Monthly Archives: July 2013

Test 4: Network Visualization with NESCENT GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner

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Test 3: Network Visualization with NESCENT GeoPhyloBuilder

From: Jessel, Tanner Monroe
Sent: Wednesday, July 17, 2013 10:16 PM
To:
Subject: FW: Evolution Visualization Tools – GeoPhyloBuilder

status.draft

From: Jessel, Tanner Monroe
Sent: Monday, February 11, 2013 4:51 PM
To: Mitchell, Chad Matthew
Subject: Evolution Visualization Tools – GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner

Network Visualization with NESCENT GeoPhyloBuilder

status.draft

From: Jessel, Tanner Monroe
Sent: Monday, February 11, 2013 4:51 PM
To: Mitchell, Chad Matthew
Subject: Evolution Visualization Tools – GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner

Network Visualization with NESCENT GeoPhyloBuilder

From: Jessel, Tanner Monroe
Sent: Monday, February 11, 2013 4:51 PM
To: Mitchell, Chad Matthew
Subject: Evolution Visualization Tools – GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner

Evolution Visualization Tools – GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner

Evolution Visualization Tools – GeoPhyloBuilder

London Experience, Day 12: Science Citation Indices

Except for two, the Pratt Students again split off from the UT Science Data scholars today for an afternoon visit to the world headquarters of Thomson Reuters.  Again, it was a very hot day, and we were lucky to avoid direct sunlight in their most Bond villain-esque office space.

We also joked about the “Ally McBeal” unisex bathroom – which had fully enclosed stalls that might have once been massage parlors, given the mood lighting, and rectangular faucets that “spilled” water rather than “poured” it.

A fun architectural space, but probably not compliant with the Americans with Disabilities Act. For that matter, I’m confident most of London isn’t compliant with the Americans with Disabilities Act.

I burned through the last pages of notes in my notebook at Thomson Reuters.  I was writing in the margins. TR might be best known for the Reuters news service.  They also deal in financial risk, legal, tax and accounting, and Intellectual property and science.

One of their big products is the “Impact Factor.” Starting with founder Eugene Garfield in 1955 in his paper in Science, “Citation indexes for science.” This is highly pertinent to my research into networks because they use a “researcher ID.” This can avoid some problems I’ve encountered in cataloging where the author is published under various names that are all the same author. E.g., “J.T Scienceguy” versus “Jeffry T. Scienceguy” or “Jeffry Tomas Scienceguy.”  A database sees those as different entities, even though it is indeed the same person.

With a researcher ID, your database does not get complicated, and you can do a lot of data science.

Another area that I’m interested in and need to follow up with TR is the Map of Science – particularly the EU collaboration.  They use something called “ScholarONe.”

There is some research analytics, and also they “peek” into repositories – I need some follow up information on how they prioritize repositories based on “who manages, how’s it updated, how frequently, and what’s the quality.” They have  a white paper on that but I have yet to find it.  It could be useful for my research with DataONE and developing/prioritizing member nodes.

The map of science I need to follow up with Patricia Brannen.

Finally they have some research out of Philadelphia, U.S.A. regarding networks, influence of research over time for individuals.  They are not yet that honed in on how to do it for an ad-hoc group of researchers. Disappointing, as that is what I’m hoping to do with research into collaborations resulting from DataONE interactions.

London Experience, Day 11: Cambridge – “Old School” & International Scholarship

Cambridge is home to Cambridge University.  A very old place where you cannot walk on the grass, people dress in caps and gowns for every day scholarly doings, and there is a big cathedral (King’s Chapel) that Frederick the III and Henry the VIII had a hand in constructing.

Obviously it’s amazing to be in a town with such a rich history – in New Mexico a couple of weeks earlier I’d visited a simple adobe church built by Spanish missionaries – the San Miguel Mission.  It’d been built in 1630 and was the oldest church structure in the U.S.  But this Cathedral – I think it was finished in the 1400s and had been under construction for several decades prior to completion. So it was unreal to be in such an old place.  The concept of preservation goes very far back.

Cambridge is also home to ProQuest, an outfit familiar to many Library Students due to scholarships and free training and access.  ProQuest must indeed love library students because they were again incredibly nice to us, from gathering coffee mugs for all 19 students, to giving us sparkling mineral water, juice, and some pastries that saved my blood sugar levels as I’d missed breakfast that morning.

We’d had a great ride on a train to Cambridge – again an unseasonably warm day. We passed over an idyllic English countryside, and once more I was surprised by the paucity of development – or rather the lack of “sprawl.”  I had to set out on my own as I’d neglected to purchase a train ticket, but caught up with students catching photos as the “9 3/4 platform at King’s Cross station.” I enjoyed some conversation on the way over.

Back on the subject of proquest, they are using the “Alchemy API” that I need to check out – apparently it’s a natural language processor that can “Integrate advanced text mining and analytics functionality into your application, service, or data-processing pipeline.”

What was most interesting to me was that scholars are concerned about “late finds.” That’s because a late find can cost a scientist’s reputation, and it’s also an economic cost.

Finally, I asked about scholarship in emerging economies, like Brazil, India, Russia, and China.  The reply was that most of the time, these scholars publish in English language journals.  Perhaps harkening back to the 1600s when England was the publishing powerhouse.  Although publishers now have locations throughout the world, English is the unofficial general language in India.

Interestingly, and more to the point of my question, there was an admission that “almost every publisher has a Chinese or Japanese interface ” and from my personal experience in a stats class, Chinese students would often switch to asking questions of each other in Chinese “because it is easier.” This could mean a lot for usability and user experience as “right to left” is the traditional way of  reading in Western societies, but not for others.  Cultural differences might be a barrier for e-publishers.

