NeSI; publishing data; open licenses #nzes

Connecting Genetics Researchers to NeSI
James Boocock & David Eyers, University of Otago
Phil Wilcox, Tony Merriman & Mik Black, Virtual Institute of Statistical Genetics (VISG) & University of Otago
Theme of conference "eResearch as an enabler" - show researchers that eresearch can benefit them and enabling them.
There's been a genomic data explosion - genomic, microarray, sequencing data. Genetics researchers need to use computers more and more. Computational cost increasing, need to use shared resources. "Compute first, ask questions later".

Galaxy aims to be web-based platform for computational biomedical research - accessible, reproducible, transparent. Has a bunch of interfaces. Recommends shared file system and splitting jobs into smaller tasks to take advantage of HPC.

Goal to create an interface between NeSI and Galaxy. Galaxy job > a job splitter > subtasks performed at NeSI then 'zipped up' and returned to Galaxy. Not just file spliting by lines, but by genetic distance. Gives different sized files.

Used git/github to track changes, and Sphynx for python documentation. Investigating Shibboleth for authentication. Some bugs they're working on. Further looking at efficiency measures for parallelization, building machine-learning approach do doing this.

Myths vs Realities: the truth about open data
Deborah Fitchett & Erin-Talia Skinner, Lincoln University
Our slides and notes available at the Lincoln University Research Archive

Some rights reserved: Copyright Licensing on our Scholarly record
Richard Hosking & Mark Gahegan, The University of Auckland

Copyright law has effect on reuse of data. Copyright = bundle of exclusive rights you get for creating work, to prevent others using it. Licensing is legal tool to transfer rights. Variety of licensing approaches, not created equal.

Linked data, combining sources with different licenses, makes licensing unclear - interoperability challenges.

* Lack of license - obvious problem
* Copyleft clauses (sharealike) - makes interoperability hard
* Proliferation of semi-custom terms - difficulties of interpretation
* Non-open public licenses (eg noncommercial) - more difficulties of interpretation

Technical, semantic, and legal challenges.
Research aims to capture semantics of licenses in a machine-readable format to align with, and interpret in context of, research practice. Need to go beyond natural language legal text. License metadata: RDF is a useful tool - allows sharing and reasoning over implications. Lets us work out whether you can combine sources.

Mapping terminology in licenses to research jargon.
Eg "reproduce" <-> "making an exact Copy"
"collaborators" <-> "other Parties"

This won't help if there's no license, or legally vague, or for novel use cases where we're waiting for precedent (eg text mining over large corpuses)

Compatibility chart of Creative Commons licenses - some very restricted. "Pathological combinations of licenses". Computing this can help measure combinability of data, degree of openness. Help understanding of propagation of rights and obligations.

Discussion of licensing choices should go beyond personal/institutional policies.

Comment: PhD student writing thesis and reusing figures from publications. For anything published by IEEE legally had to ask for permission to reuse figures he'd created himself. Not just about datasets but anything you put out.

Comment: "Best way to hide data is to publish a PhD thesis".

Q: Have you started implementing?
A: Yes but still early on coding as RDF structure and asking simple questions. Want to dig deeper.

Q: Get in trouble with practicing law - always told by institution to send questions to IP lawyers etc. Has anyone got mad at you yet?
A: I do want to talk to a lawyer at some point. Can get complex fast especially pulling in cross-jurisdiction.
Comment: This will save time (=$$$) when talking to lawyer.
A: There's a lot of situations where you don't need a lawyer - that's more for fringe cases.

How to run a podcast poetry competition

without an in-house IT infrastructure to support it
Rachel Fisher, Kris Wehipeihana
abstract (pdf)

Covering podcasting; working outside IT infrastructure; social media.

Using Blogger, Twitter, Google Calendar. But if your team isn't keen it won't happen.

Linking Montana Poetry Day activities to something that could be pushed out through to school activities. Wrote it quickly.

Clause 4 of terms and conditions - that poems are shared under Creative Commons BY-NC-ND. No questions or complaints from users.

Didn't have any speaker/microphone/sound cards/file space at all. Most work done on Rachel's own time and own computer. Used free software. Some shortcomings but advantages outweighed disadvantages.

Blogger as easy to use. Free templates can be customised but not easy if you're not familiar with html. However there's lots of instructions available online especially as Blogger is so popular.

