Description

The nanoBIO Node at Illinois is a resource for understanding and designing nanoBIO devices and systems. This NSF funded activity is a collaboration between the University of Illinois at Urbana-Champaign and the University of California at Merced. The node provides simulation building blocks and educational resources for use in nanoBIO device engineering.

Tools (1-20 of 30)

1. LegoGen

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

   Tool workflow for building DNA Brick structures automatically.

2. Molecular Dynamics Showcase Builder

   Tools | 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.

3. Traction Force Microscopy

   Tools | 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.

4. nanoDDSCAT+

   Tools | 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.

5. Nanoindentation

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

   Nanoindentation for Mechanical Characterization of Soft Materials

6. nanoDDSCAT

   Tools | 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.

7. cadnano to PDB File Converter

   Tools | 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.

8. Molecular Dynamics Showcase

   Tools | 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

9. [Illinois]: Error Gradient Estimations Due to Parallel Perturbation of Weights

   Tools | 07 Jul 2013 | Contributor(s):: AbderRahman N Sobh, Jessica S Johnson, NanoBio Node

   This tool trains two-layered networks of sigmoidal units to associate patterns using simultaneous perturbation of weights.

10. [Illinois]: Perturbative Reinforcement Learning to Develop Distributed Representations

    Tools | 10 Jul 2013 | Contributor(s):: AbderRahman N Sobh, Jessica S Johnson, NanoBio Node

    This tool trains three-layered networks of sigmoidal units to associate patterns.

11. [Illinois]: Perturbative Reinforcement Learning Using Directed Drift

    Tools | 10 Jul 2013 | Contributor(s):: AbderRahman N Sobh, Jessica S Johnson, NanoBio Node

    This tool trains two-layered networks of sigmoidal units to associate patterns using a real-valued adaptation of the directed drift algorithm.

12. [Illinois]: Temporal Difference, Iterative Dynamic Programming, and Least Mean Squares

    Tools | 11 Jul 2013 | Contributor(s):: Bara Saadah, Nahil Sobh, AbderRahman N Sobh, Jessica S Johnson

    This tool updates state values using the Temporal Difference Algorithm.

13. [Illinois]: Direction Selectivity

    Tools | 13 Jul 2013 | Contributor(s):: Bara Saadah, Nahil Sobh, AbderRahman N Sobh, Jessica S Johnson, NanoBio Node

    This tool implements a simple direction selective network.

14. [Illinois]: Predict Correct Set Up

    Tools | 15 Jul 2013 | Contributor(s):: Bara Saadah, Nahil Sobh, AbderRahman N Sobh, Jessica S Johnson, NanoBio Node

    This tool sets up a predictor-corrector model of target tracking

15. [Illiniois]: SynchUp

    Tools | 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]: AsynchUp

    Tools | 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.

17. [Illinois] KohonenSOM

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

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

18. [Illinois]: BUTDprobInference

    Tools | 17 Jul 2013 | Contributor(s):: Bara Saadah, Jessica S Johnson, NanoBio Node

    This tool stimulates bottom-up/top-down processing in the visual system using probabilistic inference.

19. [Illinois]: BUTDjointDistribution

    Tools | 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

20. [Illinois]: Error Gradient Estimations Due to Perturbation of One Weight at a Time

    Tools | 29 Jun 2013 | Contributor(s):: AbderRahman N Sobh, Jessica S Johnson, NanoBio Node

    This tool trains two-layered networks of sigmoidal units to associate patterns using perturbation of one weight at a time.