My computer often experiences trouble and I could hardly find someone to fix it for me, especially when it happens during the wee hours of the morning. My friend told me about Computer Assistance O...
I was one of the lucky few who was given access to a dump of "social" statistics for PLoS One (my term). The data were given to us to analyze as we please, to glean from them what we may (I don't really know who all the others were).
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
least radical idea you can find in modern Science 2.0 world
virtual research environment
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.
participation in online communities
important part of Science 2.0 is the fact that it has human face
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
access to real-time scientific conversation
follow current research and decide what is important to learn
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
good definition of openness acts as a standard that ensures different open datasets are ‘interoperable’
Licensing is important because it reduces uncertainty. Without a license you don’t know where you, as a user, stand: when are you allowed to use this data? Are you allowed to give to others? To distribute your own changes, etc?
licensing and definitions are important even though they are only a small part of the overall picture
If we get them wrong they will keep on getting in the way of everything else.
My opinion is that there should be no requirements, including attribution, and that standards should be community-based instead of legal.
Even if a basic license is used it can be argued that any ‘requirements’ for attribution or share-alike should not be in a license but in ‘community norms’.
Licenses and community norms are not exclusive. It's recommended to adopt a Public Domain license, and encourage attribution through community standards.
A license is likely to elicit at least as much, and almost certainly more, conformity with its provisions than community norms.
Why bother about openness and licensing for data? After all they don't matter in themselves: what we really care about are things like the progress of human knowledge or the freedom to understand and share.
Processing (BETA) library to communicate with MySQL (or any other SQL) databases.
note that due to java security restrictions this will not work with applets "out of the box"
and that many remote mysql-servers will only allow local access ("localhost")
or connections from trusted hosts. (see notes. )
also note that you should have some experience with SQL to put, change
and retrieve data from the database.