_viash.yaml

viash_version: 0.9.0

name: task_predict_modality
organization: openproblems-bio
version: dev
license: MIT

label: Predict Modality
keywords: [multi-omics, regression, single-cell]
summary: Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression).
description: |
  Experimental techniques to measure multiple modalities within the same single cell are increasingly becoming available. 
  The demand for these measurements is driven by the promise to provide a deeper insight into the state of a cell. 
  Yet, the modalities are also intrinsically linked. We know that DNA must be accessible (ATAC data) to produce mRNA 
  (expression data), and mRNA in turn is used as a template to produce protein (protein abundance). These processes 
  are regulated often by the same molecules that they produce: for example, a protein may bind DNA to prevent the production 
  of more mRNA. Understanding these regulatory processes would be transformative for synthetic biology and drug target discovery. 
  Any method that can predict a modality from another must have accounted for these regulatory processes, but the demand for 
  multi-modal data shows that this is not trivial.
references:
  doi:
    # Multimodal single cell data integration challenge: results and lessons learned
    # Christopher Lance, Malte D. Luecken, Daniel B. Burkhardt, Robrecht Cannoodt, Pia Rautenstrauch, Anna Laddach, Aidyn Ubingazhibov, Zhi-Jie Cao, Kaiwen Deng, Sumeer Khan, Qiao Liu, Nikolay Russkikh, Gleb Ryazantsev, Uwe Ohler, NeurIPS 2021 Multimodal data integration competition participants, Angela Oliveira Pisco, Jonathan Bloom, Smita Krishnaswamy, Fabian J. Theis
    # bioRxiv 2022.04.11.487796; doi: https://doi.org/10.1101/2022.04.11.487796 
    - 10.1101/2022.04.11.487796
  bibtex:
    - |
      @inproceedings{luecken2021sandbox,
        title={A sandbox for prediction and integration of DNA, RNA, and proteins in single cells},
        author={Luecken, Malte D and Burkhardt, Daniel Bernard and Cannoodt, Robrecht and Lance, Christopher and Agrawal, Aditi and Aliee, Hananeh and Chen, Ann T and Deconinck, Louise and Detweiler, Angela M and Granados, Alejandro A and others},
        booktitle={Thirty-fifth conference on neural information processing systems datasets and benchmarks track (Round 2)},
        year={2021}
      }

authors:
  - name: Alejandro Granados
    roles: [ author ]
    info:
      github: agranado
  - name: Alex Tong
    roles: [ author ]
    info:
      github: atong01
  - name: Bastian Rieck
    roles: [ author ]
    info:
      github: Pseudomanifold
  - name: Christopher Lance
    roles: [ author ]
    info:
      github: xlancelottx
      orcid: "0000-0002-1275-9802"
  - name: Daniel Burkhardt
    roles: [ author ]
    info:
      github: dburkhardt
  - name: Kai Waldrant
    roles: [ contributor ]
    info: 
      github: KaiWaldrant
      orcid: "0009-0003-8555-1361"
  - name: Kaiwen Deng
    roles: [ contributor ]
    info:
      email: dengkw@umich.edu
      github: nonztalk
  - name: Louise Deconinck
    roles: [ author ]
    info:
      github: LouiseDck
  - name: Robrecht Cannoodt
    roles: [ author, maintainer ]
    info:
      github: rcannood
      orcid: "0000-0003-3641-729X"
  - name: Xueer Chen
    roles: [ contributor ]
    info:
      github: xuerchen
      email: xc2579@columbia.edu
  - name: Jiwei Liu
    roles: [ contributor ]
    info:
      github: daxiongshu
      email: jiweil@nvidia.com
      orcid: "0000-0002-8799-9763"

links:
  issue_tracker: https://github.com/openproblems-bio/task_predict_modality/issues
  repository: https://github.com/openproblems-bio/task_predict_modality
  docker_registry: ghcr.io

info:
  image: thumbnail.svg

  test_resources:
    - type: s3
      path: s3://openproblems-data/resources_test/common/openproblems_neurips2021
      dest: resources_test/common/openproblems_neurips2021
    - type: s3
      path: s3://openproblems-data/resources_test/task_predict_modality/
      dest: resources_test/task_predict_modality

repositories:
  - name: openproblems
    type: github
    repo: openproblems-bio/openproblems
    tag: build/main

config_mods: |
  .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }