Mike Chelen - Bookmarks

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Data scraping with YQL and jQuery | kelvinluck.com

Tags: jquery, yql, yahoo on 2009-05-25 and saved by 3 people -All Annotations (13) -About

more fromwww.kelvinluck.com

need a list of all the US National Parks in XML format
grab the data from this list on Wikipedia
jQuery to parse the data
navigating a HTML DOM
XPath to your YQL
relevant table from the Wikipedia document
SELECT * FROM html WHERE url="http://en.wikipedia.org/wiki/List_of_United_States_National_Parks_by_state" AND xpath="//table[@class='wikitable sortable']"
XML or JSON
creating an XML document
AJAX call from jQuery and then loop over the JSON
documentation could maybe be clearer
CSS style selection engine as well as the XPath one
Add Sticky Note
- added recently- http://developer.yahoo.net/blog/archives/2009/04/yql_execute.html
  posted by amiigo on 2009-05-25

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XML Path Language (XPath)

Tags: xpath on 2009-05-24 and saved by 52 people -All Annotations (3) -About

more fromwww.w3.org

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Creative Commons Attribution Noncommercial ShareAlike Legal Code

Tags: no_tag on 2009-05-22 and saved by 2 people -All Annotations (13) -About

more fromcreativecommons.org

must include a
copy of, or the Uniform Resource Identifier for, this
License with every copy
the terms of this License
Derivative Work
distribute
rights granted to You
in Section 3 above
primarily
intended for or directed toward commercial advantage or
private monetary compensation
may not exercise
primarily
exchange of the Work
for other copyrighted works by means of digital
file-sharing or otherwise shall not be considered to be
intended for or directed toward commercial advantage or
private monetary compensation
provided there is no
payment of any monetary compensation in connection with
the exchange of copyrighted works
keep intact all
copyright notices for the Work
name of
the Original Author
"Attribution Parties"

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Science 2.0 – introduction and perspectives for Poland « Freelancing science

Tags: science2.0, elearning, eresearch on 2009-05-20 and saved by 2 people -All Annotations (47) -About

more fromfreelancingscience.com

transcript of Science 2.0 based on a presentation I gave on conference on open science organized in Warsaw earlier this month
prepared for mixed audience and focused on perspectives for Poland
new forms of communication between scientists
research become meaningful only after confronting results with the scientific community
peer-reviewed publication is the best communication channel we had so far
new communication channels complement peer-reviewed publication
two important attributes in which they differ from traditional models: openness and communication time
increased openness and shorter communication time happens already in publishing industry (via Open Access movement and experiments with alternative/shorter ways of peer-review)
say few words about experiments that go little or quite a lot beyond publication
My Experiment as an example of an important step towards openness
virtual research environment
least radical idea you can find in modern Science 2.0 world
focus is put on sharing scientific workflows
use case
diagram of the “methods” sections from experimental (including bioinformatics analyses) publications
make it easier for others to understand what we did
can open towards other scientists we can also open towards non-experts
people from all over the world compete in improving structural models of proteins
helps in improving protein structure prediction software and in understanding protein folding
combine teaching and data annotation
metagenome sequences in first case and chemistry spectra in the second
interactive visualizations of chemical structures, genomes, proteins or multidimensional data
communicate some difficult concepts faster
new approaches in conference reporting
report in real time from the conference
followed by a number of people, including even the ones that were already on the conference
“open notebook science” which means conducting research using publicly available, immediately updated laboratory notebook
The reason I did a model for Cameron’s grant was that I subscribed to his feed before
I didn’t subscribe to Cameron because I knew his professional profile
I read his blog, I commented on it and he commented on mine, etc.
important part of Science 2.0 is the fact that it has human face
participation in online communities
PhDs about the same time
first was from a major Polish institute, the second from a major European one
what a head of a lab both would apply to will see
gap we must fill, this is between current research and lectures we give today
follow current research and decide what is important to learn
access to real-time scientific conversation
synthetic biology
not all universities in world have synthetic biology courses
didn’t stop these students, and they plan to participate in IGEM again
not only scientists – there are librarians, science communicators, editors from scientific journals, people working in biotech industry
community of life scientists
even people without direct connection to science
diverse skills and background
online conference
interact with them and to learn from them

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Science in the open » A breakthrough on data licensing for public science?

