Hi Bryan,
please see below,
Bryan Bishop wrote:
Hey all,
I am new to the list, but I really should have known about this group
years ago. I am running a semantic web project oriented that is best
summarized as apt-get for physical automation. Today, while writing
some perl to steal the humancortex data from the Allen Institute, I
stumbled upon the AJAX + SPARQL + RDF + Google Maps API + Ruby on rails
implementation that is mentioned in some slides/PDFs. Unfortunately,
the hcls1 server on CSAIL at MIT seems to be dead -- I'd be willing to
take over some of that code. I think it was here:
http://hcls1.csail.mit.edu:8890/map/[EMAIL PROTECTED],[EMAIL PROTECTED]
And the PDF was: http://tinyurl.com/ysqm3z
Anyway, the basis of "SKDB", or the metadata for physical automation:
http://heybryan.org/exp.html
http://heybryan.org/new_exp.html
http://oscomak.net/
I am very happy to see gateways like:
http://hcls.deri.ie/hcls_demo.html
'The following queries access a SPARQL endpoint hosted at DERI. The
underlying triplestore contains over 325 million RDF triples of
biomedical information. The information covers a large array of
biomedical knowledge: from basic molecular biology over literature
annotation up to anatomy and physiology.'
Which I suspect is an integration of OBO Foundry, SBML, and other
related projects.
we are build a related system (this prototype integrates the entire
obo-foundry candidate ontologies, GOA files, swissprot, ncbi taxonomy, ...):
http://www.semantic-systems-biology.com/biogateway/querying
the system (BioGateway) is still a prototype, we are working on some
more improvements before the official release, however, you can already
try out some queries and get "interesting" results. (Actually, any
feedback is very welcome...)
and indeed there are no plug-n-play components yet at least developed
within academia. However, industry
(http://www.io-informatics.com/products/index.html) seems to be
interested also in this issue. In the case of IO- Informatics, they
propose a very interesting notion of an intelligent multidimensional
object (IMO,
http://www.io-informatics.com/news/pdfs/ABL_Vol24_No7_24-26(2006).pdf).
Erick
I've noticed, however, that the major drawback of the
majority of these semantic querying interfaces is that there's no
plug-and-play functionality that I have found yet -- I hope I am
completely wrong here -- but it's too bad that these databases have
their tables and their data structures completely hidden instead of
floating around as code. It's one of the reasons that I am a user of
YAML and object serialization.
http://yaml.org/
"YAML: YAML Ain't Markup Language / What It Is: YAML is a human friendly
data serialization standard for all programming languages."
And the python implementation details (PyYAML):
http://pyyaml.org/
I mention this for two strong reasons. First, has anyone seen PyLab? I
regret that I keep mentioning python, just because it might show bias,
but I actually do a significant amount of work not in python, so it's
really just because I was going through the majority of known
scientific number crunching packages:
http://heybryan.org/num.html like Axiom, derive, macsyma, maple,
mathematica, MATLAB, mupad, reduce, R, octave, sage, numpy, scipy, PDL,
sympy, and next up on my list is CAD/CAM packages, which I suspect will
have significant cross over with the CFD packages out there.
Anyway, PyLab:
http://scipy.org/PyLab
"SciPy (pronounced "Sigh Pie") is open-source software for mathematics,
science, and engineering. It is also the name of a very popular
conference on scientific programming with Python. The SciPy library
depends on NumPy, which provides convenient and fast N-dimensional
array manipulation. The SciPy library is built to work with NumPy
arrays, and provides many user-friendly and efficient numerical
routines such as routines for numerical integration and optimization.
Together, they run on all popular operating systems, are quick to
install, and are free of charge. NumPy and SciPy are easy to use, but
powerful enough to be depended upon by some of the world's leading
scientists and engineers. If you need to manipulate numbers on a
computer and display or publish the results, give SciPy a try!"
And PyLab is the "total lab integration" mostly on the software side.
But still, as I mentioned, I'm interested in extracting functionality
out of the web (put it to work for you) instead of static information
just sitting there. Somehow I ended up finding out about EXPO:
http://expo.sf.net/
"EXPO defines over 200 concepts for creating semantic markup about
scientific experiments, using the Web Ontology Language OWL.
