Open Science and more

I am surprised to discover I have not posted here for a couple of years. What?? Anyway - today I wanted to collect some interesting pointers to open science.

Our INSIGHT project is available on the Open Science Framework at this particular place: https://osf.io/9yuqr/.  The other IARPA project "FAST" is also posted there.  OSF has been recommended by the Center for Open Science too.

Related to our INSIGHT project, we did a survey of data repositories related to neuroscience and the social and behavioral sciences.  This survey included IPCSR,  NITRC, COINS, OpenfMRI, SumsDB, 1000 Functional Connectomes project and its successor the International Neuroimaging Data-sharing Initiative, BrainBiodiversity Bank, XNAT, and The WholeBrain Atlas.  C-PAC is the Configurable Pipeline for the Analysis of Connectomes.

I just learned of rOPenSci - open tools in the R programming language.

The National Data Service is being spearheaded by NCSA. 

Of course there is a long history of open-source software, of which two of my favorite examples are Bugzilla and NAMD.

The scientific journals are also important players here, obviously PLOS as well as others.

A bit of larger context of the Web itself:
World Wide Web Consortium and the Web Ontology Language (OWL) and the Extensible Markup Language (XML) and the IEEE Standards on metadata and the Internet of Things and the Harvard Dataverse and the Comprehensive Knowledge Archive Network (CKAN) and the Dublin Core Metadata Initiative and the DSpace open source repository application and the Open Archives Initiative  and the Registry of Research Data Repositories (RE3Data) form a complex ecosystem of philosophies, approaches, technical requirements, standards, and infrastructure.

---

Big data is a big deal

"Big data" is a big deal.  The US National Science Foundation has a Big Data initiative.  The US National Institutes of Health has a "Big Data to Knowledge (BD2K)" program.  The US Defense Advanced Research Projects Agency (DARPA) has a Big Data effort as well.  There are lots of cool examples of scientific communities that are organized around data sharing and analysis, such as the Allen Brain Atlas, the Neuroscience Information Framework,  the Worldwide Protein Data Bank, the Materials Project,  and more.  The US Government's current sites include NASA's Life Science Data Archive and the Aviation Safety Reporting System, JPL's Small Body Database Browser and Molecular Spectroscopy Catalog,  and the Department of Defense's Information Analysis Centers.

n-Disciplinarity

Back in the day, there was a lot of talk about multidisciplinary research.  As a human factors researcher, I am already used to being interdisciplinary - between the worlds of industrial engineering, psychology, and computer science. Now there is more talk of transdisciplinarity - such as the talk that Dan Stokols will give here at UIUC next month.  It is interesting to ponder this longitudinally -- that a topic that was once between disciplines, then becomes a discipline itself.

Brains!

Of course I am interested in the new White House BRAIN initiative.  There is a White House infographic, fact sheet and blog entry.  And plenty of commentary on a variety of news sites.  Part of the basis for this is the Brain Activity Map (BAM!) project described in this paper published in the peer-reviewed journal Neuron.  Certainly, creating maps is helpful, and thusly inventing technologies to help you create the maps is important.  But it is also important to focus on human health and performance issues (e.g., PTSD, TBI, dementia, etc.) that are the reason to care about such maps.

Shout out!

I just read Professor Brian Cunningham's post over at his Nanosensors blog.  Very good advice for graduate students!

On university-industry collaboration

Tomorrow I will participate in a UIUC faculty development seminar on "Working with Companies".  I think it will be a good introduction to a lot of issues, including:

• gifts versus grants versus contracts
• Conflicts of Interest and Commitment
• Publication
• Intellectual properties, patents, licenses
• Types of agreements, including Material Transfer, Sponsored Research, Technical Testing, and more
• Institutional Review Board (IRB) for human subjects research
• Institutional Animal Care and Use Committee (IACUC)

I will mention several cool examples of industry collaboration with the University of Illinois at Urbana-Champaign, including

• the Energy Biosciences Institute
• the Center for Nutrition, Learning, and Memory
• the Air Conditioning and Refrigeration Center
• the Mayo Illinois Alliance for Technology Based Healthcare

On human-in-the-loop simulation

In addition to BIC and ITG (see previous post),  the Illinois Simulator Laboratory (ISL) is a shared research facility at Beckman.  ISL supports an array of laboratories:  virtual reality systems (Cave and Cube), driving simulator, flight simulation, and motion capture suite.   When you are doing human-systems integration research (like my previous gig at NASA Ames Research Center's Human Systems Integration Division), this kind of capability is crucial.  But of course, technology keeps changing.  Mobile computing is another genre of technology that has other harmonics related to human factors and human-systems integration.  The whole area of human-computer intelligent interaction is a very active research field.

On biomedical imaging

Part of my job at Beckman is to provide oversight over our shared research facilities, which includes the Biomedical imaging Center and the Imaging Technology Group.  BIC has MRI, ultrasound, microPET/SPECT/CT, and diffuse optical imaging (fNIRS and EROS).  ITG's Microscopy Suite includes micro and nano CT.  I just read an IEEE Spectrum article on "omni-tomography" -- interesting!  see it here:   "Combined MRI and CT Scanner".  We are always thinking about how to advance the state of the art, and also how we can support the faculty.  Of course the faculty themselves are doing groundbreaking work in imaging -- such as Steve Boppart's work in biophotonics, Gabi Popescu's work on quantitative light imaging, Rohit Bhargava's work on chemical imaging, Zhi-Pei Liang's work in MRI, and Brad Sutton's work on MR functional imaging.

