Week 3: Calling all researchers! The fight against COVID-19, armed with open science
Claire-Alix Zapata Garin
Research is continuing to move quickly on the COVID-19 frontlines and we’re here again to bring you the latest developments and resources from the past week. Lifebit’s curated COVID-19 resources are intended to keep our readers, clients, and partners up-to-date on the latest developments so that together we can all contribute our time and knowledge to combat this global crisis.
Don’t forget to check out our first and second instalments of curated COVID-19 resources!
The COVID-19 Portal, set up by EMBL-EBI, brings together relevant datasets which have been submitted to EMBL-EBI and other major biomedical centres. The overall goal is to facilitate the rapid collection and sharing of available data from different sources, and making them accessible to the research community to leap forward coronavirus research. The portal consists of two components:
- SARS-CoV-2 Data Hubs: to organise the flow of SARS-CoV-2 outbreak sequence data and provide open data sharing for global research communities, and
- COVID-19 Portal: to bring together relevant COVID-19 datasets and tools, host sequence data sharing and to facilitate access to other SARS-CoV-2 resources.
If interested, your organisation can get involved in this large-scale SARS-CoV-2 data and tool collection by getting in touch with EMBL-EBI here (firstname.lastname@example.org).
The 2019 Novel Coronavirus Resource (2019nCoVR) curated by the China National Centre for Bioinformation (CNCB) features comprehensive integration of genomic and proteomic sequences, in addition to metadata from GISAID, NCBI, NMDC and CNCB/NGDC. At the time of writing, the resource contains 4,388 SARS-CoV-2 sequences submitted by laboratories throughout the world.
Besides making SARS-CoV-2 sequencing data publicly available, the 2019nCoVR resource provides great visualisation functionalities for genome variation analysis results based on all collected 2019-nCoV strains.
COVID-19 Research Communities & Challenges
A crowd-sourced repository of information, workflows, protocols and other resources for research laboratories intending to jump on the SARS-CoV-2 sequencing bandwagon. This collection is maintained and curated by Duncan MacCannel from the Office of Advanced Molecular Detection (AMD) at the Centres for Disease Control and Prevention (CDC).
hackseq is a peer-led hackathon, where individuals propose projects and the organisers help recruit teams of interdisciplinary scientists and developers to turn an original idea into reality.
The current focus of the hackseq ultra-hackathon is on high-risk, high-reward research projects on SARS-CoV-2. By bringing together world-class RNA biologists, bioinformaticians, statisticians and computer scientists the goal for this ultra-hackathon is to develop cutting-edge software, pioneer RNA analysis pipelines, and build digital infrastructure to fight the COVID-19 pandemic.
Dates: 72h ultra-hackathon from May 22nd – 24th
Let’s keep the conversation going – please share with us any COVID-19 resources that you have found valuable. We will continue to update our readers and followers regularly. We are in this together!