[SciPy-user] [OT] advice about publishing a scientific software

massimo sandal massimo.sandal@unibo...
Mon Jul 16 08:04:15 CDT 2007


I am currently developing a (Python-and-Scipy based, of course!) data 
analysis software (more precisely, a single molecule force spectroscopy 
data analysis sw). It has been thought to be not the usual 
quick-and-dirty in house script, but to be an actual application that 
can be used in general by different labs. In fact, it actually features 
an easy and working (even if slightly unpolished) plugin API, and most 
functionality is implemented by mean of independent plugin.

Now, I would like to release it as free software (probably LGPL, but 
still thinking about it) online, however there are two concerns blocking me:

- Major one: I would like to publish a peer-reviewed paper about this 
software. If I want this, do I need *first* to write the paper, get it 
accepted, *then* to publish the software online? Or, given that 
functionality is plugin-driven, can I publish the software backbone and 
later publish a paper that presents the software and some (new, to 
release) nifty plugin that does some clever kind of data analysis? Or 
what? What are the usual requirements of journals about this?

- Minor one: Where to publish it? I am used to think about SourceForge 
as THE place for publishing open source software, however a number of 
people told me about Google Code. Basically what I want, if possible, is 
no-nonsense SVN access and some integrated mailing list/forum. Google 
Code seems good at that -it also gives automatically Wiki space, which 
is a major plus for me. What do you think about? Drawbacks? Licence 
issues (i.e. something like "since you publish it on Google Code the 
code is also owned by Google" tiny-letters clause?) Is there some other 

Moreover, I'd like to know your opinions about the degree of 
"polishness" and other requirements for initial publication of a 
scientific software. As for documentation, I am working on actual, user 
manual and hacking (mainly but not only focused on plugin writing) 
manual with tutorials etc.. The sw still lacks an installer but 
"installation" is braindead (provided that you have all the correct 
dependencies): put all the files in the same directory and run "python 
software.py" from where: do you think an installer is absolutely 
necessary or it is OK to let it go this way, and add the installer later?

Thanks a lot,

Massimo Sandal
University of Bologna
Department of Biochemistry "G.Moruzzi"

snail mail:
Via Irnerio 48, 40126 Bologna, Italy


tel: +39-051-2094388
fax: +39-051-2094387
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