Tags: open, public, science, data, license on 2009-05-15 and saved by 2 people -All Annotations (30) -About

more fromblog.openwetware.org

Peter Murray-Rust and others at the Unilever Centre for Molecular Informatics at Cambridge
conversation we had over lunch with Peter, Jim Downing, Nico Adams, Nick Day and Rufus Pollock
appropriate way to license published scientific data
value of share-alike or copyleft provisions of GPL and similar licenses
spreading the message and use of Open Content
prevent “freeloaders” from being able to use Open material and not contribute back to the open community
presumption in this view is that a license is a good, or at least acceptable, way of achieving both these goals
allow people the freedom to address their concerns through copyleft approaches
Rufus
concerned more centrally with enabling re-use and re-purposing of data as far as is possible
don’t tend to be concerned about freeloading
worried by the potential for licensing to make it harder to re-use and re-mix disparate sets of data and content into new digital objects
“license”, will have scientists running screaming in the opposite direction
we focused on what we could agree on
common position statement
area of best practice for the publication of data that arises from public science
there is a window of opportunity to influence funder positions
data sharing policies
“following best practice”
make it easy for researchers to deliver on their obligations
providing clear guidance and tools
if it is widely accepted by their research communities
“best practice is X”
enable re-use and re-purposing of that data
share-alike approaches as a community expectation
Explicit statements of the status of data are required and we need effective technical and legal infrastructure to make this easy for researchers.
“Where a decision has been taken to publish data deriving from public science research, best practice to enable the re-use and re-purposing of that data, is to place it explicitly in the public domain via {one of a small set of protocols e.g. cc0 or PDDL}.”
focuses purely on what should be done once a decision to publish has been made
data generated by public science
describing this as best practice it also allows deviations that may, for whatever reason, be justified by specific people in specific circumstances

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RNA world easier to make : Nature News

Tags: rna on 2009-05-15 -All Annotations (32) -About

more fromwww.nature.com

John Sutherland and his colleagues from the University of Manchester, UK
ribonucleotide
building block of RNA
'RNA world' hypothesis, which suggests that life began when RNA, a polymer related to DNA that can duplicate itself and catalyse reactions
strong evidence for the RNA world
Donna Blackmond, a chemist at Imperial College London.
RNA polymer is a string of ribonucleotides
three distinct parts: a ribose sugar, a phosphate group and a base
chemists had thought the subunits would probably assemble themselves first, then join to form a ribonucleotide
efforts to connect ribose and base together have met with frustrating failure
researchers have now managed to synthesise
remedy is to avoid producing separate ribose-sugar and base subunits
ribonucleotides
makes a molecule whose scaffolding contains a bond that will
atoms are then added around this skeleton
be the key ribose-base connection
final connection is to add a phosphate group
influences the entire synthesis
acting as a catalyst, it guides small organic molecules into making the right connections
What we have ended up with is molecular choreography
objectors to the RNA-world theory say the RNA molecule as a whole is too complex to be created using early-Earth geochemistry
flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth
Robert Shapiro, a chemist at New York University
early-Earth scenarios
heating molecules in water, evaporating them and irradiating them with ultraviolet light
results showing that they can string nucleotides together
ultimate goal is to get a living system (RNA) emerging from a one-pot experiment
need to know what the constraints on the conditions are first
Shapiro sides with
another theory of life's origins
because RNA is too complex to emerge from small molecules, simpler metabolic processes
eventually catalysed the formation of RNA and DNA

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untitled - Twiddla.com

Tags: no_tag on 2009-05-15 -All Annotations (1) -About

more fromwww.twiddla.com

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WSJ Staff Not Allowed To Mix "Business And Pleasure" On Twitter (NWS)

