Grad student blogging/ academic life (Amber, Ania)

We looked at two graduate student blogs and one post-doc blog that discuss the mentor-mentee relationship and the disjoint between what is expected of both parties and what ends up being supported.
The blogger at ilovescience points out that what students may be encouraged to do theoretically (attending training seminars, TA training, etc) may not be what is supported in reality.
Wecansleeplater does a CBA on the mentor-mentee relationship. One point that stuck out to me was that from a purely CBA standpoint, the PI should only be invested in what happens to the student while they are currently a member of the lab. This may be why there is such a precipitous drop off of women in science after graduate school. There is little support or information available for women who wish to pursue a career and develop of a family.
Far more radical, YoungFemaleScientist, a post-doctoral researcher, rails against the sexism she perceives in the mentor-mentee relationship and follows up the comments here. I feel that there may be some truth to what she says, however, I'm not sure how much of what she is writing is colored more by poor mentor-mentee relationships that have nothing to do with gender.
Female Science Professor does dole out "street smarts" in her post on academic etiquette to both males and females who read her blog. These unwritten rules, most of which are common sense, are crucial. What would you add?

Science Tools 2.0

This week’s topic is “other web 2.0 applications”. In my opinion, this is one of the more exciting developments at the interface between science and technology over the last 5 years or so, it's also rapidly changing. The major themes in this area (as I see them) are:

- increasing integration between data sources and/or analysis strategies
- accessibility and low learning curves
- resource availability

In some cases, this simply amounts to using standard web 2.0 tools (e.g., wikis and blogs) in order to organize and present scientific information in useful ways, in other cases these tools are novel applications developed with a specific purpose in mind. I’ve linked to some resources that I’ve found useful or think are cool. This list is heavily biased toward the type of resources that I use most (phylogenetics and biodiversity informatics), feel free to add others in the comments.

Increasing integration
GBIF - Global Biodiversity Information Facility
Genbank
Scratchpads - Customizable collaboration for taxonomic research
Phylota - Mike Sanderson's database that packages genbank into phylogenetically useful clusters
dryad - Nescent funded data repository

Accessibility
Tree tapper - Former CPBer Brian O'Meara's Nescent postodoctoral project.
Phylowiki - phylogenetics tutorials as a wiki, developed as part of the Bodega Applied Phylogenetics Course
OpenWetWare - lab notebooks, blogs, protocols, etc.
BEAST user guide - example of using a wiki to develop a user guide to complicated software
Cipres - popular phylogenetic inference methods made easy
iTOL - tree visualization
automated tree inference - mor (rDNA fungal phylogeny), MatriPhy (my package, still in development, link goes to turtle example)

Resource availability
Genome browsers
RDP -ribosomal database
Treebase - database of phylogenies
uBIO - database of taxonomic information
Museum collections: specimens - MaNIS, ORNIS, HerpNET; fieldnotes
EoL - Encyclopedia of Life
Biodiversity heritage library - an effort to digitize all the biodiversity literature in 10 natural history museum libraries
Cipres - Free access to some computing resources at the San Diego Supercomputer Center


One could also argue that new online “rapid publication” journals are part of this trend (E.g. Zootaxa, Zookeys, PLoS one). I’ve only had one experience with this type of journal to date and found it to be really great for certain types of papers, I’d be interested to hear about other’s experiences.

In many ways, science is only beginning to take advantage of web 2.0 technologies and I think most would agree that there is a lot of potential for more development in this area. Aside from discussing the utility and the impact that these tools have had on science already, I would also be interested in discussing what resources people think are currently missing and what future developers should be aiming for.

Nature Editorial on Blogging

Check out the editorial appearing in this week's Nature, discussing blogging about articles before they are published. Take home message -- go ahead, but watch don't give away too much...
Then go and engage in the discussion on Nature's forum. Guess since this a blog post and not the mass email I had started, I better go share an opinion. Sounds like Nature is taking a cautious approach to authors engaging in blogging -- they talk about the advantage of all work being peer reviewed before being public, but the embargo goes beyond the point when it has been peer reviewed and accepted, but still not published. The justification for this is unclear.

Post Made on Behalf of Clarissa

Blogs as an Outreach Tool

So there are so many different types of outreach, I thought maybe we could focus on either of the following:

1) Blogs as a medium to communicate science painlessly to the public.

- Here’s an extension of what we talked about last week, a blog for biology teachers: http://blogging4biology.edublogs.org/

- A blogger who interviews scientist doing outreach as her form of outreach:

http://jendodd.com/index.php?option=com_content&view=article&id=67:interview-with-eva-amsen&catid=42:science-outreach&Itemid=54

- And a page of web resources for communicating science effectively to the public:

http://opa.faseb.org/pages/PolicyIssues/commscience.htm

2) Blogs as a yet another tool to reach out to those anti-evolutionist folks (or for them to reach out to us!).

- One interesting thing you find with these types of blogs is often very short posts followed by extended comments. Check out the following three links for examples:

http://www.bbc.co.uk/blogs/thereporters/justinwebb/2009/02/evolution_vs_creationism.html

http://blog.news-record.com/opinion/letters/archives/2008/05/most_true_scientists_do_suppor.shtml

http://firstread.msnbc.msn.com/archive/2009/02/12/1791814.aspx

Framing Science (http://scienceblogs.com/framing-science/ ) is an interesting blog I found that has commented on both of the above and uses the blog as a media tool to connect science with politics.

Education and technology

I came across this video of Sir Ken Robinson talking at the TED (Technology, Entertainment, Design) Conference in 2006 about our current education system and the effects he thinks it has on kids' creativity. Even though he is talking about lower education, I think his views are relevant to college- or graduate-level science teaching because it is at this point that students are challenged (often for the first time) to think independently and creatively about scientific ideas.

How do we plan to evaluate students in our classrooms while also fostering creativity? If anyone has good ideas about how they plan to do this or good stories about how their professors did this in the past, please share!

I am really interested in how technology can be utilized in the classroom, especially in the context of a college-level biology class. And I'm talking something other than powerpoint presentations, people. Here's an example of a class blog , made by Darren Kuropatwa, a high school math teacher in Manitoba. After each class, he has one student summarize what they learned that day and post it on the blog. He has gotten a lot of good feedback from students who benefited from reading other students' explanations of math concepts. I wonder how a similar blog could work in a college-level biology class? How would you change his model?

Finally, here's the Online Education Database's collection of their top 100 education blogs .

What Every Scientist Should Know About Open Access

Let's start by learning a little more about the Creative Commons license such as used by PLoS. To do so, we'll include a piece of media licensed under Creative Commons attribution (by) license.



We better attribute it: From Creative Commons, http://creativecommons.org/videos, found on Wikipedia, which is itself becoming Creative Commons (cc-by-sa: attribution and share alike), though currently GFDL. Okay, on to Open Access.

Green and Gold OA
Their are two basic paths to Open Access: the Green road and the Golden road. In Green Open Access, authors self-archive papers. Archiving post-publication is subject to copyright, while as pre-publication is simply a matter of journal policy. Most journals now allow pre-publication archiving -- Nature recently changed their policy to allow this. A long standing example in the physical sciences is arXiv.
Gold Open Access is the PLoS model, where researchers pay $1000 - $3000 to cover publication costs. Many journals use a hybrid model, where the authors have the option to pay and have their paper published as open access, see this list of journals accepting so called "sponsored articles" through Elsiver.

How big is Open Access?
Good question. NIH funded research requires it, as does Harvard.


Think bigger
Need More Openess? How about Open Peer Review? Check out Biology-direct, an open-source, open peer-review model. Authors solicit reviews from three board members and then can be published with or without revisions but with the reviewers comments and names included. Further alternative is Open Peer Commentary, where peer commentary on a target published article is published along with the author's response.

A natural extension of open publication is Open Text Books. Hear Richard Baraniuk discuss on TED talks, which use the cc-by-nd-nc (attribution, non-derivative, non-commercial):




How about all of science being open? Open Data and Open Notebooks? Check out the vision of Science Commons, and the example of Neurocommons.

Blogspot rules and copyright

Curious about what we are allowed to post on blogger?
the Blogspot Content Policy

Guidelines for copyright infringement, through Google