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Koene R.A.,Halcyon Molecular
International Journal of Machine Consciousness | Year: 2012

Whole brain emulation aims to re-implement functions of a mind in another computational substrate with the precision needed to predict the natural development of active states in as much as the influence of random processes allows. Furthermore, brain emulation does not present a possible model of a function, but rather presents the actual implementation of that function, based on the details of the circuitry of a specific brain. We introduce a notation for the representations of mind state, mind transition functions and transition update functions, for which elements and their relations must be quantified in accordance with measurements in the biological substrate. To discover the limits of significance in terms of the temporal and spatial resolution of measurements, we point out the importance of brain region and task specific constraints, as well as the importance of in-vivo measurements. We summarize further problems that need to be addressed. © 2012 World Scientific Publishing Company. Source


Koene R.A.,Halcyon Molecular
International Journal of Machine Consciousness | Year: 2012

Whole brain emulation aims to re-implement functions of a mind in another computational substrate by carefully emulating the function of fundamental components, and by copying the connectivity between those components. The precision with which this is done must enable prediction of the natural development of active states. To accomplish this, in vivo measurements at large scale and high resolution are critically important. We propose a set of requirements for these empirical measurements. We then outline general methods leading to acquisition of a structural and functional connectome, and to the characterization of responses at large scale and high resolution. Finally, we describe two new project developments that tackle the problem of functional recording in vivo, namely the "molecular ticker-tape" and the integrated-circuit "Cyborcell". © 2012 World Scientific Publishing Company. Source


Patent
Halcyon Molecular | Date: 2011-02-10

A transmission electron microscope includes an electron beam source to generate an electron beam. Beam optics are provided to converge the electron beam. An aberration corrector corrects the electron beam for at least a spherical aberration. A specimen holder is provided to hold a specimen in the path of the electron beam. A detector is used to detect the electron beam transmitted through the specimen. The transmission electron microscope operates in a dark-field mode in which a zero beam of the electron beam is not detected. The microscope may also be capable of operating in an incoherent illumination mode.


Patent
Halcyon Molecular | Date: 2011-11-22

A scanning transmission electron microscope includes an electron beam source to generate an electron beam. Beam optics are provided to converge the electron beam to a probe, such as a longitudinally stretched probe. A stage is provided to hold a specimen in the path of the electron beam. The specimen comprises one or more polymers to be sequenced. A beam scanner scans the electron beam across the specimen. A controller may define one or more scanning areas corresponding to the locations of the polymers, and control one or more of the beam scanner and stage to selectively scan the electron beam probe in the scanning areas. The controller may also tune the beam optics during imaging. One or more detectors are provided to detect electrons transmitted through the specimen to generate an image for each of the scanning areas. The controller may also analyze the one or more images to sequence the polymers.


News Article | August 20, 2012
Site: gigaom.com

Halcyon Molecular, a much-talked about genetics startup that was started by Andregg Brothers – William and Michael in 2008 has quietly gone away. It is not clear if the company has shut down – the web site exists – but sources familiar with the Redwood City, Calif.-based company say that it ran out of money. Its investors included Peter Thiel’s Founder’s Fund and maverick investor/entrepreneur Elon Musk. In its life, the company had snagged upwards of $20 million in funding. I am awaiting comment from Founders Found and Musk. It is a bit of a bummer since I always root for such startups whose foundation is pure technology and whose ambition to change the future. In 2009, when Founders Fund partner Luke Nosek joined Halcyon, in an email he noted that the company would one day it would be able to “sequence 100 percent complete human genome in less than ten minutes for less that $100.” Earlier this year Oxford Nanopore team had beaten Halcyon to the punch. It was one of the companies that was working on low cost DNA sequencing technologies and it is one of the reasons why I kept tabs on the company. The company listing recently went missing on the Founders Found website. Here is an article from The Independent from last year that highlights company’s plans and ambitions – it is worth reading.

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