Documenting one's work with NEURON (digital notebooks)
Posted: Sat Sep 20, 2008 7:04 am
Now I'm using NEURON on a daily basis, I've been forced to think about documenting my work.
I'm familiar with documenting wet experiments in a bound lab notebook, but what about in silico work? It seems wasteful (of my time, paper and printer toner) to repeatedly print and affix hard copies of .hoc and .mod files, and any generated data, to the bound notebook. It makes more sense to generate a digital notebook. In such a notebook I could document -- in one place -- my ideas and progress with NEURON-based experiments, including the model code as it evolves, and the subsequent data. [NB: Our lab uses Microsoft Windows exclusively, so I'm confined to that operating system.]
There is an increasing demand for lab notebook software; a Google search turned up a few options (and many discussions of this topic!), but I didn't find what I was looking for. Obviously the ideal software will rely on fairly universal (and cross-platform) file formats. We must be able to read the files years down the track, even when the original software has become obsolete.
A word processor (of some description) would probably offer the simplest solution; I could format my notes and easily paste in/keep track of the code as it changes. Upside: no need to separately archive the many superseded files of code. Downside: the document would be clogged with code, and difficult to follow.
It'd be great to create sections (i.e. of model code) in the document which only show the first line or two by default. The user would then click an inline button to expand the section of choice, and view the full body of code. Does any existing software offer this capability?
Finally:
Do you have any experience with digital lab notebooks? If so, what was your solution? Are you happy with it?
I'm familiar with documenting wet experiments in a bound lab notebook, but what about in silico work? It seems wasteful (of my time, paper and printer toner) to repeatedly print and affix hard copies of .hoc and .mod files, and any generated data, to the bound notebook. It makes more sense to generate a digital notebook. In such a notebook I could document -- in one place -- my ideas and progress with NEURON-based experiments, including the model code as it evolves, and the subsequent data. [NB: Our lab uses Microsoft Windows exclusively, so I'm confined to that operating system.]
There is an increasing demand for lab notebook software; a Google search turned up a few options (and many discussions of this topic!), but I didn't find what I was looking for. Obviously the ideal software will rely on fairly universal (and cross-platform) file formats. We must be able to read the files years down the track, even when the original software has become obsolete.
A word processor (of some description) would probably offer the simplest solution; I could format my notes and easily paste in/keep track of the code as it changes. Upside: no need to separately archive the many superseded files of code. Downside: the document would be clogged with code, and difficult to follow.
It'd be great to create sections (i.e. of model code) in the document which only show the first line or two by default. The user would then click an inline button to expand the section of choice, and view the full body of code. Does any existing software offer this capability?
Finally:
Do you have any experience with digital lab notebooks? If so, what was your solution? Are you happy with it?