[gentoo-science] elektronic lab book

[gentoo-science] elektronic lab book

[Norman Warthmann]

Hi there,

please excuse me if this is the wrong place;
I am having my eyes open for an electronic way of keeping a lab book  
for my experiments for quite some time now, however to my surprise,  
it seems there is none open source. I am wondering how people in the  
science herd are organizing their day by day experiments.
I feel time is over to use a ordinary book for this especially since  
we are all drowning in files/pics/movies that we cannot stick in a  
book and have to reference.
  I am tempted to use some sort of wiki (mediawiki or dokuwiki) for  
this, however this is of course not ideal. what do you use?

thank you for your time


regards

Norman

----
Norman Warthmann
Max-Planck-Institute for Developmental Biology
Dept. Molecular Biology
http://www.smartgradstudent.de




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Re: [gentoo-science] elektronic lab book

[Olivier Fisette]

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On Saturday, 16 September 2006 10:38, Norman Warthmann wrote:
> I am having my eyes open for an electronic way of keeping a lab book
> for my experiments for quite some time now, however to my surprise,
> it seems there is none open source. I am wondering how people in the
> science herd are organizing their day by day experiments.

Hi Norman,

There are open source ELN and LIMS such as OpenSourceELN 
(www.opensourceeln.org) and HalX (Prilusky et al. 2005, 
halx.genomics.eu.org), but I personally prefer to use text files, 
directories, vim and a few shell scripts to keep track of my day-to-day work. 
I never felt the need for anything more complex. ;)

Cheers,

-- 
Olivier Fisette (ribosome)
Gentoo Linux Developer
Scientific applications, Developer relations

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Re: [gentoo-science] elektronic lab book

[Markus Dittrich]

On Sun, 17 Sep 2006, Olivier Fisette wrote:

> On Saturday, 16 September 2006 10:38, Norman Warthmann wrote:
>> I am having my eyes open for an electronic way of keeping a lab book
>> for my experiments for quite some time now, however to my surprise,
>> it seems there is none open source. I am wondering how people in the
>> science herd are organizing their day by day experiments.
>
> Hi Norman,
>
> There are open source ELN and LIMS such as OpenSourceELN
> (www.opensourceeln.org) and HalX (Prilusky et al. 2005,
> halx.genomics.eu.org), but I personally prefer to use text files,
> directories, vim and a few shell scripts to keep track of my day-to-day work.
> I never felt the need for anything more complex. ;)
>
> Cheers,
>

Same here! I mostly use README files combined with a suitable
directory structure in addition to a good old paper lab 
notebook. I also use cvs/subversion to keep track of changes
to scripts, analysis routines, data files, and for paper writing.

The only decent and usable electronic notebook I've seen
is notetaker, which, unfortunately, is only available on OS X.
http://www.aquaminds.com/

best,
Markus

-- 
Markus Dittrich (markusle)
Gentoo Linux Developer
Scientific applications
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Re: [gentoo-science] elektronic lab book

[Markus Luisser]

Hi Norman!

> I am having my eyes open for an electronic way of keeping a lab book
> for my experiments for quite some time now, however to my surprise,
> it seems there is none open source. I am wondering how people in the
> science herd are organizing their day by day experiments.

I have to admit that similar to Oliver and Markus I use mostly text
files and plain old paper to keep track of my activities. On the
computer I use a combination of plain text files, LaTeX files, data
files and a proper directory structure, backed by a subversion
repository which I found immensely useful for working at different
computers and to keep track of my progress.

My main reason to use LaTeX is simply that I'm lazy and dont want to
type stuff twice, so when I want to publish, I simply combine what I
already have. Together with subversion (and probably viewcv) this
gives a nice system that is quite painless to keep track of stuff,
plus you always have a backup somewhere. I also found it very helpful
at times to be able to work with my documents on different operating
systems and text files are very difficult to beat in the
interoperability area ;)

I also experimented with wikis some time ago and found them quite
useful but ditched them in the end because the overhead was too large
for what I needed. But it could be that its just the right stuff for
you.

Good luck!

markus
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