SCINet Working Groups
The SCINet initiative contributes funding to various working groups that use SCINet computational resources for research. The funding is generally used to convene in-person group workshops. There are also two working groups that develop SCINet learning/training materials.
The current working groups are:
- Ag100Pest Initiative (subgroup of AGR)
- Arthropod Genomics Research (AGR) Working Group
- Geospatial Research Working Group
- Microbiome Working Group
- SCINet-Longterm Agroecosystem Research (LTAR) Phenology Working Group
- SCINet Website Developers
- Workbook Developers
Ag100Pest Initiative (subgroup of AGR)
The Ag100Pest Initiative’s goal is to produce annotated, reference quality genome assemblies for the top 100 US arthropod agricultural pests by leveraging ARS’s unique expertise in both arthropod pest management and agricultural genomics research. We are pushing the limits of current technology to produce long-read sequencing data from individual specimens, despite the challenges of small body sizes, and sometimes large genomes, presented by arthropods. Arthropod pests of US field crops, livestock, bees, trees, and stored products as well as foreign pest species considered potential invasive threats to US agriculture are being considered.
Ag100Pest teams are developing best practices in many arenas from process and data management to extraction, sequencing, assembly, and annotation that will benefit the entire genomics community. As an example, we collaborated in the development of an open-source functional annotation workflow specifically tailored to arthropods, which users can find installed on Ceres or available through CyVerse, Docker, and GitHub.
This initiative enhances the agency’s contribution to two international genome sequencing projects – i5K (the 5000 insect genomes initiative) and the Earth BioGenome Project (to sequence the genomes of all of the world’s 1.5 million animals and plants).
Executive Coordination Team
Anna Childers, Project Lead
Brian Scheffler, Technical Lead
Kevin Hackett, National Program Leader
Core Leadership Group
Brad Coates, Technology Transfer Team Lead
Scott Geib, Extraction/Pre-Sequencing Team Lead
Brian Scheffler, Sequencing Team Co-Lead
Tim Smith, Sequencing Team Co-Lead
Anna Childers, Assembly and Analysis Team Lead
Monica Poelchau, Post-Assembly Team Co-Lead
Chris Childers, Post-Assembly Team Co-Lead
Kevin Hackett, National Program Leader
Please contact a member of the Executive Coordination Team for more information.
Arthropod Genomics Research (AGR) Working Group
The AGR working group focuses on outreach within USDA-ARS aimed at enhancing the genomic analyse knowledge and skill sets of members and collaborators. This is delivered through monthly teleconferences and webinars by internal and external scientists focused on genome assembly, gene and protein expression, population genomics, and reverse genetic (RNAi and CRISPR) approaches. The AGR was initiated following two organizational meetings in 2014 (AGR Workshop I) and 2016 (AGR Workshop II), at which participants communicated needs and devised solutions for challenging analytical pipelines. The AGR facilitates internal and external collaborations by merging those with complementary knowledge, skills, and capabilities within a given research area. Collaborations among AGR members have also resulted in two published papers reviewing ARS arthropod genomics research1 and developing RNAi and CRISPR technologies2. Work within the AGR includes the Ag100Pest Initiative, which aims to provide reference quality genome sequence assemblies for arthropod pests of U.S. agricultural commodities.
The AGR is open to anyone within ARS, and those interested in joining can contact Brad Coates.
Coates BS, Poelchau M, Childers C, Evans JD, Handler A, Guerrero F, Skoda S, Hopper K, Wintermantel WM, Ling KS, Hunter WB, Oppert B, Perez de Leon AA, Hackett K, Shoemaker D. 2015. Arthropod genomics research in the United States Department of Agriculture-Agricultural Research Service: Current impacts and future prospects. Trends in Entomology 11:1-27. (opens pdf in this browser window)
Gundersen-Rindal D, Adrianos S, Allen M, Becnel JJ, Chen YP, Choi MY, Estep A, Evans JD, Garczynski S, Geib SM, Ghosh SKB, Handler AM, Hasegawa DK, Heerman M, Jull J, Hunter W, Kaur N, Li J, Li W, Ling KS, Nayduch D, Oppert B, Perera OP, Perkin L, Sanscrainte N, Sim S, Sparks M, Temeyer K, Vander Meer R, Wintermantel WM, James R, Hackett K, Coates BS. 2017. Arthropod genomics research in the United States Department of Agriculture-Agricultural Research Service: Applications of RNA interference and gene editing in pest control. Trends in Entomology 13: 109-137. (opens pdf in this browser window)
Geospatial Research Working Group
This working group was formed as the result of a September 2019 SCINet-funded workshop hosted by Deb Peters, the acting ARS Chief Science Information Officer. The focus of the group is to provide continued input on the development of SCINet, to determine the computational needs of ARS geospatial researchers, and to develop collaborative research projects. The group will also learn from each other on topics related to high-performance computing. For example, how to use Ceres (the ARS high-performance computer), optimizing code for parallel processing, getting software onto Ceres, etc. Monthly working group teleconference calls and working sessions are beginning soon. If you would like to join the group, please contact Kerrie Geil to be added to the group’s Basecamp.
Microbiome Working Group
information coming soon, contact Adam Rivers
SCINet-Longterm Agroecosystem Research (LTAR) Phenology Working Group
information coming soon, contact Dawn Browning
SCINet Website Developers
SCINet website development, led by Adam Rivers, started in 2019 to create this centralized website for the SCINet Scientific Computing Initiative. The developers are a small team of ARS scientists who manage/solicit content and respond to site feedback with input from the Scientific Advisory Committee (SAC; see FAQ’s: What is the Scientific Advisory Committee?). The SCINet website developers are currently working to expand site content, especially science tutorials, user guides, and news. If you would like to contribute to SCINet website development, contact Adam Rivers.
information coming soon, contact Andrew Severin