We propose the ontology EXPO to formalise generic knowledge about
scientific experimental design, methodology, and results
representation. Such a common ontology is both feasible and desirable
because all the sciences follow the same experimental principles. The
formal description of experiments for efficient analysis, annotation,
and sharing of results is a fundamental objective of science."
An interesting example is "The Robot Scientist":
http://www.aber.ac.uk/compsci/Research/bio/robotsci/
"The Robot Scientist is perhaps the first physical implementation of the
task of Scientific Discovery in a microbiology laboratory. It
represents the merging of increasingly automated and remotely
controllable laboratory equipment and knowledge discovery techniques.
Automation of laboratory equipment (the "Robot" of Robot Scientist) has
revolutionised laboratory practice by removing the "drudgery" of
constructing many wet lab experiments by hand, allowing an increase in
both the scope and scale of potential experiments. Most lab robots only
require a simple description of the various chemical/ biological
entities to be used in the experiments, along with their required
volumes and where these entities are stored. Automation has also given
rise to significantly increased productivity and a concomitant increase
in the production of results and data requiring interpretation, giving
rise to an "interpretation bottleneck" where the process of
understanding the results is lagging behind the production of results."
So, how are these robots and automation machinery made? Usually in CAD
programs. Admittedly the open source solutions to CAD have been known
to be, not the best, but the point is still the same -- designers build
and generate information, which is then implemented into physical
machinery. Those designs are packages and could be made accessible in
an automatic manner. At the same time, the machines that this
information is being fed into are already automated. So the cybernetic
loop, as it were, is nearly complete. It's just that the focus on
static information tends to ignore the instrumentation and automation
hardware that brought that information in the first place -- the
programming and such.
So that's how apt-get is interesting (besides being awesome):
http://en.wikipedia.org/wiki/Debian
http://debian.org/
"Debian (pronounced [ˈdɛbiən]) is a computer operating system (OS)
composed entirely of software which is both free and open source
(FOSS). Its primary form, Debian GNU/Linux, is a popular and
influential Linux distribution.[1] It is a multipurpose OS; it can be
used as a desktop or server operating system.
Debian is known for strict adherence to the Unix and free software
philosophies.[2] Debian is also known for its abundance of options —
the current release includes over twenty-six thousand software packages
for eleven computer architectures. These architectures range from the
Intel/AMD 32-bit/64-bit architectures commonly found in personal
computers to the ARM architecture commonly found in embedded systems
and the IBM eServer zSeries mainframes.[3] Throughout Debian's
lifetime, other distributions have taken it as a basis to develop their
own, including: Ubuntu, MEPIS, Dreamlinux, Damn Small Linux, Xandros,
Knoppix, Linspire, sidux, Kanotix, and LinEx among others.[4] A
university's study concluded that Debian's 283 million source code
lines would cost US$10 billion to develop by proprietary means.[5]"
"Prominent features of Debian are its APT package management system, its
strict policies regarding its packages and the quality of its releases.
[6] These practices afford easy upgrades between releases and easy
automated installation and removal of packages. Debian uses an open
development and testing process. It is developed by volunteers from
around the world and supported by donations through SPI, a non-profit
umbrella organization for various free software projects.[7]"
In particular, apt-get allows users to retrieve packages by unique
identifiers, with automatic installation and configuration to the local
environment. This involves a significant amount of metadata and lots of
overhead for actually transmitting the packages, which has been known
to redline the Cisco root nodes for weeks when debian releases major
updates. Heh. They are considering (or are they already implementing?)
debtorrents and debtags to help bring that down to something less
destructive.
SKDB/OSCOMAK is a pet project of mine and a handful of other programmers
and machine shop enthusiasts interested in making sure when gEDA and
OpenCores happens everywhere else, the same infrastructure can be
deployed, in a functionally useful manner -- like Gershenfeld's group
over at the MIT Media Lab, the 'FabLab' projects. Basically they are
quantified shop configurations (much like linux installations) for the
physical floor space, with downloadable tools that would be implemented
with whatever tools the system has wired up (obviously some things
can't make other things). Behind all of this would be a design compiler
which works just like a regular compiler except for the resolution of
dependencies between metadata describing projects that are to be
implemented, whether by hand or by machine.
