semeiotica » yeast

Organelle View 2: the cell cycle

gharp — Tue, 20 May 2008 05:48:10 +0000

Yeast Cell Cycle

Here is a new visualization of the cell cycle using a combination of Virtual Reality Markup Language (VRML), Flash, and database-driven graphics. This new version from Chris Landau and Jamie Cope’s nformation design demonstrates the yeast cell cycle in 3D cycle stages along with educational information about the process.

Try zooming in and see changes in the nucleus as the cycle progresses.

Yeast Cell Nucleus During Metaphase

This project started as a collaboration at the University of Michigan with Anuj Kumar’s lab in the Life Sciences Institute and first led to the OrganelleView project.

Organelle View published in Nucleic Acids Research

admin — Sun, 11 Mar 2007 04:26:00 +0000

The collaborative work of graduate student Gabriel Harp and Chris Landau (MFA ’06) on the Organelle View project was published in the January issue of Nucleic Acids Research.

“The project makes a gigantic leap in the distribution of biological data–moving it beyond the conventional representations of names and numbers to embrace the visual and organismal aspects of cellular and molecular forms”, says Harp.

“Organelle View is a scientific visualization application allowing users to dynamically generate a visual interpretation of data from Organelle DB. Organelle View presents a searchable interface with a three-dimensional representation of an archetypical cell. Rather than representing organelles and subcellular structures by text, Organelle View offers an artist’s rendering of a cell and its major organelles. At present, we have chosen a budding yeast cell (S.cerevisiae) as the model for Organelle View, largely because protein localization has been studied quite extensively in yeast; future versions of Organelle View will incorporate additional cell types from other organisms.”

(Wiwatwattana, N., Landau, C.M., Cope, G.J., Harp, G.A., & Kumar, A. (2007). Organelle DB: an updated resource of eukaryotic protein localization and function. Nucleic Acids Research, 35, D810-D814.)

full text via PubMed

plans for the social construction of living systems

admin — Sun, 11 Feb 2007 16:22:00 +0000

Organelle View

admin — Sat, 13 Jan 2007 18:28:00 +0000

Organelle View is a collaborative project aimed at developing the role of visual media (versus verbal) in the exploration of bioinformatic semantic networks. In cooperation with the Kumar lab and in my role as creative director and project manager, I led the team through the proof-of-concept stages of development with a successful grant application and navigation through the complex task of translation among scientific, IT, and artistic goals. In this instance, A virtual reality model dynamically linked to a bioinformatic database and designed to increase the use of rich media in collaborative learning. Developed with support from GROCS, the University of Michigan Office of the Provost, IBM, and Apple Computer, Organelle View allows users to learn about organelles and protein localization in a yeast model cell.

As a result of the Organelle View project, team members Chris Landau and Jamie Cope went on to form N Formation Design. The project is now being taken further in affiliation with the Kumar Lab. An animated version demonstrating the cell cycle in in the works.

organelleview.lsi.umich.edu