Tags: no_tag on 2009-05-13 -All Annotations (28) -About

more fromwww.businessinsider.com

"discuss articles that haven't been published, meetings you've attended or plan to attend with staff or sources, or interviews that you've conducted."
Add Sticky Note
- Reasonable for some cases, yet surely it would be okay to discuss meetings and interviews with public figures?
  posted by amiigo on 2009-05-13
whether on Dow Jones sites or in social-networking, e-mail, personal blogs, or other sites outside Dow Jones
Add Sticky Note
- This covers nearly every form of digital communication, and is tantamount to including phone calls for web-generation.
  posted by amiigo on 2009-05-13
Never misrepresent yourself using a false name when you're acting on behalf of your Dow Jones publication or service.
Add Sticky Note
- Part of good professional ethics, does this not apply already to all forms of communication?
  posted by amiigo on 2009-05-13
Base all comments posted in your role as a Dow Jones employee in the facts, drawing from and citing your reporting when appropriate.
Add Sticky Note
- Good practice for all writers, and a reasonable goal in professional capacity.
  posted by amiigo on 2009-05-13
Base all comments posted in your role as a Dow Jones employee in the facts, drawing from and citing your reporting when appropriate. Sharing your personal opinions, as well as expressing partisan political views, whether on Dow Jones sites or on the larger Web, could open us to criticism that we have biases and could make a reporter ineligible to cover topics in the future for Dow Jones.
could open us to criticism that we have biases
Add Sticky Note
- Critical perspectives can be welcomed by unbiased authors to substantiate the claim their article is based on fact.
  posted by amiigo on 2009-05-13
whether on Dow Jones sites or on the larger Web
Add Sticky Note
- Views expressed outside professional capacity should not be subject to approval by one's employer.
  posted by amiigo on 2009-05-13
Consult your editor before "connecting" to or "friending" any reporting contacts who may need to be treated as confidential sources. Openly "friending" sources is akin to publicly publishing your Rolodex.
Add Sticky Note
- Very good technical advice, which some users may not be aware of.
  posted by amiigo on 2009-05-13
Let our coverage speak for itself, and don't detail how an article was reported, written or edited.
Add Sticky Note
- These are not mutually exclusive, in that providing additional details can be valuable, if done to further an article that is already strong enough to stand on its own.
  posted by amiigo on 2009-05-13
Don't discuss articles that haven't been published, meetings you've attended or plan to attend with staff or sources, or interviews that you've conducted.
Add Sticky Note
- Overly vague, what about discussing every day meetings with other staff? Encouraging employees to talk an editor in sensitive cases would be certainly be advisable however.
  posted by amiigo on 2009-05-13
Don't disparage the work of colleagues or competitors or aggressively promote your coverage.
Add Sticky Note
- Goes back to #2, in that crticism is useful to the degree it is based on research and factual reporting.
  posted by amiigo on 2009-05-13
Don't engage in any impolite dialogue with those who may challenge your work -- no matter how rude or provocative they may seem.
Add Sticky Note
- Great media/social media advice, agreed on by popular bloggers.
  posted by amiigo on 2009-05-13
Avoid giving highly-tailored, specific advice to any individual on Dow Jones sites. Phrases such as "Travel agents are saying the best deals are X and Y..." are acceptable while counseling a reader "You should choose X..." is not. Giving generalized advice is the best approach.
Add Sticky Note
- The first phrase is indeed better, the reason is actually because it is *more* specific by providing evidence for its claim.
  posted by amiigo on 2009-05-13
Business and pleasure should not be mixed on services like Twitter.
Common sense should prevail, but if you are in doubt about the appropriateness of a Tweet or posting, discuss it with your editor before sending.
Add Sticky Note
- Educated decision making and judgment of the professional remain the surest guarantee of high quality journalism.
  posted by amiigo on 2009-05-13

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Edge of Space Found | LiveScience

