Tag: Engineering

ZiFiT 4.2 – Zinc Finger Engineering tool

ZiFiT 4.2

:: DESCRIPTION

The ZiFiT (Zinc Finger Targeter) software package is designed to aid research in the application of gene editing and expression technologies.ZiFiT identifies potential target sites in DNA sequences for several DNA binding platforms using publicly available reagents and protocols

::DEVELOPER

the Zinc Finger Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W462-8. doi: 10.1093/nar/gkq319. Epub 2010 Apr 30.
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool.
Sander JD1, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D.

Disulfide by Design 2.12 – Disulfide Engineering in Proteins

Disulfide by Design 2.12

:: DESCRIPTION

Disulfide by Design (DbD2) is a redesigned and enhanced version of original DbD application for the rational design of disulfide bonds in proteins. For a given protein structural model, all residue pairs are rapidly assessed for proximity and geometry consistent with disulfide formation, assuming the residues were mutated to cysteines.

::DEVELOPER

Dombkowski Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Craig DB, Dombkowski AA.
Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins.
BMC Bioinformatics. 2013 Dec 1;14:346. doi: 10.1186/1471-2105-14-346. PMID: 24289175; PMCID: PMC3898251.

ProFET 1.0 – Protein Feature Engineering Toolkit

ProFET 1.0

:: DESCRIPTION

ProFET: Protein Feature Engineering Toolkit for Machine Learning

::DEVELOPER

Dan Ofer , Michal Linial

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 ProFET

:: MORE INFORMATION

Citation

ProFET: Feature engineering captures high-level protein functions.
Ofer D, Linial M.
Bioinformatics. 2015 Jun 30. pii: btv345.

CellNet / CellNetR – Network Biology applied to Stem Cell Engineering

CellNet / CellNetR

:: DESCRIPTION

CellNet is a network biology-based computational platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations.

::DEVELOPER

Hu Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Max OS X
  • R

:: DOWNLOAD

 CellNetR

:: MORE INFORMATION

Citation:

CellNet: network biology applied to stem cell engineering.
Cahan P, Li H, Morris SA, Lummertz da Rocha E, Daley GQ, Collins JJ.
Cell. 2014 Aug 14;158(4):903-15. doi: 10.1016/j.cell.2014.07.020.

pyHIVE 1.0.8 – Health-related image visualization and engineering system using Python

pyHIVE 1.0.8

:: DESCRIPTION

pyHIVE was implemented as an image processing system, providing five widely used image feature engineering algorithms.

::DEVELOPER

Health Informatics Lab (HILab)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Python

:: DOWNLOAD

pyHIVE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2018 Nov 26;19(1):452. doi: 10.1186/s12859-018-2477-7.
pyHIVE, a health-related image visualization and engineering system using Python.
Zhang R, Zhao R, Zhao X, Wu D, Zheng W, Feng X, Zhou F.