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Thursday, December 29, 2011

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Sunday, November 20, 2011

B Fwd: PLoS Computational Biology Volume 7(11) November 2011

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From: "PLoS Computational Biology" <news@lists.plos.org>
Date: Nov 19, 2011 6:27 PM
Subject: PLoS Computational Biology Volume 7(11) November 2011
To: <technologiclee@gmail.com>

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PLoS Computational Biology
Volume 7(11) November 2011

View Table of Contents on web site



Perspective

PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011
Pedro Madrigal, Noa Sela, Simon M. Lin

Review

The What and Where of Adding Channel Noise to the Hodgkin-Huxley Equations
Joshua H. Goldwyn, Eric Shea-Brown

Research Articles

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
Chao Cheng, Koon-Kiu Yan, Woochang Hwang, Jiang Qian, Nitin Bhardwaj, Joel Rozowsky, Zhi John Lu, Wei Niu, Pedro Alves, Masaomi Kato, Michael Snyder, Mark Gerstein

Robust Signal Processing in Living Cells
Ralf Steuer, Steffen Waldherr, Victor Sourjik, Markus Kollmann

Significance of Input Correlations in Striatal Function
Man Yi Yim, Ad Aertsen, Arvind Kumar

Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits
Rutger Hermsen, David W. Erickson, Terence Hwa

Virus Replication Strategies and the Critical CTL Numbers Required for the Control of Infection
Andrew J. Yates, Minus Van Baalen, Rustom Antia

Gene Expression Divergence is Coupled to Evolution of DNA Structure in Coding Regions
Zhiming Dai, Xianhua Dai

Optimizing Experimental Design for Comparing Models of Brain Function
Jean Daunizeau, Kerstin Preuschoff, Karl Friston, Klaas Stephan

Sparse Gamma Rhythms Arising through Clustering in Adapting Neuronal Networks
Zachary P. Kilpatrick, Bard Ermentrout

Collective Animal Behavior from Bayesian Estimation and Probability Matching
Alfonso Pérez-Escudero, Gonzalo G. de Polavieja

Genome Majority Vote Improves Gene Predictions
Michael E. Wall, Sindhu Raghavan, Judith D. Cohn, John Dunbar

Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study
Zhuo Song, Yang Cao, David C. Samuels

Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping
Avraham Ben-Shimon, Masha Y. Niv

Phosphorylation of the Arp2 Subunit Relieves Auto-inhibitory Interactions for Arp2/3 Complex Activation
Arjun Narayanan, Lawrence L. LeClaire III, Diane L. Barber, Matthew P. Jacobson

Identification of Biochemical Network Modules Based on Shortest Retroactive Distances
Gautham Vivek Sridharan, Soha Hassoun, Kyongbum Lee

Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation
Joshua Lequieu, Anirikh Chakrabarti, Satyaprakash Nayak, Jeffrey D. Varner

Stochastic Delay Accelerates Signaling in Gene Networks
Krešimir Josić, José Manuel López, William Ott, LieJune Shiau, Matthew R. Bennett

Representational Switching by Dynamical Reorganization of Attractor Structure in a Network Model of the Prefrontal Cortex
Yuichi Katori, Kazuhiro Sakamoto, Naohiro Saito, Jun Tanji, Hajime Mushiake, Kazuyuki Aihara

Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia
Assieh Saadatpour, Rui-Sheng Wang, Aijun Liao, Xin Liu, Thomas P. Loughran, István Albert, Réka Albert

A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules
Alexandra Jilkine, Sigurd B. Angenent, Lani F. Wu, Steven J. Altschuler

Reversible and Noisy Progression towards a Commitment Point Enables Adaptable and Reliable Cellular Decision-Making
Anna Kuchina, Lorena Espinar, Jordi Garcia-Ojalvo, Gürol M. Süel

Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons
Lars Buesing, Johannes Bill, Bernhard Nessler, Wolfgang Maass

Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health
Melissa J. Morine, Audrey C. Tierney, Ben van Ommen, Hannelore Daniel, Sinead Toomey, Ingrid M. F. Gjelstad, Isobel C. Gormley, Pablo Pérez-Martinez, Christian A. Drevon, Jose López-Miranda, Helen M. Roche

How Landscape Heterogeneity Frames Optimal Diffusivity in Searching Processes
E. P. Raposo, F. Bartumeus, M. G. E. da Luz, P. J. Ribeiro-Neto, T. A. Souza, G. M. Viswanathan

High Degree of Heterogeneity in Alzheimer's Disease Progression Patterns
Natalia L. Komarova, Craig J. Thalhauser

Learning the Optimal Control of Coordinated Eye and Head Movements
Sohrab Saeb, Cornelius Weber, Jochen Triesch

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing
Paul M. Magwene, John H. Willis, John K. Kelly

Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy
Seyed Yahya Anvar, Allan Tucker, Veronica Vinciotti, Andrea Venema, Gert-Jan B. van Ommen, Silvere M. van der Maarel, Vered Raz, Peter A. C. 't Hoen

