Building Blogs of Science

Opening up [I think]

Posted in Science, Science and Society by kubke on September 23, 2010

What does it mean, in science, to be open?

I don’t know.

by Darwin Bell

I wrote a while back, that while I endorse the principles of ‘openness‘, I struggle with the issue of ‘how‘. Since then I have been trying to listen and learn. [Or, better said, shut up and listen.] I started trying to see what hurdles I encountered trying to work exclusively on Open Source Software. I joined the Learning4Content course at WikiEducator. I started looking into platforms that would fit my needs as an open lab notebook. I tried to follow the Open Science Summit. I listened hard at sessions at SciFoo Camp. I went to some New Zealand open data discussions. I became an Academic Editor at PLoS ONE. I joined the panel of the Creative Commons Aotearoa New Zealand.

And after several months of ‘listening’ the one thing that keeps popping in my head is:

kubke, you ain’t gonna figure it out by yourself.

The loudest message that I heard is, perhaps, that there is not a single, simple, one-size-fits-all answer, and that it just may come down to fumbling through until we figure it out.

So, I decided to fumble.

I am taking in Summer students this summer to work on a project that I will try to make as ‘open’ as possible.

I am leaning towards a few things:

  • I am pretty sure I want to give Mahara a go as a platform for the day-to-day ‘lab’ stuff.
  • I am pretty sure I want to regularly put as much as I can into my space in OpenWetWare.
  • I am pretty sure I want to try to shift my imaging to Open Source Software (e.g., Osirix, ImageJ, Cell Profiler)
  • am pretty sure I want to put the work out there as it is being gathered.

What I am not so sure about is how this will work. It will be a steep learning curve, but one thing that I am hoping is that by giving it a go I may begin to get the answers.

And hopefully some of the smart people out there might give me a hand and help me steer the boat in the right direction.

4 Responses

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  1. Daniel Mietchen said, on September 24, 2010 at 02:20

    From my experience with open courses (primarily through Eduzendium, Citizendium’s coursework initiative; example), it is helpful to have the students work in small groups (e.g. of three or four) rather than alone.

    Tutorials at the beginning are vital, and for them to be effective, it is best to have prepared dummy entries that have most of the kinds of contents one expects for a typical entry, so as to allow students to focus on content rather than formatting (OWW does part of this for you already, and things like ImageJ macros can be pre-configured as well).

    Also, an element of peer reviewing the things produced by the other course participants usually helps in creating awareness for what the essentials of the course are.

    Finally, if you are in open environments, it is helpful to have a clear signal in case you want to limit or broaden the ways others can interact with the students.

    • kubke said, on September 24, 2010 at 02:51

      I think you are right about the groups. I will have 3 students working collaboratively on the project (each on a different arm, but very interrelated). I had not thought about ‘dummy entries’, I tend to use templates (which students then modify to fit their own styles). But it might be good to have the entries. I am hoping to transcribe my notebook into the system before they start, so they also have access to my prior experiments, so that might do the job. I am trying to decide whether I should go for a Uni installation or get my own server. The latter would allow me to have more control over access, but of course it would mean I won’t have access to the Uni tech support. Given I am not very savvy, this will be a big hurdle for me. I am not sure what types of macros you refer to in Image J. Daniel, tanks for your feedback! It will indeed be a test to make sure the ‘process’ does not get in the way of the science!

      • Daniel Mietchen said, on September 24, 2010 at 03:42

        Templates are actually better than dummies, I would think – it’s just that you don’t always have them there yet when the research has not been done before.

        As to whether self-hosting Mahara or not, I would think that the Uni tech guys can still give you admin rights within the CMS, just not root access to the server that hosts it.

        For ImageJ macros, see here.

      • kubke said, on September 24, 2010 at 12:13

        I have to see what Uni is willing to give me if I host with them. We shall see. And thanks for pointing to the ImageJ wiki. How come I didn’t know about it? I have been using ImageJ since.. version 1.2 or 1.3 I think :)


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