Contents
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Intro to SCINet
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SCINet Website Update
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Workshops & Training
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User Stories
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Opportunities
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Useful Links
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SCINet Working Group Update
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Tech Update
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Contribute / Contact
Intro to SCINet
SCINet is an ARS-wide initiative designed to provide high-level computational resources to improve the ability of ARS scientists and staff to fulfill the ARS mission and enhance the impact of ARS science.
SCINet provides ARS and formal collaborators access to:
- a community of researchers on Basecamp (access provided with your SCINet account)
- workshops, training, and communities of practice/working groups
- parallel computational environment with IT and user support
- community nodes
- high memory nodes (GPUs) for image processing
- high-use community software maintained by the system
- ability to upload individual software to project directory
- helpful user guides and tutorials on the SCINet Website
- cloud computing resources
- emerging technologies and shared software not typically available to individuals or research units
How to get started
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Simply request a SCINet account (eAuthentication required) to get started. Upon approval, you will receive instructions for logging into SCINet and accessing Basecamp.
Checkout the new SCINet website for more info on how SCINet can enable your research.
Read the SCINet FAQs covering general info, accounts/login, software, storage, data transfer, support/policy/O&M, parallel computing, and technical issues.
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SCINet Website Update
 A new SCINet website is under development that will be the home base for all things SCINet!
The site will consolidate SCINet information from Basecamp and multiple websites and will include news, user guides and support information, science tutorials, workshop/training summaries and materials, use cases, technical specs, contact info, and much more.
Browse the new website frequently to check out progress and new user resources. Please send feedback to SCINet@usda.gov.
Workshops & Training
WHAT'S NEW? SCINet-funded self-led or SCINet-led
workshops or training due Feb 1, 2020
The SCINet initiative is currently accepting two types of requests from ARS scientists and staff:
1) proposals for SCINet-funded workshops or training led by the applicant(s)
2) suggestions for workshops/training that you would like to see SCINet conduct.
Proposals for self-led SCINet-funded workshops/training:
Successful proposals must state how the workshop/training will promote the goals of SCINet, including:
- improving high performance computing or big data analytical capabilities of ARS scientists;
- increasing use of SCINet resources (e.g., Ceres, cloud computing) by ARS scientists or disciplines not currently part of SCINet; and
- improving access to ARS data.
Click here for more information and to submit an application. Applications must be received by February 1, 2020 for full consideration.
Proposals for SCINet-led workshops/training:
Click here to make suggestions for workshops/training that you see a need for and that SCINet would need to lead.
FY19 workshops & training summaries
Four SCINet-funded events were held in FY 2019. Follow the links below for event summaries, workshop/training materials, and contact information:
User Stories
Antigenic and genetic evolution of contemporary swine H1 influenza viruses in the United States
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The continued genetic and antigenic evolution of contemporary H1 viruses has resulted in vaccines with reduced efficacy, and the observed genetic and antigenic diversity represents a challenge to public health initiatives that attempt to minimize swine-to-human IAV transmission.
Check out how ARS scientist Daniela Rajao and collaborators used SCINet/Ceres to help characterize the genetic and antigenic evolution of contemporary swine viruses in this SCINet website news post by Tavis Anderson.
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Do you use SCINet for your research?
Email your user story and published research to SCINet@usda.gov for a chance to be featured in the newsletter!
Opportunities
WHAT'S NEW? SCINet-funded postdocs
We have unique opportunities available for postdocs to gain experience working on big data problems in agriculture while learning new skills, such as machine learning, data mining, and conducting research in a high performance computing environment. These 2-year SCINet-funded positions will be based at various ARS locations across the US under the direction of ARS scientists. Each position will be administered by the Department of Energy's Oak Ridge Institute for Science and Education (ORISE).
Please see the links for more specific information on this year's open positions.
Useful Links
High-performance computing
- The Bioinformatics Workbook created by the SCINet Virtual Research Support Core at Iowa State University has guides and tutorials extending well beyond the genomics and bioinformatics communities. Researchers of all backgrounds can use the workbook for UNIX command line basics, HPC info, project management tips, and data visualization tutorials. For bioinformatics researchers there is also information on experimental design, genome assembly and annotation, RNA sequencing, variant discovery, and more.
Data management
Do you have useful links that you'd like to share?
Email them to SCINet@usda.gov to be included on the SCINet website and in future newsletters.
SCINet Working Group Update
SCINet currently supports the following working groups:
- AG100Pest Genome WG
- Arthropod Genomic Research WG
- Geospatial Research WG
- Microbiome WG
- SCINet Website Developers
- Workbook Developers: Bioinformatics and Geospatial
Visit the working group's page on the SCINet website to learn more.
Host a workshop to start your own SCINet Working Group by submitting an FY20 SCINet Workshops & Training Application.
Tech Update
Ceres is an ARS-owned high-performance computing (HPC) cluster connected to SCINet and located in Ames, IA. The original cluster build included 72 regular compute nodes (65 available compute nodes, 2 data transfer nodes, a login node, and service nodes), 5 high memory nodes, and a two Petabyte file system for a range of scientific applications. During 2018, the cluster was enlarged by 20 regular, 5 high memory, and 1 GPU “priority” nodes, all funded by individual Research Units. In December 2019, the Ceres cluster was expanded further by 64 regular-, 2 mid-, and 5 high-memory nodes. This capacity expansion included 36 regular-, 2 mid-, and 3 high-memory “priority” nodes funded by Research Units. “Priority” nodes are available to all ARS users when not in use by their funders.
In addition to the ARS in-house compute infrastructure, Amazon Web Services (AWS) are available to augment the HPC capability of Ceres with cloud resources.
ARS researchers will also have access to a Cray system in Starkville, MS through an agreement with the Mississippi State University to supplement Agency scientific computing capacity. Installation and testing of the cluster will begin in December 2019. Also, a second Agency-owned HPC cluster is planned for Beltsville, MD and will consist of a blend of compute nodes and multi-tier storage.
Contribute / Contact
For questions about this newsletter or to contribute content, please email SCINet@usda.gov
For feedback on the SCINet website, SCINet policy and development questions, or for technical assistance with your SCINet account: Contact Information
SCINet Leadership Team
Deb Peters, Acting Chief Science Information Officer
Stan Kosecki, Acting SCINet Project Manager
Adam Rivers, Science Advisory Committee (SAC) Chair
Brian Scheffler, Ex Officio
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