Tags: space, solar_wind on 2009-04-10 -All Annotations (24) -About

more fromwww.livescience.com

boundary between Earth's atmosphere and outer
space
instrument developed by scientists at the University of Calgary
73 miles (118 kilometers) above Earth's
surface
astronauts can say they've
been to space after only passing the 50-mile (80-kilometer) mark
space industry is also a somewhat
arbitrary 62 miles (100 kilometers)
United States, however, has never officially adopted a set boundary standard
overflight rights of satellites and other
orbiting bodies
NASA's
mission control uses 76 miles (122 kilometers) as their re-entry altitude
shuttle switches from steering with thrusters to
maneuvering with air surfaces
13 million miles (21
million kilometers)
the boundary
where Earth's gravity is no longer dominant
Supra-Thermal Ion Imager
tracking the relatively gentle winds of Earth's
atmosphere and the more violent flows of charged particles in space
difficult to make
measurements in this region, which is too high for balloons and too low for
satellites
second time that direct measurements of charged particle flows have
been made in this region
first time all the ingredients – such as the
upper atmospheric winds – have been included
David Knudsen of the University of Calgary
an altitude of about 124 miles (200 kilometers) above sea level and collected
data for the five minutes it was moving through the "edge of space."
carried by the JOULE-II rocket on Jan. 19, 2007
Journal of Geophysical Research on April 7
space weather and its impacts
on Earth
calculate energy flows into the Earth's atmosphere that
ultimately may be able to help us understand the interaction between space and
our environment
link between sunspots and the warming and cooling of the
Earth's climate
how space weather impacts satellites, communications,
navigation, and power systems

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Using the Google Plugin for Eclipse - Google App Engine - Google Code

Tags: google, appengine, java, eclipse, plugin on 2009-04-08 and saved by 2 people -All Annotations (21) -About

more fromcode.google.com

Eclipse 3.4 (Ganymede)
Help menu > Software Updates...
Add Site...
http://dl.google.com/eclipse/plugin/3.4
Google Web Toolkit SDK
Google App Engine Java SDK
Google Plugin for Eclipse 3.4
Install...
restart
File menu > New > Web Application Project
Project name
Guestbook
guestbook
Package
Verify that "Use Google App Engine" is checked.
Finish
Run menu, Debug As > Web Application
App Engine deploy button uploads your application to App Engine:
register an application ID with App Engine using the Admin Console
edit the appengine-web.xml file and change the <application>...</application> element to contain the new ID
administrator account username (your email address) and password

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Quick Start - Google Plugin for Eclipse - Google Code

Tags: google, eclipse, plugin on 2009-04-08 and saved by 3 people -All Annotations (2) -About

more fromcode.google.com

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Content Nation in Washington: Masters of Twittercraft Talk About Social Media's Impact on Politics and the Press [Content Nation ™]

Tags: no_tag on 2009-04-06 -All Annotations (4) -About

more fromcontentnation.com

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BioscienceWorld

Tags: no_tag on 2009-04-05 -All Annotations (5) -About

more fromwww.bioscienceworld.ca

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What Socrates Can Teach You About Social Media

Tags: social, media, socrates on 2009-04-03 and saved by 7 people -All Annotations (36) -About

more fromjessenewhart.com

get involved
Interact with people. Make mistakes. Learn.
Which relationships need more nurturing
always room for improvement
How can you better serve your community
Ask somebody
Be the person you’ve always wanted to be. Practice what you preach.
This balancing act is one of the trickiest you’ll ever have to walk, but if you make your best efforts to stay true to yourself and others it will be noticed, appreciated and respected.
Flesh out the details
follow it through
Do your best
effective word of mouth
reward you with deeper connections
it’s ok to unplug for a while and take a break
Don’t worry
Employ your time in improving yourself by other’s writings, so that you shall gain easily what others have labored hard for.
Add Sticky Note
- aka murk loar
  posted by amiigo on 2009-04-03
One who is injured ought not to return the injury, for on no account can it be right to do an injustice;
it is not right to return an injury, or to do evil to any man, however much we have suffered from him.
it is easy for a message to be misconstrued
When most messages transmitted are text
Add Sticky Note
- Occurs in any form of communication, including phone, handwritten letter, or face-to-face. With higher volume in telecom, the absolute number of misunderstandings may increase, even while the frequency stays the same.
  posted by amiigo on 2009-04-03
The only true wisdom consists in knowing that you know nothing.
Keep your mind in a constant state of openness.
Be willing to truly listen to what others have to say and don’t hold on to your ideas so strongly that you are unable to see a new and greater truth.
Earnest debate helps the truth to rise to the top for all to see.
debate respectfully while keeping an open mind
you and the person with whom you are debating will be the better for it in the end
Remember that there is nothing stable in human affairs; therefore avoid undue elation in prosperity, or undue depression in adversity.
Remain constantly moving towards your goals, ever evolving.
The important thing is that you have taken the initiative and and are moving forward.
constructive criticism
don’t be afraid to try something new
the harder you work and the better informed you strive to be, the more your intuition seems to pay off

