Tags: NanoBio Node

Tools (1-20 of 28)

  1. Accurate Chemical Master Equation (ACME)

    20 May 2013 | | Contributor(s):: Youfang Cao, Anna Terebus, John Feser, Nahil Sobh, Jie Liang

    Direct solution method of discrete Chemical Master Equation (dCME) for the steady state, the time evolution of full probability landscapes, and the first passage time distribution (FPTD) in biological networks.

  2. BioSensorLab

    14 Aug 2006 | | Contributor(s):: Pradeep R. Nair, Jonghyun Go, Graeme John Landells, Tejas Rajiv Pandit, Muhammad Alam, Xin Jin, Piyush Dak, Ankit Jain, Mohammad Ryyan Khan, Mohammad Ryyan Khan

    BioSensorLab is a tool to evaluate and predict the performance parameters of Biosensors.

  3. cadnano to PDB File Converter

    13 Nov 2013 | | Contributor(s):: Jejoong Yoo, AbderRahman N Sobh, Chen-Yu Li, Aleksei Aksimentiev

    Accepts CadNano files in the form of *.json and outputs a file in *.pdb which can be read by programs such as VMD.

  4. DBR Laser Simulator

    07 Sep 2012 | | Contributor(s):: Nikhil Sancheti, Lynford Goddard, Christopher Adam Edwards

    Describes properties of a GaAs/AlGaAs DBR laser

  5. Hydrodynamic Particle Trapping

    14 Jun 2013 | | Contributor(s):: Melikhan tanyerim@illinois.edu Tanyeri, John Feser, Nahil Sobh

    Simulates the motion of a nanoparticle in a hydrodynamic trap.

  6. LegoGen

    05 Feb 2016 | | Contributor(s):: Scott Michael Louis Slone, Chris Maffeo, AbderRahman N Sobh, Aleksei Aksimentiev

    Tool workflow for building DNA Brick structures automatically.

  7. Molecular Dynamics Showcase

    06 Jul 2013 | | Contributor(s):: Michael McLennan, Chen-Yu Li, john stone, Aleksei Aksimentiev, George A. Howlett

    View interesting features of a molecular dynamics trajectory file

  8. Molecular Dynamics Showcase Builder

    09 Nov 2015 | | Contributor(s):: Michael McLennan, Nicholas K Kisseberth, George A. Howlett, Jim Slopsema, Aleksei Aksimentiev, Chen-Yu Li

    Tool to create showcases for the Molecular Dynamics Showcase viewer.

  9. nanoDDSCAT

    23 Apr 2013 | | Contributor(s):: Prashant K Jain, Nahil Sobh, Jeremy Smith, AbderRahman N Sobh, Sarah White, Jacob Faucheaux, John Feser

    Calculate scattering and absorption of light by targets with arbitrary geometries and complex refractive index.

  10. nanoDDSCAT+

    13 Aug 2014 | | Contributor(s):: AbderRahman N Sobh, Sarah White, Jeremy Smith, Nahil Sobh, Prashant K Jain

    Combines the Discrete Dipole Scattering (DDSCAT) tool with the DDAConvert tool for a single workflow for custom shapes.

  11. Nanoindentation

    28 Oct 2013 | | Contributor(s):: Taha Goudarzi, AbderRahman N Sobh, Kathy Walsh, Nahil Sobh, Iwona Jasiuk

    Nanoindentation for Mechanical Characterization of Soft Materials

  12. Nisin Diffusion Tool

    08 Apr 2013 | | Contributor(s):: Andrew Blanchard, Ting Lu

    Simulate cell fluorescence based on nisin concentration

  13. Pattern Formation in Bacterial Populations

    03 May 2013 | | Contributor(s):: Ting Lu, John Feser, Nahil Sobh, Pratik Naik

    Synthetic biology tool for engineering patterning systems.

  14. Traction Force Microscopy

    17 Apr 2014 | | Contributor(s):: Bara Saadah, AbderRahman N Sobh, Alireza Tofangchi

    This is a tool for particle motion tracking with respect to physical forces.

  15. [Illiniois]: SynchUp

    16 Jul 2013 | | Contributor(s):: Bara Saadah, Nahil Sobh, AbderRahman N Sobh, Jessica S Johnson, NanoBio Node

    This tool computes synchronous updates of autoassociative networks.

  16. [Illinois] KohonenSOM

    09 Jul 2013 | | Contributor(s):: Bara Saadah, Nahil Sobh, Jessica S Johnson, NanoBio Node

    This tool implements the Kohonen self-organizing map (SOM) algorithm

  17. [Illinois]: AsynchUp

    16 Jul 2013 | | Contributor(s):: Bara Saadah, Nahil Sobh, AbderRahman N Sobh, NanoBio Node, Jessica S Johnson

    This tool computes asynchronous updates of autoassociative networks.

  18. [Illinois]: Avoidance Learn Simulation

    20 Jun 2013 | | Contributor(s):: AbderRahman N Sobh, NanoBio Node, Jessica S Johnson

    This script simulates avoidance conditioning as reinforcement learning with two upper motoneurons (SUMO and FUMO).

  19. [Illinois]: Avoidance Learn Simulation with 'Call' Neuron

    25 Jun 2013 | | Contributor(s):: AbderRahman N Sobh, NanoBio Node, Jessica S Johnson

    This script simulates avoidance learning as a reinforcement learning with two upper motoneurons (sumo and fumo) and one "call" neuron.

  20. [Illinois]: BUTDjointDistribution

    16 Jul 2013 | | Contributor(s):: Bara Saadah, Jessica S Johnson, NanoBio Node

    this tool simulates bottom-up/top-down processing in the visual system using the joint distribution