Stability Properties of Underdominance in Finite Subdivided Populations
Philipp M. Altrock, Arne Traulsen, Floyd A. Reed

Trade-Offs and Constraints in Allosteric Sensing
Bruno M.C. Martins, Peter S. Swain


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Wednesday, May 4, 2011

Removable ‘cloak’ for nanoparticles helps them target tumors | KurzweilAI

Removable ‘cloak’ for nanoparticles helps them target tumors | KurzweilAI

AIR for AppUp - What you need to know

AIR for AppUp - What you need to know

Waterbear is Like Scratch, but for JavaScript

Waterbear is Like Scratch, but for JavaScript

"Waterbear is a Scratch-like visual programming language for JavaScript. It was created by Dethe Elza, who gave a presentation on the project today at JSConf in Portland, OR. Waterbear brings the concepts of kid-friendly, educational programming languages, such as Logo and Scratch, to the modern, browser-oriented computer. Users can create programs by snapping together blocks.

Unlike Scratch, you can view the code generated by Waterbear."

Tuesday, May 3, 2011

Dodge leading human resistance to robocars | Brad Ideas

Dodge leading human resistance to robocars | Brad Ideas

Gabedit : A graphical user interface to computational chemistry packages

Gabedit : A graphical user interface to computational chemistry packages

Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess and Q-Chem

It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.

Major features

  • Gabedit can Creates input file for GAMESS(US), GAUSSIAN, MOLCAS, MOLPRO , MPQC, OpenMopac, Orca, PCGamess and Q-Chem.
  • Gabedit can graphically display a variety of Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess, Q-Chem and (partially) ADF calculation results, including the following
    • Molecular orbitals.
    • Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties.
    • Surfaces may be displayed in solid, translucent and wire mesh modes. they are can be colorcoded by a separate property.
    • Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes and the principal axes of the molecule.
    • Animation of the normal modes corresponding to vibrational frequencies.
    • Animation of the rotation of geometry, surfaces, contours, planes colorcoded, xyz and the principal axes of the molecule.
    • Animation of contours, Animation of planes colorcoded.
  • Gabedit can display UV-Vis, IR and Raman computed spectra.
  • Gabedit can generate a povray file for geometry (including hydrogen's bond),surfaces (including colorcoded surfaces), contours, planes colorcoded.
  • Gabedit can save picture in BMP, JPEG, PNG, PPM and PS format.
  • Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, planes colorcoded).
  • Simulated Annealing with Molecular Dynamics is implemented in Gabedit (using Amber 99 molecular mechanics parameters).

Fibre-laser system

Fibre-laser system

Fibre-based picosecond lasers, which replace solid-state, free-beam laser set-ups – the result of the PULSAR (PUlsed Laser System with Adaptive Pulse PaRameters) research project – fulfil these requirements.

The system is adaptable to different settings, not least because the laser oscillator and amplifier are separate. Also, depending on the material and the process requirements, the repetition frequency and average output are easy to change – making rapid optimisation feasible.

In this system, a laser diode with a wavelength of 1,03µm and a pulse length of 40ps serves as the pulse source. Pulse repetition rate is flexible between 50kHz and 40Mhz. Using a three-step amplifier, the pulse can be amplified from several 10µW to an average output of 14W – meaning that, at a repetition rate of 1MHz, pulse energy is 14µJ.

Meanwhile, the fibre system shows good beam quality, and is resistant to production problems, such as dust contamination, temperature fluctuation and vibration. It is also smaller and less expensive than conventional solid-state lasers.

UCSC Genome Bioinformatics: FAQ

UCSC Genome Bioinformatics: FAQ

Scientists create stable, self-renewing neural stem cells

Scientists create stable, self-renewing neural stem cells

Nano Terra licenses nanotech, ex-Surface Logix platform - Mass High Tech Business News

Nano Terra licenses nanotech, ex-Surface Logix platform - Mass High Tech Business News

Wednesday, February 9, 2011

B Nanonets give rust a boost as agent in water splitting's hydrogen harvest

Nanonets give rust a boost as agent in water splitting's hydrogen harvest
Nanonets give rust a boost as agent in water splitting's hydrogen harvest


B Microsponges from seaweed may save lives

B Glass melts near absolute zero

B World's First Programmable Nanoprocessor: Nanowire Tiles Can Perform Arithmetic and Logical Functions

World's first programmable nanoprocessor: Nanowire tiles can perform arithmetic and logical functions
World's First Programmable Nanoprocessor: Nanowire Tiles Can Perform Arithmetic and Logical Functions


Saturday, January 8, 2011

B Android blogtv broadcast

Hi, Blogtv is a great site. Do you know if a broadcast can be made from a HTC EVO running Android 2.2? The message says that I need a webcam. The Evo has front and back cameras and works with things like Skype. I did Google this question, but only found another person with the same question.

Also, when I use the 'friend' button the menu hides behind the other panels. This would probably be a quick fix.

Thanks,
Lee Nelson
Technologiclee