Tag: DSD

DSD 0.5 – Diffusion State Distance Calculation Program

DSD 0.5

:: DESCRIPTION

DSD is a diffusion state distance calculation program. It uses global topological properties of graphs through random walks to compute proximity in terms of node’s funcationality in graphs such as protein-protein interaction networks.

::DEVELOPER

Cowen Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 DSD

:: MORE INFORMATION

Citation:

Cao M, Zhang H, Park J, Daniels NM, Crovella ME, Cowen LJ, Hescott B. (2013)
Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks.
PLoS ONE 8(10): e76339. doi:10.1371/journal.pone.0076339 .

capDSD – Confidence, Augmented Pathway Diffusion State Distance

capDSD

:: DESCRIPTION

capDSD is an extension of DSD  that takes in to account a measure of interaction confidence while also incorporating directed pathway data.

::DEVELOPER

Cowen Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 capDSD

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jun 15;30(12):i219-i227. doi: 10.1093/bioinformatics/btu263.
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence.
Cao M, Pietras CM, Feng X, Doroschak KJ, Schaffner T, Park J, Zhang H, Cowen LJ, Hescott BJ.

DSD 20190308 – DNA Strand Displacement Simulator

DSD 20190308

:: DESCRIPTION

DSD is a new programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism.

::DEVELOPER

DSD team

:: SCREENSHOTS

dsd

:: REQUIREMENTS

:: DOWNLOAD

 DSD

:: MORE INFORMATION

Citation

Visual DSD: a design and analysis tool for DNA strand displacement systems.
Lakin MR, Youssef S, Polo F, Emmott S, Phillips A.
Bioinformatics. 2011 Nov 15;27(22):3211-3. doi: 10.1093/bioinformatics/btr543