Scielo – Scientific Electronic Library Online – is a Brazilian scholarship site that I’d like to check out. “The Scientific Electronic Library Online – SciELO is an electronic library covering a selected collection of Brazilian scientific journals.” To wit, there is a Portuguese version to complement the top-level .br english language domain <http://www.scielo.br/scielo.php?script=sci_home&lng=pt&nrm=iso&gt;. Note the “&lng=pt” compared to “&lng=en.” According to the English language version of the site, “SciELO is an electronic library covering a selected collection of Brazilian scientific journals.”

Some interesting FAQs pertaining to inclusion are here: http://www.scielo.br/avaliacao/faq_avaliacao_en.htm

And even more interesting is the detailed list of criteria for journals to meet for inclusion in the index: http://www.scielo.br/avaliacao/criterio/scielo_brasil_en.htm

It goes back to the question of “who do you trust?” In fact, this list of criteria might help answer the question “why do you trust them?” At least from the citation indexer’s point of view.

 

London Experience, Day 10: Data Science in the UK

On Wednesday, July 5 we had a visit and talk from Graham Parton, a self professed “data scientist.” He gave a talk on “Environmental Data Archival – Practices and Benefits.”  He’s associated with the British Atmospheric data Centre

Centre for Environmental Data Archival
National Centre for Earth Observation

While Pratt students had not been exposed to this, UTK Science Data Students felt familiar with much of the information presented due to taking Environmental Informatics in the Spring 2013 semester. Also, UT is heavily involved with DataONE, essentially a collaboration of U.S. environmental data centers.

A second development of interest to me was my attempt to visit the University College London Centre for Advanced Spatial Analysis, http://www.casa.ucl.ac.uk. I did wind up there, but spent more time in the tube getting there than actually doing anything of value.

I’d hoped to speak with the director, Dr. Andrew Hudson-Smith.  [Major aside: Unfortunately, he was busy setting up a Web cam for Jeremy Bentham, a rich old dude who gave a lot of money to UCL and made some weird requests, including to be mummified, put on display, and apparently a window on the world.  Well, now he’s got it – via a webcam and computer display. I think the campus preoccupation with Jeremy Bentham is a little creepy – he’s a mummy after all. Here in the U.S. we have taxidermy mascots – but no human beings to my knowledge].

However I did get a card from Dr. Hudson-Smith, and may follow up with him.  I spoke for literally a few seconds about the “if you build it they will come” scenario that Oak Ridge National Lab is facing with it’s visualization lab.  What exactly is being visualized?  Will the science follow on the availability of the equipment?

At UCL, apparently they are doing a lot of spatial modeling.  That includes for community planning.  There’s a blog on the business card I got, “digitalurban.org.”  In as much as I’m interested in using Geographic Information Science (Just “GI” in Europe) to enhance transportation planning, including things like “crowdsourcing” the best biking routes, this was fascinating.  They also do some agent based modelling. I’m sure LiDAR data would be useful. As has been often discussed, I’m not sure why we need to visualize data on giant screens, though. In New Mexico we joked about the University of Arizona building a visualization lab, but not budgeting in staff to work on it or maintain it.  Everyone wants that “hollywood” moment where data is visualized to tell a story on-the-fly, but finding data, making sure it’s in compatible formats, and then throwing it up into a visualization takes time – and most of all, skilled information professionals – in GIS, data visualization, information sciences.

UCL spatial analysis lab has been doing work for 20 years – what keyed me into it was a facebook event celebrating that milestone that my group had just missed – a showcase of visualizations where “real and virtual worlds collide <http://www.bartlett.ucl.ac.uk/graduate/events/veiv-projection-ucl>.  In fact there’s a new masters and phD program starting up in  “UCL Engineering Doctorate Centre in Virtual Environments, Imaging and Visualisation (EngD VEIV)” that supports evidence-based decision making.  This is one of my pet projects at <http://knox4greenways.blogspot.com> where I talk about transportation issues and community planning.

 

 

London Experience, Day 9: Oxford University Press

For July 2, the entire day was occupied by a visit to Oxford University, home to the famed “Oxford University Press.”

Much of the information presented was not particularly interesting to me; my parents and sister are the English majors.  We went over much about scholarly editions of literature such as Shakespeare, and the great work that goes into interpreting ancient texts, even those from more recent ancient history.

An example that sticks out in my mind is “Oh my too too solid flesh.” Wait, was that sullied? Or sordid? Hard to tell.  But through digital scholarship, you can leverage your current question against the works of others.  The digital version can provide rich footnotes.

This also brings up the point about providing context – because the digital version is always detatched from the real world, context is incredibly important.

Because Shakespeare had written about the solid flesh of a human being in an earlier play, either Macbeth or Hamlet, I forget which, the modern scholar can infer that it it’s most likely this sonnet was referencing the corporeal nature of a man.

There are certainly some technical challenges in providing context – it’s a lot more than making content “machine readable.” As pointed out early, “electronic” doesn’t really mean the same thing as “digital” when it comes to e-publishing.

Finally there were some more “science centric” points made at Oxford: namely, a discussion of the White House OSTP Consultation on Public Access to Federally Supported Research Output.

A link provided for further reading:

www.theurbanpolitico.com/2011/08/united-states-
congress-at-work-faa.html

Some key pieces of legislature:

-Research Works Act (RWA)
Federal Research Public Access Act (FRPAA)
FASTR bill (access to federally funded research after 5 mo.)

Library Response: SHARE: Shared Access Research Ecosystem – network of cross institutional repositories.

Publisher Response: CHORUS: Clearing House for the Open Research of the U.S. (links to publisher’s websites)