Re: [MLUG] LIMS, ELNs and such

["Jonathan King" <EMAIL:PROTECTED>]

On 11/17/06, Mike Miller <EMAIL:PROTECTED> wrote:
> I spoke recently to a professor who recommends that we use a LIMS
> (Laboratory Information Management System) instead of developing our own
> LAMP-based system.  Apparently there are LIMS out there that would be
> nearly ready to manage the kind of data we will be collecting.  We want to
> use a web-based data entry system based on PHP, have MySQL manage the data
> and of course run this all on Linux with Apache and mod-ssl.  It all seems
> pretty straightforward to me.

I think both approaches are valid, and depend on both the scope of
what you're trying to do, and how much time you have to spend building
out your own system. There were LIMS vendors at Neurosciences for the
past few years, and there is a certain charm to having a system that
can Just Work and handle all of this stuff (and, in all likelihood,
make labels for all your samples and such as well).

Of course, if the lab in question had Mike Miller hanging around, the
relative cost of doing the other thing is much larger.

> I get the impression that LIMS are expensive.

They're not cheap, but you can probably get quotes (and some nice
lunches :-)) for cheap.

> I also get the impression
> that they aren't going to do more for me than the system we can develop.
> Of course, there is cost in development, but I've seen one of my guys
> develop a nice data-entry form in only a few hours, so I don't think the
> development costs are all that tremendous.  I also think that there are
> tremendous advantages in developing our own system.  For one, it will do
> just what we want it to do.  It will also be very flexible.

It *could* be flexible. I'm not saying you shouldn't do it, but I am
saying to look around pretty carefully because I don't think the
turnkey systems are complete boondoggles, either.

> The other thing my colleague mentioned was the ELN (Electronic Lab [or
> Laboratory] Notebook).  I don't see why we need this, but I do see some
> value in the concept.

OK, so if the concept is done well, it could be really valuable. Most
lab books haven't changed AT ALL from say the 1930s, and that's a bit
nuts. At this point, most of your gels are done at digital gel
stations, and a lot of your data can be directly digitally recorded as
well. And there's the possibility (you would think) to error check
protocols and present feedback to technicians about what the next step
is, and have the notebook keep the timers for you, and you'd have
timestamps for everything, and...I think a *good* system could be
pretty amazing. That said, I really don't know what's out there at the
moment.

> On the other hand, the ELN seems to be many
> different things to many different people and I saw a lot of confusing
> verbiage that led me to wonder if it is not possible to simply say what
> the ELN can do.  What, for example, is a "generic authoring tool?"  My
> guess is that I don't want one.

Not sure about the generic authoring tool. But there's no question
that there is tremendous merit in the general concept (heh), and I'm
sure there will be a lot of movement towards this in the next decade.
Again, I would recommend visiting other labs like the one you're going
to work with, and it wouldn't hurt to talk to vendors if you can enter
the room with your full [+3] Cloak of Skepticism on. I think you
should be essentially immune to corporate hype, so if something
actually sounded good, it would mean something.

jking

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