Author: i2d

02.06.2023 London, 9:30 am to 4:30 pm (UK time)

A Student Workshop at Royal College of Art 2023

Since the era of our cave-drawing ancestors, humans have possessed innate cognitive faculties that are naturally engaged by diagrams. Diagrams notably play a key role in conveying information in biology. Such diagrams can be found, e.g., in every good handbook for biology.

The need for standardizing the representation of biological diagrams became apparent in the 2000’s with the advent of computational systems biology – that focused on building, exchanging and analysing large and complex diagrams representing the molecular events occurring in whole biological systems. Therefore, a community composed of biochemists, modellers, and computer scientists developed, the Systems Biology Graphical Notation (SBGN), a set of standard visual languages designed for the representation of biochemical  networks in a consistent and clear manner. But although this standard is now around for a few years, continuously new challenges are coming up which need to be tackled – therefore, the standard and the way it is communicated is continuously evolving.

In 2022, we kicked-off the DESIGN X BIOINFORMATICS initiative with a one day workshop. One of the presentations introduced already the idea of standardization in systems biology.

Therefore, we decided to provide this year on June 2 2023 a workshop introducing and discussing SBGN. During the workshop, you will learn the basics of network biology, get an introduction to SBGN, and you will be introduced to a tool which can be used to draw corresponding maps. Two SBGN developers will be present at the workshop.

During the design activity, the workshop will explore together with you different ideas how to improve network biology representations and visualizations. We will come up with three different briefs and you will work in groups to tackle the challenges.

Moreover, we will announce a student competition based on this design activity during the workshop which will run until 18th June!

http://desxbioinf.i2d.uk/

09.09.2022 London/Paris/Fukuoka, 1-5 pm (UK time)

With this initiative, we are intending to bring together Bioinformaticians from various fields, and designers, design researchers, as well as medical and scientific illustrators to discuss future challenges in the context of Bioinformatics and Design. Being an area which often combines abstract and spatial data, and often taking standardisation approaches into account, Bioinformatics provides a number of opportunities for future designers. In addition, we want to contextualise Design X Bioinformatics towards the newly emerging field of BioDesign, which uses the biological affordances of organisms to address some user needs, e.g. in terms of material development, applications of synthetic biology, or the creation of bio-digital hybrid systems.

http://desxbioinf.i2d.uk/

This workshop will take place hybrid: at London and Paris, in-person events will be planned!

Bioinformatics is an area which is applying computer science-related approaches to biological data analysis. It is widely known for providing genomics-based analytical approaches which were supporting, e.g., the 1000 Genomes Project. But it also relates to many other fields, such as analysis of microscopic images (e.g. organelle location), molecular modelling (e.g. proteins, biological membranes), or biological network visualisation (e.g. protein-protein interaction networks, metabolism).

Design is a highly interdisciplinary field integrating aspects, such as aesthetic, economic, functional, philosophical and/or socio-political considerations, and is usually driven by context. Whereas visualisation plays a crucial role in Bioinformatics, reflected by a number of conferences and workshops in this field, design in particular is not so well investigated in bioinformatics-related research contexts.

We are excited to present two papers at the DRS 2022 (Design Research Society Conference) in Bilbao, Spain! The papers are already published, the links are shown below!

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June 28, 2022

Immersive Exploration of Cell Localization Scenarios Using VR, Spatialized Video Communication, and Integrative Bioinformatics

Bjorn Sommer, Ayn Sayuti, Chang Hee Lee, Zidong Lin, Jenny Hu & Ashley Hall

Integrating spatially localized molecular networks into virtual cell environments is an approach which is only provided by a very small number of tools. As this task requires the combination of a set of Biotechnology/Bioinformatics-related information sources, it can be seen as an appropriate example for Integrative Bioinformatics research. Here, we want to show new immersive perspectives for cytological pathway integration by combining recent explorative technologies with the software CELLmicrocosmos 4 PathwayIntegration. A mesoscopic-localized metabolic pathway—i.e. the citrate cycle and the glycolysis—is localized based on database entries onto an abstract cell environment of Arabidopsis thaliana. The created cell model is used in three different contexts providing different degrees of immersion:

1. Web-based 2D exploration of 3D Scenarios (using Gather.town),
2. Exploration and Annotation in a VR Design Application (using Gravity Sketch), and
3. Large-Scale VR Visualization and Navigation (using the CAVE2 and zSpace).

All these examples promise to be very useful in the context of Integrative Bioinformatics-related education as well as communication.

https://doi.org/10.1007/978-981-16-6795-4_14

Stereoscopic Display & Application 2022, January 20, 2022

At the Stereoscopic Display & Application 2022 conference at the Electronic Imaging symposium, we will present on January 20, 2022, our new work “Towards an immersive virtual studio for innovation design engineering”.

http://www.stereoscopic.org/2022/index.html

Towards an immersive virtual studio for 
innovation design engineering, 
Bjorn Sommer, Ayn Sayuti, Zidong Lin, Shefali Bohra, 
Emre Kayganaci, Caroline Yan Zheng, Chang Hee Lee, 
Ashley Hall1, and Paul Anderson; 
Royal College of Art, 
Universiti Teknologi MARA (UiTM), and 
Korea Advanced Institute of Science and Technology

It started as a hobby photography project during the COVID pandemic 2020 and somehow ended up with an Android app and a paper presented at the Stereoscopic Displays and Applications XXXII conference!

More …

Hybrid Stereoscopic Photography – Analogue Stereo 
Photography meets the Digital Age with the 
StereoCompass app
B Sommer
Electronic Imaging, Stereoscopic Displays and 
Applications XXXII, pp. 58-1-58-10(10); 
Society for Imaging Science and Technology
https://doi.org/10.2352/ISSN.2470-1173.2021.2.SDA-058
2021

For the 4th time, the MolVA 2021 – Workshop on Molecular Graphics and Visual Analysis of Molecular Data is taking place in the context of the EuroVis 2021. The workshop will run from 8:00 am to 11:40 UK time and will virtually take place this year in Zurich, Switzerland.

The whole program can be found here!

The participation in the whole prestigious EuroVis2021 conference will be this year for free! If you would like to join for some of the talks, please register here.