Bio+MedVis Challenge @ IEEE VIS 2023

The Challenge

This year’s challenge will be based on a study recently published in Cancer Cell by the ProCan team (Gonçalves et al., 2022). The study aimed to generate a comprehensive pan-cancer proteomic map of human cell lines to aid in the discovery of cancer biomarkers and the development of new cancer treatments. The main challenge will be to create an integrated overview of cell-type / tissue-type / cancer-type distributions of both single proteins as well as protein categories. There will also be a re-design challenge connected to the improvement of the representation/interaction strategies used for one of the figures in the paper.

Biological Background and Data Description

The ProCan team used mass spectrometry-based proteomics to identify and quantify proteins in 949 human cell lines that represented 28 different tissue types and over 40 genetically and histologically diverse cancer types. These cell lines were treated with 625 anti-cancer drugs and over 17,000 CRISPR-Cas9 gene essentialities. The analysis resulted in a dataset of about 8,500 proteins that were quantified across the cell lines, and these data capture evidence of cell types and post-transcriptional modifications. Integrating multi-omics, drug response, and CRISPR-Cas9 gene essentiality screens with a deep learning-based pipeline revealed thousands of protein biomarkers of cancer vulnerabilities that were not significant at the transcript level. The power of the proteome to predict drug response was very similar to that of the transcriptome. Further, random downsampling to only 1,500 proteins had limited impact on predictive power, consistent with protein networks being highly connected and co-regulated. This proteomic dataset is a high-quality resource for mechanistic investigation of network organisation and regulatory principles of the proteome, as well as for translational discoveries.

The dataset and the exact description of the challenge tasks will be coming very soon. We are also planning an online Q&A session where you can ask questions directly to the ProCan team: this will be announced well in advance.

Program

The Bio+MedVis Challenge, jointly organized by the BioVis and VCBM communities, will be organized as a half-day event within the IEEE VIS 2023 conference. The program will consist of invited talks (we are happy to announce that Drew Berry already confirmed our invitation), presentations of accepted submissions, and other supplementary sessions. Details will follow soon.

Important dates

Submission

Submissions will be considered for talk and/or poster presentations. You will be requested to submit a two-page PDF abstract with unlimited additional figures and a draft of your proposed poster (max 10MB) to the PCS. The deadlines will be announced soon. Last year, the acceptance rate for presentations happened to be 89%, yet such acceptance rate is not guaranteed. Selected submissions will be invited for talk presentations during the Bio+MedVis Challenge session within the IEEE VIS 2023 conference.

Questions?

Please feel free to ask questions on our Slack channel if you need more information and details about the data or tasks:
biovis2016.slack.com » #biovis-challenge2023

Otherwise, feel free to contact us at: biovis_challenge@ieeevis.org

The chairs of the Bio+MedVis Challenge @ IEEE VIS 2023

Barbora Kozlikova, Masaryk University, Czech Republic
Daniel Jönsson, Linköping University, Sweden
Renata Raidou, TU Wien, Austria
Sean O’Donoghue, Garvan Institute of Medical Research, Sydney