I was wondering whether there existed some software to organise protocols locally?

The PI at our facility would like our protocols to all be stored in a logical way on a common drive, with links between them as appropriate and indications were to find required materials/equipment in the lab. Does some dedicated software not already exist for this?

(One could perhaps make a database but that's too involved; I don't want to have to learn anything new right now; I've already got my plate full.)

seanspotatobusiness on Jul 17 2009, 03:14 PM said:

We don't have anything quite that intricate (although it would be nice). We have a couple rolodex-type things that have all our our chemicals, reagents, etc listed, what room they're in, if they're at room temp, 4C, -20C, or -80C. We also have a recipe-card box for all of our "recipes". Anything from mixing our DNA ladders to making bacterial minimal medias. Each card has the components required, the amounts, how to mix, whether to autoclave or filter sterilize and stuff like that. As for protocols, as each person develops a new protocol in the lab, an SOP is written and put into a "protocol binder" (there's no real easy way to organize it, but we've got it grouped by "type" of project... cell culture, bacterial broth culture, challenge procedures, dilutions, blotting, PCR, etc).

All the protocols are also stored and updated on multiple computers. If anyone new comes into the lab, they are given their own copy of the protocols binder (or get one passed down from a former lab member).

The catch to this method is that it was started years ago. If we had to make this up right now, it would take a full time employee a long time to go through and catalog all the reagents, chemicals, kits, etc as well as write up all the SOPs for all the basics.

Here we simply write all protocols or hints in a word document.
Then we make a pdf file out if it.
Basically, whenever we have a new protocol, we write this out in word and then add it to the "old" pfd file. We replace the old by a new one then.
(we do place them in a so normal order as possible: things that have links with each other, we link them in the file... ) you can use "links" in a pfd file so that when you click on something that you go to the link in that file itself)
(in that file there is also stated where you find certain stuff, there is also a list of the stuff we have in the lab however we do NOT keep it updated in the matter of how much of a certain product we have...)



I know this is a very basic way of working, but in pdf you can use the search key and thus find what you need very fast in most cases.
Its important they you write it out very clear so that everyone can understand it.

But there is more specialised software avaible but you have to pay for it.
Or maybe it would even be easier for you to make a little website with everyhting linked to each other ? But offcourse you need to be able to make such websites.

We once had that too, it was very easy, but since the one who made and kept the website up to date left, we went from the website to the pdf file.

I have our protocols installed on a Mediawiki wiki (the same software Wikipedia uses) running from an Linux box under the Apache web server. There's password protection via an .htaccess file. If you're not into setting up all these things (Apache, PHP, MySQL, and Mediwiki) yourself -- though it's not very hard -- you can take a look at the BitNami MediaWiki Stack, available for just about any platform including Windows. The Bitnami Stack is a one-click installer that installs Mediawiki and all associated apps for you, then configures everything for you. Quite easy and useful.

HomeBrew on Jul 18 2009, 02:44 AM said:

hi HB,
that sounds really useful and i was thinking about establishing something similar in my lab. in my former lab this is what i had, a server with a static IP so i could manage it very well, however, in my new lab we are under a novell network and i don't think the IT people are very keen on giving static IPs (but i haven't asked for one yet).
I've got a dual boot computer here with enough space on the hard drive so that all the labmates create their backup files, and if we could store the protocols as well it would be great!! is there any way to do that under the scheme i mention? many thanks!
tj.

Hi toejam --

In addition to each of the personal computers at the desks of my lab mates, we have a separate Linux server which was assigned a static IP by our IT guys. I sold the IT folks on the idea of assigning this machine a static IP because I also have each of the individual computers backed up to it each night via the network.

There is no need for this computer to be internet-facing, so it's completely inside the firewalls established by my institution, and can use a private subnet IP (192.xx.xx.xx or 172.xx.xx.xx, for example). Thus the added security risk to establishing a static IP on this machine is minimal, and I've lessened it even more by proper configuration (running SELinux, disallowing root log-in from remote, using .htaccess files, etc.).

It is not difficult for the IP guys to set a static IP for a machine -- I'm sure they do it all the time for networked printers, for example.

Your first step should be to inquire if your IT guys is willing to assign your machine a static IP. That's the best way. If they say no, we can try some other alternatives...

thanks HB, since we don't have a specific computer assigned to each of the members of the lab i think at the end they'll have to back up everything directly into the hard drive of this computer, rather than setting up a server as i had thought, plus, it would be inconvenient to have one machine without internet connection. thanks anyway

in the old days you could make a hypercard stack (if you had a mac).

now, you can make a hypernext stack with a mac or pc.

hypernext studio

btw, this should have been posted in either the "bioinformatics" or, more appropriately, the "be a geek" forum.

toejam on Jul 20 2009, 10:07 AM said:

I did not mean to imply the server cannot connect to the internet (it can). What I meant was that no one from outside can connect to it...

Try OpenWetWare run out of MIT for free!