Michelle Kuttel

 

Software

 

We have developed a suite of software prototypes for representation, building and investigation of carbohydrate structures, listed below.

CarbBuilder

JCC cover image

CarbBuilder is software for building 3D molecular structures of carbohydrates. CarbBuilder enables researchers to build a complex 3D carbohydrate model from a textual primary structure specification. CarbBuilder supports building with a wide range of monosaccharide and other residues.

This application was developed using C# under .Net framework. It can be run from Windows, and, using the mono framework, MacOS and Linux.

LATEST version: Download CarbBuilder v2.1.25 (~792KB) [29 July 2018 - S and NS substituents added]

Previous version:Download CarbBuilder v2.1.24 (~789KB) [31 May 2018]

Previous version: Download CarbBuilder v2.1.23 (~769KB) [27 Mar 2018]

Previous version: Download CarbBuilder v2.1.20 (~769KB) [19 Aug 2017]

Previous version: Download CarbBuilder v2.1.19 (~765KB) [1 Aug 2017]

Previous version: Download CarbBuilder v2.1.18 (~765KB) [15 Jun 2017]

Previous version: Download CarbBuilder v2.1.17 (~750KB) [17 Feb 2017]

Previous version: Download CarbBuilder v2.1.16 (~750KB) [24 Jan 2017]

Previous version: Download CarbBuilder v2.1.15 (~700KB) [16 Jan 2017]

Previous version: Download CarbBuilder v2.1.14 (~700KB) [14 Sept. 2016]

Previous version: < Download CarbBuilder v2.1.13 (~700KB) [13 Sept. 2016]

Installing and running CarbBuilder

The residues currently supported by CarbBuilder for building polysaccharide structures are listed here.

If you use CarbBuilder, please reference:

CarbBuilder: Software for Building Molecular Models of Complex Oligo- and Polysaccharide Structures. M. M. Kuttel, Jonas Stahle, and Goran Widmalm, J. Comput. Chem., J. Comput. Chem., 37(22), 2098-2105 (2016), DOI: 10.1002/jcc.24428.

CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation Michelle Kuttel, Yue Mao, Goran Widmalm and Magnus Lundborg Proceedings of 7th IEEE International Conference on e-Science , 5-8 December 2011, Stockholm, Sweden, pages: 395-402 pdf (406 KB)

 

Glycano

Glycano sample strucutre

Representation of Human Bllod A antigen

Human Blood A Antigen

Glycano is a web-application for creating graphical representations of polysaccharide sequences: the simple ‘nodes-and-edges’ molecular graphs typically used to convey the structure of complex, branched glycans in research publications. Glycano enables users to rapidly build, edit, annotate, load and export molecular graphs that represent the key features of polysaccharide structure. Glycano allows the user to toggle between two symbols sets for representing the monosaccharide ’nodes’: the widely adopted Essentials of Glycobiology symbol nomenclature and our new symbol set, which conveys residue connectivity information spatially and has broad coverage of bacterial sugar residues (ketones, linear alditols etc.). Glycano is designed to have an intuitive interface which minimises mouse-clicks for rapid structure building.

The website is implemented in Javascript, with all major browsers supported.

SweetTouch

SweetTouch image

SweetTouch an Open Source Android application for the 3D visualisation of molecules in general and the identification of carbohydrate rings. It combines a 3D/2D represnetation and was developed as a 2014 UCT CS 4th year (Honours) project by Wesley Robinson and Mordechai Serraf. SweetTouch is still a prototype, which is available for download from the Google play store.

Other software projects are:

Alfred

Alfred: thecurriculum planner

Alfred, the UCT curriculum Planner is a graphical planner for UCT courses designed by myself and developed/improved by M.Sc. student Adrianna Pinska. You can use this tool to get a general idea of the structure of a UCT B.Sc. degree.

StoryMaker and StoryGame

Comparison of effectiveness of two mobile application designs for encouraging children to read,.

Erin Versveld, James Foster

Summer Undergraduate Research Experience (SURE) project: 2013-2014, in collaboration with the Nal’ibali national reading-for-enjoyment campaign.

Last updated: April 2016