Audacity - all you need to know is the location of record, stop, pause, play. Advanced functionality available if you're technically minded. Save-to-mp3 is an extra file so awkward step for users. Comes included in APNK package.

File hosting - two downsides include: sites require you to sign in regularly or you'll lose your account. Can also impose file storage and file size limits (but probably not a problem unless your competition is really popular).

Stat counters (eg StatCounter) lets you know how many people are visiting, whether they're repeat visitors, where they come from again. Google Analytics is another one they use and will use in future.

Last year people could only enter if they had their own equipment; now they have stuff through APNK it's opened things up for everyone. APNK should be self-managing but customers still ask librarians for help, so librarians require training.

Rodney Libraries uses a yahoo email address because their staff email has size limits - it also ties in with their Flickr account.

File hosting sponsor this year is Liquid Silver.

Ideal set up would have dedicated website where customers can fill in mandatory information and upload files directly. Computers would have all equipment and software preloaded; staff would be fully trained. Significant relationships with local schools to combine curriculum areas (technology, english, etc). One school in Rodney catchment area has more classes participating each year.

Intends to maintain presence in web2 sites so as to be in a good position when demand for these services increases.

First year had 32 entries; second year 56. (50 entries in short story competition, for comparison.)

Tim Spalding asked whether they've looked at sites where people can post poems and have them critiqued.

Some difficulties in first year of competition re dialup - but it could be done, so don't let dialup be your excuse not to do it!

Links of interest 12/8/09

Louisville Free Public Library, Kentucky, suffered a flash flood; a librarian there has been posting updates and photos via Twitter. There's an interview with the library director plus photos and the Library Society of the World (a grassroots organisation based on social networking, the absence of policies, and a stringent Cod of Ethics) is fundraising US$5000 to help out - latest I heard today they'd reached $2700.

Web and search
Curtin Library have created an optimised website for mobile phones.

You can now search for Creative Commons material across various sites in a single place, to find free photos, music, and videos.

If you've got an image on your computer and you're not sure where it's from (or if you've uploaded an image and want to see if anyone else has stolen it), Tineye may be able to find it. Like any search engine it only indexes a portion of the web but it's indexing more all the time.

Subject guides
Some libraries are discussing ways to use LibGuides material in other parts of their library websites.

A new edition of the Internet Resources Newsletter is out, as usual listing a whole lot of new websites in a broad variety of subject areas - many could be useful for subject guides.

Food for thought
A bunch of librarians have been writing A Day in the Life of a Librarian blog posts - interesting to see what goes on in different libraries and different positions.

Seth Godin charts media according to bandwidth/value of information vs synchronicity/speed of communication - an interesting way of thinking about the way we communicate with our users.

Links of interest 12/5/09

Lav Notes: help for the stalled (pdf) is a one-side library newsletter posted in library bathroom stalls. A colleague of its author mentions a library which posted butcher paper in the bathroom stalls and invited temporary grafitti. Cheaper than repainting!

Finding Physical Properties of Chemicals: A Practical Guide for Scientists, Engineers, and Librarians (pdf)

From Twitter, "New Zealand music month + free performances = [Dunedin Public Library's] YouTube channel http://bit.ly/7WgU0 enjoy!"

"University of Oregon Library['s] faculty unanimously passed a resolution requiring all library faculty-authored scholarly articles to be licensed CC BY-NC-ND." That is, they retain copyright but authorise anyone to copy, share and use it so long as they attribute its source (BY), use it for non-commercial purposes only (NC), and don't change it (non-derivative=ND).

Notes from a presentation "on the potential use of mobile devices and cell phones for providing library services and resources".

More and more people have web-enabled cellphones. Examples of libraries who've done this include:

• University of Virginia
• Ball State University
• Penn Libraries
• Yale Medical Library

Non-English blog roundup #11 - the sharing edition

"Non-English" seems to have turned into French, probably mostly because that's the language I read best. Must remedy this. In any case, today I've got a collection of blog posts sharing data:

The Assessment Librarian was thinking about computer posts in his library dedicated to catalogue research only and wondered how much use these got compared to computers available for any purpose. Data collected over two weeks showed:

• Arts and Sciences branch
  • Catalogue-only - 12% usage
  • 'Open' computers - 51% usage
• Law and economy branch
  • Catalogue-only - 7% usage
  • 'Open' computers - 65% usage

He concludes that, while it's not straight-forward to analyse the results, it's worth considering whether there are other possible uses for their catalogue-only computer stations.

