We will help run a scopeathon (January 16-17, 2020). This event focuses on planning and designing software to extract value from organismal and genera-level graph genomes by dynamically labeling with metadata. We’re seeking people who are interested in describing community level genomes as graphs, or solving problems involving complex phenotypic interactions with specific genomes. If this describes you, please apply! We also encourage people who will be in San Diego for the International Plant & Animal Genome XXVIII conference to apply. The event is open to anyone selected and willing to travel to San Diego. We will work with data from the following organism groups:
- Viruses
- Microbes (Bacteria and Archaea)
- Human
- Plants (corn/wheat, others)
- Animals
Logistics
The event runs from 9 am – 5 pm each day, with optional social events in the evening. We will form working groups of five or six individuals, with various backgrounds and expertise, into five to eight teams with an experienced leader. These teams will scope and design pipelines to explore the potential of graph genomes. Teams will work with existing data types and create specifications for new data types as needed. We will work with traditional metadata and indexed data such as protein domains relevant to genome subregions.
There is no registration fee for this event.
Note: Participants must bring their own laptop to this program. No financial support for travel, lodging, or meals is available for this event.
Organization
After a brief organizational session, teams will spend two days addressing a challenging set of scientific problems related to a group of datasets. Participants will plan how to analyze and combine datasets in order to work on these problems. Throughout the two days, we will come together to discuss progress on each of the topics, bioinformatics best practices, software architecture, etc.
Datasets
We will use metadata from public repositories, such as the NCBI BioSample, dbSNP and ClinVar, as well as other phenotype databases Image stacks and phenotype data may also be available from a variety of labs.
Products
We will make all pipelines, other scripts, plans and architecture generated in this event available on a dedicated public GitHub repository.
Each team may submit manuscripts describing the design and use of the software tools they created to an appropriate journal such as the F1000Research hackathons channel, BMC Bioinformatics, GigaScience, Genome Research, or PLoS Computational Biology.
Application
Please fill out the application form. Applications are due December 21, 2019 by 3 pm ET. We will select participants based on their experience and their motivation to attend.
We encourage prior participants and prior applicants to apply. International applicants or those with particular skillsets may be accepted early. If this affects your travel considerations, please note on the form and contact Ben Busby. If you confirm, please make sure that you can attend. Confirming and not attending prevents other scientists from attending this event.
Please contact Ben Busby for more information.