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Internal vs. External Cloud

Tags: no_tag on 2009-04-02 -All Annotations (15) -About

more fromwww.serverwatch.com

Many corporate data centers have many different generations of servers from a variety of vendors running different operating systems on different processors — Windows, AIX, Solaris, Linux, Intel, PowerPC, SPARC and so on. In contrast, most cloud services offer a limited choice of operating systems running on a narrow range of hardware.
Add Sticky Note
- This is actually a good reason for virtualization, because it is easier to get VM host running on a couple platforms, than maintaining more specific software.
  posted by amiigo on 2009-04-02
Steve Oberlin, chief scientist at Cassatt, a San Jose, Calif.-based IT infrastructure management software
"Internal clouds help you to pool your computing resources into a cloud and manage it, applying server resources dynamically on the fly in response to demand," he says. "What you end up with is higher utilization and efficiency."
organizations have already embarked on virtualization programs
It enables applications that are not suitable for virtualization (such as those that require the resources of an entire server at peak times) to run more efficiently, and it includes virtualized servers anyway: virtualization, in other words, is part of an internal cloud solution, he says.
Oberlin says an internal cloud goes beyond this
Which is better, implementing an internal cloud or using a public cloud?
James Staten, a principal analyst at Forrester
"Internal clouds are good because you can follow all of your workflow and security guidelines, and ensure that you are running the right code. The trade-off is that you can't reach the economies of scale that public cloud providers achieve,"
adapting to the processes of the public cloud
license management
Add Sticky Note
- Many server software components have open source versions available, including customized VM images.
  posted by amiigo on 2009-04-03
get the benefits of economies of scale
have to work with what is on offer

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Pulp Nonfiction

Tags: no_tag on 2009-04-02 and saved by 4 people -All Annotations (7) -About

more fromwww.thenation.com

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Setting up - Skulltag Wiki

Tags: skulltag, fmod, linux on 2009-04-02 -All Annotations (12) -About

more fromskulltag.com

cp fmodapi375linux/api/libfmod-3.75.so /usr/lib/
wget http://www.fmod.org/index.php/release/version/fmodapi375linux.tar.gz
tar -xvzf fmodapi375linux.tar.gz
sudo su
cp fmodapi375linux/api/libfmod-3.75.so /usr/lib/
cp fmodapi375linux/api/libfmod-3.75.so /usr/lib/
ln -s /usr/lib/libfmod-3.75.so /usr/lib/libfmod.so
apt-get install zlib1g-dev libsdl1.2-dev libflac++-dev nasm tar bzip2 p7zip libjpeg62
apt-get install timidity
create a skulltag folder in your home directory and extract the linux base (skulltag.wad) and distro binary (skulltag and skulltag.pk3) in there
put all of your iwads in that same directory
./skulltag

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skulltag [Archive] - Ubuntu Forums

Tags: skulltag, ubuntu, debian on 2009-04-02 -All Annotations (6) -About

more fromubuntuforums.org

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Voluntary amputation and extra phantom limbs : Neurophilosophy

Tags: no_tag on 2009-04-01 and saved by 3 people -All Annotations (1) -About

more fromscienceblogs.com

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Journal of Clinical Investigation -- All data are not created equal

