LegoGen
05 Feb 2016 | Tools | Contributor(s): Scott Michael Louis Slone, Chris Maffeo, AbderRahman N Sobh, Aleksei Aksimentiev
Tool workflow for building DNA Brick structures automatically.
nanoDDSCAT+
13 Aug 2014 | Tools | 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.
Traction Force Microscopy
17 Apr 2014 | Tools | Contributor(s): Bara Saadah, AbderRahman N Sobh, Alireza Tofangchi
This is a tool for particle motion tracking with respect to physical forces.
cadnano to PDB File Converter
13 Nov 2013 | Tools | 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.
Nanoindentation
28 Oct 2013 | Tools | Contributor(s): Taha Goudarzi, AbderRahman N Sobh, Kathy Walsh, Nahil Sobh, Iwona Jasiuk
Nanoindentation for Mechanical Characterization of Soft Materials
Functionalization Workbench
30 Aug 2013 | Tools | Contributor(s): AbderRahman N Sobh, Chen-Yu Li, Nahil Sobh, Aleksei Aksimentiev
Using molecular dynamic simulation - explore the interactions between a molecular structure and substrate when they are linked together.
DDSCAT Convert: A Target Generation Tool
17 Jul 2013 | Tools | Contributor(s): John Feser, AbderRahman N Sobh
Convert .obj files to DDSCAT shape files
[Illinois]: AsynchUp
16 Jul 2013 | Tools | Contributor(s): Bara Saadah, Nahil Sobh, AbderRahman N Sobh, NanoBio Node, Jessica S Johnson
This tool computes asynchronous updates of autoassociative networks.
[Illiniois]: SynchUp
16 Jul 2013 | Tools | Contributor(s): Bara Saadah, Nahil Sobh, AbderRahman N Sobh, Jessica S Johnson, NanoBio Node
This tool computes synchronous updates of autoassociative networks.
[Illinois]: Predict Correct Set Up
15 Jul 2013 | Tools | 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
[Illinois]: Direction Selectivity
13 Jul 2013 | Tools | Contributor(s): Bara Saadah, Nahil Sobh, AbderRahman N Sobh, Jessica S Johnson, NanoBio Node
This tool implements a simple direction selective network.
[Illinois]: Temporal Difference, Iterative Dynamic Programming, and Least Mean Squares
11 Jul 2013 | Tools | Contributor(s): Bara Saadah, Nahil Sobh, AbderRahman N Sobh, Jessica S Johnson
This tool updates state values using the Temporal Difference Algorithm.
[Illinois]: Perturbative Reinforcement Learning to Develop Distributed Representations
10 Jul 2013 | Tools | Contributor(s): AbderRahman N Sobh, Jessica S Johnson, NanoBio Node
This tool trains three-layered networks of sigmoidal units to associate patterns.
[Illinois]: Perturbative Reinforcement Learning Using Directed Drift
This tool trains two-layered networks of sigmoidal units to associate patterns using a real-valued adaptation of the directed drift algorithm.
[Illinois]: Error Gradient Estimations Due to Parallel Perturbation of Weights
07 Jul 2013 | Tools | 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.
[Illinois]: Error Gradient Estimations Due to Perturbation of One Weight at a Time
29 Jun 2013 | Tools | 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.
[Illinois]: Avoidance Learn Simulation with 'Call' Neuron
25 Jun 2013 | Tools | 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.
[Illinois]: Avoidance Learn Simulation
20 Jun 2013 | Tools | 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).
nanoDDSCAT
23 Apr 2013 | Tools | 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.