Hello folks, I’m looking at info/feedback on any particular software (commercial or freeware) used for organizing lab strains, primers, and other list based lab resources. Thanks!
Hi,
this is one of those questions where the phrase ‘it depends’ is immediately deployed…
to answer to your question, it depends (see) on a hold load of variables such as;
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Have you been given the job of organising ‘listy things’ in an established worm lab?
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Are you starting up a new lab or starting to work with worms?
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How big is the lab (number of people not square feet /metres)?
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How many strains /sets of primers are we talking about here?
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Who needs access?
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Who updates the information?
For example, if as in (1) you are in an established lab then presumably strains, primers and other reagents are already listed or located somehow?
In this case, it would be worthwhile asking other lab members how they use/update this information before investing time in a super-dupa new system. In any event, if the lab is not too large, you could list strains, primers and reagents in separate excel files that are shared on your network as well as having paper-based copies. the excel datafiles would be searchable and the fields indicating how much of these items you have could be locked so that only the person given the responsibility for ordering such items can change these data.
Then, it makes sense to have generic items such as strains entered in to an excel file by the person responsible for this in your lab (so everyone knows that they are frozen away, have been checked for viability and how many vials there are), chemicals (so that you know that the last bottle has been started) and reagents such as restriction enzymes listed (same logic). The latter two can be written first in a notebook, e.g. last bottle of NaCl started or 2000U EcoRI used 300U remaining so that someone allocated the task of ordering enzymes etc. can check each week and then enter the data in the excel file or oder new, or both…the possibilities are endless.
If the lab is large, e.g. more than a few post docs, PhD students and technicians, then perhaps a more flexible (and controllable)
approach would be to use Access rather than Excel.
If it is a new lab then you need to think about how this information would be used and updated and who’s going to do it. In the lab where I did my PhD we had a person/rota of people responsible for just about everything (including donuts), but then there were 30 people in the lab…now in my lab (we three other members), we kind of manage in a less regimented way.
In the end, what p***** people off is when they come to thaw out a strain and it’s not there or use a restriction enzyme that is nowhere to be found or worse, the tube is there with nothing in it. If you have the sole responsibility for orders strain maintenance etc then you need to develop a good ‘surveillance’ system for letting you know when things are running short, missing or not where they should be.
In terms of software, (hey how did we manage when we used to heat the lab with our computer monitors rather than using them to store lists), I would stick with generic spreadsheets, lockable documents or if you have the will, with Access. Forget the all-singing, all-dancing software that runs the lab resources like a multinational…think Schumacher (Ernst not Michael), Small is Beautiful…
Steve
We have developed a Labstory a free software but in beta version now. The link is below…
It works on Anroid, Mac, PC and Linux platforms . It comes with databases (LIMS system), documentation and also Excel or any kind of Table export import and also has a graphics sections for making
genetic crosses and for chemistry drawings.
exactly…a case in point in the last post…no mention of how donuts would be ordered…and how much work is it to write in a notebook or on a sheet of paper that more enzyme is needed…you need to be careful you don’t end up using sophisticated software just because you can (to misquote Jeff Goldblum in Jurrasic Park)…
I have recently been undertaking this project in my own lab, where years of post docs/grad students/techs having come and gone
has left our excel databases almost useless.
I started using quartzy I’ll admit its clunky to set up and I don’t love all the features, but I like the interactive boxes and that it backs up to excel.
With that said, I will not use it for worm stocks. We recently had a freezer malfunction and have the opportunity to move our worm database
from excel to access. I am currently at a loss of how to set up an access database for worms
Would anyone be willing to share how their worm database is set up?
We spent some time a couple of years ago organizing things using the free website Quartzy.com
You can even email them old excel lists and they will upload for you. It’s nice to have everything online.
You can download your databases automatically for safe keeping.