From ae5aca59db183d40d9652bef34d0fd4c39cea72a Mon Sep 17 00:00:00 2001 From: Jose Nimo Date: Sun, 7 Jun 2026 18:46:18 +0200 Subject: [PATCH 1/3] ADDED: vienna-hack details --- .../events/2026_09_singlecellproteomics.md | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 content/events/2026_09_singlecellproteomics.md diff --git a/content/events/2026_09_singlecellproteomics.md b/content/events/2026_09_singlecellproteomics.md new file mode 100644 index 0000000..edf425c --- /dev/null +++ b/content/events/2026_09_singlecellproteomics.md @@ -0,0 +1,38 @@ ++++ +title = "Scverse Hackathon 2026-09 Vienna" +date = 2026-03-30T00:00:05+01:00 +description = "scverse x single-cell proteomics hackathon" +draft = false ++++ + +## Welcome + +Join us for the joint [scverse](https://scverse.org) x single-cell proteomics hackathon on **September 4-5, 2026** at the Vienna Biocenter in Vienna. + +This hackathon aims to bring together users and developers of scverse tools with mass spectrometry-based single-cell proteomics (SCP) researchers. The main topic of this hackathon will center on the specialized preprocessing and downstream analysis workflows unique to SCP data. + +During this hackathon, we will tackle core computational challenges, settle on robust data formats, and establish best practices for handling low-input MS signals. You will have the opportunity to directly improve existing tools, build missing pieces of the ecosystem, and optimize scverse packages for single-cell proteomics data. All contributions will be made publicly available on GitHub under an open-source license. + +## Hackathon Main Tasks + +### Task 1: Curation of Datasets + +Task Lead: Florian Mutschler + +Identifying, collecting, and preparing MS-based single-cell proteomics datasets to start a community-curated resource for testing analysis strategies and benchmarking methods such as imputation or normalization. Establishing AnnData format from the scverse ecosystem as the main object for benchmarking and analysis. + +### Task 2: Data QC and Preprocessing + +Task lead: Jose Nimo + +Identifying best practices for analyzing different types of MS-based single-cell proteomics datasets. Including: QC metrics, imputation strategies, normalization approaches, and methods for handling biological and technical confounders such as cell cycle, cell size, and batch effects. We aim to prototype methods in a service-styled package, to deal with these problems. + +### Task 3: Downstream analysis + +Task lead: Anna Sophie Welter + +Come together, think and benchmark different challenges during downstream analysis. How to perform feature selection? How can we use proteomics for cell type annotation? + +## Registration + +Please fill out the following [Luma form](https://luma.com/pwzuldwr) From 2f1d9c1facf51722ea01776b3bb434c68da8e988 Mon Sep 17 00:00:00 2001 From: Jose Nimo Date: Sun, 7 Jun 2026 18:50:04 +0200 Subject: [PATCH 2/3] FIX: datetime of event --- content/events/2026_09_singlecellproteomics.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/content/events/2026_09_singlecellproteomics.md b/content/events/2026_09_singlecellproteomics.md index edf425c..754c253 100644 --- a/content/events/2026_09_singlecellproteomics.md +++ b/content/events/2026_09_singlecellproteomics.md @@ -1,7 +1,8 @@ +++ title = "Scverse Hackathon 2026-09 Vienna" -date = 2026-03-30T00:00:05+01:00 +date = 2026-09-04T00:00:05+01:00 description = "scverse x single-cell proteomics hackathon" +link = "https://scverse.org/sc-proteomics2026/" draft = false +++ From 750217c6bd8138569443760440948ae83f0dc793 Mon Sep 17 00:00:00 2001 From: Jose Nimo Date: Sun, 7 Jun 2026 18:52:40 +0200 Subject: [PATCH 3/3] FIX: title --- content/events/2026_09_singlecellproteomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/events/2026_09_singlecellproteomics.md b/content/events/2026_09_singlecellproteomics.md index 754c253..e08a7a8 100644 --- a/content/events/2026_09_singlecellproteomics.md +++ b/content/events/2026_09_singlecellproteomics.md @@ -1,5 +1,5 @@ +++ -title = "Scverse Hackathon 2026-09 Vienna" +title = "Scverse x sc-Proteomics Hackathon 2026-09 Vienna" date = 2026-09-04T00:00:05+01:00 description = "scverse x single-cell proteomics hackathon" link = "https://scverse.org/sc-proteomics2026/"