{"id":20425034,"url":"https://github.com/databio/bdshack2023","last_synced_at":"2026-04-20T07:04:53.835Z","repository":{"id":235699885,"uuid":"629195524","full_name":"databio/bdshack2023","owner":"databio","description":null,"archived":false,"fork":false,"pushed_at":"2023-04-18T19:37:26.000Z","size":30132,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-09-11T10:46:57.321Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/databio.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2023-04-17T20:30:16.000Z","updated_at":"2023-04-18T14:56:24.000Z","dependencies_parsed_at":"2024-04-24T09:39:29.986Z","dependency_job_id":null,"html_url":"https://github.com/databio/bdshack2023","commit_stats":null,"previous_names":["databio/bdshack2023"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/databio/bdshack2023","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbdshack2023","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbdshack2023/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbdshack2023/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbdshack2023/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/bdshack2023/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2Fbdshack2023/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32036803,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-20T00:18:06.643Z","status":"online","status_checked_at":"2026-04-20T02:00:06.527Z","response_time":94,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-15T07:12:03.875Z","updated_at":"2026-04-20T07:04:53.797Z","avatar_url":"https://github.com/databio.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 2023 SBDS Hackathon\n## Overview\nWelcome, to the 2023 Systems Biology and Data Science (SBDS) Hackathon. This is a 48-hour hackathon working to tackle open problems in single-cell analysis. The goal of this competition is to predict how DNA, RNA, and protein measurements co-vary in single cells as bone marrow stem cells develop into more mature blood cells. You will develop a model trained on a subset of 300,000-cell time course dataset of CD34+ hematopoietic stem and progenitor cells (HSPC) from four human donors at five time points generated for this competition by Cellarity, a cell-centric drug creation company. \n\n## The challenge\nThere are two main challenges for this hackathon. Both challenges must be achieved through machine learning and data science approaches. First, you must train a model that can utilize chromatin accessibility data to predict gene expression data _from the same cell_. More speficially, you must convert each row of a scATAC-seq dataset into a corresponding row of a scRNA-seq dataset. The second challenge is to convert gene expression data into protein level data. Specifically, you must convert each row of a scRNA-seq dataset into a correspodning row of a CITE-seq dataset (Fig. 1).\n\n\u003cimg src=\"assets/fig1.png\" alt=\"Two primary challenges for the SBDS 2023 hackathon.\" /\u003e\n\nAs mentioned, these tasks must be solved through machine learning and data science approaches. Anything is fair game including libraries, packages, or even previously built models to solve these challenges!\n\n## The data\nThe data for this competition lives inside `/data`. There are three main datatypes you will be working with:\n1. Chromatin accessibility (scATAC-seq)\n2. Gene expression (scRNA-seq)\n3. Protein levels (CITE-seq)\n\nThese three datasets were obtained from single-cell multiomics data collected from mobilized peripheral CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from four healthy human donors. This data was collected repeatedly over the course of many days (Fig. 2)\n\n\u003cimg src=\"assets/fig2.png\" alt=\"Collection workflow of the competition dataset\" /\u003e\n\nEach task mentioned [above](#the-challenge) works with two of the three datatypes. Task one works with scATAC-seq (input) + scRNA-seq (output), while task two works with scRNA-seq (input)  + scCITE-seq (output). As such, the tasks can be conceptualized as such:\n\n**Task 1:** Train a model with `train_multi_inputs.h5` (scATAC-seq) as input and `train_multi_targets.h5` (scRNA-seq) as output. Test your model with `test_multi_inputs.h5`.  \n**Task 2:** Train a model with `train_cite_inputs.h5` (scRNA-seq) as input and `train_cite_targets.h5` (scCITE-seq) as output. Test your model with `test_cite_targets.h5`.\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fbdshack2023","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Fbdshack2023","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Fbdshack2023/lists"}