High-Performance Computing. Training. High-Speed Networking.
What is SCINet?
The SCINet initiative is an effort by the USDA Agricultural Research Service (ARS) to grow USDA’s research capacity by providing scientists with access to high-performance computing clusters, high-speed networking for data transfer, and training in scientific computing.
Upcoming Trainings and Events
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RNA for Genome Annotation and Reproducibility in Bioinformatics
This workshop demonstrates how RNA data can be used for genome annotation. Participants will explore using RNA-derived evidence to improve genome annotations, distinguish coding from non-coding regions, and validate. We will also explore strategies for increasing reproducibility in bioinformatics.
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SCINet Corner · Commonly used Slurm parameters and the new “ceres” partition
- Understanding partitions and accounts on SCINet’s supercomputers.
- Specifying the partition, account, and time limit for compute jobs.
- Using the new “ceres” partition on Ceres.
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From Reads to Variants
DeepVariant is a DNA sequence variant caller that uses a convolutional neural network (CNN) to call genotypes relative to a reference genome assembly. In this workshop, we will discuss a workflow for calling variants from whole-genome data for multiple individuals.
Featured Stories
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Comparative genomics reveals a light-activated phytotoxin that contributes to red leaf blotch disease of soybean
*Coniothyrium glycines* causes red leaf blotch, a major disease of soybean in Africa (Figure 1). It is one of two fungal pathogens listed on the USDA APHIS Plant Protection and Quarantine Select Agents and Toxins list owing to its likely destructive potential if it spreads to major soybean growing regions.
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High-Performance Computing Facilitates Improved Understanding of Phenotypic Plasticity in Maize
In maize and other crops, important traits are often complex, affected by genetics, the environment, and their interaction. In addition, different crop varieties exhibit varying degrees of phenotypic plasticity, in which a given genotype displays different phenotype values in different environments.
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SCINet as a Resource for Safeguarding and Advancing ARS's Biological Collections
Across the USDA’s Agricultural Research Service (ARS) there are nealy 100 biological collections containing millions of preserved and viable specimens including animal tissues, seeds, fungal cultures, plant accessions, pinned insects, and viral isolates. These specimens and the data about them document and support ARS research efforts and are an integral part of delivering on the Agency’s mission.
Find out how SCINet can enable your research
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Working Groups
Information about how our collaborators currently use SCINet
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Fellowship Opportunities
SCINet-funded research fellowship opportunities for PhD and MS level graduates
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How to Use SCINet
Quick Start guide to getting up and running with SCINet
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Running Analyses
Guides for running different analyses
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Frequently Asked Questions
Answers to common questions asked about SCINet
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Need Help?
Find who you need to contact for specific issues or requests