it's worth it, or force them to follow the rules even if they don't agree. :-)

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Thanks for your answer! Indeed, it's all about getting people to keep things organized. But, how do you keep track of things? Whichever way you organize things, you'll still need to keep records of them... So how do you do that? Spreadsheet (Excel type) or database (Access, MySQL, FileMaker Pro) or pen and paper or something else? – Nicojo Jul 9 at 6:21
the fastest and easiest way probably are electronic spreadsheets (OpenOfficeCalc, Excel, etc). Which give you the advantage that they later may easily become incorporated/converted into a database if you decide to set it up. Databases give you the advantage that it's easy to incorporate and search complex lengthy additional data (eg plasmid maps, papers, sequence data, chemical structures, fotos) which is quite impractical on large scale with a spreadsheet. I think, it does not matter much what you choose as tracking system. The important thing is that you keep it consistent all the time /Wo – WS Jul 9 at 7:29
@WS: thanks for the comment! We have been trying with Excel, but it gets quickly cumbersome. It's easy to introduce mistakes. If one person is using it (and forgets to close it) then others can't use it. As for databases, my experience is that database design is an art and commercial solutions like Access get outdated too often (each time MS wants to make more money)... That's why I'm asking around for people's experience. I'm sure there's a good practical solution out there, somewhere ;) – Nicojo Jul 9 at 8:32
Google Docs has a database feature that allows you to create forms that people fill out. The results are stored in a spreadsheet, and you can search and edit in either format. I've had good experiences with Google Docs in lab settings because everyone can have access, they're automatically backed up, and you don't have to worry about compatibility or upgrades. – Rappley Jul 9 at 17:23
@Rappley: Now that's what I'm after! Thanks, it's a great idea, I'll give it a try ;) – Nicojo Jul 10 at 12:41
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