Tags: no_tag on 2009-03-28 -All Annotations (43) -About

more fromwww.jci.org

For the examples in this editorial,
let’s discuss Western blots in particular (though the rules apply to Northern,
Southern, and PCR blots too).
bands can be spliced together, but only, and I repeat
only, if they were noncontiguous but run on the same gel at the same
time
a thin line in between the spliced lanes and appropriate text
added to the figure legend to reflect the modification
there is nothing more
reliable than a blot with bubbles — there is no need to erase background noise
or doublet bands
a loading control, say β-actin or GAPDH, was probed
off the same gel
My understanding of a loading control is that it represents an analysis
of an irrelevant protein from the exact same gel lane to assess how much sample was loaded
in that particular lane.
elementary governing principle to me
an article that, among other problems, ran the
loading control on a separate gel at the same time
running a parallel gel, even if
the sample run on the gel was an aliquot from the same tube, does not demonstrate equal
loading of sample in the experimental gel
How does one control for variations in pipetting
such small volumes?
can’t you just cut off the bottom and reprobe that part for the
actin or other loading control and reprobe the top for another protein of interest?
some blots need to be stripped and reprobed several
times
run duplicate blots and present 2 rows of loading controls?
worried about the manipulations we can detect
a
heavy (or light) hand with a pipette can influence a band’s appearance when no
loading control is there to normalize it
exposure times
in a particular row of a
Western, all bands presented should be from the same exposure time
allow
band splicing — with all the appropriate caveats, as described
splicing lanes from various exposures of the same blot doesn’t prove anything
expose most any gel long enough, you’ll get bands to appear and the
results you want
can always add another row of lanes to
your figure that show a longer exposure time to verify that the protein was there
A well-annotated lab
notebook can resolve problems very quickly.
keep the raw data
Scan the film from your blot and save it on
your computer and on the lab server, and keep a copy on a USB drive or elsewhere
data were on a single USB drive that
had been lost
paste the film into your lab notebook
Label the film clearly and
annotate the date and conditions.
Do not lose it when you
move your lab
protect the lab notebook
could not substantiate the data
e-mail a scan of the uncut, labeled film to yourself and
the senior author to ensure the data are accessible
Label the data
multiple copies
print
them
clear records
If you are the senior author,
it is incumbent on you to verify all of the raw data yourself.
There is intense pressure to
produce, and to produce high-impact results.
doing
anything to please
you should be able to
verify every single piece of data in it and take responsibility
tools to be able to detect whether you have altered your figures in any way
Add Sticky Note
- These principles could be used in cooperation with authors to help them ensure accurate data records are preserved.
  posted by amiigo on 2009-03-28
I hope that the experiments themselves in our published papers have been
performed properly, but that is not something we can police.
Add Sticky Note
- The processes of peer review and reproduction of experimental results works together with careful examination and preservation of published material.
  posted by amiigo on 2009-03-28

Mike Chelen's Bookmarks

Data scraping with YQL and jQuery | kelvinluck.com

XML Path Language (XPath)

Creative Commons Attribution Noncommercial ShareAlike Legal Code

Science 2.0 – introduction and perspectives for Poland « Freelancing science

Science in the open » A breakthrough on data licensing for public science?

RNA world easier to make : Nature News

untitled - Twiddla.com

WSJ Staff Not Allowed To Mix "Business And Pleasure" On Twitter (NWS)

Edge of Space Found | LiveScience

Using the Google Plugin for Eclipse - Google App Engine - Google Code

Quick Start - Google Plugin for Eclipse - Google Code

Content Nation in Washington: Masters of Twittercraft Talk About Social Media's Impact on Politics and the Press [Content Nation ™]

BioscienceWorld

What Socrates Can Teach You About Social Media

Internal vs. External Cloud

Pulp Nonfiction

Setting up - Skulltag Wiki

skulltag [Archive] - Ubuntu Forums

Voluntary amputation and extra phantom limbs : Neurophilosophy

Journal of Clinical Investigation -- All data are not created equal

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