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Hackathon

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Multi-omics studies are available here

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**Submitted challenge analyses, vignettes, and containers now available at https://github.com/BIRSBiointegration/Hackathon/blob/master/analysis-vignettes.md**

Welcome to our repository to prepare for our upcoming workshop *Mathematical Frameworks for Integrative Analysis of Emerging Biological Data Type* **June 14-19, 2020 in Banff, Canada**. More details about the workshop can be found in [here](https://www.birs.ca/events/2020/5-day-workshops/20w5197) from the BIRS event page.

Due to covid-19, the event will go *virtual*. We have two main aims for this meeting:

- **Hackathon analyses on our three case studies** to identify hurdles, limitations and methods development strategies to move forward in the field of multi omics single cell

- **Draft of a white paper about the challenges highlighted during the hackathon**, discuss pitfalls and guidelines to develop computational methods in this fast changing area.

A publication of the white paper sumarizing the outcomes of this meeting is available as [Le Cao et al, Genome Biology, 2021](https://doi.org/10.1186/s13059-021-02433-9). Please cite this manuscript for use of these summarized datasets provided in this repository.

*Secure the date (June 15-19), and accept the BIRS invitation online*. We are currently working on an agenda that will accommodate the different time zones, and still make it an engaging meeting where we can brainstorm together, initiate new collaborations and discuss  exciting avenues for further development.
The workshop will be divided into keynote speaker sessions, participants presentations, brainstorming and panel discussions on pitfalls and guidelines to develop computational methods in this fast changing area. A white paper will be written with all participants, and there are opportunities to also submit study-specific papers. Whilst we are unable to fund travel to Banff, BIRS waives the fee registrations, covers food and accommodation for 42 participants and speakers invited to the event.

# Organisers
- [Aedin Culhane](https://www.hsph.harvard.edu/aedin-culhane/) (Harvard TH Chan School of Public Health)
- [Elana Fertig](https://fertiglab.com/) (John Hopkins)
- [Kim-Anh Lê Cao](https://lecao-lab.science.unimelb.edu.au/) (University of Melbourne)

# Multi-omics studies
*We provide easy access to our three multi-omics studies at the following links*.

## Gastrulation scNMT-seq data 
Three omics and more on 826 matching single cells, see the [scNMT-seq folder](https://github.com/BIRSBiointegration/Hackathon/tree/master/scNMT-seq) which contains a README file and guidelines (including a list of challenges to tackle, plus more if you wish to help out).

## Cortex seq-FISH data
Two omics with ~1600 single cells each and 113 matched genes, see the [Data folder seqFISH](https://github.com/BIRSBiointegration/Hackathon/tree/master/seqFISH) that contains a README and challenges to address. Links to additional data are included, if you want to explore further.

## Single-cell proteomic data
Two targeted proteomic studies investigating the tumor-immune microenvironment in breast cancer patients using different technologies (mass cytometry and MIBI-TOF), see the [Data folder sc-targeted-proteomics](https://github.com/BIRSBiointegration/Hackathon/tree/master/sc-targeted-proteomics) which contains a README and more details on the data, with some questions to begin exploring.

# Communication
All communication will be via Slack. Join our channel at birsbiointegration.slack.com at this [link](https://join.slack.com/t/birsbiointegration/shared_invite/enQtODQxNzA5OTUzMzYzLTVmNDEzNDIyMTM2MDFmYzZlM2ViMGU0NWQzYjY2ODM4OGVlYjJiOGVmNWUzYmQxYTQ1Zjc1ZTE0YmEzNDYwYWI)

## Information Webinar

* Slides now available via [this link](https://docs.google.com/presentation/d/1tcJem9mgDHW0qP9iSWjWYScZrSsjXRRykqsiQ8eeAwA/edit#slide=id.g6b7ca50076_1_8).

* The recording available via [this link](https://vimeo.com/376936827).

## BIRS workshop

* The recordings are available via [this link](http://www.birs.ca/videos/2020)

# Timelines
- Studies start to be released from the week of 14th October 2019.
- Abstract due on March 9 2020 (more details to come on the format - we expect preliminary analyses to be presented) 
- Abstract selection announced March 16 2020 
- Reproducible analyses shared on our GitHub on **June 1st 2020**

Hackathon

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