Inspired by this post, Des Bibliotheques 2.0:

• shares Google Analytics statistics for off-campus visits to the library catalogue from 1st April 2008 - 1 Jan 2009 (a good handful of pages in pdf);
• compares numbers of visitors to the homepage (site) vs the number of visitors to the catalogue (OPAC) (note the numbers were gathered using different tools;
• shows the impact of a new website - " the number of visitors has increased from 80-100%; the number of visits has increased from 30-50%; the number of pages seen per visit has tripled".

And De Tout Sur Rien has decided "I will no longer participate in projects in which the publication of my contributions in a digital format and under Creative Commons license [...] is not planned from the beginning," and calls for colleagues and/or readers to make the same decision.

Non-English blog roundup #5 (French)

Still catching up, so pulling together a bunch of French content this time:

Bernard Rentier writes "A university which wants to be on the cutting edge of information as a communication tool cannot be unfamiliar with these new practices. It must even use them, not to "reform" them, even less to control them, these two objectives not being acceptable, but if it's a tool frequently used by many students, the Institution must be able to adopt this new concept and make itself a usage of it that is "sympathetic" and perceived as positive by everyone."

Risu suggests an easy method of increasing your library's visibility: enter it into Google Business Center with contact details, website, description, photos and videos, opening hours etc. "The whole thing takes 5 minutes and it's free."

Thomas on Vagabondages talks about "Lottobook", a game where every participant pledges to send a book to the winner. The winner is drawn and receives n-1 books, while a runner-up receives 1 book (from the winner) as a consolation prize and so even the winner doesn't know they've won until all the books arrive in the mail.

A meme being passed on via Marlene's Corner: "to give you the contents of my day as a 2.0 librarian on Monday".

In Bibliobsession:

• a blog aggregator for library blogs -- that is, library blogs aimed at the public, rather than those aimed at other librarians. See the aggregator at Touti Frouti.
  
• "In other words, many vendors try to reinvent the wheel by proposing badly what is done very well by open source tools!"
  
• notes that "you can filter your Google search by license type thanks to the advanced search." (I'd long known about this on Flickr advanced search, but indeed, just expand the "date, usage rights" etc link on Google advanced search and hey presto.

On DLog, Dominique writes about The two branches of the library:

Let's not confuse

• the physical item;
  
• a particular edition of which the physical item is a clone among clones;
  
• the work, which is immaterial

And:

I draw from this a new conception of conservation: no longer only for the future or for researchers, but also for the public, here and now."

And a new report has been published, Report on the digital book (pdf) by Bruno Patino, 30 June 2008. Very roughly, from the executive summary:

The entrance into the digital age seems to be happening later for the book than for other cultural industries. However, many publishing sectors such as professional, practice or reference books are already largely digitised. This development, so far, has challenged neither the commercial model, nor relations with authors, nor the customs of readers. But what would happen if digitisation were to accelerate, even to take over? Such a hypothesis, even if it cannot be predicted with certainty, still merits that the key players in the sector prepare for it, bearing in mind the very important effects that it could lead to on the precarious equilibrium of the book industry.

A particular vigilance should especially be brought to a possible new competition between the rights holders (authors and publishers), whose remuneration of their creations should be preserved and increased, and the access and network holders, who don't necessarily have any interest in increasing the intellectual property rights.

In this context, two elements are essential: intellectual property must remain the cornerstone of publishing, and publishers must retain a central role in determining price.

The committee therefore recommends a series of measures organised into four actions:

1. Promote an attractive legal offer. [eg look at interoperability of digital content - formats as much as DRM; interoperability of existing metadata; pursue the policy of supporting digital books[
   
2. Defend intellectual property. [don't modify intellectual property law, which can accomodate digitisation; open inter-professional discussions about the rights of authors]
   
3. Put in place provisions allowing rights holders to have a central role in determining prices.
   
4. Conduct an active policy with respect to community institutions. [Establish a bureau to promote intellectual property-related policy; request a lower TVA tax for digital cultural content.]

Discussion in various venues has ensued and seems likely to continue apace....