I'm studying manufacturing engineering down at the University of Texas
at Austin, also some computational neuroscience. But I've realized that
the bootstrapping requirements to make all of this happen are difficult
to the extent that even NIST had some troubles with their Virtual
Manufacturing projects, to the extent that it would require significant
funding and a "leap of faith" from others -- which might be somewhat
unreasonable. So I've been putting most of the work in a specific
implementation in biology, I put together the do-it-yourself
biotechnology kit < http://heybryan.org/new_exp.html and
http://biohack.sf.net/ and http://heybryan.org/biotech.git >. Genes are
already highly unitized across the semantic web, and could be made to
do interesting things, see http://partsregistry.org among others in
synthetic biology. With some buddies I've been detailing the design
strategies required to make a 'writozyme', a biologically replicable
system that would allow individuals to very simply synthesize DNA
without conventional DNA synthesizers like
http://bioinformatics.org/pogo/ which admittedly already works, but the
writozyme methodology would (hopefully) inherit the self-replication
functionality. The metadata aspects are just the same as in OBO, SBML,
the bioinformatics databases, and so on. And even more importantly it's
all 'functional' in that it's not "biobricks" that are being sent
across the web, but instead the tools, machinery, and semantic snowball
backing it all up and potentially turning into this recursive data
acquisition process. Bacteria don't just sit there (unless you did your
plate wrong, ugh).
Some other interesting guys who are working with me on this:
http://diybio.org/
http://openwetware.org/
http://biopunk.org/
and a few others that I am forgetting.
I hope I have the right mailing list for talking about these topics :-).
The project that led me to the Allen Institute, and then to Science
Commons, and now to W3C's HCLSIG group, was my attention to attention:
http://heybryan.org/mediawiki/index.php/Sustained_attention
Specifically because of Henry Markram's combined work on computational
neuroscience (microcolumn simulations of the brain in ~2005) and also,
surprisingly, on autism:
http://heybryan.org/intense_world_syndrome.html
"Autism is a devastating neurodevelopmental disorder with a polygenetic
predisposition that seems to be triggered by multiple envi ronmental
factors during embryonic and/or early postnatal life. While significant
advances have been made in identifying the neuronal structures and
cells affected, a unifying theory that could explain the manifold
autistic symptoms has still not emerged. Based on recent synaptic,
cellular, molecular, microcircuit, and behavioral results obtained with
the valproic acid (VPA) rat model of autism, we propose here a unifying
hypothesis where the core pathology of the autistic brain is
hyper-reactivity and hyper-plasticity of local neuronal circuits. Such
excessive neuronal processing in circumscribed circuits is suggested to
lead to hyper-perception, hyper-attention, and hyper-memory, which may
lie at the heart of most autistic symptoms. In this view, the autistic
spectrum are disorders of hyper-functionality, which turns
debilitating, as opposed to disorders of hypo-functionality, as is
often assumed. We discuss how excessive neuronal processing may render
the world painfully intense when the neocortex is affected and even
aversive when the amygdala is affected, leading to social and
environmental withdrawal. Excessive neuronal learning is also
hypothesized to rapidly lock down the individual into a small
repertoire of secure behavioral routines that are obsessively repeated.
We further discuss the key autistic neuropathologies and several of the
main theories of autism and re-interpret them in the light of the
hypothesized Intense World Syndrome."
When combined with the humancortex datasets from the Allen Institute,
things start to get very interesting :-). Throw in some metadata
packaging dynamics, like from SKDB or apt-get, suddenly you're
programming simulations of neural slices (as we've done for many years
now) -- or the actual physical tissue plates -- and you're able to
engineer brains. Sort of :-).
http://heybryan.org/buildingbrains.html
http://heybryan.org/recursion.html
'At least' you're able to do some interesting science + neurofeedback,
one of my intentions.
So, that's the direction that I'm coming from. It looks like I
completely missed Science Commons when it showed up on the map, and I
deeply regret this. Are there any other initiatives that I should be
made aware of? I'm also approaching all of this from the aerospace
angle: http://heybryan.org/2008-05-09.html It's an email I sent to some
presenters at ISDC2008 (since I couldn't attend), the National Space
Society, OpenVirgle ( http://google.com/virgle (humor is healthy)), and
even some Google Lunar X Prize teams, like Interplanetary Ventures, and
Team FREDNET, the open source team.
Cheers,
- Bryan
________________________________________
http://heybryan.org/
--
==================================================================
Erick Antezana http://www.cellcycleontology.org
PhD student
Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
[EMAIL PROTECTED] http://www.psb.ugent.be/~erant
==================================================================