Episode 4: A new gig

I have finally reconnected with my old blog here. I had been going for a "Bridget Jones's Diary" vibe a few years ago.  Now I am at the Beckman Institute for Advanced Science and Technology, at the University of Illinois at Urbana-Champaign. It is good to be back home in Illinois! And it is super-cool to be the Associate Director for Research at Beckman.  see more at: Beckman Institute

number of months back home: nearly 3

I got back home on December 15, 2007. And then what with holidays and all, did not really get back in the swing until January 7.
Did a big all-hands meeting on February 7.
Working a lot of personnel and budget issues.
Now that I got used to 3 or 4 month detail assignments in 2007, I detect a longing for change again...but will have to work that within my current job.

number of days on external assignments: 169 so far

Been away from the family for three months, and now home but a loooong commute.
Love the work, don't love the effect on family life.

number of days on Capitol Hill: 4
number of nights in Chicago: 1

This past week I got to attend a course on Congressional operations, actually held on Capitol Hill
and, in two of the sessions, actually held in a House or Senate committee hearing room.
Cool! V. interesting to learn about the deliberately-inefficient, anti-tyranny machine
that is the legislative branch.

Flight left DC late on the last day, so missed flight in Chicago.
But got to spend the night with family, which was fun.

number of weeks our financial system will be down: 4-6
number of weeks our computer network will be partially down: 4-6

Infrastructure! Gotta have it.
Of course, in a *real* industry, they would presumably spend money on keeping a second
backup financial system running while the main one is down, and on renting new
office space with intact computer networks while our building is being upgraded.
In the absence of resources for doing that, we will just do the best we can to work around it.

number of Nintendo DS machines in the house: 4
number of Nintendo Game Boy Advance machines in the house: 1
number of PlayStation 2 machines in the house: 1

I can justify all this technology. Now that I and my husband and my two boys each have a Nintendo DS,
we can all do PictoChat and exchange games. I use my GBA during airline travel and will now have
my Nintendo DS as well to practice Brain Age. The PlayStation has the eyeToy kinetic workout program
which is good and helps keep me in shape. Although I must admit, I skipped the whole last week of working
out, but then again I was away for four days on business travel.

This week is a swirl of medical and work issues.
Thursday: dentist for root planing (ugh).
Friday: eye doctor for new prescription (yuk on exams but fun on new frames).

Every day at work is frantic replanning and rewickering of budget and workforce numbers.
Am now going on v. important trip next week.

Unconventional Leadership Books


"The Bad Popes" by E. R. Chamberlin.
As a lapsed Catholic, I do not feel guilty about learning about the history
of the Church even if it is less than flattering.
This is a fascinating and wittily-written history with many lessons
on what not to do as a leader.

"The March of Folly" by Barbara Tuchman.
There are so many good insights here that apply to our times now.


"Sorting Things Out" by Geoff Bowker and S. Leigh Star
This is about how organizations categorize things
(eg how WHO classifies diseases). It's a great reminder of the
political and social forces at work that define how we conceptualize
the world and how that shapes our processes and decisions.
I always think about these insights when dealing with categories
like "performance metrics" or "transition workforce".

data from yesterday:
number of diet cokes: 3
number of protein bars: 2
number of technical planning meetings: 2
number of technical/budget meetings: 1


Good day yesterday. Useful and interesting meetings.

From last night:
number of hours shopping with sons: 2
number of games of MASTERMIND played with sons: 4

Today is Saturday:
number of cups of coffee: 2
number of fruit washed: 10 apples, 3 peaches, 3 large tomatoes,
large quantities of cherry tomatoes and grapes

number of minutes spent dealing with budget spreadsheets: 480
number of minutes spent dealing with children: 30


Oof. Too much work to do today. Too many spreadsheets due in the next 48 hours.
Why do we persist in believing that precision equals accuracy?
WHIMS WHIMS WHIMS

number of consultations: 2
number of diet Cokes drunk: 4

Today is a day of one-on-one meetings, individual work and reflection.

Am pondering appropriate synonyms for what dear Bridget would
call "fuckwittage". Hrm. Maybe WHIMS as an acronym for
What in the Hell Idiocy is Masquerading as Strategic thinking.
which also has a logical connection the actual meaning of the
word whims -- management fads and shallow reactive thinking.
Amusingly, this is reminiscent of the acronym for our
Workforce Information Management System.

number of team-building exercises: 5 (lava lake, pictionary, maze word challenge, traffic jam, uplift/popsicle pushups)
number of alcoholic beverages drunk: 1


And so it begins.....I am in my official orientation for the executive training program.
It is so v. interesting to meet all the other people in the class -- they are such a mix of personality and communication styles. I find it heartening to have my belief reinforced: that it takes all kinds to make the world.