Publishing On OpenWetWare - Lessons Learned 1
Previously I wrote about my plan to try out OWW as an authoring platform. I have now completed the first phase of this little experiment, and I thought I would share my experiences.
The first draft of ‘Python - All A Scientist Needs’ can be seen here. I wrote the article completely on OWW, but developed and tested the code examples on my laptop, since OWW doesn’t provide a way to test and run code. The wiki worked out pretty great until the document got too long to manage easily. Below are the pros and cons of my experience.
Wiki As An Authoring Tool: Pros
- I really enjoyed having a copy of the document that I could work on from anywhere (my laptop at home, computer on the bench in the lab).
- The formatting looks nice, especially the code example highlighting.
- The biblio plugin makes citations very easy to work with (with some manual typing).
- The versioning through the article history made it very easy to see past versions.
- Having the wiki host the source code zip file is a great way to share supplementary data.
Wiki As An Authoring Tool: Cons
- The article got a little unwieldy to deal with when it got to its full length. When adding citations, I needed to edit the whole document to be able to see where the citation goes as well as plug it into the References section.
- The wiki auto-time-out could be very frustrating causing me to lose changes if I didn’t save often enough. (You can see where I got a little annoyed if you look at the history comments.)
- I had to use a web browser to do my edits, instead of a client-side text editor, which is my method of choice.
It’s now time for phase 2 - collecting comments. I have sent out an email to a few friends to collect their comments. Hopefully they will use the talk page to write their comments down. I would be very grateful if any of you would like to leave comments, either on the talk page, or at the bottom of this post.
Thanks!
Posted: February 20th, 2008 under Publishing.
Comments: 5
Comments
Comment from Reshma
Time: February 21, 2008, 9:29 pm
Very useful list of cons re using the wiki to write a paper. We should brainstorm how to address these problems at the next SC meeting.
Could you explain a bit more re the saving issue you were having? If you get that message about “loss of session data” then if you just hit the save button again, it should save everything. But it sounds like you were having some other problem?
Just fyi, another option is to write your paper in LaTex on the wiki (http://openwetware.org/wiki/User:Austin/Extensions/LatexDoc) but LaTeX isn’t attractive to most biological researchers. (Using LaTeX might enable dividing up your paper into different sections that get included together. But again the saving issue isn’t addressed.)
Regardless, thanks for running the writing experiment and blogging on it. Lots of useful info here!
Comment from Austin
Time: February 22, 2008, 9:40 am
I can’t editing using a web browser either. On linux, there’s a wikipediafs which works great with oww so you can edit pages as if they were normal files. There’s also a firefox plugin I believe that lets you use a text editor to edit any text box on a webpage.
Comment from austen
Time: February 22, 2008, 8:11 pm
Same on the web browser . . . I actually tried that with a grant and it was hell. Here’s what we need to do: Get people publishing as soon as they are done and get people publishing in HTML. That way it’s readable (in the way many in bio&chem like to read) and searchable.
If we can get people doing that everything will work itself out. I say OWW should work to help people do this. If you pick a format like writing in a wiki or using LaTeX you’re doomed. If OWW showed people how to convert to HTML or offered to publish for a price—then I think this could work.
I’m sure you could hire me or a million other howler monkeys to convert the stuff on at a per conversion rate.
http://blog.openwetware.org/brokenscience/2008/02/22/arxiv-and-the-html-wonderland/
Comment from austen
Time: February 22, 2008, 8:42 pm
How about this?
You write a paper. Before you publish somewhere else (presumably) you submit a PDF and HTML to OWW. If you don’t want to do the conversion you pay OWW a few bucks to do it.
OWW submits your PDF and HTML to arXiv. It also links to live HTML on the OWW site.
Voila…OWW publishing.
http://blog.openwetware.org/brokenscience/2008/02/22/the-type-of-publisher-oww-should-be/
Comment from austen
Time: February 22, 2008, 10:21 pm
Yeah unless you can write a program that can convert standard word processor docs into wiki text I think wiki papers are toast.
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